scholarly journals Population genetics reveals cryptic lineages and ongoing hybridization in a declining migratory fish species complex

2021 ◽  
Author(s):  
Quentin Rougemont ◽  
Charles Perrier ◽  
Anne-Laure Besnard ◽  
Isabelle Lebel ◽  
Yann Abdallah ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Demographic History ◽  
Life History Strategies ◽  
Secondary Contact ◽  
Allis Shad ◽  
Twaite Shad ◽  
Genetic Diversity And Structure ◽  
Demographic Processes ◽  
Hybridization And Introgression

AbstractDeciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression, of two species of anadromous fish with contrasted life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species allis shad that disperse stronger distance compared to the iteroparous species, twaite shad. Individuals caught at sea were assigned at the river level for twaite shad and at the region level for allis shad. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species implicated historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence of contemporary hybridization and introgression between both species. Besides, our results support the existence of cryptic species in the Mediterranean sea. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species’ populations and their hybridization should be carefully considered while implementing conservation programs.

scholarly journals The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead (Oncorhynchus mykiss) Populations across the Elwha River Watershed

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 89
Author(s):  
Alexandra K. Fraik ◽  
John R. McMillan ◽  
Martin Liermann ◽  
Todd Bennett ◽  
Michael L. McHenry ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Oncorhynchus Mykiss ◽  
Population Genetic ◽  
Dam Removal ◽  
Life History Strategies ◽  
Dam Construction ◽  
Elwha River ◽  
Population Genetic Diversity ◽  
Genetic Diversity And Structure

Dam construction and longitudinal river habitat fragmentation disrupt important life histories and movement of aquatic species. This is especially true for Oncorhynchus mykiss that exhibits both migratory (steelhead) and non-migratory (resident rainbow) forms. While the negative effects of dams on salmonids have been extensively documented, few studies have had the opportunity to compare population genetic diversity and structure prior to and following dam removal. Here we examine the impacts of the removal of two dams on the Elwha River on the population genetics of O. mykiss. Genetic data were produced from >1200 samples collected prior to dam removal from both life history forms, and post-dam removal from steelhead. We identified three genetic clusters prior to dam removal primarily explained by isolation due to dams and natural barriers. Following dam removal, genetic structure decreased and admixture increased. Despite large O. mykiss population declines after dam construction, we did not detect shifts in population genetic diversity or allele frequencies of loci putatively involved in migratory phenotypic variation. Steelhead descendants from formerly below and above dammed populations recolonized the river rapidly after dam removal, suggesting that dam construction did not significantly reduce genetic diversity underlying O. mykiss life history strategies. These results have significant evolutionary implications for the conservation of migratory adaptive potential in O. mykiss populations above current anthropogenic barriers.

scholarly journals Variation in Demography and Life-History Strategies Across the Range of a Declining Mountain Bird Species

2021 ◽  
Vol 9 ◽  
Author(s):  
Arnaud G. Barras ◽  
Sébastien Blache ◽  
Michael Schaub ◽  
Raphaël Arlettaz
Keyword(s):  
Life History ◽  
Environmental Change ◽  
Life History Traits ◽  
Local Population ◽  
Bird Species ◽  
Life History Strategies ◽  
Adult Survival ◽  
Northwestern Part ◽  
European Alps ◽  
Demographic Processes

Species- and population-specific responses to their environment may depend to a large extent on the spatial variation in life-history traits and in demographic processes of local population dynamics. Yet, those parameters and their variability remain largely unknown for many cold-adapted species, which are exposed to particularly rapid rates of environmental change. Here, we compared the demographic traits and dynamics for an emblematic bird species of European mountain ecosystems, the ring ouzel (Turdus torquatus). Using integrated population models fitted in a Bayesian framework, we estimated the survival probability, productivity and immigration of two populations from the Western European Alps, in France (over 11 years) and Switzerland (over 6 years). Juvenile apparent survival was lower and immigration rate higher in the Swiss compared to the French population, with the temporal variation in population growth rate driven by different demographic processes. Yet, when compared to populations in the northwestern part of the range, in Scotland, these two Alpine populations both showed a much lower productivity and higher adult survival, indicating a slower life-history strategy. Our results suggest that demographic characteristics can substantially vary across the discontinuous range of this passerine species, essentially due to contrasted, possibly locally evolved life-history strategies. This study therefore raises the question of whether flexibility in life-history traits is widespread among boreo-alpine species and if it might provide adaptive potential for coping with current environmental change.

Fine-scale structure within a Trillium maculatum (Liliaceae) population

Botany ◽  
2009 ◽  
Vol 87 (3) ◽  
pp. 223-230 ◽  
Author(s):  
Alana N. Walker ◽  
Stephanie A. Foré ◽  
Beverly Collins
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Vegetative Reproduction ◽  
Flowering Plants ◽  
Life History Stages ◽  
Genetic Diversity And Structure ◽  
Random Expectation ◽  
Perennial Herbs

In long-lived ant-dispersed perennial herbs of mesic forests, interactions among fruiting plants, seed dispersal, and plant mortality over life-history stages can create demographic and genetic structure. We investigated whether there was nonrandom variation in the distributions of individuals and in genetic diversity within and among life-history stages of the forest herb Trillium maculatum Raf. (Liliaceae). In 2002 and 2004, all T. maculatum plants in a 5 m × 5 m plot (1572 and 1379 individuals, respectively) were mapped and classified as seedling, one-leaf, three-leaf nonflowering, or flowering. Spatial distributions of plants within and across life-history stages were tested against random expectation. Allozyme analysis of 262 individuals from three life-history stages was used to assess genetic diversity and structure in 2004. The number of seedlings and the proportion of one-leaf plants differed between years, but the proportions of three-leaf nonflowering and flowering plants remained the same. There was little evidence of vegetative reproduction, but heterozygosity was low and there was evidence of inbreeding. Seedlings were clumped around flowering plants at distances up to 50 cm and one-leaf plants were clumped at distances up to 100 cm. There were no apparent genetic differences among life-history stages, nor any apparent spatial genetic structure among all sampled individuals. These results, like those of other demographic and allozyme studies of Trillium species, can be explained by restricted dispersal and random mortality.

scholarly journals High genetic diversity and strong genetic structure of Strongyllodes variegatus populations in oilseed rape production areas of China

2020 ◽  
Author(s):  
HaiXia Zhan ◽  
ZhongPing Hao ◽  
Rui Tang ◽  
LiNi Zhu ◽  
JingJiang Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Oilseed Rape ◽  
Demographic History ◽  
Insect Pest ◽  
Distribution Analysis ◽  
Geographical Distance ◽  
Geographical Regions ◽  
Genetic Diversity And Structure ◽  
Production Areas

Abstract Background: Strongyllodes variegatus (Fairmaire) is a major insect pest of oilseed rape in China. Despite its economic importance, the contribution of its population genetics in the development of any suitable protection control strategy for the management of oilseed rape crops is poorly studied. It is a much urgent need to prevent its spread to the rest of the world. Results: Using the sequences of mitochondrial DNA cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) as genetic markers, we analyzed the population genetic diversity and structure of 437 individuals collected from 15 S. variegates populations located in different oilseed rape production areas in China. In addition, we estimated the demographic history using neutrality test and mismatch distribution analysis. The high level of genetic diversity was detected among the COI and Cytb sequences of S. variegates. The population structure analyses strongly suggested three distinct genetic and geographical regions in China with limited gene flow. The Mantel test showed that the genetic distance was greatly influenced by the geographical distance. The demographic analyses showed that S. variegates had experienced population fluctuation during the Pleistocene Epoch, which was likely to be related to the climatic changes.Conclusion: Overall, these results demonstrate that the strong genetic structure of S. variegates populations in China, which is attributed by the isolation through the geographical distance among populations, their weak flight capacity and subsequent adaptation to the regional ecological conditions.

scholarly journals Human demographic history has amplified the effects of background selection across the genome

2017 ◽  
Author(s):  
Raul Torres ◽  
Zachary A. Szpiech ◽  
Ryan D. Hernandez
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Demographic History ◽  
Background Selection ◽  
Dynamic Changes ◽  
Genome Wide ◽  
Neutral Genetic Diversity ◽  
African Populations ◽  
Demographic Processes ◽  
Non Equilibrium

AbstractNatural populations often grow, shrink, and migrate over time. Demographic processes such as these can impact genome-wide levels of genetic diversity. In addition, genetic variation in functional regions of the genome can be altered by natural selection, which drives adaptive mutations to higher frequencies or purges deleterious ones. Such selective processes impact not only the sites directly under selection but also nearby neutral variation through genetic linkage through processes referred to as genetic hitch-hiking in the context of positive selection and background selection (BGS) in the context of purifying selection. While there is extensive literature examining the impact of selection at linked sites at demographic equilibrium, less is known about how non-equilibrium demographic processes impact the effects of hitchhiking and BGS. Utilizing a global sample of human whole-genome sequences from the Thousand Genomes Project and extensive simulations, we investigate how non-equilibrium demographic processes magnify and dampen the consequences of selection at linked sites across the human genome. When binning the genome by inferred strength of BGS, we observe that, compared to Africans, non-African populations have experienced larger proportional decreases in neutral genetic diversity in such regions. We replicate these findings in admixed populations by showing that non-African ancestral components of the genome have also been impacted more severely in these regions. We attribute these differences to the strong, sustained/recurrent population bottlenecks that non-Africans experienced as they migrated out of Africa and throughout the globe. Furthermore, we observe a strong correlation between FST and inferred strength of BGS, suggesting a stronger rate of genetic drift. Forward simulations of human demographic history with a model of BGS support these observations. Our results show that non-equilibrium demography significantly alters the consequences selection at linked sites and support the need for more work investigating the dynamic process of multiple evolutionary forces operating in concert.Author summaryPatterns of genetic diversity within a species are affected at broad and fine scales by population size changes (“demography”) and natural selection. From both population genetics theory and observation of genomic sequence data, it is known that demography can alter genome-wide average neutral genetic diversity. Additionally, natural selection can affect neutral genetic diversity regionally across the genome via selection at linked sites. During this process, natural selection acting on adaptive or deleterious variants in the genome will also impact diversity at nearby neutral sites due to genetic linkage. However, less is well known about the dynamic changes to diversity that occur in regions impacted by selection at linked sites when a population undergoes a size change. We characterize these dynamic changes using thousands of human genomes and find that the population size changes experienced by humans have shaped the consequences of linked selection across the genome. In particular, population contractions, such as those experienced by non-Africans, have disproportionately decreased neutral diversity in regions of the genome inferred to be under strong background selection (i.e., selection at linked sites that is caused by natural selection acting on deleterious variants), resulting in large differences between African and non-African populations.

scholarly journals Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data

2020 ◽  
Author(s):  
Lisa N. Barrow ◽  
Emanuel Masiero da Fonseca ◽  
Coleen E. P. Thompson ◽  
Bryan C. Carstens
Keyword(s):  
Machine Learning ◽  
Genetic Diversity ◽  
Life History ◽  
Life History Traits ◽  
Phylogenetic Signal ◽  
Species Traits ◽  
Intraspecific Diversity ◽  
Northern Latitudes ◽  
Demographic Processes ◽  
Salamander Species

AbstractThe growing availability of genetic datasets, in combination with machine learning frameworks, offer great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What determines intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative importance of these factors varies across taxonomic and geographic scales. Furthermore, interpreting the influence of numerous, potentially correlated variables is difficult with traditional statistical approaches. To address these challenges, we combined repurposed data with machine learning and investigated predictors of genetic diversity, focusing on Nearctic amphibians as a case study. We aggregated species traits, range characteristics, and >42,000 genetic sequences for 299 species using open-access scripts and various databases. After identifying important predictors of nucleotide diversity with random forest regression, we conducted follow-up analyses to examine the roles of phylogenetic history, geography, and demographic processes on intraspecific diversity. Although life history traits were not important predictors for this dataset, we found significant phylogenetic signal in genetic diversity within amphibians. We also found that salamander species at northern latitudes contain lower genetic diversity. Data repurposing and machine learning provide valuable tools for detecting patterns with relevance for conservation, but concerted efforts are needed to compile meaningful datasets with greater utility for understanding global biodiversity.

scholarly journals Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation

Diversity ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 62 ◽  
Author(s):  
Yasmin G. S. Carvalho ◽  
Luciana C. Vitorino ◽  
Ueric J. B. de Souza ◽  
Layara A. Bessa
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Plant Species ◽  
Life History Traits ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Molecular Techniques ◽  
Fixation Index ◽  
Relative Contribution ◽  
Recent Trends

Genetic diversity and its distribution, both within and between populations, may be determined by micro-evolutionary processes, such as the demographic history of populations, natural selection, and gene flow. In plants, indices of genetic diversity (e.g., k, h and π) and structure (e.g., FST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. We also used phylogenetic modeling to assess the relative contribution of relatedness or ecological and reproductive characters to the genetic diversity of plants. We postulated that genetic diversity could be defined not only by microevolutionary factors and life history traits, but also by relatedness, so that species more closely related phylogenetically would have similar genetic diversities. We found a clear tendency for an increase in the number of studies over time, confirming the hypothesis that the advances in the area of molecular genetics have supported the accumulation of data on the genetic diversity of plants. However, we found that the vast majority of these data have been produced by Chinese authors, and refer specifically to populations of Chinese plants. Most of the data on genetic diversity have been obtained for species in the International Union for Conservation of Nature (IUCN) category NE (Not Evaluated), which indicates a relative lack of attention on threatened species. In general, we observed very high FST values in the groups analyzed and, as we focused primarily on species that have not been evaluated by the IUCN, the number of plant species that are threatened with extinction may be much greater than that indicated by the listing of this organization. We also found that the number of haplotypes (k) was influenced by the type of geographic distribution of the plant, while haplotype diversity (h) was affected by the type of flower, and the fixation index (FST), by the type of habitat. The plant species most closely-related phylogenetically have similar levels of genetic diversity. Overall, then, it will important to consider phylogenetic dependence in future studies that evaluate the effects of life-history traits on plant genetic diversity.

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