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Phylogenetics and phylogeography

Section edited by Craig Moritz and Herve Philippe

This section considers studies in the phylogeny and phylogeography of organisms.

Page 1 of 12

  1. The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic and Jurassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely h...

    Authors: Timothy J. Colston, Pallavi Kulkarni, Walter Jetz and R. Alexander Pyron

    Citation: BMC Evolutionary Biology 2020 20:81

    Content type: Research article

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  2. Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negl...

    Authors: Edson Fiedler de Abreu-Jr, Silvia E. Pavan, Mirian T. N. Tsuchiya, Don E. Wilson, Alexandre R. Percequillo and Jesús E. Maldonado

    Citation: BMC Evolutionary Biology 2020 20:77

    Content type: Research article

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  3. The New World Tropics has experienced a dynamic landscape across evolutionary history and harbors a high diversity of flora and fauna. While there are some studies addressing diversification in Neotropical ver...

    Authors: Melissa Sánchez-Herrera, Christopher D. Beatty, Renato Nunes, Camilo Salazar and Jessica L. Ware

    Citation: BMC Evolutionary Biology 2020 20:74

    Content type: Research article

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  4. Disentangling the drivers of genetic differentiation is one of the cornerstones in evolution. This is because genetic diversity, and the way in which it is partitioned within and among populations across space...

    Authors: Antonio R. Castilla, Belén Méndez-Vigo, Arnald Marcer, Joaquín Martínez-Minaya, David Conesa, F. Xavier Picó and Carlos Alonso-Blanco

    Citation: BMC Evolutionary Biology 2020 20:71

    Content type: Research article

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  5. The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has be...

    Authors: Alexandros Vasilikopoulos, Bernhard Misof, Karen Meusemann, Doria Lieberz, Tomáš Flouri, Rolf G. Beutel, Oliver Niehuis, Torsten Wappler, Jes Rust, Ralph S. Peters, Alexander Donath, Lars Podsiadlowski, Christoph Mayer, Daniela Bartel, Alexander Böhm, Shanlin Liu…

    Citation: BMC Evolutionary Biology 2020 20:64

    Content type: Research article

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  6. The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying exten...

    Authors: Gunilla Ståhls, Rudolf Meier, Christoph Sandrock, Martin Hauser, Ljiljana Šašić Zorić, Elina Laiho, Andrea Aracil, Jovana Doderović, Rozane Badenhorst, Phira Unadirekkul, Nur Arina Binte Mohd Adom, Leo Wein, Cameron Richards, Jeffery K. Tomberlin, Santos Rojo, Sanja Veselić…

    Citation: BMC Evolutionary Biology 2020 20:60

    Content type: Research article

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  7. Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive ef...

    Authors: Jingchun Li, Sarah Lemer, Lisa Kirkendale, Rüdiger Bieler, Colleen Cavanaugh and Gonzalo Giribet

    Citation: BMC Evolutionary Biology 2020 20:50

    Content type: Research article

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  8. Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogen...

    Authors: Jairo Arroyave, John S. S. Denton and Melanie L. J. Stiassny

    Citation: BMC Evolutionary Biology 2020 20:48

    Content type: Research article

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  9. Copepods are key components of aquatic ecosystems and can help regulate the global carbon cycle. Much attention has been paid to the species diversity of copepods worldwide, but the phylogeography and genetic ...

    Authors: Yijun Ni, Chike Chukwuenyem Ebido, Elijah Chibueze Odii, Jinhui Wang, Chinemerem Hodges Orakwelu, Francis Chukwuemeka Abonyi, Chinedu Innocent Ngene, Joseph Onyekwere Okoro, Patience Obiageli Ubachukwu, Wei Hu and Mingbo Yin

    Citation: BMC Evolutionary Biology 2020 20:45

    Content type: Research article

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  10. The Mexican hand tree or Canac (Chiranthodendron pentadactylon) is a temperate tree species of cloud and pine-oak forests of southern Mexico and Guatemala. Its characteristic hand-shaped flower is used in folk me...

    Authors: Diana Gabriela Hernández-Langford, María Elena Siqueiros-Delgado and Eduardo Ruíz-Sánchez

    Citation: BMC Evolutionary Biology 2020 20:44

    Content type: Research article

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  11. Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptom...

    Authors: Dustin J. Wcisel, J. Thomas Howard III, Jeffrey A. Yoder and Alex Dornburg

    Citation: BMC Evolutionary Biology 2020 20:41

    Content type: Software

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  12. Most cinquefoils (Potentilla L., Rosaceae) are polyploids, ranging from tetraploid (4x) to dodecaploid (12x), diploids being a rare exception. Previous studies based on ribosomal and chloroplast data indicated th...

    Authors: Nannie L. Persson, Torsten Eriksson and Jenny E. E. Smedmark

    Citation: BMC Evolutionary Biology 2020 20:38

    Content type: Research article

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  13. Various ecological groups of earthworms very likely constitute sharply isolated niches that might permit speciation of their symbiotic ciliates, even though no distinct morphological features appear to be reco...

    Authors: Tomáš Obert and Peter Vďačný

    Citation: BMC Evolutionary Biology 2020 20:37

    Content type: Research article

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  14. The family Aegisthidae is known as typical component of deep-sea hyperbenthic waters that gradually colonized other marine environments. The phylogenetic relationships within this family have been examined her...

    Authors: Sahar Khodami, Nancy F. Mercado-Salas and Pedro Martìnez Arbizu

    Citation: BMC Evolutionary Biology 2020 20:36

    Content type: Research article

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  15. In recent years, Ecuador and other South American countries have experienced an increase in arboviral diseases. A rise in dengue infections was followed by introductions of chikungunya and Zika, two viruses ne...

    Authors: Irina Maljkovic Berry, Wiriya Rutvisuttinunt, Rachel Sippy, Efrain Beltran-Ayala, Katherine Figueroa, Sadie Ryan, Abhinaya Srikanth, Anna M. Stewart-Ibarra, Timothy Endy and Richard G. Jarman

    Citation: BMC Evolutionary Biology 2020 20:31

    Content type: Research article

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  16. Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their...

    Authors: Shunde Chen, Jiao Qing, Zhu Liu, Yang Liu, Mingkun Tang, Robert W. Murphy, Yingting Pu, Xuming Wang, Keyi Tang, Keji Guo, Xuelong Jiang and Shaoying Liu

    Citation: BMC Evolutionary Biology 2020 20:29

    Content type: Research article

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  17. Climatic variation and geologic change both play significant roles in shaping species distributions, thus affecting their evolutionary history. In Sahara-Sahel, climatic oscillations shifted the desert extent ...

    Authors: Ana Filipa Moutinho, Nina Serén, Joana Paupério, Teresa Luísa Silva, Fernando Martínez-Freiría, Graciela Sotelo, Rui Faria, Tapio Mappes, Paulo Célio Alves, José Carlos Brito and Zbyszek Boratyński

    Citation: BMC Evolutionary Biology 2020 20:26

    Content type: Research article

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  18. The flat periwinkles, Littorina fabalis and L. obtusata, are two sister species widely distributed throughout the Northern Atlantic shores with high potential to inform us about the process of ecological speciati...

    Authors: Graciela Sotelo, Mårten Duvetorp, Diana Costa, Marina Panova, Kerstin Johannesson and Rui Faria

    Citation: BMC Evolutionary Biology 2020 20:23

    Content type: Research article

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  19. Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and ev...

    Authors: Iker Irisarri, Juan E. Uribe, Douglas J. Eernisse and Rafael Zardoya

    Citation: BMC Evolutionary Biology 2020 20:22

    Content type: Research article

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  20. The current Brazilian population is the product of centuries of admixture between intercontinental founding groups. Although previous results have revealed a heterogeneous distribution of mitochondrial lineage...

    Authors: Ana Paula Schaan, Leonor Gusmão, Juliana Jannuzzi, Antonio Modesto, Marcos Amador, Diego Marques, Silvia Helena Rabenhorst, Raquel Montenegro, Thayson Lopes, France Keiko Yoshioka, Giovanny Pinto, Sidney Santos, Lorenna Costa, Vivian Silbiger and Ândrea Ribeiro-dos-Santos

    Citation: BMC Evolutionary Biology 2020 20:15

    Content type: Research article

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  21. Early Cambrian Lagerstätten from China have greatly enriched our perspective on the early evolution of animals, particularly arthropods. However, recent studies have shown that many of these early fossil arthr...

    Authors: Cédric Aria, Fangchen Zhao, Han Zeng, Jin Guo and Maoyan Zhu

    Citation: BMC Evolutionary Biology 2020 20:4

    Content type: Research article

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  22. The biodiversity and distributions of terrestrial snails at local and regional scales are influenced by their low vagility and microhabitat specificity. The accessibility of large-bodied species and their char...

    Authors: Z. W. Dempsey, C. P. Goater and T. M. Burg

    Citation: BMC Evolutionary Biology 2020 20:3

    Content type: Research article

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  23. Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research...

    Authors: Michael Bradshaw, Felix Grewe, Anne Thomas, Cody H. Harrison, Hanna Lindgren, Lucia Muggia, Larry L. St. Clair, H. Thorsten Lumbsch and Steven D. Leavitt

    Citation: BMC Evolutionary Biology 2020 20:2

    Content type: Research article

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  24. African annual killifishes (Nothobranchius spp.) are adapted to seasonally desiccating habitats (ephemeral pools), surviving dry periods as dormant eggs. Given their peculiar life history, geographic aspects of t...

    Authors: Veronika Bartáková, Béla Nagy, Matej Polačik, Radim Blažek, Hieromin Lamtane and Martin Reichard

    Citation: BMC Evolutionary Biology 2020 20:1

    Content type: Research article

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  25. Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptiona...

    Authors: Alberto Rocha-Méndez, Luis A. Sánchez-González, Clementina González and Adolfo G. Navarro-Sigüenza

    Citation: BMC Evolutionary Biology 2019 19:237

    Content type: Research article

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  26. Understanding the phylogenetic relationships among species is one of the main goals of systematic biology. Simultaneously, credible phylogenetic hypotheses are often the first requirement for unveiling the evo...

    Authors: Russell J. S. Orr, Marianne N. Haugen, Björn Berning, Philip Bock, Robyn L. Cumming, Wayne K. Florence, Masato Hirose, Emanuela Di Martino, Mali H. Ramsfjell, Maja M. Sannum, Abigail M. Smith, Leandro M. Vieira, Andrea Waeschenbach and Lee Hsiang Liow

    Citation: BMC Evolutionary Biology 2019 19:235

    Content type: Research article

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  27. Attributes of pest species like host range are frequently reported as being evolutionarily constrained and showing phylogenetic signal. Because these attributes in turn could influence the abundance and impact...

    Authors: Peng-Yu Jin, Jing-Tao Sun, Ary Hoffmann, Yan-Fei Guo, Jin-Cheng Zhou, Yu-Xi Zhu, Lei Chen and Xiao-Yue Hong

    Citation: BMC Evolutionary Biology 2019 19:223

    Content type: Research article

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  28. The coincidence of long distance dispersal (LDD) and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here,...

    Authors: Michael D. Pirie, Martha Kandziora, Nicolai M. Nürk, Nicholas C. Le Maitre, Ana Mugrabi de Kuppler, Berit Gehrke, Edward G. H. Oliver and Dirk U. Bellstedt

    Citation: BMC Evolutionary Biology 2019 19:222

    Content type: Research article

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  29. Phylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediat...

    Authors: Yang Fang, Chengcheng Liu, Jiangyi Lin, Xufeng Li, Kambiz N. Alavian, Yi Yang and Yulong Niu

    Citation: BMC Evolutionary Biology 2019 19:219

    Content type: Software

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  30. Despite decades of research, the horse domestication scenario in East Asia remains poorly understood.

    Authors: Tiao Ning, Yinghui Ling, Shaoji Hu, Arman Ardalan, Jing Li, Bikash Mitra, Tapas Kumar Chaudhuri, Weijun Guan, Qianjun Zhao, Yuehui Ma, Peter Savolainen and Yaping Zhang

    Citation: BMC Evolutionary Biology 2019 19:217

    Content type: Research article

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  31. The flood of genomic data to help build and date the tree of life requires automation at several critical junctures, most importantly during sequence assembly and alignment. It is widely appreciated that autom...

    Authors: Yan Du, Shaoyuan Wu, Scott V. Edwards and Liang Liu

    Citation: BMC Evolutionary Biology 2019 19:203

    Content type: Research article

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  32. Understanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genus Quercus is a species-rich and ecologically diverse woody genus that dominates a wid...

    Authors: Mengxiao Yan, Ruibin Liu, Ying Li, Andrew L. Hipp, Min Deng and Yanshi Xiong

    Citation: BMC Evolutionary Biology 2019 19:202

    Content type: Research article

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  33. Helicobacter pylori, a bacterium that infects the human stomach, has high genetic diversity. Because its evolution is parallel to human, H. pylori is used as a tool to trace human migration. However, there are fe...

    Authors: Takaaki Ono, Modesto Cruz, José A. Jiménez Abreu, Hiroyuki Nagashima, Phawinee Subsomwong, Celso Hosking, Seiji Shiota, Rumiko Suzuki and Yoshio Yamaoka

    Citation: BMC Evolutionary Biology 2019 19:197

    Content type: Research article

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  34. Genetic processes shape the modern-day distribution of genetic variation within and between populations and can provide important insights into the underlying mechanisms of evolution. The resulting genetic var...

    Authors: Endre Gy Tóth, Francine Tremblay, Johann M. Housset, Yves Bergeron and Christopher Carcaillet

    Citation: BMC Evolutionary Biology 2019 19:190

    Content type: Research article

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  35. Studying site-specific amino acid frequencies by eye can reveal biologically significant variability and lineage-specific adaptation. This so-called ‘sequence gazing’ often informs bioinformatics and experimen...

    Authors: Christopher Monit, Richard A. Goldstein and Greg J. Towers

    Citation: BMC Evolutionary Biology 2019 19:186

    Content type: Software

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  36. Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular f...

    Authors: C. A. Hamilton, R. A. St Laurent, K. Dexter, I. J. Kitching, J. W. Breinholt, A. Zwick, M. J. T. N. Timmermans, J. R. Barber and A. Y. Kawahara

    Citation: BMC Evolutionary Biology 2019 19:182

    Content type: Research article

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  37. Marine invertebrates are abundant and diverse on the continental shelf in Antarctica, but little is known about their parasitic counterparts. Endoparasites are especially understudied because they often posses...

    Authors: Kara K. S. Layton, Greg W. Rouse and Nerida G. Wilson

    Citation: BMC Evolutionary Biology 2019 19:180

    Content type: Research article

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  38. The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept ...

    Authors: Terrence C. Demos, Paul W. Webala, Steven M. Goodman, Julian C. Kerbis Peterhans, Michael Bartonjo and Bruce D. Patterson

    Citation: BMC Evolutionary Biology 2019 19:166

    Content type: Research article

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  39. Artiopodan euarthropods represent common and abundant faunal components in sites with exceptional preservation during the Cambrian. The Chengjiang biota in South China contains numerous taxa that are exclusive...

    Authors: Xiaohan Chen, Javier Ortega-Hernández, Joanna M. Wolfe, Dayou Zhai, Xianguang Hou, Ailin Chen, Huijuan Mai and Yu Liu

    Citation: BMC Evolutionary Biology 2019 19:165

    Content type: Research article

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  40. Ancestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology,...

    Authors: François Chevenet, Guillaume Castel, Emmanuelle Jousselin and Olivier Gascuel

    Citation: BMC Evolutionary Biology 2019 19:163

    Content type: Software

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  41. Geological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded respondin...

    Authors: Jiande Li, Gang Song, Naifa Liu, Yongbin Chang and Xinkang Bao

    Citation: BMC Evolutionary Biology 2019 19:161

    Content type: Research article

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  42. Flathead fishes of the genus Platycephalus are economically important demersal fishes that widely inhabit the continental shelves of tropical and temperate sea waters. This genus has a long history of taxonomic r...

    Authors: Jie Cheng, Zhiyang Wang, Na Song, Takashi Yanagimoto and Tianxiang Gao

    Citation: BMC Evolutionary Biology 2019 19:159

    Content type: Research article

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  43. With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from usin...

    Authors: Kevin Debray, Jordan Marie-Magdelaine, Tom Ruttink, Jérémy Clotault, Fabrice Foucher and Valéry Malécot

    Citation: BMC Evolutionary Biology 2019 19:152

    Content type: Methodology article

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  44. Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unpara...

    Authors: Per G. P. Ericson, Yanhua Qu, Pamela C. Rasmussen, Mozes P. K. Blom, Frank E. Rheindt and Martin Irestedt

    Citation: BMC Evolutionary Biology 2019 19:151

    Content type: Research article

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  45. China is an important biogeographical zone in which the genetic legacies of the Tertiary and Quaternary periods are abundant, and the contemporary geography environment plays an important role in species distr...

    Authors: Liufu Wang, Hang Zhuang, Yingying Zhang and Wenzhi Wei

    Citation: BMC Evolutionary Biology 2019 19:145

    Content type: Research article

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