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opencc-by-4.0Nov 2022View details →

F I G U R E 1 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

F I G U R E 1 Map showing the location of rivers sampled for brown trout within the UK, France and Ireland. The left panel shows the rivers used to assess the performance of the single nucleotide polymorphisms (SNP) panel at characterising genetic parameters within and outside the target region. The top right (blue) panel shows the locations of the four sampled rivers in Mount's Bay, Cornwall (Case Study 1). The bottom right (red) panel shows the location of the sample locations in the Camel catchment (Case Study 2). The red box within the bottom right panel gives the position of the impassable De Lank quarry site

opencc-by-4.0Nov 2022View details →

F I G U R E 2 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

F I G U R E 2 A priori discriminant analysis of principal components (DAPC) of trout genotypes from rivers flowing into Mount's Bay, Cornwall. Individuals are represented by individual points, with centroids for each river labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis

opencc-by-4.0Apr 2015View details →

Fig. 3 in Prevalence and genetic diversity of haematozoa in South American waterfowl and evidence for intercontinental redistribution of parasites by migratory birds

Fig. 3. Bayesian phylogenetic tree of haematozoa mitochondrial DNA cytochrome b haplotypes obtained from infected waterfowl. Trees were rooted with mammalian Plasmodium outgroups. Node tips are labeled with parasite genus (Haem = Haemoproteus, Leuc = Leucocytozoon, and Plas = Plasmodium), followed by the lineage name, GenBank accession number for each sequence, host order (passerine/waterfowl), and the country/state from which the samples were collected. All haplotypes identified in this study are highlighted in red. Numbers on branches represent posterior probabilities from the analysis. Asterisks after node tip labels indicate sequences from our study that were identical to lineages previously found in non-waterfowl hosts. All reference sequences were obtained from the National Center for Biotechnology Information website.

opencc-by-4.0Apr 2015View details →

Fig. 2. Minimum spanning network for haematozoa mitochondrial DNA cytochrome b in Prevalence and genetic diversity of haematozoa in South American waterfowl and evidence for intercontinental redistribution of parasites by migratory birds

Fig. 2. Minimum spanning network for haematozoa mitochondrial DNA cytochrome b haplotypes detected in South American waterfowl. Shaded circles represent unsampled nodes. All circles are drawn proportional to the frequency at which haplotypes were observed. Lines separating nodes are drawn to scale based on the number of nucleotide mutations, unless otherwise indicated by hash marks. Only haplotypes with a length of 358 bp or greater were included. Haplotype name abbreviations are as follows: Haem = Haemoproteus, Leuc = Leucocytozoon, and Plas = Plasmodium.

opencc-by-4.0Apr 2015View details →

Fig. 1 in Prevalence and genetic diversity of haematozoa in South American waterfowl and evidence for intercontinental redistribution of parasites by migratory birds

Fig. 1. Map of sampling locations in Peru and Argentina. The number of waterfowl blood samples collected at each site is provided in parentheses.

opencc-by-4.0Nov 2022View details →

F I G U R E 4 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

F I G U R E 4 Correlation between geographic distance (km) against genetic distance (linear FST) for the trout samples from the River Camel. The red points represent those between the De Lank and all other sites, the black points for all pair-wise comparisons excluding the De Lank. Linear regression for all sites including the De Lank is given by the red line (r2 = 0.321, P = 0.231), and linear regression for all pair-wise sites excluding the De Lank is given by the black line (r2 = 0.658, P = 0.0671)

opencc-by-4.0May 2024View details →

Tilapia genetic diversity across the Lake Victoria Basin

Genotypes for Oreochromis niloticus, O. leucosticus, O. variabilis, O. esculentus, Coptodon rendalli, C. zillii collected in water bodies in Kenya, Tanzania, and Uganda within the Lake Victoria Basin.

opencc-by-4.0Sep 2021View details →

Genetic diversity of wild and cultivated Coffea canephora in northeastern DR Congo and the implications for conservation - Additional Data

List of wild and cultivated Coffea canephora accessions from northeastern Democratic Republic of the Congo included in Vanden Abeele et al. 2021 - American Journal of Botany, and the corresponding alleles for each of the 18 microsatellite markers (0 indicates missing alleles).

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

FIG. 4 in Genetic diversity of Malagasy baobabs: implications for conservation

FIG. 4. — Observed nucleotide diversity PI (π) for the six Adansonia L. species endemic to Madagascar. Northern and southern populations of A. za Baill. are combined here. When distinguishing between geographic populations of A. za, nucleotide diversity was the same as combined for southern populations (π = 0.0029), but less for northern populations (π = 0.0026).

FIG. 3 in Genetic diversity of Malagasy baobabs: implications for conservation

FIG. 3. — Principal components analysis (PCA) of Malagasy Adansonia L. colored by species. Panels represent different PCA axes from: A, 2089 SNPs for all Malagasy Adansonia for axis 1 vs axis 2; B, axis 3 vs axis 4; C, 1873 SNPs for Longitubae taxa only for axis 1 vs axis 2; and D), axis 3 vs axis 4. Northern and southern populations of A. za Baill. labeled.

FIG. 2 in Genetic diversity of Malagasy baobabs: implications for conservation

FIG. 2. — SNP-based tree from 2089 biallelic SNPs as inferred by IQ-TREE. Values on the branches represent bootstrap support for the primary clades: A, broad scale relationships with monophyletic taxa collapsed and number of samples per clade indicated in parentheses; B, detailed phylogeny for the core Longitubae clade (A. perrieri Capuron, A. madagascariensis Baill., and A. za Baill.), with individual accessions mapped to their respective geographic localities in Madagascar (B). Adansonia za (Aza) accessions are listed in red; A. madagascariensis (Ama), in blue; and A. perrieri (Ape) accessions in yellow.

FIG. 1 in Genetic diversity of Malagasy baobabs: implications for conservation

FIG. 1. — Flowers of the six species of baobabs endemic to Madagascar: A, Adansonia grandidieri Baill.; B, A. madagascariensis Baill.; C, A. perrieri Capuron; D, A. rubrostipa Jum. & H. Perrier; E, A. suarezensis H. Perrier; F, A. za Baill. Photographs by David A. Baum and Nisa Karimi.

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-by-4.0Sep 2019View details →

Fig. 2 in Genetic Diversity And Place In The General Phylogeographic Structure Of Capercaillie,Tetrao Urogallus (Galliformes, Phasianidae), From Belarus

Fig. 2. Reconstruction of the phylogeny of the capercaillie according to the polymorphism of the control region of mtDNA. Red dots — sequences from Belarus (this study).

opencc-by-4.0Sep 2019View details →

Fig. 3 in Genetic Diversity And Place In The General Phylogeographic Structure Of Capercaillie,Tetrao Urogallus (Galliformes, Phasianidae), From Belarus

Fig. 3. Network of capercaillie haplotypes according to the mtDNA control region. Balkans — the Balkan Peninsula, E_Europe — Eastern Europe, N_Europe — Northern Europe, W_Russia — Western Russia (up to Ural Mountains), W_Europe — Western Europe, NW_Russia — Northwest Russia, C_Europe — Central Europe.

opencc-by-4.0Sep 2019View details →

Fig. 1 in Genetic Diversity And Place In The General Phylogeographic Structure Of Capercaillie,Tetrao Urogallus (Galliformes, Phasianidae), From Belarus

Fig. 1. Distribution of samples of the capercaillie. Black circles are samples obtained independently, black squares are mtDNA sequences (control region) downloaded from the GenBank database (see Appendix, table 1).

opencc-zeroMay 2022View details →

Phenotypic plasticity and genetic diversity in a polyploid Arabidopsis complex

Polyploid species possess more than two sets of chromosomes and may show high gene redundancy, hybrid vigor and masking of deleterious alleles compared to their parent species. Following this, it is hypothesized that this makes them better at adapting to novel environments than their parent species, possibly due to phenotypic plasticity. The allopolyploid Arabidopsis suecica and its parent species A. arenosa and A. thaliana were chosen as a model system to investigate relationships between phenotypic plasticity, fitness and genetic variation. Particularly, we test if A. suecica is more plastic, show higher genetic diversity and/or have higher fitness than its parent species. Wild Norwegian populations of each species were analyzed for phenotypic responses to differences in availability of nutrient, water and light, while genetic diversity was assessed through analysis of AFLP markers. Arabidopsis arenosa showed a higher level of phenotypic plasticity and higher levels of genetic diversity than the two other species, probably related to its outbreeding reproduction strategy. Furthermore, a general positive relationship between genetic diversity and phenotypic plasticity was found. Low genetic diversity were found in the inbreeding A. thaliana. Geographic spacing of populations might explain the clear genetic structure in A. arenosa, while the lack of structure in A. suecica could be due to coherent populations. Fitness measured as allocation of resources to reproduction, pointed towards A. arenosa having lower fitness under poor environmental conditions. Arabidopsis suecica, on the other hand, showed tendencies towards keeping up fitness under different environmental conditions.

opencc-zeroMay 2022View details →

Effects of insularity on genetic diversity within and among natural populations

We conducted a review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together "insularity"). Using populations from within the same studies, we were able to control for between-study variation in methodology, as well as demographic and life histories. Contradictory to typical expectations, insularity had relatively minor effects on GD within and among population, which points to the more important roles of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen – particularly in systems (i.e. studies) where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non-insular populations of the same system – suggesting an important role for the "scope" of influences on GD. These conclusions were more robust for within - population GD than among - population GD, although a number of biases might underlie this difference. Overall, our findings indicate that population-level genetic assumptions need to be tested rather than assumed in nature, particularly for topics highly relevant to current conservation management practices.