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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 8 of 12

  1. Early methods for estimating divergence times from gene sequence data relied on the assumption of a molecular clock. More sophisticated methods were created to model rate variation and used auto-correlation of...

    Authors: Mathieu Fourment and Edward C Holmes

    Citation: BMC Evolutionary Biology 2014 14:163

    Content type: Research article

    Published on:

  2. Skipper butterflies (Hesperiidae) are a relatively well-studied family of Lepidoptera. However, a combination of DNA barcodes, morphology, and natural history data has revealed several cryptic species complexe...

    Authors: Claudia Bertrand, Daniel H Janzen, Winnie Hallwachs, John M Burns, Joel F Gibson, Shadi Shokralla and Mehrdad Hajibabaei

    Citation: BMC Evolutionary Biology 2014 14:153

    Content type: Research article

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  3. Recent molecular hypotheses suggest that some traditional suprageneric taxa of Characiformes require revision, as they may not constitute monophyletic groups. This is the case for the Bryconidae. Various studi...

    Authors: Kelly T Abe, Tatiane C Mariguela, Gleisy S Avelino, Fausto Foresti and Claudio Oliveira

    Citation: BMC Evolutionary Biology 2014 14:152

    Content type: Research article

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  4. The origin and colonisation history after the Quaternary ice ages remain largely unresolved for many plant lineages, mainly owing to a lack of fine-scale studies. Here, we present a molecular phylogeny and a p...

    Authors: Isabel M Liberal, Monique Burrus, Claire Suchet, Christophe Thébaud and Pablo Vargas

    Citation: BMC Evolutionary Biology 2014 14:146

    Content type: Research article

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  5. Lethal amanitas (Amanita section Phalloideae) are a group of wild, fatal mushrooms causing many poisoning cases worldwide. However, the diversity and evolutionary history of these lethal mushrooms remain poorly k...

    Authors: Qing Cai, Rodham E Tulloss, Li P Tang, Bau Tolgor, Ping Zhang, Zuo H Chen and Zhu L Yang

    Citation: BMC Evolutionary Biology 2014 14:143

    Content type: Research article

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  6. Haldane’s Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it i...

    Authors: Fiona C Gowen, James M Maley, Carla Cicero, A Townsend Peterson, Brant C Faircloth, T Caleb Warr and John E McCormack

    Citation: BMC Evolutionary Biology 2014 14:135

    Content type: Research article

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  7. The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, a...

    Authors: Esther Ibáñez-Marcelo and Marta Casanellas

    Citation: BMC Evolutionary Biology 2014 14:132

    Content type: Methodology article

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  8. Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondr...

    Authors: Yong-Fang Yao, Qiu-Xia Dai, Jing Li, Qing-Yong Ni, Ming-Wang Zhang and Huai-Liang Xu

    Citation: BMC Evolutionary Biology 2014 14:130

    Content type: Research article

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  9. The origin and early radiation of archosaurs and closely related taxa (Archosauriformes) during the Triassic was a critical event in the evolutionary history of tetrapods. This radiation led to the dinosaur-do...

    Authors: Richard J Butler, Corwin Sullivan, Martín D Ezcurra, Jun Liu, Agustina Lecuona and Roland B Sookias

    Citation: BMC Evolutionary Biology 2014 14:128

    Content type: Research article

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  10. The Kalligrammatidae are distinctive, large, conspicuous, lacewings found in Eurasia from the Middle Jurassic to mid Early Cretaceous. Because of incomplete and often inadequate fossil preservation, an absence...

    Authors: Qiang Yang, Yongjie Wang, Conrad C Labandeira, Chungkun Shih and Dong Ren

    Citation: BMC Evolutionary Biology 2014 14:126

    Content type: Research article

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  11. Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid...

    Authors: Dan Chang and Thomas F Duda Jr

    Citation: BMC Evolutionary Biology 2014 14:123

    Content type: Research article

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  12. Considered a biodiversity hotspot, the Canary Islands have been the key subjects of numerous evolutionary studies concerning a large variety of organisms. The genus Cheirolophus (Asteraceae) represents one of the...

    Authors: Daniel Vitales, Teresa Garnatje, Jaume Pellicer, Joan Vallès, Arnoldo Santos-Guerra and Isabel Sanmartín

    Citation: BMC Evolutionary Biology 2014 14:118

    Content type: Research article

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  13. Despite its high number of endemic deciduous broad-leaved species in China’s warm-temperate zone, far less attention has been paid to phylogeographic studies in this region. In this work, the phylogeographic h...

    Authors: Zi-Zhen Fu, Yong-Hua Li, Kai-Ming Zhang and Yong Li

    Citation: BMC Evolutionary Biology 2014 14:114

    Content type: Research article

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  14. Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western...

    Authors: Derek D Houston, Dennis K Shiozawa, Brian Tilston Smith and Brett R Riddle

    Citation: BMC Evolutionary Biology 2014 14:111

    Content type: Research article

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  15. Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Pa...

    Authors: Bernard Secher, Rosa Fregel, José M Larruga, Vicente M Cabrera, Phillip Endicott, José J Pestano and Ana M González

    Citation: BMC Evolutionary Biology 2014 14:109

    Content type: Research article

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  16. The aquatic flowering-plant family Hydatellaceae has a classic Gondwanan distribution, as it is found in Australia, India and New Zealand. To shed light on the biogeographic history of this apparently ancient ...

    Authors: William J D Iles, Christopher Lee, Dmitry D Sokoloff, Margarita V Remizowa, Shrirang R Yadav, Matthew D Barrett, Russell L Barrett, Terry D Macfarlane, Paula J Rudall and Sean W Graham

    Citation: BMC Evolutionary Biology 2014 14:102

    Content type: Research article

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  17. Most previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (BMC Evol Biol 9...

    Authors: Teng Li, Jimeng Hua, April M Wright, Ying Cui, Qiang Xie, Wenjun Bu and David M Hillis

    Citation: BMC Evolutionary Biology 2014 14:99

    Content type: Research article

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  18. The Malili Lakes system in central Sulawesi (Indonesia) is a hotspot of freshwater biodiversity in the Wallacea, characterized by endemic species flocks like the sailfin silversides (Teleostei: Atherinomorpha:...

    Authors: Björn Stelbrink, Isabella Stöger, Renny K Hadiaty, Ulrich K Schliewen and Fabian Herder

    Citation: BMC Evolutionary Biology 2014 14:94

    Content type: Research article

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  19. Army ants are dominant invertebrate predators in tropical and subtropical terrestrial ecosystems. Their close relatives within the dorylomorph group of ants are also highly specialized predators, although much...

    Authors: Seán G Brady, Brian L Fisher, Ted R Schultz and Philip S Ward

    Citation: BMC Evolutionary Biology 2014 14:93

    Content type: Research article

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  20. The Indo-Pacific region has the largest number of seagrass species worldwide and this region is considered as the origin of the Hydrocharitaceae. Halophila ovalis and its closely-related species belonging to the ...

    Authors: Vy X Nguyen, Matsapume Detcharoen, Piyalap Tuntiprapas, U Soe-Htun, Japar B Sidik, Muta Z Harah, Anchana Prathep and Jutta Papenbrock

    Citation: BMC Evolutionary Biology 2014 14:92

    Content type: Research article

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  21. Recent work has shown that Fusarium species and genotypes most commonly associated with human infections, particularly of the cornea (mycotic keratitis), are the same as those most commonly isolated from plumbing...

    Authors: Dylan PG Short, Kerry O’Donnell and David M Geiser

    Citation: BMC Evolutionary Biology 2014 14:91

    Content type: Research article

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  22. Determining the presence or absence of gene flow between populations is the target of some statistical methods in population genetics. Until recently, these methods either avoided the use of recombining genes,...

    Authors: Miguel Navascués, Delphine Legrand, Cécile Campagne, Marie-Louise Cariou and Frantz Depaulis

    Citation: BMC Evolutionary Biology 2014 14:89

    Content type: Methodology article

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  23. The pantropical genus Bauhinia, along with the northern temperate Cercis and several tropical genera, bear bilobate, bifoliolate, or sometimes unifoliolate leaves, which constitute the tribe Cercideae as sister t...

    Authors: Qi Wang, Zhuqiu Song, Yunfa Chen, Si Shen and Zhenyu Li

    Citation: BMC Evolutionary Biology 2014 14:88

    Content type: Research article

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  24. Mangroves are key components of coastal ecosystems in tropical and subtropical regions worldwide. However, the patterns and mechanisms of modern distribution of mangroves are still not well understood. Histori...

    Authors: Eugenia YY Lo, Norman C Duke and Mei Sun

    Citation: BMC Evolutionary Biology 2014 14:83

    Content type: Research article

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  25. Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for esti...

    Authors: Robert Lanfear, Brett Calcott, David Kainer, Christoph Mayer and Alexandros Stamatakis

    Citation: BMC Evolutionary Biology 2014 14:82

    Content type: Methodology article

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  26. Manchurochelys manchoukuoensis is an emblematic turtle from the Cretaceous Yixian Formation of Liaoning, China, a geological rock unit that is famous for yielding perfectly preserved skeletons of fossil vertebrat...

    Authors: Chang-Fu Zhou, Márton Rabi and Walter G Joyce

    Citation: BMC Evolutionary Biology 2014 14:77

    Content type: Research article

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  27. Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by...

    Authors: Ross Barnett, Nobuyuki Yamaguchi, Beth Shapiro, Simon YW Ho, Ian Barnes, Richard Sabin, Lars Werdelin, Jacques Cuisin and Greger Larson

    Citation: BMC Evolutionary Biology 2014 14:70

    Content type: Research article

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  28. Hybridization, the interbreeding of diagnosably divergent species, is a major focus in evolutionary studies. Eels, both from North America and Europe migrate through the Atlantic to mate in a vast, overlapping...

    Authors: Sébastien Wielgoss, Aude Gilabert, Axel Meyer and Thierry Wirth

    Citation: BMC Evolutionary Biology 2014 14:61

    Content type: Research article

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  29. Across heterogeneous environments selection and gene flow interact to influence the rate and extent of adaptive trait evolution. This complex relationship is further influenced by the rarely considered role of...

    Authors: Lizelle J Odendaal, David S Jacobs and Jacqueline M Bishop

    Citation: BMC Evolutionary Biology 2014 14:60

    Content type: Research article

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  30. Numerous studies have investigated cospeciation (or cophylogeny) in various host-symbiont systems, and different patterns were inferred, from strict cospeciation where symbiont phylogeny mirrors host phylogeny...

    Authors: Laure Bellec, Camille Clerissi, Roseline Edern, Elodie Foulon, Nathalie Simon, Nigel Grimsley and Yves Desdevises

    Citation: BMC Evolutionary Biology 2014 14:59

    Content type: Research article

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  31. Despite considerable progress in systematics, a comprehensive scenario of the evolution of phenotypic characters in the mega-diverse Holometabola based on a solid phylogenetic hypothesis was still missing. We ...

    Authors: Ralph S Peters, Karen Meusemann, Malte Petersen, Christoph Mayer, Jeanne Wilbrandt, Tanja Ziesmann, Alexander Donath, Karl M Kjer, Ulrike Aspöck, Horst Aspöck, Andre Aberer, Alexandros Stamatakis, Frank Friedrich, Frank Hünefeld, Oliver Niehuis, Rolf G Beutel…

    Citation: BMC Evolutionary Biology 2014 14:52

    Content type: Research article

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  32. Because of their fragmented nature, inselberg species are interesting biological models for studying the genetic consequences of disjoint populations. Inselbergs are commonly compared with oceanic islands, as ...

    Authors: Fábio Pinheiro, Salvatore Cozzolino, David Draper, Fábio de Barros, Leonardo P Félix, Michael F Fay and Clarisse Palma-Silva

    Citation: BMC Evolutionary Biology 2014 14:49

    Content type: Research article

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  33. The phylogenetic relationships of many taxa remain poorly known because of a lack of appropriate data and/or analyses. Despite substantial recent advances, amphibian phylogeny remains poorly resolved in many i...

    Authors: Karen Siu-Ting, David J Gower, Davide Pisani, Roman Kassahun, Fikirte Gebresenbet, Michele Menegon, Abebe A Mengistu, Samy A Saber, Rafael de Sá, Mark Wilkinson and Simon P Loader

    Citation: BMC Evolutionary Biology 2014 14:44

    Content type: Research article

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  34. Interactions with pollinators are proposed to be one of the major drivers of diversity in angiosperms. Specialised interactions with pollinators can lead to specialised floral traits, which collectively are kn...

    Authors: Alicia Toon, Lyn G Cook and Michael D Crisp

    Citation: BMC Evolutionary Biology 2014 14:43

    Content type: Research article

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  35. The formation of the East African Rift System has decisively influenced the distribution and evolution of tropical Africa’s biota by altering climate conditions, by creating basins for large long-lived lakes, ...

    Authors: Roland Schultheiß, Bert Van Bocxlaer, Frank Riedel, Thomas von Rintelen and Christian Albrecht

    Citation: BMC Evolutionary Biology 2014 14:42

    Content type: Research article

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  36. In East Asia, an increasing number of studies on temperate forest tree species find evidence for migration and gene exchange across the East China Sea (ECS) land bridge up until the last glacial maximum (LGM)....

    Authors: Xin-Shuai Qi, Na Yuan, Hans Peter Comes, Shota Sakaguchi and Ying-Xiong Qiu

    Citation: BMC Evolutionary Biology 2014 14:41

    Content type: Research article

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  37. Modern flamingos (Phoenicopteridae) occupy a highly specialized ecology unique among birds and represent a potentially powerful model system for informing the mechanisms by which a lineage of birds adapts and ...

    Authors: Chris R Torres, Lisa M Ogawa, Mark AF Gillingham, Brittney Ferrari and Marcel van Tuinen

    Citation: BMC Evolutionary Biology 2014 14:36

    Content type: Research article

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  38. Phytomyxids (plasmodiophorids and phagomyxids) are cosmopolitan, obligate biotrophic protist parasites of plants, diatoms, oomycetes and brown algae. Plasmodiophorids are best known as pathogens or vectors for...

    Authors: Sigrid Neuhauser, Martin Kirchmair, Simon Bulman and David Bass

    Citation: BMC Evolutionary Biology 2014 14:33

    Content type: Research article

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  39. The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and th...

    Authors: Liang Liu, Guan-Nan Huo, Hong-Bin He, Benjiang Zhou and Stephen W Attwood

    Citation: BMC Evolutionary Biology 2014 14:29

    Content type: Research article

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  40. Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous...

    Authors: Brad R Ruhfel, Matthew A Gitzendanner, Pamela S Soltis, Douglas E Soltis and J Gordon Burleigh

    Citation: BMC Evolutionary Biology 2014 14:23

    Content type: Research article

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  41. The role of tectonic uplift in stimulating speciation in South Africa’s only alpine zone, the Drakensberg, has not been explicitly examined. Tectonic processes may influence speciation both through the creatio...

    Authors: Joanne Bentley, G Anthony Verboom and Nicola G Bergh

    Citation: BMC Evolutionary Biology 2014 14:27

    Content type: Research article

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  42. Myanmar is the largest country in mainland Southeast Asia with a population of 55 million people subdivided into more than 100 ethnic groups. Ruled by changing kingdoms and dynasties and lying on the trade rou...

    Authors: Monika Summerer, Jürgen Horst, Gertraud Erhart, Hansi Weißensteiner, Sebastian Schönherr, Dominic Pacher, Lukas Forer, David Horst, Angelika Manhart, Basil Horst, Torpong Sanguansermsri and Anita Kloss-Brandstätter

    Citation: BMC Evolutionary Biology 2014 14:17

    Content type: Research article

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  43. Survival in microrefugia represents an important paradigm in phylogeography for explaining rapid postglacial re-colonization by species in temperate regions. Microrefugia may allow populations to persist in ar...

    Authors: Robert W Bryson Jr, Lorenzo Prendini, Warren E Savary and Peter B Pearman

    Citation: BMC Evolutionary Biology 2014 14:9

    Content type: Research article

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