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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 11

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. The ancient Lake Baikal is characterized by an outstanding diversity of endemic faunas with more than 350 amphipod species and subspecies. We determined the genetic diversity within the endemic littoral amphip...

    Authors: Anton Gurkov, Lorena Rivarola-Duarte, Daria Bedulina, Irene Fernández Casas, Hendrik Michael, Polina Drozdova, Anna Nazarova, Ekaterina Govorukhina, Maxim Timofeyev, Peter F. Stadler and Till Luckenbach

    Citation: BMC Evolutionary Biology 2019 19:138

    Content type: Research article

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  17. Nuclear progesterone receptor (nPR) is an evolutionary innovation in vertebrates that mediates genomic responses to progesterone. Vertebrates also respond to progesterone via membrane progesterone receptors (m...

    Authors: Jianfeng Ren, Yu-Wen Chung-Davidson, Liang Jia and Weiming Li

    Citation: BMC Evolutionary Biology 2019 19:136

    Content type: Research article

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  18. Speciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary c...

    Authors: Xuejing Wang, Pinjia Que, Gerald Heckel, Junhua Hu, Xuecong Zhang, Chung-Yu Chiang, Nan Zhang, Qin Huang, Simin Liu, Jonathan Martinez, Emilio Pagani-Núñez, Caroline Dingle, Yu Yan Leung, Tamás Székely, Zhengwang Zhang and Yang Liu

    Citation: BMC Evolutionary Biology 2019 19:135

    Content type: Research article

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  19. The classification of the family Psilotrichidae, a curious group of ciliated protists with unique morphological and ontogenetic features, is ambiguous and poorly understood particularly due to the lack of mole...

    Authors: Xiaotian Luo, Jie A. Huang, Lifang Li, Weibo Song and William A. Bourland

    Citation: BMC Evolutionary Biology 2019 19:125

    Content type: Research article

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  20. Nematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms. Free-living nematodes, particularly from the clades Enoplia...

    Authors: Ashleigh B. Smythe, Oleksandr Holovachov and Kevin M. Kocot

    Citation: BMC Evolutionary Biology 2019 19:121

    Content type: Research article

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  21. The evolution of male pregnancy is the most distinctive characteristic of syngnathids, and their specialized life history traits make syngnathid species excellent model species for many issues in biological ev...

    Authors: Xin Wang, Yanhong Zhang, Huixian Zhang, Geng Qin and Qiang Lin

    Citation: BMC Evolutionary Biology 2019 19:119

    Content type: Research article

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  22. There is a biogeographic break located at 30°S in the southeast Pacific, in a coastal area of strong environmental discontinuities. Several marine benthic taxa with restricted dispersal have a coincident phylo...

    Authors: Pilar A. Haye, Nicolás I. Segovia, Andrea I. Varela, Rodrigo Rojas, Marcelo M. Rivadeneira and Martin Thiel

    Citation: BMC Evolutionary Biology 2019 19:118

    Content type: Research article

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  23. Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been c...

    Authors: Andrea M. Quattrini, Tiana Wu, Keryea Soong, Ming-Shiou Jeng, Yehuda Benayahu and Catherine S. McFadden

    Citation: BMC Evolutionary Biology 2019 19:116

    Content type: Research article

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  24. The Taklimakan Desert in China is characterized by unique geological and historical dynamics and endemic flora and fauna, but the influence of historical climate oscillations on the evolutionary history of end...

    Authors: Brawin Kumar, Jilong Cheng, Deyan Ge, Lin Xia and Qisen Yang

    Citation: BMC Evolutionary Biology 2019 19:113

    Content type: Research article

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  25. Avian avulavirus (commonly known as avian paramyxovirus-1 or APMV-1) can cause disease of varying severity in both domestic and wild birds. Understanding how viruses move among hosts and geography would be use...

    Authors: Joseph T. Hicks, Kiril M. Dimitrov, Claudio L. Afonso, Andrew M. Ramey and Justin Bahl

    Citation: BMC Evolutionary Biology 2019 19:108

    Content type: Research article

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  26. The Pleistocene cyclic sea-level fluctuations are thought to have markedly affected the distribution and genetic architecture of Atlanto-Mediterranean biota. Despite the acknowledged key role played by these h...

    Authors: Temim Deli, Christina Kiel and Christoph D. Schubart

    Citation: BMC Evolutionary Biology 2019 19:105

    Content type: Research article

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  27. RNA interference (RNAi) related pathways provide defense against viruses and transposable elements, and have been implicated in the suppression of meiotic drive elements. Genes in these pathways often exhibit ...

    Authors: Danang Crysnanto and Darren J. Obbard

    Citation: BMC Evolutionary Biology 2019 19:99

    Content type: Research article

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  28. Recent studies have demonstrated that Bayesian species delimitation based on the multispecies coalescent model can produce inaccurate results by misinterpreting population splits as species divergences. An app...

    Authors: Kin Onn Chan and L. Lee Grismer

    Citation: BMC Evolutionary Biology 2019 19:95

    Content type: Research article

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  29. Cichlids are a prime model system in evolutionary research and several of the most prominent examples of adaptive radiations are found in the East African Lakes Tanganyika, Malawi and Victoria, all part of the...

    Authors: Frederic Dieter Benedikt Schedel, Zuzana Musilova and Ulrich Kurt Schliewen

    Citation: BMC Evolutionary Biology 2019 19:94

    Content type: Research article

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  30. Tropical rainforests (TRFs) harbour almost half of the world’s vascular plant species diversity while covering only about 6–7% of land. However, why species richness varies amongst the Earth’s major TRF region...

    Authors: Alexander Gamisch and Hans Peter Comes

    Citation: BMC Evolutionary Biology 2019 19:93

    Content type: Research article

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  31. Species diversity is determined by both local environmental conditions that control differentiation and extinction and the outcome of large-scale processes that affect migration. The latter primarily comprises...

    Authors: Qian H. Gu, Martin Husemann, Hui H. Wu, Jing Dong, Chuan J. Zhou, Xian F. Wang, Yun N. Gao, Man Zhang, Guo R. Zhu and Guo X. Nie

    Citation: BMC Evolutionary Biology 2019 19:82

    Content type: Research article

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  32. Congruent patterns in the distribution of biodiversity between regions or habitats suggest that key factors such as climatic and topographic variation may predictably shape evolutionary processes. In a number ...

    Authors: Paul M. Oliver, Lauren G. Ashman, Sarah Bank, Rebecca J. Laver, Renae C. Pratt, Leonardo G. Tedeschi and Craig C. Moritz

    Citation: BMC Evolutionary Biology 2019 19:81

    Content type: Research article

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  33. Dictyostelid cellular slime molds (dictyostelids) are microscopic throughout their entire life cycle. The vegetative phase consists of single-celled amoeboid forms which live in the soil/leaf litter microhabit...

    Authors: Pu Liu, Yue Zou, Jiangan Hou, Steven L. Stephenson and Yu Li

    Citation: BMC Evolutionary Biology 2019 19:78

    Content type: Research article

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  34. Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and ev...

    Authors: T. Aghová, K. Palupčíková, R. Šumbera, D. Frynta, L. A. Lavrenchenko, Y. Meheretu, J. Sádlová, J. Votýpka, J. S. Mbau, D. Modrý and J. Bryja

    Citation: BMC Evolutionary Biology 2019 19:69

    Content type: Research article

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  35. Despite attempts in retracing the history of the Thao people in Taiwan using folktales, linguistics, physical anthropology, and ethnic studies, their history remains incomplete. The heritage of Thao has been a...

    Authors: Jean A. Trejaut, Frank Muyard, Ying-Hui Lai, Lan-Rong Chen, Zong-Sian Chen, Jun-Hun Loo, Jin-Yuan Huang and Marie Lin

    Citation: BMC Evolutionary Biology 2019 19:64

    Content type: Research article

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  36. Understanding the relative influence of vicariance and dispersal in shaping Old World tropical biodiversity remains a challenge. We aimed to infer the roles of these alternative biogeographic processes using a...

    Authors: Jahnavi Joshi and Gregory D. Edgecombe

    Citation: BMC Evolutionary Biology 2019 19:41

    Content type: Research article

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    The Correction to this article has been published in BMC Evolutionary Biology 2019 19:56

  37. For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the ‘Saccharum Complex’, an...

    Authors: Dyfed Lloyd Evans, Shailesh V. Joshi and Jianping Wang

    Citation: BMC Evolutionary Biology 2019 19:33

    Content type: Research article

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  38. Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed siz...

    Authors: Warren M. Cardinal-McTeague, Kenneth J. Wurdack, Erin M. Sigel and Lynn J. Gillespie

    Citation: BMC Evolutionary Biology 2019 19:29

    Content type: Research article

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  39. The polyamine oxidases (PAOs) catabolize the oxidative deamination of the polyamines (PAs) spermine (Spm) and spermidine (Spd). Most of the phylogenetic studies performed to analyze the plant PAO family took i...

    Authors: Cesar Daniel Bordenave, Carolina Granados Mendoza, Juan Francisco Jiménez Bremont, Andrés Gárriz and Andrés Alberto Rodríguez

    Citation: BMC Evolutionary Biology 2019 19:28

    Content type: Research article

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  40. Knowledge about the distribution of the genetic variation of marine species is fundamental to address species conservation and management strategies, especially in scenarios with mass mortalities. In the Medit...

    Authors: Ana Riesgo, Sergi Taboada, Rocío Pérez-Portela, Paolo Melis, Joana R. Xavier, Gema Blasco and Susanna López-Legentil

    Citation: BMC Evolutionary Biology 2019 19:24

    Content type: Research article

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  41. Peninsulas often harvest high genetic diversity through repeated southward migrations of species during glacial maxima. Studies addressing within-species evolutionary responses to climate fluctuations in north...

    Authors: Michael Joseph Jowers, Santiago Sánchez-Ramírez, Euigeun Song, Samer Angelone, Taeyoung Choi, Inna Voloshina and Donggul Woo

    Citation: BMC Evolutionary Biology 2019 19:23

    Content type: Research article

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  42. Multiple Sequence Alignments (MSAs) are the starting point of molecular evolutionary analyses. Errors in MSAs generate a non-historical signal that can lead to incorrect inferences. Therefore, numerous efforts...

    Authors: Arnaud Di Franco, Raphaël Poujol, Denis Baurain and Hervé Philippe

    Citation: BMC Evolutionary Biology 2019 19:21

    Content type: Research article

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  43. The Carpathians and the Alps are the largest mountain ranges of the European Alpine System and important centres of endemism. Among the distinctive endemic species of this area is Saxifraga wahlenbergii, a Wester...

    Authors: Natalia Tkach, Martin Röser, Tomasz Suchan, Elżbieta Cieślak, Peter Schönswetter and Michał Ronikier

    Citation: BMC Evolutionary Biology 2019 19:18

    Content type: Research article

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  44. The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocat...

    Authors: Themistoklis Giannoulis, Dimitrios Plageras, Costas Stamatis, Eleni Chatzivagia, Andreas Tsipourlianos, Periklis Birtsas, Charalambos Billinis, Franz Suchentrunk and Zissis Mamuris

    Citation: BMC Evolutionary Biology 2019 19:17

    Content type: Research article

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  45. The impressive adaptive radiation of notothenioid fishes in Antarctic waters is generally thought to have been facilitated by an evolutionary key innovation, antifreeze glycoproteins, permitting the rapid evol...

    Authors: Santiago G. Ceballos, Marius Roesti, Michael Matschiner, Daniel A. Fernández, Malte Damerau, Reinhold Hanel and Walter Salzburger

    Citation: BMC Evolutionary Biology 2019 19:13

    Content type: Research article

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2018 Journal Metrics

  • Citation Impact
    3.045 - 2-year Impact Factor
    3.559 - 5-year Impact Factor
    1.15 - Source Normalized Impact per Paper (SNIP)
    1.687 - SCImago Journal Rank (SJR)

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