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 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 Inference of complex population histories using whole-genome sequences from multiple populations

2019 ◽  
Vol 116 (34) ◽  
pp. 17115-17120 ◽  
Author(s):  
Matthias Steinrücken ◽  
Jack Kamm ◽  
Jeffrey P. Spence ◽  
Yun S. Song
Keyword(s):  
Sequence Data ◽  
Model Complexity ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
East Asians ◽  
Multiple Populations ◽  
Demographic Models ◽  
Dna Sequence Data ◽  
Complex Population ◽  
And Migration

There has been much interest in analyzing genome-scale DNA sequence data to infer population histories, but inference methods developed hitherto are limited in model complexity and computational scalability. Here we present an efficient, flexible statistical method, diCal2, that can use whole-genome sequence data from multiple populations to infer complex demographic models involving population size changes, population splits, admixture, and migration. Applying our method to data from Australian, East Asian, European, and Papuan populations, we find that the population ancestral to Australians and Papuans started separating from East Asians and Europeans about 100,000 y ago, and that the separation of East Asians and Europeans started about 50,000 y ago, with pervasive gene flow between all pairs of populations.

scholarly journals Inversions shape the divergence of Drosophila pseudoobscura and D. persimilis on multiple timescales

2019 ◽  
Author(s):  
Katharine L Korunes ◽  
Carlos A Machado ◽  
Mohamed AF Noor
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Whole Genome Sequence ◽  
Drosophila Pseudoobscura ◽  
Ancestral Polymorphism ◽  
Chromosomal Inversions ◽  
History Of ◽  
Ancient Gene

AbstractBy shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage-disequilibrium pre-speciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of chromosomal inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and D. persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between Drosophila pseudoobscura and D. persimilis over three distinct timescales: 1) pre-speciation segregation of ancestral polymorphism, 2) post-speciation ancient gene flow, and 3) recent gene flow. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in similar datasets in other systems.

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.

scholarly journals The comparative genomics and complex population history ofPapiobaboons

2019 ◽  
Vol 5 (1) ◽  
pp. eaau6947 ◽  
Author(s):  
Jeffrey Rogers ◽  
Muthuswamy Raveendran ◽  
R. Alan Harris ◽  
Thomas Mailund ◽  
Kalle Leppälä ◽  
...  
Keyword(s):  
Sequence Data ◽  
Population History ◽  
Whole Genome Sequence ◽  
Evolutionary Divergence ◽  
Papio Anubis ◽  
Phenotypic Differences ◽  
Extant Species ◽  
Complex Population ◽  
In The Wild ◽  
History Of

Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genusPapio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation ofPapiobaboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.

Genetic structure of the benthic amphipod Diporeia (Amphipoda: Pontoporeiidae) and its relationship to abundance in Lake Superior

2009 ◽  
Vol 66 (8) ◽  
pp. 1318-1327 ◽  
Author(s):  
Erik M. Pilgrim ◽  
Jill V. Scharold ◽  
John A. Darling ◽  
John R. Kelly
Keyword(s):  
Great Lakes ◽  
Dreissena Polymorpha ◽  
Sequence Data ◽  
Lake Superior ◽  
The Other ◽  
Dna Sequence Data ◽  
Population Structuring ◽  
History Of ◽  
Potential Population ◽  
Distinct Lineage

The freshwater amphipod Diporeia is a crucial part of the food web in the Laurentian Great Lakes, but has faced serious declines correlated with the invasion of zebra mussels ( Dreissena polymorpha ), except in Lake Superior, which has seen an increase in Diporeia abundance. Speculation on the mechanisms causing changes in Diporeia densities has not included the possibility of evolutionarily distinct lineages of Diporeia within the Great Lakes. In this study, we use cytochrome c oxidase subunit I (COI) DNA sequence data to investigate the evolutionary history of Lake Superior Diporeia relative to the other Great Lakes and consider potential population structuring within Lake Superior based upon depth or geography. Our analyses reveal that Lake Superior Diporeia represent a distinct lineage that diverged from populations of the other lakes at least several hundred thousand years ago. F statistics show that two localities within Lake Superior were significantly differentiated from all other locales, but analysis of molecular variance did not find significant structure based on depth or geography. Genetic diversity within Lake Superior was not correlated with depth, although abundance was significantly negatively correlated with increasing depth.

scholarly journals Inference of complex population histories using whole-genome sequences from multiple populations

2015 ◽  
Author(s):  
Matthias Steinrücken ◽  
Jack Kamm ◽  
Jeffrey P. Spence ◽  
Yun S. Song
Keyword(s):  
Sequence Data ◽  
Model Complexity ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
East Asians ◽  
Multiple Populations ◽  
Demographic Models ◽  
Dna Sequence Data ◽  
Complex Population ◽  
And Migration

AbstractThere has been much interest in analyzing genome-scale DNA sequence data to infer population histories, but inference methods developed hitherto are limited in model complexity and computational scalability. Here we present an efficient, flexible statistical method, diCal2, that can utilize whole-genome sequence data from multiple populations to infer complex demographic models involving population size changes, population splits, admixture, and migration. Applying our method to data from Australian, East Asian, European, and Papuan populations, we find that the population ancestral to Australians and Papuans started separating from East Asians and Europeans about 100,000 years ago, and that the separation of East Asians and Europeans started about 50,000 years ago, with pervasive gene flow between all pairs of populations.

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.

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