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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 7 of 12

  1. Ultraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has yet to be extensively compared with that of traditional Sanger s...

    Authors: Bonnie B. Blaimer, Seán G. Brady, Ted R. Schultz, Michael W. Lloyd, Brian L. Fisher and Philip S. Ward
    Citation: BMC Evolutionary Biology 2015 15:271
    Content type: Research article Published on:

  2. Teleosts constitute more than 99 % of living actinopterygian fishes and fossil teleosts have been studied for about two centuries. However, a general consensus on the definition of Teleostei and the relationsh...

    Authors: Emilia Sferco, Adriana López-Arbarello and Ana María Báez
    Citation: BMC Evolutionary Biology 2015 15:268
    Content type: Research article Published on:

  3. The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) ...

    Authors: Claude Lemieux, Antony T. Vincent, Aurélie Labarre, Christian Otis and Monique Turmel
    Citation: BMC Evolutionary Biology 2015 15:264
    Content type: Research article Published on:

  4. Geological events in the latter Cenozoic have influenced the distribution, abundance and genetic structure of tree populations in temperate and tropical North America. The biogeographical history of temperate ...

    Authors: Yalma L. Vargas-Rodriguez, William J. Platt, Lowell E. Urbatsch and David W. Foltz
    Citation: BMC Evolutionary Biology 2015 15:257
    Content type: Research article Published on:

  5. The Osprey (Pandion haliaetus) is one of only six bird species with an almost world-wide distribution. We aimed at clarifying its phylogeographic structure and elucidating its taxonomic status (as it is currently...

    Authors: Flavio Monti, Olivier Duriez, Véronique Arnal, Jean-Marie Dominici, Andrea Sforzi, Leonida Fusani, David Grémillet and Claudine Montgelard
    Citation: BMC Evolutionary Biology 2015 15:255
    Content type: Research article Published on:

  6. Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Ar...

    Authors: Sean B. Reilly, Ammon Corl and David B. Wake
    Citation: BMC Evolutionary Biology 2015 15:241
    Content type: Research article Published on:

  7. Recent genetic studies have suggested that the colonization of East Asia by modern humans was more complex than a single origin from the South, and that a genetic contribution via a Northern route was probably...

    Authors: Da Di, Alicia Sanchez-Mazas and Mathias Currat
    Citation: BMC Evolutionary Biology 2015 15:240
    Content type: Research article Published on:

  8. Population structure and genetic diversity of marine organisms in the Northwestern Pacific Ocean exhibited complex patterns. Saccharina japonica is a commercially and ecologically important kelp species widely di...

    Authors: Jie Zhang, Jian-Ting Yao, Zhong-Min Sun, Gang Fu, Dmitry A. Galanin, Chikako Nagasato, Taizo Motomura, Zi-Min Hu and De-Lin Duan
    Citation: BMC Evolutionary Biology 2015 15:237
    Content type: Research article Published on:

  9. The Commerson’s leaf-nosed bat, Hipposideros commersoni sensu stricto, is endemic to Madagascar and is relatively common in the western portion of the island, where it is found in areas, including forested zones,...

    Authors: Andrinajoro R. Rakotoarivelo, Sandi Willows-Munro, M. Corrie Schoeman, Jennifer M. Lamb and Steven M. Goodman
    Citation: BMC Evolutionary Biology 2015 15:235
    Content type: Research article Published on:

  10. How species ranges form in landscapes is a matter of long-standing evolutionary interest. However, little is known about how natural phenotypic variations of ecologically important traits contribute to species...

    Authors: Yoshihiro Matsuoka, Shigeo Takumi and Taihachi Kawahara
    Citation: BMC Evolutionary Biology 2015 15:213
    Content type: Research article Published on:

  11. The plastid maturase MatK has been implicated as a possible model for the evolutionary “missing link” between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigat...

    Authors: Michelle M. Barthet, Keenan Moukarzel, Kayla N. Smith, Jaimin Patel and Khidir W. Hilu
    Citation: BMC Evolutionary Biology 2015 15:210
    Content type: Research article Published on:

  12. Divergent selection can be a major driver of ecological speciation. In insects of medical importance, understanding the speciation process is both of academic interest and public health importance. In the West...

    Authors: Bruno Gomes, Craig S. Wilding, David Weetman, Carla A. Sousa, Maria T. Novo, Harry M. Savage, António P. G. Almeida, João Pinto and Martin J. Donnelly
    Citation: BMC Evolutionary Biology 2015 15:197
    Content type: Research article Published on:

  13. Butterflies of the subtribe Mycalesina have radiated successfully in almost all habitat types in Africa, Madagascar, the Indian subcontinent, Indo-China and Australasia. Studies aimed at understanding the reas...

    Authors: Kwaku Aduse-Poku, Oskar Brattström, Ullasa Kodandaramaiah, David C. Lees, Paul M. Brakefield and Niklas Wahlberg
    Citation: BMC Evolutionary Biology 2015 15:167
    Content type: Research article Published on:

  14. Squaliform sharks represent approximately 27 % of extant shark diversity, comprising more than 130 species with a predominantly deep-dwelling lifestyle. Many Squaliform species are highly specialized, includin...

    Authors: Nicolas Straube, Chenhong Li, Julien M. Claes, Shannon Corrigan and Gavin J. P. Naylor
    Citation: BMC Evolutionary Biology 2015 15:162
    Content type: Research article Published on:

  15. The populations of Soldanella (Primulaceae) of the southern Apennines (Italy) are unique within the genus for their distribution and ecology. Their highly fragmented distribution range, with three main metapopula...

    Authors: Alessandro Bellino, Leonardo Bellino, Daniela Baldantoni and Antonio Saracino
    Citation: BMC Evolutionary Biology 2015 15:158
    Content type: Research Article Published on:

  16. The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large siz...

    Authors: Stephen A Smith, Michael J Moore, Joseph W Brown and Ya Yang
    Citation: BMC Evolutionary Biology 2015 15:150
    Content type: Methodology Article Published on:

  17. The European mink (Mustela lutreola, L. 1761) is a critically endangered mustelid, which inhabits several main river drainages in Europe. Here, we assess the genetic variation of existing populations of this spec...

    Authors: Maria Teresa Cabria, Elena G. Gonzalez, Benjamin J. Gomez-Moliner, Johan R. Michaux, Dimitry Skumatov, Andreas Kranz, Pascal Fournier, Santiago Palazon and Rafael Zardoya
    Citation: BMC Evolutionary Biology 2015 15:141
    Content type: Research Article Published on:

  18. Influenza A/H3N2 has been circulating in humans since 1968, causing considerable morbidity and mortality. Although H3N2 incidence is highly seasonal, how such seasonality contributes to global phylogeographic ...

    Authors: Daniel Zinder, Trevor Bedford, Edward B Baskerville, Robert J Woods, Manojit Roy and Mercedes Pascual
    Citation: BMC Evolutionary Biology 2014 14:272
    Content type: Research article Published on:

  19. Snails species belonging to the genus Bulinus (Planorbidae) serve as intermediate host for flukes belonging to the genus Schistosoma (Digenea, Platyhelminthes). Despite its importance in the transmission of these...

    Authors: Rima Zein-Eddine, Félicité Flore Djuikwo-Teukeng, Mustafa Al-Jawhari, Bruno Senghor, Tine Huyse and Gilles Dreyfuss
    Citation: BMC Evolutionary Biology 2014 14:271
    Content type: Research article Published on:

  20. Estimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimate...

    Authors: Michael D Crisp, Nate B Hardy and Lyn G Cook
    Citation: BMC Evolutionary Biology 2014 14:263
    Content type: Research article Published on:

  21. Rodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the ...

    Authors: Josef Bryja, Ondřej Mikula, Radim Šumbera, Yonas Meheretu, Tatiana Aghová, Leonid A Lavrenchenko, Vladimír Mazoch, Nicholas Oguge, Judith S Mbau, Kiros Welegerima, Nicaise Amundala, Marc Colyn, Herwig Leirs and Erik Verheyen
    Citation: BMC Evolutionary Biology 2014 14:256
    Content type: Research article Published on:

  24. Fossil lobopodians, including animals proposed to have close affinity to modern onychophorans, are crucial to understanding the evolution of the panarthropod body plan and the phylum-level relationships betwee...

    Authors: Duncan JE Murdock, Sarah E Gabbott, Georg Mayer and Mark A Purnell
    Citation: BMC Evolutionary Biology 2014 14:222
    Content type: Research article Published on:

  25. The Central and Southern European mountain ranges represent important biodiversity hotspots and show high levels of endemism. In the land snail genus Orcula Held, 1837 nine species are distributed in the Alps and...

    Authors: Josef Harl, Barna Páll-Gergely, Sandra Kirchner, Helmut Sattmann, Michael Duda, Luise Kruckenhauser and Elisabeth Haring
    Citation: BMC Evolutionary Biology 2014 14:223
    Content type: Research article Published on:

  26. Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the...

    Authors: Nora Hohmann, Roswitha Schmickl, Tzen-Yuh Chiang, Magdalena Lučanová, Filip Kolář, Karol Marhold and Marcus A Koch
    Citation: BMC Evolutionary Biology 2014 14:224
    Content type: Research article Published on:

  27. Rhynchocypris oxycephalus is a cold water fish with a wide geographic distribution including the relatively warm temperate regions of southern China. It also occurs in second- and third-step geomorphic areas in C...

    Authors: Dan Yu, Ming Chen, Qiongying Tang, Xiaojuan Li and Huanzhang Liu
    Citation: BMC Evolutionary Biology 2014 14:225
    Content type: Research article Published on:

  28. The margins of a species’ range might be located at the margins of a species’ niche, and in such cases, can be highly vulnerable to climate changes. They, however, may also undergo significant evolutionary cha...

    Authors: Makiko Mimura, Misako Mishima, Martin Lascoux and Tetsukazu Yahara
    Citation: BMC Evolutionary Biology 2014 14:209
    Content type: Research article Published on:

  29. The current taxonomy of the African giraffe (Giraffa camelopardalis) is primarily based on pelage pattern and geographic distribution, and nine subspecies are currently recognized. Although genetic studies have b...

    Authors: Friederike Bock, Julian Fennessy, Tobias Bidon, Andy Tutchings, Andri Marais, Francois Deacon and Axel Janke
    Citation: BMC Evolutionary Biology 2014 14:219
    Content type: Research article Published on:

  30. As attested by the fossil record, Cretaceous environmental changes have significantly impacted the diversification dynamics of several groups of organisms. A major biome turnover that occurred during this peri...

    Authors: Gael J Kergoat, Patrice Bouchard, Anne-Laure Clamens, Jessica L Abbate, Hervé Jourdan, Roula Jabbour-Zahab, Gwenaelle Genson, Laurent Soldati and Fabien L Condamine
    Citation: BMC Evolutionary Biology 2014 14:220
    Content type: Research article Published on:

  31. Vetulicolians are one of the most problematic and controversial Cambrian fossil groups, having been considered as arthropods, chordates, kinorhynchs, or their own phylum. Mounting evidence suggests that vetuli...

    Authors: Diego C García-Bellido, Michael S Y Lee, Gregory D Edgecombe, James B Jago, James G Gehling and John R Paterson
    Citation: BMC Evolutionary Biology 2014 14:214
    Content type: Research article Published on:

  32. Annual Nothobranchius fishes are distributed in East and Southern Africa and inhabit ephemeral pools filled during the monsoon season. Nothobranchius show extreme life-history adaptations: embryos survive by ente...

    Authors: Alexander Dorn, Zuzana Musilová, Matthias Platzer, Kathrin Reichwald and Alessandro Cellerino
    Citation: BMC Evolutionary Biology 2014 14:210
    Content type: Research article Published on:

  33. Glaciations were recurrent throughout the Quaternary and potentially shaped species genetic structure worldwide by affecting population dynamics. Here, we implemented a multi-model inference approach to recove...

    Authors: Rosane G Collevatti, Matheus S Lima-Ribeiro, Levi Carina Terribile, Ludymila B S Guedes, Fernanda F Rosa and Mariana P C Telles
    Citation: BMC Evolutionary Biology 2014 14:213
    Content type: Research article Published on:

  34. Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least...

    Authors: Miroslava Derenko, Boris Malyarchuk, Galina Denisova, Maria Perkova, Andrey Litvinov, Tomasz Grzybowski, Irina Dambueva, Katarzyna Skonieczna, Urszula Rogalla, Iosif Tsybovsky and Ilya Zakharov
    Citation: BMC Evolutionary Biology 2014 14:217
    Content type: Research article Published on:

  35. Understanding the evolutionary history of morphologically cryptic species complexes is difficult, and made even more challenging when geographic distributions have been modified by human-mediated dispersal. Th...

    Authors: Enric Planas, Erin E Saupe, Matheus S Lima-Ribeiro, A Townsend Peterson and Carles Ribera
    Citation: BMC Evolutionary Biology 2014 14:195
    Content type: Research article Published on:

  36. Mountain landscapes are topographically complex, creating discontinuous `islands’ of alpine and sub-alpine habitat with a dynamic history. Changing climatic conditions drive their expansion and contraction, le...

    Authors: Rachel A Slatyer, Michael A Nash, Adam D Miller, Yoshinori Endo, Kate DL Umbers and Ary A Hoffmann
    Citation: BMC Evolutionary Biology 2014 14:204
    Content type: Research article Published on:

  37. The green algae represent one of the most successful groups of photosynthetic eukaryotes, but compared to their land plant relatives, surprisingly little is known about their evolutionary history. This is in g...

    Authors: Claude Lemieux, Christian Otis and Monique Turmel
    Citation: BMC Evolutionary Biology 2014 14:211
    Content type: Research article Published on:

  38. With more than 100000 living species, mollusks are the second most diverse metazoan phylum. The current taxonomic classification of mollusks recognizes eight classes (Neomeniomorpha, Chaetodermomorpha, Polypla...

    Authors: David Osca, Iker Irisarri, Christiane Todt, Cristina Grande and Rafael Zardoya
    Citation: BMC Evolutionary Biology 2014 14:197
    Content type: Research article Published on:

  39. Partulid tree snails are endemic to Pacific high islands and have experienced extraordinary rates of extinction in recent decades. Although they collectively range across a 10,000 km swath of Oceania, half of ...

    Authors: Taehwan Lee, Jingchun Li, Celia KC Churchill and Diarmaid Ó Foighil
    Citation: BMC Evolutionary Biology 2014 14:202
    Content type: Research article Published on:

  40. Symbiotic relationships have contributed to major evolutionary innovations, the maintenance of fundamental ecosystem functions, and the generation and maintenance of biodiversity. However, the exact nature of ...

    Authors: Clive T Darwell, Sarah al-Beidh and James M Cook
    Citation: BMC Evolutionary Biology 2014 14:189
    Content type: Research article Published on:

  41. Calisto is the largest butterfly genus in the West Indies but its systematics, historical biogeography and the causes of its diversification have not been previously rigorously evaluated. Several studies attempti...

    Authors: Pável Matos-Maraví, Rayner Núñez Águila, Carlos Peña, Jacqueline Y Miller, Andrei Sourakov and Niklas Wahlberg
    Citation: BMC Evolutionary Biology 2014 14:199
    Content type: Research article Published on:

  43. New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nu...

    Authors: Myriam Gaudeul, Martin F Gardner, Philip Thomas, Richard A Ennos and Pete M Hollingsworth
    Citation: BMC Evolutionary Biology 2014 14:171
    Content type: Research article Published on:

  44. Species thermal requirements are one of the principal determinants of their ecology and biogeography, although our understanding of the interplay between these factors is limited by the paucity of integrative ...

    Authors: Amparo Hidalgo-Galiana, David Sánchez-Fernández, David T Bilton, Alexandra Cieslak and Ignacio Ribera
    Citation: BMC Evolutionary Biology 2014 14:187
    Content type: Research article Published on:

  45. The evolutionary history of the Old World monkey tribe Papionini comprising the genera Macaca, Mandrillus, Cercocebus, Lophocebus, Theropithecus, Rungwecebus and Papio is still matter of debate. Although the Afri...

    Authors: Rasmus Liedigk, Christian Roos, Markus Brameier and Dietmar Zinner
    Citation: BMC Evolutionary Biology 2014 14:176
    Content type: Research article Published on:

  46. Myzostomids are marine annelids, nearly all of which live symbiotically on or inside echinoderms, chiefly crinoids, and to a lesser extent asteroids and ophiuroids. These symbionts possess a variety of adult b...

    Authors: Mindi M Summers and Greg W Rouse
    Citation: BMC Evolutionary Biology 2014 14:170
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Evolutionary Biology 2015 15:53

  47. Fleas, the most notorious insect ectoparasites of human, dogs, cats, birds, etc., have recently been traced to its basal and primitive ancestors during the Middle Jurassic. Compared with extant fleas, these la...

    Authors: Taiping Gao, Chungkun Shih, Alexandr P Rasnitsyn, Xing Xu, Shuo Wang and Dong Ren
    Citation: BMC Evolutionary Biology 2014 14:168
    Content type: Research article Published on:

  48. The genetic diversity of the human microbiome holds great potential for shedding light on the history of our ancestors. Helicobacter pylori is the most prominent example as its analysis allowed a fine-scale resol...

    Authors: Karsten Henne, Jing Li, Mark Stoneking, Olga Kessler, Hildegard Schilling, Anne Sonanini, Georg Conrads and Hans-Peter Horz
    Citation: BMC Evolutionary Biology 2014 14:190
    Content type: Research article Published on:

  49. Specific host-parasite systems often embody a particular co-distribution phenomenon, in which the parasite’s phylogeographic pattern is dependent on its host. In practice, however, both congruent and incongrue...

    Authors: Gonghua Lin, Fang Zhao, Hongjian Chen, Xiaogong Deng, Jianping Su and Tongzuo Zhang
    Citation: BMC Evolutionary Biology 2014 14:180
    Content type: Research article Published on:

  50. Aquaporins (AQPs) and aquaglyceroporins (AQGPs) belong to the superfamily of Major Intrinsic Proteins (MIPs) and are involved in the transport of water and neutral solutes across the membranes. MIP channels pl...

    Authors: Ravi Kumar Verma, Neel Duti Prabh and Ramasubbu Sankararamakrishnan
    Citation: BMC Evolutionary Biology 2014 14:173
    Content type: Research article Published on:
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