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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 11 of 12

  1. The fern genus Dryopteris (Dryopteridaceae) is among the most common and species rich fern genera in temperate forests in the northern hemisphere containing 225–300 species worldwide. The circumscription of Dryop...

    Authors: Li-Bing Zhang, Liang Zhang, Shi-Yong Dong, Emily B Sessa, Xin-Fen Gao and Atsushi Ebihara
    Citation: BMC Evolutionary Biology 2012 12:180
    Content type: Research article Published on:

  2. Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent esti...

    Authors: Steven D Leavitt, Theodore L Esslinger, Pradeep K Divakar and H Thorsten Lumbsch
    Citation: BMC Evolutionary Biology 2012 12:176
    Content type: Research article Published on:

  3. Galeommatoidea is a superfamily of bivalves that exhibits remarkably diverse lifestyles. Many members of this group live attached to the body surface or inside the burrows of other marine invertebrates, includ...

    Authors: Ryutaro Goto, Atsushi Kawakita, Hiroshi Ishikawa, Yoichi Hamamura and Makoto Kato
    Citation: BMC Evolutionary Biology 2012 12:172
    Content type: Research article Published on:

  4. Physarales represents the largest taxonomic order among the plasmodial slime molds (myxomycetes). Physarales is of particular interest since the two best-studied myxomycete species, Physarum polycephalum and Didy...

    Authors: Satish CR Nandipati, Kari Haugli, Dag H Coucheron, Edward F Haskins and Steinar D Johansen
    Citation: BMC Evolutionary Biology 2012 12:166
    Content type: Research article Published on:

  5. If the geographical displacement of one species by another is accompanied by hybridization, mitochondrial DNA can introgress asymmetrically, from the outcompeted species into the invading species, over a large...

    Authors: Ben Wielstra and Jan W Arntzen
    Citation: BMC Evolutionary Biology 2012 12:161
    Content type: Research article Published on:

  6. Indehiscent sporangia are reported for only a few of derived leptosporangiate ferns. Their evolution has been likely caused by conditions in which promotion of self-fertilization is an evolutionary advantageou...

    Authors: Li Wang, Harald Schneider, Zhiqiang Wu, Lijuan He, Xianchun Zhang and Qiaoping Xiang
    Citation: BMC Evolutionary Biology 2012 12:158
    Content type: Research article Published on:

  7. The circumscription of the avian superfamily Sylvioidea is a matter of long ongoing debate. While the overall inclusiveness has now been mostly agreed on and 20 families recognised, the phylogenetic relationsh...

    Authors: Silke Fregin, Martin Haase, Urban Olsson and Per Alström
    Citation: BMC Evolutionary Biology 2012 12:157
    Content type: Research article Published on:

  8. The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Compari...

    Authors: Yi-Chiao Chan, Christian Roos, Miho Inoue-Murayama, Eiji Inoue, Chih-Chin Shih and Linda Vigilant
    Citation: BMC Evolutionary Biology 2012 12:150
    Content type: Research article Published on:

  9. The Pleistocene Ice Ages were the most recent geohistorical event of major global impact, but their consequences for most parts of the Southern hemisphere remain poorly known. We investigate a radiation of ten...

    Authors: Oliver Hawlitschek, Lars Hendrich, Marianne Espeland, Emmanuel FA Toussaint, Martin J Genner and Michael Balke
    Citation: BMC Evolutionary Biology 2012 12:142
    Content type: Research article Published on:

  10. Patagonia extends for more than 84,000 km of irregular coasts is an area especially apt to evaluate how historic and contemporary processes influence the distribution and connectivity of shallow marine benthic...

    Authors: Claudio A González-Wevar, Mathias Hüne, Juan I Cañete, Andrés Mansilla, Tomoyuki Nakano and Elie Poulin
    Citation: BMC Evolutionary Biology 2012 12:139
    Content type: Research article Published on:

  11. Fungus farming is an unusual life style in insects that has evolved many times in the wood boring weevils named ‘ambrosia beetles’. Multiple occurrences of this behaviour allow for a detailed comparison of the...

    Authors: Bjarte H Jordal and Anthony I Cognato
    Citation: BMC Evolutionary Biology 2012 12:133
    Content type: Research article Published on:

  12. The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagi...

    Authors: Annie R Lindgren, Molly S Pankey, Frederick G Hochberg and Todd H Oakley
    Citation: BMC Evolutionary Biology 2012 12:129
    Content type: Research article Published on:

  13. Duikers in the subfamily Cephalophinae are a group of tropical forest mammals believed to have first originated during the late Miocene. However, knowledge of phylogenetic relationships, pattern and timing of ...

    Authors: Anne R Johnston and Nicola M Anthony
    Citation: BMC Evolutionary Biology 2012 12:120
    Content type: Research article Published on:

  14. Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and w...

    Authors: Knud A Jønsson, Pierre-Henri Fabre and Martin Irestedt
    Citation: BMC Evolutionary Biology 2012 12:72
    Content type: Research article Published on:

  15. House mice (Mus musculus) are commensals of humans and therefore their phylogeography can reflect human colonization and settlement patterns. Previous studies have linked the distribution of house mouse mitochond...

    Authors: EP Jones, K Skirnisson, TH McGovern, MTP Gilbert, E Willerslev and JB Searle
    Citation: BMC Evolutionary Biology 2012 12:35
    Content type: Research article Published on:

  16. Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different ...

    Authors: Lyndall L Pereira-da-Conceicoa, Benjamin W Price, Helen M Barber-James, Nigel P Barker, Ferdy C de Moor and Martin H Villet
    Citation: BMC Evolutionary Biology 2012 12:26
    Content type: Research article Published on:

  17. The trans-Atlantic slave trade dramatically changed the demographic makeup of the New World, with varying regions of the African coast exploited differently over roughly a 400 year period. When compared to the...

    Authors: Michael L Deason, Antonio Salas, Simon P Newman, Vincent A Macaulay, Errol Y st A Morrison and Yannis P Pitsiladis
    Citation: BMC Evolutionary Biology 2012 12:24
    Content type: Research article Published on:

  18. Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that speci...

    Authors: Christine D Bacon, Miles J McKenna, Mark P Simmons and Warren L Wagner
    Citation: BMC Evolutionary Biology 2012 12:23
    Content type: Research article Published on:

  19. Oxygen transport in the hemolymph of many arthropod species is facilitated by large copper-proteins referred to as hemocyanins. Arthropod hemocyanins are hexamers or oligomers of hexamers, which are characteri...

    Authors: Peter Rehm, Christian Pick, Janus Borner, Jürgen Markl and Thorsten Burmester
    Citation: BMC Evolutionary Biology 2012 12:19
    Content type: Research article Published on:

  20. The Ampelopsis clade (Ampelopsis and its close allies) of the grape family Vitaceae contains ca. 43 species disjunctly distributed in Asia, Europe, North America, South America, Africa, and Australia, and is a ra...

    Authors: Ze-Long Nie, Hang Sun, Steven R Manchester, Ying Meng, Quentin Luke and Jun Wen
    Citation: BMC Evolutionary Biology 2012 12:17
    Content type: Research article Published on:

  21. The pronounced morphological conservatism within Tarentola geckos contrasted with a high genetic variation in North Africa, has led to the hypothesis that this group could represent a cryptic species complex, a c...

    Authors: Catarina Rato, Salvador Carranza and David J Harris
    Citation: BMC Evolutionary Biology 2012 12:14
    Content type: Research article Published on:

  23. For phylogenetic reconstructions, conflict in signal is a potential problem for tree reconstruction. For instance, molecular data from different cellular components, such as the mitochondrion and nucleus, may ...

    Authors: Min Zhong, Benjamin Hansen, Maximilian Nesnidal, Anja Golombek, Kenneth M Halanych and Torsten H Struck
    Citation: BMC Evolutionary Biology 2011 11:369
    Content type: Research article Published on:

  24. The rapidly increasing number of available plant genomes opens up almost unlimited prospects for biology in general and molecular phylogenetics in particular. A recent study took advantage of this data and ide...

    Authors: Julia Naumann, Lars Symmank, Marie-Stéphanie Samain, Kai F Müller, Christoph Neinhuis, Claude W dePamphilis and Stefan Wanke
    Citation: BMC Evolutionary Biology 2011 11:357
    Content type: Research article Published on:

  25. The avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. T...

    Authors: Per Alström, Sebastian Höhna, Magnus Gelang, Per GP Ericson and Urban Olsson
    Citation: BMC Evolutionary Biology 2011 11:352
    Content type: Research article Published on:

  26. Genetic, phenotypic and ecological divergence within a lineage is the result of past and ongoing evolutionary processes, which lead ultimately to diversification and speciation. Integrative analyses allow link...

    Authors: Patrick S Fitze, Virginia Gonzalez-Jimena, Luis M San-Jose, Diego San Mauro, Pedro Aragón, Teresa Suarez and Rafael Zardoya
    Citation: BMC Evolutionary Biology 2011 11:347
    Content type: Research article Published on:

  27. Understanding how freshwater assemblages have been formed and maintained is a fundamental goal in evolutionary and ecological disciplines. Here we use a historical approach to test the hypothesis of codivergen...

    Authors: Brian R Barber, Peter J Unmack, Marcos Pérez-Losada, Jerald B Johnson and Keith A Crandall
    Citation: BMC Evolutionary Biology 2011 11:343
    Content type: Research article Published on:

  28. Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed ...

    Authors: Omar Fiz-Palacios, Harald Schneider, Jochen Heinrichs and Vincent Savolainen
    Citation: BMC Evolutionary Biology 2011 11:341
    Content type: Research article Published on:

  29. The nematode Caenorhabditis elegans is a major laboratory model in biology. Only ten Caenorhabditis species were available in culture at the onset of this study. Many of them, like C. elegans, were mostly isolate...

    Authors: Karin C Kiontke, Marie-Anne Félix, Michael Ailion, Matthew V Rockman, Christian Braendle, Jean-Baptiste Pénigault and David HA Fitch
    Citation: BMC Evolutionary Biology 2011 11:339
    Content type: Research article Published on:

  30. Environmental preferences and past climatic changes may determine the length of time during which a species range has contracted or expanded from refugia, thereby influencing levels of genetic diversification....

    Authors: Jesus T Garcia, Fernando Alda, Julien Terraube, François Mougeot, Audrey Sternalski, Vincent Bretagnolle and Beatriz Arroyo
    Citation: BMC Evolutionary Biology 2011 11:333
    Content type: Research article Published on:

  31. From a common ancestor with animals, the earliest fungi inherited flagellated zoospores for dispersal in water. Terrestrial fungi lost all flagellated stages and reproduce instead with nonmotile spores. Olpidium ...

    Authors: Satoshi Sekimoto, D'Ann Rochon, Jennifer E Long, Jaclyn M Dee and Mary L Berbee
    Citation: BMC Evolutionary Biology 2011 11:331
    Content type: Research article Published on:

  32. DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from ...

    Authors: Sebastian Lippold, Nicholas J Matzke, Monika Reissmann and Michael Hofreiter
    Citation: BMC Evolutionary Biology 2011 11:328
    Content type: Research article Published on:

  33. Species of the Fusarium genus are important fungi which is associated with health hazards in human and animals. The taxonomy of this genus has been a subject of controversy for many years. Although many researche...

    Authors: Maiko Watanabe, Takahiro Yonezawa, Ken-ichi Lee, Susumu Kumagai, Yoshiko Sugita-Konishi, Keiichi Goto and Yukiko Hara-Kudo
    Citation: BMC Evolutionary Biology 2011 11:322
    Content type: Research article Published on:

  34. The major islands of the Western Mediterranean--Corsica, Sardinia, and the Balearic Islands--are continental terrenes that drifted towards their present day location following a retreat from their original pos...

    Authors: Leticia Bidegaray-Batista and Miquel A Arnedo
    Citation: BMC Evolutionary Biology 2011 11:317
    Content type: Research article Published on:

  35. Scleractinian corals are currently a focus of major interest because of their ecological importance and the uncertain fate of coral reefs in the face of increasing anthropogenic pressure. Despite this, remarka...

    Authors: Jarosław Stolarski, Marcelo V Kitahara, David J Miller, Stephen D Cairns, Maciej Mazur and Anders Meibom
    Citation: BMC Evolutionary Biology 2011 11:316
    Content type: Research article Published on:

  36. A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress h...

    Authors: Zhuo Chen, Shixia Xu, Kaiya Zhou and Guang Yang
    Citation: BMC Evolutionary Biology 2011 11:314
    Content type: Research article Published on:

  38. The 5S ribosomal DNA (5S rDNA) is organized in tandem arrays with repeat units that consist of a transcribing region (5S) and a variable nontranscribed spacer (NTS), in higher eukaryotes. Until recently the 5S...

    Authors: Alejandra Perina, David Seoane, Ana M González-Tizón, Fernanda Rodríguez-Fariña and Andrés Martínez-Lage
    Citation: BMC Evolutionary Biology 2011 11:304
    Content type: Research article Published on:

  39. The use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA) to estimate phylogeny are common, especially in vertebrates. ...

    Authors: M Caitlin Fisher-Reid and John J Wiens
    Citation: BMC Evolutionary Biology 2011 11:300
    Content type: Research article Published on:

  40. Reconstructing the higher relationships of pulmonate gastropods has been difficult. The use of morphology is problematic due to high homoplasy. Molecular studies have suffered from low taxon sampling. Forty-ei...

    Authors: Tracy R White, Michele M Conrad, Roger Tseng, Shaina Balayan, Rosemary Golding, António Manuel de Frias Martins and Benoît A Dayrat
    Citation: BMC Evolutionary Biology 2011 11:295
    Content type: Research article Published on:

  41. The Asian origin of Native Americans is largely accepted. However uncertainties persist regarding the source population(s) within Asia, the divergence and arrival time(s) of the founder groups, the number of e...

    Authors: Satish Kumar, Claire Bellis, Mark Zlojutro, Phillip E Melton, John Blangero and Joanne E Curran
    Citation: BMC Evolutionary Biology 2011 11:293
    Content type: Research article Published on:

  42. Two Calyptogena clam intracellular obligate symbionts, Ca. Vesicomyosocius okutanii (Vok; C. okutanii symbiont) and Ca. Ruthia magnifica (Rma; C. magnifica symbiont), have small genomes (1.02 and 1.16 Mb, respect...

    Authors: Hirokazu Kuwahara, Yoshihiro Takaki, Shigeru Shimamura, Takao Yoshida, Taro Maeda, Takekazu Kunieda and Tadashi Maruyama
    Citation: BMC Evolutionary Biology 2011 11:285
    Content type: Research article Published on:

  43. Parasites are evolutionary hitchhikers whose phylogenies often track the evolutionary history of their hosts. Incongruence in the evolutionary history of closely associated lineages can be explained through a ...

    Authors: Jan Štefka, Paquita EA Hoeck, Lukas F Keller and Vincent S Smith
    Citation: BMC Evolutionary Biology 2011 11:284
    Content type: Research article Published on:

  44. The family Pteropodidae comprises bats commonly known as megabats or Old World fruit bats. Molecular phylogenetic studies of pteropodids have provided considerable insight into intrafamilial relationships, but...

    Authors: Francisca C Almeida, Norberto P Giannini, Rob DeSalle and Nancy B Simmons
    Citation: BMC Evolutionary Biology 2011 11:281
    Content type: Research article Published on:

  45. The most frequent case of horizontal transfer in plants involves a group I intron in the mitochondrial gene cox1, which has been acquired via some 80 separate plant-to-plant transfer events among 833 diverse angi...

    Authors: Maria V Sanchez-Puerta, Cinthia C Abbona, Shi Zhuo, Eric J Tepe, Lynn Bohs, Richard G Olmstead and Jeffrey D Palmer
    Citation: BMC Evolutionary Biology 2011 11:277
    Content type: Research article Published on:

  46. With nearly 1,100 species, the fish family Characidae represents more than half of the species of Characiformes, and is a key component of Neotropical freshwater ecosystems. The composition, phylogeny, and cla...

    Authors: Claudio Oliveira, Gleisy S Avelino, Kelly T Abe, Tatiane C Mariguela, Ricardo C Benine, Guillermo Ortí, Richard P Vari and Ricardo M Corrêa e Castro
    Citation: BMC Evolutionary Biology 2011 11:275
    Content type: Research article Published on:

  47. Schmidtea mediterranea (Platyhelminthes, Tricladida, Continenticola) is found in scattered localities on a few islands and in coastal areas of the western Mediterranean. Although S. mediterranea is the object of ...

    Authors: Eva M Lázaro, Abdul Halim Harrath, Giacinta A Stocchino, Maria Pala, Jaume Baguñà and Marta Riutort
    Citation: BMC Evolutionary Biology 2011 11:274
    Content type: Research article Published on:

  48. The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversifica...

    Authors: Trinidad Pérez, Sabine E Hammer, Jesús Albornoz and Ana Domínguez
    Citation: BMC Evolutionary Biology 2011 11:272
    Content type: Research article Published on:

  50. The genus Pyrus belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of Pyrus has not been defini...

    Authors: Xiaoyan Zheng, Chunyun Hu, David Spooner, Jing Liu, Jiashu Cao and Yuanwen Teng
    Citation: BMC Evolutionary Biology 2011 11:255
    Content type: Research article Published on:
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