Complex patterns of sex-biased demography in canines

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.

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Diverse demographic histories in a guild of hymenopteran parasitoids

10.1101/2019.12.20.884403 ◽

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.

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Understanding the Hidden Complexity of Latin American Population Isolates

10.1101/340158 ◽

2018 ◽

Cited By ~ 1

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.

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The Genetic History of France

10.1101/712497 ◽

2019 ◽

Author(s):

Aude Saint Pierre ◽

Joanna Giemza ◽

Matilde Karakachoff ◽

Isabel Alves ◽

Philippe Amouyel ◽

...

Keyword(s):

Genetic Structure ◽

Demographic History ◽

Migration Routes ◽

Effective Population ◽

Genetic Studies ◽

Independent Population ◽

Genome Wide Data ◽

Population Sizes ◽

History Of ◽

Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

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Characterizing mutagenic effects of recombination through a sequence-level genetic map

Science ◽

10.1126/science.aau1043 ◽

2019 ◽

Vol 363 (6425) ◽

pp. eaau1043 ◽

Cited By ~ 62

Author(s):

Bjarni V. Halldorsson ◽

Gunnar Palsson ◽

Olafur A. Stefansson ◽

Hakon Jonsson ◽

Marteinn T. Hardarson ◽

...

Keyword(s):

Genetic Map ◽

Meiotic Recombination ◽

De Novo ◽

Sequence Data ◽

Mutagenic Effect ◽

Whole Genome Sequence ◽

De Novo Mutation ◽

Base Pairs ◽

Males And Females ◽

Mutagenic Effects

Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.

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

10.1101/2020.07.11.198358 ◽

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.

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

10.1101/103275 ◽

2017 ◽

Cited By ~ 2

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.

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

10.1101/2020.02.21.959205 ◽

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.

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

10.1101/022194 ◽

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.

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Molecular phylogenetic, population genetic and demographic studies of Nodularia douglasiae and Nodularia breviconcha based on CO1 and 16S rRNA

Scientific Reports ◽

10.1038/s41598-020-72015-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Eun Hwa Choi ◽

Gyeongmin Kim ◽

Seung Hyun Cha ◽

Jun-Sang Lee ◽

Shi Hyun Ryu ◽

...

Keyword(s):

16S Rrna ◽

East Asia ◽

Korean Peninsula ◽

Population Genetic ◽

Demographic History ◽

Taxonomic Status ◽

Genetic Studies ◽

Molecular Phylogenetic ◽

History Of ◽

Independent Species

Abstract Freshwater mussels belonging to the genus Nodularia (Family Unionidae) are known to be widely distributed in East Asia. Although phylogenetic and population genetic studies have been performed for these species, there still remain unresolved questions in their taxonomic status and biogeographic distribution pathways. Here, the nucleotide sequences of CO1 and 16S rRNA were newly determined from 86 N. douglasiae and 83 N. breviconcha individuals collected on the Korean Peninsula. Based on these data, we revealed the following results: (1) N. douglasiae can be divided into the three genetic clades of A (only found in Korean Peninsula), B (widely distributed in East Asia), and C (only found in the west of China and Russia), (2) the clade A is not an independent species but a concrete member of N. douglasiae given the lack of genetic differences between the clades A and B, and (3) N. breviconcha is not a subspecies of N. douglasiae but an independent species apart from N. douglasiae. In addition, we suggested the plausible scenarios of biogeographic distribution events and demographic history of Nodularia species.

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The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenic position of Lobotiformes and biological conservation

10.1101/787077 ◽

2019 ◽

Author(s):

Shuai Sun ◽

Yue Wang ◽

Xiao Du ◽

Lei Li ◽

Xiaoning Hong ◽

...

Keyword(s):

Demographic History ◽

Whole Genome Sequence ◽

Biological Conservation ◽

Whole Genome ◽

Effective Population ◽

Phylogenetic Tree Analysis ◽

Pigment Synthesis ◽

Long Time ◽

History Of ◽

Immune Related Genes

AbstractMekong tiger perch (Datnioides undecimradiatus) is one ornamental fish and a vulnerable species, which belongs to order Lobotiformes. Here, we report a ∼595 Mb D. undecimradiatus genome, which is the first whole genome sequence in the order Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that Lobotiformes and Sciaenidae are closer than Tetraodontiformes, resolving a long-time dispute. We depicted the pigment synthesis pathway in Mekong tiger perch and result confirmed that this pathway had evolved from the shared whole genome duplication. We also estimated the demographic history of Mekong tiger perch, showing the effective population size suffered a continuous reduction possibly related to the contraction of immune-related genes. Our study provided a reference genome resource for the Lobotiformes, as well as insights into the phylogeny of Eupercaria and biological conservation.

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