scholarly journals Brown rat demography reveals pre-commensal structure in eastern Asia prior to expansion into Southeast Asia

2018 ◽  
Author(s):  
Emily E. Puckett ◽  
Jason Munshi-South
Keyword(s):  
Range Expansion ◽  
Eastern China ◽  
Human Migration ◽  
Genomic Diversity ◽  
Ancestral Population ◽  
Pest Species ◽  
Effective Population ◽  
Northern Asia ◽  
Se Asia ◽  
Brown Rat

ABSTRACTFossil evidence indicates that the globally-distributed brown rat (Rattus norvegicus) originated in northern China and Mongolia. Historical records report the human-mediated invasion of rats into Europe in the 1500s, followed by global spread due to European imperialist activity during the1600s-1800s. We analyzed 14 genomes representing seven previously identified evolutionary clusters and tested alternative demographic models to infer patterns of range expansion, divergence times, and changes in effective population (Ne) size for this globally important pest species. We observed three range expansions from the ancestral population that produced the Pacific (~4.8kya), eastern China (diverged ~0.55kya), and Southeast (SE) Asia (~0.53kya) lineages. Our model shows a rapid range expansion from SE Asia into the Middle East then continued expansion into central Europe 537 years ago (1478 AD). We observed declining Ne within all brown rat lineages from 150-1kya, reflecting population contractions during glacial cycles. Ne increased since 1kya in Asian and European, but not Pacific, evolutionary clusters. Our results support the hypothesis that northern Asia was the ancestral range for brown rats. We suggest that southward human migration across China between 800-1550s AD resulted in the introduction of rats to SE Asia, from which they rapidly expanded via existing maritime trade routes. Finally, we discovered that North America was colonized separately on both the Atlantic and Pacific seaboards, yet by evolutionary clusters of vastly different ages and genomic diversity levels. Our results should stimulate discussions among historians and zooarcheologists regarding the relationship between humans and rats.

scholarly journals Genomic characterisation and conservation genetics of the indigenous Irish Kerry cattle breed

2017 ◽  
Author(s):  
Sam Browett ◽  
Gillian McHugo ◽  
Ian W. Richardson ◽  
David A. Magee ◽  
Stephen D. E. Park ◽  
...  
Keyword(s):  
Gene Flow ◽  
Phylogenetic Trees ◽  
Principal Component ◽  
Physical Geography ◽  
Genomic Diversity ◽  
Ancestral Population ◽  
Effective Population ◽  
Cattle Breeds ◽  
Genome Wide ◽  
European Cattle

AbstractKerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP data (Illumina® BovineSNP50 array) to evaluate genomic diversity within the Kerry cattle population and between Kerry cattle and other European cattle breeds. Visualisation of patterns of genetic differentiation and gene flow among cattle breeds using phylogenetic trees with ancestry graphs highlighted, in particular, historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.Note 1: This is an Associate Editor (D.E.M) Inaugural Article submission to Frontiers in Genetics: Livestock GenomicsNote 2: British English language style preferred for publication of this article.

scholarly journals Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

2019 ◽  
Vol 286 (1916) ◽  
pp. 20191989 ◽  
Author(s):  
M. C. Yates ◽  
E. Bowles ◽  
D. J. Fraser
Keyword(s):  
Genetic Diversity ◽  
Body Size ◽  
Population Size ◽  
Brook Trout ◽  
Habitat Degradation ◽  
Species Conservation ◽  
Empirical Work ◽  
Genomic Diversity ◽  
Effective Population ◽  
Isolated Populations

Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size ( N e ), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had no effect on either fitness correlate, which was determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low N e , and long-term isolation can represent important sources of variation and are capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.

scholarly journals Genome Assembly and Population Resequencing Reveal the Geographical Divergence of 'Shanmei'(Rubus corchorifolius)

2021 ◽  
Author(s):  
Yinqing Yang ◽  
Kang Zhang ◽  
Ya Xiao ◽  
Lingkui Zhang ◽  
Yile Huang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Ancestral Population ◽  
Effective Population ◽  
High Quality ◽  
Local Environments ◽  
Rubus Species ◽  
Rubus Chingii ◽  
Rubus Chingii Hu ◽  
Genomic Regions ◽  
High Quality Genome

Rubus corchorifolius (Shanmei or mountain berry, 2n =14) is widely distributed in China, and its fruit has high nutritional and medicinal values. Here, we report a high-quality chromosome-scale genome assembly of Shanmei, with a size of 215.69 Mb and encompassing 26696 genes. Genome comparisons among Rosaceae species show that Shanmei and Fupenzi(Rubus chingii Hu) are most closely related, and then is blackberry (Rubus occidentalis). Further resequencing of 101 samples of Shanmei collected from four regions in provinces of Yunnan, Hunan, Jiangxi and Sichuan in South China reveals that the Hunan population of Shanmei possesses the highest diversity and may represent the relatively more ancestral population. Moreover, the Yunnan population undergoes strong selection based on nucleotide diversity, linkage disequilibrium and the historical effective population size analyses. Furthermore, genes from candidate genomic regions that show strong divergence are significantly enriched in flavonoid biosynthesis and plant hormone signal transduction, indicating the genetic basis of adaptation of Shanmei to the local environments. The high-quality genome sequences and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

scholarly journals Evidence that the rate of strong selective sweeps increases with population size in the great apes

2017 ◽  
Vol 114 (7) ◽  
pp. 1613-1618 ◽  
Author(s):  
Kiwoong Nam ◽  
Kasper Munch ◽  
Thomas Mailund ◽  
Alexander Nater ◽  
Maja Patricia Greminger ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Large Population ◽  
Great Apes ◽  
Genomic Diversity ◽  
Comparative Approach ◽  
Selective Sweeps ◽  
Effective Population ◽  
Intergenic Sequences ◽  
The Right

Quantifying the number of selective sweeps and their combined effects on genomic diversity in humans and other great apes is notoriously difficult. Here we address the question using a comparative approach to contrast diversity patterns according to the distance from genes in all great ape taxa. The extent of diversity reduction near genes compared with the rest of intergenic sequences is greater in a species with larger effective population size. Also, the maximum distance from genes at which the diversity reduction is observed is larger in species with large effective population size. In Sumatran orangutans, the overall genomic diversity is ∼30% smaller than diversity levels far from genes, whereas this reduction is only 9% in humans. We show by simulation that selection against deleterious mutations in the form of background selection is not expected to cause these differences in diversity among species. Instead, selective sweeps caused by positive selection can reduce diversity level more severely in a large population if there is a higher number of selective sweeps per unit time. We discuss what can cause such a correlation, including the possibility that more frequent sweeps in larger populations are due to a shorter waiting time for the right mutations to arise.

scholarly journals On the estimation of ancestral population sizes of modern humans

1997 ◽  
Vol 69 (2) ◽  
pp. 111-116 ◽  
Author(s):  
ZIHENG YANG
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Divergence Time ◽  
Ancestral Population ◽  
Rate Variation ◽  
Effective Population ◽  
Modern Humans ◽  
Extant Species ◽  
Population Sizes ◽  
Highly Correlated

The theory developed by Takahata and colleagues for estimating the effective population size of ancestral species using homologous sequences from closely related extant species was extended to take account of variation of evolutionary rates among loci. Nuclear sequence data related to the evolution of modern humans were reanalysed and computer simulations were performed to examine the effect of rate variation on estimation of ancestral population sizes. It is found that the among-locus rate variation does not have a significant effect on estimation of the current population size when sequences from multiple loci are sampled from the same species, but does have a significant effect on estimation of the ancestral population size using sequences from different species. The effects of ancestral population size, species divergence time and among-locus rate variation are found to be highly correlated, and to achieve reliable estimates of the ancestral population size, effects of the other two factors should be estimated independently.

scholarly journals Human migration activities drive the fluctuation of ARGs: Case study of landfills in Nanjing, eastern China

2016 ◽  
Vol 315 ◽  
pp. 93-101 ◽  
Author(s):  
Mingming Sun ◽  
Mao Ye ◽  
Arthur P. Schwab ◽  
Xu Li ◽  
Jinzhong Wan ◽  
...  
Keyword(s):  
Eastern China ◽  
Human Migration

scholarly journals Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration

2001 ◽  
Vol 98 (8) ◽  
pp. 4558-4562 ◽  
Author(s):  
M. C. Fisher ◽  
G. L. Koenig ◽  
T. J. White ◽  
G. San-Blas ◽  
R. Negroni ◽  
...  
Keyword(s):  
South America ◽  
Range Expansion ◽  
New World ◽  
Human Migration ◽  
Coccidioides Immitis

scholarly journals Genomic insights into the recent population history of Mapuche Native Americans

2021 ◽  
Author(s):  
Lucas Vicuña ◽  
Anastasia Mikhailova ◽  
Tomás Norambuena ◽  
Anna Ilina ◽  
Olga Klimenkova ◽  
...  
Keyword(s):  
Native American ◽  
Native Americans ◽  
Amazon Basin ◽  
Genomic Data ◽  
Population History ◽  
Ancestral Population ◽  
Effective Population ◽  
Southern Patagonia ◽  
History Of ◽  
Demographic Shifts

The last few years have witnessed an explosive generation of genomic data from ancient and modern Native American populations. These data shed light on key demographic shifts that occurred in geographically diverse territories of South America, such as the Andean highlands, Southern Patagonia and the Amazon basin. We used genomic data to study the recent population history of the Mapuche, who are the major Native population from the Southern Cone (Chile and Argentina). We found evidence of specific shared genetic ancestry between the Mapuche and ancient populations from Southern Patagonia, Central Chile and the Argentine Pampas. Despite previous evidence of cultural influence of Inca and Tiwanaku polities over the Mapuche, we did not find evidence of specific shared ancestry between them, nor with Amazonian groups. We estimated the effective population size dynamics of the Mapuche ancestral population during the last millennia, identifying a population bottleneck around 1650 AD, coinciding with a period of Spaniards invasions into the territory inhabited by the Mapuche. Finally, we show that admixed Chileans underwent post-admixture adaptation in their Mapuche subancestry component in genes related with lipid metabolism, suggesting adaptation to scarce food availability.

scholarly journals Genomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance inKlebsiella aerogenes

2019 ◽  
Author(s):  
Hemanoel Passarelli-Araujo ◽  
Jussara K. Palmeiro ◽  
Kanhu C. Moharana ◽  
Francisnei Pedrosa-Silva ◽  
Libera M. Dalla-Costa ◽  
...  
Keyword(s):  
Population Structure ◽  
Genomic Analysis ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Single Nucleotide ◽  
Deleterious Alleles ◽  
Large Effective Population Size ◽  
Healthcare Associated ◽  
Antibiotic Efflux

ABSTRACTKlebsiella aerogenesis an important pathogen in healthcare-associated infections. Nevertheless, in comparison to other clinically important pathogens,K. aerogenespopulation structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidateK. aerogenesclonal complexes (CCs) and genomic features associated with resistance and virulence. We present a detailed description of the population structure ofK. aerogenesbased on 97 publicly available genomes by using both, multilocus sequence typing and single nucleotide polymorphisms extracted from core genome. We also assessed virulence and resistance profiles using VFDB and CARD, respectively. We show thatK. aerogeneshas an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least ten CCs, including two novel ones identified here, CC9 and CC10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow and extended spectrum β-lactamases. Regarding the population structure, we identified two clusters based on virulence profile due to the presence of the toxin-encodingclboperon and the siderophore production genes,irpandybt.Notably, CC3 comprises the majority ofK. aerogenesisolates associated with hospital outbreaks, emphasizing the importance of its constant monitoring. Collectively, our results can be useful in the development of new therapeutic and surveillance strategies worldwide.

scholarly journals Population Genetic Structure of Raccoons as a Consequence of Multiple Introductions and Range Expansion in the Boso Peninsula, Japan

2021 ◽  
Author(s):  
Miki Hirose ◽  
Kazuya Yoshida ◽  
Eiji Inoue ◽  
Masami Hasegawa
Keyword(s):  
Range Expansion ◽  
Population Control ◽  
Large Population ◽  
Genetic Admixture ◽  
Effective Population ◽  
Genetic Barrier ◽  
Management Units ◽  
Multiple Introductions ◽  
Boso Peninsula ◽  
Chiba Prefecture

Abstract Raccoon (Procyon lotor) is a globally introduced invasive carnivore. Although controlling feral raccoon populations is important to reduce serious threats to local ecosystems, raccoons are not under rigid population control in Europe and Japan. We examined the D-loop and nuclear microsatellite regions to identify spatially explicit and feasible management units for effective population control and further range expansion retardation. Through the identification of five mitochondrial DNA haplotypes and three nuclear genetic groups, we identified at least three independent introductions, range expansion, and subsequent genetic admixture in the Boso Peninsula. Admitting that the currently recognizable two genetic clusters can be treated as different management units, these management units will soon fuse to a single but large population to which the effective population control will no longer be applicable due to the absence of a genetic barrier between southern and northern Chiba Prefecture.

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