Molecular Phylogenetics and Evolution (Mol Phylogenet Evol )

Publisher: Elsevier


Molecular Phylogenetics and Evolution is dedicated to bringing Darwin's dream - to "have fairly true genealogical trees of each great kingdom of Nature" - within grasp. The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution. This journal plays an important role by publishing the results of molecular studies that identify the actual clades to which different species and higher taxa belong. Such knowledge will further the development of phylogenetically more accurate taxonomic classifications and ultimately lead to a unified classification for all the ramifying lines of life.

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    Molecular phylogenetics and evolution (Online), Molecular phylogenetics and evolution
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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Determining factors that facilitate the transition from a solitary to a social lifestyle is a major challenge in evolutionary biology, especially in taxa that are usually aggressive towards conspecifics. Most spiders live solitarily and few species are known to be social. Nevertheless, sociality has evolved multiple times across several families and nearly all studied social lineages have originated from a periodically social (subsocial) ancestor. Group-living crab spiders (Thomisidae) are exclusively found in Australia and differ from most other social spiders because they lack a communal capture web. Three of the group-living species were placed in the genus Diaea and another in the genus Xysticus. Most Australian thomisids are, however, difficult to identify as most descriptions are old and of poor quality, and the genera Diaea and Xysticus may not correspond to monophyletic groups. Here, we clarify the phylogenetic relationships of the four group-living Australian thomisids and conclude that amongst these subsociality has evolved two to three times independently. The subsocial Xysticus bimaculatus is not closely related to any of the social Diaea and an independent origin of subsociality is likely in this case. The presented data indicates that within Diaea two origins of subsociality are possible. Our results help to understand the evolution of sociality in thomisids and support the hypothesis that permanent sociality in spiders has evolved multiple times relatively recently from subsocial ancestors.
    Molecular Phylogenetics and Evolution 01/2015; 82:330–340.
  • Meng Mao, Tracey Gibson, Mark Dowton
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    ABSTRACT: Higher-level hymenopteran relationships remain unresolved in both morphological and molecular analyses. In this study, we present the most comprehensive analyses of hymenopteran relationships based on 48 mitochondrial (mt) genomes. One complete and two nearly complete mt genomes representing three hymenopteran superfamilies were newly sequenced. We assessed the influence of inclusion/exclusion of 3(rd) codon positions, alignment approaches, partition schemes and phylogenetic approaches on topology and nodal support within the Hymenoptera. The results showed that the topologies were sensitive to the variation of dataset and analytical approach. However, some robust and highly supported relationships were recovered: the Ichneumonomorpha was monophyletic; the Trigonalyoidea + Megalyroidea and the Diaprioidea + Chalcidoidea were consistently recovered; the Cynipoidea was generally recovered as the sister group to the Diaprioidea + Chalcidoidea. In addition, the monophyletic Aculeata and Proctotrupomorpha were recovered in some analyses. Several gene rearrangements were detected in each of the three newly sequenced mt genomes. Specifically, the Ibalia leucospoides mt genome harbors a large inversion of a gene block from trnE to trnS2. Inverted, duplicated A+T rich regions were detected in the Ibalia leucospoides mt genome, which probably played an important role during the formation of the large gene block inversion via recombination. Copyright © 2014. Published by Elsevier Inc.
    Molecular Phylogenetics and Evolution 12/2014;
  • Søren Faurby, Jens-Christian Svenning
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    ABSTRACT: Across large clades, two problems are generally encountered in the estimation of species-level phylogenies: a) the number of taxa involved is generally so high that computation-intensive approaches cannot readily be utilized and b) even for clades that have received intense study (e.g., mammals), attention has been centered on relatively few selected species, and most taxa must therefore be positioned on the basis of very limited genetic data. Here, we describe a new heuristic-hierarchical Bayesian approach and use it to construct a species-level phylogeny for all extant and late Quaternary extinct mammals. In this approach, species with large quantities of genetic data are placed nearly freely in the mammalian phylogeny according to these data, whereas the placement of species with lower quantities of data is performed with steadily stricter restrictions for decreasing data quantities. The advantages of the proposed method include a) an improved ability to incorporate phylogenetic uncertainty in downstream analyses based on the resulting phylogeny, b) a reduced potential for long-branch attraction or other types of errors that place low-data taxa far from their true position, while maintaining minimal restrictions for better-studied taxa, and c) likely improved placement of low-data taxa due to the use of closer outgroups. Copyright © 2014 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 12/2014;
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    ABSTRACT: We used mitochondrial DNA sequence data from 151 individuals to estimate population genetic structure across the range of the Western Diamondback Rattlesnake (Crotalus atrox), a widely distributed North American pitviper. We also tested hypotheses of population structure using double-digest restriction site associated DNA (ddRADseq) data, incorporating thousands of nuclear genome-wide SNPs from 42 individuals. We found strong mitochondrial support for a deep divergence between eastern and western C. atrox populations, and subsequent intermixing of these populations in the Inter-Pecos region of the United States and Mexico. Our nuclear RADseq data also identify these two distinct lineages of C. atrox, and provide evidence for nuclear admixture of eastern and western alleles across a broad geographic region. We identified contrasting patterns of mitochondrial and nuclear genetic variation across this genetic fusion zone that indicate partially restricted patterns of gene flow, which may be due to either pre- or post-zygotic isolating mechanisms. The failure of these two lineages to maintain complete genetic isolation, and evidence for partially-restricted gene flow, imply that these lineages were in the early stages of speciation prior to secondary contact. Copyright © 2014 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 12/2014;
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    ABSTRACT: The giant sable antelope is one of the most endangered African bovids. Populations of this iconic animal, the national symbol of Angola, were recently rediscovered, after many decades of presumed extinction. Even so, their numbers are scarce and hence conservation plans are essential. However, fundamental information such as its taxonomic position, time of divergence and degree of genetic variation are still lacking. Here, we used a museum preserved horn as a source of DNA to describe, for the first time, the complete mitochondrial genome of the giant sable antelope, and provide insights into its evolutionary history. Reads generated by shotgun sequencing were mapped against the mitochondrial genome of common sable antelope and the nuclear genomes of cow and sheep. Phylogenetic reconstruction and divergence time estimate give support to the monophyly of the giant sable and a maximum divergence time of 170 thousand years to the closest subspecies. About 7% of the nuclear genome was mapped against the reference. The genetic resources reported here are now available for future work in the field of conservation genetics and phylogeny, in this and related species. Copyright © 2014 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 12/2014;
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    ABSTRACT: The phylogeny and historical demography of small Eurasian vipers of the Vipera ursinii and V. renardi complexes were studied using mitochondrial DNA sequences analysed with Bayesian inference, Maximum Likelihood and Maximum Parsimony approaches, and mismatch distributions. Diversification in the group resulted from an initial dispersion in the later Pliocene - Pleistocene in two directions: north-westwards via the Balkans (V. ursinii complex) and north-eastwards from Asia Minor via the Caucasus (V. renardi complex). An independent, comparatively recent transition occurred from montane habitats to lowland grasslands in different mitochondrial lineages during the Late Pleistocene, when representatives of both complexes had reached lowland steppes to the north. Effective population size showed clear signs of rapid growth in eastern V. renardi, triggered by colonization of vast lowland steppes, but in western V. ursinii complex grew during the Last Glaciation and experienced stabilization in Holocene. Expansion and population growth in lowland lineages of V. renardi was not strongly affected by Pleistocene climatic oscillations, when cold, dry conditions could have favoured species living in open grasslands. The high diversity of closely related haplotypes in the Caucasus and Tien-Shan could have resulted from repetitive expansion-constriction-isolation events in montane regions during Pleistocene climate fluctuations. The mitochondrial phylogeny pattern conflicts with the current taxonomy. Copyright © 2014 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 12/2014;
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    ABSTRACT: The placenta of ruminants contains characteristic binucleate cells (BNC) with a highly conserved glycan structure which evolved early in Ruminant phylogenesis. Giraffe and Okapi placentae also contain these cells and it is not known whether they have a similar glycan array. We have used lectin histochemistry to examine the glycosylation of these cells in these species and compare them with bovine BNC which have a typical ruminant glycan composition. Two placentae, mid and near term, from Giraffe (Giraffa camelopardalis) and two term placenta of Okapi (Okapia johnstoni) were embedded in resin and stained with a panel of 23 lectins and compared with near-term bovine (Bos taurus) placenta. Significant differences were found in the glycans of Giraffe and Okapi BNC compared with those from the bovine, with little or no expression of terminal αN-acetylgalactosamine bound by Dolichos biflorus and Vicia villosa agglutinins which instead bound to placental blood vessels. Higher levels of N-acetylglucosamine bound by Lycopersicon esculentum and Phytolacca americana agglutinins were also apparent. Some differences between Okapi and Giraffe were evident. Most N-linked glycans were similarly expressed in all three species as were fucosyl residues. Interplacentomal areas in Giraffe and Bovine showed differences from the placentomal cells though no intercotyledonary BNC were apparent in Okapi. In conclusion, Giraffidae BNC developed different glycan biosynthetic pathways following their split from the Bovidae with further differences evolving as Okapi and Giraffe diverged from each other, affecting both inter and placentomal BNC which may have different functions during development. Copyright © 2014. Published by Elsevier Inc.
    Molecular Phylogenetics and Evolution 12/2014;
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    ABSTRACT: Betanodavirus is a small bipartite RNA virus of global economical significance that can cause severe neurological disorders to an increasing number of marine fish species. Herein, to further the understanding of the evolution of betanodavirus, Bayesian coalescent analyses were conducted to the time-stamped entire coding sequences of their RNA polymerase and coat protein genes. Similar moderate nucleotide substitution rates were then estimated for the two genes. According to age calculations, the divergence of the two genes into the four genotypes initiated nearly simultaneously at ∼700years ago, despite the different scenarios, whereas the seven analyzed chimeric isolates might be the outcomes of a single genetic reassortment event taking place in the early 1980s in Southern Europe. Furthermore, codon usage bias analyses indicated that each gene had influences in addition to mutational bias and codon choice of betanodavirus was not completely complied with that of fish host. Copyright © 2014 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 12/2014;
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    ABSTRACT: Bioluminescence is essential to the survival of many organisms, particularly in the deep sea where light is limited. Shrimp of the family Oplophoridae exhibit a remarkable mechanism of bioluminescence in the form of a secretion used for predatory defense. Three of the ten genera possess an additional mode of bioluminescence in the form of light-emitting organs called photophores. Phylogenetic analyses can be useful for tracing the evolution of bioluminescence, however, the few studies that have attempted to reconcile the relationships within Oplophoridae have generated trees with low-resolution. We present the most comprehensive phylogeny of Oplophoridae to date, with 90% genera coverage using seven genes (mitochondrial and nuclear) across 30 oplophorid species. We use our resulting topology to trace the evolution of bioluminescence within Oplophoridae. Previous studies have suggested that oplophorid visual systems may be tuned to differentiate the separate modes of bioluminescence. While all oplophorid shrimp possess a visual pigment sensitive to blue-green light, only those bearing photophores have an additional pigment sensitive to near-ultraviolet light. We attempt to characterize opsins, visual pigment proteins essential to light detection, in two photophore-bearing species (Systellaspis debilis and Oplophorus gracilirostris) and make inferences regarding their function and evolutionary significance. Copyright © 2014. Published by Elsevier Inc.
    Molecular Phylogenetics and Evolution 12/2014;
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    ABSTRACT: European tree frogs (Hyla) characterized by short temporal parameters of the advertisement call form six genetically differentiated but morphologically cryptic taxa, H. arborea sensu stricto, H. orientalis and H. molleri from across Europe to western Asia (together referred to as H. arborea sensu lato), two putative taxa within H. intermedia (Northern and Southern) from the Italian Peninsula and Sicily, and H. sarda from Sardinia and Corsica. Here, we assess species limits and phylogenetic relationships within these 'short-call tree frogs' based on mitochondrial DNA and nuclear protein-coding markers. The mitochondrial and nuclear genes show partly incongruent phylogeographic patterns, which point toa complex history of gene flow across taxa, particularly in the Balkans. To test the species limits in the short-call tree frogs and to infer the species tree, we used coalescent-based approaches. The monophyly of H. arborea sensu lato is supported by the mtDNA as well as by the all-gene species tree. The Northern and Southern lineages of H. intermediahave been connected by nuclear gene flow (despite their deep mtDNA divergence) and should be treated as conspecific. On the contrary, the parapatric taxa within H. arborea sensu lato should be considered distinct species (H. arborea, H. orientalis, H. molleri) based on the coalescent analysis, although signs of hybridizationwere detected between them (H. arborea x H. orientalis; H. arborea x H. molleri). A mitochondrial capture upon secondary contact appears to explain the close mtDNA relationship between the geographically remote Iberian H. molleri and H. orientalisfromaround the Black Sea. Introgressive hybridization occurred also between the Balkan H. arborea and northern Italian H. intermedia, and between the Minor Asiatic H. orientalis and Arabian H. felixarabica (the latter belonging to a different acoustic group/clade). Our results shed light on the species limits in the European short-call tree frogs and show that introgression played an important role in the evolutionary history of the short-call tree frogs and occurred even between taxa supported as distinct species. Copyright © 2014 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 12/2014;
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    ABSTRACT: Sequence data were obtained for five different loci, both mitochondrial (cox1, mtMutS, 16S) and nuclear (18S, 28S rDNA) from 64 species representing 25 genera of the common deep-sea octocoral family Primnoidae. We tested the hypothesis that Primnoidae have an Antarctic origin, as this is where they currently have high species richness, using Maximum likelihood and Bayesian inference methods of phylogenetic analysis. Using a time-calibrated molecular phylogeny we also investigated the time of species radiation in sub-Antarctic Primnoidae. Our relatively wide taxon sampling and phylogenetic analysis supported Primnoidae as a monophyletic family. The base of the well-supported phylogeny was Pacific in origin, indicating Primnoidae sub-Antarctic diversity is a secondary species radiation. There is also evidence for a subsequent range extension of sub-Antarctic lineages into deep-water areas of the Indian and Pacific Oceans. Conservative and speculative fossil-calibration analyses resulted in two differing estimations of sub-Antarctic species divergence times. Conservative analysis suggested a sub-Antarctic species radiation occurred ∼52 MYA (95% HPD: 36-73 MYA), potentially before the opening of the Drake Passage and Antarctic Circumpolar Current (ACC) formation (41-37 MYA). Speculative analysis pushed this radiation back into the late Jurassic, 157 MYA (95% HPD: 118-204 MYA). Genus-level groupings were broadly supported in this analysis with some notable polyphyletic exceptions: Callogorgia, Fanellia, Primnoella, Plumarella, Thouarella. Molecular and morphological evidence supports the placement of Tauroprimnoa austasensis within Dasystenella and Fannyella kuekenthali within Metafannyella. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 12/2014;
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    ABSTRACT: The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika constitute the most diverse extant adaptive radiations in vertebrates. Lake Tanganyika, the oldest of the lakes, harbors the morphologically and genetically most diverse assemblage of cichlids and contains the highest number of endemic cichlid genera of all African lakes. Based on morphological grounds, the Tanganyikan cichlid species have been grouped into 12 to 16 distinct lineages, so-called tribes. While the monophyly of most of the tribes is well established, the phylogenetic relationships among the tribes remain largely elusive. Here, we present a new tribal level phylogenetic hypothesis for the cichlid fishes of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length of close to 18 kb. Using next-generation amplicon sequencing with the 454 pyrosequencing technology, we compiled a dataset consisting of 42 nuclear loci in 45 East African cichlid species, which we subjected to maximum likelihood and Bayesian inference phylogenetic analyses. We analyzed the entire concatenated dataset and each marker individually, and performed a Bayesian concordance analysis and gene tree discordance tests. Overall, we find strong support for a position of the Oreochromini, Boulengerochromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprologini and the mouthbrooding tribes of the ‘H-lineage’, which are both strongly supported to be monophyletic. The Eretmodini are firmly placed within the ‘H-lineage’, as sister-group to the most species-rich tribe of cichlids, the Haplochromini. The phylogenetic relationships at the base of the ‘H-lineage’ received less support, which is likely due to high speciation rates in the early phase of the radiation. Discordance among gene trees and marker sets further suggests the occurrence of past hybridization and/or incomplete lineage sorting in the cichlid fishes of Lake Tanganyika.
    Molecular Phylogenetics and Evolution 11/2014;
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    ABSTRACT: The unrivalled level of biodiversity across the tropical Indo-Australian Archipelago (IAA) has been the subject of wide debate. Attempts to understand its origins have focussed on the timing of speciation, rates of diversification and the directionality of colonization across geographical and climatic gradients in an array of marine groups. We investigate origins and evolution in the Choerodon tuskfishes, a group of labrids whose centre of diversity coincides with this region. Mitochondrial (COI, 16S) and nuclear (RAG2, Tmo4c4) molecular phylogenies and biogeographic analyses, coupled with molecular clock dating, were inferred from 18 of the 23 valid Choerodon species. Two additional, undescribed Choerodon species were also included, showing reciprocal monophyly in both genomes, confirming their species level status. Choerodon diverged from their ancestral sister group, the Odacines, at the onset of the Miocene, coinciding with the collision of the Australian and Eurasian Plates when extensive areas of shallow-water habitat formed. Despite subsequent evolutionary patterns being partially obscured by overlapping distribution ranges between many species and a lack of clear evidence for climatically driven lineage divergences, our data support an evolutionary scenario of peripheral endemics budding from once widespread populations across this biodiversity hotspot. Interestingly, these peripheral endemics tend to occupy more specialised reef or non-reef habitats whereas widespread groups appear to generally take advantage of both reef and non-reef environments. Our results are discussed in light of the most accredited hypotheses proposed to explain species richness in the IAA, with some support for processes such as centrifugal speciation. Copyright © 2014 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 11/2014;