The widespread adoption of RAD-Seq data in phylogeography means genealogical relationships previously evaluated using relatively few genetic markers can now be addressed with thousands of loci. One ...challenge, however, is that RAD-Seq generates complete genotypes for only a small subset of loci or individuals. Simulations indicate that loci with missing data can produce biased estimates of key population genetic parameters, although the influence of such biases in empirical studies is not well understood. Here we compare microsatellite data (8 loci) and RAD-Seq data (six datasets ranging from 239 to 25,198 loci) from red mangroves (Rhizophora mangle) in Florida to evaluate how different levels of data filtering influence phylogeographic inferences. For all datasets, we calculated population genetic statistics and evaluated population structure, and for RAD-Seq datasets, we additionally examined population structure using coalescence. We found higher F
using microsatellites, but that RAD-Seq-based estimates approached those based on microsatellites as more loci with more missing data were included. Analyses of RAD-Seq datasets resolved the classic Gulf-Atlantic coastal phylogeographic break, which was not significant in the microsatellite analyses. Applying multiple levels of filtering to RAD-Seq datasets can provide a more complete picture of potential biases in the data and elucidate subtle phylogeographic patterns.
Primula secundiflora is an insect-pollinated, perennial herb belonging to section Proliferae (Primulaceae) and exhibits considerable variation in mating system with predominantly outcrossing ...populations comprising long-styled and short-styled floral morphs and selfing populations comprising only homostyles. To facilitate future investigations of the population genetics and mating patterns of this species, we developed 25 microsatellite markers from P. secundiflora using next-generation sequencing and measured polymorphism and genetic diversity in a sample of 30 individuals from three natural populations. The markers displayed relatively high polymorphism, with the number of observed alleles per locus ranging from three to 16 (mean = 8.36). The observed and expected heterozygosities ranged from 0.100 to 1.000 and 0.145 to 0.843, respectively. Twenty-one of the loci were also successfully amplified in P. denticulata. These microsatellite markers could provide powerful tools for investigating patterns of population genetic diversity and the evolutionary relationships between distyly and homostyly in this species.
ABSTRACT
The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long ...represented a primary source of human–carnivore conflict, which has led to long‐term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the ‘pre‐genomic era’ and the first insights of the ‘genomics era’. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental autosomal microsatellites and single nucleotide polymorphisms (SNPs). To describe large‐scale trends and patterns of genetic variation in European wolf populations, we conducted a meta‐analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south‐west (lowest genetic diversity) to north‐east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650−850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science‐based wolf conservation and management at regional and Europe‐wide scales.
Somatic mutations occur during brain development and are increasingly implicated as a cause of neurogenetic disease. However, the patterns in which somatic mutations distribute in the human brain are ...unknown. We used high-coverage whole-genome sequencing of single neurons from a normal individual to identify spontaneous somatic mutations as clonal marks to track cell lineages in human brain. Somatic mutation analyses in >30 locations throughout the nervous system identified multiple lineages and sublineages of cells marked by different LINE-1 (L1) retrotransposition events and subsequent mutation of poly-A microsatellites within L1. One clone contained thousands of cells limited to the left middle frontal gyrus, whereas a second distinct clone contained millions of cells distributed over the entire left hemisphere. These patterns mirror known somatic mutation disorders of brain development and suggest that focally distributed mutations are also prevalent in normal brains. Single-cell analysis of somatic mutation enables tracing of cell lineage clones in human brain.
Genotypic study of Tunisian Arabian stallions Jlassi, Mariam; Jemmali, Bayrem; Ahmed, Hatem Ouled ...
ACTA BIOLOGICA SZEGEDIENSIS (Print),
11/2022, Letnik:
66, Številka:
1
Journal Article
Odprti dostop
Diversity of Arabian stallions distributed throughout the territory of Tunisia has been evaluated. Seventeen microsatellite markers were used for the determination of genetic variation. A total of 95 ...alleles were detected in the 50 stallions studied. The number of alleles per locus ranged from 2 to 9 with an average of 5.6. The observed mean number of genetically diverse alleles (Na) was 5.6 (0.44). The mean number of expected alleles (Ne) was 3.42 (0.28). The average expected and observed heterozygosity was approximately 0.675 (0.026) and 0.593 (0.044), respectively. Principal component analysis showed the presence of 2 subpopulations in the studied sample set. These findings demonstrate the potential of microsatellites as a tool for designing and controlling animal breeds. Results show that the population under study has sufficient levels of genetic variations, which can be used as a foundation for developing plans for species conservation and long-term sustainability.
One of the most common questions asked before starting a new population genetic study using microsatellite allele frequencies is "how many individuals do I need to sample from each population?" This ...question has previously been answered by addressing how many individuals are needed to detect all of the alleles present in a population (i.e. rarefaction based analyses). However, we argue that obtaining accurate allele frequencies and accurate estimates of diversity are much more important than detecting all of the alleles, given that very rare alleles (i.e. new mutations) are not very informative for assessing genetic diversity within a population or genetic structure among populations. Here we present a comparison of allele frequencies, expected heterozygosities and genetic distances between real and simulated populations by randomly subsampling 5-100 individuals from four empirical microsatellite genotype datasets (Formica lugubris, Sciurus vulgaris, Thalassarche melanophris, and Himantopus novaezelandia) to create 100 replicate datasets at each sample size. Despite differences in taxon (two birds, one mammal, one insect), population size, number of loci and polymorphism across loci, the degree of differences between simulated and empirical dataset allele frequencies, expected heterozygosities and pairwise F(ST) values were almost identical among the four datasets at each sample size. Variability in allele frequency and expected heterozygosity among replicates decreased with increasing sample size, but these decreases were minimal above sample sizes of 25 to 30. Therefore, there appears to be little benefit in sampling more than 25 to 30 individuals per population for population genetic studies based on microsatellite allele frequencies.
Mitochondrial DNA (mtDNA) has been the workhorse of research in phylogeography for almost two decades. However, concerns with basing evolutionary interpretations on mtDNA results alone have been ...voiced since the inception of such studies. Recently, some authors have suggested that the potential problems with mtDNA are so great that inferences about population structure and species limits are unwarranted unless corroborated by other evidence, usually in the form of nuclear gene data. Here we review the relative merits of mitochondrial and nuclear phylogeographical studies, using birds as an exemplar class of organisms. A review of population demographic and genetic theory indicates that mitochondrial and nuclear phylogeographical results ought to concur for both geographically unstructured populations and for populations that have long histories of isolation. However, a relatively common occurrence will be shallow, but geographically structured mtDNA trees--without nuclear gene corroboration--for populations with relatively shorter periods of isolation. This is expected because of the longer coalescence times of nuclear genes (approximately four times that of mtDNA); such cases do not contradict the mtDNA inference of recent isolation and evolutionary divergence. Rather, the nuclear markers are more lagging indicators of changes in population structure. A review of the recent literature on birds reveals the existence of relatively few cases in which nuclear markers contradict mitochondrial markers in a fashion not consistent with coalescent theory. Preliminary information from nuclear genes suggests that mtDNA patterns will prove to be robust indicators of patterns of population history and species limits. At equilibrium, mitochondrial loci are generally a more sensitive indicator of population structure than are nuclear loci, and mitochondrial estimates of FST-like statistics are generally expected to exceed nuclear ones. Hence, invoking behavioural or ecological explanations of such differences is not parsimonious. Nuclear genes will prove important for quantitative estimates of the depths of haplotype trees, rates of population growth and values of gene flow.
Loche is an ancient landrace of squash from Northern Peru, notable for its vegetative reproduction and lack of seeds in fruits. To date, very little is known about its genetics. Here, we used 21 ...simple sequence repeats to assess the genetic diversity and population structure of a collection of 100 samples of loche from three localities in Peru, and 10 samples of related species, C. pepo and C. maxima (110 accessions in total). A total 85 bands were manually scored, obtaining an average of 4.05 alleles per locus. The UPGMA clustering method and principal coordinate analysis showed a clear identification between the three species of Cucurbita. Population structure analysis clustered the 110 accessions into the following five populations: (i) three of loche, (ii) one of C. pepo, and (iii) one of C. maxima. Genetic diversity estimation was conducted considering only the three groups (populations) of loche identified, which was 0.024 as an average. AMOVA revealed the greatest variation between populations (79.66%) and indicated that variability within populations is 20.33%. Vegetative propagation by means of stem cuttings and cultivation in a very restricted geographical area would explain the rather low diversity of loche. This in turn would suggest that the apparent variation observed in fruit shape may be explained by somatic mutation and/or environmental factors.
Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, ...but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species' true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.
The spatial genetic structure is a topical issue in the studies of various aspects of ecology and evolution. Using the multilocus autocorrelation method with hypervariable microsatellite genetic ...markers, we investigated a fine‐scale pattern of genetic structure in 5 local populations of the common shrew Sorex araneus separated by distances of 300–1000 m (the Moscow chromosomal race). Spatial genetic autocorrelation analysis based on 5 microsatellite loci (expected heterozygosity >0.79) with 90 alleles revealed a consistent pattern of significant positive genetic structure. By testing the autocorrelation at multiple scales from 25 to 500 m, we found that positive spatial genetic structure is detectable in distance classes of <500 m. The weaker spatial genetic structure positively correlated with a higher ratio of nonresident individuals to residents’ activity (number of captures). In contrast to nonresident animals, the residents demonstrated prominent genetic structure. Genetic difference (FST) between the populations was significant (0.016–0.051) and comparable with that between populations of different races analyzed previously (0.016–0.038). FST was not associated with geographic distance. These demographic patterns allowed us to propose a scheme of genetic‐structure dynamics involving periodic appearance of more related local groups and renewal of allelic profiles from а common pool where the alleles are mixed. The scheme predicts fluctuating genetic structure and random similar differences among local populations.
Graphical
Fluctuations in the relative abundance of resident and nonresident shrews create situations with different rates of immigration and changing of alleles. Considering population system in the common shrew as a number of local populations with periodic renewing from common pool—cocktail of alleles, one may expect random genetic differentiation of local populations. We found that the FST values were not correlated with geographic distances and, at the smallest distances, were comparable with that between populations of different chromosomal races of this species.
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