6,153 results match your criteria Molecular phylogenetics and evolution[Journal]


Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic Buzzards.

Mol Phylogenet Evol 2019 Feb 11. Epub 2019 Feb 11.

CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto. Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; Department of Zoology, University of Johannesburg, PO Box 534, Auckland Park 2006, South Africa.

Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903183060
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http://dx.doi.org/10.1016/j.ympev.2019.02.004DOI Listing
February 2019
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Phylogenomic analyses of brachyuran crabs support early divergence of primary freshwater crabs.

Mol Phylogenet Evol 2019 Feb 11. Epub 2019 Feb 11.

Simon F. S. Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong. Electronic address:

Recent fossil calibrated molecular phylogenies have revealed that the Brachyura underwent rapid radiation during the Cretaceous and Early Tertiary, resulting in many early diverging lineages separated by short internodes that remain difficult to resolve. Here we present the first phylogenomic analyses of Brachyura using transcriptome data from 30 brachyuran species and 22 families. Analyses were carried out on a dataset containing 372 putative homologous loci (246,590 bps) and included data from 22 newly generated transcriptomes. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.001DOI Listing
February 2019

New lineages and old species: lineage diversity and regional distribution of Moina (Crustacea: Cladocera) in China.

Mol Phylogenet Evol 2019 Feb 9. Epub 2019 Feb 9.

MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China. Electronic address:

The distribution and genetic diversity of freshwater zooplankton is understudied in the Eastern Palearctic. Here, we explored the lineage diversity and regional distribution of the genus Moina in China. Members of this genus are often keystone components of freshwater ecosystems and have been frequently subjected to toxicological and physiological studies. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.007DOI Listing
February 2019

Mitogenomic evidence of close relationships between New Zealand's extinct giant raptors and small-sized Australian sister-taxa.

Mol Phylogenet Evol 2019 Feb 9. Epub 2019 Feb 9.

Canterbury Museum, 8013 Christchurch, New Zealand.

Prior to human arrival in the 13th century, two large birds of prey were the top predators in New Zealand. In the absence of non-volant mammals, the extinct Haast's eagle (Hieraaetus moorei), the largest eagle in the world, and the extinct Eyles' harrier (Circus teauteensis) the largest harrier in the world, had filled ecological niches that are on other landmasses occupied by animals such as large cats or canines. The evolutionary and biogeographic history of these island giants has long been a mystery. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.026DOI Listing
February 2019

Cryptic diversity and dynamic chromosome evolution in Alpine scorpions (Euscorpiidae: Euscorpius).

Mol Phylogenet Evol 2019 Feb 8. Epub 2019 Feb 8.

Department of Zoology, Faculty of Science, Charles University, Viničná 7, CZ-12844, Prague, Czech Republic.

Over time, mountain biota has undergone complex evolutionary histories that have left imprints on its genomic arrangement, geographical distribution and diversity of contemporary lineages. Knowledge on these biogeographical aspects still lags behind for invertebrates inhabiting the Alpine region. In the present study, we examined three scorpion species of the subgenus Euscorpius (Alpiscorpius) from the European Alps using cytogenetic and molecular phylogenetic approaches to determine the variation and population structure of extant lineages at both chromosome and genetic level, and to provide an insight into the species diversification histories. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.002DOI Listing
February 2019
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Plastomes resolve generic limits within tribe Clusieae (Clusiaceae) and reveal the new genus Arawakia.

Mol Phylogenet Evol 2019 Feb 8. Epub 2019 Feb 8.

Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138 USA. Electronic address:

Clusieae is an exclusively Neotropical tribe in the family Clusiaceae sensu stricto. Although tribes within Clusiaceae are morphologically and phylogenetically well-delimited, resolution among genera within these tribes remains elusive. The tribe Clusieae includes an estimated ∼500 species distributed among five genera: Chrysochlamys, Clusia, Dystovomita, Tovomita, and Tovomitopsis. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.02.005DOI Listing
February 2019

Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants.

Mol Phylogenet Evol 2019 Feb 7. Epub 2019 Feb 7.

Department of Entomology and Nematology, One Shields Avenue, University of California at Davis, Davis, California, 95616, USA.

Knowledge of the internal phylogeny and evolutionary history of ants (Formicidae), the world's most species-rich clade of eusocial organisms, has dramatically improved since the advent of molecular phylogenetics. A number of relationships at the subfamily level, however, remain uncertain. Key unresolved issues include placement of the root of the ant tree of life and the relationships among the so-called poneroid subfamilies. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.024DOI Listing
February 2019

Plastid phylogenomic insights into the evolution of Caryophyllales.

Mol Phylogenet Evol 2019 Feb 5. Epub 2019 Feb 5.

Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China. Electronic address:

The Caryophyllales includes 40 families and 12,500 species, representing a large and diverse clade of angiosperms. Collectively, members of the clade grow on all continents and in all terrestrial biomes and often occupy extreme habitats (e.g. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.023DOI Listing
February 2019
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Not always young: The first vertebrate ancient origin of true parthenogenesis found in an Amazon leaf litter lizard with evidence of mitochondrial DNA haplotypes surfing on the wave of a range expansion.

Mol Phylogenet Evol 2019 Feb 4. Epub 2019 Feb 4.

Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Campus Diadema, Diadema, São Paulo, Brasil.

In vertebrates, true parthenogenesis is found only in squamate reptiles and (mostly) originates via interspecific hybridization after a secondary contact. In many cases, parthenogenesis is followed by an increase of ploidy, resulting in triploid lineages. Phylogenetic analyses derived from nuclear and maternally inherited markers can help to clarify the mechanisms of origin and the potential parental species involved. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.023DOI Listing
February 2019
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Assessing Phylogenetic Information to Reveal Uncertainty in Historical Data: An Example Using Goodeinae (Teleostei: Cyprinodontiformes: Goodeidae).

Mol Phylogenet Evol 2019 Feb 4. Epub 2019 Feb 4.

Southeastern Louisiana University, Dept. of Biological Sciences, Hammond, LA 70402.

A major emerging challenge to resolution of a stable phylogenetic Tree of Life has been incongruent inference among studies. Given the increasing ubiquity of incongruent studies, analyzing the predicted phylogenetic utility and quantitative evidence regarding contributions toward resolution of commonly-used markers in historical studies over the last decade represents an important, yet neglected, component of phylogenetics. Here we examine the phylogenetic utility of two sets of commonly-used legacy markers for understanding the evolutionary relationships among goodeines, a group of viviparous freshwater fishes endemic to central Mexico. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.025DOI Listing
February 2019

Hiding in the lianas of the tree of life: molecular phylogenetics and species delimitation reveal considerable cryptic diversity of New World Vine Snakes.

Mol Phylogenet Evol 2019 Feb 1. Epub 2019 Feb 1.

Science and Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, USA; 2564 E. Murdoch Ct., Green Valley, AZ 85614(2).

The Brown Vine Snake, Oxybelis aeneus, is considered a single species despite the fact its distribution covers an estimated 10% of the Earth's land surface, inhabiting a variety of ecosystems throughout North, Central, and South America and is distributed across numerous biogeographic barriers. Here we assemble a multilocus molecular dataset (i.e. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.022DOI Listing
February 2019
2 Reads

A well supported multi gene phylogeny of 52 dictyostelia.

Mol Phylogenet Evol 2019 Jan 31. Epub 2019 Jan 31.

School of Life Sciences, University of Dundee, Dundee DD15EH, UK. Electronic address:

The Dictyostelid social amoebas are a popular model system for cell- and developmental biology and for evolution of sociality. Small subunit (SSU) ribosomal DNA-based phylogenies subdivide the known 150 species into four major and some minor groups, but lack resolution within groups, particularly group 4, and, as shown by genome-based phylogenies of 11 species, showed errors in the position of the root and nodes separating major clades. We are interested in the evolution of cell-type specialization, which particularly expanded in group 4. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.017DOI Listing
January 2019

Phylogenetic analysis of plant calreticulin homologs.

Mol Phylogenet Evol 2019 Jan 31. Epub 2019 Jan 31.

Laboratory of Molecular and Isotope Methods, Department of Cellular and Molecular Biology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland. Electronic address:

Calreticulin (CRT) is a multifunctional resident endoplasmic reticulum (ER) luminal protein implicated in regulating a variety of cellular processes, including Ca storage/mobilization and protein folding. These multiple functions may be carried out by different CRT genes and protein isoforms. The plant CRT family consist of three genes: CRT1 and CRT2 classified in the common subclass (CRT1/2), and CRT3. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.014DOI Listing
January 2019

Bayesian Phylogenetic Analysis of the Influenza-A virus genomes isolated in Tunisia, and Determination of Potential Recombination Events.

Mol Phylogenet Evol 2019 Jan 29. Epub 2019 Jan 29.

Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, KSA; Institut National des Sciences Appliquées et de Technologie (INSAT), Tunis, Tunisia.

The influenza-A virus (IAV) causes seasonal epidemics and presents a pandemic risk with the possibility of genetic re-assortment, allowing the emergence of new strains. The evolution of IAVes is done most often by relatively frequent re-assortment between gene segments, but the hypothesis of their evolution by recombination between RNA segments has not been justified to this date. Here, we examine this hypothesis by Bayesian phylogenetic analysis, to test if recombination events have occurred between genomic RNA segments. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.019DOI Listing
January 2019
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Wolbachia symbionts in mosquitoes: Intra- and intersupergroup recombinations, horizontal transmission and evolution.

Mol Phylogenet Evol 2019 Jan 29;134:24-34. Epub 2019 Jan 29.

Institute of Cytology and Genetics of SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia; Immanuel Kant Baltic Federal University, Kaliningrad 236041, Russia. Electronic address:

Many mosquitoes harbour Wolbachia symbionts that could affect the biology of their host in different ways. Evolutionary relationships of mosquitoes' Wolbachia infection, geographical distribution and symbiont prevalence in many mosquito species are not yet clear. Here, we present the results of Wolbachia screening of 17 mosquito species of four genera-Aedes, Anopheles, Coquillettidia and Culex collected from five regions of Eastern Europe and the Caucasus in 2012-2016. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.020DOI Listing
January 2019

Ancient diversification, biogeography, and the role of climatic niche evolution in the Old World cat snakes (Colubridae, Telescopus).

Mol Phylogenet Evol 2019 Jan 29;134:35-49. Epub 2019 Jan 29.

Hielscherstr. 25, 13158 Berlin, Germany.

The process of species diversification is often associated with niche shifts in the newly arising lineages so that interspecific competition is minimized. However, an opposing force known as niche conservatism causes that related species tend to resemble each other in their niche requirements. Due to the inherent multidimensionality of niche space, some niche components may be subject to divergent evolution while others remain conserved in the process of speciation. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.015DOI Listing
January 2019

Diversification of bent-toed geckos (Cyrtodactylus) on Sumatra and west Java.

Mol Phylogenet Evol 2019 Jan 29;134:1-11. Epub 2019 Jan 29.

Department of Biology and the Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA.

Complex geological processes often drive biotic diversification on islands. The islands of Sumatra and Java have experienced dramatic historical changes, including isolation by marine incursions followed by periodic connectivity with the rest of Sundaland across highland connections. To determine how this geological history influenced island invasions, we investigated the colonization history and diversification of bent-toed geckos (genus Cyrtodactylus) on Sumatra and west Java. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.021DOI Listing
January 2019
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A plastid phylogeny of the Old World fern genus Leptochilus (Polypodiaceae): Implications for cryptic speciation and progressive colonization from lower to higher latitudes.

Mol Phylogenet Evol 2019 Jan 24. Epub 2019 Jan 24.

CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China; Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110, USA. Electronic address:

The newly defined fern genus Leptochilus contains about 50 species occurring in subtropical to tropical Asia and adjacent Pacific islands. The circumscription and phylogeny of the genus have been ambiguous and its species had been included in various genera such as Colysis, Dendroglossa, Kontumia, Microsorum, and Paraleptochilus. Previous molecular studies sampled only 2-4 molecular markers and 2-16 accessions of Leptochilus. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.013DOI Listing
January 2019
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Antioxidant activity and phycoremediation ability of four cyanobacterial isolates obtained from a stressed aquatic system.

Mol Phylogenet Evol 2019 Jan 24. Epub 2019 Jan 24.

Department of Physiology, National Organization for Drug Control and Research (NODCAR), Giza 12553, Egypt.

Cyanobacteria are natural enormous sources of various biologically active compounds with great contributions in different industries. This study aimed to explore and characterize novel cyanobacterial isolates with antioxidant activity and potent phycoremediation ability from Egyptian wastewater canals. The in vitro biological activity of these isolates and their potential ability to take up nutrients and heavy metals from wastewater were examined. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.018DOI Listing
January 2019
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Effects of missing data and data type on phylotranscriptomic analysis of stony corals (Cnidaria: Anthozoa: Scleractinia).

Mol Phylogenet Evol 2019 Jan 22;134:12-23. Epub 2019 Jan 22.

Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Tropical Marine Science Institute, National University of Singapore, Singapore 119227, Singapore.

Across the tree of life, phylogenetic analysis is increasingly being performed using transcriptome data. As a result of heterogeneous gene expression within individual organisms and unequal sequencing depth between samples, coverage of homologous loci in such datasets is typically inhomogeneous. Consequently, missing data are a common feature of phylotranscriptomic inference, but their impact on phylogenetic analysis remains poorly characterised empirically. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.012DOI Listing
January 2019
2 Reads

Phylogeographic variation within the Buff-browed Foliage-gleaner (Aves: Furnariidae: Syndactyla rufosuperciliata) supports an Andean-Atlantic forests connection via the Cerrado.

Mol Phylogenet Evol 2019 Jan 17;133:198-213. Epub 2019 Jan 17.

Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina.

We evaluated whether the Andean and the Atlantic forests acted as refugia during the Quaternary, and tested biogeographic hypotheses about the regions involved in the connectivity between those biomes (through the Chaco or the Cerrado). To achieve these goals we selected the Buff-browed Foliage-gleaner Syndactyla rufosuperciliata (Aves, Furnariidae) as a study system, a taxon distributed between the Andean and Atlantic forest. We first explored the historical connectivity between regions through niche modeling. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.011DOI Listing
January 2019
2 Reads

Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis.

Mol Phylogenet Evol 2019 Jan 16;133:189-197. Epub 2019 Jan 16.

Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany.

We reconstruct the molecular phylogeny of Near Eastern mountain brook newts of the genus Neurergus (family Salamandridae) based on newly determined RADseq data, and compare the outcomes of concatenation-based phylogenetic reconstruction with species-tree inference. Furthermore, we test the current taxonomy of Neurergus (with four species: Neurergus strauchii, N. crocatus, N. 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.2019.01.003DOI Listing
January 2019
8 Reads

Convergent evolution misled taxonomy in schizothoracine fishes (Cypriniformes: Cyprinidae).

Mol Phylogenet Evol 2019 Jan 11. Epub 2019 Jan 11.

Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China. Electronic address:

Highly specialized grade (HSG; genera Gymnocypris, Oxygymnocypris, Schizopygopsis, Platypharodon and Chuanchia) of the Schizothoracinae (Cypriniformes: Cyprinidae) are endemic to the Qinghai-Tibet Plateau (QTP). Previously, two distinct ecomorphs were recognized according to trophic traits. One was a limnetic omnivore with normal lower jaw morphology, terminal mouth, and moderate or dense gill rakers, mostly inhabiting in open water of lakes, including Gymnocypris and Oxygymnocypris. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.008DOI Listing
January 2019
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An integrative study of island diversification: Insights from the endemic Haemodracon geckos of the Socotra Archipelago.

Mol Phylogenet Evol 2019 Jan 11;133:166-175. Epub 2019 Jan 11.

Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.

The Socotra Archipelago in the Arabian Sea is considered one of the most geo-politically isolated landforms on earth and a center of endemism. The archipelago is located at the western edge of the Indian Ocean and comprises four islands: Socotra, Darsa, Samha, and Abd al Kuri. Here we provide an integrative study on Haemodracon geckos, the sole genus of geckos strictly endemic to the archipelago. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.009DOI Listing
January 2019
2 Reads

Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi).

Mol Phylogenet Evol 2019 Jan 11;133:152-163. Epub 2019 Jan 11.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States. Electronic address:

Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.006DOI Listing
January 2019
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Species delimitation and interspecific relationships of the endangered herb genus Notopterygium inferred from multilocus variations.

Mol Phylogenet Evol 2019 Jan 11;133:142-151. Epub 2019 Jan 11.

Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China. Electronic address:

Species identification and discrimination is the basis of biodiversity research. In general, it is considered that numerous nucleotide variations (e.g. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903183000
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http://dx.doi.org/10.1016/j.ympev.2019.01.002DOI Listing
January 2019
7 Reads
3.916 Impact Factor

Tempo and mode in coevolution of Agave sensu lato (Agavoideae, Asparagaceae) and its bat pollinators, Glossophaginae (Phyllostomidae).

Mol Phylogenet Evol 2019 Jan 11;133:176-188. Epub 2019 Jan 11.

Departamento Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma México, Ciudad de México 04510, Mexico. Electronic address:

The genus Agave sensu lato contains ca. 211 described species, many of which are considered keystone species because of their ecological dominance and the quantity of resources they provide with their massive, nectar-rich inflorescences. The large diversity of Agave species has been hypothesized as being related to their reproductive strategy (predominantly monocarpic) and diverse pollinators (e. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.004DOI Listing
January 2019
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Incorporating older literature into genomic studies: A response to Zunino & Halffter.

Mol Phylogenet Evol 2019 Jan 10;133:164-165. Epub 2019 Jan 10.

Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Life Sciences, Silwood Park Campus, Imperial College London, Buckhurst Road, Ascot SL5 7PY, United Kingdom.

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http://dx.doi.org/10.1016/j.ympev.2019.01.010DOI Listing
January 2019
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Genetic structure, phylogeography, and migration routes of Bouteloua gracilis (Kunth) Lag. ex Griffiths (Poaceae:Chloridoideae).

Mol Phylogenet Evol 2019 Jan 9;134:50-60. Epub 2019 Jan 9.

Universidad Autónoma de Aguascalientes, Av. Universidad 940, Aguascalientes 20130, Mexico. Electronic address:

Blue grama grass (Bouteloua gracilis) populations are found in widely variable environments, tolerating drought, alkaline soils and different levels of grazing. Many ploidy levels have been reported for this species that is also considered to be phenotypically plastic and morphologically variable. Recently a decline in its cover and frequency in the North American shortgrass steppe and central Mexico has been reported although much about the biology of the species is unknown, including genetic diversity throughout its distribution. Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.005DOI Listing
January 2019
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Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle.

Mol Phylogenet Evol 2019 Jan 7;133:120-127. Epub 2019 Jan 7.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA; La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.

Newts of the genus Triturus (marbled and crested newts) exhibit substantial variation in the number of trunk vertebrae (NTV) and a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny has thwarted resolution to date, the evolutionary history of NTV, annual aquatic period, and their potential coevolution has remained unclear. To resolve the phylogeny of Triturus, we generated a c. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.032DOI Listing
January 2019
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Birth of an order: Comprehensive molecular phylogenetic study excludes Herpomyces (Fungi, Laboulbeniomycetes) from Laboulbeniales.

Mol Phylogenet Evol 2019 Jan 6;133:286-301. Epub 2019 Jan 6.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.

The class Laboulbeniomycetes comprises biotrophic parasites associated with arthropods and fungi. Two orders are currently recognized, Pyxidiophorales and Laboulbeniales. Herpomyces is an isolated genus of Laboulbeniales, with species that exclusively parasitize cockroaches (Blattodea). Read More

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http://dx.doi.org/10.1016/j.ympev.2019.01.007DOI Listing
January 2019
2 Reads

About the origin of American Onthophagus (Coleoptera: Scarabaeidae). A critical appraisal of a recent paper by Breeschoten et al. (2016) on phylogenetics and biogeography.

Mol Phylogenet Evol 2019 Jan 3;133:141. Epub 2019 Jan 3.

Instituto de Ecología A. C., Carretera Antigua a Coatepec 361, El Haya, 91070 Xalapa, Veracruz, Mexico. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2019.01.001DOI Listing
January 2019
3 Reads

Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes.

Mol Phylogenet Evol 2018 Dec 30;133:352-361. Epub 2018 Dec 30.

Institute of Natural and Mathematical Sciences, Massey University Auckland, Auckland 0632, New Zealand; School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand. Electronic address:

Mammalian genomes contain a number of duplicated genes, and sequence identity between these duplicates can be maintained by purifying selection. However, between-duplicate recombination can also maintain sequence identity between copies, resulting in a pattern known as concerted evolution where within-genome repeats are more similar to each other than to orthologous repeats in related species. Here we investigated the tandemly-repeated keratin-associated protein 1 (KAP1) gene family, KRTAP1, which encodes proteins that are important components of hair and wool in mammals. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.031DOI Listing
December 2018
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Phylogeny, historical biogeography and diversification rates in an economically important group of Neotropical palms: Tribe Euterpeae.

Mol Phylogenet Evol 2018 Dec 27;133:67-81. Epub 2018 Dec 27.

Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL A1B3X9, Canada. Electronic address:

Tribe Euterpeae is an economically and ecologically important group of Neotropical palms (Arecaceae). Some species are hyperdominant in the Neotropics, and many constitute a good source of revenue. To reconstruct the biogeographical history and diversification of the Euterpeae, we inferred a robust dated molecular phylogenetic hypothesis including 82% of the species sequenced for five DNA regions (trnD-trnT, CISP4, WRKY6, RPB2, and PHYB). Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.030DOI Listing
December 2018
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Multilocus phylogeography of the brown-spotted pitviper Protobothrops mucrosquamatus (Reptilia: Serpentes: Viperidae) sheds a new light on the diversification pattern in Asia.

Mol Phylogenet Evol 2018 Dec 28;133:82-91. Epub 2018 Dec 28.

School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Gwynedd LL57 2UW, UK.

Understanding the influence of geographical events and climate changes on genetic diversity is essential in explaining current patterns of genetic structure and geographic distribution of organisms. We inferred phylogenetic relationships, investigated historical demography, explored the evolutionary history, and clarified intraspecific taxonomy of Protobothrops mucrosquamatus, which is one of the commonest and most wide-ranging Asian pitvipers. A total of 184 samples from 54 localities were sequenced and analyzed for two mitochondrial gene fragments and two nuclear genes. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903183005
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http://dx.doi.org/10.1016/j.ympev.2018.12.028DOI Listing
December 2018
18 Reads
3.916 Impact Factor

Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko.

Mol Phylogenet Evol 2018 Dec 24;133:54-66. Epub 2018 Dec 24.

Department of Biological Sciences, Marquette University, Milwaukee, WI, USA; Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, USA; Milwaukee Public Museum, Milwaukee, WI, USA. Electronic address:

Amazonia harbors the greatest biological diversity on Earth. One trend that spans Amazonian taxa is that most taxonomic groups either exhibit broad geographic ranges or small restricted ranges. This is likely because many traits that determine a species range size, such as dispersal ability or body size, are autocorrelated. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.029DOI Listing
December 2018
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Analyzing the functional divergence of Slo1 and Slo3 channel subfamilies.

Mol Phylogenet Evol 2018 Dec 23;133:33-41. Epub 2018 Dec 23.

Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250 Cuernavaca, Mexico.

Slo1 and Slo3 encode close paralogues of the Slo potassium (K) channels family. Despite their evolutionary relatedness, Slo1 and Slo3 channels show marked functional differences and evolutionary dynamics. Whereas Slo1 is a highly conserved and widely expressed channel, Slo3 is a rapidly evolving channel restricted to sperm. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S10557903173094
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http://dx.doi.org/10.1016/j.ympev.2018.12.026DOI Listing
December 2018
7 Reads

High cryptic diversity of bitterling fish in the southern West Palearctic.

Mol Phylogenet Evol 2018 Dec 23;133:1-11. Epub 2018 Dec 23.

The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65 Brno, Czech Republic. Electronic address:

South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) species complex (Cyprinidae) across its range in the western Palearctic, but with a particular emphasis in the region of Balkan, Pontic and Caspian refugia. We genotyped 12 polymorphic microsatellite loci and a partial sequence of mitochondrial gene cytochrome b (CYTB) for a set of 1,038 individuals from 60 populations. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.025DOI Listing
December 2018
2 Reads

Contrasting patterns of diversification between Amazonian and Atlantic forest clades of Neotropical lianas (Amphilophium, Bignonieae) inferred from plastid genomic data.

Mol Phylogenet Evol 2018 Dec 22;133:92-106. Epub 2018 Dec 22.

Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil; University of California, Berkeley, Department of Integrative Biology, Berkeley, CA, USA. Electronic address:

The mechanisms and processes underlying patterns of species distributions have intrigued ecologists and biogeographers for a long time. The Neotropics is the most species-rich region in the World, representing an excellent model for studying the drivers of diversification. In this study, we used a phylogenomic approach to infer relationships and examine the role of major geological and climatic events in shaping biogeographic patterns within Amphilophium (Bignonieae, Bignoniaceae), a genus of Neotropical lianas. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.021DOI Listing
December 2018
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Phylogenetic relationships and divergence dating in the Glass Lizards (Anguinae).

Mol Phylogenet Evol 2018 Dec 22;133:128-140. Epub 2018 Dec 22.

Department of Biology, Sonoma State University, 1801 East Cotati Ave, Rohnert Park, CA 94928, USA. Electronic address:

The Glass Lizards are a subfamily (Anguinae) of Anguid Lizards with an elongated limbless body plan that occur throughout the Northern Hemisphere primarily in North America, Europe, and Asia, but also have a presence in North Africa and Indonesia. We used twenty-five nuclear loci (15,191 bp) and 2090 bp of the mtDNA genome to generate a phylogeny containing all known species groups to explore species relationships within the group as well as divergence dating. We also examined the group in the context of a coalescent species tree analysis and species delimitation. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.022DOI Listing
December 2018
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Molecular phylogeny and evolution of world Tachinidae (Diptera).

Mol Phylogenet Evol 2018 Dec 22. Epub 2018 Dec 22.

Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA.

We reconstructed phylogenetic relationships within the diverse parasitoid fly family Tachinidae using four nuclear loci (7800 bp) and including an exceptionally large sample of more than 500 taxa from around the world. The position of the earthworm-parasitizing Polleniinae (Calliphoridae s.l. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.002DOI Listing
December 2018
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Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data.

Mol Phylogenet Evol 2018 Dec 21;133:263-285. Epub 2018 Dec 21.

cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal. Electronic address:

The evolutionary history of western Iberian Leuciscinae, obligatory freshwater fish, is directly linked to the evolution of the hydrographic network of the Iberian Peninsula after its isolation from the rest of Europe, which involved dramatic rearrangements such as the transition from endorheic lakes to open basins draining to the Atlantic. Previous phylogenetic research on western Iberian leuciscines, using mainly mitochondrial DNA and more recently one or two nuclear genes, has found contradictory results and there remain many unresolved issues regarding species relationships, taxonomy, and evolutionary history. Moreover, there is a lack of integration between phylogenetic and divergence time estimates and information on the timing of geomorphological changes and paleobasin rearrangements in the Iberian Peninsula. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.020DOI Listing
December 2018
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Game of clones: Is Wolbachia inducing speciation in a weevil with a mixed reproductive mode?

Mol Phylogenet Evol 2018 Dec 21;133:42-53. Epub 2018 Dec 21.

Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IEGEBA (CONICET-UBA), Intendente Güiraldes y Av. Costanera Norte s/n, 4to. Piso, Pabellón II, Ciudad Universitaria, CI1428 EHA Ciudad Autónoma de Buenos Aires, Argentina.

Parthenogenesis is widely distributed in Metazoa but it is especially frequent in weevils (Coleoptera, Curculionidae) with one fifth of all known cases. Previous studies have shown that in the tribe Naupactini parthenogenetic reproduction most likely originated with an infection of the endoparasitic bacterium Wolbachia pipientis. In particular, Pantomorus postfasciatus possess a mixed reproductive mode: some populations have males while in others they are absent, and females produce clones by thelytoky. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.027DOI Listing
December 2018
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Placing the regionally threatened moss Orthodontium gracile in the big picture - Phylogeny, genome incongruence and anthropogenic dispersal in the order Orthodontiales.

Mol Phylogenet Evol 2018 Dec 20. Epub 2018 Dec 20.

Botanicheskaya 4, Main Botanical Garden, Russian Academy of Sciences, 127276 Moscow, Russia; Faculty of Biology, Moscow State University 119991 Moscow, Russia. Electronic address:

The Orthodontiaceae is a small family of predominantly Southern Hemisphere temperate and South East Asian mosses that has a key phylogenetic position for research into the evolution of pleurocarpy. In the United Kingdom it is represented by the rare conservation priority species Orthodontium gracile and the abundant exotic O. lineare, introduced from the Southern Hemisphere around a century ago. 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.2018.12.024DOI Listing
December 2018
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Usual alga from unusual habitats: Biodiversity of Klebsormidium (Klebsormidiophyceae, Streptophyta) from the phylogenetic superclade G isolated from biological soil crusts.

Mol Phylogenet Evol 2018 Dec 18;133:236-255. Epub 2018 Dec 18.

Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany.

Seven new species and two varieties of Klebsormidium were described using an integrative approach on the base of 28 strains from the poorly studied phylogenetic superclade G. These strains originated from the unusual and exotic habitats (semi-deserts, semi-arid shrublands, Mediterranean shrub and deciduous vegetation, temperate Araucaria forests, peat bogs, dumps after coal mining, maritime sand dunes etc.) of four continents (Africa, South and North America, and Europe). Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.018DOI Listing
December 2018
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New patellogastropod mitogenomes help counteracting long-branch attraction in the deep phylogeny of gastropod mollusks.

Mol Phylogenet Evol 2018 Dec 17;133:12-23. Epub 2018 Dec 17.

Dept. Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain. Electronic address:

Long-branch attraction (LBA) is a well-known artifact in phylogenetic reconstruction. Sparse taxon sampling and extreme heterogeneity of evolutionary rates among lineages generate propitious situations for LBA, even defying probabilistic methods of phylogenetic inference. A clear example illustrating LBA challenges is the difficulty of reconstructing the deep gastropod phylogeny, particularly using mitochondrial (mt) genomes. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.019DOI Listing
December 2018
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Cetartiodactyla: Updating a time-calibrated molecular phylogeny.

Mol Phylogenet Evol 2018 Dec 15;133:256-262. Epub 2018 Dec 15.

Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36124, United States. Electronic address:

Cetartiodactyla comprises one of the most diverse mammal radiations. Currently, 23 families, 131 genera and more than 330 species are recognized. Several studies have been trying to resolve its phylogenetic relationships. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.015DOI Listing
December 2018
3 Reads

Complex patterns of hybridization and introgression across evolutionary timescales in Mexican whiptail lizards (Aspidoscelis).

Mol Phylogenet Evol 2019 Mar 15;132:284-295. Epub 2018 Dec 15.

Department of Biology, University of Hawai'i, Honolulu, HI 96822, USA.

Identifying patterns of introgression across the tree of life is foundational to understanding general mechanisms that govern the impacts of gene flow on the speciation process. There are few vertebrate groups in which hybridization is associated with as large a diversity of outcomes as in North American whiptail lizards (Aspidoscelis). Of particular interest is that hybridization among divergent whiptail species has repeatedly led to the formation of unisexual (parthenogenetic) lineages. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.016DOI Listing
March 2019
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Evolutionary history of Manihot carthagenensis (Euphorbiaceae) and allied species in eastern South America.

Mol Phylogenet Evol 2019 Mar 15;132:207-218. Epub 2018 Dec 15.

Laboratório de Biologia Molecular e Filogeografia, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil. Electronic address:

Intermittent episodes of climate changes, such as those that occurred during the Pleistocene, likely shaped the diversification of the young genus Manihot Mill. (Euphorbiacheae). One of such recently-derived congeners ─ M. Read More

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http://dx.doi.org/10.1016/j.ympev.2018.12.017DOI Listing
March 2019
2 Reads