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 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 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 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 The counteracting effects of demography on functional genomic variation: the Roma paradigm

2021 ◽  
Author(s):  
Neus Font-Porterias ◽  
Rocio Caro-Consuegra ◽  
Marcel Lucas-Sánchez ◽  
Marie Lopez ◽  
Aaron Giménez ◽  
...  
Keyword(s):  
Gene Flow ◽  
Rare Variants ◽  
Demographic History ◽  
Genomic Variation ◽  
Human Populations ◽  
History Plays ◽  
High Coverage ◽  
Roma Population ◽  
Genome Wide ◽  
Whole Exome

Abstract Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomes is not fully resolved in human populations. Here we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events and extensive gene flow from non-Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homozygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from pre-admixture adaptation in the Roma population sources. The present study shows how two demographic forces, bottlenecks and admixture, act in opposite directions and have long-term balancing effects on the Roma genomes. Understanding how demography and gene flow shape the genome of an admixed population provides an opportunity to elucidate how genomic variation is modelled in human populations.

scholarly journals Selection and gene flow define polygenic barriers between incipient butterfly species

2020 ◽  
Author(s):  
Steven M. Van Belleghem ◽  
Jared M. Cole ◽  
Gabriela Montejo-Kovacevich ◽  
Caroline N. Bacquet ◽  
W. Owen McMillan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Recombination Rate ◽  
Genomic Variation ◽  
Species Boundaries ◽  
Secondary Contact ◽  
Butterfly Species ◽  
Demographic Modeling ◽  
Incipient Species ◽  
Genome Wide ◽  
Genomic Divergence

AbstractCharacterizing the genetic architecture of species boundaries remains a difficult task. Hybridizing species provide a powerful system to identify the factors that shape genomic variation and, ultimately, identify the regions of the genome that maintain species boundaries. Unfortunately, complex histories of isolation, admixture and selection can generate heterogenous genomic landscapes of divergence which make inferences about the regions that are responsible for species boundaries problematic. However, as the signal of admixture and selection on genomic loci varies with recombination rate, their relationship can be used to infer their relative importance during speciation. Here, we explore patterns of genomic divergence, admixture and recombination rate among hybridizing lineages across the Heliconius erato radiation. We focus on the incipient species, H. erato and H. himera, and distinguish the processes that drive genomic divergence across three contact zones where they frequently hybridize. Using demographic modeling and simulations, we infer that periods of isolation and selection have been major causes of genome-wide correlation patterns between recombination rate and divergence between these incipient species. Upon secondary contact, we found surprisingly highly asymmetrical introgression between the species pair, with a paucity of H. erato alleles introgressing into the H. himera genomes. We suggest that this signal may result from a current polygenic species boundary between the hybridizing lineages. These results contribute to a growing appreciation for the importance of polygenic architectures of species boundaries and pervasive genome-wide selection during the early stages of speciation with gene flow.

scholarly journals Spatial and host related genomic variation in partially sympatric cactophagous moth species

2021 ◽  
Author(s):  
Daniel Poveda-Martínez ◽  
Laura Varone ◽  
Malena Fuentes Corona ◽  
Stephen Hight ◽  
Guillermo Logarzo ◽  
...  
Keyword(s):  
Gene Flow ◽  
Host Plants ◽  
Genomic Variation ◽  
South American ◽  
Moth Population ◽  
Cactoblastis Cactorum ◽  
Genome Wide ◽  
Mitochondrial Data ◽  
Distribution Ranges ◽  
Host Plant Use

Surveys of patterns of genetic variation in natural sympatric and allopatric populations of recently diverged species are necessary to understand the processes driving intra and interspecific diversification. The South American moths Cactoblastis cactorum, Cactoblastis doddi and Cactoblastis bucyrus are specialized in the use of cacti as host plants. These species have different distribution ranges and differ in patterns of host plant use. However, there are areas in which their ranges overlap, as in northwestern Argentina, where they are largely sympatric. Using a combination of genome-wide SNPs and mitochondrial data we investigated the phylogeographic patterns of these cactophilic moths and searched for footprints of hybridization. Additionally, we evaluated a moth population feeding on Cleistocactus baumannii, a plant never reported as a host for the genus. We identified three well delimited species and detected signs of historical gene flow. Our survey also revealed intraspecific geographic structure in both C. doddi and C. cactorum and showed that the moth population feeding on C. baumannii may be considered as conspecific to C. bucyrus. Overall, our results indicated historical events of genetic interchange occurred in Cactoblastis cactophagous moths, but host plants likely played an important role during divergence limiting gene flow across species.

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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