scholarly journals Conservation genomics of the threatened western spadefoot, Spea hammondii, in urbanized southern California

2020 ◽  
Author(s):  
Kevin M Neal ◽  
Robert N Fisher ◽  
Milan J Mitrovich ◽  
H Bradley Shaffer
Keyword(s):  
Los Angeles ◽  
Population Size ◽  
Effective Population Size ◽  
Southern California ◽  
Orange County ◽  
Genetic Connectivity ◽  
Gene Pools ◽  
Conservation Genomics ◽  
Effective Population ◽  
Artificial Ponds

Abstract Populations of the western spadefoot (Spea hammondii) in southern California occur in one of the most urbanized and fragmented landscapes on the planet and have lost up to 80% of their native habitat. Orange County is one of the last strongholds for this pond-breeding amphibian in the region, and ongoing restoration efforts targeting S. hammondii have involved habitat protection and the construction of artificial breeding ponds. These efforts have successfully increased breeding activity, but genetic characterization of the populations, including estimates of effective population size and admixture between the gene pools of constructed artificial and natural ponds, has never been undertaken. Using thousands of genome-wide single-nucleotide polymorphisms, we characterized the population structure, genetic diversity, and genetic connectivity of spadefoots in Orange County to guide ongoing and future management efforts. We identified at least two, and possibly three major genetic clusters, with additional substructure within clusters indicating that individual ponds are often genetically distinct. Estimates of landscape resistance suggest that ponds on either side of the Los Angeles Basin were likely interconnected historically but intense urban development has rendered them essentially isolated, and the resulting risk of interruption to natural metapopulation dynamics appears to be high. Resistance surfaces show that the existing artificial ponds were well-placed and connected to natural populations by low-resistance corridors. Toad samples from all ponds (natural and artificial) returned extremely low estimates of effective population size, possibly due to a bottleneck caused by a recent multi-year drought. Management efforts should focus on maintaining gene flow among natural and artificial ponds by both assisted migration and construction of new ponds to bolster the existing pond network in the region.

scholarly journals Assessment of the state of population gene pools of the slightly mobile animal species on the example of the land snail Bradybaena fruticum Müll. (Gastropoda, Pulmonata) based on the DNA markers

2017 ◽  
Vol 15 (3) ◽  
pp. 4-19 ◽  
Author(s):  
Eduard A. Snegin ◽  
Elena A. Snegina
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Markers ◽  
Allelic Diversity ◽  
Land Snail ◽  
Shannon Index ◽  
Forest Steppe ◽  
Gene Pools ◽  
Effective Population ◽  
Industrial Enterprises

Using the polymorphic DNA markers (RAPD and ISSR), the genetic structure was examined and the viability of 26 populations of the terrestrial gastropod Bradybaena (Fruticicola) fruticum Müll., most of which lives in the south of the Central Russian Upland, was estimated. Samples from Romania, the Urals and Vyatka regions for comparison were taken. In total, 1153 individuals were examined. The level of expected heterozygosity averaged He = 0.208 ± 0.028, the Shannon index Ish = 0.320 ± 0.039. The lowered level of variability, both actual and theoretically expected (estimated by the methods of Chao1-bc and 1st order jackknife) in groups of anthropogenically disturbed biotopes inhabiting the zones of industrial enterprises is noted. The indices of the genetic disunity of the populations were Fst = 0.298, Gst = 0.254, and the level of the gene flow Nm = 0.708. The cluster analysis and the Mantel correlation coefficient Rm = –0.024 showed the absence of a reliable relationship between the geographic and genetic distance between populations, which indicates the violation of the isolation model by distance and confirms the thesis advanced earlier that the urbanized forest-steppe landscape disrupts the natural migration processes, leads to the strong isolation and of the genetic drift in populations of snails. At the same time, the observed phenomenon of increasing the degree of subdivision of populations against the background of a decrease in the allelic diversity noted by us in many groups of bush snail can be regarded as the shift of genetic equilibrium toward increasing interpopopulation diversity (according to Wright's model). The calculation of the effective population size with the help of the Slatkin model turned out to be the lowest of the background mollusks in the study area (Ne = 0.39-0.83). However, the level of the effective population size calculated with the subdivision index (Fst and Gst) was equal to 6.2 and 7.3, respectively, which is comparable with other species of mollusks.

scholarly journals Preferred habitat and effective population size drive landscape genetic patterns in an endangered species

2013 ◽  
Vol 280 (1769) ◽  
pp. 20131756 ◽  
Author(s):  
Byron V. Weckworth ◽  
Marco Musiani ◽  
Nicholas J. DeCesare ◽  
Allan D. McDevitt ◽  
Mark Hebblewhite ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Environmental Variables ◽  
Spatial Configuration ◽  
Genetic Relationships ◽  
Empirical Support ◽  
Genetic Connectivity ◽  
Effective Population ◽  
Resistance Distance ◽  
Preferred Habitat

Landscape genetics provides a framework for pinpointing environmental features that determine the important exchange of migrants among populations. These studies usually test the significance of environmental variables on gene flow, yet ignore one fundamental driver of genetic variation in small populations, effective population size, N e . We combined both approaches in evaluating genetic connectivity of a threatened ungulate, woodland caribou. We used least-cost paths to calculate matrices of resistance distance for landscape variables (preferred habitat, anthropogenic features and predation risk) and population-pairwise harmonic means of N e , and correlated them with genetic distances, F ST and D c . Results showed that spatial configuration of preferred habitat and N e were the two best predictors of genetic relationships. Additionally, controlling for the effect of N e increased the strength of correlations of environmental variables with genetic distance, highlighting the significant underlying effect of N e in modulating genetic drift and perceived spatial connectivity. We therefore have provided empirical support to emphasize preventing increased habitat loss and promoting population growth to ensure metapopulation viability.

scholarly journals High genetic diversity and low future habitat suitability: will Cupressus atlantica, endemic to the High Atlas, survive under climate change?

2020 ◽  
Vol 20 (4) ◽  
Author(s):  
Katarzyna Sękiewicz ◽  
Łukasz Walas ◽  
Berika Beridze ◽  
Mohamed Fennane ◽  
Monika Dering
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Endemic Species ◽  
Spatial Genetic Structure ◽  
Species Range ◽  
Ex Situ ◽  
Genetic Connectivity ◽  
Effective Population ◽  
High Atlas ◽  
Cupressus Atlantica

AbstractCupressus atlantica is a narrow endemic species of semi-arid and sub-humid habitats in the western High Atlas, Morocco. We explored the possible dynamics of the species’ range under climatic changes using species distribution modelling (SDM) to identify populations vulnerable to range changes. Additionally, we investigated the spatial genetic structure (SGS), the effective population size and genetic connectivity in natural populations, which may provide important data on demo-genetic processes and support the conservation management of this critically endangered species. The SDM results showed that the current species range constitutes only 49% of the potential distribution. Under the most pessimistic scenarios (RCP6.0 and RCP8.5), a significant reduction in the species range was predicted. However, the projection based on RPC4.5 revealed possible extensions of the habitats suitable for C. atlantica. Potentially, these areas could serve as new habitats that could be used with the assisted migration approach aiming to mitigate the current fragmentation. In terms of the SGS, significant and positive aggregation of relatives was detected up to ca. 100 m. In comparison to other fragmented and endemic species, the detected SGS was weak (Sp = 0.0112). The estimated level of recent gene flow was considerable, which likely prevented a strong SGS and allowed diversity to accumulate (HE = 0.894). The most alarming results concern the effective population size, which was very low in the studied populations (< 53), suggesting a possible increase in inbreeding and loss of diversity in the near future. More effective conservation actions integrating in situ and ex situ measures should be undertaken to prevent extirpation of the species.

scholarly journals A phylogenetic estimator of effective population size or mutation rate.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 685-692 ◽  
Author(s):  
Y X Fu
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Dna Sequences ◽  
High Efficiency ◽  
Minimum Variance ◽  
Population Subdivision ◽  
Effective Population ◽  
Fisher Model ◽  
Mitochondrial Sequences

Abstract A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

scholarly journals Alu Evolution in Human Populations: Using the Coalescent to Estimate Effective Population Size

Genetics ◽  
1997 ◽  
Vol 147 (4) ◽  
pp. 1977-1982
Author(s):  
Stephen T Sherry ◽  
Henry C Harpending ◽  
Mark A Batzer ◽  
Mark Stoneking
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genomic Library ◽  
Diploid Cell ◽  
Human Populations ◽  
Effective Population ◽  
Alu Repeats ◽  
Branch Lengths ◽  
Diploid Cell Line ◽  
Coalescence Theory

Abstract There are estimated to be ~1000 members of the Ya5 Alu subfamily of retroposons in humans. This Subfamily has a distribution restricted to humans, with a few copies in gorillas and chimpanzees. Fifty-seven Ya5 elements were previously cloned from a HeLaderived randomly sheared total genomic library, sequenced, and screened for polymorphism in a panel of 120 unrelated humans. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. The observed distribution of sample frequencies of the 13 dimorphic elements is consistent with the theoretical expectation for elements ascertained in a single diploid cell line. Coalescence theory is used to compute expected total pedigree branch lengths for monomorphic and dimorphic elements, leading to an estimate of human effective population size of ~18,000 during the last one to two million years.

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