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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 3 of 12

  1. 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 Published on:

  2. 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 Published on:

  4. 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 Published on:

  5. 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 Published on:

  6. 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 Published on:

  7. 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 Published on:

  8. 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 Published on:

  9. 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 Published on:

  10. 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 Published on:

  11. 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 Published on:

  12. 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 Published on:

  14. 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 Published on:

  15. 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

  16. 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

  18. 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 Published on:

  19. 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 Published on:

  20. 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 Published on:

  21. 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 Published on:

  22. 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 Published on:

  23. 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 Published on:

  24. 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 Published on:

  25. 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 Published on:

  26. 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 Published on:

  27. Clupeid fisheries in Lake Tanganyika (East Africa) provide food for millions of people in one of the world’s poorest regions. Due to climate change and overfishing, the clupeid stocks of Lake Tanganyika are de...

    Authors: Els L. R. De Keyzer, Zoë De Corte, Maarten Van Steenberge, Joost A. M. Raeymaekers, Federico C. F. Calboli, Nikol Kmentová, Théophile N’Sibula Mulimbwa, Massimiliano Virgilio, Carl Vangestel, Pascal Masilya Mulungula, Filip A. M. Volckaert and Maarten P. M. Vanhove
    Citation: BMC Evolutionary Biology 2019 19:6
    Content type: Research article Published on:

  28. Geographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as compet...

    Authors: Yunxiang Liu, Christopher H. Dietrich and Cong Wei
    Citation: BMC Evolutionary Biology 2019 19:5
    Content type: Research article Published on:

  29. Septins are cytoskeletal proteins important in cell division and in establishing and maintaining cell polarity. Although septins are found in various eukaryotes, septin genes had the richest history of duplica...

    Authors: Benjamin Auxier, Jaclyn Dee, Mary L. Berbee and Michelle Momany
    Citation: BMC Evolutionary Biology 2019 19:4
    Content type: Research article Published on:

  30. The lake deposits of the informal Ruby Paper Shale unit, part of the Renova Formation of Montana, have yielded abundant plant fossils that document Late Eocene – Early Oligocene global cooling in western North...

    Authors: Tobin L. Hieronymus, David A. Waugh and Julia A. Clarke
    Citation: BMC Evolutionary Biology 2019 19:3
    Content type: Research article Published on:

  31. Climate oscillation may have a profound effect on species distributions, gene flow patterns and population demography. In response to environmental change, those species restricted to montane habitats experien...

    Authors: Tao Pan, Hui Wang, Pablo Orozcoterwengel, Chao-Chao Hu, Gui-You Wu, Li-Fu Qian, Zhong-Lou Sun, Wen-Bo Shi, Peng Yan, Xiao-Bing Wu and Bao-Wei Zhang
    Citation: BMC Evolutionary Biology 2019 19:1
    Content type: Research article Published on:

  32. The diversity and phylogeny of whitefish of the genus Coregonus is complex, and includes many endemic species of high conservation concern. However, because of commercial importance of whitefish fisheries, stocki...

    Authors: Thomas Mehner, Kirsten Pohlmann, David Bittner and Jörg Freyhof
    Citation: BMC Evolutionary Biology 2018 18:208
    Content type: Research article Published on:

  34. Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities s...

    Authors: Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E. G. Briggs, Rich Mooi and Greg W. Rouse
    Citation: BMC Evolutionary Biology 2018 18:189
    Content type: Research article Published on:

  35. Understanding the factors shaping population genetic structure is important for evolutionary considerations as well as for management and conservation. While studies have revealed the importance of palaeogeogr...

    Authors: Ka Yan Ma, Lynne van Herwerden, Stephen J. Newman, Michael L. Berumen, John Howard Choat, Ka Hou Chu and Yvonne Sadovy de Mitcheson
    Citation: BMC Evolutionary Biology 2018 18:180
    Content type: Research article Published on:

  36. Phylogenies provide critical information about convergence during adaptive radiation. To test whether there have been multiple origins of a distinctive trophic phenotype in one of the most rapidly radiating gr...

    Authors: C. Darrin Hulsey, Jimmy Zheng, Roi Holzman, Michael E. Alfaro, Melisa Olave and Axel Meyer
    Citation: BMC Evolutionary Biology 2018 18:179
    Content type: Research article Published on:

  37. The Pantosteus plebeius-nebuliferus species-group is a group of freshwater fishes distributed in endo- and exorheic drainage basins in the Mexican Sierra Madre Occidental mountain range system and central North M...

    Authors: Diushi Keri Corona-Santiago, Omar Domínguez-Domínguez, Llanet Tovar-Mora, José Ramón Pardos-Blas, Yvonne Herrerías-Diego, Rodolfo Pérez-Rodríguez and Ignacio Doadrio
    Citation: BMC Evolutionary Biology 2018 18:173
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Evolutionary Biology 2018 18:206

  38. Transcriptome sequencing has become a method of choice for evolutionary studies in microbial eukaryotes due to low cost and minimal sample requirements. Transcriptome data has been extensively used in phylogen...

    Authors: Yonas I. Tekle and Fiona C. Wood
    Citation: BMC Evolutionary Biology 2018 18:170
    Content type: Research article Published on:

  39. The cartilaginous fishes diverged from other jawed vertebrates ~ 450 million years ago (mya). Despite this key evolutionary position, the only high-quality cartilaginous fish genome available is for the elepha...

    Authors: Anthony K. Redmond, Daniel J. Macqueen and Helen Dooley
    Citation: BMC Evolutionary Biology 2018 18:169
    Content type: Research article Published on:

  40. Drylands cover nearly 41% of Earth’s land surface and face a high risk of degradation worldwide. However, the actual timeframe during which dryland floras rose on a global scale remains unknown. Zygophyllaceae...

    Authors: Sheng-Dan Wu, Lin-Jing Zhang, Li Lin, Sheng-Xiang Yu, Zhi-Duan Chen and Wei Wang
    Citation: BMC Evolutionary Biology 2018 18:166
    Content type: Research article Published on:

  41. Southern Appalachian forests are dominated by second-growth vegetation following decades of intensive forestry and agricultural use, although some old-growth patches remain. While it’s been shown that second-g...

    Authors: Michael S. Caterino and Shelley S. Langton-Myers
    Citation: BMC Evolutionary Biology 2018 18:165
    Content type: Research article Published on:

  42. Islands have traditionally been the centre of evolutionary biological research, but the dynamics of immigration and differentiation at continental islands have not been well studied. Therefore, we focused on t...

    Authors: Takumi Saito, Takahiro Hirano, Larisa Prozorova, Van Tu Do, Anna Sulikowska-Drozd, Tatiana Sitnikova, Purevdorj Surenkhorloo, Daishi Yamazaki, Yuta Morii, Yuichi Kameda, Hiroshi Fukuda and Satoshi Chiba
    Citation: BMC Evolutionary Biology 2018 18:164
    Content type: Research article Published on:

  43. Past climatological events and contemporary geophysical barriers shape the distribution, population genetic structure, and evolutionary history of many organisms. The Himalayan region, frequently referred to a...

    Authors: Laxman Khanal, Mukesh Kumar Chalise, Tao Wan and Xuelong Jiang
    Citation: BMC Evolutionary Biology 2018 18:159
    Content type: Research article Published on:

  44. Previous molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa, we perform target gene capturing and subsequent ne...

    Authors: Nicolas Straube, Chenhong Li, Matthias Mertzen, Hao Yuan and Timo Moritz
    Citation: BMC Evolutionary Biology 2018 18:158
    Content type: Research article Published on:

  45. Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origi...

    Authors: Johanna L. A. Paijmans, Axel Barlow, Daniel W. Förster, Kirstin Henneberger, Matthias Meyer, Birgit Nickel, Doris Nagel, Rasmus Worsøe Havmøller, Gennady F. Baryshnikov, Ulrich Joger, Wilfried Rosendahl and Michael Hofreiter
    Citation: BMC Evolutionary Biology 2018 18:156
    Content type: Research article Published on:

  46. Quaternary climatic oscillations had tremendous effects on the current distribution of species. Here, we aim to elucidate the glacial history of Rhodiola crenulata, a perennial herb almost exclusively restricted ...

    Authors: Yuan-Zhen Zhang, Ruo-Wei Zhu, Da-Lv Zhong and Jian-Qiang Zhang
    Citation: BMC Evolutionary Biology 2018 18:154
    Content type: Research article Published on:

  47. Refugial populations in Quaternary glaciations are critical to understanding the evolutionary history and climatic interactions of many extant species. Compared with the well-studied areas of Europe and Northe...

    Authors: Wei Song, Li-Jun Cao, Bing-Yan Li, Ya-Jun Gong, Ary Anthony Hoffmann and Shu-Jun Wei
    Citation: BMC Evolutionary Biology 2018 18:152
    Content type: Research article Published on:

  48. Intraspecific variation in chromosome structure may cause genetic incompatibilities and thus provides the first step in the formation of species. In ants, chromosome number varies tremendously from 2n = 2 to 2...

    Authors: Danon Clemes Cardoso, Jürgen Heinze, Mariana Neves Moura and Maykon Passos Cristiano
    Citation: BMC Evolutionary Biology 2018 18:146
    Content type: Research article Published on:

  49. Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmet...

    Authors: Jeremy M. Bono, Helen K. Pigage, Peter J. Wettstein, Stephanie A. Prosser and Jon C. Pigage
    Citation: BMC Evolutionary Biology 2018 18:139
    Content type: Research article Published on:

  50. Chytridiomycota species (chytrids) belong to a basal lineage in the fungal kingdom. Inhabiting terrestrial and aquatic environments, most are free-living saprophytes but several species cause important disease...

    Authors: Bart T. L. H. van de Vossenberg, Balázs Brankovics, Hai D. T. Nguyen, Marga P. E. van Gent-Pelzer, Donna Smith, Kasia Dadej, Jarosław Przetakiewicz, Jan F. Kreuze, Margriet Boerma, Gerard C. M. van Leeuwen, C. André Lévesque and Theo A. J. van der Lee
    Citation: BMC Evolutionary Biology 2018 18:136
    Content type: Research article Published on:
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