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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 soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropica...

    Authors: Dario Karmeinski, Karen Meusemann, Jessica A. Goodheart, Michael Schroedl, Alexander Martynov, Tatiana Korshunova, Heike Wägele and Alexander Donath
    Citation: BMC Ecology and Evolution 2021 21:226
    Content type: Research article Published on:

  2. Historical and ecological processes shape patterns of genetic diversity in plant species. Colonization to new environments and geographical landscape features determine, amongst other factors, genetic diversit...

    Authors: Gustavo A. Silva-Arias, Lina Caballero-Villalobos, Giovanna C. Giudicelli and Loreta B. Freitas
    Citation: BMC Ecology and Evolution 2021 21:196
    Content type: Research article Published on:

  3. The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are class...

    Authors: Huijuan Zhou, Yiheng Hu, Aziz Ebrahimi, Peiliang Liu, Keith Woeste, Peng Zhao and Shuoxin Zhang
    Citation: BMC Ecology and Evolution 2021 21:191
    Content type: Research article Published on:

  4. Conserved syntenic gene complexes are rare in Arthropods and likely only retained due to functional constraint. Numerous sHSPs have been identified in the genomes of insects, some of which are located clustere...

    Authors: Megan Leask, Mackenzie Lovegrove, Abigail Walker, Elizabeth Duncan and Peter Dearden
    Citation: BMC Ecology and Evolution 2021 21:154
    Content type: Research article Published on:

  6. Understanding how island ecosystems change across habitats is a major challenge in ecological conservation under the conditions of habitat degradation. According to a 2-year investigation on Dong Island of the...

    Authors: Yingcan Li, Zhiwen Chen, Chao Peng, Guangchuan Huang, Hongyu Niu and Hongmao Zhang
    Citation: BMC Ecology and Evolution 2021 21:137
    Content type: Research article Published on:

  7. Delimiting cryptic species in elasmobranchs is a major challenge in modern taxonomy due the lack of available phenotypic features. Employing stand-alone genetics in splitting a cryptic species may prove proble...

    Authors: Fahmi, Ian R. Tibbetts, Michael B. Bennett and Christine L. Dudgeon
    Citation: BMC Ecology and Evolution 2021 21:121
    Content type: Research article Published on:

  8. The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species ...

    Authors: J. S. Eriksson, C. D. Bacon, D. J. Bennett, B. E. Pfeil, B. Oxelman and A. Antonelli
    Citation: BMC Ecology and Evolution 2021 21:107
    Content type: Research article Published on:

  10. Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial spec...

    Authors: Olli H. Laitinen, Tanja P. Kuusela, Sampo Kukkurainen, Anssi Nurminen, Aki Sinkkonen and Vesa P. Hytönen
    Citation: BMC Ecology and Evolution 2021 21:53
    Content type: Research article Published on:

  11. The New Guinean archipelago has been shaped by millions of years of plate tectonic activity combined with long-term fluctuations in climate and sea level. These processes combined with New Guinea’s location at...

    Authors: Emmanuel F. A. Toussaint, Lloyd T. White, Helena Shaverdo, Athena Lam, Suriani Surbakti, Rawati Panjaitan, Bob Sumoked, Thomas von Rintelen, Katayo Sagata and Michael Balke
    Citation: BMC Ecology and Evolution 2021 21:51
    Content type: Research article Published on:

  12. Comparative phylogeographic studies on rainforest species that are widespread in Central Africa often reveal genetic discontinuities within and between biogeographic regions, indicating (historical) barriers t...

    Authors: Samuel Vanden Abeele, Steven B. Janssens, Rosalía Piñeiro and Olivier J. Hardy
    Citation: BMC Ecology and Evolution 2021 21:50
    Content type: Research article Published on:

  13. Identifying factors shaping population genetic structure across continuous landscapes in the context of biogeographic boundaries for lineage diversification has been a challenging goal. The red muntjacs cover ...

    Authors: Bhim Singh, Ajit Kumar, Virendra Prasad Uniyal and Sandeep Kumar Gupta
    Citation: BMC Ecology and Evolution 2021 21:49
    Content type: Research article Published on:

  14. Nbp35-like proteins (Nbp35, Cfd1, HCF101, Ind1, and AbpC) are P-loop NTPases that serve as components of iron-sulfur cluster (FeS) assembly machineries. In eukaryotes, Ind1 is present in mitochondria, and its ...

    Authors: Jan Pyrih, Vojtěch Žárský, Justin D. Fellows, Christopher Grosche, Dorota Wloga, Boris Striepen, Uwe G. Maier and Jan Tachezy
    Citation: BMC Ecology and Evolution 2021 21:46
    Content type: Research article Published on:

  15. Natural model systems are indispensable for exploring adaptations in response to environmental pressures. Sinocyclocheilus of China, the most diverse cavefish clade in the world (75 species), provide unique oppor...

    Authors: Ting-Ru Mao, Ye-Wei Liu, Madhava Meegaskumbura, Jian Yang, Gajaba Ellepola, Gayani Senevirathne, Cheng-Hai Fu, Joshua B. Gross and Marcio R. Pie
    Citation: BMC Ecology and Evolution 2021 21:45
    Content type: Research article Published on:

  16. Phylogenomic approaches have great power to reconstruct evolutionary histories, however they rely on multi-step processes in which each stage has the potential to affect the accuracy of the final result. Many ...

    Authors: Jennifer L. Spillane, Troy M. LaPolice, Matthew D. MacManes and David C. Plachetzki
    Citation: BMC Ecology and Evolution 2021 21:43
    Content type: Research article Published on:

  17. The bearded vulture is sparsely distributed across a wide geographic range that extends over three continents (Africa, Europe and Asia). Restriction to high-altitude mountainous habitats, low breeding rates, l...

    Authors: Melanie Streicher, Sonja Krüger, Franziska Loercher and Sandi Willows-Munro
    Citation: BMC Ecology and Evolution 2021 21:42
    Content type: Research article Published on:

  18. Cherleria (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was...

    Authors: Abigail J. Moore, Jennifer A. Messick and Joachim W. Kadereit
    Citation: BMC Ecology and Evolution 2021 21:40
    Content type: Research article Published on:

  19. Pyrenoids are protein microcompartments composed mainly of Rubisco that are localized in the chloroplasts of many photosynthetic organisms. Pyrenoids contribute to the CO2-concentrating mechanism. This organelle ...

    Authors: Ryo Matsuzaki, Shigekatsu Suzuki, Haruyo Yamaguchi, Masanobu Kawachi, Yu Kanesaki, Hirofumi Yoshikawa, Toshiyuki Mori and Hisayoshi Nozaki
    Citation: BMC Ecology and Evolution 2021 21:11
    Content type: Research article Published on:

  20. The earliest records in Britain for the western European house mouse (Mus musculus domesticus) date from the Late Bronze Age. The arrival of this commensal species in Britain is thought to be related to human tra...

    Authors: Oxala García-Rodríguez, Emilie A. Hardouin, Ellen Hambleton, Jonathan Monteith, Clare Randall, Martin B. Richards, Ceiridwen J. Edwards and John R. Stewart
    Citation: BMC Ecology and Evolution 2021 21:9
    Content type: Research article Published on:

  21. Heterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a num...

    Authors: Rebecca M. Varney, Bastian Brenzinger, Manuel António E. Malaquias, Christopher P. Meyer, Michael Schrödl and Kevin M. Kocot
    Citation: BMC Ecology and Evolution 2021 21:6
    Content type: Research article Published on:

  22. The SARS-CoV-2 pandemic is one of  the greatest  global medical and social challenges that have emerged in recent history. Human coronavirus strains discovered during previous SARS outbreaks have been hypoth...

    Authors: Vladimir Makarenkov, Bogdan Mazoure, Guillaume Rabusseau and Pierre Legendre
    Citation: BMC Ecology and Evolution 2021 21:5
    Content type: Research article Published on:

  23. Salmonids are of major importance both as farmed and wild animals. With the changing environment comes changes in pathogenic pressures so understanding the immune system of all salmonid species is of essence. ...

    Authors: U. Grimholt and M. Lukacs
    Citation: BMC Ecology and Evolution 2021 21:3
    Content type: Research article Published on:

  24. Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects ...

    Authors: Kelly B. Klingler, Joshua P. Jahner, Thomas L. Parchman, Chris Ray and Mary M. Peacock
    Citation: BMC Ecology and Evolution 2021 21:2
    Content type: Research article Published on:

  26. Ecdysozoa are the moulting protostomes, including arthropods, tardigrades, and nematodes. Both the molecular and fossil records indicate that Ecdysozoa is an ancient group originating in the terminal Proterozo...

    Authors: Richard J. Howard, Gregory D. Edgecombe, Xiaomei Shi, Xianguang Hou and Xiaoya Ma
    Citation: BMC Evolutionary Biology 2020 20:156
    Content type: Research article Published on:

  27. Parasitoidism, a specialized life strategy in which a parasite eventually kills its host, is frequently found within the insect order Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two do...

    Authors: Bonnie B. Blaimer, Dietrich Gotzek, Seán G. Brady and Matthew L. Buffington
    Citation: BMC Evolutionary Biology 2020 20:155
    Content type: Research article Published on:

  28. Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-thi...

    Authors: Zhongning Zhao, Neil Heideman, Phillip Bester, Adriaan Jordaan and Margaretha D. Hofmeyr
    Citation: BMC Evolutionary Biology 2020 20:153
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Ecology and Evolution 2021 21:142

  29. Although the processes of co-evolution between parasites and their hosts are well known, evidence of co-speciation remains scarce. Microsporidian intracellular parasites, due to intimate relationships with the...

    Authors: Adrien Quiles, Rémi A. Wattier, Karolina Bacela-Spychalska, Michal Grabowski and Thierry Rigaud
    Citation: BMC Evolutionary Biology 2020 20:149
    Content type: Research article Published on:

  30. Austropotamobius torrentium is a freshwater crayfish species native to central and south-eastern Europe, with an intricate evolutionary history and the highest genetic diversity recorded in the northern-central D...

    Authors: Leona Lovrenčić, Lena Bonassin, Ljudevit Luka Boštjančić, Martina Podnar, Mišel Jelić, Göran Klobučar, Martina Jaklič, Valentina Slavevska-Stamenković, Jelena Hinić and Ivana Maguire
    Citation: BMC Evolutionary Biology 2020 20:146
    Content type: Research article Published on:

  31. Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic r...

    Authors: Nikolaus U. Szucsich, Daniela Bartel, Alexander Blanke, Alexander Böhm, Alexander Donath, Makiko Fukui, Simon Grove, Shanlin Liu, Oliver Macek, Ryuichiro Machida, Bernhard Misof, Yasutaka Nakagaki, Lars Podsiadlowski, Kaoru Sekiya, Shigekazu Tomizuka, Björn M. Von Reumont…
    Citation: BMC Evolutionary Biology 2020 20:144
    Content type: Research article Published on:

  32. The three-spined stickleback (Gasterosteus aculeatus) is a remarkable system to study the genetic mechanisms underlying parallel evolution during the transition from marine to freshwater habitats. Although the ma...

    Authors: Ryo Kakioka, Seiichi Mori, Tomoyuki Kokita, Takuya K. Hosoki, Atsushi J. Nagano, Asano Ishikawa, Manabu Kume, Atsushi Toyoda and Jun Kitano
    Citation: BMC Evolutionary Biology 2020 20:143
    Content type: Research article Published on:

  33. The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophylet...

    Authors: Guilherme Rezende Dias, Eduardo Guimarães Dupim, Thyago Vanderlinde, Beatriz Mello and Antonio Bernardo Carvalho
    Citation: BMC Evolutionary Biology 2020 20:141
    Content type: Research article Published on:

  34. The aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidificat...

    Authors: Deborah Wall-Palmer, Arie W. Janssen, Erica Goetze, Le Qin Choo, Lisette Mekkes and Katja T. C. A. Peijnenburg
    Citation: BMC Evolutionary Biology 2020 20:124
    Content type: Research article Published on:

  35. As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imp...

    Authors: Erica S. Nielsen, Romina Henriques, Maria Beger, Robert J. Toonen and Sophie von der Heyden
    Citation: BMC Evolutionary Biology 2020 20:121
    Content type: Research article Published on:

  36. The Chinese Isoetes L. are distributed in a stairway pattern: diploids in the high altitude and polyploids in the low altitude. The allopolyploid I. sinensis and its diploid parents I. yunguiensis and I. taiwanen...

    Authors: Xiaokang Dai, Xiang Li, Yuqian Huang and Xing Liu
    Citation: BMC Evolutionary Biology 2020 20:118
    Content type: Research article Published on:

  37. The distribution of genetic diversity and the underlying processes are important for conservation planning but are unknown for most species and have not been well studied in many regions. In East Asia, the Sic...

    Authors: Yuchi Zheng, Qiang Dai, Xianguang Guo and Xiaomao Zeng
    Citation: BMC Evolutionary Biology 2020 20:111
    Content type: Research article Published on:

  38. Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investiga...

    Authors: Simon T. Maddock, Ronald A. Nussbaum, Julia J. Day, Leigh Latta, Mark Miller, Debra L. Fisk, Mark Wilkinson, Sara Rocha, David J. Gower and Michael E. Pfrender
    Citation: BMC Evolutionary Biology 2020 20:110
    Content type: Research article Published on:

  39. Was there a mid-Cenozoic vertebrate extinction and recovery event in Madagascar and, if so, what are its implications for the evolution of lemurs? The near lack of an early and mid-Cenozoic fossil record on Ma...

    Authors: Laurie R. Godfrey, Karen E. Samonds, Justin W. Baldwin, Michael R. Sutherland, Jason M. Kamilar and Kristen L. Allfisher
    Citation: BMC Evolutionary Biology 2020 20:97
    Content type: Research article Published on:

  40. Old World porcupines (Family: Hystricidae) are the third-largest rodents and inhabit southern Europe, Asia, and most regions of Africa. They are a typical indicator of warm climate and their distribution is re...

    Authors: Guilian Sheng, Jiaming Hu, Haowen Tong, Bastien Llamas, Junxia Yuan, Xindong Hou, Shungang Chen, Bo Xiao and Xulong Lai
    Citation: BMC Evolutionary Biology 2020 20:88
    Content type: Research article Published on:

  41. Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates...

    Authors: Qi Zhang, Jiahui Xu, Alan Warren, Ran Yang, Zhuo Shen and Zhenzhen Yi
    Citation: BMC Evolutionary Biology 2020 20:86
    Content type: Research article Published on:

  42. We have described the diversity of complete mtDNA sequences from ‘relic’ groups of the Russian Far East, primarily the Nivkhi (who speak a language isolate with no clear relatedness to any others) and Oroki of...

    Authors: Stanislav V. Dryomov, Elena B. Starikovskaya, Azhar M. Nazhmidenova, Igor V. Morozov and Rem I. Sukernik
    Citation: BMC Evolutionary Biology 2020 20:83
    Content type: Research article Published on:

  43. Quaternary climate fluctuations are an engine of biotic diversification. Global cooling cycles, such as the Last Glacial Maximum (LGM), are known to have fragmented the ranges of higher-latitude fauna and flor...

    Authors: Kritika M. Garg, Balaji Chattopadhyay, Bonny Koane, Katerina Sam and Frank E. Rheindt
    Citation: BMC Evolutionary Biology 2020 20:82
    Content type: Research article Published on:

  44. 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 Published on:

  45. 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 Published on:

  46. 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 Published on:

  47. 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 Published on:

  48. 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 Published on:

    The Correction to this article has been published in BMC Evolutionary Biology 2020 20:133

  49. 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 Published on:
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