Genomic diversity and Demographic History of the Dromiciops genus (Marsupialia: Microbiotheriidae)

How urbanization shapes population genomic diversity and evolution of urban wildlife is largely unexplored. We investigated the impact of urbanization on white-footed mice, Peromyscus leucopus, in the New York City (NYC) metropolitan area using coalescent-based simulations to infer demographic history from the site-frequency spectrum. We assigned individuals to evolutionary clusters and then inferred recent divergence times, population size changes and migration using genome-wide single nucleotide polymorphisms genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modelling indicates that post-glacial sea-level rise led to isolation of mainland and Long Island populations. These models also indicate that several urban parks represent recently isolated P. leucopus populations, and the estimated divergence times for these populations are consistent with the history of urbanization in NYC.

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Impact of past climate warming on genomic diversity and demographic history of collared lemmings across the Eurasian Arctic

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1913596117 ◽

2020 ◽

Vol 117 (6) ◽

pp. 3026-3033 ◽

Cited By ~ 4

Author(s):

Vadim B. Fedorov ◽

Emiliano Trucchi ◽

Anna V. Goropashnaya ◽

Eric Waltari ◽

Susan Erin Whidden ◽

...

Keyword(s):

Climate Warming ◽

Demographic History ◽

Genomic Diversity ◽

Northern Eurasia ◽

Last Interglacial ◽

Effective Population ◽

The West ◽

Past Climate ◽

History Of ◽

Late Pleistocene To Holocene

The Arctic climate was warmer than today at the last interglacial and the Holocene thermal optimum. To reveal the impact of past climate-warming events on the demographic history of an Arctic specialist, we examined both mitochondrial and nuclear genomic variation in the collared lemming (Dicrostonyx torquatus, Pallas), a keystone species in tundra communities, across its entire distribution in northern Eurasia. The ancestral phylogenetic position of the West Beringian group and divergence time estimates support the hypothesis of continental range contraction to a single refugial area located in West Beringia during high-magnitude warming of the last interglacial, followed by westward recolonization of northern Eurasia in the last glacial period. The West Beringian group harbors the highest mitogenome diversity and its inferred demography indicates a constantly large effective population size over the Late Pleistocene to Holocene. This suggests that northward forest expansion during recent warming of the Holocene thermal optimum did not affect the gene pool of the collared lemming in West Beringia but reduced genomic diversity and effective population size in all other regions of the Eurasian Arctic. Demographic inference from genomic diversity was corroborated by species distribution modeling showing reduction in species distribution during past climate warming. These conclusions are supported by recent paleoecological evidence suggesting smaller temperature increases and moderate northward forest advances in the extreme northeast of Eurasia during the Late Pleistocene-to-Holocene warming events. This study emphasizes the importance of West Beringia as a potential refugium for cold-adapted Arctic species under ongoing climate warming.

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Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City

10.1101/032979 ◽

2015 ◽

Cited By ~ 1

Author(s):

Stephen E. Harris ◽

Alexander T. Xue ◽

Diego Alvarado-Serrano ◽

Joel T. Boehm ◽

Tyler Joseph ◽

...

Keyword(s):

New York ◽

New York City ◽

York City ◽

Demographic History ◽

Peromyscus Leucopus ◽

Genomic Diversity ◽

Divergence Times ◽

Island Populations ◽

History Of ◽

The Impact

ABSTRACTHow urbanization shapes population genomic diversity and evolution of urban wildlife is largely unexplored. We investigated the impact of urbanization on white-footed mice, Peromyscus leucopus, in the New York City metropolitan area using coalescent-based simulations to infer demographic history from the site frequency spectrum. We assigned individuals to evolutionary clusters and then inferred recent divergence times, population size changes, and migration using genome-wide SNPs genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modeling indicates that post-glacial sea level rise led to isolation of mainland and Long Island populations. These models also indicate that several urban parks represent recently-isolated P. leucopus populations, and the estimated divergence times for these populations are consistent with the history of urbanization in New York City.

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Understanding the Hidden Complexity of Latin American Population Isolates

10.1101/340158 ◽

2018 ◽

Cited By ~ 1

Author(s):

Jazlyn A. Mooney ◽

Christian D. Huber ◽

Susan Service ◽

Jae Hoon Sul ◽

Clare D. Marsden ◽

...

Keyword(s):

Latin American ◽

Sequence Data ◽

Demographic History ◽

Costa Rican ◽

Genomic Diversity ◽

Whole Genome Sequence ◽

Ancestral Population ◽

Long Run ◽

History Of ◽

Admixed Population

AbstractMost population isolates examined to date were founded from a single ancestral population. Consequently, there is limited knowledge about the demographic history of admixed population isolates. Here we investigate genomic diversity of recently admixed population isolates from Costa Rica and Colombia and compare their diversity to a benchmark population isolate, the Finnish. These Latin American isolates originated during the 16th century from admixture between a few hundred European males and Amerindian females, with a limited contribution from African founders. We examine whole genome sequence data from 449 individuals, ascertained as families to build mutigenerational pedigrees, with a mean sequencing depth of coverage of approximately 24X. We find that Latin American isolates have increased genetic diversity relative to the Finnish. However, there is an increase in the amount of identity by descent (IBD) segments in the Latin American isolates relative to the Finnish. The increase in IBD segments is likely a consequence of a very recent and severe population bottleneck during the founding of the admixed population isolates. Furthermore, the proportion of the genome that falls within a long run of homozygosity (ROH) in Costa Rican and Colombian individuals was significantly greater than that in the Finnish, suggesting more recent consanguinity in the Latin American isolates relative to that seen in the Finnish. Lastly, we found that recent consanguinity increased the number of deleterious variants found in the homozygous state, which is relevant if deleterious variants are recessive. Our study suggests there is no single genetic signature of a population isolate.

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Population structure, genomic diversity and demographic history of Komodo dragons inferred from whole‐genome sequencing

Molecular Ecology ◽

10.1111/mec.16121 ◽

2021 ◽

Author(s):

Alessio Iannucci ◽

Andrea Benazzo ◽

Chiara Natali ◽

Evy Ayu Arida ◽

Moch Samsul Arifin Zein ◽

...

Keyword(s):

Population Structure ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Demographic History ◽

Genomic Diversity ◽

Whole Genome ◽

History Of

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Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽

10.1093/genetics/164.4.1511 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1511-1518 ◽

Cited By ~ 1

Author(s):

Ning Yu ◽

Michael I Jensen-Seaman ◽

Leona Chemnick ◽

Judith R Kidd ◽

Amos S Deinard ◽

...

Keyword(s):

Nucleotide Diversity ◽

Nuclear Dna ◽

Demographic History ◽

Nuclear Genome ◽

Limited Data ◽

Effective Population ◽

East Central ◽

Dna Diversity ◽

History Of ◽

Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

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Corrigendum to: Demographic history of the human commensal Drosophila melanogaster

Genome Biology and Evolution ◽

10.1093/gbe/evab046 ◽

2021 ◽

Vol 13 (3) ◽

Author(s):

J Roman Arguello ◽

Stefan Laurent ◽

Andrew G Clark

Keyword(s):

Drosophila Melanogaster ◽

Demographic History ◽

History Of

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Reference genome and demographic history of the most endangered marine mammal, the vaquita

Molecular Ecology Resources ◽

10.1111/1755-0998.13284 ◽

2020 ◽

Author(s):

Phillip A. Morin ◽

Frederick I. Archer ◽

Catherine D. Avila ◽

Jennifer R. Balacco ◽

Yury V. Bukhman ◽

...

Keyword(s):

Marine Mammal ◽

Reference Genome ◽

Demographic History ◽

History Of

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Temporal fluctuations of Y-chromosomal variation in Bos taurus

Biology Letters ◽

10.1098/rsbl.2008.0342 ◽

2008 ◽

Vol 4 (6) ◽

pp. 752-754 ◽

Cited By ~ 29

Author(s):

Emma Svensson ◽

Anders Götherström

Keyword(s):

Single Nucleotide Polymorphism ◽

Bos Taurus ◽

Demographic History ◽

Northern Europe ◽

Chromosomal Gene ◽

Chromosomal Variation ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Domestic Species ◽

History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

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Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

Animal Biology ◽

10.1163/157075610x523314 ◽

2010 ◽

Vol 60 (4) ◽

pp. 449-465

Author(s):

Wen Longying ◽

Zhang Lixun ◽

An Bei ◽

Luo Huaxing ◽

Liu Naifa ◽

...

Keyword(s):

Demographic History ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Population Expansion ◽

Population History ◽

Tibet Plateau ◽

Phylogeographic Structure ◽

Mitochondrial Cytochrome B ◽

History Of ◽

Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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