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Molecular Phylogenetics and Evolution

Martin Carr, Daniel J Richter, Parinaz Fozouni, Timothy J Smith, Alexandra Jeuck, Barry S C Leadbeater, Frank Nitsche
Recent studies have shown that molecular phylogenies of the choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other choanoflagellate taxa...
October 17, 2016: Molecular Phylogenetics and Evolution
Jiyeon Kim, Elizabeth Kern, Taeho Kim, Mikang Sim, Jaebum Kim, Yuseob Kim, Chungoo Park, Steven A Nadler, Joong-Ki Park
Plectida is an important nematode order with species that occupy many different biological niches. The order includes free-living aquatic and soil-dwelling species, but its phylogenetic position has remained uncertain. We sequenced the complete mitochondrial genomes of two members of this order, Plectus acuminatus and Plectus aquatilis and compared them with those of other major nematode clades. The genome size and base composition of these species are similar to other nematodes; 14,831 and 14,372 bp, respectively, with AT contents of 71...
October 13, 2016: Molecular Phylogenetics and Evolution
Akinori Suzuki, Hidero Komata, Shogo Iwashita, Shotaro Seto, Hironobu Ikeya, Mitsutoshi Tabata, Takashi Kitano
In vertebrates, there are four major genes in the RH (Rhesus) gene family, RH, RHAG, RHBG, and RHCG. These genes are thought to have been formed by the two rounds of whole-genome duplication (2R-WGD) in the common ancestor of all vertebrates. In our previous work, where we analyzed details of the gene duplications process of this gene family, three nucleotide sequences belonging to this family were identified in Far Eastern brook lamprey (Lethenteron reissneri), and the phylogenetic positions of the genes were determined...
October 13, 2016: Molecular Phylogenetics and Evolution
Juan E Uribe, Suzanne T Williams, José Templado, Barbara Buge, Rafael Zardoya
The subfamily Cantharidinae Gray, 1857 (Trochoidea: Trochidae) includes 23 recognized genera and over 200 known living species. These marine top shell snails are microphagous grazers that generally live in shallow rocky shores and in macroalgae and seagrass beds of sub-tropical and temperate waters from the Central and Western Indo-Pacific biogeographic regions to the Mediterranean Sea and the Eastern Atlantic Ocean. Recent molecular phylogenetic studies revising the family Trochidae supported the monophyly of the subfamily Cantharidinae and its sister group relationship to the subfamily Stomatellinae...
October 13, 2016: Molecular Phylogenetics and Evolution
Benjamin E Carter, Juan Larraín, Alžběta Manukjanová, Blanka Shaw, A Jonathan Shaw, Jochen Heinrichs, Peter de Lange, Monica Suleiman, Louis Thouvenot, Matt von Konrat
Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere...
October 13, 2016: Molecular Phylogenetics and Evolution
Sereina Rutschmann, Harald Detering, Sabrina Simon, David H Funk, Jean-Luc Gattolliat, Samantha J Hughes, Pedro M Raposeiro, Rob DeSalle, Michel Sartori, Michael T Monaghan
The study of processes driving diversification requires a fully sampled and well resolved phylogeny. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L...
October 11, 2016: Molecular Phylogenetics and Evolution
Federico Lopez-Osorio, Kurt M Pickett, James M Carpenter, Bryan A Ballif, Ingi Agnarsson
The phylogenetic relationships among genera of the subfamily Vespinae (yellowjackets and hornets) remain unclear. Yellowjackets and hornets constitute one of the only two lineages of highly eusocial wasps, and the distribution of key behavioral traits correlates closely with the current classification of the group. The potential of the Vespinae to elucidate the evolution of social life, however, remains limited due to ambiguous genus-level relationships. Here, we address the relationships among genera within the Vespinae using transcriptomic (RNA-seq) data...
October 11, 2016: Molecular Phylogenetics and Evolution
Adrián Nieto-Montes de Oca, Anthony J Barley, Rubi N Meza-Lázaro, Uri O García-Vázquez, Joan G Zamora-Abrego, Robert C Thomson, Adam D Leaché
Middle American knob-scaled lizards of the genus Xenosaurus are a unique radiation of viviparous species that are generally characterized by a flattened body shape and a crevice-dwelling ecology. Only eight species of Xenosaurus, one of them with five subspecies (X. grandis), have been formally described. However, species limits within Xenosaurus have never been examined using molecular data, and no complete phylogeny of the genus has been published. Here, we used ddRADseq data from all of the described and potentially undescribed taxa of Xenosaurus to investigate species limits, and to obtain a phylogenetic hypothesis for the genus...
October 5, 2016: Molecular Phylogenetics and Evolution
James F Smith, John L Clark, Marisol Amaya-Márquez, Oscar H Marín-Gómez
Speciation by hybridization has long been recognized among plants and includes both homoploid and allopolyploid speciation. The numbers of presumed hybrid species averages close to 11% and tends to be concentrated in a subset of angiosperm families. Recent advances in molecular methods have verified species of hybrid origin that had been presumed on the basis of morphology and have identified species that were not initially considered hybrids. Identifying species of hybrid origin is often a challenge and typically based on intermediate morphology, or discrepancies between molecular datasets...
October 5, 2016: Molecular Phylogenetics and Evolution
Yuan Tian, Laura S Kubatko
Although it is widely appreciated that gene trees may differ from the overall species tree and from one another due to various evolutionary processes (e.g., incomplete lineage sorting (ILS), horizontal gene transfer, etc.), the extent of this incongruence is rarely quantified and discussed. Here we consider the expected amount of incongruence arising from ILS, as modeled by the coalescent process. In particular, we compute the probability that two gene trees randomly sampled from the same species tree agree with one another as well as the distribution of the Robinson-Foulds distance between them, for species trees with three to eight taxa...
October 4, 2016: Molecular Phylogenetics and Evolution
Harold Sungani, Benjamin P Ngatunga, Stephan Koblmüller, Tuuli Mäkinen, Paul H Skelton, Martin J Genner
It has been proposed that the fish faunas of African rivers assemble through multiple colonisation events, while lake faunas form additionally through intralacustine speciation. While this pattern has been established for many lineages, most notably cichlids, there are opportunities to further investigate the concept using phylogenies of congeneric endemic species within ancient lake catchments. The Lake Malawi catchment contains three river-spawning cyprinids of the genus Opsaridium, two of which are endemic...
September 30, 2016: Molecular Phylogenetics and Evolution
S J Wallace, J A Morris-Pocock, J González-Solís, P Quillfeldt, V L Friesen
Phylogenetic relationships among species can provide insight into how new species arise. For example, careful consideration of both the phylogenetic and geographic distributions of species in a group can reveal the geographic models of speciation within the group. One such model, sympatric speciation, may be more common than previously thought. The Hydrobatinae (Aves: Procellariformes) is a diverse subfamily of Northern Hemisphere storm-petrels for which the taxonomy is unclear. Previous studies showed that Hydrobates (formally Oceanodroma) castro breeding in the Azores during the cool season is sister species to H...
September 29, 2016: Molecular Phylogenetics and Evolution
Takuya Akiyama, Chizuko Nishida, Kunikazu Momose, Manabu Onuma, Kazutoshi Takami, Ryuichi Masuda
The gene duplication in mitochondrial DNA (mtDNA) has been reported in diverse bird taxa so far. Although many phylogenetic and population genetic analyses of cranes were carried out based on mtDNA diversity, whether mtDNA contains duplicated regions is unknown. To address the presence or absence of gene duplication in cranes and investigate the molecular evolutionary features of crane mtDNA, we analyzed the gene organization and the molecular phylogeny of mtDNA from 13 crane species. We found that the mtDNA in 13 crane species shared a tandem duplicated region, which consists of duplicated sequence sets including cytochrome b (Cytb), NADH6, control region (CR) and three genes of tRNA...
September 28, 2016: Molecular Phylogenetics and Evolution
Marwa Al Arab, Christian Höner Zu Siederdissen, Kifah Tout, Abdullah H Sahyoun, Peter F Stadler, Matthias Bernt
Mitochondrial genome sequences are available in large number and new sequences become published nowadays with increasing pace. Fast, automatic, consistent, and high quality annotations are a prerequisite for downstream analyses. Therefore, we present an automated pipeline for fast de novo annotation of mitochondrial protein-coding genes. The annotation is based on enhanced phylogeny-aware hidden Markov models (HMMs). The pipeline builds taxon-specific enhanced multiple sequence alignments (MSA) of already annotated sequences and corresponding HMMs using an approximation of the phylogeny...
September 28, 2016: Molecular Phylogenetics and Evolution
R Paul Scofield, Kieren J Mitchell, Jamie R Wood, Vanesa L De Pietri, Scott Jarvie, Bastien Llamas, Alan Cooper
The relationships of the extinct New Zealand ravens (Corvus spp.) are poorly understood. We sequenced the mitogenomes of the two currently recognised species and found they were sister-taxa to a clade comprising the Australian raven, little raven, and forest raven (C.coronoides, C. mellori and C. tasmanicus respectively). The divergence between the New Zealand ravens and Australian raven clade occurred in the latest Pliocene, which coincides with the onset of glacial deforestation. We also found that the divergence between the two putative New Zealand species C...
September 24, 2016: Molecular Phylogenetics and Evolution
Amanda E Haponski, Taehwan Lee, Diarmaid Ó Foighil
Natural history museum collections provide a biodiversity window into the past and are of particular importance to the study of extinction-impacted clades such as the Pacific Island tree snail family Partulidae. Deliberate introduction of the predatory rosy wolf snail Euglandina rosea in the late 20th century led to the extinction/extirpation of 55/61 Society Island Partulidae species. In this study, we phylogenomically investigated the inter-relationships of the three surviving Society Island valley Partula species: P...
September 24, 2016: Molecular Phylogenetics and Evolution
Jairo Patiño, Jian Wang, Matt A M Renner, S Robbert Gradstein, Benjamin Laenen, Nicolas Devos, A Jonathan Shaw, Alain Vanderpoorten
Why some species exhibit larger geographical ranges than others, and to what extent does variation in range size affect diversification rates, remains a fundamental, but largely unanswered question in ecology and evolution. Here, we implement phylogenetic comparative analyses and ancestral area estimations in Radula, a liverwort genus of Cretaceous origin, to investigate the mechanisms that explain differences in geographical range size and diversification rates among lineages. Range size was phylogenetically constrained in the two sub-genera characterized by their almost complete Australasian and Neotropical endemicity, respectively...
September 21, 2016: Molecular Phylogenetics and Evolution
Mitzy Pepper, David G Hamilton, Thomas Merkling, Nina Svedin, Bori Cser, Renee A Catullo, Sarah R Pryke, J Scott Keogh
The spectacular threat display of the savannah specialist Australo-Papuan frilled lizards has made them one of the world's most iconic reptiles. They are increasingly used as a model system for research in evolutionary biology and ecology but little is known of their population structure. Their distribution across northern Australia and southern New Guinea also provides an opportunity to examine biogeographic patterns as they relate to the large-scale movement of savannah habitat during the Plio/Pleistocene and the associated increase in aridity...
September 21, 2016: Molecular Phylogenetics and Evolution
Prashant P Sharma, Marc A Santiago, Ricardo Kriebel, Savana M Lipps, Perry A C Buenavente, Arvin C Diesmos, Milan Janda, Sarah L Boyer, Ronald M Clouse, Ward C Wheeler
The taxonomy and systematics of the armored harvestmen (suborder Laniatores) are based on various sets of morphological characters pertaining to shape, armature, pedipalpal setation, and the number of articles of the walking leg tarsi. Few studies have tested the validity of these historical character systems in a comprehensive way, with reference to an independent data class, i.e., molecular sequence data. We examined as a test case the systematics of Podoctidae, a family distributed throughout the Indo-Pacific...
September 21, 2016: Molecular Phylogenetics and Evolution
Breda M Zimkus, Lucinda P Lawson, Michael Barej, Christopher D Barratt, Alan Channing, Katrina M Dash, J Maximilian Dehling, Louis Du Preez, Philip-Sebastian Gehring, Eli Greenbaum, Václav Gvoždík, James Harvey, Jos Kielgast, Chifundera Kusamba, Zoltán T Nagy, Maciej Pabijan, Johannes Penner, Mark-Oliver Rödel, Miguel Vences, Stefan Lötters
The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals...
September 21, 2016: Molecular Phylogenetics and Evolution
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