scholarly journals Understanding the Hidden Complexity of Latin American Population Isolates

2018 ◽  
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.

scholarly journals Complex patterns of sex-biased demography in canines

2019 ◽  
Vol 286 (1903) ◽  
pp. 20181976 ◽  
Author(s):  
Tanya N. Phung ◽  
Robert K. Wayne ◽  
Melissa A. Wilson ◽  
Kirk E. Lohmueller
Keyword(s):  
Sequence Data ◽  
Demographic History ◽  
Multiple Paternity ◽  
Whole Genome Sequence ◽  
Evolutionary Time ◽  
Genetic Studies ◽  
History Of ◽  
Males And Females ◽  
Dog Domestication ◽  
Number Of Males

The demographic history of dogs is complex, involving multiple bottlenecks, admixture events and artificial selection. However, existing genetic studies have not explored variance in the number of reproducing males and females, and whether it has changed across evolutionary time. While male-biased mating practices, such as male-biased migration and multiple paternity, have been observed in wolves, recent breeding practices could have led to female-biased mating patterns in breed dogs. For example, breed dogs are thought to have experienced a popular sire effect, where a small number of males father many offspring with a large number of females. Here we use genetic variation data to test how widespread sex-biased mating practices in canines are during different evolutionary time points. Using whole-genome sequence data from 33 dogs and wolves, we show that patterns of diversity on the X chromosome and autosomes are consistent with a higher number of reproducing males than females over ancient evolutionary history in both dogs and wolves, suggesting that mating practices did not change during early dog domestication. By contrast, since breed formation, we found evidence for a larger number of reproducing females than males in breed dogs, consistent with the popular sire effect. Our results confirm that canine demography has been complex, with opposing sex-biased processes occurring throughout their history. The signatures observed in genetic data are consistent with documented sex-biased mating practices in both the wild and domesticated populations, suggesting that these mating practices are pervasive.

scholarly journals Complex introgression history of the erato-sara clade of Heliconius butterflies

2021 ◽  
Author(s):  
Yuttapong Thawornwattana ◽  
Fernando A. Seixas ◽  
Ziheng Yang ◽  
James Mallet
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Hybrid Origin ◽  
Ancestral Population ◽  
Ancestral Gene ◽  
Species Phylogeny ◽  
Full Likelihood ◽  
History Of

AbstractIntrogression plays a key role in adaptive evolution and species diversification in many groups of species including Heliconius butterflies. However, frequent hybridization and subsequent gene flow between species makes estimation of the species phylogeny challenging. Here, we infer species phylogeny and introgression events from whole-genome sequence data of six members of the erato-sara clade of Heliconius using a multispecies coalescent model with introgression (MSci) and an isolation-with-migration (IM) model. These approaches probabilistically capture the genealogical heterogeneity across the genome due to introgression and incomplete lineage sorting in a full likelihood framework. We detect robust signals of introgression across the genome, and estimate the direction, timing and magnitude of each introgression event. The results clarify several processes of speciation and introgression in the erato-sara group. In particular, we confirm ancestral gene flow between the sara clade and an ancestral population of H. telesiphe, a hybrid origin of H. hecalesia, and gene flow between the sister species H. erato and H. himera. The ability to confidently infer the presence, timing and magnitude of introgression events using genomic sequence data is helpful for understanding speciation in the presence of gene flow and will be useful for understanding the adaptive consequences of introgressed regions of the genome. Our analysis serves to highlight the power of full likelihood methods under the MSci model to the history of species divergence and cross-species introgression from genome-scale data.

scholarly journals Diverse demographic histories in a guild of hymenopteran parasitoids

2019 ◽  
Author(s):  
William Walton ◽  
Graham N Stone ◽  
Konrad Lohse
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Demographic History ◽  
Whole Genome Sequence ◽  
Parasitoid Wasps ◽  
Effective Population ◽  
Glacial Cycles ◽  
Genome Wide ◽  
History Of ◽  
Hymenopteran Parasitoids

AbstractSignatures of changes in population size have been detected in genome-wide variation in many species. However, the causes of such changes and the extent to which they are shared across co-distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles have been widely studied, little is known about the demographic history of refugial populations, and the extent and causes of demographic variation among codistributed species. We used whole genome sequence data to reconstruct and compare demographic histories during the Quaternary for Iberian refuge populations in a single ecological guild (seven species of chalcid parasitoid wasps associated with oak cynipid galls). We find support for large changes in effective population size (Ne) through the Pleistocene that coincide with major climate change events. However, there is little evidence that the timing, direction and magnitude of demographic change are shared across species, suggesting that demographic histories are largely idiosyncratic. Our results are compatible with the idea that specialist parasitoids attacking a narrow range of hosts experience greater fluctuations in Ne than generalists.

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

2022 ◽  
pp. 107405
Author(s):  
Julian F. Quintero-Galvis ◽  
Pablo Saenz-Agudelo ◽  
Guillermo C. Amico ◽  
Soledad Vazquez ◽  
Aaron B.A. Shafer ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Diversity ◽  
History Of

scholarly journals Genomic Evidences Support an Independent History of Grapevine Domestication in the Levant

2020 ◽  
Author(s):  
Aviad Sivan ◽  
Oshrit Rahimi ◽  
Mail Salmon-Divon ◽  
Ehud Weiss ◽  
Elyashiv Drori ◽  
...  
Keyword(s):  
Sequence Data ◽  
Genetic Load ◽  
Whole Genome Sequence ◽  
Local Varieties ◽  
Caucasus Region ◽  
Demographic Models ◽  
Comprehensive Survey ◽  
History Of ◽  
Distinct Lineage ◽  
Pedigree Relationship

AbstractThe ancient grapevines of the Levant have inspired beliefs and rituals in human societies which are still practiced today in religious and traditional ceremonies around the world. Despite their importance, the original Levantine wine-grapes varieties were lost due to cultural turnovers commencing in the 7th century CE, which lead to the collapse of a flourishing winemaking industry in this region. Recently, a comprehensive survey of feral grapevines was conducted in Israel in an attempt to identify local varieties, yet the origin of these domesticated accessions is unclear. Here we study the origin of Levantine grapevines using whole-genome sequence data generated for a diversity panel of wild and cultivated accessions. Comparison between Levantine and Eurasian grapevines indicated that the Levantine varieties represent a distinct lineage from the Eurasian varieties. Demographic models further supported this observation designating that domestication in the Caucasus region predated the emergence of the Levantine samples in circa 5000 years and that authentic descendants of ancient varieties are represented among the Levantine samples. We further explore the pedigree relationship among cultivated grapevines, identify footprints of selective sweeps, and estimate the extent of genetic load in each group. We conclude that the Levantine varieties are distinct from the Eurasian varieties and that resistance to disease and abiotic stress are key traits in the development of both Eurasian and Levantine varieties.

scholarly journals Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation

2017 ◽  
Author(s):  
Julien Jouganous ◽  
Will Long ◽  
Simon Gravel
Keyword(s):  
Diffusion Approximation ◽  
Sequence Data ◽  
Demographic History ◽  
Allele Frequencies ◽  
Human Sequence ◽  
Medical Study ◽  
Joint Frequency ◽  
Classical Models ◽  
History Of ◽  
Demographic Inference

AbstractUnderstanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution of allele frequencies, using forward simulation, coalescent theory, or the diffusion approximation, have been applied extensively for demographic inference, medical study design, and evolutionary studies. Here we propose a tractable model of ordinary differential equations for the evolution of allele frequencies that is closely related to the diffusion approximation but avoids many of its limitations and approximations. We show that the approach is typically faster, more numerically stable, and more easily generalizable than the state-of-the-art software implementation of the diffusion approximation. We present a number of applications to human sequence data, including demographic inference with a five-population joint frequency spectrum and a discussion of the transferability of demographic histories across populations.

scholarly journals Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation

2021 ◽  
Vol 288 (1961) ◽  
Author(s):  
Anna Brüniche-Olsen ◽  
Kenneth F. Kellner ◽  
Jerrold L. Belant ◽  
J. Andrew DeWoody
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Management Practices ◽  
Sequence Data ◽  
Extinction Risk ◽  
Conservation Status ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Habitat Availability

More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes ( N e ) and current genomic variability ( H ), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that N e and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.

scholarly journals Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

2020 ◽  
Author(s):  
Lisa Cooper ◽  
Lynsey Bunnefeld ◽  
Jack Hearn ◽  
James M Cook ◽  
Konrad Lohse ◽  
...  
Keyword(s):  
Gene Flow ◽  
Rain Forest ◽  
Sequence Data ◽  
Dry Forest ◽  
Whole Genome Sequence ◽  
Model Organisms ◽  
Eastern Coast ◽  
Population Divergence ◽  
Fig Wasp ◽  
History Of

AbstractPopulation divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide datasets allows discrimination between alternative scenarios for these processes even in non-model taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum (bSFS), the second on the Pairwise Sequentially Markovian Coalescent (PSMC)) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia, and are separated into northern and southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of post divergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, non-model organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.

scholarly journals Whole genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

2015 ◽  
Author(s):  
PingHsun Hsieh ◽  
Krishna R Veeramah ◽  
Joseph Lachance ◽  
Sarah A Tishkoff ◽  
Jeffrey D Wall ◽  
...  
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Muscle Development ◽  
Demographic History ◽  
Single Pulse ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Anatomically Modern Humans ◽  
History Of ◽  
African Pygmies

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 years ago. We also find that bi-directional asymmetric gene-flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

scholarly journals Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations

2019 ◽  
Author(s):  
Haige Han ◽  
Kenneth Bryan ◽  
Wunierfu Shiraigol ◽  
Dongyi Bai ◽  
Yiping Zhao ◽  
...  
Keyword(s):  
Sequence Data ◽  
Genomic Diversity ◽  
Data Sets ◽  
Domestic Horse ◽  
Snp Data ◽  
Genome Wide ◽  
History Of ◽  
Genomic Characterization ◽  
Mongolian Horse ◽  
Free Ranging

Abstract The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that represent 5 distinct populations. These animals were genotyped for 670K SNPs and the data were analyzed in conjunction with 35K SNP data for 35 distinct breeds. Analyses of these integrated SNP data sets demonstrated that the Chinese Mongolian populations were genetically distinct from other modern horse populations. In addition, compared to other domestic horse breeds, the Chinese Mongolian horse populations exhibited relatively high genomic diversity. These results suggest that, in genetic terms, extant Chinese Mongolian horses may be the most similar modern populations to the animals originally domesticated in this region of Asia. Chinese Mongolian horse populations may therefore retain ancestral genetic variants from the earliest domesticates. Further genomic characterization of these populations in conjunction with archaeogenetic sequence data should be prioritized for understanding recent horse evolution and the domestication process that has led to the wealth of diversity observed in modern global horse breeds.

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