scholarly journals Long-term isolation at a low effective population size greatly reduced genetic diversity in Gulf of California fin whales

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vania E. Rivera-León ◽  
Jorge Urbán ◽  
Sally Mizroch ◽  
Robert L. Brownell ◽  
Tom Oosting ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Gulf Of California ◽  
Effective Population ◽  
Fin Whales

scholarly journals Life histories predict genetic diversity and population structure within three species of Octopus targeted by small-scale fisheries in Northwest Mexico

2017 ◽  
Author(s):  
José F Domínguez-Contreras ◽  
Adrian Munguia-Vega ◽  
Bertha P Ceballos-Vázquez ◽  
Marcial Arellano-Martínez ◽  
Francisco J García-Rodríguez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Gulf Of California ◽  
Life Histories ◽  
Local Population ◽  
Small Scale ◽  
Effective Population ◽  
Northwest Mexico

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species with varying life histories targeted by artisanal fisheries in the region, lack of information about the distribution of each species and metapopulation size and structure could impede effective fisheries management to avoid overexploitation. Here we tested if different life histories in three species of octopus help to predict observed patterns of genetic diversity, population dynamics, structure and connectivity that could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the Pacific coast of the Baja California peninsula. We tested four a priori hypothesis derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We found that the species with low fecundity and without a planktonic larval stage (Octopus bimaculoides) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, suggesting limited dispersal and high local recruitment. In contrast, two species with higher fecundity and planktonic larvae (O. bimaculatus, O. hubbsorum) showed higher effective population size and genetic diversity, and overall lower kinship and population structure, supporting higher levels of gene flow over a larger geographical scale. Even among the latter, there were differences in the calculated parameters possibly associated with increased connectivity in the species with the longest planktonic larval duration (O. bimaculatus). We consider that O. bimaculoides could be more susceptible to over exploitation of small, isolated populations that could have longer recovery times, and suggest that management should take place within each local population. For the two species with pelagic larvae, management should consider metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal between localities driven by ocean currents. The distribution of each species and variations in their reproductive timing should also be considered when establishing marine reserves or seasonal fishing closures.

scholarly journals Life histories predict genetic diversity and population structure within three species of Octopus targeted by small-scale fisheries in Northwest Mexico

2017 ◽  
Author(s):  
José F Domínguez-Contreras ◽  
Adrian Munguia-Vega ◽  
Bertha P Ceballos-Vázquez ◽  
Marcial Arellano-Martínez ◽  
Francisco J García-Rodríguez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Gulf Of California ◽  
Life Histories ◽  
Local Population ◽  
Small Scale ◽  
Effective Population ◽  
Northwest Mexico

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species with varying life histories targeted by artisanal fisheries in the region, lack of information about the distribution of each species and metapopulation size and structure could impede effective fisheries management to avoid overexploitation. Here we tested if different life histories in three species of octopus help to predict observed patterns of genetic diversity, population dynamics, structure and connectivity that could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the Pacific coast of the Baja California peninsula. We tested four a priori hypothesis derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We found that the species with low fecundity and without a planktonic larval stage (Octopus bimaculoides) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, suggesting limited dispersal and high local recruitment. In contrast, two species with higher fecundity and planktonic larvae (O. bimaculatus, O. hubbsorum) showed higher effective population size and genetic diversity, and overall lower kinship and population structure, supporting higher levels of gene flow over a larger geographical scale. Even among the latter, there were differences in the calculated parameters possibly associated with increased connectivity in the species with the longest planktonic larval duration (O. bimaculatus). We consider that O. bimaculoides could be more susceptible to over exploitation of small, isolated populations that could have longer recovery times, and suggest that management should take place within each local population. For the two species with pelagic larvae, management should consider metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal between localities driven by ocean currents. The distribution of each species and variations in their reproductive timing should also be considered when establishing marine reserves or seasonal fishing closures.

scholarly journals Life histories predict genetic diversity and population structure within three species of Octopus targeted by small-scale fisheries in Northwest Mexico

2017 ◽  
Author(s):  
José F Domínguez-Contreras ◽  
Adrian Munguia-Vega ◽  
Bertha P Ceballos-Vázquez ◽  
Marcial Arellano-Martínez ◽  
Francisco J García-Rodríguez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Gulf Of California ◽  
Life Histories ◽  
Local Population ◽  
Small Scale ◽  
Effective Population ◽  
Northwest Mexico

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species with varying life histories targeted by artisanal fisheries in the region, lack of information about the distribution of each species and metapopulation size and structure could impede effective fisheries management to avoid overexploitation. Here we tested if different life histories in three species of octopus help to predict observed patterns of genetic diversity, population dynamics, structure and connectivity that could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the Pacific coast of the Baja California peninsula. We tested four a priori hypothesis derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We found that the species with low fecundity and without a planktonic larval stage (Octopus bimaculoides) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, suggesting limited dispersal and high local recruitment. In contrast, two species with higher fecundity and planktonic larvae (O. bimaculatus, O. hubbsorum) showed higher effective population size and genetic diversity, and overall lower kinship and population structure, supporting higher levels of gene flow over a larger geographical scale. Even among the latter, there were differences in the calculated parameters possibly associated with increased connectivity in the species with the longest planktonic larval duration (O. bimaculatus). We consider that O. bimaculatus could be more susceptible to over exploitation of small, isolated populations that could have longer recovery times, and suggest that management should take place within each local population. For the two species with pelagic larvae, management should consider metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal between localities driven by ocean currents. The distribution of each species and variations in their reproductive timing should also be considered when establishing marine reserves or seasonal fishing closures.

scholarly journals Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species

2021 ◽  
Author(s):  
Zachariah Gompert ◽  
Amy Springer ◽  
Megan Brady ◽  
Samridhi Chaturvedi ◽  
Lauren K. Lucas
Keyword(s):  
Genetic Diversity ◽  
Time Series ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Time Series Data ◽  
Series Data ◽  
Effective Population ◽  
Population Sizes

AbstractEffective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show thatLycaeidesbutterfly populations maintain low contemporary (variance) effective population sizes (e.g., ∼200 individuals) and thus evolve rapidly by genetic drift. Contemporary effective sizes were consistent with local census populations sizes. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift inLycaeideshas implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.

scholarly journals Low genetic diversity in the endangered Taxus yunnanensis following a population bottleneck, a low effective population size and increased inbreeding

2016 ◽  
Vol 65 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Y. C. Miao ◽  
Z. J. Zhang ◽  
J. R. Su
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Population Bottleneck ◽  
Effective Population ◽  
Taxus Yunnanensis ◽  
Low Genetic Diversity ◽  
Two Populations

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

scholarly journals Genetic diversity, population structure, and effective population size in two yellow bat species in south Texas

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10348
Author(s):  
Austin S. Chipps ◽  
Amanda M. Hale ◽  
Sara P. Weaver ◽  
Dean A. Williams
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
North America ◽  
Wind Energy ◽  
Population Size ◽  
Effective Population Size ◽  
Microsatellite Loci ◽  
South Texas ◽  
Population Substructure ◽  
Effective Population

There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D. intermedius (D. i. floridanus and D. i. intermedius) which are sympatric in this region of Texas, yet little differentiation using microsatellite loci. We suggest this pattern is due to secondary contact and hybridization and possibly incomplete lineage sorting at microsatellite loci. We also found evidence of some hybridization between D. ega and D. intermedius in this region of Texas. We recommend that our data serve as a starting point for the long-term genetic monitoring of these species in order to better understand the impacts of wind-related mortality on these populations over time.

scholarly journals Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 361 ◽  
Author(s):  
Shuqi Diao ◽  
Shuwen Huang ◽  
Zhiting Xu ◽  
Shaopan Ye ◽  
Xiaolong Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Conservation Status ◽  
Snp Array ◽  
Size Analysis ◽  
Selection Signatures ◽  
Effective Population ◽  
Low Genetic Diversity ◽  
Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

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