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opencc-zeroDec 2009View details →

Data from: Can clone size serve as a proxy for clone age? An exploration using microsatellite divergence in Populus tremuloides

In long-lived clonal plant species, the overall size of a clone has previously been used to estimate clone age. The size of a clone, however, might be largely determined by physical or biotic interactions, obscuring the relationship between clone size and age. Here, we use the accumulation of mutations at 14 microsatellite loci to estimate clone age in trembling aspen, Populus tremuloides, from southwestern Canada. We show that the observed patterns of genetic divergence are consistent with a model of clonal growth, allowing us to use pairwise genetic divergence as an estimator of clone age. In the populations studied, clone size did not exhibit a significant relationship with microsatellite divergence, indicating that clone size is not a good proxy for clone age.

opencc-zeroDec 2019View details →

Microsatellite genotypes, cluster membership and metadata of Central European wolves (Canis lupus)

Local extinction and recolonization events can shape genetic structure of subdivided animal populations. The gray wolf (Canis lupus) was extirpated from most of Europe, but recently recolonized big part of its historical range. An exceptionally dynamic expansion of wolf population is observed in the western part of the Great European Plain. Nonetheless, genetic consequences of this process have not yet been fully understood. We aimed to assess genetic diversity of this recently established wolf population in Western Poland (WPL), determine its origin and provide novel data regarding the population genetic structure of the grey wolf in Central Europe. We utilized both spatially explicit and non-explicit Bayesian clustering approaches, as well as a model-independent, multivariate method DAPC, to infer genetic structure in large dataset of wolf microsatellite genotypes. To put the patterns observed in studied population into a broader biogeographic context we also analyzed a mtDNA control region fragment widely used in previous studies. In comparison to a source population, we found slightly reduced allelic richness and heterozygosity in the newly recolonized areas west of the Vistula river. We discovered relatively strong west-east structuring in lowland wolves, probably reflecting founder-flush and allele surfing during range expansion, resulting in clear distinction of WPL, eastern lowland and Carpathian genetic groups. Interestingly, wolves from recently recolonized mountainous areas (Sudetes Mts, SW Poland) clustered together with lowland, but not Carpathian wolf populations. We also identified an area in Central Poland that seems to be a melting pot of western, lowland eastern and Carpathian wolves. We conclude that the process of dynamic recolonization of Central European lowlands lead to the formation of a new, genetically distinct wolf population. Together with the settlement and establishment of packs in mountains by lowland wolves and vice versa, it suggests that demographic dynamics and possibly anthropogenic barriers rather than ecological factors (e.g. natal habitat-biased dispersal patterns) shape the current wolf genetic structure in Central Europe.

opencc-zeroDec 2013View details →

Data from: Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs)

Ex situ germ plasm collections of woody crops are necessary to ensure the optimal use of plant genetic resources. The fig tree (Ficus carica L.) germ plasm bank, consisting of 229 accessions, is located in Centro de Investigación 'La Orden'. Despite great progress in conservation, ex situ collections face size and organization problems. Core collections obtained from structured samples of bigger collections are a useful tool to improve germ plasm management. In this work, we used simple sequence repeat (SSR) markers to establish a core collection in this underutilised Mediterranean fruit tree species. Four approaches have been carried out (random sampling, maximization, simulated annealing and stepwise clustering) to determine the best method to develop a core collection in this woody plant. The genetic diversity obtained with each subset was compared with that of the complete collection. It was found that the most efficient way to achieve the maximum diversity was the maximization strategy, which, with 30 accessions, recovers all the SSR alleles and does not show significant differences in allele frequency distribution in any of the loci or in the variability parameters (H O, H E) between the whole and core collections. Thus, this core collection, a representative of most fig diversity conserved in the germ plasm bank, could be used as a basis for plant material exchange among researchers and breeders.

opencc-zeroDec 2017View details →

Data from: Development of 15 nuclear EST microsatellite markers for the palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae)

Premise of the study: Nuclear microsatellite markers were developed for population genetic analysis of the threatened palaeoendemic conifer Pherosphaera hookeriana W. Archer (Podocarpaceae). Methods and Results: Fifteen variable loci were identified showing 1 to 13 alleles per population with seven loci displaying over four alleles in all populations and the average number of alleles per locus ranging from 4.8 to 5.93 per population. The observed heterozygosity per locus varied from 0.00 to 0.91 and overall heterozygosity was markedly consistent between populations (from 0.54 to 0.57). All loci also amplified in the endangered congener P. fitzgeraldii but only five of the loci had more than one allele. Conclusions: These 15 loci are the first microsatellite markers developed in the genus Pherosphaera. These loci will be useful for investigating the species' extant genetic diversity and structure, the impact of past environmental change and the significance of asexual reproduction.

opencc-zeroDec 2018View details →

Data from: Dissimilarity of individual microsatellite profiles under different mutation models: empirical approach

Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.

opencc-zeroDec 2013View details →

Data from: A rapid and cost-effective quantitative microsatellite genotyping protocol to estimate intraspecific competition in protist microcosm experiments

High levels of intra-specific variation are commonly observed in natural microbial populations, yet the consequences of this variation for ecological and evolutionary processes remains poorly understood. Protists are excellent experimental models for investigating fundamental and applied questions in ecology and evolution, but studying intra-specific variation remains a challenge due to a lack of molecular resources to aid in quantifying and distinguishing strains during experiments. Here we present a molecular method, quantitative microsatellite genotyping, to accurately quantify strain specific frequencies from microcosm experiments of the marine flagellate Oxyrrhis marina, both between many pairs of strains and between strains in a multi-strain mixture. We find that for pairs of strains the method is effective for relative frequencies as low as 0.02 and with around 99% accuracy. The method is able to quantify four strains reasonably well, though less accurately than for pairs (range 92%-97% accuracy). This makes accessible a cheap and easy to implement method for quantifying strain (or allele) frequencies, and is suitable for use in a broad range of single celled eukaryotes (Protists) where copy number should correlate well with number of individuals (i.e. cells). This opens up the possibility of examining the role of intra-specific variation using experimental protist microcosms.

Figure 4. Individual multilocus genotype clustering analysis for Podarcis carbonelli. A in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers

Figure 4. Individual multilocus genotype clustering analysis for Podarcis carbonelli. A, inferred population structure from the number of clusters (K) = 2 to 5. These plots were obtained from the runs producing the highest values of Ln probability for each value of K, assuming correlated allele frequencies. In these plots, each individual is represented by a column divided into K segments, the size of each corresponding to the individual's estimated membership fraction in each of the K clusters. See Table 1 for locality name abbreviations. B, variation of the value of DK with the number of clusters, following Evanno et al. (2005). C, pie charts representing the mean proportion of membership for K = 4 (chosen by the previous method) for each locality.

Figure 3. Individual multilocus genotype clustering analysis for Podarcis bocagei. A in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers

Figure 3. Individual multilocus genotype clustering analysis for Podarcis bocagei. A, inferred population structure from the number of clusters (K) = 2 to 5. These plots were obtained from the runs producing the highest values of Ln probability for each value of K, assuming correlated allele frequencies. In these plots, each individual is represented by a column divided into K segments, the size of each corresponding to the individual's estimated membership fraction in each of the K clusters. See Table 1 for locality name abbreviations. B, variation of the value of DK with the number of clusters, following Evanno et al. (2005). C, pie charts representing the mean proportion of membership for K = 3 and 5 (chosen by the previous method) for each locality.

Figure 2 in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers

Figure 2. Synthetic maps showing patterns of geographical variation in allele frequencies across species distribution ranges based on the inversed distance weighted interpolation of the values calculated for each locality of Podarcis bocagei (top) and Podarcis carbonelli (bottom) for the first (A, D), second (B, E), and third (C, F) axes of factorial correspondence analyses. White represents higher and black lower factor score values.

Figure 1 in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers

Figure 1. Distribution and localities analysed in this study for Podarcis bocagei (dark grey, circles) and Podarcis carbonelli (light grey, squares) (A), and median-joining networks of mtDNA haplotypes for P. bocagei (B) and P. carbonelli (C) reproduced from Pinho et al., 2007a. Dashed lines indicate the mtDNA groups and corresponding geographical distributions in P. carbonelli. Locality codes and sampling details are given in Table 1. Notice that the distribution shown for P. carbonelli is based on a 20 km buffer of occupied 10 ¥ 10 km UTM (Universal Transverse Mercator) squares and is therefore amplified compared to that in Pinho et al., 2007a. This was necessary in order to visualize geographical patterns of genetic variation (see Material and methods).

opencc-zeroSep 2021View details →

Lampsilis siliquoidea and L. radiata seven microsatellite loci data set

The data set corresponds to genotypes of individuals belonging to Lampsilis siliquoidea and L. radiata which are two closely related freshwater mussel species [Bivalvia: Unionidae]. Individual genotypes consist of seven microsatellite loci developed by Eackles and King 2002. Genotypes were used to asses population genetic structure above and below waterfalls in the lower Great Lakes (USA) and to investigate the degree of hybridization between these two species.

opencc-zeroSep 2021View details →

Larval A. bishopi microsatellite data from: Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape

The dataset consists of 9 microsatellite markers used to analyze reticulated flatwoods salamanders' (Ambystoma bishopi) population structure on Eglin AFB. Samples came from various breeding ponds and allele sizes were scored using GeneMapper (GeneMapper v4.0; Applied Biosystems). Data was collected via allele scoring in GeneMapper by two independent researchers. Allele sizes for each individual have been re-formatted for various programs using the microsatellite Add-in in Excel as well as by using the GenAlEx extension in Excel.

opencc-zeroOct 2021View details →

Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence

Three subspecies of Northern Bahamian Rock Iguanas, Cyclura cychlura, are currently recognized: C. c. cychlura,restricted to Andros Island, and C. c. figginsi and C. c. inornata, native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the two currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than two. That inference also ignores evidence that populations of C. cychlura are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: C. cychlura iguanas, their ticks (genus Amblyomma, preferentially parasitizing these reptiles), and Rickettsia spp. endosymbionts (within tick ectoparasites). Our results indicate that while C. c. cychlura on Andros is consistently supported as a separate clade, patterns of relatedness among populations of C. c. figginsi and C. c. inornata within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and Rickettsia spp., supports the evolutionary independence of C. c. inornata. Further, these patterns are also consistent with two independent evolutionarily significant units within C. c. figginsi. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.

opencc-zeroJan 2023View details →

Genotypes at 10 microsatellite loci for 8 perennial, polygyne colonies of Vespula squamosa

Many highly social species show plasticity in their social structure in response to different environmental conditions. For example, typical colonies of the yellowjacket wasp Vespula squamosa are headed by a single reproductive queen and survive for only a single season. However, in warmer climates, V. squamosa colonies sometimes persist for multiple years and can grow to extremely large size. We used genetic markers to understand patterns of reproduction and recruitment within these perennial colonies. We genotyped V. squamosa workers, pre-reproductive queens, and males from perennial colonies in the southeastern United States at 10 polymorphic microsatellite loci and one mitochondrial DNA locus. We found that V. squamosa from perennial nests were produced by multiple reproductives, in contrast to typical annual colonies. Relatedness of nestmates from perennial colonies was significantly lower than relatedness of nestmates from annual colonies. Our analyses of mitochondrial DNA indicated that most V. squamosa perennial colonies represented semi-closed systems whereby all individuals belonged to a single matriline despite the presence of multiple reproductive females. However, new queens recruited into perennial colonies apparently mated with non-nestmate males. Notably, perennial and annual colonies did not show significant genetic differences, supporting the hypothesis that perennial colony formation represents an instance of social phenotypic plasticity. Overall, our results indicate that perennial V. squamosa colonies show substantial changes to their social biology compared to typical annual colonies.

opencc-byNov 2022View details →

Microsatellite genotypes and associated data for: Tetrasporophyte bias coupled with heterozygote deficiency in Antarctic Plocamium sp. (Rhodophyta)

Meiosis and syngamy generate an alternation between two ploidy stages, but the timing of these two processes varies widely across taxa, thereby generating life cycle diversity. One hypothesis suggests that life cycles with long-lived haploid stages are correlated with selfing, asexual reproduction, or both. Though mostly studied in angiosperms, selfing and asexual reproduction are often associated with marginal habitats. Yet, in haploid-diploid macroalgae, these two reproductive modes have subtle, but unique consequences whereby predictions from angiosperms may not apply. Along the western Antarctic Peninsula, there is a thriving macroalgal community, providing an opportunity to explore reproductive system variation in haploid-diploid macroalgae at high latitudes where endemism is common. Plocamium sp. is a widespread and abundant red macroalga found within this ecosystem. We sampled twelve sites during 2017 and 2018 field seasons and used ten microsatellite loci to describe the reproductive system. Overall genotypic richness and evenness were high, suggesting sexual reproduction. Eight sites were dominated by tetrasporophytes, but there was strong heterozygote deficiency, suggesting intergametophytic selfing. We found slight differences in the prevailing reproductive mode among sites, possibly due to local conditions (e.g., disturbance) that may contribute to site-specific variation. It remains to be determined whether high levels of selfing are characteristic of macroalgae more generally at high latitudes or due to the haploid-diploid life cycle. Further investigations of algal life cycles will likely reveal the processes underlying the maintenance of sexual reproduction more broadly across eukaryotes, but more studies of natural populations are required.

opencc-zeroFeb 2023View details →

Development of microsatellite markers for colony delineation of the invasive Asian subterranean termite in South Florida and Taiwan

Delineating the colony identity of Coptotermes gestroi (Wasmann) is a core issue of colony elimination in the implementation of subterranean termite baiting systems. Invasion history is believed the possible cause of genetic variabilities among colonies. Haplotype network analysis of mitochondrial cytochrome c oxidase subunit II revealed the multiple origins of American C. gestroi from the Philippines and Southeast Asia and the Taiwan population only from the Philippines. We further developed 21 new microsatellite markers for the comparison of genetic variabilities on colony delineation of C. gestroi colonies from South Florida (invaded ~30 years; 3–7 generations) and Taiwan (~110 years; 13–27 generations). The present microsatellite markers with 1–4 alleles per locus have validated the effectiveness of colony delineation for three incipient colonies reared in the laboratory and three field colonies from Taiwan. Genetic admixture of the Floridian C. gestroi probably caused by recent invasion history, multiple invasions, and anthropogenic activities among regions. A possible introduction event likely occurred through human-mediated activities between Fort Lauderdale and Miami. Overall, these new microsatellite markers provide suitable and efficient candidate genetic markers for colony delineation of C. gestroi to consolidate the effectiveness of the colony elimination system in termite management.

opencc-by-4.0Mar 2023View details →

Data of the paper "The ionospheric exploration based on TJU#01 meteorological microsatellite mission: initial results"

Ionospheric occultation data of the paper "The ionospheric exploration based on TJU#01 meteorological microsatellite mission: initial results"

opencc-by-4.0Jul 2023View details →

Microsatellite and morphological data for Carpobrotus species sampled from 40 different populations

Microsatellite data for six loci and 698 individuals of Carpobrotus species sampled from 40 different population Morphological data for individuals of Carpobrotus species from 40 different populations

opencc-zeroOct 2023View details →

Physaria thamnophila microsatellite dataset

Taxonomy, genetics and biogeography each make key contributions to biological conservation. However, integrating these disciplines to obtain a coherent account of the status of a taxon of concern is not always straightforward. This is the case for the cross-border endemic plant Physaria thamnophila (Brassicaceae). This US federally-listed endangered species is restricted to a set of unique geological sites just north of the Rio Grande (Rio Bravo del Norte) river in south Texas, USA. A single highly-disjunct occurrence of this species is found on a geologically and ecologically distinct site 260 km to the south, in Tamaulipas, Mexico. In this work, we quantify the genetic differentiation between the U.S. and Mexican populations using four microsatellite markers and sequences from three nuclear genes. In both sets of data, we find a high level of genetic divergence consistent with geographic isolation on a time scale of 1–2.5 million years. Further, we provide a hypothesis for the geological basis of this geographic isolation. Integrating our data with ecological, taxonomic and conservation considerations, we propose the sub-specific designation of Physaria thamnophila subsp. loretensis for the Mexican population. The evolutionary and conservation implications of this designation are presented.