scholarly journals Contribution of spatial heterogeneity in effective population sizes to the variance in pairwise measures of genetic differentiation

2015 ◽  
Author(s):  
Jérôme G. Prunier ◽  
Vincent Dubut ◽  
Lounès Chikhi ◽  
Simon Blanchet
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Spatial Heterogeneity ◽  
Landscape Genetics ◽  
Isolation By Distance ◽  
List Type ◽  
Unique Contribution ◽  
Landscape Resistance ◽  
Effective Population ◽  
Population Sizes

SummaryPairwise measures of neutral genetic differentiation are supposed to contain information about past and on-going dispersal events and are thus often used as dependent variables in correlative analyses to elucidate how neutral genetic variation is affected by landscape connectivity. However, spatial heterogeneity in the intensity of genetic drift, stemming from variations in population sizes, may inflate variance in measures of genetic differentiation and lead to erroneous or incomplete interpretations in terms of connectivity. Here, we tested the efficiency of two distance-based metrics designed to capture the unique influence of spatial heterogeneity in local drift on genetic differentiation. These metrics are easily computed from estimates of effective population sizes or from environmental proxies for local carrying capacities, and allow us to introduce the hypothesis of Spatial-Heterogeneity-in-Effective-Population-Sizes (SHNe). SHNe can be tested in a way similar to isolation-by-distance or isolation-by-resistance within the classical landscape genetics hypothesis-testing framework.We used simulations under various models of population structure to investigate the reliability of these metrics to quantify the unique contribution of SHNe in explaining patterns of genetic differentiation. We then applied these metrics to an empirical genetic dataset obtained for a freshwater fish (Gobio occitaniae).Simulations showed that SHNe explained up to 60% of variance in genetic differentiation (measured as Fst) in the absence of gene flow, and up to 20% when migration rates were as high as 0.10. Furthermore, one of the two metrics was particularly robust to uncertainty in the estimation of effective population sizes (or proxies for carrying capacity). In the empirical dataset, the effect of SHNe on spatial patterns of Fst was five times higher than that of isolation-by-distance, uniquely contributing to 41% of variance in pairwise Fst. Taking the influence of SHNe into account also allowed decreasing the signal-to-noise ratio, and improving the upper estimate of effective dispersal distance.We conclude that the use of SHNe metrics in landscape genetics will substantially improve the understanding of evolutionary drivers of genetic variation, providing substantial information as to the actual drivers of patterns of genetic differentiation in addition to traditional measures of Euclidean distance or landscape resistance.

scholarly journals Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

2019 ◽  
Vol 190 (1) ◽  
pp. 65-78 ◽  
Author(s):  
Kin Onn Chan ◽  
Rafe M Brown
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Variance Partitioning ◽  
Nucleotide Polymorphisms ◽  
Landscape Genomics ◽  
Mountain Ranges ◽  
Historical Factors ◽  
Environmental Attributes

Abstract The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

scholarly journals Reducing bias in population and landscape genetic inferences: the effects of sampling related individuals and multiple life stages

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1813 ◽  
Author(s):  
William Peterman ◽  
Emily R. Brocato ◽  
Raymond D. Semlitsch ◽  
Lori S. Eggert
Keyword(s):  
Best Practice ◽  
Isolation By Distance ◽  
Life Stage ◽  
Population Sample ◽  
Life Stages ◽  
Effective Population ◽  
Data Set ◽  
Sibling Pairs ◽  
Population Sizes ◽  
Landscape Genetic

In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. Additionally, the removal of siblings from a data set is considered best-practice, but direct comparisons of inferences made with and without siblings are limited. In this study, we sampled embryos, larvae, and adultAmbystoma maculatumfrom five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FSTandDC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. We also assessed the effect of reducing the number of microsatellites used to make inference. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. We found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when usingDC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Further, power to detect an IBD relationship was reduced when fewer microsatellites were used in the analysis.

scholarly journals Spatial, climate, and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra

2019 ◽  
Author(s):  
CW Ahrens ◽  
EA James ◽  
AD Miller ◽  
NC Aitken ◽  
JO Borevitz ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Isolation By Distance ◽  
Management Strategies ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
List Type ◽  
Themeda Triandra ◽  
Reduced Representation ◽  
Isolation By Environment ◽  
Susceptible Populations

SummaryFragmented grassland ecosystems, and the species that shape them, are under immense pressure. Restoration and management strategies should include genetic diversity and adaptive capacity to improve success but these data are generally unavailable. Therefore, we use the foundational grass, Themeda triandra, to test how spatial, environmental, and ploidy factors shape patterns of genetic variation.We used reduced-representation genome sequencing on 487 samples from 52 locations to answer fundamental questions about how the distribution of genomic diversity and ploidy polymorphism supports adaptation to harsher climates. We explicitly quantified isolation-by-distance (IBD), isolation-by-environment (IBE), and predicted population genomic vulnerability in 2070.We found that a majority (54%) of the genomic variation could be attributed to IBD, while 22% of the genomic variation could be explained by four climate variables showing IBE. Results indicate that heterogeneous patterns of vulnerability across populations are due to genetic variation, multiple climate factors, and ploidy polymorphism, which lessened genomic vulnerability in the most susceptible populations.These results indicate that restoration and management of T. triandra should incorporate knowledge of genomic diversity and ploidy polymorphisms to increase the likelihood of population persistence and restoration success in areas that will become hotter and more arid.

scholarly journals Quantifying the individual impact of artificial barriers in freshwaters: A standardized and absolute genetic index of fragmentation

2019 ◽  
Author(s):  
Jérôme G. Prunier ◽  
Camille Poesy ◽  
Vincent Dubut ◽  
Charlotte Veyssière ◽  
Géraldine Loot ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Molecular Data ◽  
Freshwater Biodiversity ◽  
Effective Population ◽  
Barrier Effects ◽  
Population Sizes ◽  
The Individual ◽  
Independent Assessment ◽  
Objective Tool ◽  
Genetic Index

AbstractFragmentation by artificial barriers is an important threat to freshwater biodiversity. Mitigating the negative aftermaths of fragmentation is of crucial importance, and it is now essential for environmental managers to benefit from a precise estimate of the individual impact of weirs and dams on river connectivity. Although the indirect monitoring of fragmentation using molecular data constitutes a promising approach, it is plagued with several constraints preventing a standardized and individual quantification of barrier effects. Indeed, observed levels of genetic differentiation depend on both the age of the obstacle and the effective size of the populations it separates, making difficult comparisons of the actual barrier effect of different obstacles. Here, we developed a standardized genetic index of fragmentation (FINDEX), allowing an absolute and independent assessment of the individual effects of obstacles on connectivity. The FINDEX is the standardized ratio (expressed as a percentage) between the observed genetic differentiation between pairs of populations located on either side of an obstacle and the genetic differentiation expected if this obstacle completely prevented gene flow. The expected genetic differentiation is calculated from simulations taking into account two nuisance parameters: the number of generations since barrier creation (the age of the obstacle) and the expected heterozygosity of the targeted populations, a proxy for effective population sizes. Using both simulated and published empirical datasets, we explored and discussed the validity and the limits of the FINDEX. We demonstrated that it allows quantifying genetic effects of fragmentation only from a few generations after barrier creation and provides valid comparisons among populations (or species) of different effective populations sizes and obstacles of different ages. The computation of the FINDEX requires a minimum amount of fieldwork and genotypic data, and solves some of the difficulties inherent to the study of artificial fragmentation in rivers and potentially in other ecosystems. This makes the FINDEX a promising and objective tool for managers aiming at at planning restoration programs and at evaluating the efficiency of these programs.

Genetic differentiation among populations of Weidemeyer's admiral butterfly

1989 ◽  
Vol 67 (9) ◽  
pp. 2294-2300 ◽  
Author(s):  
Risa H. Rosenberg
Keyword(s):  
Genetic Differentiation ◽  
Social Systems ◽  
Starch Gel Electrophoresis ◽  
Effective Population ◽  
Isolated Populations ◽  
Genetic Structure Of Populations ◽  
Two Factors ◽  
Population Sizes ◽  
Starch Gel ◽  
Allozyme Loci

I assessed the genetic differentiation of populations of Weidemeyer's admiral butterfly (Limenitis weidemeyerii) in central and eastern Colorado by using starch-gel electrophoresis. Wright's F-statistics indicated that there was significant differentiation, both within and between years, among the same populations analyzed for 2 successive years, and among populations, even those in close geographic proximity. Consequently, no correlation was found between the genetic identities and geographic distances between pairs of populations. To explain the genetic structure of populations, I estimated patterns of movement and effective sizes of populations. I assessed movement of individuals by using mark–recapture techniques, which indicated that travel over the season for both sexes was negligible (range 0–2850 m, mean 166 m). I estimated effective population sizes by using Pollak's methods, and as would be expected for populations with territorial social systems, effective sizes were small (ranging from 17 to 131, mean 61). These two factors, small and isolated populations, suggest that a significant portion of the genetic differentiation observed at allozyme loci among populations of Weidemeyer's admiral butterfly in Colorado is mediated by random genetic drift.

Genetic variation in the greenback flounder Rhombosolea tapirina GÜnther (Teleostei, Pleuronectidae) and the implications for aquaculture

2000 ◽  
Vol 51 (1) ◽  
pp. 23 ◽  
Author(s):  
Tony van den Enden ◽  
Robert W. G. White ◽  
Nicholas G. Elliott
Keyword(s):  
Genetic Variation ◽  
New Zealand ◽  
Genetic Distance ◽  
West Coast ◽  
Gel Electrophoresis ◽  
Effective Population ◽  
Average Heterozygosity ◽  
The West ◽  
Order Of Magnitude ◽  
Population Sizes

Samples of the greenback flounder, Rhombosolea tapirina, were collected from five Tasmanian sites and from one site each off Victoria and New Zealand. Thirty enzyme-coding loci were analysed by gel electrophoresis. Seventeen loci were variable, nine of which were polymorphic in at least four samples. Average heterozygosity across all 30 loci was relatively high at 0.086 ± 0.032. There were significant genetic differences between the Australian and New Zealand samples, with a genetic distance of 0.041, which was an order of magnitude larger than that observed between any Australian samples. Samples from the west coast of Tasmania and from Victoria were genetically isolated from each other and from the remaining four Tasmanian samples; the latter showed little variation among themselves. Reductions in genetic variation (heterozygosity and alleles) were observed in two cultured cohorts when compared with the wild-caught samples, with corresponding low estimates of effective population sizes compared with putative breeding numbers. No genetic variation was detected between normal and malpigmented individuals from the same culture cohort.

scholarly journals Low genetic variation in a Pacific cycad: conservation concerns for Cycas seemannii (Cycadaceae)

Oryx ◽  
2002 ◽  
Vol 36 (1) ◽  
pp. 41-49 ◽  
Author(s):  
Gunnar Keppel
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
New Caledonia ◽  
Conservation Status ◽  
Iucn Red List ◽  
Factors Affecting ◽  
Abundance Estimates ◽  
In The Wild ◽  
Population Sizes ◽  
Fragmented Population

The conservation status of Cycas seemannii, native to Vanuatu, New Caledonia, Fiji and Tonga, is assessed based on isozyme analysis, abundance estimates and factors affecting the survival of the species. Genetic variation in the species is low and genetic differentiation between populations is high, as compared to plants in general and to other cycads. Lower genetic variation was detected in a fragmented population as compared to less disturbed populations. Low gene flow was also detected, implying little contact between the various populations. A conservative estimate of 17,000 individuals remaining in the wild was obtained, with more than half of these located on the islands of Vanuatu. Accounts of past abundance suggest declining population sizes, most likely the result of repeated burning. Other factors that may be contributing to the decline are decreasing importance to and protection by humans, habitat alteration for agricultural and developmental purposes, and poor dispersal and recolonisation potential. An assessment based on the present estimated abundance and what is known of recent declines in numbers, indicates that the species should be categorised as Vulnerable on the IUCN Red List. On some of the densely populated islands, such as Viti Levu in Fiji and Nukualofa in Tonga, the species is locally Endangered or Critically Endangered. Possible conservation measures are suggested, and it is emphasised that populations on different islands must be considered separately because of their genetic differentiation.

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