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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. 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

    Published on:

  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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

    Published on:

    The Correction to this article has been published in BMC Evolutionary Biology 2019 19:212

  46. 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

    Published on:

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

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