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

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.

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The role of environmental factors in the formation of the genetic structure of P. аbies populations

Ecological genetics ◽

10.17816/ecogen15211-20 ◽

2017 ◽

Vol 15 (2) ◽

pp. 11-20

Author(s):

Kseniia V Zakharova ◽

Kirill S Seits

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Geographic Region ◽

Genetic Differences ◽

Environment Impact ◽

Geographical Regions ◽

Adult Trees ◽

Isolation By Environment

Background. Norway spruce (Picea abies (L.) Karst.) is one of the main forest forming spruce species in Europe. Their populations are characterized by the genetic heterogeneity between individuals in population. The genetic structure of P. abies populations studied supported a hypothesis of an environment impact on the degree of genetic differentiation among populations. Materials and methods. Analysis of genetic diversity of natural populations in distinct geographical regions from North-West Russia, South-West Russia, South Norway were done using nuclear microsatellites. The needles were collected from the 20-30 adult trees in each geographical spot taking into account the local environment. The statistical calculations were performed with GenAlEx 6.5.03 and Structure 2.3.4. Results. The analysis highlighted the environmental impact on the genetic diversity. The genetic structure of spruce cenopopulations from poor conditions are extremely different from those of cenopopulations growing under rich environmental conditions in one geographic region. The genetic differences between them are comparable with the genetic differences between spatially remote populations. Conclusion. The role of the isolation by environment as a pattern in which genetic differentiation increases with environmental differences independent of the geographic distance is essential for genetic structure of spruce populations.

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Landscape and climatic features drive genetic differentiation processes in a South American coastal plant

10.1101/2020.07.02.184366 ◽

2020 ◽

Author(s):

Gustavo A. Silva-Arias ◽

Lina Caballero-Villalobos ◽

Giovanna C. Giudicelli ◽

Loreta B. Freitas

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Coastal Plain ◽

Population Differentiation ◽

Water Bodies ◽

Marginal Populations ◽

Landscape Features ◽

Precipitation Seasonality ◽

Isolation By Environment

ABSTRACTBackground and aimsHistorical and ecological processes shaped the patterns of genetic diversity in plant species; among these, colonization to new environments such as coastal regions generate multiple signals of interest to understand the influence of landscape features on the population differentiation.MethodsWe analysed the genetic diversity and population structure of Calibrachoa heterophylla to infer the influence of abiotic landscape features on this coastal species’ gene flow in the South Atlantic Coastal Plain (SACP). We used ten microsatellite loci to genotype 253 individuals from 15 populations, covering the species’ entire geographical range. We applied population genetics analyses to determine population diversity and structure along the SACP, migration model inference and correlative analyses to disentangle the most likely drivers of gene flow in the SACP.Key ResultsThe C. heterophylla populations located more distantly from the seashore showed higher genetic diversity than those closer to the sea. The genetic differentiation had a consistent signal of isolation-by-distance. Landscape features, such as water bodies and wind corridors, and raw geographical distances equally explained the genetic differentiation, whereas the precipitation seasonality showed a strong signal for isolation-by-environment in marginal populations. The estimated gene flow suggested that marginal populations had restricted immigration rates, which could enhance the genetic differentiation.ConclusionsThe influence of topographical features in population differentiation in C. heterophylla is related with the history of the coastal plain deposition. Gene flow is mainly restricted to nearby populations and facilitated by wind fields but with no apparent influence of large water bodies. Furthermore, differential rainfall regimes in marginal populations can promote local genetic differentiation.

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Landscape and climatic features drive genetic differentiation processes in a South American coastal plant

BMC Ecology and Evolution ◽

10.1186/s12862-021-01916-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Gustavo A. Silva-Arias ◽

Lina Caballero-Villalobos ◽

Giovanna C. Giudicelli ◽

Loreta B. Freitas

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Coastal Plain ◽

Atlantic Coastal Plain ◽

Water Bodies ◽

Marginal Populations ◽

Landscape Features ◽

Precipitation Seasonality ◽

Isolation By Environment

Abstract Background Historical and ecological processes shape patterns of genetic diversity in plant species. Colonization to new environments and geographical landscape features determine, amongst other factors, genetic diversity within- and differentiation between-populations. We analyse the genetic diversity and population structure of Calibrachoa heterophylla to infer the influence of abiotic landscape features on the level of gene flow in this coastal species of the South Atlantic Coastal Plain. Results The C. heterophylla populations located on early-deposited coastal plain regions show higher genetic diversity than those closer to the sea. The genetic differentiation follows a pattern of isolation-by-distance. Landscape features, such as water bodies and wind corridors, and geographical distances equally explain the observed genetic differentiation, whereas the precipitation seasonality exhibits a strong signal for isolation-by-environment in marginal populations. The estimated levels of gene flow suggest that marginal populations had restricted immigration rates enhancing differentiation. Conclusions Topographical features related to coastal plain deposition history influence population differentiation in C. heterophylla. Gene flow is mainly restricted to nearby populations and facilitated by wind fields, albeit without any apparent influence of large water bodies. Furthermore, differential rainfall regimes in marginal populations seem to promote genetic differentiation.

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

10.21203/rs.3.rs-779119/v1 ◽

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.

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

Australian Journal of Zoology ◽

10.1071/zo18059 ◽

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.

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The role of environment, local adaptation, and past climate fluctuation on the amount and distribution of genetic diversity in two subspecies of Mexican wild Zea mays

American Journal of Botany ◽

10.1002/ajb2.1561 ◽

2020 ◽

Vol 107 (11) ◽

pp. 1542-1554

Author(s):

Jaime Gasca‐Pineda ◽

Yocelyn T. Gutiérrez‐Guerrero ◽

Erika Aguirre‐Planter ◽

Luis E. Eguiarte

Keyword(s):

Genetic Diversity ◽

Zea Mays ◽

Local Adaptation ◽

Past Climate ◽

Climate Fluctuation

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Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

10.1101/500041 ◽

2018 ◽

Author(s):

Marco A. Escalante ◽

Charles Perrier ◽

Francisco J. García-De León ◽

Arturo Ruiz-Luna ◽

Enrique Ortega-Abboud ◽

...

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Genetic Variation ◽

Local Adaptation ◽

Population Genomics ◽

Landscape Heterogeneity ◽

Genotyping By Sequencing ◽

Anthropogenic Factors ◽

Nucleotide Polymorphisms ◽

Evolutionary Potential

AbstractHow environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

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

10.21203/rs.3.rs-640424/v1 ◽

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.

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

Frontiers in Genetics ◽

10.3389/fgene.2021.705337 ◽

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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Different Habitats Show Similar Genetic Structure of Bunias orientalis L. (Brassicaceae)in Lithuania

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha4129186 ◽

2013 ◽

Vol 41 (2) ◽

pp. 396 ◽

Cited By ~ 5

Author(s):

Jolanta PATAMSYTĖ ◽

Tatjana ČĖSNIENĖ ◽

Donatas NAUGŽEMYS ◽

Violeta KLEIZAITĖ ◽

Virginija TUNAITIENĖ ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Genetic Difference ◽

Habitat Type ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Baltic Countries ◽

Bunias Orientalis ◽

The Impact

We studied genetic diversity within and among populations of warty cabbage (Bunias orientalis L.), which is an alien species in Lithuania and other Baltic countries. In Lithuania, this weed colonises two main types of habitats: railway/roadsides and meadows on riversides. The aim of this study was to assess the genetic structure of invasive populations of B. orientalis in Lithuania and consider the impact of diverse habitats on the partitioning of genetic diversity using inter-simple sequence repeat (ISSR) markers. An analysis of molecular variance (AMOVA) carried out on the basis of ISSR showed that there is high genetic differentiation (46%) among populations of B. orientalis, which is probably caused by the founder effect and limited gene flow. However, we observed no impact of habitat on the genetic difference among populations. Similar levels of ISSR polymorphic loci were observed in riverside (P = 31.67%) and railway/roadsides (P = 30.51%) populations. UPGMA cluster analysis and principal coordinate analysis (PCoA) also did not show grouping of studied populations according to habitat type. High genetic differentiation among populations, as indicated by ISSR markers, confirm multiple independent introductions of this species in Lithuania.

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