scholarly journals Long distance migration is a major factor driving local adaptation at continental scale in Coho Salmon

2021 ◽  
Author(s):  
Quentin Rougemont ◽  
Amanda Xuereb ◽  
Xavier Dallaire ◽  
Jean-Sebastien Moore ◽  
Eric Normandeau ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Evolutionary Biology ◽  
Coho Salmon ◽  
Demographic History ◽  
Long Distance ◽  
Homing Behavior ◽  
Association Analyses ◽  
Continental Scale ◽  
History Of ◽  
Genomic Basis

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species homing behavior may promote the establishment of local adaptation. We genotyped 7,829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. Results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidates SNP associated with long distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

scholarly journals Long distance migration is a major factor driving local adaptation at continental scale in Coho Salmon

2022 ◽  
Author(s):  
Quentin Rougemont ◽  
Amanda Xuereb ◽  
Xavier Dallaire ◽  
Jean‐Sébastien Moore ◽  
Eric Normandeau ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Coho Salmon ◽  
Long Distance ◽  
Continental Scale

scholarly journals Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1910 ◽  
Author(s):  
Quentin Rougemont ◽  
Camille Roux ◽  
Samuel Neuenschwander ◽  
Jerome Goudet ◽  
Sophie Launey ◽  
...  
Keyword(s):  
Gene Flow ◽  
Life Histories ◽  
Evolutionary Biology ◽  
Demographic History ◽  
Secondary Contact ◽  
Isolation With Migration ◽  
Genome Wide Data ◽  
History Of ◽  
Parameterized Model ◽  
Approximate Bayesian

Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey(L. planeri)show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.

scholarly journals Efficiently inferring the demographic history of many populations with allele count data

2018 ◽  
Author(s):  
John A. Kamm ◽  
Jonathan Terhorst ◽  
Richard Durbin ◽  
Yun S. Song
Keyword(s):  
Evolutionary Biology ◽  
Demographic History ◽  
Directed Acyclic Graphs ◽  
Population History ◽  
Demographic Model ◽  
Natural Processes ◽  
Acyclic Graphs ◽  
Open Source Software Package ◽  
History Of ◽  
Allele Count

AbstractThe sample frequency spectrum (SFS), or histogram of allele counts, is an important summary statistic in evolutionary biology, and is often used to infer the history of population size changes, migrations, and other demographic events affecting a set of populations. The expected multipopulation SFS under a given demographic model can be efficiently computed when the populations in the model are related by a tree, scaling to hundreds of populations. Admixture, back-migration, and introgression are common natural processes that violate the assumption of a tree-like population history, however, and until now the expected SFS could be computed for only a handful of populations when the demographic history is not a tree. In this article, we present a new method for efficiently computing the expected SFS and linear functionals of it, for demographies described by general directed acyclic graphs. This method can scale to more populations than previously possible for complex demographic histories including admixture. We apply our method to an 8-population SFS to estimate the timing and strength of a proposed “basal Eurasian” admixture event in human history. We implement and release our method in a new open-source software package momi2.

scholarly journals Eocene origin, Miocene diversification and intercontinental dispersal of the genus Drosera (Droseraceae)

2020 ◽  
Author(s):  
Sandeep Sen ◽  
Neha Tiwari ◽  
R Ganesan
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Charles Darwin ◽  
Long Distance ◽  
Data Set ◽  
Origin And Evolution ◽  
Fossil Calibration ◽  
History Of ◽  
Nuclear Its

AbstractResolving the evolutionary history of plant carnivory is of great interest to biologists throughout the world. Among the carnivorous plants, Genus Drosera (Droseraceae) is highly diverse with a wide pantropical distribution. Despite being a group of interest for evolutionary biology studies since the time of Charles Darwin, the historical biogeography of this group remains poorly understood. In this study, with an improved species sampling from Genbank, we present a reanalyzed phylogenetic hypothesis of the genus Drosera. We developed a dated molecular phylogeny of Drosera from DNA sequences of nuclear ITS and chloroplast rbcL genes. Divergence times were estimated on the combined dataset using an uncorrelated lognormal relaxed clock model and a known fossil calibration implemented in BEAST. The maximum clade credibility tree was then used for ancestral range estimations using DEC+J model implemented in BioGeoBEARS. Our analysis suggests that Drosera evolved during the Mid Eocene 36 Ma [95% HPD: 49.5-26] and have diversified and dispersed from the late Miocene onwards. Ancestral areas estimated using the DEC+J models suggest an African origin followed major radiation within Australia. Diversification in Drosera is temporally congruent with the prevailing drier conditions during the Miocene. From Miocene, grasslands and open habitats dominated across continents and might have provided ecological opportunities for their dispersal and diversification. Several long-distance dispersals and range extensions and in situ radiations coinciding with the evolution of drier conditions can explain their extant distribution across continents. Overall our data set provides fresh insights into the biogeographic factors that shaped the origin and evolution of the genus Drosera.

scholarly journals Demographic history and genomics of local adaptation in blue tit populations

2019 ◽  
Author(s):  
Perrier Charles ◽  
Rougemont Quentin ◽  
Charmantier Anne
Keyword(s):  
Local Adaptation ◽  
Evolutionary Biology ◽  
Demographic History ◽  
Habitat Type ◽  
Divergent Selection ◽  
Effective Population ◽  
Blue Tit ◽  
Demographic Modeling ◽  
Local Selection ◽  
Spatio Temporal

AbstractUnderstanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.004 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long-lasting gene flow between populations, inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migrations, followed by isolation since the end of the last glaciation. Effective population sizes were overall large, yet smaller on the island than on the mainland. Weak and non-parallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds, and were more often found in regions of low recombination as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.

Religious Norms, Human Capital, and Money Lending in Jewish European History

2011 ◽  
pp. 56-80 ◽  
Author(s):  
Maristella Botticini ◽  
Zvi Eckstein
Keyword(s):  
Human Capital ◽  
Jewish History ◽  
Southern Italy ◽  
European History ◽  
Long Distance ◽  
Common View ◽  
Jewish Diaspora ◽  
Medieval Europe ◽  
History Of ◽  
Muslim Spain

Circa 1000, the main occupations of the large Jewish community in Muslim Spain and of the small Jewish communities in southern Italy, France, and Germany were local trade and long-distance commerce, as well as handicrafts. A common view states that the usury ban on Christians segregated European Jews into money lending. A similar view contends that the Jews were forced to become money lenders because they were not permitted to own land, and therefore, they were banned from farming. This article offers an alternative argument which is consistent with the main features that mark the history of the Jews: the Jews in medieval Europe voluntarily selected themselves into money lending because they had the key assets for being successful players in credit markets. After providing an overview of Jewish history during 70–1492, it discusses religious norms and human capital in Jewish European history, Jews in the Talmud era, the massive transition of the Jews from farming to crafts and trade, the golden age of the Jewish diaspora (ca. 800–ca. 1250), and the legacy of Judaism.

scholarly journals Influence of environmental factors on the genetic variation of the aquatic macrophyte Ranunculus subrigidus on the Qinghai-Tibetan Plateau

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhigang Wu ◽  
Xinwei Xu ◽  
Juan Zhang ◽  
Gerhard Wiegleb ◽  
Hongwei Hou
Keyword(s):  
Genetic Diversity ◽  
Tibetan Plateau ◽  
Environmental Factors ◽  
Local Adaptation ◽  
Aquatic Macrophyte ◽  
Spatial Genetic Structure ◽  
Long Distance ◽  
Elevation Gradients ◽  
Mantel Tests ◽  
Genetic Patterns

Abstract Background Due to the environmental heterogeneity along elevation gradients, alpine ecosystems are ideal study objects for investigating how ecological variables shape the genetic patterns of natural species. The highest region in the world, the Qinghai-Tibetan Plateau, is a hotspot for the studies of evolutionary processes in plants. Many large rivers spring from the plateau, providing abundant habitats for aquatic and amphibious organisms. In the present study, we examined the genetic diversity of 13 Ranunculus subrigidus populations distributed throughout the plateau in order to elucidate the relative contribution of geographic distance and environmental dissimilarity to the spatial genetic pattern. Results A relatively low level of genetic diversity within populations was found. No spatial genetic structure was suggested by the analyses of molecular variance, Bayesian clustering analysis and Mantel tests. Partial Mantel tests and multiple matrix regression analysis showed a significant influence of the environment on the genetic divergence of the species. Both climatic and water quality variables contribute to the habitat heterogeneity of R. subrigidus populations. Conclusions Our results suggest that historical processes involving long-distance dispersal and local adaptation may account for the genetic patterns of R. subrigidus and current environmental factors play an important role in the genetic differentiation and local adaptation of aquatic plants in alpine landscapes.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

COMBINING ORAL TRADITIONS AND BAYESIAN CHRONOLOGICAL MODELING TO UNDERSTAND VILLAGE DEVELOPMENT IN THE GULF OF PAPUA (PAPUA NEW GUINEA)

Radiocarbon ◽  
2021 ◽  
pp. 1-21
Author(s):  
Chris Urwin ◽  
Quan Hua ◽  
Henry Arifeae
Keyword(s):  
Papua New Guinea ◽  
New Guinea ◽  
Oral Traditions ◽  
Long Distance ◽  
Spatial History ◽  
The Past ◽  
History Of ◽  
Gulf Of Papua ◽  
The Village

ABSTRACT When European colonists arrived in the late 19th century, large villages dotted the coastline of the Gulf of Papua (southern Papua New Guinea). These central places sustained long-distance exchange and decade-spanning ceremonial cycles. Besides ethnohistoric records, little is known of the villages’ antiquity, spatiality, or development. Here we combine oral traditional and 14C chronological evidence to investigate the spatial history of two ancestral village sites in Orokolo Bay: Popo and Mirimua Mapoe. A Bayesian model composed of 35 14C assays from seven excavations, alongside the oral traditional accounts, demonstrates that people lived at Popo from 765–575 cal BP until 220–40 cal BP, at which time they moved southwards to Mirimua Mapoe. The village of Popo spanned ca. 34 ha and was composed of various estates, each occupied by a different tribe. Through time, the inhabitants of Popo transformed (e.g., expanded, contracted, and shifted) the village to manage social and ceremonial priorities, long-distance exchange opportunities and changing marine environments. Ours is a crucial case study of how oral traditional ways of understanding the past interrelate with the information generated by Bayesian 14C analyses. We conclude by reflecting on the limitations, strengths, and uncertainties inherent to these forms of chronological knowledge.

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