Open Access

A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda)

  • Heather D Bracken-Grissom1Email author,
  • Maren E Cannon2,
  • Patricia Cabezas2, 3,
  • Rodney M Feldmann4,
  • Carrie E Schweitzer5,
  • Shane T Ahyong6,
  • Darryl L Felder7,
  • Rafael Lemaitre8 and
  • Keith A Crandall3, 8
BMC Evolutionary Biology201313:128

DOI: 10.1186/1471-2148-13-128

Received: 3 December 2012

Accepted: 21 May 2013

Published: 20 June 2013

Abstract

Background

The infraorder Anomura has long captivated the attention of evolutionary biologists due to its impressive morphological diversity and ecological adaptations. To date, 2500 extant species have been described but phylogenetic relationships at high taxonomic levels remain unresolved. Here, we reconstruct the evolutionary history—phylogeny, divergence times, character evolution and diversification—of this speciose clade. For this purpose, we sequenced two mitochondrial (16S and 12S) and three nuclear (H3, 18S and 28S) markers for 19 of the 20 extant families, using traditional Sanger and next-generation 454 sequencing methods. Molecular data were combined with 156 morphological characters in order to estimate the largest anomuran phylogeny to date. The anomuran fossil record allowed us to incorporate 31 fossils for divergence time analyses.

Results

Our best phylogenetic hypothesis (morphological + molecular data) supports most anomuran superfamilies and families as monophyletic. However, three families and eleven genera are recovered as para- and polyphyletic. Divergence time analysis dates the origin of Anomura to the Late Permian ~259 (224–296) MYA with many of the present day families radiating during the Jurassic and Early Cretaceous. Ancestral state reconstruction suggests that carcinization occurred independently 3 times within the group. The invasion of freshwater and terrestrial environments both occurred between the Late Cretaceous and Tertiary. Diversification analyses found the speciation rate to be low across Anomura, and we identify 2 major changes in the tempo of diversification; the most significant at the base of a clade that includes the squat-lobster family Chirostylidae.

Conclusions

Our findings are compared against current classifications and previous hypotheses of anomuran relationships. Many families and genera appear to be poly- or paraphyletic suggesting a need for further taxonomic revisions at these levels. A divergence time analysis provides key insights into the origins of major lineages and events and the timing of morphological (body form) and ecological (habitat) transitions. Living anomuran biodiversity is the product of 2 major changes in the tempo of diversification; our initial insights suggest that the acquisition of a crab-like form did not act as a key innovation.

Keywords

Anomura Phylogeny Divergence times Diversification rates Molecular Morphology Character evolution Next-generation sequencing

Background

The infraorder Anomura represents a highly diverse group of decapod crustaceans comprised of hermit crabs, mole crabs, king crabs, squat-lobsters and porcelain crabs. The fossil record contains representatives of nearly all extant families and spans the Norian/Rhaetian (Late Triassic) [1] to Holocene. Anomurans have colonized a wide variety of ecosystems including freshwater, anchialine cave, terrestrial and hydrothermal vent habitats, and are distributed from the ocean’s surface to depths more than 5000 m [2]. Their morphological and ecological diversity are of doubtless scientific interest, but anomurans also represent an important economic commodity as evident in major commercial fisheries for some king crab and squat lobster genera [35] and the common use of hermit crabs as pets in the aquarium trade. Moreover, some species are threatened or endangered due to rarity in nature, e.g., Pylochelidae [6], overfishing, e.g., Lithodidae [7], or habitat loss, e.g., Aeglidae [810]. Thus, improved understanding of these groups bears not only on appreciation of their diversity and ecology, but also strategies for their conservation.

Anomuran classification has long been fraught with controversy [see reviews by [1113]]. Early classifications from the 19th to the first half of the 20th centuries were based on adult morphological characters including mouthparts, antennae, gills, pleon type, and/or larval characteristics. These classifications often differed in higher-level composition and, in some cases, the infraordinal name (e.g. Anomura vs. Anomala). Since these studies, various researchers have proposed changes in the classification scheme [1418], many of which remain actively debated. More recently, molecular and/or morphological data have been used to reevaluate anomuran relationships [1921]. As currently defined, extant Anomura contains 7 superfamilies, 20 families, 335 genera, and more than 2500 species [17, 18, 22, 23]. Although the monophyly of Anomura is widely accepted [2426], the elucidation of internal relationships among families, genera, and species using modern methods is dynamic and under continuous debate [11, 17, 18, 20, 23, 27].

One of the most debated evolutionary questions within Anomura is phylogenetic relationships between hermit and king crabs. Since the early 1800’s [e.g., [28, 29]], studies have suggested king crabs and hermit crabs are close relatives, despite first appearances to the contrary. King crabs are among the largest arthropods and have a crab-like body shape, whereas hermit crabs are relatively small and depend on a shell for protection. Despite glaring morphological differences as adults, an affinity between king crabs (lithodoids) and hermit crabs (paguroids) has been long suggested [30, 31]. Although most accept this claim, the evolutionary pathways and hypothesized ancestor of both groups has been debated for decades, with two major hypotheses being proposed. The first suggests that the lithodids (Lithodes or Paralithodes) evolved from a pagurid-like ancestor (Pagurus) (“hermit to king hypothesis”) while the second suggests the opposite evolutionary pathway (“king to hermit hypothesis”). Here we revisit these hypotheses in light of new phylogenetic data to test the “hermit to king”/“king to hermit” evolutionary pathway.

Additional controversy over anomuran relationships stems from apparently rampant examples of convergent and/or parallel evolution in body forms. Anomurans span an impressive array of body configurations that include: 1) crab-like forms 2) squat-lobster forms 3) hermit crab forms with pleonal (abdomen) symmetry (found in 1 hermit crab family) and 4) hermit crab forms with pleonal asymmetry (found in 4 hermit crab families). Recent studies suggest that the acquisition of a crab-like body form, known as carcinization [see, [32] for a review of this concept], has occurred multiple times during evolution of the group [20, 33]. Brachyura, all of which possess a “crab-like” body shape or slight modifications to this form, dominates decapod diversity with 6550+ species [34], and is considered the sister clade to Anomura [2426, 3538]. Given the success of brachyuran crabs, it has been hypothesized that acquisition of a crab-like form may have acted as a key innovation [33], possibly impacting diversification rates within these lineages. For the first time, we explore diversification patterns in Anomura and specifically test if carcinized lineages underwent unusually rapid diversification rates. If the emergence of the crab-like form promoted diversification we would expect the overall rate in carcinized lineages to be high compared to net of diversification across Anomura. Additionally, we test if the acquisition of different body forms (i.e., crab-like, squat-lobster-like, pleonal asymmetry and symmetry (hermit)) arose once or multiple times during the emergence of the anomurans and reconstruct the evolutionary pathways of these transitions.

Divergence dating is a powerful tool used to estimate the timing and origins of diversity, morphological traits, habitat shifts, and diversification. Although nearly all the family-level groups of Anomura are represented in the fossil record, the discovery has not been as frequent as that of other decapod groups (i.e., true crabs, lobsters). Two factors, variations in cuticular sclerotization and habitat preference, are likely responsible for the limited occurrence of anomuran fossils. Many taxa are weakly calcified, whereas others possess well-calcified claws and poorly calcified carapaces and pleons. In addition, habitats currently occupied by anomurans, including freshwater, terrestrial, intertidal marine, deep marine, and hydrothermal vent areas are strongly underrepresented in the fossil record. Despite these limitations, we incorporate 31 fossil calibrations to estimate the origin of lineages and major events during anomuran evolutionary history, including the transition of body forms and shift into freshwater and terrestrial environments.

Here, we present the taxonomically broadest and largest dataset yet assembled. We combine sequences generated by traditional Sanger and next-generation 454 sequencing methods with morphological characters, including 19/20 extant families and 137 species, to estimate phylogenetic relationships, character state evolution, divergence times, and diversification patterns among major lineages of this diverse clade of crustaceans. Our comprehensive sampling, in combination with modern integrative approaches, allows us to present the most complete evolutionary picture for the infraorder Anomura to date.

Results

Our study includes representatives from 19 of the 20 anomuran families and 18 outgroup taxa sampled across Decapoda (Dendrobranchiata, Caridea, Axiidea, Gebiidea, Brachyura) (Table 1). Alternative outgroup sampling schemes did not affect internal relationships among Anomura. The optimal models of evolution for each gene selected in MODELTEST were as follows: GTR + I + G 18S, 28S, H3 and TVM + I + G 12S, 16S. Several sequences downloaded from GenBank were excluded from the analysis due to contamination after a BLAST search and/or strange alignment results (see Additional file 1).
Table 1

Taxonomy, voucher catalog numbers, and GenBank accession numbers for gene sequences used in this study

Infraorder

Family

Species

Catalog ID

16SrRNA

18SrRNA

28SrRNA

H3

12SrRNA

Ingroup

        

Anomura

Aeglidae

Aegla abtao Schmitt, 1942

KAC-Aa5/KC_Aa004

AY050067

AF439390

AY595966

DQ079658

AY050021

Anomura

Aeglidae

Aegla alacalufi Jara & Lopez, 1981

KACa1144/KaC798/KACa0090/KAC-A90

FJ472207

EU920958

AY595958

EU921042

AY050013

Anomura

Aeglidae

Aegla camargoi Buckup & Rossi, 1977

KACa0358

AY595874

N/A

AY596045

N/A

AY595493

Anomura

Aeglidae

Aegla cholchol Jara & Palacios, 1999

KAC-A71

AY050050

N/A

AY595948

N/A

AY050004

Anomura

Aeglidae

Aegla jarai Bond-Buckup & Buckup, 1994

KACa0273

AY595849

N/A

AY596020

N/A

AY595468

Anomura

Aeglidae

Aegla papudo Schmitt, 1942

KAC-A7

AY050032

AY595796

AY595930

N/A

AY049986

Anomura

Aeglidae

Aegla platensis Schmitt, 1942

KACa0495

AY595917

AY595800

AY596088

N/A

AY595536

Anomura

Aeglidae

Aegla uruguayana Schmitt, 1942

KACaB395

AF436051

AF436012

AF435992

N/A

AY595505

Anomura

Aeglidae

Aegla violacea Bond-Buckup & Buckup, 1994

KACa0379

AY595880

AY595799

AY596051

N/A

AY595499

Anomura

Albuneidae

Albunea catherinae Boyko, 2002

KC6848/ULLZ10315

KF182559

KF182445

KF182607

N/A

KF182439

Anomura

Albuneidae

Albunea gibbesii Stimpson, 1859

KC4754/ULLZ7376

KF182558

KF182440

KF182604

KF182698

KF182373

Anomura

Albuneidae

Lepidopa californica Efford, 1971

N/A

AF436054

AF436015

AF435996

N/A

N/A

Anomura

Albuneidae

Lepidopa dexterae Abele & Efford, 1972

KC6846/ULLZ4867

KF182561

KF182442

KF182606

KF182704

KF182375

Anomura

Albuneidae

Paraleucolepidopa myops (Stimpson, 1860)

KC4756/ULLZ10659

KF182560

KF182441

KF182605

KF182703

KF182374

Anomura

Albuneidae

Zygopa michaelis Holthuis, 1961

KC6849/ULLZ7565

KF182562

KF182443

KF182608

KF182699

KF182387

Anomura

Blepharipodidae

Blepharipoda occidentalis Randall, 1840

N/A

AF436053

AF436014

AF435994

N/A

N/A

Anomura

Chirostylidae

Chirostylus novaecaledoniae Baba, 1991

MNHN:Ga 2072

EU821539

EU821555

EU821572

N/A

N/A

Anomura

Chirostylidae

Gastroptychus novaezelandiae Baba, 1974

NIWA:23496

EU821538

EU821554

EU821571

N/A

N/A

Anomura

Chirostylidae

Gastroptychus rogeri Baba, 2000

NIWA:14598

HQ380260

HQ380285

HQ380272

N/A

N/A

Anomura

Chirostylidae

Gastroptychus spinifer (A. Milne-Edwards, 1880)

KC6839/ULLZ11351

KF182520

KF182511

KF182657

KF182720

KF182438

Anomura

Chirostylidae

Uroptychus nitidus (A. Milne-Edwards, 1880)

KACurni

AY595925

AF439387

AY596096

N/A

AY595544

Anomura

Chirostylidae

Uroptychus parvulus (Henderson, 1885)

KACurpa

AY595926

AF439386

AY596097

DQ079703

AY595545

Anomura

Chirostylidae

Uroptychus scambus Benedict, 1902

NIWA:10198

EU831282

EU821553

EU831283

N/A

N/A

Anomura

Chirostylidae

Uroptychus spinirostris (Ahyong & Poore, 2004)

NIWA:8992

N/A

EU821582

EU821570

N/A

N/A

Anomura

Coenobitidae

Birgus latro (Linnaeus, 1767)

KC6694

KF182532

KF182470

KF182625

KF182696

KF182421

Anomura

Coenobitidae

Coenobita clypeatus (Fabricius, 1787)

KC4759/ULLZ9968

KF182531

KF182467

KF182624

KF182695

KF182420

Anomura

Coenobitidae

Coenobita compressus (H. Milne Edwards)

N/A

AF436059

AF436023

AF435999

N/A

N/A

Anomura

Coenobitidae

Coenobita perlatus H. Milne Edwards, 1836

MNHN:IU200816162

HQ241512

HQ241524

HQ241535

HQ241557

HQ241501

Anomura

Diogenidae

Areopaguristes hewatti (Wass, 1963)

KC4766/ULLZ6876

KF182535

KF182485

KF182643

KF182733

KF182377

Anomura

Diogenidae

Areopaguristes hewatti (Wass, 1963)

KC6865/ULLZ6876

KF182536

KF182481

KF182644

KF182734

N/A

Anomura

Diogenidae

Areopaguristes hewatti (Wass, 1963)

KC6976/ULLZ6861

N/A

KF182482

KF182645

KF182735

KF182378

Anomura

Diogenidae

Areopaguristes hummi (Wass, 1955)

KC6866/ULLZ6880

KF182541

KF182483

KF182641

KF182730

KF182379

Anomura

Diogenidae

Areopaguristes hummi (Wass, 1955)

KC6984/ULLZ6926

KF182542

KF182484

KF182642

KF182731

KF182380

Anomura

Diogenidae

Areopaguristes pilosus H. Milne Edwards, 1836

NIWA:28030

HQ380271

HQ380296

HQ380283

N/A

N/A

Anomura

Diogenidae

Calcinus laevimanus (Randall, 1840)

KC6994/ULLZ10120

N/A

KF182471

KF182632

KF182691

KF182426

Anomura

Diogenidae

Calcinus obscurus Stimpson, 1859

H111

AF436058

AF436022

AF435998

FJ620465

N/A

Anomura

Diogenidae

Clibanarius albidigitus Nobili, 1901

N/A

AF425323

AF438751

AF425342

N/A

N/A

Anomura

Diogenidae

Clibanarius antillensis Stimpson, 1859

KC6973/ULLZ9433

KF182529

KF182472

KF182628

KF182693

KF182424

Anomura

Diogenidae

Clibanarius corallinus (H. Milne-Edwards, 1848)

KC6975/ULLZ10121

KF182528

KF182473

KF182629

KF182694

KF182423

Anomura

Diogenidae

Clibanarius vittatus (Bosc, 1802)

KC6855/ULLZ4781

KF182527

KF182474

KF182630

KF182692

KF182422

Anomura

Diogenidae

Dardanus fucosus Biffar & Provenzano, 1972

KC6858/ULLZ7122

KF182586

N/A

KF182654

N/A

KF182430

Anomura

Diogenidae

Dardanus insignis (de Saussure, 1858)

KC6857/ULLZ7964

KF182585

KF182498

KF182631

N/A

KF182429

Anomura

Diogenidae

Dardanus sp.

KC4761/ULLZ6711

KF182533

KF182468

KF182626

KF182697

KF182428

Anomura

Diogenidae

Isocheles pilosus (Holmes, 1900)

N/A

AF436057

AF436021

N/A

N/A

N/A

Anomura

Diogenidae

Isocheles wurdemanni Stimpson, 1859

KC6856/ULLZ5683

KF182530

KF182475

KF182633

N/A

KF182425

Anomura

Diogenidae

Paguristes cadenati Forest, 1954

KC6862/ULLZ7624

KF182540

KF182493

KF182637

N/A

KF182386

Anomura

Diogenidae

Paguristes grayi (Benedict, 1901)

KC6859/ULLZ11744

KF182537

KF182488

KF182636

KF182728

KF182382

Anomura

Diogenidae

Paguristes nr. moorei

KC6863/ULLZ11765

KF182552

KF182490

KF182640

N/A

KF182385

Anomura

Diogenidae

Paguristes punticeps Benedict, 1901

KC6861/ULLZ6801

KF182538

KF182487

KF182639

KF182727

KF182383

Anomura

Diogenidae

Paguristes sericeus A. Milne Edwards, 1880

KC4762/ULLZ7331

N/A

KF182486

KF182635

KF182726

KF182381

Anomura

Diogenidae

Paguristes tortugae Schmitt, 1933

KC4763/ULLZ6800

KF182534

KF182480

N/A

KF182732

KF182376

Anomura

Diogenidae

Paguristes triangulatus A. Milne-Edwards & Bouvier, 1893

KC6860/ULLZ6892

KF182539

KF182489

KF182638

KF182729

KF182384

Anomura

Diogenidae

Paguristes turgidus (Stimpson, 1857)

N/A

AF436056

AF436020

AF435997

N/A

N/A

Anomura

Diogenidae

Petrochirus diogenes (Linnaeus, 1758)

KC4764/ULLZ8129

N/A

KF182469

KF182627

KF182719

KF182427

Anomura

Eumunididae

Eumunida funambulus Gordon, 1930

KC3100

EU920922

EU920957

EU920984

EU921056

EU920892

Anomura

Eumunididae

Eumunida picta Smith, 1883

KC6872

KF182518

KF182463

KF182619

KF182690

KF182368

Anomura

Eumunididae

Eumunida picta Smith, 1883

KC6874

KF182519

KF182464

KF182620

N/A

KF182369

Anomura

Eumunididae

Pseudomunida fragilis Haig, 1979

KC6707

KF182517

KF182462

KF182618

KF182665

KF182370

Anomura

Galatheidae

Alainius crosnieri Baba, 1991

MNHN:Norfolk I Stn DW 1703

HQ380263

HQ380287

HQ380275

N/A

N/A

Anomura

Galatheidae

Galathea rostrata A. Milne-Edwards, 1880

KC4767/ULLZ7681

KF182523

KF182504

KF182664

KF182684

KF182388

Anomura

Galatheidae

Galathea sp.

KES-2008

EU821544

EU821561

EU821578

N/A

N/A

Anomura

Hapalogastridae

Hapalogaster mertensii Brandt, 1850

KC6175/ULLZ11535

KF182573

KF182451

KF182601

KF182667

KF182401

Anomura

Hapalogastridae

Oedignathus inermis (Stimpson, 1860)

N/A

AF425334

Z14062

AF425353

N/A

N/A

Anomura

Hippidae

Emerita brasiliensis Schmitt, 1935

KCembr

DQ079712

AF439384

DQ079786

DQ079673

N/A

Anomura

Hippidae

Emerita emeritus (Linnaeus 1767)

AMSP67874

AY583898

AY583971

AY583990

N/A

N/A

Anomura

Hippidae

Emerita talpoida (Say, 1817)

KC6850/ULLZ9434

KF182557

KF182444

KF182587

KF182702

KF182419

Anomura

Kiwaidae

Kiwa hirsuta Macpherson, Jones & Segonzac, 2005

MNHN:Ga 5310

EU831284

DQ219316

EU831286

EU921065

N/A

Anomura

Lithodidae

Cryptolithodes sp.

KC6971/ULLZ11844

KF182574

KF182453

KF182603

KF182669

KF182402

Anomura

Lithodidae

Glyptolithodes cristatipes (Faxon, 1893)

N/A

AF425326

N/A

AF425346

N/A

N/A

Anomura

Lithodidae

Lithodes santolla (Molina, 1782)

KC6340/ULLZ11875

KF182572

KF182452

KF182602

KF182671

KF182400

Anomura

Lithodidae

Lithodes santolla (Molina, 1782)

KAClisa

AY595927

AF439385

AY596100

DQ079679

AY595546

Anomura

Lithodidae

Lopholithodes mandtii Brandt, 1848

N/A

AF425333

N/A

AF425352

N/A

N/A

Anomura

Lithodidae

Paralithodes brevipes (H. Milne Edwards & Lucas, 1841)

N/A

AF425337

N/A

AF425356

N/A

N/A

Anomura

Lithodidae

Paralithodes camtschaticus Tilesius, 1815

N/A

AF425338

N/A

AF425357

N/A

N/A

Anomura

Lithodidae

Paralithodes platypus (Brandt, 1850)

N/A

N/A

N/A

AB193822

N/A

N/A

Anomura

Lithodidae

Paralomis sp.

KC3506

KF182571

KF182446

KF182588

KF182666

KF182399

Anomura

Lithodidae

Phyllolithodes papillosus Brandt, 1848

N/A

AF425340

N/A

AF425359

N/A

N/A

Anomura

Lomisidae

Lomis hirta (Lamarck, 1818)

KClohi

AF436052

AF436013

AF435993

DQ079680

AY595547

Anomura

Munididae

Agononida procera Ahyong & Poore, 2004

NIWA:9017

EU821540

EU821556

EU821573

N/A

N/A

Anomura

Munididae

Anoplonida inermis (Baba, 1994)

MNHN:SANTO Stn AT9

HQ380265

HQ380289

HQ380276

N/A

N/A

Anomura

Munididae

Babamunida kanaloa Schnabel, Martin & Moffitt, 2009

LACM:CR 2006-014.21

N/A

HQ380294

HQ380281

N/A

N/A

Anomura

Munididae

Bathymunida balssi Van Dam, 1838

MNHN:SANTO Stn AT5

HQ380266

HQ380290

HQ380277

N/A

N/A

Anomura

Munididae

Cervimunida johni Porter, 1903

NIWA:46109

EU821546

EU821563

EU821580

N/A

N/A

Anomura

Munididae

Munida iris A. Milne-Edwards, 1880

KC4768/ULLZ8366

KF182521

KF182491

KF182622

KF182685

KF182389

Anomura

Munididae

Munida pusilla Benedict, 1902

KC6837/ULLZ8322

KF182522

KF182492

KF182623

KF182686

KF182390

Anomura

Munididae

Munida quadrispina Benedict, 1902

N/A

AF436050

AF436010

AF435990

N/A

N/A

Anomura

Munididae

Munida gregaria (Fabricius, 1793)

KAC-mso1/Kcmusu

AY050075

AF439382

AY596099

DQ079688

AY050029

Anomura

Munididae

Neonida grandis Baba & de Saint Laurent, 1996

MNHN:Lifou Stn CP2

HQ380264

HQ380288

N/A

N/A

N/A

Anomura

Munididae

Pleuroncodes monodon (H. Milne Edwards, 1837)

NIWA:46108

EU821545

EU821562

EU821579

N/A

N/A

Anomura

Munididae

Sadayoshia sp.

MNHN:SANTO

EU821547

EU821564

EU821581

N/A

N/A

Anomura

Munidopsidae

Galacantha rostrata A. Milne-Edwards, 1880

NIWA:9002

HQ380261

EU821559

EU821576

N/A

N/A

Anomura

Munidopsidae

Galacantha valdiviae Balss, 1913

KC3102

EU920928

EU920961

EU920985

EU921066

EU920898

Anomura

Munidopsidae

Leiogalathea laevirostris (Balss, 1913)

NIWA:10197

EU821541

EU821557

EU821574

N/A

N/A

Anomura

Munidopsidae

Munidopsis bairdii (Smith, 1884)

NIWA:19175

EU821542

EU821558

EU821575

N/A

N/A

Anomura

Munidopsidae

Munidopsis erinacea (A. Milne-Edwards, 1880)

KC4769/ULLZ7810

KF182524

KF182479

KF182621

KF182689

KF182391

Anomura

Munidopsidae

Shinkaia crosnieri Baba & Williams, 1998

NTOU:Chan, Lee & Lee, 2000

NC_011013

N/A

EU831285

N/A

NC_011013

Anomura

Paguridae

Agaricochirus alexandri (A. Milne-Edwards & Bouvier, 1893)

KC4772/ULLZ6891

N/A

KF182447

KF182593

KF182672

KF182404

Anomura

Paguridae

Bythiopagurus macrocolus McLaughlin, 2003

NIWA:29632

EU821532

EU821548

EU821565

N/A

N/A

Anomura

Paguridae

Discorsopagurus schmitti (Stevens, 1925)

N/A

AF436055

AF436017

N/A

N/A

N/A

Anomura

Paguridae

Goreopagurus piercei Wass, 1963

KC6991/ULLZ8570

N/A

KF182456

KF182592

KF182670

KF182416

Anomura

Paguridae

Iridopagurus caribbensis (A. Milne-Edwards & Bouvier, 1893)

KC4774/ULLZ6759

KF182580

KF182448

KF182598

KF182687

KF182412

Anomura

Paguridae

Iridopagurus reticulatus García-Gómez, 1983

KC6827/ULLZ10032

KF182581

KF182449

KF182599

KF182688

KF182413

Anomura

Paguridae

Labidochirus splendescens (Owen, 1839)

N/A

AF425332

N/A

AF425351

N/A

N/A

Anomura

Paguridae

Manucomplanus ungulatus (Studer, 1883)

KC6833/ULLZ7851

KF182575

KF182457

KF182612

KF182681

N/A

Anomura

Paguridae

Pagurus bernhardus (Linnaeus, 1758)

N/A

AF425335

N/A

AF425354

N/A

N/A

Anomura

Paguridae

Pagurus brevidactylus (Stimpson, 1859)

KC4776/ULLZ7065

KF182563

KF182495

KF182610

KF182679

KF182407

Anomura

Paguridae

Pagurus bullisi Wass, 1963

KC6832/ULLZ11056

KF182568

KF182454

KF182595

KF182668

KF182410

Anomura

Paguridae

Pagurus maclaughlinae García-Gómez, 1982

KC6831/ULLZ11975

KF182566

KF182460

KF182611

KF182680

KF182408

Anomura

Paguridae

Pagurus nr. carolinensis

KC6830/ULLZ8576

KF182565

KF182465

KF182609

N/A

N/A

Anomura

Paguridae

Pagurus pollicaris Say, 1817

KC6829/ULLZ11954

N/A

KF182458

KF182589

KF182737

KF182403

Anomura

Paguridae

Pagurus stimpsoni (A. Milne-Edwards & Bouvier, 1893)

KC6828/ULLZ11110

KF182564

KF182466

KF182613

KF182682

KF182409

Anomura

Paguridae

Phimochirus holthuisi (Provenzano, 1961)

KC6834/ULLZ7973

KF182578

KF182455

KF182594

KF182678

KF182415

Anomura

Paguridae

Phimochirus randalli (Provenzano, 1961)

KC4777/ULLZ7071

KF182576

KF182461

KF182591

KF182676

KF182417

Anomura

Paguridae

Phimochirus randalli (Provenzano, 1961)

KC4778/ULLZ7345

KF182577

KF182450

KF182596

KF182677

KF182418

Anomura

Paguridae

Porcellanopagurus filholi de Saint Laurent & McLaughlin, 2000

NIWA:29628

HQ380267

HQ380291

HQ380278

N/A

N/A

Anomura

Paguridae

Pylopaguridium markhami McLaughlin & Lemaitre, 2001

KC4779/ULLZ6780

KF182570

KF182478

KF182597

KF182674

KF182414

Anomura

Paguridae

Pylopagurus discoidalis (A. Milne-Edwards, 1880)

KC4780/ULLZ7675

KF182569

KF182496

KF182614

KF182675

KF182405

Anomura

Paguridae

Tomopagurus merimaculosus (Glassell, 1937)

KC4782/ULLZ9441

KF182567

KF182497

KF182590

KF182673

KF182411

Anomura

Paguridae

Xylopagurus cancellarius Walton, 1950

KC4783/ULLZ9443

KF182584

KF182459

KF182600

KF182683

KF182406

Anomura

Parapaguridae

Parapagurus latimanus Henderson, 1888

NIWA:29621

N/A

EU821550

EU821567

N/A

N/A

Anomura

Parapaguridae

Sympagurus acinops Lemaitre, 1989

KC6977/ULLZ11020

KF182526

KF182476

KF182616

KF182701

KF182371

Anomura

Parapaguridae

Sympagurus dimorphus (Studer, 1883)

NIWA:29594

EU821533

EU821549

EU821566

N/A

N/A

Anomura

Parapaguridae

Sympagurus pictus Smith, 1883

KC7247/KC6835 (ULLZ 10849 16S/H3only)

KF182579

KF182477

KF182617

KF182700

KF182372

Anomura

Porcellanidae

Allopetrolisthes spinifrons (H. Milne Edwards, 1837)

KC6965/ULLZ5979

KF182550

KF182499

KF182662

KF182714

KF182398

Anomura

Porcellanidae

Euceramus sp.

KC6974/ULLZ10235

KF182555

KF182513

KF182634

KF182716

N/A

Anomura

Porcellanidae

Megalobrachium poeyi (Guérin-Méneville, 1855)

KC6964/ULLZ6094

N/A

KF182512

N/A

KF182713

KF182397

Anomura

Porcellanidae

Neopisosoma angustifrons (Benedict, 1901)

KC6968/ULLZ5385

KF182545

KF182501

KF182652

KF182712

KF182434

Anomura

Porcellanidae

Pachycheles ackleianus A. Milne-Edwards, 1880

KC6988/ULLZ8341

KF182554

KF182503

KF182651

KF182706

N/A

Anomura

Porcellanidae

Pachycheles haigae Rodrigues da Costa, 1960

KAC-pha1

AY050076

AF439389

N/A

N/A

AY050030

Anomura

Porcellanidae

Pachycheles pilosus (H. Milne Edwards, 1837)

KC6986/ULLZ10036

KF182544

KF182502

KF182653

KF182707

N/A

Anomura

Porcellanidae

Pachycheles rudis Stimpson, 1859

N/A

AF260598

AF436008

AF435988

N/A

N/A

Anomura

Porcellanidae

Pachycheles rugimanus A. Milne-Edwards, 1880

KC4787/ULLZ6903

KF182543

KF182500

KF182650

KF182705

KF182392

Anomura

Porcellanidae

Parapetrolisthes tortugensis (Glassell, 1945)

KC4788/ULLZ6726

KF182546

KF182507

KF182658

KF182709

KF182393

Anomura

Porcellanidae

Parapetrolisthes tortugensis (Glassell, 1945)

KC6979/ULLZ7560

KF182547

KF182508

KF182660

KF182710

KF182394

Anomura

Porcellanidae

Petrolisthes armatus (Gibbes, 1850)

KC6993/ULLZ10098

KF182549

KF182510

KF182661

KF182708

KF182396

Anomura

Porcellanidae

Petrolisthes armatus (Gibbes, 1850)

N/A

AF436049

AF436009

AF435989

N/A

N/A

Anomura

Porcellanidae

Petrolisthes galathinus (Bosc, 1802)

KC4789/ULLZ6897

KF182548

KF182509

KF182659

KF182711

KF182395

Anomura

Porcellanidae

Petrolisthes laevigatus (Guérin, 1835)

N/A

AF260606

AF439388

N/A

N/A

N/A

Anomura

Porcellanidae

Pisidia magdalenensis (Glassell, 1936)

KC6980/ULLZ5986

KF182556

KF182514

N/A

KF182718

N/A

Anomura

Porcellanidae

Polyonyx gibbesii Haig, 1956

KC6987/ULLZ12061& KC6983/ULLZ8943

KF182553

KF182515

KF182663

KF182717

N/A

Anomura

Porcellanidae

Porcellana sayana (Leach, 1820)

KC4790/ULLZ8092

KF182551

KF182516

N/A

KF182715

N/A

Anomura

Pylochelidae

Pomatocheles jeffreysii Miers, 1879

KC3097

EU920930

EU920965

EU920983

EU921070

EU920903

Anomura

Pylochelidae

Trizocheles spinosus (Henderson, 1888)

NIWA:29348

N/A

EU821551

EU821568

N/A

N/A

Anomura

Pylochelidae

Xylocheles macrops Forest, 1987

AMSP57955

AY583897

AY583970

AY583989

N/A

N/A

Outgroup

        

Brachyura

Calappidae

Calappa gallus (Herbst, 1803)

KC3083

EU920916

EU920947

EU920977

EU921049

EU920886

Brachyura

Varunidae

Cyclograpsus cinereus (Dana, 1851)

KC3417

EU920914

EU920945

EU920997

EU921046

EU920884

Brachyura

Leucosiidae

Praebebalia longidactyla (Yokoya, 1933)

KC3086

EU920931

EU920946

EU920979

EU921071

EU920904

Brachyura

Epialtidae

Chorilia longipes (Dana, 1852)

KC3089

EU920919

EU920948

EU920981

EU921052

EU920889

Brachyura

Rainidae

Cosmonotus grayi (White, 1848)

KC3092

EU920918

EU920949

EU920982

EU921051

EU920888

Axiidea

Callianassidae

Lepidophthalmus louisianensis (Schmitt,1935)

KAC1852

DQ079717

DQ079751

DQ079792

DQ079678

EU920897

Axiidea

Callianassidae

Sergio mericeae (Manning & Felder, 1995)

KAC1865

DQ079733

DQ079768

DQ079811

DQ079700

EU920909

Axiidea

Axiidae

Calaxius manningi Kensley et al., 2000

NTOUA0053

EF585447

EF585458

EF585469

N/A

N/A

Axiidea

Calocarididae

Calastacus crosnieri Kensley & Chan, 1998

NTOUA00212

EF585446

EF585457

EF585468

N/A

N/A

Gebiidea

Laomediidae

Laomedia astacina de Haan, 1841

NTOUA00366

EF585450

EF585461

EF585472

N/A

N/A

Gebiidea

Thalassinidae

Thalassina anomala (Herbst, 1804)

ZRC1998-.2263

AY583896

AY583969

EF585476

N/A

N/A

Gebiidea

Upogebiidae

Austinogebia narutensis (Sakai, 1986)

NTOUA00416

EF585443

EF585454

EF585465

N/A

N/A

Penaeoidea

Solenoceridae

Hymenopenaeus debilis Smith, 1882

KC 4444/ULLZ 8531

KF182582

KF182505

KF182655

KF182721

KF182431

Penaeoidea

Solenoceridae

Solenocera sp.

KC 4454/ULLZ 6705

KF182583

KF182506

KF182656

KF182722

KF182432

Caridea

Hippolytidae

Latreutes fucorum (Fabricius, 1798)

KC 4498/ULLZ 9135

EU868664

EU868755

KF182646

KF182723

KF182435

Caridea

Atyidae

Atyopsis sp.

KC 4517/ULLZ 9174

EU868634

EU868724

KF182647

KF182724

KF182433

Caridea

Palaemonidae

Palaemonetes pugio Holthuis, 1949

KC 4523/ULLZ7458

EU868697

EU868791

KF182648

KF182725

KF182437

Caridea

Ogyrididae

Ogyrides sp.

KC 4542/ULLZ 7755

EU868679

EU868772

KF182649

KF182736

KF182436

An “N/A” not available indicates missing sequence data. New sequences are indicated as KFXXXXXX.

Phylogenetic analyses

Alternative outgroup selections did not affect internal anomuran relationships. With all outgroups included, Brachyura was recovered as the sister taxon. The Bayesian analysis from the combined molecular + morphology dataset recovers Anomura as a monophyletic group with high support (100 = Pp, Figure 1). The majority of the nodes (86%) are recovered with very high support (>95). Three families are recovered as para- or polyphyletic (Diogenidae, Paguridae, Munididae). With the exception of three families (Blepharipodidae, Kiwaidae, Lomisidae) each having a single representative, the remaining families were found to be monophyletic (Hippidae, Albuneidae, Munidopsidae, Galatheidae, Porcellanidae, Parapaguridae, Aeglidae, Eumunididae, Chirostylidae, Lithodidae, Hapalogastridae, Pylochelidae, and Coenobitidae) with high support. Blepharipodidae, Hippidae, and Albuneidae (Hippoidea) group together with very high support (100), being sister to the remaining 16 anomuran families. Lomisidae, Eumunididae, Kiwaidae, and Chirostylidae (Lomisoidea + Chirostyloidea) form a clade with high support (100) and are sister to Aeglidae (Aegloidea). Munidopsidae, Galatheidae, Munididae, and Porcellanidae (Galatheoidea) form a clade with high Bayesian support (100). Within the Galatheoidea, Munididae is paraphyletic with the galatheids nested within the group. Pylochelidae, Parapaguridae, Diogenidae, Coenobitidae, Paguridae, Hapalogastridae, and Lithodidae (= Paguroidea + Lithodoidea) form a statistically supported clade (97). Six of the seven anomuran superfamilies are monophyletic (Hippoidea, Galatheoidea, Aegloidea, Lomisoidea [monotypic], Chirostyloidea, and Lithodoidea). The remaining superfamily, Paguroidea is found to be paraphyletic and includes the superfamily Lithodoidea (Lithodidae + Hapalogastridae). 11 genera were found to be poly- or paraphyletic (Eumunida, Gastroptychus, Munidopsis, Munida, Pachycheles, Petrolisthes, Sympagurus, Areopaguristes, Paguristes, Pagurus, and Paralithodes).
https://static-content.springer.com/image/art%3A10.1186%2F1471-2148-13-128/MediaObjects/12862_2012_Article_2378_Fig1_HTML.jpg
Figure 1

Combined Bayesian phylogram based on molecular (3669 characters) and morphological (156 characters) data. Vertical colored bars represent anomuran families, grey brackets represent superfamilies, and the black vertical line represents outgroups. Bayesian posterior probabilities represented as percentages and >70% are noted above or below branches.

The molecular-only phylogeny (Figure 2) is similar to our combined phylogeny, with most differences being found in placement and composition of Paguroidea. Unlike the combined phylogeny, which recovered Paguroidea as paraphyletic, Paguroidea was found to be polyphyletic. The family Pylochelidae was recovered as polyphyletic according to molecular data but was monophyletic when morphology was added. Parapaguridae was sister to a clade containing Pylochelidae, Aeglidae, Lomisidae, Eumunididae, Kiwaidae, and Chirostylidae, similar to the results of Tsang et al. [20] based on nuclear protein coding genes. As in the combined phylogeny, Coenobitidae is nested within the Diogenidae, and Lithodoidea nested within the Paguroidea. Within Lithodoidea of the molecular–only phylogeny, Hapalogastridae was found to be paraphyletic, with representatives of the genera Hapalogaster and Oedignathus at the basal (H. mertensi) and derived (O. inermis) end of the tree. However lithodoid relationships in the molecular-only phylogeny should be interpreted with caution as many were recovered with little to no support. In the combined phylogeny Hapalogastridae was found to be a monophyletic and sister to Lithodidae (Figure 1). The remaining superfamilies were monophyletic as recovered in the combined tree (Figures 1 and 2). Twelve genera were found to be poly- or paraphyletic (Munidopsis, Munida, Pachycheles, Petrolisthes, Sympagurus, Eumunida, Gastroptychus, Uroptychus, Paguristes, Areopaguristes, Pagurus, and Paralithodes). Some deep splits and short branches in the molecular-only phylogeny should be interpreted with caution, as support is low.
https://static-content.springer.com/image/art%3A10.1186%2F1471-2148-13-128/MediaObjects/12862_2012_Article_2378_Fig2_HTML.jpg
Figure 2

Bayesian phylogram based on 5 genes 12S, 16S, 18S, 28S, H3 and 3669 characters. Vertical colored bars represent anomuran families, grey brackets represent superfamilies, and the black vertical line represents outgroups. Bayesian posterior probabilities represented as percentages and maximum likelihood bootstrap values are noted above or below branches.

Alternative hypotheses

Alternative hypotheses regarding monophyly of the families Paguridae, Diogenidae, Hapalogastridae, Lithodidae, Munididae, Pylochelidae, and the superfamily Paguroidea [1418, 23, 39] were tested using the Shimodaira-Hasegawa test (S-H). Three of the seven hypotheses were found to be significantly worse than our unconstrained topology (P < 0.05; MLbest = −68420.363272; MLDiogenidae = −68667.853268, MLPaguridae = −68497.123254; MLPaguroidea = −68825.722919). The remaining four hypotheses were not found to be significantly worse than our unconstrained topology (P > 0.05; MLHapalogastridae = −68432.438825; MLLithodidae = −68438.309801; MLMunididae = −68428.284597; MLPylochelidae = −68430.951016). Hypotheses that tested a “king to hermit” evolutionary pathway were all significantly worse than the alternative (i.e., “hermit to king”) as recovered in our best ML tree (P < 0.05; MLbest = −68420.363272; MLking-Paguroidea = −68777.179402; MLking-Paguridae = −68713.171227).

Character evolution

To infer evolutionary pathways, body forms (crab-like, squat lobster, asymmetrical hermit pleon, symmetrical hermit pleon) and habitat types (marine, freshwater, semi-terrestrial) were optimized across our combined phylogeny using ancestral state reconstruction methods (Figure 3A). Analyses indicated that a crab-like ancestor gave rise to all extant anomuran lineages. In addition to the earliest branching clade, Hippoidea, carcinization occurred independently three times during the evolution of the group, twice through squat lobster-like intermediaries (squat intermediary = SI on tree) and once through an asymmetrical hermit crab-like ancestor (asymmetrical hermit intermediary = AHI on tree) (Figure 3A). The squat lobster-like form arose once as an early branching lineage and gave rise to the crab-like clades, Lomisidae and Porcellanidae. Within the hermit crab lineages, the symmetrical pleon arose once within the Pylochelidae. The asymmetrical pleon arose once within the Paguroidea, but was subsequently partially reverted to the ancestral symmetrical condition (in males only) within the crab-like Lithodidae and Hapalogastridae (= Lithodoidea, Figure 3A). We traced the colonization of freshwater and semi-terrestrial habitats by the families Aeglidae and Coenobitidae (Figure 3B). Both transitions occurred via marine ancestors (marine intermediary = MI in Figure 3B). In combination with divergence time results, we can make predictions about the timing of these events (see Discussion). Maximum parsimony and maximum likelihood methods recovered similar ancestral state reconstructions for body form and habitat (Figure 3A and B), so only the likelihood analyses are presented.
https://static-content.springer.com/image/art%3A10.1186%2F1471-2148-13-128/MediaObjects/12862_2012_Article_2378_Fig3_HTML.jpg
Figure 3

Ancestral state reconstruction analysis using maximum likelihood methods for body shape and habitat transition within Anomura. Colored taxa correspond to anomuran families as noted in legend. Pie charts represent the likelihood of the ancestral state. (A) Character states for body shape were defined as crab-like white, squat lobster blue, symmetrical hermit green and asymmetrical hermit black. (B) Character states for habitat were defined as freshwater white, semi-terrestrial green, and marine black. Subtrees are shown for the transition into freshwater (Aeglidae) and semi-terrestrial habitats (Coenobitidae).

Divergence time analysis

The divergence dating program BEAST was used to estimated origins and radiations of major lineages based on 31 fossil calibrations (Table 2). All parameters reached convergence for individual runs. BEAST estimated the divergence of the anomurans from the true crabs, Brachyura, to be in the Permian (~259 (224–296) MYA, Figure 4, Square A). The most recent common ancestor of all present-day families radiated shortly afterwards in the Triassic representing the origin of the earliest branching clade (Blepharipodidae-Albuneidae-Hippidae) estimated in the Norian (~221 MYA, Square B). Additional speciation events leading to these present-day families occurred throughout the Cretaceous (~111-90.7 MYA). The exclusively freshwater family Aeglidae diverged in the Early Cretaceous (~137 MYA, Square C) with rapid speciation of present day species occurring since the mid-Miocene (~12 MYA). The families Lomisidae, Eumunididae, Chirostylidae, and Kiwaidae all originated in the Cretaceous (~122, 109, 95, and 95 MYA respectively). Squat lobsters and porcelain crabs within the superfamily Galatheoidea originated in the Early Jurassic (Hettangian) and split into the Munidopsidae and remaining families during the Pliensbachian, Early Jurassic (~180 MYA, Square D). The other galatheoid families, Munididae and Galatheidae, arose soon thereafter within the Tithonian, Late Jurassic (~150 MYA, Square E) while Porcellanidae emerged in the Aalenian, Middle Jurassic (~173 MYA, Square F). The oldest family of hermit crabs, the symmetrical pylochelids, branched from the remaining hermits around 200 MYA in the Norian, Late Triassic (Figure 4, Square G). The origin of the asymmetrical hermit crab lineages followed soon after in the Pliensbachian, Early Jurassic (~187 MYA, Square H). Two hermit crab families were recovered as non-monophyletic assemblages (Diogenidae, Paguridae), which resulted in multiple timing of origins for these families. Parapaguridae split from one clade of Diogenidae (Areopaguristes and Paguristes) in the Bathonian, Middle Jurassic (~167 MYA, Square I), while the family Coenobitidae is found nested within a slightly older clade of Diogenidae (~173 MYA, Square J), which includes most present day genera. Paguridae is not monophyletic, because of the internally nested Lithodidae and Haplogastridae. The most recent common ancestor of the pagurid + lithodid + hapalogastrid clade was placed in the Late Cretaceous (Cenomanian, ~98 MYA, Square K) with Lithodidae and Hapalogastridae splitting from one another around 18 MYA (Burdigalian, Miocene).
https://static-content.springer.com/image/art%3A10.1186%2F1471-2148-13-128/MediaObjects/12862_2012_Article_2378_Fig4_HTML.jpg
Figure 4

Divergence time chronogram using Bayesian evolutionary analysis by sampling trees using BEAST. Fossil calibration points are indicated by numbers 1–31 embedded in black circles (refer to Table 2). Divergence time estimates (MY) are noted adjacent to their respective nodes and blue nodal bars correspond to the 95% highest posterior density regions. Geological periods are superimposed onto the phylogeny and listed as follows: D, Devonian; C, Carboniferous; P, Permian; TR, Triassic; J, Jurassic; K, Cretaceous; T, Tertiary. Colored taxa correspond to anomuran families as noted in the legend. Green boxes indicate a diversification shift.

Table 2

Fossil calibrations used in BEAST divergence time analyses

Taxonomy

Species

Geological Age (MYA)

Node

Outgroup

   

Natantia

   

Suborder Dendrobranchiata

   

Superfamily Penaeoidea

Aciculopoda mapesi Feldmann and Schweitzer, 2010

Late Devonian (Fammenian) 359-374

1

Suborder Pleocyemata

   

Infraorder caridea

Pinnacaris dentata Garassino and Teruzzi, 1993

Late Triassic (Norian) 204-228

2

Reptantia

Palaeopalaemon newberryi Whitfield, 1880

Late Devonian 354-370

3

Infraorder axiidea

Callianassa s.l. bonjouri Étallon, 1861

Early Jurassic (Toarcian) 176-183

8

Infraorder gebiidea

Upogebia s. l. obscura von Meyer, 1834

Early Triassic 245-251

9

Ingroup

   

Infraorder anomura

Platykotta akaina Chablais, Feldmann and Schweitzer, 2011

Late Triassic (Norian/Rhaetian) 201.6-228

4

Superfamily Aegloidea

   

Family Aeglidae

Protaegla miniscula Feldmann, Vega, Applegate, and Bishop, 1998

Early Cretaceous (Albian) 99.6-112

14

Superfamily Chirostyloidea

Pristinaspina gelasina Schweitzer and Feldmann, 2001

Late Cretaceous 65.5-99.6

15

Superfamily Galatheoidea

   

Family Galatheidae

Galatheites zitteli (Moericke, 1889)

Late Jurassic (Tithonian) 145.5-151

23

Genus Shinkaia

Shinkaia katapsyxis Schweitzer and Feldmann, 2008

Eocene 33.9-55.8

19

Family Munididae

Juracrista perculta Robins, Feldmann, and Schweitzer, 2012

Late Jurassic (Tithonian) 145.5-151

22

Genus Munida

Munida konara Schweitzer and Feldmann, 2000

Oligocene-Miocene 5.3-36.6

21

Genus Sadayoshia

Sadayoshia pentacantha (Muller and Collins, 1991)

Late Eocene (Priabonian) 33.9-37.2

20

Family Munidopsidae

Based upon a drawing and description only, type material apparently destroyed: Palaeomunidopsis moutieri Van Straelen, 1925

Middle Jurassic (Bathonian) 168-165

16

 

Based upon actual fossil material: Gastrosacus wetzleri Von Meyer, 1851

Late Jurassic (Oxfordian-Tithonian) 161-145

 

Genus Munidopsis

Munidopsis foersteri Feldmann et al., 1993

Late Cretaceous (Campanian) 70.6-83.5

18

Family Porcellanidae

Jurellana tithonia Schweitzer and Feldmann, 2010

Late Jurassic (Tithonian) 145.5-151

17

Genus Pachycheles

Pachycheles dorsosulcatus Beschin, Busulini, De Angeli, and Tessier, 2007

Eocene 36.6-57.8

25

Genus Petrolisthes

Petrolisthes bittneri De Angeli and Garassino, 2002

Oligocene 23.7-36.6

26

Genus Pisidia

Pisidia dorsosinuata De Angeli and Garassino, 2002

Eocene 36.6-57.8

24

Superfamily Hippoidea

   

Family Albuneidae

Praealbunea rickorum Fraaije, 2002

Late Cretaceous (Maastrichtian) 65.5-70.6

11

Genus Albunea

Albunea cuisiana Beschin and De Angeli, 1984

Eocene 33.9-55.8

13

Genus Zygopa

Zygopa galantensis De Angeli and Marangon, 2001

Oligocene 23-33.9

12

Family Blepharipodidae

Lophomastix antiqua Schweitzer and Boyko, 2000

Eocene 33.9-55.8

10

Superfamily Lithodoidea

   

Family Lithodidae

Paralomis debodeorum Feldmann, 1998

Miocene 5.3-23

31

Superfamily Paguroidea

Based upon claws only: Palaeopagurus deslongchampsi Van Straelen, 1925

Early Jurassic (Pliensbachian) 190-183

5

 

Based upon carapace material: Diogenicheles theodorae Fraaije et al., 2012

Late Jurassic (Oxfordian) 161-156

 

Family Coenobitidae

Birgus latro Linnaeus, 1767

Pliocene 2.6-5.3

29

Family Diogenidae

Annuntidiogenes ruizdegaonai Fraaije et al., 2008

Early Cretaceous (Albian) 99.6-112

7

Genus Calcinus

Calcinus agnoensis Beschin et al., 2005

Eocene 33.9-55.8

28

Family Paguridae

Pagurus malloryi Schweitzer and Feldmann 2001

Oligocene 23.7-36.6

30

Family Parapaguridae

Eotylaspis wehnerae van Bakel et al., 2008

Late Jurassic (Kimmeridgian) 151-156

27

Family Pylochelidae

Jurapylocheles malutka, Ammopylocheles mclaughlinae Van Bakel et al. 2008

Late Jurassic (Kimmeridgian) 151-156

6

Number corresponds to nodal placement as assigned in Figure 4.

Diversification analyses

The reworked version of MEDUSA [40] was used to detect whether any clade within the anomuran tree was best explained by independent diversification models, and to specifically address whether acquisition of the crab-like form resulted in an increase of diversification rates. The background tempo of diversification across the anomuran tree is characterized by a speciation rate lambda of 0.032572 lineages/Myr, and our results suggest that the diversification of anomurans is characterized by two periods where the tempo of diversification changes (Figure 4). A slow speciation rate is detected in the lineage leading to the monotypic and carcinized family Lomisidae, and an increase rate occurred in the squat-lobster family Chirostylidae. The ancient but species-depauperate branch leading to the monotypic family Lomisidae was optimally modelled separately with maximum likelihood estimate of lambda = 0 (rate reduction). The rate shift that occurred in the branch leading to the family Chirostylidae was characterized by a speciation rate lambda of 0.054182 (rate acceleration). All three resulting clade-specific diversification models were optimally fit as Yule models (AIC = 339.3032).

Discussion

Phylogenetic relationships

Recent studies on anomuran evolution have used molecular data [20, 21, 25, 38], morphological (including developmental) data [4143], or a combination of the two [19] to resolve phylogenetic relationships. These studies have dramatically increased our understanding of anomuran relationships and resulted in several major changes within higher-level classification [17, 18, 27]. The instability of anomuran taxonomy in recent years highlights the need for continued phylogenetic study of this group at many levels, and we for now elect to follow the most recent and up-to-date classification scheme [17, 18, 22, 4446].

Our total evidence approach combines 3669 molecular (nuclear and mitochondrial) and 156 morphological (adult, sperm and larval) characters from 137 species to recover the anomuran phylogeny (Figure 1). The addition of morphological data increased the support for many intra-familial and superfamily relationships that were poorly supported in the molecular-only phylogeny (Figure 2). As mentioned previously, anomurans have undergone dramatic changes in higher-level classification based on recent phylogenetic studies. Galatheoidea has been revised recently to exclude Aeglidae, Kiwaidae, and Chirostylidae [18, 23], and include only Galatheidae, Munididae, Munidopsidae, and Porcellanidae [18]. With the recent revision of Galatheoidea, all superfamilies were recovered as monophyletic (i.e., Hippoidea, Aegloidea, Lomisoidea, Chirostyloidea, Galatheoidea, Lithodoidea), except for Paguroidea (Figures 1 and 2). We found Lithodoidea to be nested within Paguroidea, which is in accordance with all recent combined (molecular + morphology) and molecular-based phylogenetic studies [1921, 33, 41]. An affinity between certain Lithodidae (Lithodes) and Paguridae (Pagurus) has been suggested since the early 1800’s [see [32] for review of literature], based on morphological characters including mouthparts, gills, and pleonal characters. However, the evolutionary pathways of the two groups continue to be debated (see also “Hermit to King, King to Hermit Evolutionary Hypotheses”) with all recent evidence pointing to a “hermit to king” hypothesis.

Family-level relationships were well resolved in the combined analysis (Figure 1) and in accordance with recent changes in classification [17, 19]. In 2010, Eumunida and Pseudomunida were removed from Chirostylidae and included in the newly erected Eumunididae, and the new family Munididae was erected on the basis of morphological and molecular evidence [17, 18]. Our results generally support these taxonomic revisions, recovering the Eumunididae as a monophyletic group, but finding Munididae to be possibly paraphyletic (Figure 1). Galatheidae was found nested inside Munididae, but alternative topologies that recovered Munididae as monophyletic were not significantly worse than our best estimate (see Results). Deeper sampling within both families is needed to resolve family and genus level relationships. The families Galatheidae, Munidopsidae, and Porcellanidae were all recovered as monophyletic with high support (Figure 1). The paraphyly and/or polyphyly of Diogenidae and Paguridae is consistent across the combined and molecular phylogenies and in accordance with recent phylogenies that have sampled sufficiently within these families [1921, 25, 26, 41]. Alternative hypotheses proposing the monophyly of these families (i.e., Diogenidae, Paguridae) were rejected using S-H tests, confirming our findings (see Results). Coenobitidae (semi-terrestrial hermit crab) was deeply nested within Diogenidae (left-handed hermit crabs) while Paguristes and Areopaguristes are more closely related to Parapaguridae (deep-water hermit crabs) than to other members of Diogenidae (Figure 1). This relationship was first proposed by Boas [47], which he collectively called the Paguristinen. The families Pylochelidae and Hapalogastridae were found to be polyphyletic in the molecular analysis (Figure 2), but monophyletic in the combined analysis (Figure 1). Although we did not find Pylochelidae to be polyphyletic in our combined tree, alternative molecular-based and morphological phylogenies have recovered similar results that suggest a polyphyletic Pylochelidae [20, 48]. Additionally, there is morphological support for polyphyly among pylochelids separating Trizocheles and Mixtopagurus from the remaining pylochelid genera (based on form of ocular acicles, eye type and larval forms [20, 48]).

Generic relationships within Anomura seem to be much less resolved than superfamily and family level relationships. We found several genera to be poly- or paraphyletic (i.e., Munida, Munidopsis, Paguristes), in agreement with previous studies [19, 20, 41, 49]. Most instances of non-monophyly occur within highly speciose genera (i.e., Paguristes = ~115 spp., Pagurus = ~170 spp., Munida = ~240 spp.), suggesting deeper sampling and continued research needs to be undertaken on these groups.

King to hermit and hermit to king evolution: historical to recent hypotheses

Although past studies have shown an affinity between Paguridae (hermit crabs) and Lithodidae (king crabs), the evolutionary pathways and ancestry of these anomuran lineages have been debated for the past two centuries. The traditional and prevalent hypothesis posits that lithodids are free-living hermit crabs that abandoned shell use and underwent a series of morphological changes (carcinization) resulting in a crab-like form. It has been argued that the asymmetry of the lithodid female pleon, in particular, is evidence of asymmetrical hermit crab ancestry. Boas [31, 50] was the first to suggest the evolution of lithodids specifically from pagurid ancestors, and based on morphology proposed the ancestral pagurid to be closely related to Nematopagurus and Pylopagurus. Bouvier [5153] similarly derived the lithodids from the pagurids, agreeing with Boas on the structural pleonal similarities between these two groups. However, Bouvier also proposed a series of gradual and linear progressive stages in the transformation of the pagurid pleon, starting from a pagurid precursor to various genera of hapalogastrids (Hapalogaster, Dermaturus) and lithodids (from Neolithodes, Paralithodes, Lithodes, Lopholithodes, Paralomis, Rhinolithodes, to Cryptolithodes). In modern times, this concept of pagurid and lithodid evolution was brought to attention when Cunningham et al. [54] coined the phrase “from hermit to king” in applying molecular analysis to study hermit crab and lithodid phylogeny, and was then widely popularized [55]. A subsequent morphologically-based phylogenetic study by Richter and Scholtz [56] supported this same evolutionary view of pagurid and lithodid evolution. Recently, a study that examines the hemolymph vascular system in hermit and king crabs found close similarities in arterial systems of the dorsal cephalothorax [57].

An alternate, opposite view, often stated as the “king to hermit” evolutionary hypothesis, was proposed by McLaughlin and Lemaitre [32]. Using morphological characters and an unusual application of cladistic methodology, McLaughlin and Lemaitre explored possible evolutionary pathways of carcinization across Anomura (rather than attempt to determine precise phylogenetic relationships among taxa). They acknowledged that the crab-like form might have arisen multiple times across the Anomura, but in the case of pagurid/lithodid evolution they concluded that the opposite evolutionary trajectory was more plausible, i.e., the transition was from a “crab-like” body form to a ‘hermit-crab” body form through a series of habitat change, calcium loss, and consequential adult morphological adaptations. Subsequent studies showed that the linear evolutionary scenario proposed by Bouvier did not correspond to the ontogenetic changes that take place in the megalopa to juvenile crab stages in at least 10 species of eight lithodid genera [43, 58]. Based on observations of the complex changes in pleonal tergites from megalopa to juvenile crab stages, these studies demonstrated that adult lithodid pleonal tergite structure in several species was the result of decalcification and sundering, not secondary calcification and fusion as had been proposed by Bouvier.

Our recent phylogenetic reconstruction of anomurans based on molecular and morphological data supports the traditional “hermit to king” hypothesis in congruence with all recent studies [1921, 33, 59]. With the largest number of taxa and most robust molecular/morphological dataset ever used in a phylogenetic study of anomurans, our study once again shows Lithodoidea to be nested within Paguridae. Moreover, our conclusions are consistent with the fossil record, which suggest hermits are much older (Jurassic) than king crabs (Miocene, Table 2). Finally, topology testing rejects the “king to hermit” hypothesis and finds it as significantly worse than the alternative (P < 0.05) (i.e., “hermit to king”) (see Results).

While there is undeniable evidence of a close relationship between hermits and king crabs, it is less clear how morphological changes associated with carcinization may have proceeded within the Lithodoidea. A recent study comparing hermit and king crab circulatory systems identified several vascular changes that occurred as the result of carcinization, arguing for more comparative studies that look at morphology (both internal and external) and development [57]. However, only with a clear phylogenetic hypothesis can many of these studies be correctly interpreted. Recent molecular or combined morphological-molecular phylogenies recover conflicting evolutionary relationships, although only three lithodoid genera (and not always the same, or excluding Hapalogastridae) have been used in previous analyses [1921, 33]. Our phylogenetic reconstruction (Figure 3) shows the less carcinized and less calcified Hapalogastridae as sister to Lithodidae, in agreement with virtually every study since Bouvier’s in the 19th century. But within Lithodidae, and in contrast to Bouvier’s linear hypothesis, our study places Cryptolithodes, the most heavily calcified and carcinized lithodid, as an early branching lineage followed by more derived genera (see also McLaughlin and Lemaitre, 1997, Figure 2). It thus appears that the process of heavy calcification may have appeared at least twice in lithodid lineages. More lithodoid genera/species are needed to examine the process of carcinization within the Lithodoidea and to properly test Bouvier’s and Boas’ earlier hypotheses (explaining the transition of a shell-dwelling hermit crab to a fully calcified lithodid crab). In conclusion, while recent, modern studies, including ours, overwhelmingly and clearly support a “hermit to king” evolutionary scenario, it is also clear that the evolutionary process and concomitant morphological changes (particularly in pleonal tergal plates and pleopods) that occurred within the Lithodoidea to produce the various degrees of crab-like forms in that family, is at best poorly understood.

In our reaffirmation here of the “hermit to king” hypothesis, we revealed a close relationship between Lithodoidea and the pagurid, Discorsopagurus (Figures 1, 2, 3 and 4). Curiously, the same close relationship has surfaced in previous studies [21, 33]. This revelation is important to highlight because the “hermit [Paguridae] to king [Lithodidae]” hypothesis presupposes a distinctly asymmetrical shell-dwelling hermit crab-like ancestor from or close to the Paguridae, or more precisely Pagurus, as proposed by early [52] as well as modern studies [54]. However, Pagurus is currently a taxonomic and paraphyletic conundrum of more than 160 species, and it remains unknown which of the different lineages within “Pagurus” could be the most likely candidate for lithodoid ancestry. The close relationship between Discorsopagurus and Lithodoidea may suggest a Discorsopagurus-like hermit crab as the precursor to the crab-like lithodoids. All species of Discorsopagurus are tube-dwellers, not shell-dwellers, and show pleonal asymmetry only in having unpaired pleopods. The genus is relatively small in size compared to the typically large-sized lithodoids with a distribution across both sides of the North Pacific, from the Sea of Japan to Puget Sound and the Straits of Juan de Fuca, Washington [60]. The relationship between Discorsopagurus and lithodoids may not be coincidental in the North Pacific region where D. schmitti (this analysis) and all other Discorsopagurus species are found [6163]. This region harbors the highest diversity of lithodoids, so it is plausible to expect closely related species (Discorsopagurus) in similar areas. Future studies with increased sampling within these groups will shed light into the evolutionary pathway of lithodoids from paguroid (possibly Discorsopagurus-like) ancestors.

Divergence times and character evolution

Our divergence dating analysis estimated the origin of Anomura to be in the Late Permian (~259 MYA) from a symmetrical crab-like ancestor (Figures 3 and 4). This is consistent with many higher-level decapod phylogenies finding Anomura and Brachyura as sister clades [26, 35, 37, 56], including the present study (Figure 1). Results estimate that the earliest diverging anomurans are the hippoids (~221 MYA), consistent with recent molecular estimates [20]. Although this date is considerably older than the hippoid fossil record, closely related extinct forms extend into the Triassic and present day Hippoidea are found in substrates underrepresented in the fossil record. The superfamily Hippoidea containing Blepharipodidae, Hippidae, and Albuneidae, has been described as being similar to primitive brachyurans [20, 64], and ancestral reconstruction analysis confirms that the present day hippoids were derived from crab-like (brachyuran-like) predecessors (Figure 3A). The next radiation occurred in the Late Triassic, giving rise to the squat-lobsters and crab-like superfamilies Chirostyloidea and Galatheoidea, Aegloidea, Lomisoidea, and the hermit crab and crab-like superfamilies Paguroidea and Lithodoidea. Our results suggest these superfamily clades were derived from a squat-lobster-like ancestor approximately ~205 MYA (Figures 3A and 4). Interestingly, our divergence time and character reconstruction analyses (Figures 3A and 4) are consistent with fossil evidence, and more specifically, the discovery of Platykotta akaina, the oldest known anomuran fossil [1]. Platykotta akaina, with a possibly squat-lobster-like body form, dates back to the Late Triassic (~201.6-228 MYA) and has strong morphological affinity with the superfamilies Chirostyloidea and Galatheoidea. This fossil was found as part of a biotic assemblage suggesting that Platykotta akaina thrived in tropical-subtropical waters and lived in the subtidal with connections to the open ocean [1, 65].

Around 137 MYA a squat-lobster like ancestor gave rise to a unique superfamily of anomurans, Aegloidea. Aegloid crabs represent the only freshwater anomuran family and can be found in caves, lakes, and streams throughout the Neotropical region of South America [66]. Apart from a single species of freshwater hermit crab, Clibanarius fonticola[67], the transition into a completely freshwater environment only occurred in extant Aeglidae (Figure 3B). Fossil evidence suggests freshwater aeglids once inhabited marine waters, based on the fossil representative, Haumuriaegla glawssneri, found in New Zealand from Late Cretaceous rocks [68]. In combination with our divergence time analyses, we hypothesize that the complete transition in freshwater occurred sometime between the Late Cretaceous and Miocene. This transition appears to have allowed for rapid diversification approximately 13 MYA (20–7.4 MYA).

From approximately 180 MYA to 147 MYA, the families of Galatheoidea radiated and diversified. These include the squat lobsters families Munidopsidae, Munididae and Galatheidae, and the porcelain crab family Porcellanidae. The porcellanids diverged in the Middle Jurassic (~172 MYA) from squat-lobster like ancestors, but a crab-like body form evolved by the Tithonian (~151-145.5 MYA) based on fossil evidence and ancestral reconstruction analyses. This was the first occurrence of carcinization from a squat-lobster or hermit-like ancestor within Anomura (Figures 3A and 4). Interestingly, Henderson [69] and Ortmann [70] suggested porcellanid crabs were derived galatheids despite the differences in body shape and form, and this is consistent with our current evolutionary hypothesis.

Lomisoidea and Chirostyloidea diverged around 122 MYA from a squat-lobster like ancestor. This body form was retained within the chirostyloids and underwent further carcinization, attaining a crab-like form in the monotypic Lomisidae, endemic to Australia.

Early hypotheses based on larval evidence proposed hermit crabs evolved as two independent lineages, Coenobitoidea and Paguroidea [71] and recent studies continue to explore superfamily and family level relationships [20, 23, 39]. In our combined analysis, the hermit crab families, Pylochelidae, Parapaguridae, Diogenidae, Coenobitidae, and Paguridae, formed a monophyletic group with the inclusion of Lithodidae or king crabs, and Hapalogastridae. We estimated these families arose early in the evolution of Anomura, approximately 205 MYA. The symmetrical hermit crabs, Pylochelidae, are unique with most having complete body symmetry and in utilizing broken gastropod shells, siboglinid tubes, and coral pieces for shelter and protection, in contrast to other hermit groups that commonly use coiled gastropod shells [42]. Our analysis suggests pylochelids branched early in the evolution of hermit and king crabs, consistent with morphological and fossil evidence that place them as a basal primitive lineage [39]. The oldest hermit crab fossils, Jurapylocheles malutka, Ammopylocheles mclaughlinae and Eotylaspis wehnerae[72] of Kimmeridgian age (~151-156 MYA), belong to the families Pylochelidae and Parapaguridae (Table 2). This is consistent with our divergence time analysis, which recovers these families as early branching lineages. Diogenidae, Coenobitidae, and Paguridae typically possess an asymmetrical pleon accompanied by an enlarged right or left chela. According to our combined analysis, pleonal asymmetry in hermits appears to have been derived once in the evolution of the anomurans, most probably between 200–187 MYA. This contrasts with the results obtained by Tsang et al. [20], who proposed that the pleonal asymmetry evolved independently in two different hermit crab lineages, once in Parapaguridae, and a second time in Diogenidae, Coenobitidae, and Paguridae. These contrasting differences are the result of incongruent phylogenies based on total evidence (molecular + morphology, this paper) and molecular only approaches [20]. Note, however, that our molecular-only analyses recover similar results to those of Tsang et al. [20]. The semiterrestrial coenobitids colonized land from a marine ancestor sometime between 84 and 39 MYA (Figures 3B and 4). The emergence of Diogenidae (~173-167 MYA), Coenobitidae (~84 MYA), and Paguridae (~173 MYA) all predate their first appearance in the fossil record (Table 2, Figure 4). Carcinization occurred for the third time in the crab-like superfamily Lithodoidea between 29–18 MYA from an asymmetrical hermit-like ancestor. This estimation is consistent with other timing estimates of king crab carcinization [54].

Carcinization

The crab-like body form was recovered in our study as the ancestral state for all the anomurans. In our study, all alternative body forms were present (crab-like, squat lobster, symmetrical hermit, and asymmetrical hermit) early in the divergence of the anomurans. From these ancestral character states, carcinization occurred independently three times during the evolution of Anomura, once in the Lithodoidea through an asymmetrical hermit intermediate, and twice in Lomisidae and Porcellanidae through squat lobster intermediates (see AHI and SI, Figure 3A). These evolutionary pathways of the crab-like form, twice from squat lobster intermediaries and once through an asymmetrical ancestor, corroborates recent hypotheses [20]. However, our tree differs significantly from Tsang et al.’s study [17] in the deep ancestral origins of carcinization. Tsang et al.’s hypothesis suggests a symmetrical hermit crab-like ancestor predated the squat lobster and asymmetrical intermediaries, whereas we recovered a crab-like ancestor to predate these intermediaries. We acknowledge that our analysis recovers two deep nodes that are unresolved, however symmetrical reconstruction at these nodes seems unlikely (Figure 3A). It must also be noted that the most recent common ancestor of Anomura is unresolved in the Tsang et al. analysis, although it appears to be a crab-like or symmetrical hermit ancestor. The major differences in the two analyses stems from the differences in phylogeny and more specifically the monophyly (our study) or polyphyly [17] of Paguroidea and families therein (i.e., Pylochelidae). There is agreement with Tsang et al. in the sister group relationship between Paguridae and Lithodoidea, although Tsang et al. used only four lithodid genera (vs. eight in our study) and did not include representatives of Hapalogastridae. In addition, both studies provide strong evidence for the intermediary ancestors directly predating carcinization across Anomura (twice through squat lobster (SI) and once through asymmetrical hermit (ASI), Figure 3A).

The multiple cases of carcinization among the anomurans have been noted since the early 1900s. Borradaile (1916) was the first to propose the term carcinization to explain the crab-like aspects of the hermit crab Porcellanopagurus and the tendency of anomurans to achieve this form, a phenomenon unique to Anomura not evident in other decapod lineages (e.g., lobsters, shrimp). The emergence of the crab-like form is not ‘evenly distributed’ across our phylogeny, first occurring in the older lineages Porcellanidae and Lomisidae and only more recently within the superfamily Lithodoidea. Some questions naturally arise. Why did carcinization occur independently three times during the evolution of the Anomura? Why did the presumably shell-dwelling asymmetrical hermit crab ancestors of lithodid king crabs forsake the use of shells for protection, which already provided them with survival advantage? Morrison et al. [33] suggest that the crab-like form might represent a key innovation that is associated with an evolutionary advantage, possibly due to the greater mobility and agility provided by this morphology. This seems to be evident within the true crabs, or Brachyura, which dominate decapods in terms of species richness [>6,559 species; 34] and have thrived in marine, freshwater, and terrestrial environments. Although diversification seems to be low in the crab-like anomurans when compared to the brachyurans, fossil evidence and divergence time analyses suggest crab-like anomurans are much younger when compared to the closely related true crabs (Table 2, Figure 4). Furthermore, the crab-like porcellanids are one of the oldest (~172 MYA, MRCA = 139 MYA) and most diverse families of anomurans [~247 species, 22]. Lithodids represent an even younger lineage, originating ~18 MYA, but comprising over 100 extant species. It is plausible that a crab-like form may hold some evolutionary advantage when considering age and diversification within Anomura, although this does not seem to hold true for all groups that underwent the crab-like transition (i.e., monotypic family Lomisidae). A second hypothesis explains the possible advantage of carcinization from a hermit-like ancestor. Previous studies have suggested a free-living body form may have a selective advantage in obtaining food resources when unconstrained by a gastropod shell [54, 73]. An example can be seen in the semi-terrestrial hermit crab, Birgus latro, a species that in the adult stages has lost dependence on shells as protection for the pleon, and instead has developed a calcified body [74].

Diversification rates

The extraordinary morphological and ecological diversity of anomurans has long fascinated evolutionary biologists. Previous studies covering a wide range of faunas have shown how morphological or ecological factors may influence the course of subsequent evolutionary diversification [7577], and in particular for anomurans it has been hypothesized that the acquisition of the crab-like form may have acted as a key-innovation [33].

Our analysis reports the pattern of diversification in Anomura to be characterized by a low net rate of diversification, with two major changes in the rates of speciation along its evolutionary history. The initial diversification of the group during the Late Permian was characterized by slow rates of diversification and it was not concomitant with major family radiations, which took place from the Jurassic onwards.

A significant change in the tempo of diversification was identified within the speciose squat-lobster family Chirostylidae, which has a higher speciation rate than the overall tempo of diversification across the anomuran tree (Figure 4). Recent studies based on the munidid squat-lobster genus Paramunida suggest that dramatic environmental change may provide great geological and habitat complexity, which in turn promotes isolation and rapid diversification [78]. The fact that both families, chirostylids and munidids, diverged during the Late Triassic (see Figure 4) and currently occupy deep-sea habitats suggests that similar geological and environmental changes may also have driven major diversification within the Munididae, which shifted habitats at some point because the Jurassic forms are nearly all coral-reef associated. Currently, the family Chirostylidae accounts for 7% of all anomuran species, but the true diversity is underestimated and about 100 new species are in hand of taxonomists [79]. Clearly, a more accurate phylogenetic framework is needed to interpret in detail the exceptionally high speciation rates reported here.

The monotypic family Lomisidae showed a strikingly lower rate than the overall tempo of diversification in Anomura. Lomis hirta is anomalous in its prolonged persistence despite an inferred speciation rate of zero (as recovered by the MEDUSA analysis, see Results). These taxa, old lineages with few extant species, have been reported in several invertebrates and vertebrates [40, 80, 81] and more recently in butterflies [82], suggesting that extremely low rates of diversification characterize these groups. High extinction rates could also account for this pattern; however, we report that a pure-birth Yule model best explains our data. Under a high-extinction scenario we would expect to see an overabundance of more recently arisen species that simply have not yet gone extinct; such a pattern is not observed in our phylogeny.

Our analysis failed to identify a correlation between the timing of branching events (speciation) and the evolutionary history of carcinized lineages, which suggests that the acquisition of a crab-like form did not play a major role in shaping extant anomuran biodiversity. However, a major limitation of the MEDUSA approach is that rate shifts cannot be assigned below the level of phylogenetic resolution [40], which prevents us from evaluating if the highly carcinized family Lithodidae underwent an unusual rapid diversification event. The lack of a rate shift in the branch leading to the three collapsed families (Paguridae, Hapalogastridae, and Lithodidae) does not necessarily imply that subclades within that group have not experienced changes in the tempo of diversification, which may be masked by the lack of taxonomic resolution among these taxa. Thus, further studies which focus on clarifying the systematics of the infraorder, with particular emphasis on the families Paguridae, Hapalogastridae, and Lithodidae, are necessary to examine the role of carcinization in anomuran diversification.

Conclusions

Anomuran relationships have been the topic of long debate, likely because of their extraordinary morphological and ecological diversity and their common targeting in fisheries. Here we estimate evolutionary relationships among 19 families, 7 superfamilies, and 137 species of anomurans based on morphological and molecular data to provide the most robust anomuran phylogeny to date. Many families and genera appear to be poly- or paraphyletic suggesting further taxonomic revisions at these levels. Carcinization evolved multiple times during the evolution of Anomura whereas transition into exclusively freshwater or semi-terrestrial environment occurred in the families Aeglidae and Coenobitidae, respectively. Divergence times date the origin of the group in the Late Permian, with subsequent radiations through the Jurassic and Cretaceous. Results suggest that anomurans diversified under low speciation rates with two major changes in the tempo of diversification. First insights suggest that the acquisition of the crab-like form did not play a major role in shaping the extant diversity of Anomura, but further examination is required in order to confirm this pattern.

Methods

Taxon sampling

Our study included extant representatives from 19 families, 77 genera, and 137 species of anomurans. The exceptionally rare family Pylojaquesidae is excluded for lack of molecular grade tissue samples. A total of 345 sequences from 76 of 144 anomuran specimens were new to this study, while sequences for all five genes from 68 taxa were obtained from GenBank. Newly included specimens were collected on cruise and field expeditions, from collaborators, or from the University of Louisiana at Lafayette Zoological (ULLZ) collection of molecular grade specimen and tissue samples (Table 1). Specimens were stored in 80% ethyl alcohol.

The sister group of Anomura is widely accepted to be Brachyura [2426, 3538], but because some molecular studies have recovered alternative arrangements [24, 25, 38] we included 18 outgroup taxa (see Table 1) spanning several decapod lineages. Different outgroups were included/excluded to explore sister relationships to Anomura and the impact of outgroup selection on anomuran relationships. They consist of representatives from infraorders Brachyura (5), Axiidea (4), Gebiidea (3), Caridea (4), and suborder Dendrobranchiata (2).

Morphological matrix

Our morphological data matrix consisted of 156 characters and 154 species (including outgroups) and was constructed in MacClade 4.0 (see Additional files 2 and 3). Citations of previously recognized characters and states are given following characters in Additional file 3. Codings for somatic morphological characters were scored based on examination of sequenced species (Table 1) supplemented by literature. For spermatozoal (130–143) and larval characters (144–156) that are highly conserved (but not available for every sequenced species), reasonable assumptions of monophyly were made in order to optimize the potential contribution of these data. Thus, for these spermatozoal characters, all members of a particular family for which data were available for some members were scored as uniform. For larval characters (primarily first zoeal stage), all members of a particular genus for which data were available for some members were scored as uniform. The larval characters that could be meaningfully scored across the breadth of taxa were included. Others are typically invariant within the family-level (and often superfamily-level) clades, as defined by recent revisionary classifications, and could have been effectively scored at family level. In deference to the possibility that some families might not be monophyletic, however, we took a more conservative, genus-level approach to larval character scoring. Monophyly (or not) of genera, however, with respect to the first zoeal characters employed does not affect results because of the level of generality of characters operating at low taxonomic levels.

Missing data were scored as unknown (?) and polymorphisms were scored as such rather than assuming a plesiomorphic state. Just as alignment gaps in molecular data have been variously treated as a fifth position or as missing in different studies, inapplicable character states in the morphological data may be scored as missing or as an additional character state, ‘inapplicable’ [83]. We scored inapplicable character states as unknown (indicated by ‘-’), rather than an additional state, in order to avoid the possibility of nodes being supported by a non-existent character state [84].

DNA extraction, PCR, sequencing, and next-generation approaches

Total genomic DNA was extracted from the pleon or gills using the QiagenDNeasy® Blood and Tissue Kit Cat. No. 69582. Two partial mitochondrial genes, 16S and 12S, were amplified by PCR using the following primers, respectively: L2/L9 & 16S1472 or 16SF & 16S1472 [~580 bps, [8587]] and 12S1F & 12SR or 12SF & 12S1R [~350 bps, [88]]. The nuclear large subunit 28S rRNA was amplified in sections by 1.3 F/4b, 3.25/4.4b, sA/5b, and 4.8/6b [~2200 bps, [89, 90]]. The nuclear small subunit 18S rRNA was amplified by A/L, C/Y, O/B [~1800 bps, [91, 92]] or by 1 F/2.9, 0.7/bi, 2.0/9R [89, 90], or by shorter internal primers (~1700 bps, B/D18s1R, D18s2F-D18s2R, D18s3F-D18s3R, D18s4F-D18s4R and D18s5F-A [93]). The histone H3 gene was amplified by H3AF/H3AR [~350 bps, [94]]. The majority of target gene regions were obtained through traditional Sanger sequencing and data for seven taxa were obtained through next-generation 454 sequencing (see below).

PCR amplifications were performed in 25 μl volumes containing 1 μl of Taq polymerase HotMaster or REDTaq, PCR buffer, 2.5 mM of deoxyribonucleotide triphosphate mix dNTPs, 0.5 μM forward and reverse primer, and extracted DNA. The thermal profile used an initial denaturation for 1 min at 94°C followed by 35–40 cycles of 30 sec at 94°C, 45 sec at 45-60°C depending on gene region, 1 min at 72º and a final extension of 10 min at 72°C. PCR products were purified using plate filters PrepEase™ PCR Purification 96-well Plate Kit, USB Corporation and sequenced with ABI BigDye® terminator mix (Applied Biosystems, Foster City, CA, USA). Cycle sequencing reactions were performed in an Applied Biosystems 9800 Fast Thermal Cycler (Applied Biosystems, Foster City, CA, USA), and sequencing products were run forward and reverse on an ABI 3730xl DNA Analyzer 96-capillary automated sequencer in the Brigham Young University (BYU) sequencing center.

Sequence data for seven taxa were obtained using a novel next-generation sequencing technique TAS: Targeted Amplification Sequencing on the 454 platform [95, 96]. The process required a two-step PCR to prepare selected DNA regions for targeted/directed sequencing. The first PCR used a locus specific primer (e.g., 16S, 12S, etc.) with a 22 bp adapter. These amplicons were cleaned using plate filters PrepEase™ PCR Purification 96-well Plate Kit, USB Corporation. One μl of cleaned PCR product was used as template for the second PCR. PCR II incorporated a 10 bp barcode multiplex identifier, MID, 4 bp key, and a 21 bp 454 Titanium primer. Samples were again cleaned using the Millipore system and subsequently combined in emulsion PCR and sequenced via 454 GS FLX Titanium pyrosequencing technology (Roche) at the BYU sequencing center. The bioinformatic pipeline, BarcodeCruncher, allowed us to exclude short reads, trim adapters, identify contamination, parse barcoded sequences, and assembly consensus sequences for phylogenetic reconstruction [for full description of methods see [95, 96]].

Phylogenetic analyses

Sequences were cleaned and assembled using Sequencher 4.9 (GeneCodes, Ann Arbor, MI, USA). To check for pseudogenes, we followed suggestions by Song et al. (2008), which included extracting DNA from tissue with high amounts of mitochondrial gill tissue, translating protein-coding sequences H3 to check for indels and stop codons, comparing sequences among closely-related species, and building individual gene trees to ensure similar topologies [97]. Comparing gene trees and BLAST searches helped identify contamination. Two datasets were assembled: 1) molecular dataset including all 5 gene regions 2) combined dataset including molecular + morphological data.

Individual gene alignments were performed using MAFFT, implementing the “E-INS-i” option. For non-protein coding genes 12S, 16S, 18S, 28S, GBlocks v0.91b were used to exclude regions of the alignment with questionable positional homology [98]. The parameters used in GBlocks for 12S, 16S, 18S, 28S, were as follow: minimum number of sequences for a conserved position = 50/77/77/79; minimum number of sequences for a flanking position = 50/77/80/79; maximum number of contiguous non-conserved positions = 8/8/8/8; minimum length of a block = 5/5/5/5; allowed gap positions = half/half/half/half. Final alignments included 300, 474, 1632, and 931 base pairs for 12S, 16S, 18S, and 28S, respectively. After trimming for primer residue, the H3 alignment resulted in 332 base pairs. In MESQUITE [99], all genes were concatenated 3669 basepairs and partitioned for analysis. The final molecular dataset included 162 individuals as 3669 basepairs (5 genes) while the combined data set included the molecular dataset plus an additional 156 morphological characters.

The Maximum Likelihood (ML) analysis was conducted using RAxML Randomized Axelerated Maximum Likelihood [100102]. Likelihood settings followed the General Time Reversible Model GTR with a gamma distribution and RAxML estimated all free parameters following a partitioned dataset. The first algorithm used in the analysis was the “-f a” option, for a rapid bootstrap analysis and search for the best tree in a single pass. The second algorithm implemented another search for the best tree implementing a “-f d” option of -#200 iterations of random starting trees. Likelihoods were compared to determine the best tree and bootstraps were mapped on the resulting topology. Confidence in the resulting topology was assessed using non-parametric bootstrap estimates [103] with 1000 pseudoreplicates and values > 50% are presented on the resulting phylogeny.

Bayesian analyses (BA) were performed in MrBayes v3.1.2b4 [104] for the molecular and combined datasets morphology + molecular. We used the Markov k Mk, [105] model for the morphological characters equal state frequencies, combined with gamma distributes rates across sites. The model of evolution that best fit the individual datasets was determined by MODELTEST 3.7 [106] and these parameters were applied to our molecular dataset. Three independent BA analyses were implemented each with 20 chains and a starting tree obtained from the ML analysis to help reach convergence. The molecular analysis ran for 30,000,000 generations, sampling one tree every 1000 generations. The combined analysis ran for 50,000,000 generations, sampling one tree every 5000 generations. To ensure that independent analyses converged on similar values, we graphically compared all likelihood parameters and scored means and variances using the program Tracer v1.4 [107]. Burn-in and stationary distributions were determined by observing the likelihood -LnL scores and split frequencies for the data (~10 million generations). A 50% majority-rule consensus tree was obtained from the remaining saved trees, once the data reached convergence. Posterior probabilities Pp for clades were compared for congruence and post-burn-in-trees were combined between individual runs. Values > 0.5 are presented on the BA phylogram presented as percentages. All analyses were run on Marylou6 Dell PowerEdge M610 computing cluster at Brigham Young University. High support is defined as ≥ 95/70 Pp/bs, marginal support is ≥ 85/65 and low support is ≤ 84/64.

Alternative hypothesis testing

A partitioned S-H test [108] was used to test whether previous hypotheses of anomuran evolution implicit in modern, morphologically-based classifications [1416] and morphological and/or molecular phylogenies [19, 20, 23] were significantly worse than our best ML tree. The test was implemented in RAxML using the same data partitions used to estimate our phylogeny. As in the ML analysis, the GTRGAMMA model was applied to each partition. Seven independent constrained tree topologies were constructed in Mesquite v.2.71 [99]. Topological constraints were forced to the following monophyletic clades: Diogenidae, Hapalogastridae, Lithodidae, Munididae, Paguridae, Paguroidea, and Pylochelidae. These clades were tested to examine the validity of current generic assignments by testing the poly- and paraphyly of the families and superfamilies in the tree. Lastly, to test the king to hermit hypothesis, we forced the topologies: 1) king crabs (Lithodidae) ancestral to hermit crab superfamily Paguroidea and 2) king crabs (Lithodidae) ancestral to hermit crab family Paguridae to test if these hypotheses are significantly worse than a “hermit to king” evolutionary pathway.

Character evolution

We used ancestral state reconstruction (ASR) methods implemented in Mesquite v.2.71 [99] to examine character evolution across the anomurans. We traced evolutionary pathways of two characters: body form and habitat. Body form was assigned as follows: 0: crab-like (carcinized), 1: squat lobster form, 2: asymmetrical pleon, 3: symmetrical pleon. Habitat was assigned as 0: semi-terrestrial, 1: freshwater, 2: marine. These characters were optimized across our best estimate of anomuran relationships (=combined (molecular + morphology) Bayesian phylogeny). Because the importance of employing different methods for ASR has been documented, we used both maximum parsimony and maximum likelihood methods [109]. Likelihood methods are often preferred over parsimony reconstructions since they take into account branch lengths, all character state possibilities, and model evolution [110]. The model of evolution used in the maximum likelihood analysis was the Markov k-state 1 (Mk1) parameter model, which allows equal probability for any character state change. All characters were scored and compiled based on specimen observation and/or literature searches. Reconstructions among all outgroup taxa are not shown.

Divergence time analyses

To estimate the relative timing of origins, diversification, body form evolution and transition in habitat, Bayesian molecular dating methods were implemented in BEAST v1.5.2 (Bayesian evolutionary analysis by sampling trees) [111]. BEAST allows for missing data, multiple calibration points, relaxed clock models, and increased flexibility of model parameters when compared to other dating methods (e.g., Multidivtime). Substitution and clock models were unlinked and the dataset was partitioned by gene following models of evolution generated by MODELTEST v3.7. A relaxed uncorrelated lognormal clock model and Yule speciation tree prior were selected. We recognize that there are varied models to consider when using relaxed dating methods. Simulation studies that have compared accuracy of relaxed clock methods have recovered conflicting results, with some favoring uncorrelated models [112], others favoring autocorrelated models [113] and some favoring both (autocorrelated and uncorrelated) depending on the dataset [114]. We chose an uncorrelated relaxed clock method due to the biological data under investigation and evidence from our divergence time analysis. It has been suggested that autocorrelation in life history traits (one biological assumption underlying autocorrelated relaxed clocks) would be less relevant in studies focused at high taxonomic levels, divergent taxa [112, 115], and sparely sampled datasets [116]. We had little reason to believe we had autocorrelation in our anomuran dataset considering we were reconstructing a phylogeny across an infraorder that originated over 250 MYA (oldest fossil evidence = 201–228 MYA). Moreover, our sampling method focused at the superfamily and family level (and not within genera or species). Secondly, it has been suggested that rate autocorrelation can be measured by comparing the posterior and prior distributions of covariance in rates on neighboring branches [112, 116]. All covariance estimates in our divergence time analyses suggested we had no strong evidence for autocorrelation of rates in our phylogeny. The statistic measure between parent and child branches contained values that span zero suggesting branches with slow and fast rates are adjacent on the tree. For abovementioned reasons, we did not assume autocorrelated rates across our tree. Our best estimate of phylogeny (=combined (morphology + molecular) tree) was used as a starting tree and the tree searching parameters were removed from the BEAUTI xml file.

Using the non-parametric rate smoothing algorithm in r8s [117], we made branch lengths proportional to the timing chronogram rather than the substitutions per site phylogram. This allowed the tree to adhere to the topological and temporal constraints of using fossil calibrations. We implemented two runs in BEAST with MCMC chain length of 350 million generations logging parameters every 3,500 samples. To ensure that analyses converged on similar values with acceptable mixing, likelihood stationary and burn-in values, we used the program Tracer v1.4 [107]. The runs were combined using LogCombiner [112]. Estimates of the mean divergence times with 95% highest posterior density regions HPD and posterior probabilities represented as percentages are noted on the chronogram. The BEAST analyses were performed on the Marylou6 Dell PowerEdge M610 computing cluster at Brigham Young University.

Fossil and time calibrations

A total of 31 fossils were included in the analysis. We included fossils that represented the oldest known specimen for a particular family and/or genus (Table 2). Only fossils that could be confidently assigned to clades based on personal observation and/or previous literature were included in the analysis [[118], Table 2]. We followed recommendations by Parham et al. [119] when justifying fossil placement. Both deep and shallow fossil representatives were included. All fossils were placed at the crown (i.e., most recent common ancestor MRCA) or stem (i.e., node directly preceding the MRCA node of the clade). There was disagreement among authors about the familial assignment of Juracrista, as either a munidid or galatheid. The munidids and galatheids, however, are closely related so the affect on calibration is minimal. Therefore, we have followed the original taxonomy [120] and retained Juracrista in Munididae. Because divergence time should predate the fossil occurrence, all calibrations followed an exponential prior with the offset value set to the minimum calibration age. This distribution is suitable for modeling fossil calibrations, because it allows us to avoid a hard upper bound while providing an increased probability with the age range of fossil discovery [121].

Diversification rates

We analysed patterns of diversification along the anomuran tree using a reworked version of MEDUSA [40]http://www.webpages.uidaho.edu/~lukeh/software/index.html. This method infers clade-specific changes in the tempo of diversification (rate acceleration and rate reduction) across a tree from phylogenetic branch lengths and taxonomic extant species richness information, the latter to account for incomplete taxon sampling [77]. MEDUSA utilized a stepwise AIC approach to adding clade-wise diversification models Yule or birth-death to a tree until the decrease in AIC failed to exceed a set threshold, which was dependent on tree size. Diversification analysis implemented in MEDUSA required that in the analysed tree terminal tips represented monophyletic taxonomic groups with known species richness. We attempted to resolve clades to the taxonomic level of family; however our best phylogenetic hypothesis did not support the monophyly of the families Munididae, Diogenidae, and Paguridae (Figure 2). This non-monophyly was also observed in molecular trees, (Additional file 4). Therefore, assuming the current family classification would lead us to infer shifts in diversification rates inconsistent with the phylogenetic relationships found in this study. Recent studies have suggested that further subdivisions are conceivable within Munididae [21], with the recognition of a well-differentiated clade including the genera Munida, Cervimunida, and Pleuroncodes and a second clade including the rest of the genera [19, 122, 123]. Our study highly supports the existence of the Munida, Cervimunida, and Pleuroncodes clade (Pp = 100), yielding also moderate support for the inclusion of the genus Sadayoshia (Pp = 91). Hence, species richness within the family Munididae was assigned to two different monophyletic subclades (see Additional file 4). In agreement with our data, Diogenidae has been recently recovered as paraphyletic [20]. Previous studies have showed the genera Paguristes or Areopaguristes to be separated from other diogenids [19, 33, 95, 124], and closely related to Pseudopaguristes and Tetralobistes[125]. Thus, in order to assign a known species richness value, we pruned this clade to include all the species belonging to those 4 genera, and recognized a second clade to accommodate the rest of species of Diogenidae plus Coenobitidae (See Additional file 4). Finally, the family Paguridae is recognized as one of the most challenging groups within Anomura and its monophyletic origin (in relation to Lithodidae and Hapalogastridae) has been debated [1921]. Given the high species richness of this family (~ 542 species) and the lack of an appropriate taxonomic framework, it is not possible to account for the phylogenetic position of each unsampled extant species or all possible lineages. Thus, subdividing this clade into smaller subclades to assign species richness would be arbitrary, potentially leading to spurious results. Although suboptimal, the family Paguridae was collapsed together with the families Hapalaogastridae and Lithodidae in order to satisfy the monophyly assumption of MEDUSA.

We obtained information about species richness for major lineages of Anomura using the most recent published checklists [22, 44, 46, 126130]. This information was assigned to 18 lineages of our phylogeny after pruning terminals belonging to the same monophyletic groups according to the aforementioned criteria (see Additional file 4).

Abbreviations

MRCA: 

Most recent common ancestor

MYA: 

Million years ago

YA: 

Years ago.

Declarations

Acknowledgements

We would like to thank a wide variety of friends and colleagues who have helped us collect anomurans from around the world. Staff and scientists at the Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution; Universidad Nacional Autónoma de México; Smithsonian Tropical Research Institute’ Marine Station, Bocas del Toro, and R/V Urraca; and Louisiana Universities Marine Consortium LUMCON, R/V Pelican, kindly assisted with research cruises, shipping of loans, or hosting our visits. We are deeply grateful to Joseph Brown and Matthew Pennell for their advice to perform diversification analyses and useful comments. We are thankful to T.Y Chan, Museum of Victoria, Melbourne (photo by M. Marmach), DLF, RL, S. DeJouannet, K. Schnabel (NIWA) whom provided anomuran photographs. Our work was partially supported by Brigham Young University and a Tree of Life grant from the US NSF EF-0531762 awarded to KAC, DLF, CES, RMF, Joel Martin, and Nikki Hannegan. This work was also partially funded by a grant from the U.S. National Science Foundation (NSF) PIRE for research on Patagonian Biodiversity to support collaboration among the following institutions (listed alphabetically): Brigham Young University, Centro Nacional Patagónico (AR), Dalhousie University, Instituto Bota´nico Darwinion (AR), Universidad Austral de Chile, Universidad Nacional del Comahue, Universidad de Concepción, and George Washington University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. PC was supported by a grant from the Fundación Caja Madrid. This is contribution no. 160 for the UL Laboratory for Crustacean Research and no. 915 for the Smithsonian Marine Station,-Ft. Pierce.

Authors’ Affiliations

(1)
Department of Biology, Florida International University-Biscayne Bay Campus
(2)
Department of Biology, Brigham Young University
(3)
Computational Biology Institute, George Washington University
(4)
Department of Geology, Kent State University
(5)
Kent State University at Stark
(6)
Australian Museum
(7)
Department of Biology, University of Louisiana at Lafayette
(8)
Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution

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