Cryptic Lineages and a Population Dammed to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

2019 ◽  
Vol 110 (5) ◽  
pp. 535-547 ◽  
Author(s):  
Amanda S Ackiss ◽  
Binh T Dang ◽  
Christopher E Bird ◽  
Ellen E Biesack ◽  
Phen Chheng ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Natural Populations ◽  
Principal Component ◽  
Flood Pulse ◽  
Mekong River ◽  
Effective Population ◽  
Long Distance ◽  
Genetic Lineages ◽  
Low Genetic Diversity ◽  
Population Size Estimates

Abstract An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller subpopulations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development—the Mekong River basin. Our results revealed the presence of 2 highly divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal component analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically important resources.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

Monitoring of the genetic structure of natural populations: change of the effective population size and inversion polymorphism in Drosophila subobscura

Genetica ◽  
2007 ◽  
Vol 133 (1) ◽  
pp. 57-63 ◽  
Author(s):  
Marina Stamenkovic-Radak ◽  
Gordana Rasic ◽  
Tatjana Savic ◽  
Predrag Kalajdzic ◽  
Zorana Kurbalija ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Natural Populations ◽  
Drosophila Subobscura ◽  
Inversion Polymorphism ◽  
Effective Population ◽  
And Inversion

Genetic diversity and population genetic structure in fragmented Allocasuarina verticillata (Allocasuarinaceae) – implications for restoration

2011 ◽  
Vol 59 (8) ◽  
pp. 770 ◽  
Author(s):  
Linda M. Broadhurst
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Gene Diversity ◽  
Natural Populations ◽  
Long Distance ◽  
Study Region ◽  
Allocasuarina Verticillata ◽  
Seed Crops

Vegetation restoration in fragmented regions is constrained by limited supplies of high quality seed and an understanding of the scale over which seed can be moved without causing negative outcomes. ‘Local’ seed is often prescribed for restoration but in fragmented landscapes this restricts collecting to small, inbred populations. Six polymorphic microsatellites were used to examine genetic diversity and population genetic structure in seed collected from 18 fragmented natural populations and three restored populations of the wind-pollinated and dispersed tree Allocasuarina verticillata, a key restoration species. Smaller populations produced seed crops with significantly fewer alleles, lower allelic richness and less gene diversity. Most of the populations assessed, including the restored sites, produce genetically diverse seed crops suitable for restoration but smaller populations (<30 plants) should be augmented with seed from larger populations. Principal coordinate analysis, graph-theory and Bayesian analyses found little evidence of spatially predictable genetic structure across the study region, which probably reflects long distance gene dispersal preventing the development of strong spatial structure. The absence of strong spatial patterns suggests that seed can be moved beyond current 5–50-km limits while being mindful of strong selection gradients or conditions that might indicate locally adapted populations.

scholarly journals Impacts of Seed and Pollen Flow on Population Genetic Structure for Plant Genomes With Three Contrasting Modes of Inheritance

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 441-450 ◽  
Author(s):  
Xin-Sheng Hu ◽  
Richard A Ennos
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Nuclear Genes ◽  
Effective Population ◽  
Long Distance ◽  
Stepping Stone ◽  
Animal Populations ◽  
And Migration ◽  
Stepping Stone Model

Abstract The classical island and one-dimensional stepping-stone models of population genetic structure developed for animal populations are extended to hermaphrodite plant populations to study the behavior of biparentally inherited nuclear genes and organelle genes with paternal and maternal inheritance. By substituting appropriate values for effective population sizes and migration rates of the genes concerned into the classical models, expressions for genetic differentiation and correlation in gene frequency between populations can be derived. For both models, differentiation for maternally inherited genes at migration-drift equilibrium is greater than that for paternally inherited genes, which in turn is greater than that for biparentally inherited nuclear genes. In the stepping-stone model, the change of genetic correlation with distance is influenced by the mode of inheritance of the gene and the relative values of long- and short-distance migration by seed and pollen. In situations where it is possible to measure simultaneously Fst for genes with all three types of inheritance, estimates of the relative rates of pollen to seed flow can be made for both the short- and long-distance components of migration in the stepping-stone model.

scholarly journals Genetic diversity and structure in the Endangered Allen Cays Rock Iguana,Cyclura cychlura inornata

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1793 ◽  
Author(s):  
Andrea C. Aplasca ◽  
John B. Iverson ◽  
Mark E. Welch ◽  
Giuliano Colosimo ◽  
Evon R. Hekkala
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Gene ◽  
Population Decline ◽  
Natural Populations ◽  
Unknown Origin ◽  
Source Population ◽  
Effective Population ◽  
The Bahamas ◽  
Low Genetic Diversity ◽  
Genetic Diversity And Structure

The Endangered Allen Cays Rock Iguana (Cyclura cychlura inornata) is endemic to the Allen Cays, a tiny cluster of islands in the Bahamas. Naturally occurring populations exist on only two cays (<4 ha each). However, populations of unknown origin were recently discovered on four additional cays. To investigate patterns of genetic variation among these populations, we analyzed nuclear and mitochondrial markers for 268 individuals. Analysis of three mitochondrial gene regions (2,328 bp) and data for eight nuclear microsatellite loci indicated low genetic diversity overall. Estimates of effective population sizes based on multilocus genotypes were also extremely low. Despite low diversity, significant population structuring and variation in genetic diversity measures were detected among cays. Genetic data confirm the source population for an experimentally translocated population while raising concerns regarding other, unauthorized, translocations. Reduced heterozygosity is consistent with a documented historical population decline due to overharvest. This study provides the first range-wide genetic analysis of this subspecies. We suggest strategies to maximize genetic diversity during ongoing recovery including additional translocations to establish assurance populations and additional protective measures for the two remaining natural populations.

scholarly journals Genetic structure of natural populations of Cryptocarya moschata Nees (Lauraceae) from southeastern Brazilian Atlantic rain forest

2004 ◽  
Vol 4 (1) ◽  
pp. 01-16 ◽  
Author(s):  
Pedro Luís Rodrigues de Moraes ◽  
Maria Teresa Vitral de Carvalho Derbyshire
Keyword(s):  
Genetic Structure ◽  
Rain Forest ◽  
Evolutionary Dynamics ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Natural Populations ◽  
Conservation Strategies ◽  
Atlantic Rain Forest ◽  
Effective Population ◽  
Allozyme Loci

This study was accomplished on a more comprehensive basis to evaluate previous questions that were raised from a preliminary article about the genetic structure of Cryptocarya moschata populations. Thus, through the analysis of 40 polymorphic allozyme loci, allele frequencies were estimated from 335 individuals of 11 natural populations of C. moschata from six hydrographic basins of São Paulo state and Serra da Estrela, Rio de Janeiro, Brazil. Estimates of Wright's F statistics were done through the analysis of variance, presenting average values of <img border=0 width=32 height=32 id="_x0000_i1026" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f).jpg" align=absmiddle > or = 0.352, <img border=0 width=32 height=32 id="_x0000_i1027" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle > or = 0.285 and <img border=0 width=32 height=32 id="_x0000_i1028" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f2).jpg" align=absmiddle > or = 0.097. These results indicated that individuals within populations must be panmitic, and that the diversity among populations is fairly high, being superior to what would be expected for groups of plants having a full-sib family structure. From estimates of <img border=0 width=32 height=32 id="_x0000_i1029" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>obtained for populations taken two at a time, the model of isolation by distance was tested; data did not fit the model, showing that <img border=0 width=32 height=32 id="_x0000_i1030" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>did not increase by the respective increasing of the geographic distance. The estimated gene flow of 0.55 migrants per generation corroborated the pronounced populational differentiation, indicating that drift effects should be more important than the selection ones. The effective population sizes found from the sampled populations showed that there was an adequate genetic representativeness of the samples for those with relatively low values of <img border=0 width=32 height=32 id="_x0000_i1031" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f2).jpg" align=absmiddle>. Though, under a metapopulation context, the effective population size was 17.07 individuals, indicating that sampling performed for the species corresponded to 88.44% of the maximum effective size obtained from 11 populations with a <img border=0 width=32 height=32 id="_x0000_i1032" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>of 0.285, equivalent to only 5.09% individuals for the total sampled. Management and conservation strategies aimed at preserving high intrapopulation genetic variation in C. moschata would imply in the maintenance of populations with great number of individuals. Moreover, for the preservation of the species as a whole, the maintenance of many such populations would be mandatorily recommended, which denotes that the conservation of large areas of Atlantic rain forest should be necessary to hold its evolutionary dynamics.

scholarly journals Genetic evidence supports polygamous mating system in a wild population of Prochilodus lineatus (Characiformes: Prochilodontidae), a Neotropical shoal spawner fish

2020 ◽  
Vol 18 (2) ◽  
Author(s):  
Josiane Ribolli ◽  
Carolina Isabel Miño ◽  
Bianca Maria Soares Scaranto ◽  
David Augusto Reynalte-Tataje ◽  
Evoy Zaniboni Filho
Keyword(s):  
Mating System ◽  
Wild Population ◽  
Natural Populations ◽  
Genetic Evidence ◽  
Effective Population ◽  
Long Distance ◽  
Prochilodus Lineatus ◽  
Behavioral Observations ◽  
Inference Methods ◽  
Uruguay River

ABSTRACT Behavioral observations made on fish have revealed remarkably diverse reproductive strategies, including polygamy by both sexes. Still, to date, most Neotropical species remain unstudied as to whether the observed reproductive behavior in natural populations correlates with their genetic mating systems. Here, we investigated the genetic mating system of a wild population of Prochilodus lineatus settled in the Middle Uruguay River basin. By using sibship reconstruction and parental inference methods based on microsatellites’ genotypes, we inferred 45 females and 47 males as potential parents of the 87 larvae analyzed. We found evidence supporting polygamous mating in both sexes: while a high percentage of males (44.7%) fertilized the eggs of one female, 55.3% of the inferred males fertilized eggs of up to four females. Likewise, while 44.5% of the inferred females had their eggs fertilized by one only male, 55.5% of females were fertilized by multiple males. The estimated proxy of the effective population size (Nb) was 126, exhibiting moderate to high levels of genetic diversity. The genetic evidence contributed in this study complements earlier behavioral observations of formation of spawning nuclei of aggregating breeders, which may be promoting a polygamous mating strategy in this long-distance migratory fish.

scholarly journals Population structure of Pyrenophora teres f. teres barley pathogens from different continents

2021 ◽  
Author(s):  
Buddhika Amarasinghe Dahanayaka ◽  
Niloofar Vaghefi ◽  
Noel L. Knight ◽  
József Bakonyi ◽  
Renée Prins ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Principal Component ◽  
Pyrenophora Teres ◽  
Neighbor Joining ◽  
Long Distance ◽  
Disease Epidemiology ◽  
Genetic Diversity And Structure ◽  
Pathogen Control ◽  
Multiple Introduction ◽  
Pathogen Populations

Net-form net blotch disease caused by Pyrenophora teres f. teres (Ptt) results in significant yield losses to barley industries. Up-to-date knowledge of the genetic diversity and structure of pathogen populations is critical for better understanding the disease epidemiology and unravelling pathogen survival and dispersal mechanisms. Thus, this study investigated long distance dispersal and adaptation by analysing the genetic structure of 250 Ptt isolates collected from Australia, Canada, Hungary and Republic of South Africa (RSA), and historical isolates from Canada, Denmark, Japan and Sweden. The population genetic structure detected by discriminant analysis of principal component, using 5890 Diversity Arrays Technology (DArT) markers, revealed the presence of four clusters. Two of these contained isolates from all regions, and all isolates from RSA were grouped in these two. Australia and Hungary showed three clusters each. One of the Australian clusters contained only Australian isolates. One of the Hungarian clusters contained only Hungarian isolates and one Danish isolate. STRUCTURE analysis indicated that some isolates from Australia and Hungary shared recent ancestry with RSA, Canada and historical isolates and were thus admixed. Subdivisions of the Neighbor-joining network indicated that isolates from distinct countries were closely related, suggesting multiple introduction events conferred genetic heterogeneity in these countries. Through a Neighbor-joining analysis and amplification with form-specific DNA markers two hybrid isolates, CBS 281.31 from Japan and H-919 from Hungary collected in 1931 and 2018, respectively, were detected. These results provide a foundation for exploring improved management of disease incursions and pathogen control through strategic deployment of resistances.

scholarly journals Genetic Diversity and Relatedness among Captive African Painted Dogs in North America

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1463
Author(s):  
Cassandra M. Miller-Butterworth ◽  
Karen Vacco ◽  
Amy L. Russell ◽  
Joseph C. Gaspard
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Mhc Class Ii ◽  
Captive Breeding ◽  
Management Plan ◽  
Captive Population ◽  
Effective Population ◽  
Breeding Programs ◽  
Low Genetic Diversity ◽  
Population Size Estimates

African painted dogs (Lycaon pictus, APD) are highly endangered, with fewer than 7000 remaining in nature. Captive breeding programs can preserve a genetically diverse population and provide a source of individuals for reintroductions. However, most programs are initiated from few founders and suffer from low genetic diversity and inbreeding. The aims of this study were to use molecular markers to assess genetic variation, inbreeding, and relatedness among APDs in the North American captive population, to use these data to realign studbook records, and to compare these data to wild populations and to the European captive population to facilitate the development of a global management plan. We sequenced mitochondrial and major histocompatibility (MHC) class II loci and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in North America. We identified three likely studbook errors and resolved ten cases of uncertain paternity. Overall, microsatellite heterozygosity was higher than reported in Europe, but effective population size estimates were lower. Mitochondrial sequence variation was extremely limited, and there were fewer MHC haplotypes than in Europe or the wild. Although the population did not show evidence of significant inbreeding overall, several individuals shared high relatedness values, which should be incorporated into future breeding programs.

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