scholarly journals Long-term reciprocal gene flow in wild and domestic geese reveals complex domestication history

2019 ◽  
Author(s):  
Marja E. Heikkinen ◽  
Minna Ruokonen ◽  
Thomas A. White ◽  
Michelle M. Alexander ◽  
İslam Gündüz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Gene Pools ◽  
Large Contribution ◽  
Wild Form ◽  
Wild Progenitor ◽  
Genome Wide ◽  
Domestication Process ◽  
Historical Writings ◽  
The Impact

AbstractHybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in genus Anser have been domesticated providing excellent opportunity for joint study of domestication and hybridization. Until now, knowledge on the details of the goose domestication process has come from archaeological findings and historical writings supplemented with few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the greylag goose (Anser anser). Our dataset consisted of 58 wild greylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that greylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that domestication process can progress despite continued and pervasive gene flow from the wild form.Significance StatementReproductive isolation between conspecific wild and domestic populations is a cornerstone of the domestication process, yet gene flow between such wild and domestic populations has been frequently documented. European domestic geese and their wild progenitor (greylags) co-occur and can hybridize and we show that they represent a particularly persuasive case where wild and domestic populations are not isolated gene pools. Our study makes a first genome-based estimate of goose domestication, which up to now has mostly relied on archaeological findings and historical writings. We show ongoing gene flow between greylags and European domestic geese following domestication, but we also observe a surprisingly large contribution of Chinese domestic geese (a separate species) to the genetic make-up of European domestic geese.

scholarly journals Long-Term Reciprocal Gene Flow in Wild and Domestic Geese Reveals Complex Domestication History

2020 ◽  
Vol 10 (9) ◽  
pp. 3061-3070 ◽  
Author(s):  
Marja E Heikkinen ◽  
Minna Ruokonen ◽  
Thomas A White ◽  
Michelle M Alexander ◽  
İslam Gündüz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Wild Form ◽  
Nucleotide Polymorphisms ◽  
Anser Anser ◽  
Domestic Species ◽  
Genome Wide ◽  
Domestication Process ◽  
Historical Writings ◽  
The Impact

Abstract Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in the genus Anser have been domesticated providing an excellent opportunity for a joint study of domestication and hybridization. Until now, knowledge of the details of the goose domestication process has come from archaeological findings and historical writings supplemented with a few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the graylag goose (Anser anser). Our dataset consisted of 58 wild graylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that graylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with the Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that the domestication process can progress despite continued and pervasive gene flow from the wild form.

scholarly journals Genome-wide local ancestries discriminate homoploid hybrid speciation from secondary introgression in the red wolf (Canidae: Canis rufus)

2020 ◽  
Author(s):  
Tyler K. Chafin ◽  
Marlis R. Douglas ◽  
Michael E. Douglas
Keyword(s):  
Gene Flow ◽  
X Chromosome ◽  
North American ◽  
Gene Trees ◽  
Canis Rufus ◽  
Red Wolf ◽  
Genome Wide ◽  
Homoploid Hybrid ◽  
Divergence Estimates ◽  
The Impact

AbstractHybridization is well recognized as a driver of speciation, yet it often remains difficult to parse phylogenomically in that post-speciation gene flow frequently supersedes an ancestral signal. Here we examined how interactions between recombination and gene flow shaped the phylogenomic landscape of red wolf to create non-random retention of introgressed ancestry. Our re-analyses of genomic data recapitulate fossil evidence by demonstrating red wolf was indeed extant and isolated prior to more recent admixture with other North American canids. Its more ancient divergence, now sequestered within low-recombinant regions on the X-chromosome (i.e., chromosomal ‘refugia’), is effectively masked by multiple, successive waves of secondary introgression that now dominate its autosomal ancestry. These interpretations are congruent with more theoretical explanations that describe the manner by which introgression can be localized within the genome through recombination and selection. They also tacitly support the large-X effect, i.e., the manner by which loci that contribute to reproductive isolation can be enriched on the X-chromosome. By contrast, similar, high recombinant regions were also found as enriched within very shallow gene trees, thus reflecting post-speciation gene flow and a compression of divergence estimates to 1/20th of that found in recombination ‘cold spots’. Our results effectively reconcile conflicting hypotheses regarding the impact of hybridization on evolution of North American canids and support an emerging framework within which the analysis of a phylogenomic landscape structured by recombination can be used to successfully address the macroevolutionary implications of hybridization.

scholarly journals The genomic impact of European colonization of the Americas

2019 ◽  
Author(s):  
Linda Ongaro ◽  
Marilia O. Scliar ◽  
Rodrigo Flores ◽  
Alessandro Raveane ◽  
Davide Marnetto ◽  
...  
Keyword(s):  
Gene Flow ◽  
Demographic History ◽  
Colonial Era ◽  
Genome Wide ◽  
A Genome ◽  
European Colonization ◽  
High Degree ◽  
The Impact ◽  
North And South America ◽  
North And South

AbstractThe human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored.Here we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected i) the genetic structure, ii) the admixture profile, iii) the demographic history and iv) sex-biased gene-flow dynamics, of the Americas.We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East and to specific regions of Africa.

scholarly journals Increased individual homozygosity is correlated with low fitness in a fragmented lizard population

2019 ◽  
Vol 128 (4) ◽  
pp. 952-962 ◽  
Author(s):  
Javier Pérez-Tris ◽  
Alejandro Llanos-Garrido ◽  
Paul Bloor ◽  
Roberto Carbonell ◽  
José Luis Tellería ◽  
...  
Keyword(s):  
Gene Flow ◽  
Restricted Gene Flow ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Anthropogenic Habitat ◽  
Geographical Scale ◽  
Psammodromus Algirus ◽  
Fragmented Population ◽  
The Impact

Abstract Isolation owing to anthropogenic habitat fragmentation is expected to increase the homozygosity of individuals, which might reduce their fitness as a result of inbreeding depression. Using samples from a fragmented population of the lizard Psammodromus algirus, for which we had data about two correlates of fitness, we genotyped individuals for six microsatellite loci that correctly capture genome-wide individual homozygosity of these lizards (as validated with an independent sample of lizards genotyped for both these microsatellites and > 70 000 single nucleotide polymorphisms). Our data revealed genetic structure at a very small geographical scale, which was compatible with restricted gene flow among populations disconnected in a matrix of inhospitable habitat. Lizards from the same fragment were genetically more related to one another than expected by chance, and individual homozygosity was greater in small than in large fragments. Within fragments, individual homozygosity was negatively associated with adult body size and clutch mass, revealing a link among reduced gene flow, increased homozygosity and lowered fitness that might reduce population viability deterministically. Our results contribute to mounting evidence of the impact of the loss of genetic diversity on fragmented wild populations.

scholarly journals Genomic signatures of inbreeding and genetic load in a threatened rattlesnake

2021 ◽  
Author(s):  
Alexander Ochoa ◽  
H. Lisle Gibbs
Keyword(s):  
Threatened Species ◽  
Empirical Studies ◽  
Genetic Load ◽  
Population History ◽  
Deleterious Mutations ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Genome Wide ◽  
The Impact

Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their negative genetic load but recent work suggests that the impact of load may be minimized by purging resulting from long term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use genome resequencing data to compare levels of inbreeding, levels of genetic load and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus) which exist in small isolated populations and closely-related yet outbred Western massasauga rattlesnakes (S. tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of ROHs of varying sizes indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of genetic load in the form of greater numbers of derived deleterious mutations compared to S. catenatus presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped the “drift sieve” and were polymorphic within S. catenatus populations were more abundant and more often found in homozygote genotypes than in S. tergeminus suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present which impacts implementation of conservation actions such as genetic rescue.

scholarly journals Genetic rescue without genomic swamping in wild populations

2019 ◽  
Author(s):  
Sarah W. Fitzpatrick ◽  
Gideon S. Bradburd ◽  
Colin T. Kremer ◽  
Patricia E. Salerno ◽  
Lisa M. Angeloni ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genomic Variation ◽  
Adaptive Variation ◽  
Genetic Rescue ◽  
Genome Wide ◽  
Evolutionary Force ◽  
Locally Adaptive ◽  
Fitness Benefits ◽  
Evolutionary Consequences

AbstractGene flow is an enigmatic evolutionary force because it can limit adaptation but can also help populations escape inbreeding depression. Manipulating gene flow for conservation purposes is a controversial, but potentially powerful management strategy. We use multigenerational pedigrees and genomics to test demographic and evolutionary consequences of manipulating gene flow in two isolated wild Trinidadian guppy populations. We found that on average, hybrids lived longer and reproduced more. Despite overall genome-wide homogenization, alleles potentially associated with local adaptation were not entirely swamped by gene flow. Our results suggest that combining new genomic variation from immigrants with potentially adaptive variation from the recipient population resulted in highly fit hybrids and subsequent increases in population size. Contrary to the prevailing view that gene flow constrains adaptation, our study shows that immigration can produce long-term fitness benefits in small populations without swamping locally adaptive variation.

scholarly journals Urban rat races: spatial population genomics of brown rats ( Rattus norvegicus ) compared across multiple cities

2018 ◽  
Vol 285 (1880) ◽  
pp. 20180245 ◽  
Author(s):  
Matthew Combs ◽  
Kaylee A. Byers ◽  
Bruno M. Ghersi ◽  
Michael J. Blum ◽  
Adalgisa Caccone ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
Gene Flow ◽  
New Orleans ◽  
York City ◽  
Rattus Norvegicus ◽  
Animal Movement ◽  
Neutral Evolution ◽  
Genome Wide ◽  
The Impact

Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats ( Rattus norvegicus ) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; and New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15 000 genome-wide single nucleotide polymorphisms. Levels of genome-wide diversity were similar across cities, but varied across neighbourhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (less than 500 m) owing to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.

scholarly journals An additional area of apple domestication with crop-wild gene flow, and also cultivation of the local wild apple, in the Caucasus

2021 ◽  
Author(s):  
Hamid Bina ◽  
Hamed Yousefzadeh ◽  
Anthony Venon ◽  
Carine Remoue ◽  
Agnes Rousselet ◽  
...  
Keyword(s):  
Gene Flow ◽  
Fruit Tree ◽  
Plant Domestication ◽  
Gene Pools ◽  
The Caucasus ◽  
Wild Fruit ◽  
Apple Cultivars ◽  
Cultivated Populations ◽  
The Impact

Anthropogenic and natural divergence processes in crop-wild fruit tree complexes are less studied than in annual crops, especially in the Caucasus, a pivotal region for plant domestication. We investigated anthropogenic and natural divergence processes in apples in the Caucasus from using 26 microsatellite markers amplified on 508 wild and cultivated samples. We found two specific Iranian cultivated populations that were differentiated from Malus domestica, the standard cultivated apple worldwide, suggesting a specific local domestication process in Iran. Some Iranian apple cultivars belonged to the Caucasian wild apple gene pools, indicating that farmers also use local wild apple for cultivation. Substantial wild-crop and crop-crop gene flow were also inferred. We identified seven genetically differentiated populations of wild apples (Malus orientalis) in the Caucasus. Niche modeling indicated that these populations likely resulted from range changes linked to the last glaciation. This study pinpoints Iran as a key region in the evolution and domestication of apple and further demonstrates the role of gene flow during fruit tree domestication as well as the impact of climate change on the natural divergence of a wild fruit tree. The results also provide a practical base for apple conservation and breeding programs in the Caucasus.

scholarly journals Distinguishing among modes of convergent adaptation using population genomic data

2017 ◽  
Author(s):  
Kristin M. Lee ◽  
Graham Coop
Keyword(s):  
Gene Flow ◽  
Fundulus Heteroclitus ◽  
Copper Toxicity ◽  
Genomic Data ◽  
Composite Likelihood ◽  
Allele Frequencies ◽  
Standing Variation ◽  
Genome Wide ◽  
Genetic Level ◽  
The Impact

AbstractGeographically separated populations can convergently adapt to the same selection pressure. Convergent evolution at the level of a gene may arise via three distinct modes. The selected alleles can (1) have multiple independent mutational origins, (2) be shared due to shared ancestral standing variation, or (3) spread throughout subpopulations via gene flow. We present a model-based, statistical approach that utilizes genomic data to detect cases of convergent adaptation at the genetic level, identify the loci involved and distinguish among these modes. To understand the impact of convergent positive selection on neutral diversity at linked loci, we make use of the fact that hitchhiking can be modeled as an increase in the variance in neutral allele frequencies around a selected site within a population. We build on coalescent theory to show how shared hitchhiking events between subpopulations act to increase covariance in allele frequencies between subpopulations at loci near the selected site, and extend this theory under different models of migration and selection on the same standing variation. We incorporate this hitchhiking effect into a multivariate normal model of allele frequencies that also accounts for population structure. Based on this theory, we present a composite-likelihood-based approach that utilizes genomic data to identify loci involved in convergence, and distinguishes among alternate modes of convergent adaptation. We illustrate our method on genome-wide polymorphism data from two distinct cases of convergent adaptation. First, we investigate the adaptation for copper toxicity tolerance in two populations of the common yellow monkey flower, Mimulus guttatus. We show that selection has occurred on an allele that has been standing in these populations prior to the onset of copper mining in this region. Lastly, we apply our method to data from four populations of the killifish, Fundulus heteroclitus, that show very rapid convergent adaptation for tolerance to industrial pollutants. Here, we identify a single locus at which both independent mutation events and selection on an allele shared via gene flow, either slightly before or during selection, play a role in adaptation across the species’ range.

scholarly journals Interactions between gene pools of russian and finnish-speaking populations from Tver region: analysis of 4 million SNP markers

2020 ◽  
Author(s):  
OP Balanovsky ◽  
IO Gorin ◽  
YuS Zapisetskaya ◽  
AA Golubeva ◽  
ES Kostryukova ◽  
...  
Keyword(s):  
Gene Flow ◽  
Gene Pool ◽  
Population Decline ◽  
Principal Component ◽  
Genetic Admixture ◽  
Gene Pools ◽  
Genome Wide ◽  
A Genome ◽  
Tver Region ◽  
Snp Panel

This study explored the gene pools of Russian and Karelian populations of Tver region. Forty-one samples representing Tver Karels (n = 11) and Russians residing in the Western, Central and Eastern districts of Tver region (n = 30) were genotyped using a genome-wide panel of 4,559,465 SNPs. In order to investigate the phenomenon of genetic admixture between Slavic and Finnish-speaking populations, the obtained results were compared to the data on the Russian populations inhabiting the neighboring territories, Karels from Karelia and other North Eastern Europeans. Studying the gene pools of Russian populations with a genome-wide SNP panel is essential for cataloging their genetic diversity and identifying the distinct features of regional gene pools; in addition, it provides valuable data for practical pharmacogenomics and forensics. Using the principal component analysis, the ADMIXTURE method and D- and f3-statistics, we demonstrated that the gene pool of Tver Karels is closest to the gene pool of Karelian Karels, despite a long (300 to 500 years) history of living among the larger Russian population and the twentyfold population decline during the 20th century. At the same time, the gene pool of Tver Karels exhibits more pronounced similarity to the gene pool of the studied Russian populations than does any other Karelian population. The genetic admixture between Tver Russians and Tver Karels occurred due to a more intense gene flow from Russians to Karels whereas the gene flow from Karels to Russians was much weaker: Tver Russians turned out to be as genetically different from Karels as Pskov Russians. The genetic similarity of Tver Karels to Karelian Karels assessed with the autosomal SNP panel exhibits a slight shift towards the Russian gene pool and is consistent with the previously published analysis of Y-chromosome lineages in these populations that detected no admixture between Tver Karels and Russians.

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