Genetic variance distribution of SSR markers and economically important quantitative traits in a progeny trial of Prosopis chilensis (Leguminosae): implications for the ‘Algarrobo’ management programme

2020 ◽  
Author(s):  
Daniela Chequer Charan ◽  
Carolina Pometti ◽  
Mariano Cony ◽  
Juan Cesar Vilardi ◽  
Beatriz O Saidman ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Morphological Variation ◽  
Management Programme ◽  
Stabilizing Selection ◽  
Basal Diameter ◽  
Spine Length ◽  
Prosopis Chilensis ◽  
Progeny Trial ◽  
Neutrality Tests

Abstract Prosopis chilensis (Molina) Stuntz (Leguminosae) is a valuable native species in Argentina included in the Prosopis Management Programme. Natural provenances show important height and shape differentiation throughout their distribution in the Monte Desert. The availability of progeny trials provides an opportunity to quantify genetic differentiation among provenances and test the relative importance of demographic vs adaptive processes on morphological variation. We quantified both genetic and quantitative differentiation of neutral markers and five economically important traits, respectively, among four provenances in a provenance-progeny trial. We aimed to quantify the genetic basis of variations in height, basal diameter, tree shape, spine length and biomass. Two hypotheses were tested: (1) economically important traits have significant heritability, and (2) the phenotypic variation among provenances is the result of local adaptation to particular environmental conditions. Our results indicate that most morphological variation was found among individuals within families (~95 per cent). The h2 estimates were heterogeneous among traits and ranged from low (0 for number of stems) to moderate (0.22 and 0.28 for spine length and biomass, respectively). Variance among families (~5 per cent) was evenly distributed within and among provenances. Morphological differentiation among provenances was low, but significant, and could be attributed mainly to individuals from Villa Unión. Based on molecular markers, genetic differentiation among provenances was low and significant (FST = 0.03; P = 5 × 10−4) but was able to differentiate the groups from Villa Unión, Fiambalá and Mogna-Chilecito. Neutrality tests were conducted using the FST–QST test and DJSOST and δGREGORIUS alternative coefficients of differentiation. Neutrality tests yielded no evidence of local adaptation and were rather consistent in showing a trend toward stabilizing selection, particularly for spine length. The selection strategy for breeding programmes should depend on the trait to be improved and should consider both provenance and familiar information. Considering an intra-familiar ranking is encouraged in order to maximize the genetic gain. Additionally, in order to recover germplasm provenance diversity, based on morphological and microsatellite results, our recommendation would be to include seeds from individuals from at least the Villa Unión, Fiambalá and Mogna-Chilecito areas.

scholarly journals Provenance Trials of the Mexican Spruces in Nursery Conditions: Three Species Endangered by Climatic Variation

2020 ◽  
Vol 3 (1) ◽  
pp. 12
Author(s):  
José Marcos Torres-Valverde ◽  
José Ciro Hernández-Díaz ◽  
Artemio Carrillo-Parra ◽  
Eduardo Mendoza-Maya ◽  
Christian Wehenkel
Keyword(s):  
Cluster Analysis ◽  
Genetic Differentiation ◽  
Local Adaptation ◽  
Quantitative Traits ◽  
Climatic Factors ◽  
Climatic Variation ◽  
Climatic Variables ◽  
Provenance Trials ◽  
Survival And Growth ◽  
Picea Species

The three Mexican spruces’ distributions are fragmented, which could lead to phenological, morphological and genetic differentiation, partially caused by local adaptation. In this study, we examined the effect that climatic variables had on the survival and growth of 5641 Picea seedlings, coming from eight seed provenances of three species and produced in identical nursery conditions. The respective responses of each species and provenance can be considered as a proxy of the genetic differentiation and adaptation of each population. A cluster analysis revealed: (i) significant differences in genetic quantitative traits among the three Picea species and (ii) significant correlations between genetic quantitative traits and climatic factors.

The Use of Protein Electrophoresis for Determining Species Boundaries in Amphipods

Crustaceana ◽  
1993 ◽  
Vol 65 (2) ◽  
pp. 265-277 ◽  
Author(s):  
Barbara A. Stewart
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Morphological Variation ◽  
Protein Electrophoresis ◽  
Species Boundaries ◽  
Allopatric Populations ◽  
A Value ◽  
Electrophoretic Data

AbstractThe use of protein electrophoretic data for determining species boundaries in amphipods is addressed. Analysis of published literature on genetic differentiation in amphipods showed that pairs of allopatric populations which have genetic identities (I) above a value of 0.85 probably represent intraspecific populations, whereas pairs of populations which have genetic identities below about 0.45 probably represent different species. It was recommended that if I values fall between 0.45 and 0.85, additional factors such as evidence of a lack of gene flow between the populations, and concordant morphological variation should be considered.

Geographic and morphological variation in the presence and absence of the pelvic skeleton in the brook stickleback, Culaea inconstans (Kirtland), in Alberta and Saskatchewan

1971 ◽  
Vol 49 (3) ◽  
pp. 343-352 ◽  
Author(s):  
Joseph S. Nelson ◽  
F. Mervyn Atton
Keyword(s):  
Morphological Variation ◽  
Fishery Management ◽  
Fish Introduction ◽  
Spine Length ◽  
Culaea Inconstans ◽  
Full Development ◽  
Normal Individuals ◽  
Brook Stickleback ◽  
Presence And Absence ◽  
Skeleton Formation

Brook sticklebacks, Culaea inconstans (Kirtland), are known from 20 locations in Alberta and Saskatchewan in which a high proportion of the individuals lack all or part of the pelvic skeleton. These locations are interspersed and surrounded by other locations containing individuals with a normal pelvic skeleton. Individuals which lack the skeleton are of both sexes and are fertile in at least one of the lakes.Considerable variation exists between locations in the proportion of individuals with and without the pelvic skeleton. Morphological intermediates are known from most of the 20 locations and virtually all degrees of pelvic skeleton formation exist between its absence and its full development. Little or no gradation exists, however, in pelvic spine length between their absence and presence. Although the pelvic spines are the first part of the pelvic skeleton to appear during ontogeny, they are present only in intermediates with a virtually complete skeleton base. In addition, many intermediates are highly asymmetrical in their pelvic skeleton while development during the ontogeny of normal individuals is symmetrical.There is a greater tendency for individuals in which the pelvic skeleton is deficient to occur in lakes which lack an outlet rather than to occur in lakes with a permanent outlet. An unusually high proportion of the lakes with these aberrant individuals have been subject to fishery management activities (fish introduction and poisoning), but these disturbances are not causing the loss of the pelvic skeleton.

scholarly journals SNP-level FST outperforms window statistics for detecting soft sweeps in local adaptation

2022 ◽  
Author(s):  
Tiago da Silva Ribeiro ◽  
José A Galván ◽  
John E Pool
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Genetic Variant ◽  
Real Data ◽  
Selective Sweeps ◽  
Functional Categories ◽  
Genome Scans ◽  
Genome Wide ◽  
A Genome ◽  
Local Selection

Local adaptation can lead to elevated genetic differentiation at the targeted genetic variant and nearby sites. Selective sweeps come in different forms, and depending on the initial and final frequencies of a favored variant, very different patterns of genetic variation may be produced. If local selection favors an existing variant that had already recombined onto multiple genetic backgrounds, then the width of elevated genetic differentiation (high FST) may be too narrow to detect using a typical windowed genome scan, even if the targeted variant becomes highly differentiated. We therefore used a simulation approach to investigate the power of SNP-level FST (specifically, the maximum SNP FST value within a window) to detect diverse scenarios of local adaptation, and compared it against whole-window FST and the Comparative Haplotype Identity statistic. We found that SNP FST had superior power to detect complete or mostly complete soft sweeps, but lesser power than window-wide statistics to detect partial hard sweeps. To investigate the relative enrichment and nature of SNP FST outliers from real data, we applied the two FST statistics to a panel of Drosophila melanogaster populations. We found that SNP FST had a genome-wide enrichment of outliers compared to demographic expectations, and though it yielded a lesser enrichment than window FST, it detected mostly unique outlier genes and functional categories. Our results suggest that SNP FST is highly complementary to typical window-based approaches for detecting local adaptation, and merits inclusion in future genome scans and methodologies.

Strong genetic differentiation but not local adaptation toward the range limit of a coastal dune plant

Evolution ◽  
2016 ◽  
Vol 70 (11) ◽  
pp. 2520-2536 ◽  
Author(s):  
Karen E. Samis ◽  
Adriana López-Villalobos ◽  
Christopher G. Eckert
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Coastal Dune ◽  
Range Limit ◽  
Dune Plant

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 Climate-driven divergent selection in a foundation tree species: QST-FST evidence from multiple common gardens

2021 ◽  
Author(s):  
Hillary Cooper ◽  
Gerard Allan ◽  
Lela Andrews ◽  
Rebecca Best ◽  
Kevin Grady ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Tree Species ◽  
Divergent Selection ◽  
Population Variation ◽  
Population Divergence ◽  
Phenotypic Traits ◽  
Local Conditions ◽  
Basal Diameter ◽  
Common Gardens ◽  
Fremont Cottonwood

Widespread tree species span large climatic gradients that often lead to high levels of local adaptation and phenotypic divergence across their range. To evaluate the relative roles of selection and drift in driving divergence in phenotypic traits, we compared molecular and quantitative genetic variation in Populus fremontii (Fremont cottonwood), using data from > 9000 SNPs and genotypes from 16 populations reciprocally planted in three common gardens that span the species’ climatic range. We present three major findings: 1) There is significant within- and among-population variation in functional traits expressed in each of the common gardens. 2) There is evidence from all three gardens that population divergence in leaf phenology and specific leaf area has been driven by divergent selection (QST > FST). In contrast, QST-FST comparisons for performance traits like height and basal diameter were highly dependent on growing environment, indicating divergent, stabilizing, or no selection across the three gardens. We show this is likely due to local adaptation of source populations to contrasting growing environments. 3) Climate is a primary selective force driving trait divergence, where the traits showing the strongest correlations with a genotype’s provenance climate also had the highest QST values. We conclude that climatic gradients have contributed to significant phenotypic differences and local adaptation in Fremont cottonwood. These results are important because as climate is changing much more rapidly, traits such as phenology that are finely tuned to local conditions may now be subject to intense selection or quickly become maladaptive.

scholarly journals Female northern grass lizards judge mates by body shape to reinforce local adaptation

2020 ◽  
Author(s):  
Kun Guo ◽  
Chen Chen ◽  
Xiao-Fang Liang ◽  
Yan-Fu Qu ◽  
Xiang Ji
Keyword(s):  
Genetic Differentiation ◽  
Genetic Distance ◽  
Local Adaptation ◽  
Body Shape ◽  
Mate Preferences ◽  
Mate Preference ◽  
Population Divergence ◽  
Female Mate Preference ◽  
Local Adaptations ◽  
Female Mate

Abstract Background: Identifying the factors that contribute to divergence among populations in mate preferences is important for understanding of the manner in which premating reproductive isolation might arise and how this isolation may in turn contribute to the evolutionary process of population divergence. Here, we offered female northern grass lizards (Takydromus septentrionalis) a choice of males between their own population and another four populations to test whether the preferences that females display in the mating trials correlate with phenotypic adaptation to local environments, or to the neutral genetic distance measured by divergence of mitochondrial DNA sequence loci. Results: Females showed a strong preference for native over foreign males. Females that mated with native versus foreign males did not differ from each other in mating latency, or copulation duration. From results of the structural equation modelling we knew that: 1) geographical distance directly contributed to genetic differentiation and environmental dissimilarity; 2) genetic differentiation and environmental dissimilarity indirectly contributed to female mate preference, largely through their effects on morphological divergence; and 3) females judged mates by body shape (appearance) and discriminated more strongly against morphologically less familiar allopatric males.Conclusions: Local adaptation rather than neutral genetic distance influences female mate preference in T. septentrionalis. The tendency to avoid mating with foreign males may indicate that, in T. septentrionalis, local adaptations are more valuable than genetic novelties. Our results highlight the importance of comprehensive studies integrating ecological, molecular and behavioral approaches to understand population divergence in female mate preferences as the consequence of local adaptations.

Crossbreeding reveals the scale and genetic architecture of local adaptation in a predominantly selfing Hordeum spontaneum

2022 ◽  
Vol 1 (1) ◽  
Author(s):  
S Volis ◽  
I Shulgina ◽  
B Dyuzgenbekova
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Spatial Scales ◽  
Hordeum Spontaneum ◽  
Term Effect ◽  
Negev Desert ◽  
Experimental Conditions ◽  
Local Selection ◽  
Wide Range ◽  
F2 Generation

Environmental variation can be large across a wide range of spatial scales resulting in complex patterns of local adaptation across species ranges. We analyzed the scale, genetic mechanism and direct climatic causes of local adaptation in a widely distributed grass Hordeum spontaneum. We performed artificial crosses of maternal plants representing the same Negev desert population with plants originating elsewhere. Pollen donors were plants from other Negev desert populations, non-desert Israeli populations sampled along an aridity gradient, and accessions covering the entire species range. Our study included planting of inter-population hybrids under favorable and simulated desert experimental conditions, followed by analysis of their performance, variation in adaptive traits and relationship with climatic parameters at sampling locations. The combined results of parental phenotypic variation and performance of hybrids were consistent with local selection, reflecting the importance of both regional and local climates. The adaptive genetic differentiation of barley desert populations had a complex architecture. None of the three effects (additive, dominance and epistasis) were fully responsible for this differentiation. Although genetic effects not related to extrinsic selection appear to contribute to genetic differentiation in barley, epistatic effects arising from local selection clearly predominated. The short-term effect of gene flow by pollen was generally negative, indicating that a majority of the new allele combinations created by recombination were maladaptive. However, the long-term effect of occasional pollen flow from other desert populations appears to be positive, as some new recombined genotypes were superior in fitness to the maternal plants even in the F2 generation.

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