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opencc-by-4.0Apr 2019View details →

Fig. 3 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction

Fig. 3. Haplotype network based on partial sequencing of the D-loop region (mtDNA) of 92 individuals of Brycon nattereri from the Laranjinha River. Circle sizes are pro- portional to haplotype frequency.

opencc-zeroDec 2016View details →

Data from: Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host

Genetic comparisons of parasitoids and their hosts are expected to reflect ecological and evolutionary processes that influence the interactions between species. The parasitoid wasp, Cotesia vestalis, and its host diamondback moth (DBM), Plutella xylostella, provide opportunities to test whether the specialist natural enemy migrates seasonally with its host or occurs as resident population. We genotyped 17 microsatellite loci and two mitochondrial genes for 158 female adults of C. vestalis collected from 12 geographical populations, as well as nine microsatellite loci for 127 DBM larvae from six separate sites. The samplings covered both the likely source (southern) and immigrant (northern) areas of DBM from China. Populations of C. vestalis fell into three groups, pointing to isolation in northwestern and southwestern China and strong genetic differentiation of these populations from others in central and eastern China. In contrast, DBM showed much weaker genetic differentiation and high rates of gene flow. TESS analysis identified the immigrant populations of DBM as showing admixture in northern China. Genetic disconnect between C. vestalis and its host suggests that the parasitoid did not migrate yearly with its host but likely consisted of resident populations in places where its host could not survive in winter.

opencc-by-4.0Dec 2020View details →

Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia

Microsatellite loci calls, sex, and mean centre detection per individual (GrizzlyMicroLociMeanXY.csv) and code associated with the paper: "Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia". All code is from published R packages or GitHub repositories not created by the author. Code used is best described in these alternate resources.

opencc-zeroDec 2021View details →

Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe

Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations. Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters. Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations. Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation. Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation per se. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.

opencc-by-4.0Jan 2021View details →

Data from: Chrysolaena obovata, A SPECIES NATIVE OF BRAZILIAN CERRADO: GENETIC DIVERSITY AND STRUCTURE OF NATURAL POPULATIONS AND POTENTIAL FOR INULIN PRODUCTION

Chrysolaena obovata (Less.) M. Dematteis, an herbaceous Asteraceae species widely distributed across different Brazilian Cerrado physiognomies, has underground organs, named rhizophores, that accumulate high concentrations of inulin-type fructans. These carbohydrates are recognized as beneficial soluble fibers for human health and are currently used in the food and pharmaceutical industries. Considering that fructans, in addition to their economic potential, provide plants with greater tolerance to drought, heat and cold, it is important to understand whether their metabolism is conserved in natural populations. In this work, we aimed to investigate if the levels of genetic diversity in the populations studied allow the selection of localities with a high genetic base and higher fructan content for future programs of in situ conservation and genetic improvement for inulin production. Therefore, we characterized the diversity, structure, and gene flow of seven natural populations from Brazilian Cerrado, using nine microsatellite loci (SSR). In addition, we compared whether the fructan composition varied between populations of different Cerrado phytophysiognomies. Overall, we found that C. obovata populations exhibited moderate levels of genetic diversity, low genetic differentiation, and high gene flow. This study identified two populations with less genetic diversity and therefore, greater attention should be given to conservation programs including these populations. Fructan metabolism is conserved in all populations, indicating that C. obovata is an important genetic resource with high potential for inulin production. File descriptions Population_code.txt - Contains a matrix that indicates the population_code, Population_name, Brazilian-state, Phytophysiognomy, Collection coordinates and Altitudes (m). Date_ Diaz et al.xlsx – Contains Genotypes crude of the individuals analyzed. Primer used for nine microsatellite loci (Camacho et al 2017).  Carbohydrates_Diaz et al  - Contains data for carbohydrates in C. obovata plant rhizophores in each population (BRA, UB, SD, SP). Location: Brazilian Cerrado

opencc-zeroMar 2022View details →

Genetic structure in patchy populations of a candidate foundation plant: a case study of Leymus chinensis using genetic and clonal diversity

PREMISE: The distribution of genetic diversity on the landscape has critical ecological and evolutionary implications. This may be especially the case on a local scale for foundation plant species since they create and define ecological communities, contributing disproportionately to ecosystem function. METHODS: We examined the distribution of genetic diversity and clones, which we defined first as unique multilocus genotypes (MLG), and then by grouping similar MLGs into multilocus lineages (MLL). We used 186 markers from inter-simple sequence repeats (ISSR) across 358 ramets from 13 patches of the foundation grass Leymus chinensis. We examined the relationship between genetic and clonal diversities, their variation with patch-size, and the effect of the number of markers used to evaluate genetic diversity and structure in this species. RESULTS: Every ramet had a unique MLG. Almost all patches consisted of individuals belonging to a single MLL. We confirmed this with a clustering algorithm to group related genotypes. The predominance of a single lineage within each patch could be the result of the accumulation of somatic mutations, limited dispersal, some sexual reproduction with partners mainly restricted to the same patch, or a combination of all three. CONCLUSIONS: We found strong genetic structure among patches of L. chinensis. Consistent with previous work on the species, the clustering of similar genotypes within patches suggests that clonal reproduction combined with somatic mutation, limited dispersal, and some degree of sexual reproduction among neighbors causes individuals within a patch to be more closely related than among patches.

opencc-zeroMay 2024View details →

Data and code from: Evaluating genomic offset predictions in a forest tree with high population genetic structure

Predicting how tree populations will respond to climate change is an urgent societal concern. An increasingly popular way to make such predictions is the genomic offset (GO) approach, which aims to use genomic and climate data to identify populations that may experience climate maladaptation in the near future. More precisely, GO tries to represent the change in allele frequencies required to maintain the current gene-climate relationships under climate change. However, the GO approach has major limitations and, despite promising validation of its predictions using height data from common gardens, it still lacks broad empirical testing. In the present study, we evaluated the consistency and empirical validity of GO predictions in maritime pine (Pinus pinaster Ait.), a tree species from southwestern Europe and North Africa with a marked population genetic structure. First, gene-climate relationships were estimated using 9,817 SNPs genotyped in 454 trees from 34 populations; and candidate SNPs potentially involved in climate adaptation were identified. Second, GO was predicted using four methods, namely Gradient Forest (GF), Redundancy Analysis (RDA), latent factor mixed model (LFMM) and Generalised Dissimilarity Modeling (GDM), two sets of SNPs (candidate and control SNPs) and five climate general circulation models (GCMs) to account for uncertainty in future climate predictions. Last, the empirical validity of GO predictions was evaluated within a Bayesian framework by estimating the associations between GO predictions and two independent data sources: mortality data from National Forest Inventories (NFI), and mortality and height data from five common gardens in contrasting environments. We found high variability in GO predictions across methods, SNP sets and GCMs. Regarding validation, GO predictions with GDM and GF (and to a lesser extent RDA) based on the candidate SNPs showed the strongest and most consistent associations with mortality rates in common gardens and NFI plots. We found almost no association between GO predictions and tree height in common gardens, most likely due to the overwhelming effect of population genetic structure on tree height in this species. Our study demonstrates the imperative to validate GO predictions with a range of independent data sources before they can be used as informative and reliable metrics in conservation or management strategies.

opencc-by-4.0Dec 2019View details →

Figure 3 in Infraspecific genetic variation and population structure of Salvia nemorosa L. (Lamiaceae) in Iran

Figure 3. PCoA plot of the studied populations based on ISSR data (population numbers are according to Table 1).

opencc-by-4.0Dec 2019View details →

Figure 2 in Infraspecific genetic variation and population structure of Salvia nemorosa L. (Lamiaceae) in Iran

Figure 2. MDS plot of the studied populations based on ISSR data (population numbers are according to Table 1).

opencc-by-4.0Dec 2019View details →

Figure 4 in Infraspecific genetic variation and population structure of Salvia nemorosa L. (Lamiaceae) in Iran

Figure 4. NJ tree of S. nemorosa populations based on ISSR results (population numbers are according to Table 1).

Figure 8 in Genetic variability and population structure of some Iranian Salvia limbata C. A. Mey. populations

Figure 8. TCS network of the studied S. limbata and their individuals (numbers indicated the populations based on Table 1).

Figure 6 in Genetic variability and population structure of some Iranian Salvia limbata C. A. Mey. populations

Figure 6. STRUCTURE analysis of the studied populations, which revealed the best number of K=7 (numbers indicated the populations based on Table 1).

Figure 5 in Genetic variability and population structure of some Iranian Salvia limbata C. A. Mey. populations

Figure 5. NJ tree of the evaluated populations and their individuals based on ISSR data (numbers indicated the populations based on Table 1).

Figure 4 in Genetic variability and population structure of some Iranian Salvia limbata C. A. Mey. populations

Figure 4. UPGMA tree of the studied populations and their members according to ISSR data (numbers indicated the populations based on Table 1).

Figure 2 in Genetic variability and population structure of some Iranian Salvia limbata C. A. Mey. populations

Figure 2. PCA plot of the evaluated populations and their individuals (numbers indicated populations according to Table 1).

Figure 7 in Genetic variability and population structure of some Iranian Salvia limbata C. A. Mey. populations

Figure 7. Reticulation dendrogram of the studied populations that indicating gene flow among. Abbreviations: Arak (1- 3), Sangak (4-6), Semnan (7-9), Vidar (10-12), Ahovan (13-15), Zarandiyeh (16-18), Ghoochan (19-21) and Lashkarak (22-24).