Evolutionary history of a Scottish harbour seal population

Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour seal populations revealed three clusters in the UK, with a northeastern cluster that included our Moray Firth study population. Our analysis revealed that the Moray Firth cluster is an independent genetic group, with similar levels of genetic diversity across each of the localities sampled. These samples were used to assess historic abundance and demographic events in the Moray Firth population. Estimates of current genetic diversity and effective population size were low, but the results indicated that this population has remained at broadly similar levels following the population bottleneck that occurred after post-glacial recolonization of the area.

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Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽

10.3390/v13050737 ◽

2021 ◽

Vol 13 (5) ◽

pp. 737

Author(s):

Issiaka Bagayoko ◽

Marcos Giovanni Celli ◽

Gustavo Romay ◽

Nils Poulicard ◽

Agnès Pinel-Galzi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Sierra Leone ◽

Evolutionary History ◽

Molecular Diversity ◽

Genomic Data ◽

Gene Recombination ◽

Necrosis Virus ◽

History Of ◽

Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

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The history of genetic diversity and effective population size of an isolated Microtus oeconomus population on Kis Balaton

Mammalian Biology ◽

10.1007/s42991-021-00199-y ◽

2021 ◽

Author(s):

Veronika Sládkovičová ◽

Dávid Žiak ◽

Peter Miklós ◽

András Gubányi ◽

Győző Horváth

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Effective Population ◽

Microtus Oeconomus ◽

History Of

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SARS-Like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020

Viruses ◽

10.3390/v14010113 ◽

2022 ◽

Vol 14 (1) ◽

pp. 113

Author(s):

Sergey Alkhovsky ◽

Sergey Lenshin ◽

Alexey Romashin ◽

Tatyana Vishnevskaya ◽

Oleg Vyshemirsky ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

Structural Proteins ◽

Rt Pcr ◽

Phylogenetic Lineage ◽

History Of ◽

Horseshoe Bats ◽

Regions Of Russia ◽

Nonstructural Genes

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.

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Population structure and demographic history of the chukar partridge Alectoris chukar in China

Current Zoology ◽

10.1093/czoolo/59.4.458 ◽

2013 ◽

Vol 59 (4) ◽

pp. 458-474 ◽

Cited By ~ 2

Author(s):

Sen Song ◽

Shijie Bao ◽

Ying Wang ◽

Xinkang Bao ◽

Bei An ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

North America ◽

Demographic History ◽

Population Expansion ◽

Northwest China ◽

Population History ◽

Extant Species ◽

History Of ◽

Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

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Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

Israel Journal of Ecology and Evolution ◽

10.1163/22244662-20191081 ◽

2020 ◽

Vol 66 (3-4) ◽

pp. 142-150

Author(s):

Jessica Worthington Wilmer ◽

Andrew P. Amey ◽

Carmel McDougall ◽

Melanie Venz ◽

Stephen Peck ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

The West ◽

European Settlement ◽

Low Genetic Diversity ◽

Eastern Australia ◽

Wide Range ◽

History Of ◽

Open Forests ◽

Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

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First monk seal from the Southern Hemisphere rewrites the evolutionary history of true seals

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.2318 ◽

2020 ◽

Vol 287 (1938) ◽

pp. 20202318

Author(s):

James P. Rule ◽

Justin W. Adams ◽

Felix G. Marx ◽

Alistair R. Evans ◽

Alan J. D. Tennyson ◽

...

Keyword(s):

Southern Hemisphere ◽

North Atlantic ◽

Marine Mammals ◽

Evolutionary History ◽

Major Change ◽

The North ◽

History Of ◽

Entire History ◽

The North Atlantic ◽

Monk Seals

Living true seals (phocids) are the most widely dispersed semi-aquatic marine mammals, and comprise geographically separate northern (phocine) and southern (monachine) groups. Both are thought to have evolved in the North Atlantic, with only two monachine lineages—elephant seals and lobodontins—subsequently crossing the equator. The third and most basal monachine tribe, the monk seals, have hitherto been interpreted as exclusively northern and (sub)tropical throughout their entire history. Here, we describe a new species of extinct monk seal from the Pliocene of New Zealand, the first of its kind from the Southern Hemisphere, based on one of the best-preserved and richest samples of seal fossils worldwide. This unanticipated discovery reveals that all three monachine tribes once coexisted south of the equator, and forces a profound revision of their evolutionary history: rather than primarily diversifying in the North Atlantic, monachines largely evolved in the Southern Hemisphere, and from this southern cradle later reinvaded the north. Our results suggest that true seals crossed the equator over eight times in their history. Overall, they more than double the age of the north–south dichotomy characterizing living true seals and confirms a surprisingly recent major change in southern phocid diversity.

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Gene flow from multiple sources maintains high genetic diversity and stable population history of Common MoorhenGallinula chloropusin China

Ibis ◽

10.1111/ibi.12579 ◽

2018 ◽

Vol 160 (4) ◽

pp. 855-869 ◽

Cited By ~ 4

Author(s):

Luzhang Ruan ◽

Wei Xu ◽

Yuqing Han ◽

Chaoying Zhu ◽

Bicai Guan ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Population History ◽

Stable Population ◽

Multiple Sources ◽

High Genetic Diversity ◽

History Of

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Origin and genetic diversity of an introduced wall lizard population and its cryptic congener

Amphibia-Reptilia ◽

10.1163/156853812x626160 ◽

2012 ◽

Vol 33 (1) ◽

pp. 129-140 ◽

Cited By ~ 8

Author(s):

Ulrich Schulte ◽

Franz Gassert ◽

Philippe Geniez ◽

Michael Veith ◽

Axel Hochkirch

Keyword(s):

Genetic Diversity ◽

Geographic Origin ◽

Effective Population ◽

Lower Saxony ◽

Sympatric Populations ◽

Podarcis Muralis ◽

Eastern Pyrenees ◽

Native Populations ◽

The Uk ◽

Introduced Population

The Common Wall Lizard (Podarcis muralis) has been introduced within large parts of Central Europe, the UK and parts of North America. In an introduced population of this species in Lower Saxony, Germany, we found in addition to mtDNA haplotypes of P. muralis also haplotypes of its congener Podarcis liolepis, a species that hitherto has never been recorded outside its native range. We therefore, (1) wanted to identify the geographic origin of the founder individuals of both non-native populations, (2) test for hybridization between introduced individuals of both species in Germany and (3) compare levels of genetic diversity between native and introduced populations. We sequenced a fragment of the mitochondrial cytochrome b gene and genotyped individuals of the introduced as well as native populations of both species at eleven microsatellite loci. Our results suggest that the founders presumably stem from a region in the eastern Pyrenees, where sympatric populations of P. muralis and P. liolepis are known. No evidence for gene flow between the two species was found in the introduced population. These results are consistent with behavioural observations indicating agonistic interactions of P. muralis towards P. liolepis rather than cross-species attraction. Compared to the native populations, high levels of genetic diversity have been retained in the introduced population of both species and no evidence for a genetic bottleneck was found. The effective population size was high in P. muralis, but substantially smaller in P. liolepis.

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