Weak genetic structuring suggests historically high genetic connectivity among recently fragmented urban populations of the scincid lizard, Ctenotus fallens

2015 ◽  
Vol 63 (4) ◽  
pp. 279 ◽  
Author(s):  
Josef Krawiec ◽  
Siegfried L. Krauss ◽  
Robert A. Davis ◽  
Peter B. S. Spencer
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Large Population ◽  
Geographic Distance ◽  
Genetic Erosion ◽  
Genetic Connectivity ◽  
Genetic Structuring ◽  
Low Genetic Diversity ◽  
Population Sizes

Populations in fragmented urban remnants may be at risk of genetic erosion as a result of reduced gene flow and elevated levels of inbreeding. This may have serious genetic implications for the long-term viability of remnant populations, in addition to the more immediate pressures caused by urbanisation. The population genetic structure of the generalist skink Ctenotus fallens was examined using nine microsatellite markers within and among natural vegetation remnants within a highly fragmented urban matrix in the Perth metropolitan area in Western Australia. These data were compared with samples from a large unfragmented site on the edge of the urban area. Overall, estimates of genetic diversity and inbreeding within all populations were similar and low. Weak genetic differentiation, and a significant association between geographic and genetic distance, suggests historically strong genetic connectivity that decreases with geographic distance. Due to recent fragmentation, and genetic inertia associated with low genetic diversity and large population sizes, it is not possible from these data to infer current genetic connectivity levels. However, the historically high levels of gene flow that our data suggest indicate that a reduction in contemporary connectivity due to fragmentation in C. fallens is likely to result in negative genetic consequences in the longer term.

scholarly journals Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhe Zhang ◽  
Stephan W. Gale ◽  
Ji-Hong Li ◽  
Gunter A. Fischer ◽  
Ming-Xun Ren ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Polynomial Regression ◽  
Genetic Erosion ◽  
Population Level ◽  
Hainan Island ◽  
Paternity Analysis ◽  
Genetic Structuring ◽  
Long Distance ◽  
High Genetic Diversity

Abstract Background Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchid Phalaenopsis pulcherrima on Hainan Island, China. Results Phalaenopsis pulcherrima is self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules of P. pulcherrima to each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next. Conclusions Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity in P. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.

Low genetic diversity and small long-term population sizes in the spring endemic watercress darter, Etheostoma nuchale

2010 ◽  
Vol 11 (6) ◽  
pp. 2267-2279 ◽  
Author(s):  
Brook L. Fluker ◽  
Bernard R. Kuhajda ◽  
Nicholas J. Lang ◽  
Phillip M. Harris
Keyword(s):  
Genetic Diversity ◽  
Low Genetic Diversity ◽  
Population Sizes

RESTRICTION FRAGMENT LENGTH POLYMORPHISM IN WILD AND CULTIVATED TETRAPLOID WHEAT

1999 ◽  
Vol 47 (4) ◽  
pp. 213-224 ◽  
Author(s):  
Li Huang ◽  
Eitan Millet ◽  
Junkang Rong ◽  
Jonathan F. Wendel ◽  
Yehoshua Anikster ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Triticum Turgidum ◽  
Large Population ◽  
Tetraploid Wheat ◽  
Nuclear Genome ◽  
Wild Emmer ◽  
Long Term Study ◽  
In The Wild

RFLP diversity in the nuclear genome was estimated within and among Israeli populations of wild emmer wheat (Triticum turgidumvar.dicoccoides) from a long-term study site at Ammiad (NE Israel), and from several other geographical locations. Using 55 enzyme-probe combinations, high levels of genetic diversity were revealed in wild emmer in general and within the Ammiad site. In spite of high diversity, observed heterozygosity was low and populations consisted of a patchwork of alternate multilocus homozygotes, consistent with the reproductive biology of a predominant self-fertilizing species. Retention of genetic diversity in wild emmer may be promoted by large population sizes, microhabitat diversity, and occasional gene flow through both pollen and seed. Population genetic structure in wild emmer appears to have been influenced by historical founder events as well as selective factors. Multivariate analyses indicated that individuals tend to cluster together according to their population of origin, and that there is little geographical differentiation among populations. Sampling of 12 domesticated land-races and both primitive and modern cultivars ofT. turgidumrevealed high levels of diversity and a large number of alleles that were not detected in the wild emmer populations. This may reflect a long-term domestication process in which wild, semi-domesticated, and domesticated types grew sympatrically, continuing introgression from wild populations, and perhaps also gene flow from trans-specific sources.

scholarly journals Assessing genetic diversity and connectivity in a tule elk (Cervus canadensis nannodes) metapopulation in Northern California

2021 ◽  
Author(s):  
Thomas J. Batter ◽  
Joshua P. Bush ◽  
Benjamin N. Sacks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Expansion ◽  
Active Management ◽  
Genetic Connectivity ◽  
Effective Population ◽  
Sex Marker ◽  
Cervus Canadensis ◽  
Population Sizes ◽  
Tule Elk

AbstractThe tule elk (Cervus canadensis nannodes) is a California endemic subspecies that experienced an extreme bottleneck (potentially two individuals) in the mid-1800s. Through active management, including reintroductions, the subspecies has grown to approximately 6000 individuals spread across 22 recognized populations. The populations tend to be localized and separated by unoccupied intervening habitat, prompting targeted translocations to ensure gene flow. However, little is known about the genetic status or connectivity among adjacent populations in the absence of active translocations. We used 19 microsatellites and a sex marker to obtain baseline data on the genetic effective population sizes and functional genetic connectivity of four of these populations, three of which were established since the 1980s and one of which was established ~ 100 years ago. A Bayesian assignment approach suggested the presence of 5 discrete genetic clusters, which corresponded to the four primary populations and two subpopulations within the oldest of them. Effective population sizes ranged from 15 (95% CI 10–22) to 51 (95% CI 32–88). We detected little or no evidence of gene flow among most populations. Exceptions were a signature of unidirectional gene flow to one population founded by emigrants of the other 30 years earlier, and bidirectional gene flow between subpopulations within the oldest population. We propose that social cohesion more than landscape characteristics explained population structure, which developed over many generations corresponding to population expansion. Whether or which populations can grow and reach sufficient effective population sizes on their own or require translocations to maintain genetic diversity and population growth is unclear. In the future, we recommend pairing genetic with demographic monitoring of these and other reintroduced elk populations, including targeted monitoring following translocations to evaluate their effects and necessity.

scholarly journals Genetic Diversity and Population Structure of Medemia argun (Mart.) Wurttenb. ex H.Wendl. Based on Genome-Wide Markers

2021 ◽  
Vol 9 ◽  
Author(s):  
Sakina Elshibli ◽  
Helena Korpelainen
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Conservation Status ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Genetic Structuring ◽  
Ancestral Gene ◽  
Low Genetic Diversity

Medemia argun is a wild, dioecious palm, adapted to the harsh arid environment of the Nubian Desert in Sudan and southern Egypt. There is a concern about its conservation status, since little is known about its distribution, abundance, and genetic variation. M. argun grows on the floodplains of seasonal rivers (wadis). The continuing loss of suitable habitats in the Nubian Desert is threatening the survival of this species. We analyzed the genetic diversity, population genetic structure, and occurrence of M. argun populations to foster the development of conservation strategies for M. argun. Genotyping-by-sequencing (GBS) analyses were performed using a whole-genome profiling service. We found an overall low genetic diversity and moderate genetic structuring based on 40 single-nucleotide polymorphisms (SNPs) and 9,866 SilicoDArT markers. The expected heterozygosity of the total population (HT) equaled 0.036 and 0.127, and genetic differentiation among populations/groups (FST) was 0.052 and 0.092, based on SNP and SilicoDArT markers, respectively. Bayesian clustering analyses defined five genetic clusters that did not display any ancestral gene flow among each other. Based on SilicoDArT markers, the results of the analysis of molecular variance (AMOVA) confirmed the previously observed genetic differentiation among generation groups (23%; p < 0.01). Pairwise FST values indicated a genetic gap between old and young individuals. The observed low genetic diversity and its loss among generation groups, even under the detected high gene flow, show genetically vulnerable M. argun populations in the Nubian Desert in Sudan. To enrich and maintain genetic variability in these populations, conservation plans are required, including collection of seed material from genetically diverse populations and development of ex situ gene banks.

scholarly journals Genetic Diversity, Inbreeding Level, and Genetic Load in Endangered Snub-Nosed Monkeys (Rhinopithecus)

2020 ◽  
Vol 11 ◽  
Author(s):  
Weimin Kuang ◽  
Jingyang Hu ◽  
Hong Wu ◽  
Xiaotian Fen ◽  
Qingyan Dai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Large Population ◽  
Population Decline ◽  
Genetic Load ◽  
Term Survival ◽  
Population Sizes ◽  
Genomic Inbreeding ◽  
Inbreeding Level

The snub-nosed monkey genus (Rhinopithecus) comprises five closely related species (R. avunculus, R. bieti, R. brelichi, R. roxellana, and R. strykeri). All are among the world's rarest and most endangered primates. However, the genomic impact associated with their population decline remains unknown. We analyzed population genomic data of all five snub-nosed monkey species to assess their genetic diversity, inbreeding level, and genetic load. For R. roxellana, R. bieti, and R. strykeri, population size is positively correlated with genetic diversity and negatively correlated with levels of inbreeding. Other species, however, which possess small population sizes, such as R. brelichi and R. avunculus, show high levels of genetic diversity and low levels of genomic inbreeding. Similarly, in the three populations of R. roxellana, the Shennongjia population, which possesses the lowest population size, displays a higher level of genetic diversity and lower level of genomic inbreeding. These findings suggest that although R. brelichi and R. avunculus and the Shennongjia population might be at risk, it possess significant genetic diversity and could thus help strengthen their long-term survival potential. Intriguingly, R. roxellana with large population size possess high genetic diversity and low level of genetic load, but they show the highest recent inbreeding level compared with the other snub-nosed monkeys. This suggests that, despite its large population size, R. roxellana has likely been experiencing recent inbreeding, which has not yet affected its mutational load and fitness. Analyses of homozygous-derived deleterious mutations identified in all snub-nosed monkey species indicate that these mutations are affecting immune, especially in smaller population sizes, indicating that the long-term consequences of inbreeding may be resulting in an overall reduction of immune capability in the snub-nosed monkeys, which could provide a dramatic effect on their long-term survival prospects. Altogether, our study provides valuable information concerning the genomic impact of population decline of the snub-nosed monkeys. We revealed multiple counterintuitive and unexpected patterns of genetic diversity in small and large population, which will be essential for conservation management of these endangered species.

scholarly journals Genetic variability and conservation of the endangered Pannonian root vole in fragmented habitats of an agricultural landscape

2021 ◽  
Vol 43 ◽  
pp. 167-191
Author(s):  
Krisztina A. Kelemen ◽  
Felicita Urzi ◽  
Elena Buzan ◽  
Győző F. Horváth ◽  
Filip Tulis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Variability ◽  
Agricultural Landscape ◽  
Isolation By Distance ◽  
Term Survival ◽  
Long Term Survival ◽  
Root Vole ◽  
Low Genetic Diversity

The distribution of the endangered glacial relict subspecies, the Pannonian root vole Alexandromys oeconomus mehelyi Éhik, 1928, is restricted to scattered localities in south-western Slovakia, which belong to the north-eastern zone of its range. Human-induced changes and fragmentation of the landscape have led to the gradual loss of suitable habitats and threaten its long-term survival. The study area in the Danubian Lowland is characterised by small habitat fragments and temporal fluctuations of the habitat area. Root voles were sampled at nine sites to study the level of genetic variability and structure of local subpopulations by scoring 13 microsatellite loci in 69 individuals. Genetic differentiation varied amongst local populations and we did not find a significant isolation-by-distance pattern. Bayesian clustering analysis suggested that dispersal effectively prevents marked genetic subdivision between studied habitat fragments. Significant pairwise differentiation between some subpopulations, however, may be the result of putatively suppressed gene flow. Low genetic diversity in the recent populations probably reflects the isolated location of the study area in the agricultural landscape, suggesting that long-term survival may not be assured. In order to maintain genetic diversity, it is essential to preserve (or even restore) habitats and ensure the possibility of gene flow; habitat protection is, therefore, recommended. Continuous assessment is necessary for effective conservation management and to predict the long-term survival chances of the Pannonian root vole in the study area.

scholarly journals Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 299
Author(s):  
Colette Blyth ◽  
Matthew J. Christmas ◽  
Doug C. Bickerton ◽  
Renate Faast ◽  
Jasmin G. Packer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
South Australia ◽  
Genomic Analysis ◽  
Unknown Origin ◽  
Genetic Connectivity ◽  
Conservation Genomics ◽  
Low Genetic Diversity ◽  
Pollinator Community ◽  
Management Recommendations

In this paper we apply a conservation genomics approach to make evidence-based management recommendations for Acacia whibleyana, an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess genetic connectivity, diversity, and historical inbreeding across all known stands of the species sampling remnant stands, revegetated stands of unknown origin, and a post-fire seedling cohort. Our results indicate a degree of historical connectivity across the landscape, but habitat loss and/or pollinator community disruption are potential causes of strong genetic structure across the remnant stands. Remnant stands had low genetic diversity and showed evidence of historical inbreeding, but only low levels of intra-stand relatedness indicating that risks of contemporary inbreeding are low. Analysis of a post-fire first generation cohort of seedlings showed they likely resulted from intra-stand matings, resulting in reduced genetic diversity compared to the parents. However, admixed seedlings in this cohort showed an increase in heterozygosity relative to likely sources and the non-admixed seedlings of the same stand. Assisted inter-stand gene flow may prove an effective management strategy to boost heterozygosity and corresponding increases in adapting capacity in this endangered species.

scholarly journals Conservation genetics of the yellow-bellied toad (Bombina variegata): population structure, genetic diversity and landscape effects in an endangered amphibian

2021 ◽  
Author(s):  
Heike Pröhl ◽  
Jana Auffarth ◽  
Tjard Bergmann ◽  
Holger Buschmann ◽  
Niko Balkenhol
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Urban Areas ◽  
Negative Relationship ◽  
Genetic Connectivity ◽  
Isolated Populations ◽  
Management Units ◽  
Low Genetic Diversity ◽  
Bombina Variegata ◽  
Genetic Clusters

AbstractRevealing patterns of genetic diversity and barriers for gene flow are key points for successful conservation in endangered species. Methods based on molecular markers are also often used to delineate conservation units such as evolutionary significant units and management units. Here we combine phylo-geographic analyses (based on mtDNA) with population and landscape genetic analyses (based on microsatellites) for the endangered yellow-bellied toad Bombina variegata over a wide distribution range in Germany. Our analyses show that two genetic clusters are present in the study area, a northern and a southern/central one, but that these clusters are not deeply divergent. The genetic data suggest high fragmentation among toad occurrences and consequently low genetic diversity. Genetic diversity and genetic connectivity showed a negative relationship with road densities and urban areas surrounding toad occurrences, indicating that these landscape features act as barriers to gene flow. To preserve a maximum of genetic diversity, we recommend considering both genetic clusters as management units, and to increase gene flow among toad occurrences with the aim of restoring and protecting functional meta-populations within each of the clusters. Several isolated populations with especially low genetic diversity and signs of inbreeding need particular short-term conservation attention to avoid extinction. We also recommend to allow natural gene flow between both clusters but not to use individuals from one cluster for translocation or reintroduction into the other. Our results underscore the utility of molecular tools for species conservation, highlight outcomes of habitat fragmentation onto the genetic structure of an endangered amphibian and reveal particularly threatened populations in need for urgent conservation efforts.

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.

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