6,214 results match your criteria Molecular phylogenetics and evolution[Journal]


Phylogenomics of the longitarsal Colossendeidae: The evolutionary history of an Antarctic sea spider radiation.

Mol Phylogenet Evol 2019 Apr 16. Epub 2019 Apr 16.

Zoological Research Museum Alexander Koenig, Statistical Phylogenetics and Phylogenomics, Adenauerallee 160, D-53113 Bonn, Germany; Faculty of Mathematics and Natural Sciences, University of Bonn, D-53012 Bonn, Germany.

Sea spiders (Pycnogonida) constitute a group of marine benthic arthropods that has a particularly high species diversity in the Southern Ocean. The "longitarsal" group of the sea spider family Colossendeidae is especially abundant in this region. However, this group also includes some representatives from other oceans, which raises the question where the group originates from. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903183051
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http://dx.doi.org/10.1016/j.ympev.2019.04.017DOI Listing
April 2019
2 Reads

Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae).

Mol Phylogenet Evol 2019 Apr 15. Epub 2019 Apr 15.

Department of Biology, Boston University, Boston, MA, USA.

The West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent conclusions about taxonomic status in groups with many endemic island populations. Here we present a phylogenetic study of the West Indian thrashers, tremblers, and allies, an assemblage of at least 5 species found on 29 islands, including what is considered the Lesser Antilles' only avian radiation. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903193003
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http://dx.doi.org/10.1016/j.ympev.2019.04.016DOI Listing
April 2019
1 Read

A brainstorm on the systematics of Turnera (Turneraceae, Malpighiales) caused by insights from molecular phylogenetics and morphological evolution.

Mol Phylogenet Evol 2019 Apr 15. Epub 2019 Apr 15.

Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Programa de Pós-graduação em Botânica, Av. Transnordestina s.n., Feira de Santana, 44036-900 Bahia, Brazil. Electronic address:

With 145 species, Turnera is the largest genus of Turneraceae (Malpighiales). Despite several morphotaxonomic and cytogenetic studies, our knowledge about the phylogenetic relationships in Turnera remains mainly based on morphological data. Here, we reconstruct the most comprehensive phylogeny of Turnera with molecular data to understand the morphological evolution within this group and to assess its circumscription and infrageneric classification. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.015DOI Listing

Dark offshoot: Phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star.

Mol Phylogenet Evol 2019 Apr 11;136:151-163. Epub 2019 Apr 11.

Museum Victoria, GPO Box 666, Melbourne 3001, Australia.

Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only three are regarded as true cave-dwellers. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.014DOI Listing

Introgressive hybridisation between two widespread sharks in the east Pacific region.

Mol Phylogenet Evol 2019 Apr 11;136:119-127. Epub 2019 Apr 11.

Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, 4811 QLD, Australia; Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, 4811 QLD, Australia; Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, B-3000 Leuven, Belgium; Laboratory for Cytogenetics and Genome Research, Center for Human Genetics, Genomics Core, KU Leuven, 3000 Leuven, Belgium.

With just a handful of documented cases of hybridisation in cartilaginous fishes, shark hybridisation remains poorly investigated. Small amounts of admixture have been detected between Galapagos (Carcharhinus galapagensis) and dusky (Carcharhinus obscurus) sharks previously, generating a hypothesis of ongoing hybridisation. We sampled a large number of individuals from areas where the species co-occur (contact zones) across the Pacific Ocean and used both mitochondrial and nuclear-encoded SNPs to examine genetic admixture and introgression between the two species. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903183041
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http://dx.doi.org/10.1016/j.ympev.2019.04.013DOI Listing
April 2019
6 Reads

A comprehensive kelp phylogeny sheds light on the evolution of an ecosystem.

Mol Phylogenet Evol 2019 Apr 10;136:138-150. Epub 2019 Apr 10.

Department of Botany & Biodiversity Research Centre, The University of British Columbia, 6270 University Blvd., Vancouver V6T 1Z4, Canada; Bamfield Marine Sciences Centre, 100 Pachena Rd., Bamfield V0R 1B0, Canada; Hakai Institute, Heriot Bay, Quadra Island, Canada.

Reconstructing phylogenetic topologies and divergence times is essential for inferring the timing of radiations, the appearance of adaptations, and the historical biogeography of key lineages. In temperate marine ecosystems, kelps (Laminariales) drive productivity and form essential habitat but an incomplete understanding of their phylogeny has limited our ability to infer their evolutionary origins and the spatial and temporal patterns of their diversification. Here, we reconstruct the diversification of habitat-forming kelps using a global genus-level phylogeny inferred primarily from organellar genome datasets, and investigate the timing of kelp radiation. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.012DOI Listing
April 2019
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Evolution of the human cold/menthol receptor, TRPM8.

Mol Phylogenet Evol 2019 Apr 10;136:104-118. Epub 2019 Apr 10.

Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France; Univ Lyon, CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, 69550 Bron, France; Hospices Civils de Lyon, Groupement Hospitalier EST, Département de Cardiologie, IHU-OPERA Bâtiment B13, 69550 Bron, France. Electronic address:

Genes showing versatile functions or subjected to fast expansion and contraction during the adaptation of species to specific ecological conditions, like sensory receptors for odors, pheromones and tastes, are characterized by a great plasticity through evolution. One of the most fascinating sensory receptors in the family of TRP channels, the cold and menthol receptor TRPM8, has received significant attention in the literature. Recent studies have reported the existence of TRPM8 channel isoforms encoded by alternative mRNAs transcribed from alternative promoters and processed by alternative splicing. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.011DOI Listing

The genetic structure of flax illustrates environmental and anthropogenic selections that gave rise to its eco-geographical adaptation.

Mol Phylogenet Evol 2019 Apr 9. Epub 2019 Apr 9.

Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, Canada K1A 0C6; Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa ON Canada K1N 6N5. Electronic address:

Flax, one of the eight founder crops of agriculture, has been cultivated for its oil and/or fiber for millennia. Understanding genetic divergence and geographic origins of germplasm in line with their cultivation history and ecological adaptation are essential for conservation and breeding. Here we performed a genome-wide assessment based on more than 51,000 single nucleotide polymorphic sites defining 383 flax accessions from a core collection representing 37 growing countries. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.010DOI Listing

Assessing the diversity of Western North American Juga (Semisulcospiridae, Gastropoda).

Mol Phylogenet Evol 2019 Apr 8;136:87-103. Epub 2019 Apr 8.

United States Fish and Wildlife Service, Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, Auburn, AL 36849, USA; School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.

Juga is a genus of freshwater gastropods distributed in Pacific and Interior drainages of the Pacific Northwest from central California to northern Washington. The current classification has relied heavily on features of the shell, which vary within and across drainages, and often intergrade without sharp distinctions between species. The only previous molecular analysis included limited population sampling, which did not allow robust assessment of intra- versus interspecific levels of genetic diversity, and concluded almost every sampled population to be a distinct OTU. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.009DOI Listing

Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments.

Mol Phylogenet Evol 2019 Apr 8. Epub 2019 Apr 8.

Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, U.K. Electronic address:

Although the majority of cichlid diversity occurs in the African Great Lakes, these fish have also diversified across the African continent. Such continental radiations, occurring in both rivers and lakes have received far less attention than lacustrine radiations despite some members, such as the oreochromine cichlids (commonly referred to as 'tilapia'), having significant scientific and socio-economic importance both within and beyond their native range. Unique among cichlids, several species of the genus Oreochromis exhibit adaptation to soda conditions (including tolerance of elevated temperatures and salinity), which are of interest from evolutionary biology research and aquaculture perspectives. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.008DOI Listing

A species-level phylogeny of Trachylepis (Scincidae: Mabuyinae) provides insight into their reproductive mode evolution.

Mol Phylogenet Evol 2019 Apr 6. Epub 2019 Apr 6.

Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA, 19085, USA.

Trachylepis (Mabuyinae) includes ∼80 species of fully-limbed skinks found primarily in Africa and Madagascar, but a robust species-level phylogeny for this genus is lacking and this impedes studies on a wide-range of topics from biogeography to character evolution. Trachylepis and its close relatives (which together form the Mabuya group or Mabuyinae) are notable in that they have undergone multiple transitions and remarkable specializations in their reproductive modes. A Trachylepis phylogeny will be particularly useful for investigating reproductive evolution, because it includes species that exhibit oviparity, viviparity, and bimodal parity (species with both oviparous and viviparous populations). Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.002DOI Listing
April 2019
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New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean.

Mol Phylogenet Evol 2019 Apr 4;136:53-64. Epub 2019 Apr 4.

Al Jaraf Fisheries, Abu Dhabi, United Arab Emirates.

Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.007DOI Listing
April 2019
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Chloroplast genome analysis of box-ironbark Eucalyptus.

Mol Phylogenet Evol 2019 Apr 4;136:76-86. Epub 2019 Apr 4.

School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia. Electronic address:

Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.001DOI Listing

Hunting the wolf: A molecular phylogeny of the wolf spiders (Araneae, Lycosidae).

Mol Phylogenet Evol 2019 Apr 3. Epub 2019 Apr 3.

División de Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Av. Angel Gallardo 470, C1405DJR, Buenos Aires, Argentina.

Lycosids are a diverse family of spiders distributed worldwide. Previous studies recovered some of the deeper splits of the family, but with little support. We present a broad phylogenetic analysis of the Lycosidae including a wide geographic sampling of representatives and all the subfamilies described to date. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.004DOI Listing
April 2019
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Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus).

Mol Phylogenet Evol 2019 Apr 2;136:65-75. Epub 2019 Apr 2.

Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan.

Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.003DOI Listing
April 2019
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A multi-locus phylogeny for the Neotropical Anomospermeae (Menispermaceae): Implications for taxonomy and biogeography.

Mol Phylogenet Evol 2019 Apr 2;136:44-52. Epub 2019 Apr 2.

State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

Neotropical rainforests cover about half of the world's tropical rainforests and house most of the biodiversity available on Earth. Australasia has been suggested as a potential source for Neotropical diversity. However, it remains unclear whether megathermal lineages could indeed have migrated to South America though Antarctica. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.006DOI Listing
April 2019
3.916 Impact Factor

From seascape ecology to population genomics and back. Spatial and ecological differentiation among cryptic species of the red algae Lithophyllum stictiforme/L. cabiochiae, main bioconstructors of coralligenous habitats.

Mol Phylogenet Evol 2019 Apr 2. Epub 2019 Apr 2.

Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.

Ecosystem engineering species alter the physical structure of their environment and can create or modify habitats, having a massive impact on local biodiversity. Coralligenous reefs are highly diverse habitats endemic to the Mediterranean Sea built by calcareous benthic organisms among which Crustose Coralline Algae are the main engineering species. We analyzed the diversity of Lithophyllum stictiforme or L. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.04.005DOI Listing
April 2019
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Synteny footprints provide clearer phylogenetic signal than sequence data for prokaryotic classification.

Mol Phylogenet Evol 2019 Apr 1;136:128-137. Epub 2019 Apr 1.

Dept. of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel. Electronic address:

Background: Extensive research efforts have been made to reconstruct the Tree of Life, aiming to explain the evolutionary history of life on earth. We expect the advent of next generation sequencing methods to bring us close to solving this challenge. Notwithstanding, with the accumulation of this mass of molecular data, it becomes evident that this solution is more complex and far from reach, especially among prokaryotes. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.010DOI Listing

Saffron (Crocus sativus) is an autotriploid that evolved in Attica (Greece) from wild Crocus cartwrightianus.

Mol Phylogenet Evol 2019 Apr 1;136:14-20. Epub 2019 Apr 1.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany. Electronic address:

Crocus sativus, the saffron crocus, is the source of saffron, which is made from the dried stigmas of the plant. It is a male-sterile triploid lineage that ever since its origin has been propagated vegetatively. Its mode of evolution and area of origin are matters of long-lasting debates. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.022DOI Listing
April 2019
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Molecular phylogeny of Paraonidae (Annelida).

Mol Phylogenet Evol 2019 Mar 29;136:1-13. Epub 2019 Mar 29.

Department of Biology, University of Pisa, via Derna 1, 56126 Pisa, Italy. Electronic address:

A molecular phylogeny of the family Paraonidae was reconstructed on the basis of 16S rDNA, COI and 18S rDNA sequences obtained from 66 individuals belonging to 38 nominal species and subspecies. In agreement with previous findings, Paraonidae represent a monophyletic group, closely related to Sternaspidae. The topology obtained by the Bayesian and Maximum Likelihood analyses on the combined dataset was not consistent with the traditional view on Paraonidae evolution, nor with a recent cladistic analysis. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.023DOI Listing
March 2019
2 Reads

Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands.

Mol Phylogenet Evol 2019 Mar 28;136:29-34. Epub 2019 Mar 28.

Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, United States; Biology Department, Occidental College, Los Angeles, CA 90041, United States. Electronic address:

Natural history collections are increasingly valued as genomic resources. Their specimens reflect the combined efforts of collectors and curators over hundreds of years. For many rare or endangered species, specimens are the only readily available source of DNA. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.017DOI Listing
March 2019
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On the uniqueness of the maximum parsimony tree for data with up to two substitutions: an extension of the classic Buneman theorem in phylogenetics.

Authors:
Mareike Fischer

Mol Phylogenet Evol 2019 Mar 27. Epub 2019 Mar 27.

Institute of Mathematics and Computer Science, Greifswald University, Greifswald, Germany. Electronic address:

One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist of various characters (also often referred to as sites). Often, however, tree reconstruction methods based on criteria like maximum parsimony may fail to provide a unique tree for a given dataset, or, even worse, reconstruct the 'wrong' tree (i. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.013DOI Listing
March 2019
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Plastome based phylogenetics and younger crown node age in Pelargonium.

Mol Phylogenet Evol 2019 Mar 26. Epub 2019 Mar 26.

Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. Electronic address:

The predominantly South-African plant genus Pelargonium L'Hér. (Geraniaceae) displays remarkable morphological diversity, several basic chromosome numbers as well as high levels of organelle genomic rearrangements, and represents the 7 largest Cape Floristic Region clade. In this study, we reconstructed a phylogenetic tree based on 74 plastome exons and nuclear rDNA ITS regions for 120 species, which represents 43 % taxon coverage for Pelargonium. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.021DOI Listing
March 2019
2 Reads

Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae).

Mol Phylogenet Evol 2019 Mar 23;136:21-28. Epub 2019 Mar 23.

Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden. Electronic address:

The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.018DOI Listing
March 2019
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Wolbachia of phylogenetic supergroup E identified in oribatid mite Gustavia microcephala (Acari: Oribatida).

Mol Phylogenet Evol 2019 Mar 23;135:230-235. Epub 2019 Mar 23.

Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland.

Heritable endosymbionts have been observed in arthropod and nematode hosts. The most-known among them is Wolbachia. Although the bacterium was previously identified in oribatid mites (Acari: Oribatida), it was not assigned to any phylogenetic group. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903183053
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http://dx.doi.org/10.1016/j.ympev.2019.03.019DOI Listing
March 2019
3 Reads

The mystery of the phylogeographic structural pattern in rodent-borne hantaviruses.

Mol Phylogenet Evol 2019 Mar 23;136:35-43. Epub 2019 Mar 23.

Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.

Hantaviruses (order Bunyavirales, family Hantaviridae) are important zoonotic pathogens. Because of the great diversity of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. To understand the mechanisms behind the evolutionary history of hantaviruses through virus-reservoir interactions, it is important to know how the radiation and diversity of hantaviruses occurred. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.020DOI Listing
March 2019
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Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.

Mol Phylogenet Evol 2019 Mar 23. Epub 2019 Mar 23.

Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden.

Old World orioles (Oriolidae) are medium-sized passerine birds confined largely to forested areas of Africa, Eurasia and Australasia. We present a new complete molecular (mtDNA) subspecies level phylogeny of the Oriolidae including all 113 taxa (35 species) together with a backbone phylogeny of 19 taxa from the main Oriolus clades based on i) 21 nuclear genes, ii) whole mito-genomes, and iii) genome-wide ultraconserved elements. We use this phylogeny to assess systematic relationships and the biogeographical history of this avian family. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903183064
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http://dx.doi.org/10.1016/j.ympev.2019.03.015DOI Listing
March 2019
2 Reads

Phylogenomics shows lignotuber state is taxonomically informative in closely related eucalypts.

Mol Phylogenet Evol 2019 Mar 23;135:236-248. Epub 2019 Mar 23.

Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Western Australia 6983, Australia. Electronic address:

Plant taxa can be broadly divided based on the mechanisms enabling persistence through whole-crown disturbances, specifically whether individuals resprout, populations reseed, or both or neither of these mechanisms are employed. At scales from species through to communities, the balance of disturbance-response types has major ramifications for ecological function and biodiversity conservation. In some lineages, morphologically identical populations except for differences in a disturbance-response trait (e. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.016DOI Listing
March 2019
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Plastome reduction and gene content in New World Pilostyles (Apodanthaceae) unveils high similarities to African and Australian congeners.

Mol Phylogenet Evol 2019 Mar 23;135:193-202. Epub 2019 Mar 23.

Instituto de Biología, Universidad de Antioquia UdeA, Medellín, Colombia. Electronic address:

Holoparasitism has led to extreme plastome reduction. Plastomes in the legume holoparasite Pilostyles (Apodanthaceae) are the most reduced in both size and gene content known so far in Embryophytes. Here, we found that the Pilostyles boyacensis plastome, the only American species sequenced so far, is reduced to seven functional genes, accD, rpl2, rrn16 (=16S), rrn23 (=23S), rps3, rps12 and a putative oxidoreductase (PbOx). Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.014DOI Listing
March 2019
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Phylogenetic delineation of regional biota: A case study of the Chinese flora.

Mol Phylogenet Evol 2019 Mar 22;135:222-229. Epub 2019 Mar 22.

State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Sino-African Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China. Electronic address:

Biogeographical regionalization schemes have traditionally been constructed based on taxonomic endemism of families, genera, and/or species, and rarely incorporated the phylogenetic relationships between taxa. However, phylogenetic relationships are important for understanding historical connections within and among biogeographical regions. Phylogeny-based delineation of biota is a burgeoning and fruitful field that is expected to provide novel insights into the conservation of regional diversity and the evolutionary history of biota. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.011DOI Listing
March 2019
4 Reads
3.916 Impact Factor

Mechanisms of antiviral resistance in influenza neuraminidase revealed by a mass spectrometry based phylonumerics approach.

Mol Phylogenet Evol 2019 Mar 20;135:286-296. Epub 2019 Mar 20.

Infectious Disease Responses Laboratory, University of New South Wales, Sydney, NSW, Australia. Electronic address:

A mass based phylonumerics approach is shown to be able to investigate the origins of the emergence of antiviral resistance mutations in influenza neuraminidase through a global view of mutational trends. Frequent ancestral and descendant mutations that precede and follow the manifestation of antiviral resistance mutations are identified in N2 neuraminidase. The majority occur in the head region around the active site and drive hydrophilicity changes, primarily through the incorporation or loss of hydroxyl groups. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.009DOI Listing
March 2019
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Spatio-temporal evolution of climbing habit in the Dahlia-Hidalgoa group (Coreopsidae, Asteraceae).

Mol Phylogenet Evol 2019 Mar 20;135:166-176. Epub 2019 Mar 20.

Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, Mexico. Electronic address:

In this paper we focus on Hidalgoa, a small genus distributed in cloud forest from Mexico to Colombia with the uncommon climbing habit of enlarging its petioles. This genus belongs to tribe Coreopsideae (Asteraceae), a group mostly from the Neotropics with a few taxa in Oceania and Polynesia. The phylogenetic position of Hidalgoa has not yet been determined though it will most probably be closely related to Dahlia. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.012DOI Listing
March 2019
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Multiple new species: Cryptic diversity in the widespread mite species Cymbaeremaeus cymba (Oribatida, Cymbaeremaeidae).

Mol Phylogenet Evol 2019 Mar 18;135:185-192. Epub 2019 Mar 18.

Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria. Electronic address:

The absence of obvious morphological differences between species impedes species identification in many groups of organisms. Such cryptic species appear to be particularly common in small-bodied animals, impacting species richness estimates. In this study we aimed at characterizing the molecular diversity of the Palearctic arboreal oribatid mite species Cymbaeremaeus cymba across large parts of Europe. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.008DOI Listing

Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily.

Mol Phylogenet Evol 2019 Mar 15. Epub 2019 Mar 15.

ISEM, Univ Montpellier, CNRS, IRD, EPHE, Montpellier, France.

Next generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of caviomorph rodents exhibiting a striking diversity of species and life history traits. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.007DOI Listing

Inferring hypothesis-based transitions in clade-specific models of chromosome number evolution in sedges (Cyperaceae).

Mol Phylogenet Evol 2019 Mar 15;135:203-209. Epub 2019 Mar 15.

Department of Plant Biology and Ecology, University of Seville, Reina Mercedes sn, ES-41012 Seville, Spain.

Large-scale changes in chromosome number have been associated with diversification rate shifts in many lineages of plants. For instance, several ancient rounds of polyploidization events have been inferred to promote genomic differentiation and/or isolation and, consequently, angiosperm diversification. Dysploidy, although less studied, has been suggested to also play an important role in angiosperm diversification. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.006DOI Listing

The phylogeny and evolutionary timescale of stoneflies (Insecta: Plecoptera) inferred from mitochondrial genomes.

Mol Phylogenet Evol 2019 Mar 12;135:123-135. Epub 2019 Mar 12.

Department of Entomology, China Agricultural University, Beijing, China. Electronic address:

Phylogenetic analysis based on mitochondrial genomic data from 25 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera (stoneflies). The monophyly of both currently recognized suborders was strongly supported, concordant with previous molecular analyses of Plecoptera. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae + Diamphipnoidae and Austroperlidae + Gripopterygidae; consistent with relationships proposed based on morphology. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.005DOI Listing
March 2019
2 Reads

Unraveling patterns and processes of diversification in the South Andean-Patagonian Nassauvia subgenus Strongyloma (Asteraceae, Nassauvieae).

Mol Phylogenet Evol 2019 Mar 8;136:164-182. Epub 2019 Mar 8.

Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, C.C. 22, B1642HYD, San Isidro, Provincia de Buenos Aires, Argentina.

Congruence among different sources of data is highly desirable in phylogenetic analyses. However, plastid and nuclear DNA may record different evolutionary processes such that incongruence among results from these sources can help unravel complex evolutionary histories. That is the case of Nassauvia subgenus Strongyloma (Asteraceae), a taxon with five putative species distributed in the southern Andes and Patagonian steppe. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.004DOI Listing
March 2019
1 Read

A novel gene arrangement among the Stylommatophora by the complete mitochondrial genome of the terrestrial slug Meghimatium bilineatum (Gastropoda, Arionoidea).

Mol Phylogenet Evol 2019 Mar 8;135:177-184. Epub 2019 Mar 8.

School of Life Sciences, Nanchang University, Nanchang 330031, China. Electronic address:

Stylommatophora is a main clade of Gastropoda that encompasses approximately 112 gastropod families and may exceed a total of 30,000 species. Twenty-four complete stylommatophoran mitogenomes have been sequenced to date, yet our understanding of mitochondrial evolution in stylommatophorans is still in its infancy. To further expand the set of available mitogenomes, we sequenced the mitogenome of Meghimatium bilineatum (Arionoidea: Philomycidae), a widespread land slug in East Asia. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.002DOI Listing

Incorporation of deep-sea and small-sized species provides new insights into gastropods phylogeny.

Mol Phylogenet Evol 2019 Mar 7;135:136-147. Epub 2019 Mar 7.

Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE CP 26, 57 rue Cuvier, 75005 Paris, France.

The use of phylogeny with uneven or limited taxon sampling may bias our interpretation of organismal evolution, for instance, the origin(s) of the deep-sea animals. The Mollusca is the second most speciose phylum, in which the Gastropoda forms the largest group. However, the currently proposed hypotheses of gastropod phylogeny are mainly based on part of their taxonomic diversity, notably on the large-sized and shallow-water species. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.003DOI Listing

Frozen Antarctic path for dispersal initiated parallel host-parasite evolution on different continents.

Mol Phylogenet Evol 2019 Mar 6;135:67-77. Epub 2019 Mar 6.

Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic. Electronic address:

After the break-up of Gondwana dispersal of organisms between America, Australia and Africa became more complicated. One of the possible remaining paths led through Antarctica, that was not yet glaciated and it remained habitable for many organisms. This favourable climate made Antarctica an important migration corridor for organisms with good dispersal ability, such as Aculeata (Hymenoptera), till the Oligocene cooling. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.023DOI Listing
March 2019
3 Reads

Molecular phylogeny of the ghost knifefishes (Gymnotiformes: Apteronotidae).

Mol Phylogenet Evol 2019 Mar 4;135:297-307. Epub 2019 Mar 4.

University of Louisiana at Lafayette Department of Biology, Lafayette, LA 70504-2451, USA.

Ghost knifefishes (Gymnotiformes: Apteronotidae) are weakly electric fishes that possess a high-frequency, neurogenic electric organ discharge. They are found throughout the humid Neotropics from Panama to Argentina and are most diverse and abundant in the channels of large lowland rivers. Apteronotidae is the most species-rich family of Neotropical electric knifefishes with 96 valid species in 15 genera. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.019DOI Listing
March 2019
3 Reads

Phylogeny, phylogeography and hybridization of Caucasian barbels of the genus Barbus (Actinopterygii, Cyprinidae).

Mol Phylogenet Evol 2019 Mar 4;135:31-44. Epub 2019 Mar 4.

Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain.

Phylogenetic relationships and phylogeography of six species of Caucasian barbels, the genus Barbus s. str., were studied based on extended geographic coverage and using mtDNA and nDNA markers. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.025DOI Listing

Positive selection of cereblon modified function including its E3 ubiquitin ligase activity and binding efficiency with AMPK.

Mol Phylogenet Evol 2019 Mar 2;135:78-85. Epub 2019 Mar 2.

Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan; Research Organization for Nano & Life Innovation, Waseda University, Japan. Electronic address:

Cereblon (CRBN) is a substrate receptor for an E3 ubiquitin ligase that directly binds to target proteins resulting in cellular activities, such as energy metabolism, membrane potential regulation, and transcription factor degradation. Genetic mutations in human CRBN lead to intellectual disabilities. In addition, it draws pathological attention because direct binding with immunomodulatory drugs can cure multiple myeloma (MM) and lymphocytic leukemia. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.03.001DOI Listing
March 2019
7 Reads

Phylogenomics facilitates stable scorpion systematics: Reassessing the relationships of Vaejovidae and a new higher-level classification of Scorpiones (Arachnida).

Mol Phylogenet Evol 2019 Mar 1;135:22-30. Epub 2019 Mar 1.

Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA.

The Neartic family Vaejovidae (Scorpiones: Chactoidea) has long been treated as a diverse and systematically cohesive group of scorpions, but its monophyly and relationship to other scorpion families have historically been questioned. Morphological data have supported its monophyly and a variety of phylogenetic placements within the superfamily Chactoidea. Recent phylogenomic analyses have instead recovered vaejovids as polyphyletic (albeit with minimal taxonomic sampling) and Chactoidea as paraphyletic. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903183045
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http://dx.doi.org/10.1016/j.ympev.2019.02.021DOI Listing
March 2019
3 Reads
3.916 Impact Factor

Evolutionary history of the Pasque-flowers (Pulsatilla, Ranunculaceae): Molecular phylogenetics, systematics and rDNA evolution.

Mol Phylogenet Evol 2019 Mar 1;135:45-61. Epub 2019 Mar 1.

Division of Molecular Biology, Department of Biology, Faculty of Science, Horvatovac 102a, HR-10000 Zagreb, Croatia. Electronic address:

Pulsatilla (Anemoneae, Ranunculaceae) is sister to Anemone s.s. and contains ca 40 perennial species of considerable horticultural and medical importance. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.015DOI Listing
March 2019
3 Reads

An exhaustive phylogeny of the combtooth blenny genus Salaria (Pisces, Blenniidae) shows introgressive hybridization and lack of reciprocal mtDNA monophyly between the marine species Salaria basilisca and Salaria pavo.

Mol Phylogenet Evol 2019 Mar 1;135:210-221. Epub 2019 Mar 1.

University of Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), via Archirafi 18, 90123 Palermo, Italy. Electronic address:

A comprehensive phylogeny of the genus Salaria based on mitochondrial and nuclear markers grouped the extant species of the genus in well-characterised marine and freshwater clades, thus rejecting the hypothesis of a polytypic origin of the freshwater Salaria populations and supporting the occurrence of a single invasion event of the inland waters by the genus. Based on both mitochondrial and nuclear DNA datasets, the Salaria species of the freshwater clade proved to be vicariant taxa originating from a common ancestor which could possibly spread throughout the circum-Mediterranean inland waters during the late Miocene Messinian salinity crisis, then experiencing a process of allopatric differentiation after the re-flooding of the Mediterranean basin. Within the marine clade, although the nuDNA datasets showed the existence of well-supported subclades in accordance to the morphological identification of the studied specimens, one of the two subclades obtained in the phylogenetic tree based on the mtDNA dataset included both S. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.026DOI Listing
March 2019
1 Read

Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae.

Mol Phylogenet Evol 2019 Feb 28;135:12-21. Epub 2019 Feb 28.

College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China. Electronic address:

The family Ranunculaceae, a member of early-diverging eudicots that is increasingly being used as a model for the study of plant developmental evolution, has been the focus of systematic studies for centuries. Recent studies showed that the family can be divided into 14 tribes, with Glaucideae, Hydrastideae, and Coptideae being the successive basal-most lineages. The relationships among the remaining 11 tribes, however, remain controversial, so that a clear picture of character evolution within the family is still lacking. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.024DOI Listing
February 2019
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Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error.

Mol Phylogenet Evol 2019 Feb 26;135:270-285. Epub 2019 Feb 26.

Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany. Electronic address:

The beetle superfamily Dytiscoidea, placed within the suborder Adephaga, comprises six families. The phylogenetic relationships of these families, whose species are aquatic, remain highly contentious. In particular the monophyly of the geographically disjunct Aspidytidae (China and South Africa) remains unclear. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.022DOI Listing
February 2019
9 Reads

Target sequence capture in the Brazil nut family (Lecythidaceae): Marker selection and in silico capture from genome skimming data.

Mol Phylogenet Evol 2019 Feb 25;135:98-104. Epub 2019 Feb 25.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama.

Reconstructing species trees from multi-loci datasets is becoming a standard practice in phylogenetics. Nevertheless, access to high-throughput sequencing may be costly, especially with studies of many samples. The potential high cost makes a priori assessments desirable in order to make informed decisions about sequencing. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.020DOI Listing
February 2019
3 Reads

Phylogenomic conflict resulting from ancient introgression following species diversification in Stewartia s.l. (Theaceae).

Mol Phylogenet Evol 2019 Feb 23;135:1-11. Epub 2019 Feb 23.

Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address:

Phylogenetic analyses using diverse datasets can yield conflicting inference of evolutionary history. Phylogenetic conflicts observed in both animal and plant systems have often been explained by two competing (but not mutually exclusive) hypotheses, i.e. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.018DOI Listing
February 2019
1 Read