Low Genetic Diversity and Low Gene Flow Corresponded to a Weak Genetic Structure of Ruddy-Breasted Crake (Porzana fusca) in China

2018 ◽  
Vol 56 (6) ◽  
pp. 586-617 ◽  
Author(s):  
Chaoying Zhu ◽  
Peng Chen ◽  
Yuqing Han ◽  
Luzhang Ruan
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Low Genetic Diversity

scholarly journals Population Genetic Structure and Habitat Connectivity for Jaguar (Panthera onca) Conservation in Central Belize.

2019 ◽  
Author(s):  
Angelica Menchaca ◽  
Natalia Rossi ◽  
Jeremy Froidevaux ◽  
Isabela Dias-freedman ◽  
Anthony Caragiulo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Connectivity ◽  
Suitable Habitat ◽  
Fine Scale ◽  
Panthera Onca ◽  
Wildlife Sanctuary ◽  
Landscape Permeability ◽  
Forest Reserve

Abstract Connectivity among jaguar (Panthera onca) populations will ensure natural gene flow and the long-term survival of the species throughout its range. Jaguar conservation efforts have focused primarily on connecting suitable habitat in a broad-scale. Accelerated habitat reduction, human-wildlife conflict, limited funding, and the complexity of jaguar behaviour have proven challenging to maintain connectivity between populations effectively. Here, we used non-invasive genetic sampling and individual-based conservation genetic analyses to assess genetic diversity and levels of genetic connectivity between individuals in the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We used expert knowledge and scientific literature to develop models of landscape permeability based on circuit theory with fine-scale landscape features as ecosystem types, distance to human settlements and roads to predict the most probable jaguar movement across central Belize. Results We used 12 highly polymorphic microsatellite loci to identify 50 individual jaguars. We detected high levels of genetic diversity across loci (HE= 0.61, HO= 0.55, and NA=9.33). Using Bayesian clustering and multivariate models to assess gene flow and genetic structure, we identified one single group of jaguars (K = 1). We identified critical areas for jaguar movement that fall outside the boundaries of current protected areas in central Belize. We detected two main areas of high landscape permeability in a stretch of approximately 18 km between Sittee River Forest Reserve and Manatee Forest Reserve that may increase functional connectivity and facilitate jaguar dispersal from and to Cockscomb Basin Wildlife Sanctuary. Our analysis provides important insights on fine-scale genetic and landscape connectivity of jaguars in central Belize, an area of conservation concern. Conclusions The results of our study demonstrate high levels of relatively recent gene flow for jaguars between two study sites in central Belize. Our landscape analysis detected corridors of expected jaguar movement between the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We highlight the importance of maintaining already established corridors and consolidating new areas that further promote jaguar movement across suitable habitat beyond the boundaries of currently protected areas. Continued conservation efforts within identified corridors will further maintain and increase genetic connectivity in central Belize.

scholarly journals Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications

2021 ◽  
Vol 9 ◽  
Author(s):  
Heather R. Kates ◽  
Fernando López Anido ◽  
Guillermo Sánchez-de la Vega ◽  
Luis E. Eguiarte ◽  
Pamela S. Soltis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Morphological Diversity ◽  
Cucurbita Maxima ◽  
Wild Progenitor ◽  
Breeding Potential ◽  
Trait Improvement ◽  
Wild Progenitors

Studies of domestication genetics enrich our understanding of how domestication shapes genetic and morphological diversity. We characterized patterns of genetic variation in two independently domesticated pumpkins and their wild progenitors to assess and compare genetic consequences of domestication. To compare genetic diversity pre- and post-domestication and to identify genes targeted by selection during domestication, we analyzed ∼15,000 SNPs of 48 unrelated accessions, including wild, landrace, and improved lines for each of two pumpkin species, Cucurbita argyrosperma and Cucurbita maxima. Genetic diversity relative to its wild progenitor was reduced in only one domesticated subspecies, C. argyrosperma ssp. argyrosperma. The two species have different patterns of genetic structure across domestication status. Only 1.5% of the domestication features identified for both species were shared between species. These findings suggest that ancestral genetic diversity, wild-crop gene flow, and domestication practices shaped the genetic diversity of two similar Cucurbita crops in different ways, adding to our understanding of how genetic diversity changes during the processes of domestication and how trait improvement impacts the breeding potential of modern crops.

Intact genetic structure and high levels of genetic diversity in bottlenecked sockeye salmon (Oncorhynchus nerka) populations of the Fraser River, British Columbia, Canada

2000 ◽  
Vol 57 (10) ◽  
pp. 1985-1998 ◽  
Author(s):  
Ruth E Withler ◽  
Khai D Le ◽  
R John Nelson ◽  
Kristina M Miller ◽  
Terry D Beacham
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Allelic Diversity ◽  
Lower Proportion ◽  
Fraser River ◽  
Rare Alleles ◽  
Genetic Bottlenecks

Analysis of six microsatellite loci in 5800 sockeye salmon (Oncorhynchus nerka) from 29 Fraser River populations provided little evidence of genetic bottlenecks or mass straying in upper Fraser sockeye salmon resulting from reduced abundances following 1913-1914 rockslides in the Fraser canyon and successive decades of high exploitation. Upper Fraser populations were not characterized by a paucity of rare alleles, a sensitive indicator of populations in which effective size has been recently reduced. Heterozygosity and allelic diversity did not differ consistently between lower and upper Fraser populations. Throughout the watershed, early-migrating populations had lower allelic diversity and a lower proportion of rare alleles than did late-migrating ones. Genetic differentiation between upper and lower Fraser populations and heterogeneity among lower Fraser populations supported the suggestion that Fraser sockeye salmon are descendants of at least two postglacial "races." Variation among lakes within regions was the strongest component of genetic structure, accounting for five times the variation among populations within lakes and more than two times the variation among regions. Extensive historical transplants of eggs and juveniles apparently resulted in lit tle gene flow among regions, but three populations were reestablished or rebuilt as the result of more recent transplants.

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 Pronounced genetic structure and low genetic diversity in European red-billed chough (Pyrrhocorax pyrrhocorax) populations

2012 ◽  
Vol 13 (5) ◽  
pp. 1213-1230 ◽  
Author(s):  
Marius A. Wenzel ◽  
Lucy M. I. Webster ◽  
Guillermo Blanco ◽  
Malcolm D. Burgess ◽  
Christian Kerbiriou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Low Genetic Diversity

scholarly journals Genetic structure of Oryza glumaepatula wild rice populations and evidence of introgression from O. sativa in Costa Rica

2015 ◽  
Author(s):  
Eric J Fuchs ◽  
Allan Meneses Martínez ◽  
Amanda Calvo ◽  
Melania Muñoz ◽  
Griselda Arrieta-Espinoza
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Costa Rica ◽  
Genetic Structure ◽  
Wild Species ◽  
Wild Rice ◽  
Wild Rice Species ◽  
Genetic Diversity And Structure ◽  
Diversity Estimates ◽  
Oryza Glumaepatula

Wild crop relatives are an important source of genetic diversity for crop improvement. However, gene flow from cultivated species into wild species may prove detrimental. Introgression may lead to changes in wild species by incorporating alleles from domesticated species, which may increase the likelihood of extinction. The objective of the present study is to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated if there is evidence of introgression between wild rice and commercial varieties of O. sativa since it is cultivated commonly in close proximity to wild rice populations. Individuals from all known O. glumaepatula populations in Costa Rica were collected. With the aid of 455 AFLP markers, we characterized the genetic diversity and structure among seven populations in northern Costa Rica. Given the dominant nature of our markers, Bayesian estimates of genetic structure were used. We also compared genetic diversity estimates between O. glumaepatula individuals and O. sativa commercial rice. Our results show that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. This is likely a result of large population size. Despite the restricted distributions of this wild species, in Costa Rica most populations are composed of several thousand individuals, thus reducing the effects of drift on genetic diversity. Our results also found low but significant structure (\theta=0.03±0.001) among populations that are separated by ~10 Km within a single river. The position of the population along the river did not influence genetic diversity estimates or differences among populations. This river does not have a strong current and meadows or seeds may easily move upstream, thus homogenizing genetic diversity across populations regardless of river position. Ample gene flow through pollen, seeds or detached culms within the same river reduces genetic structure. A Bayesian structure analysis showed that individuals from two populations share a significant proportion of their genomes with O. sativa genome. These results suggest that the low levels of genetic structure found in these populations are likely the result of introgression from cultivated O. sativa populations. These results expose an important biohazard as recurrent hybridization may reduce genetic diversity of this wild rice species. Introgression may transfer commercial traits into the only populations of O. glumaepatula in Costa Rica, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

scholarly journals Landscape genomics of an obligate mutualism: discordant population structures between a leafcutter-ant and its fungal cultivars

2018 ◽  
Author(s):  
Chad C. Smith ◽  
Jesse N. Weber ◽  
Alexander S. Mikheyev ◽  
Flavio Roces ◽  
Martin Bollazzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Abiotic Factors ◽  
Genotyping By Sequencing ◽  
Range Limit ◽  
Range Margin ◽  
Landscape Genomics ◽  
Temperature And Precipitation ◽  
Obligate Mutualism

AbstractTo explore landscape genomics at the range limit of an obligate mutualism, we used genotyping-by-sequencing (ddRADseq) to quantify population structure and the effect of hostsymbiont interactions between the northernmost fungus-farming leafcutter ant Atta texana and its two main types of cultivated fungus. At local scales, genome-wide differentiation between ants associated with either of the two fungal types is greater than the differentiation associated with the abiotic factors temperature and precipitation, suggesting that specific ant-fungus genome-genome combinations may have been favored by selection. For the ant hosts, we found a broad cline of genetic structure across the range, and a reduction of genetic diversity along the axis of range expansion towards the range margin. In contrast, genetic structure was patchy in the cultivated fungi, with no consistent reduction of fungal genetic diversity at the range margins. This discordance in population-genetic structure between ant hosts and fungal symbionts is surprising because the ant farmers co-disperse with their vertically-transmitted fungal symbionts, but apparently the fungi disperse occasionally also through between-nest horizontal transfer or other unknown dispersal mechanisms. The discordance in populationgenetic structure indicates that genetic drift and gene flow differ in magnitude between each partner in this leafcutter mutualism. Together, these findings imply that variation in the strength of drift and gene flow experienced by each mutualistic partner affects adaptation to environmental stress at the range margin, and genome-genome interactions between host and symbiont influences adaptive genetic differentiation of the host during range evolution in this obligate mutualism.

scholarly journals Population Genetic Structure and Habitat Connectivity for Jaguar (Panthera onca) Conservation in Central Belize.

2019 ◽  
Author(s):  
Angelica Menchaca ◽  
Natalia Rossi ◽  
Jeremy Froidevaux ◽  
Isabela Dias-freedman ◽  
Anthony Caragiulo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Connectivity ◽  
Suitable Habitat ◽  
Fine Scale ◽  
Panthera Onca ◽  
Wildlife Sanctuary ◽  
Landscape Permeability ◽  
Forest Reserve

Abstract Background Connectivity among jaguar (Panthera onca) populations will ensure natural gene flow and the long-term survival of the species throughout its range. Jaguar conservation efforts have focused primarily on connecting suitable habitat in a broad-scale. Accelerated habitat reduction, human-wildlife conflict, limited funding, and the complexity of jaguar behaviour have proven challenging to maintain connectivity between populations effectively. Here, we used non-invasive genetic sampling and individual-based conservation genetic analyses to assess genetic diversity and levels of genetic connectivity between individuals in the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We used expert knowledge and scientific literature to develop models of landscape permeability based on circuit theory with fine-scale landscape features as ecosystem types, distance to human settlements and roads to predict the most probable jaguar movement across central Belize. Results We used 12 highly polymorphic microsatellite loci to identify 50 individual jaguars. We detected high levels of genetic diversity across loci (HE= 0.61, HO= 0.55, and NA=9.33). Using Bayesian clustering and multivariate models to assess gene flow and genetic structure, we identified one single group of jaguars (K = 1). We identified critical areas for jaguar movement that fall outside the boundaries of current protected areas in central Belize. We detected two main areas of high landscape permeability in a stretch of approximately 18 km between Sittee River Forest Reserve and Manatee Forest Reserve that may increase functional connectivity and facilitate jaguar dispersal from and to Cockscomb Basin Wildlife Sanctuary. Our analysis provides important insights on fine-scale genetic and landscape connectivity of jaguars in central Belize, an area of conservation concern. Conclusions The results of our study demonstrate high levels of relatively recent gene flow for jaguars between two study sites in central Belize. Our landscape analysis detected corridors of expected jaguar movement between the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We highlight the importance of maintaining already established corridors and consolidating new areas that further promote jaguar movement across suitable habitat beyond the boundaries of currently protected areas. Continued conservation efforts within identified corridors will further maintain and increase genetic connectivity in central Belize.

scholarly journals Genetic structure of the threatened West-Pannonian population of Great Bustard (Otis tarda)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1759
Author(s):  
Jose L. Horreo ◽  
Rainer Raab ◽  
Péter Spakovszky ◽  
Juan Carlos Alonso
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Structure ◽  
Great Bustard ◽  
Single Population ◽  
Current Conservation ◽  
Otis Tarda ◽  
Hungarian Population ◽  
First Time

The genetic diversity, population structure and gene flow of the Great Bustards (Otis tarda) living in Austria-Slovakia-West Hungary (West-Pannonian region), one of the few populations of this globally threatened species that survives across the Palaearctic, has been assessed for the first time in this study. Fourteen recently developed microsatellite loci identified one single population in the study area, with high values of genetic diversity and gene flow between two different genetic subunits. One of these subunits (Heideboden) was recognized as a priority for conservation, as it could be crucial to maintain connectivity with the central Hungarian population and thus contribute to keeping contemporary genetic diversity. Current conservation efforts have been successful in saving this threatened population from extinction two decades ago, and should continue to guarantee its future survival.

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