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opennotspecifiedJul 2013View details →

Figure 1 in Cryptic diversity in coastal Australasia: a morphological and mitonuclear genetic analysis of habitat-forming sibling species

Figure 1. Scanning electron microscope photographs of the siphonal spines of the species comprising the Pyura stolonifera species complex. A, Pyura doppelgangera sp. nov., B, Pyura praeputialis, C, Pyura dalbyi, D, Pyura herdmani, E, P. stolonifera. Scale bars: A = 100 Mm; B, D = 40 Mm; C = 50 Mm; E = 10 Mm.

opencc-zeroDec 2020View details →

Genetic diversity and population structure of two endangered neotropical parrots inform In Situ and Ex Situ conservation strategies

A key aspect in the conservation of endangered populations is understanding patterns of genetic variation and structure, which can provide managers with critical information to support evidence-based status assessments and management strategies. This is especially important for species with small wild and larger captive populations, as found in many endangered parrots. We used genotypic data to assess genetic variation and structure in wild and captive populations of two endangered parrots, the blue-throated macaw, Ara glaucogularis, of Bolivia, and the thick-billed parrot, Rhynchopsitta pachyrhyncha, of Mexico. In the blue-throated macaw, we found evidence of weak genetic differentiation between wild northern and southern subpopulations, and between wild and captive populations. In the thick-billed parrot we found no signal of differentiation between the Madera and Tutuaca breeding colonies or between wild and captive populations. Similar levels of genetic diversity were detected in the wild and captive populations of both species, with private alleles detected in captivity in both, and in the wild in the thick-billed parrot. We found genetic signatures of a bottleneck in the northern blue-throated macaw subpopulation, but no such signal was identified in any other subpopulation of either species. Our results suggest both species could potentially benefit from reintroduction of genetic variation found in captivity, and emphasize the need for genetic management of captive populations.

opencc-zeroAug 2021View details →

Using niche centrality within the scope of the nearly neutral theory of evolution to predict genetic diversity in a tropical conifer species-pair

Aim: Estimating genetic diversity is key for understanging biogeographic and evolutionary processes. However, gathering genetic information is not feasible for all taxa or populations, particularly in the tropical regions. Identifying proxies for inferring such values has thus become essential. Here, we built on the niche centrality hypothesis (NCH; or central-abundance hypothesis) and the nearly neutral theory of evolution (NNT) to identify some of such proxies using a montane tropical conifer species-pair as model. The NCH predicts more genetic diversity under optimal ecological conditions, which should also allow for more efficient purifying selection, according to the NNT. Location: The Transmexican Volcanic Belt, central Mexico. Taxa: A fir species-pair endemic to central Mexico, Abies flinckii and A. religiosa. Methods: We estimated patterns of genetic diversity from nuclear SSRs (A, HE), and gene-coding sequences (πS, πN), together with the efficacy of purifying selection, measured as πN/πS. After testing for niche overlap, we used several geographic and ecological proxies (i.e. longitude, latitude, elevation, estimated area, and distance to the niche centroid in the present and in the LGM) to predict genetic diversity and πN/πS using general linear models. Results: Populations at the west of the Trans Mexican Volcanic Belt (TVB) had lower genetic diversity than populations in the east of this mountain chain. Both species had significant niche overlap. The principal predictors for neutral genetic diversity (HE, A and πS) were longitude and latitude, followed by the current distance to the niche centroid; the efficiency of purifying selection was mostly accounted for by the current distance to the niche centroid (which was also correlated to elevation). No correlation was observed between genetic diversity or πN/πS and current population area. Main conclusions: Historical and ecological factors have to be taken into account for explaining the amounts of genetic diversity in mountain tropical species. Following the NTT, populations closer to the niche centroid are more efficient at eliminating slightly deleterious mutations than marginal stands, independently of their size or geographical location (longitude). Expanding the central-abundance theory within the scope of the NTT might help reconciling conflicting views concerning the extent of its empirical support.

opencc-zeroOct 2021View details →

IUCN Red List protects avian genetic diversity

Despite well-established links between low genetic diversity and extinction processes, intra-specific genetic diversity is rarely considered in global conservation assessments, potentially leading to biased estimates of species' extinction risk. We show that birds ranked as "threatened" by the IUCN Red List have lower intra-specific genetic diversity than "non-threatened" species, confirming that threat criteria, used by the IUCN, effectively protect genetically depleted species. However, some "non-threatened" species harbour low levels of genetic diversity, indicating an undetected vulnerability to global change. Global conservation assessments will benefit from explicitly integrating relevant genetic and genomic diversity-based measures in estimates of species' extinction risk.

opencc-zeroNov 2022View details →

Data from: Increasing temperature weakens the positive effect of genetic diversity on population growth

Genetic diversity and temperature increases associated with global climate change are known to independently influence population growth and extinction risk. Whether increasing temperature may influence the effect of genetic diversity on population growth, however, is not known. We address this issue in the model protist system Tetrahymena thermophila. We test the hypothesis that at temperatures closer to the species' thermal optimum (i.e., the temperature at which population growth is maximal, or Topt), genetic diversity should have a weaker effect on population growth compared to temperatures away from the thermal optimum. To do so, we grew populations of T. thermophila with varying levels of genetic diversity at increasingly warmer temperatures and quantified their intrinsic population growth rate, r. We found that genetic diversity increases population growth at cooler temperatures, but that as temperature increases, this effect weakens. We also show that a combination of changes in the amount of expressed genetic diversity (G), plastic changes in population growth across temperatures (E), and strong GxE interactions, underlie this temperature effect. Our results uncover important but largely overlooked temperature effects that have implications for the management of small populations with depauperate genetic stocks in an increasingly warming world. --

opencc-zeroNov 2022View details →

Genetic loci associated with winter survivorship in diverse lowland switchgrass populations: SNP read count data

High winter mortality is the most important factor limiting biomass yield of lowland switchgrass planted in the northern latitudes of North America. Due to the perennial growth habit and strong dependence on weather conditions to generate sufficient selection pressure to identify winter-hardy individuals, breeding of cold tolerant switchgrass cultivars requires many years. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 population with differential winter survivorship was used for BSA. A maximum of 10% of the individuals per population (8-20) was bulked to create survivor and non-survivor DNA pools. The DNA pools were evaluated using exome capture sequencing and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine QTL from tetraploid populations and seven QTL from octoploid populations. Some markers were identified in multiple populations that originated across a broad geographic landscape, while other markers were site-specific. QTL at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.

opencc-zeroNov 2022View details →

Demographic changes and life-history strategies predict the genetic diversity in crabs

Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analyzed across 150 species (16,992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration, and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.

opencc-zeroDec 2022View details →

Supplementary material 1 from: Leonhardt F, Arranz Aveces C, Müller A, Angin B, Jegu M, Haynes P, Ernst R (2022) Low genetic diversity in a widespread whistling alien: A comparison of Eleutherodactylus johnstonei Barbour, 1914 (Eleutherodactylidae) and congeners in native and introduced ranges. NeoBiota 79: 31-50. https://doi.org/10.3897/neobiota.79.86778

Detailed information on all populations of the three congeneric taxa used in the molecular data sets of this study

opencc-zeroFeb 2023View details →

Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers

Water yam (Dioscorea alata L.) is among the most cultivated species used as a source of food and income for small-scale farmers in Tanzania. However, little is documented about Dioscorea species available in Tanzania, including their genetic diversity. This study used ten polymorphic microsatellite markers to determine the genetic diversity and relationship of 63 D. alata accessions from six major producing regions. Results revealed a polymorphic information content (PIC) of 0.63, while the number of alleles per locus ranged from 4 to 12 with a mean of 7.60. The expected heterozygosity ranged from 0.17 to 0.74, with a mean of 0.49, which suggests moderate genetic diversity of D. alata accessions. Kagera region had the highest mean number of (1.5) private alleles. Analysis of molecular variance revealed that 91% of the variation was attributed to within-population while among-population contributed 9% of the total variation. The highest Nei's genetic distance (0.65) was for accessions sampled from Arusha and Mtwara regions. Principal coordinate analysis and cluster analysis using Unweighted Paired Group Method using Arithmetic (UPGMA) grouped D. alata accessions into two major clusters regardless of geographical origin and local names. The Bayesian structure analysis confirmed the two clusters obtained in UPGMA and revealed an admixture of D. alata accessions in all six regions suggesting farmers' extensive exchange of planting materials. These results are helpful in the selection of D. alata accessions for breeding programs in Tanzania.

opencc-zeroApr 2023View details →

Data for: Invasion history of Lycium ferocissimum in Australia – the impact of admixture on genetic diversity and differentiation

Aim: We investigated the invasion history of Lycium ferocissimum, a spine-covered shrub native to South Africa that has developed into a damaging invasive plant of undisturbed landscapes and pastures across southern and eastern Australia. In addition to identifying the provenance of the Australian plants, we tested for evidence of admixture, and contrasted genetic diversity and structuring across the native and introduced ranges. Location: Samples were collected across South Africa (24 localities) and Australia (26 localities). Methods: We used genotyping-by-sequencing (3,130 SNPs across 381 individuals) to assess population genetic structuring in L. ferocissimum across Australia and South Africa. Coalescent analyses were used to explicitly test contrasting invasion scenarios. Results: Clear geographic genetic structuring was detected across South Africa, with distinct clusters in the Eastern and Western Cape provinces. The L. ferocissimum plants in Australia form their own genetic cluster, with a similar level of genetic diversity as plants in South Africa. Coalescent analyses demonstrated that the lineage in Australia was formed by admixture between Eastern Cape and Western Cape plants, with analyses suggesting that plants from both African regions were originally introduced to South Australia. We detected little evidence of geographic genetic structure across Australia, although many of the populations were genetically distinct from one another. Main conclusions: Our results illustrate how admixture can result in genetically diverse and distinct invasive populations. The complex invasion history of L. ferocissimum in Australia poses particular challenges for biological control. We suggest potential biological control agents should be screened against admixed plants (in addition to plants from the Eastern and Western Cape) to test whether they provide effective control of the genetically distinct invasive lineage.

Figure 3 in Well-known species, unexpected results: high genetic diversity in declining Vipera ursinii in central, eastern and southeastern Europe

Figure 3. Genetic relationship between locations calculated using Cavalli-Sforza and Edwards Dc distance (Cavalli-Sforza and Edwards, 1967) using the software POPULATIONS 1.2.28 (Langella, 1999). The distances were calculated with 5 microsatellite markers and branches with bootstrap support>40 were indicated.

Figure 2 in Well-known species, unexpected results: high genetic diversity in declining Vipera ursinii in central, eastern and southeastern Europe

Figure 2. Maximum-likelihood tree from combined data (Cytochrome b and ND4, totalling 1920 bp) for different subspecies of Vipera ursinii. Values of bootstrap support for maximum likelihood (first) maximum parsimony (middle) are shown for nodes found in more than 50% of 1000 trees, as well as posterior probability from Bayesian inference (right). The population number (see fig. 1 and supplementary table S1) where the haplotypes have been found are added to the haplotype label. Drawing of Vipera ursinii rakosiensis courtesy of Márton Zsoldos.

Figure 1 in Well-known species, unexpected results: high genetic diversity in declining Vipera ursinii in central, eastern and southeastern Europe

Figure 1. Location of the samples used in the study: squares represent mtDNA data, round symbols represent microsatellites data. The size of the round symbols is proportional to the number of samples used. Locality numbers correspond with supplementary table S1 (in black when microsatellite data are available; in white when mtDNA data). The colours of the marks are different between subspecies: green: V. ursinii rakosiensis, yellow: V. u. moldavica, blue: V. u. macrops, grey: V. u. macrops from Bistra Mt., red: V. renardi. White striped grids show distribution of each subspecies/species on a 100x100 UTM grid resolution (after Sillero et al., 2014). Distribution area of V. greaca (from IUCN red list, Mizsei et al., 2018) is colored in pink. On the top left, insert A shows a zoom in the V. ursinii macrops region, while insert B illustrates the location of study area within Europe.

Figure 4. Comparative phylogenetic relationship between the 11 in Well-known species, unexpected results: high genetic diversity in declining Vipera ursinii in central, eastern and southeastern Europe

Figure 4. Comparative phylogenetic relationship between the 11 regions with both mtDNA (left) and nDNA (right). left: Mitochondrial DNA tree based on the genetic distances of the different haplotypes (combining cytochrome b and ND4; 1920 bp) within each region. right: Nuclear tree based on Cavalli-Sforza and Edwards Dc distances (Cavalli-Sforza and Edwards, 1967) calculated with the software POPULATIONS 1.2.28 (Langella, 1999) based on 5 microsatellites markers. Dashed branches correspond to discrepancies between both phylogenetic reconstructions. Both trees were not rooted. The colours are different between subspecies: green: V. ursinii rakosiensis, yellow: V. u. moldavica, blue: V. u. macrops, grey: V. u. macrops from Bistra Mt., red: V. renardi.

opencc-by-4.0May 2023View details →

Data for Selfing species has greater genetic diversity and less structure than related outcrossing species due to seed dispersal and population history in Roscoea (Zingiberaceae)

Data matrix of two species with nexus format.

opencc-zeroJun 2023View details →

Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

The Carpathian Mountains were always inhabited by grey wolves and present one of the largest distribution areas in Europe, comprising between 2,300 to 2,700 individuals in Romania. To date, however, relatively little is known about the Romanian wolf population. We aimed to provide a first assessment of genetic diversity, population structure and wolf-dog hybridisation based on 444 mostly non-invasively collected samples in the Eastern Romanian Carpathians. Pack reconstruction and analysis of population genetic parameters were performed with mitochondrial DNA control-region sequencing and microsatellite genotyping. We found relatively high levels of genetic diversity, which is similar to values found in previous studies on Carpathian wolves from Poland and Slovakia, as well as to the long-lasting Dinaric-Balkan wolf population. We found no significant population structure in our study region, suggesting effective dispersal and admixture. Analysis of wolf-dog hybridisation using a Single Nucleotide Polymorphism panel optimised for hybrid detection revealed low rates of admixture between wolves and domestic dogs. Our results provide evidence for the existence of a genetically viable wolf population in the Romanian Carpathians. The genetic data obtained in this study may serve as valuable baseline information for the elaboration of monitoring standards and management plans for wolves in Romania.

FIGURE 4 in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia

FIGURE 4. An unrooted Neighbor Joining tree of Lake Tana Labeobarbus species constructed by APE (an R-package) using pair-wise genetic distances among individuals based on analysis of 10 microsatellite loci. Bootstrap percentage values shown at nodes are from 100 pseudo-replicates and indicate the level of support for each group; only bootstrap values higher than 50% are indicated.

FIGURE 3 in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia

FIGURE 3. Scatter plot from Discriminant analysis of Principal Components (DPC; Jombart et al. 2010) of microsatellite data from 161 Lake Tana Labeobarbus individuals. The 95% confidence ellipses of each group based on the common covariance matrix assumption for the multivariate normal distribution are presented. Points represent individual genotypes and symbols represent species (A) or spawning populations (B). A. Using species as grouping factor with asterisks representing the estimated means for each population: Pop A = L. acutirostris, Pop B = L. brevicephalus, Pop C = L. crassibarbus, Pop D = L. gorgorensis, Pop E = L. gorguari, Pop F = L. intermedius, Pop G = L. longissimus, Pop H = L. macrophtalmus, Pop I = L. megastoma, Pop J = L. nedgia, Pop K = L. platydorsus, Pop L = L. surkis, Pop M = L. tsanensis, Pop N = L. truttiformis. B. Using spawning strategy as grouping criteria: ▲riverine spawning population, ●lacustrine spawning population.

FIGURE 2 in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia

FIGURE 2. Bayesian clustering assignment of individuals based on Structure analysis of 10 microsatellite loci of Labeobarbus populations from Lake Tana and adjacent water bodies. A. Analysis of whole dataset without a priori population definitions (K=1–15). B. Lake Tana Labeobarbus populations only with K = 2 inferred clusters. 1. L. acitirostris, 2. L. brevicephalus, 3. L. crassibarbus, 4. L. gorgorensis, 5. L. gorguari, 6. L. longissimus, 7. L. macrophtalmus, 8. L. megastoma, 9. L. nedgia, 10. L. platydorsus, 11. L. surkis, 12. L. truttiformis, 13. L. tsanensis, 14. L. intermedius, 15. L. beso.

FIGURE 1. A in Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia

FIGURE 1. A. Map showing major river drainages of Ethiopia; B. Map of Lake Tana. All samples of Lake Tana were drawn from sites (area lying within the red rectangle) located in the Bahir Dar Gulf.