scholarly journals The Genomic Basis of the Genetic Differentiation and Local Adaptive Evolution of Pampus Echinogaster based on SLAF-seq

2021 ◽  
Author(s):  
Yuan Li ◽  
Fangrui Lou ◽  
Hai Li ◽  
Rui Wang ◽  
Zizi Cai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Expansion ◽  
Nucleotide Polymorphisms ◽  
Stress Reactions ◽  
Long Distance ◽  
Evolutionary Mechanisms ◽  
Inflammatory Reactions ◽  
Genomic Study

Abstract Background: Factors such as climate change (especially ocean warming) and overfishing have led to a decline in the supply of Pampus echinogaster and a trend of decreasing age. Exploring the genetic structure and local adaptive evolutionary mechanisms is crucial for the management of P. echinogaster. Results: This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the overall genetic diversity among the nine P. echinogaster populations was high. The Shantou population had the lowest genetic diversity, and the Tianjin population had the highest. Meanwhile, the population genetic structure based on all SNPs revealed significant gene exchange and insignificant genetic differentiation between the nine P. echinogaster populations. Based on pairwise genetic differentiation (FST), we further screened 1,852 outlier SNPs that might have been affected by habitat selection and annotated SLAF tags containing these 1,852 outlier SNPs using Blast2GO. The annotation results showed that the genomic sequences at the outlier SNPs were mainly related to material metabolism, ion transport, breeding, stress response, and inflammatory reactions, which may be related to the adaptation of P. echinogaster to different environmental conditions (such as water temperature and salinity) in different sea areas.Conclusions: The high genetic similarity of nine P. echinogaster populations may have been caused by the population expansion after the last glacial period, the lack of balance between migration and genetic drift, and the long-distance diffusion of eggs and larvae. We suspected that variation of these genes associated with material metabolism, ion transfer, breeding, stress reactions, and inflammatory reactions were critical for adaptation to spatially heterogeneous temperatures in natural P. echinogaster populations.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Genetic Diversity and Population Structure in the Ryukyu Flying Fox Inferred from Remote Sampling in the Yaeyama Archipelago

2020 ◽  
Author(s):  
Yuto Taki ◽  
Christian E. Vincenot ◽  
Yu Sato ◽  
Miho Inoue-Murayama
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Haplotype Network ◽  
Iucn Red List ◽  
The Philippines ◽  
Conservation Units ◽  
Long Distance ◽  
Flying Fox

AbstractThe Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. Although P. dasymallus is listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species.mtDNA analysis was conducted with 142 DNA remote samples, mostly from feces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure.Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population.We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among populations of the archipelago. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.

scholarly journals Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2764 ◽  
Author(s):  
Pilar Suárez-Montes ◽  
Mariana Chávez-Pesqueira ◽  
Juan Núñez-Farfán
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Mating System ◽  
Population Expansion ◽  
Outcrossing Rate ◽  
Mixed Mating ◽  
Long Distance ◽  
Mixed Mating System ◽  
Genetic Structure Of Populations

IntroductionTheory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herbAphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios.MethodsTwelve populations ofA. aurantiacawere sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population.ResultsDespite prevailing habitat fragmentation, populations ofA. aurantiacapossess high genetic variation (He = 0.61), weak genetic structure (Rst = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected.Aphelandra aurantiacashows a mixed mating system (tm = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum.DiscussionHabitat fragmentation has not increased genetic differentiation or reduced genetic diversity ofA. aurantiacadespite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure ofA. aurantiacaseem to have been buffered owing to its large effective populations and long-distance dispersal events. In particular, its mixed-mating system, mostly of outcrossing, suggests high efficiency of pollinators promoting connectivity and reducing inbreeding. However, some results point that the effects of fragmentation are underway, as two small fragments showed higher membership probabilities to their population of origin, suggesting genetic isolation. Our findings underscore the importance of fragment size to maintain genetic connectivity across the landscape.

scholarly journals Genetic diversity and population structure in the Ryukyu flying fox inferred from remote sampling in the Yaeyama archipelago

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248672
Author(s):  
Yuto Taki ◽  
Christian E. Vincenot ◽  
Yu Sato ◽  
Miho Inoue-Murayama
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Haplotype Network ◽  
Iucn Red List ◽  
The Philippines ◽  
Conservation Units ◽  
Long Distance ◽  
Flying Fox

The Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. AlthoughP.dasymallusis listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species. mtDNA analysis was conducted with 142 DNA remote samples, mostly from faeces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure. Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population. We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among the archipelago’s populations. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.

scholarly journals Serial founder effects and genetic differentiation during worldwide range expansion of monarch butterflies

2014 ◽  
Vol 281 (1797) ◽  
pp. 20142230 ◽  
Author(s):  
Amanda A. Pierce ◽  
Myron P. Zalucki ◽  
Marie Bangura ◽  
Milan Udawatta ◽  
Marcus R. Kronforst ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Genetic Drift ◽  
North American ◽  
Range Expansion ◽  
Dispersal Ability ◽  
Founder Effects ◽  
Long Distance ◽  
Mobile Species ◽  
High Dispersal

Range expansions can result in founder effects, increasing genetic differentiation between expanding populations and reducing genetic diversity along the expansion front. However, few studies have addressed these effects in long-distance migratory species, for which high dispersal ability might counter the effects of genetic drift. Monarchs ( Danaus plexippus ) are best known for undertaking a long-distance annual migration in North America, but have also dispersed around the world to form populations that do not migrate or travel only short distances. Here, we used microsatellite markers to assess genetic differentiation among 18 monarch populations and to determine worldwide colonization routes. Our results indicate that North American monarch populations connected by land show limited differentiation, probably because of the monarch's ability to migrate long distances. Conversely, we found high genetic differentiation between populations separated by large bodies of water. Moreover, we show evidence for serial founder effects across the Pacific, suggesting stepwise dispersal from a North American origin. These findings demonstrate that genetic drift played a major role in shaping allele frequencies and created genetic differentiation among newly formed populations. Thus, range expansion can give rise to genetic differentiation and declines in genetic diversity, even in highly mobile species.

Genetic differentiation of regional populations of the widespread Asiatic toad (Bufo gargarizans), as revealed by development of novel microsatellite markers

2018 ◽  
Vol 66 (6) ◽  
pp. 335
Author(s):  
T. Pan ◽  
P. Yan ◽  
M. Yang ◽  
H. Wang ◽  
I. Ali ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Yangtze River ◽  
The Yangtze River ◽  
Geographic Scale ◽  
Widespread Species ◽  
Bufo Gargarizans ◽  
Toad Bufo

Dispersal is a key component of a species’ life history, by influencing population persistence, genetic structure, adaptation and maintenance of genetic diversity. The Asiatic toad (Bufo gargarizans) is a widespread species in east Asia. However, we still have no knowledge of what kind of geographical scale equates to genetic differentiation within B. gargarizans. In this study, the population genetics of B. gargarizans was studied at five localities, with the Yangtze River running through the sampling area, in order to detect the level of genetic differentiation and the natural barriers to the species’ dispersal on a small geographic scale, by means of the development and use of novel microsatellite loci. These markers revealed a relatively high level of genetic diversity. Distinct genetic structure among populations in B. gargarizans was observed, as described by genetic distance, AMOVA, PCA and Geneland results. A weak but significant positive correlation between genetic distance and geographical distance. The combination of these findings suggests that the Yangtze River and geographic distance may act as effective barriers for B. gargarizans. These results serve as benchmark data for understanding the impacts of dispersal barriers and continued landscape research on B. gargarizans.

scholarly journals First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes (Canis latrans)

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 66 ◽  
Author(s):  
Javier Monzón
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Canis Latrans ◽  
Regional Analysis ◽  
Model Organism ◽  
Nucleotide Polymorphisms ◽  
Genomic Markers

Previous genetic studies of eastern coyotes (Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

scholarly journals Influence of isolation by environment and landscape heterogeneity on genetic structure of wild rice Zizania latifolia along a latitudinal gradient

2020 ◽  
Author(s):  
Godfrey Kinyori Wagutu ◽  
Xiangrong Fan ◽  
Wenlong Fu ◽  
Wei Li ◽  
Yuanyuan Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Local Adaptation ◽  
Landscape Heterogeneity ◽  
Maximum Temperature ◽  
Zizania Latifolia ◽  
Precipitation Seasonality ◽  
Isolation By Environment

AbstractGlobal aquatic habitats are undergoing rapid degradation and fragmentation as a result of land-use change and climate change. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the role of environment, landscape heterogeneity and geographical distance in shaping the genetic structure of 28 natural populations of Zizania latifolia (Griseb.) Turcz. Ex Stapf in China based on 25 microsatellite markers. Genetic structure was investigated by analysis of molecular variance (AMOVA), estimation of FST, Bayesian clustering and Thermodynamic Integration (TI) methods. Isolation by environment (IBE), isolation by resistance (IBR) and isolation by distance (IBD) hypotheses were compared using a reciprocal causal model (RCM). Further, generalized linear models and spatially explicit mixed models, by using geographic, landscape and genetic variables, were developed to elucidate the role of environment in driving Z. latifolia genetic diversity. The genetic differentiation across all populations was high: FST = 0.579; Øpt = 0.578. RCM exclusively supported IBE in shaping genetic structuring, only partial support for IBR, but not for IBD. Maximum temperature of the warmest month and precipitation seasonality were the plausible parameters responsible for genetic diversity. After controlling for spatial effect and landscape complexity, precipitation seasonality was significantly associated with genetic diversity. Based on these findings, genetic structure of Z. latifolia across China seem to be as a result of local adaptation. Environmental gradient and topographical barriers, rather than geographical isolation, influence genetic differentiation of aquatic species across China resulting in instances of local adaptation.

scholarly journals Assessment of local genetic structure and connectivity of the common eelgrass Zostera marina for seagrass restoration in northern Europe

2021 ◽  
Vol 664 ◽  
pp. 103-116
Author(s):  
L Martínez-García ◽  
B Hansson ◽  
J Hollander
Keyword(s):  
Climate Change ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Baltic Sea ◽  
Zostera Marina ◽  
Anthropogenic Impacts ◽  
Ecosystem Functions ◽  
Long Distance ◽  
Seagrass Meadows

Seagrass meadows are one of the most important habitats in coastal regions since they constitute a multifunctional ecosystem providing high productivity and biodiversity. They play a key role in carbon sequestration capacity, mitigation against coastal erosion and as nursery grounds for many marine fish and invertebrates. However, despite these ecosystem functions and services, seagrass meadows are a threatened ecosystem worldwide. In the Baltic Sea, seagrass meadows have declined rapidly, mainly because of eutrophication, anthropogenic activities and climate change. This decline has the potential to erode the genetic variation and genetic structure of the species. In this study, we assessed how genetic variation and genetic differentiation vary among Zostera marina meadows and with a number of environmental characteristics in the county of Scania in southern Sweden. A total of 205 individuals sampled at 12 locations were analysed with 10 polymorphic microsatellite loci. Results showed that in spite of anthropogenic impacts and climate change pressures, locations of Z. marina possessed high genetic variation and weak genetic differentiation, with 3 major genetic clusters. Long-distance dispersal and/or stepping-stone dispersal was found among locations, with higher migration rates within the west coast. Organic matter, salinity and maximum depth appeared to be factors most strongly associated with the genetic structure and morphological variation of Z. marina. These findings contribute significantly in the identification of potential donor sites and the viability of impacted areas to recover from natural recruitment, for the development of effective transplantation measures of Z. marina in the southern Baltic Sea and temperate regions elsewhere.

scholarly journals Genetic Differentiation of Reintroduced Père David’s Deer (Elaphurus davidianus) Based on Population Genomics Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Shumiao Zhang ◽  
Chao Li ◽  
Yiping Li ◽  
Qi Chen ◽  
Defu Hu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Size ◽  
Population Genomics ◽  
Distribution Area ◽  
History Of ◽  
Père David’S Deer ◽  
Free Ranging ◽  
Elaphurus Davidianus

The reintroduction is an important conservation tool to restore a species in its historically distribution area, but the rate of reintroduction success varies across species or regions due to different reasons. Genetic evaluation is important to the conservation management of reintroduced species. Conservation concerns relate to genetic threats for species with a small population size or severely historically bottle-necked species, such as negative consequences associated with loss of genetic diversity and inbreeding. The last 40years have seen a rapid increasing of population size for Père David’s deer (Elaphurus davidianus), which originated from a limited founder population. However, the genetic structure of reintroduced Père David’s deer has not been investigated in terms of population genomics, and it is still not clear about the evolutionary history of Père David’s deer and to what extent the inbreeding level is. Conservation genomics methods were used to reconstruct the demographic history of Père David’s deer, evaluate genetic diversity, and characterize genetic structure among 18 individuals from the captive, free-ranging and wild populations. The results showed that 1,456,457 single nucleotide polymorphisms (SNPs) were obtained for Père David’s deer, and low levels of genome-wide genetic diversity were observed in Père David’s deer compared with Red deer (Cervus elaphus) and Sika deer (Cervus nippon). A moderate population genetic differentiation was detected among three populations of Père David’s deer, especially between the captive population in Beijing Père David’s deer park and the free-ranging population in Jiangsu Dafeng National Nature Reserve. The effective population size of Père David’s deer started to decline ~25.8ka, and the similar levels of three populations’ LD reflected the genetic impacts of long-term population bottlenecks in the Père David’s deer. The findings of this study could highlight the necessity of individual exchange between different facilities, and genetic management should generally be integrated into conservation planning with other management considerations.

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