scholarly journals Estimating movement rates between Eurasian and North American birds that are vectors of avian influenza (AI)

2021 ◽  
Author(s):  
Fern Spaulding ◽  
Jessica F. McLaughlin ◽  
Travis C. Glenn ◽  
Kevin Winker
Keyword(s):  
Gene Flow ◽  
Relative Risk ◽  
Avian Influenza ◽  
North American ◽  
Population Genomics ◽  
Effective Population ◽  
Anas Acuta ◽  
Movement Rates ◽  
Census Size

Avian influenza (AI) is an emerging zoonotic disease that will likely be involved in future pandemics. Because waterbird movements are difficult to quantify, determining the host-specific risk of Eurasian-origin AI movements into North America is challenging. We estimated relative rates of movements, based on long-term evolutionary averages of gene flow, between Eurasian and North American waterbird populations to obtain bidirectional baseline rates of the intercontinental movements of these AI hosts. We used population genomics and coalescent-based demographic models to obtain these gene-flow-based movement estimates. Inferred rates of movement between these populations varies greatly among species. Within dabbling ducks, gene flow, relative to effective population size, varies from ~3-24 individuals/generation between Eurasian and American wigeons (Mareca penelope — M. americana) to ~100-300 individuals/generation between continental populations of northern pintails (Anas acuta). These are evolutionary long-term averages and provide a solid foundation for understanding the relative risks of each of these host species in potential intercontinental AI movements. We scale these values to census size for evaluation in that context. In addition to being AI hosts, many of these species are also important in the subsistence diets of Alaskans, increasing the risk of direct bird-to-human exposure to Eurasian-origin AI virus. We contrast species-specific rates of intercontinental movements with the importance of each species in Alaskan diets to understand the relative risk of these taxa to humans. Greater scaup (Aythya marila), mallard (Anas platyrhynchos), and northern pintail (Anas acuta) were the top three species presenting the highest risks for intercontinental AI movement both within the natural system and through exposure to subsistence hunters. These directly comparable, species-based intercontinental movement rates and relative risk rankings should help in modeling, monitoring, and mitigating the impacts of intercontinental host and AI movements.

scholarly journals Long-term ‘islands’ in the landscape: low gene flow, effective population size and genetic divergence in the shrubHakea oldfieldii(Proteaceae)

2015 ◽  
Vol 179 (2) ◽  
pp. 319-334 ◽  
Author(s):  
Jane F. Sampson ◽  
Maggie Hankinson ◽  
Shelley McArthur ◽  
Sarah Tapper ◽  
Margaret Langley ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Divergence ◽  
Effective Population

scholarly journals Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259124
Author(s):  
Damian C. Lettoof ◽  
Vicki A. Thomson ◽  
Jari Cornelis ◽  
Philip W. Bateman ◽  
Fabien Aubret ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Drift ◽  
Urban Areas ◽  
Population Genomics ◽  
Genomic Structure ◽  
Genomic Diversity ◽  
Effective Population ◽  
Population Genomic ◽  
Population Sizes ◽  
Urban Matrix

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.

scholarly journals Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

2018 ◽  
Author(s):  
Kevin Winker ◽  
Travis C Glenn ◽  
Brant C Faircloth
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Divergence Time ◽  
Demographic Model ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Ultraconserved Elements ◽  
Genomic Markers ◽  
Allelic Differences ◽  
Analytical Approaches

Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (~18-74 Kya). With a sequencing depth of ~30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (~3.6 single nucleotide polymorphisms [SNPs]/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (~92,500 - 240,500 individuals), a deeper divergence time (~241,000 yrs), and lower gene flow (2.8-5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.

scholarly journals Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

2018 ◽  
Author(s):  
Kevin Winker ◽  
Travis C Glenn ◽  
Brant C Faircloth
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Divergence Time ◽  
Demographic Model ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Ultraconserved Elements ◽  
Genomic Markers ◽  
Allelic Differences ◽  
Analytical Approaches

Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (~18-74 Kya). With a sequencing depth of ~30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (~3.6 single nucleotide polymorphisms [SNPs]/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (~92,500 - 240,500 individuals), a deeper divergence time (~241,000 yrs), and lower gene flow (2.8-5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.

scholarly journals Accounting for Gene Flow from Unsampled ‘Ghost’ Populations while Estimating Evolutionay History under the Isolation with Migration Model

2019 ◽  
Author(s):  
Arun Sethuraman ◽  
Melissa Lynch
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Population Genomics ◽  
Divergence Times ◽  
Effective Population ◽  
Migration Rates ◽  
Isolation With Migration ◽  
Population Sizes ◽  
And Migration ◽  
Erroneous Inferences

AbstractUnsampled or extinct ‘ghost’ populations leave signatures on the genomes of individuals from extant, sampled populations, especially if they have exchanged genes with them over evolutionary time. This gene flow from ‘ghost’ populations can introduce biases when estimating evolutionary history from genomic data, often leading to data misinterpretation and ambiguous results. Here we assess these biases while accounting, or not accounting for gene flow from ‘ghost’ populations under the Isolation with Migration (IM) model. We perform extensive simulations under five scenarios with no gene flow (Scenario A), to extensive gene flow to- and from- an unsampled ‘ghost’ population (Scenarios B, C, D, and E). Estimates of evolutionary history across all scenarios A-E (effective population sizes, divergence times, and migration rates) indicate consistent a) under-estimation of divergence times between sampled populations, (b) over-estimation of effective population sizes of sampled populations, and (c) under-estimation of migration rates between sampled populations, with increased gene flow from the unsampled ‘ghost’ population. Without accounting for an unsampled ‘ghost’, summary statistics like FST are under-estimated, and π is over-estimated with increased gene flow from the‘ghost’. To show this persistent issue in empirical data, we use a 355 locus dataset from African Hunter-Gatherer populations and discuss similar biases in estimating evolutionary history while not accounting for unsampled ‘ghosts’. Considering the large effects of gene flow from these ‘ghosts’, we propose a multi-pronged approach to account for the presence of unsampled ‘ghost’ populations in population genomics studies to reduce erroneous inferences.

scholarly journals Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species

2021 ◽  
Author(s):  
Zachariah Gompert ◽  
Amy Springer ◽  
Megan Brady ◽  
Samridhi Chaturvedi ◽  
Lauren K. Lucas
Keyword(s):  
Genetic Diversity ◽  
Time Series ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Time Series Data ◽  
Series Data ◽  
Effective Population ◽  
Population Sizes

AbstractEffective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show thatLycaeidesbutterfly populations maintain low contemporary (variance) effective population sizes (e.g., ∼200 individuals) and thus evolve rapidly by genetic drift. Contemporary effective sizes were consistent with local census populations sizes. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift inLycaeideshas implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.

scholarly journals Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5735 ◽  
Author(s):  
Kevin Winker ◽  
Travis C. Glenn ◽  
Brant C. Faircloth
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Divergence Time ◽  
Demographic Model ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Ultraconserved Elements ◽  
Genomic Markers ◽  
Allelic Differences ◽  
Analytical Approaches

Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.

Anthropologic Relationships among Prehistoric Northeastern Amerindians

1980 ◽  
Vol 1 (2) ◽  
pp. 145-159
Author(s):  
Edward F. Harris ◽  
Nicholas F. Bellantoni
Keyword(s):  
New York ◽  
Gene Flow ◽  
Material Culture ◽  
New England ◽  
Cultural Barriers ◽  
Group Differences ◽  
Phenetic Analysis ◽  
Trade Relationships ◽  
Good Agreement

Archaeologically defined inter-group differences in the Northeast subarea ate assessed with a phenetic analysis of published craniometric information. Spatial distinctions in the material culture are in good agreement with those defined by the cranial metrics. The fundamental dichotomy, between the Ontario Iroquois and the eastern grouping of New York and New England, suggests a long-term dissociation between these two groups relative to their ecologic adaptations, trade relationships, trait-list associations, and natural and cultural barriers to gene flow.

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