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MICRO-CHECKER: Software for identifying and correcting genotyping errors in microsatellite data
Abstract
DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO-CHECKER is WINDOWS(R)-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO-CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
... The bullfrog populations were genotyped using 17 microsatellite loci (GenBank sequences to calculate genetic diversity and genetic structure [29]: AY323934, AY323931, AY323932, AY323930, AY323929, AY323928, HQ439092, HQ439093, HQ439094, HQ439096, HQ439097, AB911223, AB911228, AB911299, AB911231, AB911236, and AB911222. Primer sequences and the procedures used during DNA amplification were based on previously published data [30,31] (Table S2, Supplementary Materials). All primers were tagged with 5 ′ -fluorescein bases (TAMRA, FAM, or HEX). ...
... MICRO-CHECKER 2.2.3 was applied to quantify the scoring errors resulting from factors such as the large allele dropout [31], stuttering, or null alleles. GENEPOP version 4.0 was employed to test the linkage disequilibrium and Hardy-Weinberg equilibrium [36]. ...
The introduction and subsequent range expansion of the American bullfrog (Lithobates catesbeianus) is part of a rising trend of troublesome biological invasions happening in China. This detrimental amphibious invasive species has strong adaptability. After its introduction and spread, it established its own ecological niche in many provinces of China, and its range has continued to expand to more areas. Previous studies recorded the introduction time of bullfrogs and calculated the changes in their genetic diversity in China using mitochondria, but the specific introduction route in China is still unknown. Expanding upon previous research, we employed whole-genome scans (utilizing 2b-RAD genomic sequencing) to examine single nucleotide polymorphisms (SNPs) and microsatellites within Lithobates catesbeianus to screen the genomes of these invasive amphibian species from eight Chinese provinces and two U.S. states, including Kansas, where bullfrogs originate. A total of 1,336,475 single nucleotide polymorphic loci and 17 microsatellite loci were used to calculate the genetic diversity of bullfrogs and their migration pathways. Our results suggest that the population in Hunan was the first to be introduced and to spread, and there may have been multiple introductions of subpopulations. Additionally, the genetic diversity of both the SNP and microsatellite loci in the Chinese bullfrog population was lower than that of the US population due to bottleneck effects, but the bullfrogs can adapt and spread rapidly. This study will offer crucial insights for preventing and controlling future introductions into the natural habitats in China. Additionally, it will assist in devising more precise strategies to manage the existing populations and curtail their continued expansion, as well as aim to improve clarity and originality while mitigating plagiarism risk.
... which also performed data binning. A Micro-Checker was run to check for genotyping errors like stutter bands, large allele dropouts, and null alleles (Van Oosterhout et al. 2004). To assess the genetic structure in the data, Structure 2.2. ...
... The MICROCHECKER software v. 2.2.3 [47] was used to examine the presence or absence of scoring errors in the microsatellite loci. Genetic diversity was measured as the number of alleles (NA), expected heterozygosity (H E ), and observed heterozygosity (H O ) using the CERVUS software v. 3.0 [46]. ...
This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8–2387) and contractions (16–2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii.
... These indices included the percentage of polymorphic loci (P), effective number of alleles (A e ), Shannon information index (I), observed heterozygosity Nei's (1973) gene diversity (h), inbreeding coefficient (F is ), coefficient of genetic differentiation between populations (F st ), and the effective number of migrants (N m ). The presence of null alleles was tested using Micro-Checker 2.2.3 (Van Oosterhout et al. 2004). Assuming inbreeding equilibrium without inbreeding depression of the investigated populations, the outcrossing rates were calculated using the formula t = (1 − F is )∕(1 + F is ) (Fyfe and Bailey 1951;Weir and Cockerham 1984). ...
Oryza rufipogon Griff. and O. nivara Sharma et Shastry are wild ancestors of Asian cultivated rice, harboring a wealth of genetic variation valuable for rice breeding. Mating systems play an important role in shaping genetic variation within species, and could shed light on germplasm conservation. Despite the importance, previous research on the mating systems of O. rufipogon and O. nivara has been hindered by limited sample sizes and the use of unsuitable genetic markers. In this study, by collecting a large number of maternal plants and seeds from representative populations of both species, we estimated their outcrossing rates using an extended mixed-mating model along with 12 simple sequence repeats markers. Our results revealed distinct mating strategies between the two species. Oryzarufipogon exhibited a mixed mating system with an average outcrossing rate of 0.478, while O. nivara was predominantly selfing, with an average outcrossing rate of 0.256. In addition, compared to O. nivara, O. rufipogon has a higher genetic diversity within populations and lower differentiation among populations. The contrasting genetic variation patterns between the two wild rice species could result from demographic bottlenecks and a shift from mixed mating to primarily selfing in O. nivara. Overall, through our geographically widespread sampling, we have obtained reliable outcrossing rate estimates for O. rufipogon and O. nivara, thus facilitating both in situ and ex situ conservation of their germplasm.
... The number of alleles (Na), polymorphic information content (PIC) and probability of identity (PI) of each microsatellite locus were calculated in Cervus v. 3.0 [52]. Microsatellite data were checked for scoring errors due to stuttering, large allele dropout and the presence of null alleles using Micro-Checker v. 2.2.3 [53]. Null allele frequencies were estimated with the expectation-maximisation algorithm using FreeNA [54]. ...
In this work, we analyzed the morphology and genetic structure of Teucrium montanum, T. capitatum and their hybrid T. × rohlenae from three syntopic populations. A morphometric study showed that the parents and their hybrids exhibited continuous morphological variation, with the hybrid positioned exactly between the parents. Genetic analysis revealed that plants morphologically identified as T. × rohlenae are fertile hybrids that produce hybrid swarms dominated by later-generation hybrids. This suggests that introgression, rather than speciation, is the more likely outcome of hybridization between these plant species. The extent and direction of gene flow between the two species differed markedly between the three syntopic localities. At the Trilj locality, it was clearly unidirectional, with T. capitatum playing the dominant role. At the Sićevo locality, gene flow was slightly asymmetric, favoring the genetic background of T. capitatum, while at the Sliven site, it was completely asymmetric in the opposite direction. The extreme case of unidirectional gene flow was observed at the Trilj locality where plants morphologically identified as T. montanum could not be genetically distinguished from T. capitatum. This suggests that interspecific hybridization occurred long ago, leading to introgression and cryptic hybrids, blurring of species boundaries and generating evolutionary noise.
... Genotyping errors and the presence of null alleles were checked using MICRO-CHECKER. If null alleles were detected or the loci failed to amplify in >50% of the samples, it was discarded (Van Oosterhout et al. 2004). ...
False killer whales (Pseudorca crassidens) are globally distributed cetaceans, often found in deep oceanic waters but occasionally near coastlines. Despite their broad distribution, information on their abundance, genetics, and ecology remains limited. In New Zealand waters, these whales occur year-round, with increased sightings during the warmer months due to the East Auckland Current. This study investigates the genetic diversity and population structure of New Zealand false killer whales using 17 samples collected from 2005 to 2018 in four locations, comparing them to global studies. New Zealand samples revealed four unique haplotypes with low genetic diversity (h = 0.42 ± 0.141; π = 0.29%± 0.002). No genetic differentiation was observed between South Pacific and New Zealand populations (F ST = 0.05 p = 0.1602 F ST = 0.058 p = 0.145). These findings suggest low genetic diversity for New Zealand false killer whales, but within values expected for other cetaceans with matrilineal social structures. The presence of shared haplotypes suggests potential historical or ongoing connections with wider Pacific populations. However, further research is needed due to the short mtDNA-CR fragment analysed and small sample size, which may have resulted in an inability to capture the full extent of the genetic variation. This study contributes to our understanding of this species and its conservation within New Zealand. ARTICLE HISTORY
... Estimates of genotyping errors allelic dropout (ADO) and false alleles (FA) from replicate genotyping were executed in Gimlet v.1.3.3 (Valiere 2002). The presence and frequency of null alleles were estimated using the Micro-Checker 2.2.3 software and Brookfield 1 (Oosterhout et al. 2004). Estimates of probability of identity (PID) and probability of identity for siblings (PIDsibs) were executed in Gimlet v.1.3.3. ...
This study traced the maternal lineage of the domestic swine populations using mitochondrial DNA control region markers and genetic diversity using microsatellite markers in Uttarakhand, an Indian state situated at the foothills of the world’s youngest (geo-dynamically sensitive) mountain system, “the Himalayas”. Analysis of 68 maternally unrelated individuals revealed 20 haplotypes. The maternal signature of the Pacific, Southeast Asian, European, and ubiquitously distributed Chinese haplotypes was present in Uttarakhand’s domestic pig population. The D3 haplotype reported in wild pigs from North India was also identified in 47 domestic samples. A unique gene pool, UKD (Uttarakhand Domestic), as another lineage specific to this region has been proposed. Genotypes were analyzed, using 13 sets of microsatellite markers. The observed (Ho) and expected (He) heterozygosities were 0.83 ± 0.02 and 0.84 ± 0.01, respectively. The average polymorphic information content value of 0.83 ± 0.01 indicated the high informativeness of the marker. The overall mean FIS value for all the microsatellite markers was low (F = 0.04, P < 0.01). Seven loci deviated from Hardy-Weinberg equilibrium (HWE) at a significant level (p < 0.05). Two clusters were identified, indicating overlapping populations. These results suggested that though belonging to different maternal lineages, the traditional management practices in Uttarakhand have allowed for genetic mixing and the sharing of genetic material among pig populations. It could contribute to increased genetic diversity but might also result in the loss of distinct genetic characteristics or breed purity of the local breeds if not carefully managed.
... Micro-checker ver. 2.2.3 (Van Oosterhout et al. 2004) was used to test for the presence of null alleles with 10,000 randomizations (95% confidence levels). LOSI-TAN (Antao et al. 2008) was used to detect loci that may be under positive selection, using 50,000 simulations following the infinite allele model (IAM) and stepwise mutation model (SMM) at the 95% confidence level. ...
Seagrass beds are ecologically and economically important coastal ecosystems, and seagrass-associated organisms are a key part of their biodiversity. Marine organisms that reproduce through broadcast spawning are likely to have less genetic differentiation among populations than those that use other modes of reproduction, but this has not been well studied. Here, we investigated the genetic diversity, genetic differentiation, and migration patterns of the seagrass-associated sea star Protoreaster nodosus across 12 sites spanning approximately 2500 km from the Ryukyu Archipelago, Japan, to the Philippines. We genotyped 405 individuals by using seven microsatellite loci and analyzed allelic richness and expected heterozygosity as indices of genetic diversity. Of these two indices, only expected heterozygosity decreased slightly with increasing latitude. These results suggest that genetic diversity has not clearly decreased, even in the isolated Ryukyu Archipelago populations. Geographic distance was significantly correlated with genetic differentiation (pairwise FST: − 0.005 to 0.049). However, populations in the Ryukyu Archipelago and the Philippines showed relatively low genetic structuring and the pairwise genetic differentiation between these regions was often non-significant. Analysis of historical migration rates showed bidirectional north–south migration, which appears to be influenced by the Kuroshio Current and its countercurrents.
... The presence of null alleles (NullA) was tested using Micro-Checker (ver. 2.2.3) (Van Oosterhout et al., 2004). The FSTAT v. 2.9.3 was used to calculate allelic richness (AR), and inbreeding coefficient (FIS) (Goudet, 1995), while linkage disequilibrium test was carried out using GENEPOP v. 4.7.3 (Raymond & Rousset, 1995) using 10000 iterations and 1000 de-memorization steps. ...
The Far Eastern freshwater mussel Sinanodonta lauta has recently been recorded in European Russia outside of its native range. As an invasive species affecting native ecosystems, this mussel is still poorly investigated in many aspects, including population genetics. In this study, we describe for the first time eight microsatellite loci that were developed based on a previously published set of microsatellite markers of the Chinese Pond Mussel (Sinanodonta woodiana).
... [25]. The presence of null alleles and estimated allele frequencies was analyzed by MICRO-CHECKER software v.2.2.3 [26]. GENETIX. ...
The sterlet (Acipenser ruthenus) is the smallest-bodied endangered species among the six native sturgeon species of the Danube River, and self-sustaining populations still inhabit the Hungarian section of the Danube River and its largest tributary, the Tisza River. Their populations are drastically decreasing; however, they still have natural reproduction in these habitats. For the genetic conservation of the species, an ex situ gene bank is maintained in Hungary. The present study aimed to analyze the genetic resources of a gene bank with a near 40-year history and to compare it with natural populations and farmed stocks. Twelve microsatellites were used for population genetics analyses and individual genotyping of 268 specimens from two natural habitats (Danube and Tisza Rivers) and three captive stocks (a gene bank broodstock and two farms). Microsatellites revealed similar patterns among wild populations and gene bank stocks and did not show genetic differentiation (FST: 0.016–0.017) among them. These results confirmed that the gene bank broodstock properly represents the genetic background of the Danube and Tisza populations and is suitable as a source of breeding materials for the restocking programs. Negative trends were detected in the farmed stocks, reflected in reduced polymorphism at a few loci. The results of the principal component analyses indicate the farm stocks’ separation from the wild and gene bank stocks. The present genetic characterization study reveals a valuable captive stock of the endangered sterlet populations and provides unique information about the genetic similarities and differences among farms and wild stocks in Hungary. Our results provide information that contributes to preserving the genetic structure and variability in sterlet populations and supports the management of gene bank broodstock—avoiding inbreeding and preserving the unique genetic background of the Carpathian basin.
... Deviations from Hardy-Weinberg expectation were detected in 3 out of 10 loci (Table A3) and were not the consequence of null allele presence. All markers were checked for null alleles with MicroChecker software (van Oosterhout et al., 2004). This finding was expected because our study population was open, non-panmitic, and characterized by a relatively high level of genetic relatedness . ...
Recent evidence indicates that individual behavioural variation in animals, defined as consistent individual differences in behaviour across contexts and time, influence ecological and evolutionary processes, and a growing number of studies demonstrate that individual behavioural variation can play a large role in shaping grouping dynamics among social animals. We studied the common degu, Octodon degus , a social rodent, to evaluate whether individual behavioural variation underlies social organization and the reproductive success of individuals within groups. We examined social groups in a population in central-north Chile during one breeding season, tested 67 adults in an open field test (i.e., the propensity to explore an unfamiliar environment) and 62 adults in a poke test (i.e., the propensity to charge an object) to quantify individual behavioural variation, determined assortment based on individual behavioural differences across 19 social groups, and performed genetic analyses to assess reproductive success. We found that the response to the poke test was repeatable, while none of the behaviours from an open field test were. The repeatable behaviour during the poke test was not associated to components of social organization (group composition), or to reproductive success. These findings imply that individual behavioural variation did not affect grouping patterns or direct fitness in this degu population.
... The number of distinct genotypes (genets) was established by deciding that missing data would not be counted. After the removal of duplicate genotypes (clones; Table 1), the presence of null alleles, stutter peaks and allele dropout was checked in the diploid populations (SP7, AU3, AU4, RO3, IT1, PL, GEO, KYR) using the MICRO-CHECKER 2.2.3 [31]. The frequency of null alleles and P-values for heterozygote deficiency were calculated using 10,000 Monte Carlo randomisations implemented in the ML-NullFreq software [32]. ...
Trees and shrubs belonging to the genus Juniperus L. are pivotal species in arid and semi-arid ecosystems in the Northern Hemisphere. However, unfavourable phenomena are observed in their populations due to global warming. We aimed to investigate the soil requirements, genetic diversity and population history of Juniperus sabina L. from Europe, Georgia, and Kyrgyzstan. Genetic resources were evaluated in 16 populations using nuclear microsatellites, while past demographic events were described based on the chloroplast DNA haplotypes. Seven chemical parameters in 36 soil samples from the European range of J. sabina were compared. In the studied area, three distinct phylogenetic lineages corresponding to different varieties of J. sabina, namely var. sabina, var. balkanensis, and the Asian variety, were revealed. Unimodal mismatch distributions and significantly negative Tajima's D and Fu's Fs parameters indicated that the sabina and balkanensis varieties underwent a population expansion. Microsatellite variation was moderate, potentially influenced by inbreeding, clonal propagation, and limited gene flow between populations. Bayesian clustering revealed five genetic groups. Compared to var. sabina, the balkanensis variety occupies areas with significantly higher potassium content in the soil, which probably mitigates the adverse effects of drought in its localities.
... Microsatellite genotypes were determined using GeneMarker 6.4 (SoftGenetics LLC). Genotyping problems, such as null alleles, large allele drop-out, and scoring errors (Guichoux et al., 2011) were verified using Microchecker 2.2.3 (Van Oosterhout et al., 2004). Loci or sampling sites with more than 10% of null alleles were removed from further analyses. ...
Neglected cryptic diversity can lead to the permanent loss of locally adapted alleles, which can reduce resilience to rapid environmental change. It can also result in overestimation of fisheries stock sizes that can result from treating different species as if they belonged to one. Bluefish ( Pomatomus saltatrix ) is considered a circumtropical and subtropical species and an important fishery resource all over the world. Differences in ecologically relevant traits are observed among isolated populations. Also, in the Southwestern Atlantic, molecular data suggest multiple populations, but these are treated as a single fish stock by regulatory agencies due to a lack of definitive information. We used whole mitogenome sequences, nuclear ( rho ) and mitochondrial ( coxI and cytb ) genes, as well as microsatellites to investigate historical and current genetic population structure and parameters of bluefish in the Western Atlantic. A total of 263 samples were collected along the Brazilian coast and in the USA (New Jersey, Northwest Atlantic). Data revealed the existence of two evolutionarily significant units (ESU) of bluefish along the South American coast, later confirmed by whole mitogenome sequencing of both haplogroups. These two ESUs have a mostly parapatric distribution, with some areas of overlap, which vary along the year. We also conducted seasonal sampling in Brazil to investigate migration patterns. ESUs occur mostly north and south of parallel 23° 40′ S, with an overlap area that varied seasonally. The level of differentiation between those two ESUs in the SW Atlantic, even in sympatry, is as high as that found between them and those from the NW Atlantic and Europe. Parapatric distribution and restricted gene flow suggest the existence of ecological barriers and local adaptation. The splitting of an ancient population from the Southwestern Atlantic into two putative species is important to understand bluefish evolutionary diversification and has implications for fishery regulatory measures in Brazil.
... other than B. griseocollis, the amplification may include null alleles that falsely inflate the level of homozygosity in the populations. We tested for null alleles and linkage disequilibrium within our loci using the program MICRO-CHECKER (Van Oosterhout et al. 2004). No null allele or linkage disequilibrium was detected, and therefore all the loci were included in the analysis. ...
The decline of wild bee pollinators has prompted habitat reconstruction in many regions around the world in order to increase the floral resources available to pollinators. Relatively little research has monitored the genetic differentiation and the relatedness of founding bumblebee populations during the colony recruitment process after vegetation is planted in the landscape. We surveyed nine 3-year post-planting reconstructed prairie sites located in the corn belt of the U.S. Midwest, where the landscape is largely dominated by industrialized row crops. Using seven microsatellite loci from 103 Bombus griseocollis, we examined the population genetics of this generalist bee's colonies established on these newly constructed prairie sites. When analyzed, B. griseocollis populations from an older reconstructed site were more genetically distinct from newly established bumblebee populations on reconstructed sites, while the new reconstructed sites exhibited no genetic structure. The floral richness or abundance at the reconstructed sites did not contribute to the allelic richness of the recolonized bumblebee populations. We did, however, find significant negative correlations between the bumblebee populations' allelic richness and the percent coverage of row-crop farmland in the surrounding landscape and positive correlations between the allelic richness and forest and woody wetland habitat covers. This finding strongly indicates the importance of the composition of the surrounding landscape in the recruitment period of the founding pollinator populations.
... Hardy-Weinberg equilibrium (HWE) was analyzed (Guo & Thompson, 1992) using Genepop (Raymond & Rousset, 1995;Rousset, 2008). MICROCHECKER version 2.2.3 was applied for the detection of null alleles, large allele dropout, stuttering and scoring errors (Van Oosterhout et al., 2004). Analysis of molecular variance (AMOVA) was applied for analysis of variance components at different hierarchical levels for domesticated and commercial stocks and for phylogenetic groups using Arlequin 3.5.2.2 (Excoffier & Lischer, 2010). ...
... The significance value for this parameter was estimated using 999 permutations. Previously, MICRO-CHECKER v2.23 [44] was used to explore the existence of null alleles and evaluate their impact on the estimation of genetic differentiation. Eighty-one individuals were collected from the sampling points using nets. ...
Biodiversity conservation entails not only the preservation of specific taxa but also genetic diversity. Despite the crucial role of molecular data in freshwater fish conservation management, there is a scarcity of information regarding the genetic diversity of Luciobarbus Heckel, 1843 (Actinopterygii, Cyprinidae) populations in the Aral system. Therefore, the primary aim of this study was to provide genetic information on two native species of the Luciobarbus genus found in the Aral system: L. conocephalus (Kessler, 1872) and L. brachycephalus (Kessler, 1872). These species, like many others in the Aral system, confront the imminent threat of extinction due to system alterations. However, genetic studies on these species at the nuclear level are challenging because Luciobarbus is an allotetraploid genus. Consequently, genetic investigations thus far have focused mainly on sequencing mitochondrial genes due to their haploid nature. This study has successfully developed fifteen new polymorphic microsatellite loci, which can prove to be valuable for population genetics, conservation, and other pertinent research on these species.
... To check whether each EST-SSR locus met the requirements for population genetic analyses, we used BayeScan 2.1 (1,000,000 simulations) (Foll 2012) to identify outlier loci, which we defined as those with excessively high or low F ST compared to neutral expectations. The existence of null alleles was checked using Micro-Checker version 2.2.3 (Van Oosterhout et al. 2004) and linkage disequilibrium between loci in each population was tested using GENEPOP version 4.7 (Raymond and Rousset 1995;Rousset 2008). For these analyses, seven populations in the Hahajima Islands that did not have a pattern of admixture in Sugai et al. (2019), listed in Table S1, were used. ...
Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Postmating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.
... function within the "stats" package of R version 4.2.0 [31]. AR was calculated using FSTAT version 1.2 [32], and MicroChecker version 2.2.3 was used to identify null alleles [33]. Polymorphic information content (PIC) was estimated for each locus using the Excel Microsatellite Toolkit. ...
The North African catfish ( Clarias gariepinus ) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding.
... MICRO CHECKER V2.2.3 was used to test for the presence of null alleles for all loci (Van Oosterhout et al. 2004). GENAIEX V6.5 was used to analyze the number of alleles (AO), observed heterozygosity (HO), Figure 1 Difference in individuals' genetic relatedness between lightly and severely degraded grasslands. ...
Grassland degradation is challenging the health of grassland ecosystems globally and causing biodiversity decline. Previous studies have demonstrated the impact of grassland degradation on the abundance and behavior of small mammals. Little is known about how it affects the genetic structure of gregarious mammals in the wild. This study explores the effects of grassland degradation on the genetic structure of a small burrowing mammal, plateau pika ( Ochotona curzoniae ). We used nine microsatellite loci to analyze the genetic diversity and genetic differentiation between colonies and genetic relatedness between individuals within the colony. We found that pikas in severely degraded grasslands had a significantly higher genetic diversity within colonies, a higher level of gene flow between colonies, and a lower genetic differentiation between colonies compared to pikas in less degraded grasslands. Individuals within colonies had a significantly lower genetic relatedness in severely degraded grasslands than in less degraded grasslands. This study has provided potential evidence of a significant impact of grassland degradation on the genetic structure of pikas, which has caused a breakdown of their kin‐selected colony structure.
... The significance criteria of all multiple tests were corrected by the continuous Bonferroni method. Invalid alleles were detected using Micro-Checker software (van Oosterhout et al. 2004). ...
The sea urchin Tripneustes gratilla holds substantial ecological and economic importance in tropical marine ecosystems. To better understand the population structure and genetic diversity of T. gratilla, here we developed a suite of 29 polymorphic microsatellite makers based on high-throughput sequencing. The range of alleles characterized by these primers varied from 6 to 19, with an average number of 12.31. The observed and expected heterozygosities ranged from 0.250 to 1.000 and from 0.808 to 0.955, respectively. All the polymorphism information content values of the 29 loci were above 0.5, suggestive of highly informative. Demonstrating adherence to Hardy–Weinberg equilibrium, these 29 primer pairs present robust candidates for conducting population genetics and phylogeographic analyses in T. gratilla, which may provide valuable information for sustainable management and conservation efforts of this urchin.
... Allele sizes were determined using a GS-600 LIZ size standard and Gene-Mapper v. 5.0 (ABI) software. The computer program MICRO-CHECKER [39] was used to check for null alleles and reading/typing errors for the microsatellite data. All samples were genotypes at all loci. ...
This study investigated the close kinship structure of southern right whales on feeding grounds during austral summer seasons. The study was based on biopsy samples of 171 individual whales, which were genotyped with 14 microsatellite DNA loci. Kinship was investigated by using the LOD (Log Odds) score, a relatedness index for a pair of genotypes. Based on a cut-off point of LOD PO > 6, which was chosen to balance false positives and negatives, a total of 28 dyads were inferred. Among these, 25 were classified as parent-offspring pairs. Additional genetic (mitochondrial DNA haplotypes) and biological (estimated body length, sex) data were used to provide additional information on the inferred close kin pairs. The elapsed time between sampling varied from 0 (close kin detected in the same austral summer season) to 17 years. All the kin pairs occurred within the Antarctic Indo sector (85°-135°E) and no pair occurred between whales within and outside of this sector. Six pairs were between individuals in high (Antarctic) and lower latitudes. Results of the present analysis on kinship are consistent with the views that whales in the Indo sector of the Antarctic are related with the breeding ground in Southwest Australia, and that whales from this population can occupy different feeding grounds. The present study has the potential to contribute to the conservation of the southern right whales through the monitoring of important population parameters such as population sizes and growth rate, in addition to assist the interpretation of stock structure derived from standard population genetic analyses.
... Possible genotyping errors, allele dropout and non-amplified alleles (null alleles) were detected using MICRO-CHECKER (van Oosterhout et al., 2004). Deviations from Hardy-Weinberg Equilibrium (HWE) and gametic disequilibrium were calculated using Arlequin v 3.5.2.2 (Excoffier and Lischer, 2010). ...
The Southern Ground-hornbill (SGH) (Bucorvus leadbeateri) is considered an umbrella species for biodiversity conservation in savannah biomes since they require large territories and significant protection measures that help to conserve a wide range of biodiversity with similar savanna and grassland requirements. Declines of the species are attributed to low reproductive rates coupled with multiple anthropogenic threats, including secondary poisoning, and persecution. Little is known about connectivity and population structure of SGH populations in Africa, south of the equator. Knowledge of population differentiation is needed to ensure that targeted conservation management plans can be implemented to slow population declines and ensure survival of the species. To inform a long-term conservation strategy, we investigated the broad-scale population structure of Southern Ground-hornbill across their sub-equatorial range. Our study based on 16 microsatellite loci identified moderate variation (average of 5.889 alleles per locus and a mean observed heterozygosity of 0.546) similar to other long-lived avian species. In contrast, mito-chondrial DNA sequences analysis identified low diversity (Hd = 0.3313, π = 0.0015). A Bayesian assignment approach, principal component analysis, analysis of molecular variance and phylo-genetic analysis identified weak to moderate population structuring across long distances and mitochondrial data showed a shallow phylogeny. Restriction to long-distance dispersal was detected that could not be attributed to isolation by distance, suggesting that other factors, such as their dispersal biology, are shaping the observed genetic differentiation. Although our study does not support the designation of populations as independent conservation units, we advocate that population management should continue to follow the Precautionary Principle (mixing founders from the same range state, rather than allowing mixing of founders from the extremes of the range) until there is scientific certainty. Following further research, if no independent Global Ecology and Conservation 52 (2024) e02963 2 conservation units are detected, then the global captive population can contribute to reintro-ductions across the range. In the wild, populations at the edge of the species range may need additional management strategies and gene flow should be promoted between neighbouring populations. Fig. 1. The distribution of the Southern Ground-Hornbill in sub-Saharan Africa with areas with high bioclimatic suitability and thus probability of occurrence.
... For these loci, amplification was carried out for each primer pair individually, while genotyping was done in multiplex (Supplemental File S1-sheet 3), except for the 99_CT locus which was performed individually. Putative null alleles were detected using Micro-Checker v. 2.2.3 (Van Oosterhout et al. 2004). Population genetic parameters (number of alleles (Na), expected and observed heterozygosity (He and Ho), Hardy-Weinberg equilibrium (HWe), linkage disequilibrium (LD)) per locus and population were calculated using GenAlEx v6.502 (Peakall and Smouse 2012) and the web version of GENEPOP (Raymond and Rousset 1995;Rousset 2008) in a set of 10 individuals for each species. ...
Centranthus is a small genus belonging to the family Caprifoliaceae, comprising approximately 16 taxa (nine species plus seven subspecies). Currently, it is incorporated into the Valeriana genus, which is the most species-rich in the world (> 400 species), even though its phylogeny is not clear. Despite its botanical relevance, genetic markers for assessing the genetic diversity and population structure of its members are scarce, thus hindering the management and conservation of wild populations. In this study, we conducted a genome screening of the critically endangered C. trinervis to develop a set of nuclear microsatellite markers (SSRs) for population genetic studies across this species and five congeneric species. After data filtering, we selected 8747 contigs from which 100 primer pairs were tested in PCR. Amplification profiles returned 37 candidate microsatellites, with 13 proving informative for C. trinervis. These markers successfully cross-amplified in C. calcitrapae (9/13), C. lecoqii (7/13), C. longiflorus (9/13), C. nevadensis (8/13), and C. ruber (8/13). The observed high level of polymorphism and the favourable amplification rates in other congeneric species underscore the utility of these microsatellite markers as valuable tools for conservation and population genetic studies in a genus such as Centranthus or Valeriana.
... The main parameters of genetic diversity, including the level of polymorphism, allele frequencies, values of observed and expected heterozygosity, compliance with the Hardy-Weinberg equilibrium and linkage disequilibrium were assessed using cErvus v 3.0.7 (Kalinowski et al., 2007) Possible errors in interpretation of genetic profiles caused by absence of alleles, allele dropouts or other possible PCR artifacts were detected using Micro-chEckEr v.2.2.1 (van Oosterhout et al., 2004) and cErvus v.3.0.7. ...
Commercial panels of microsatellite (STR) loci are focused on the use of DNA of the domestic dog (Canis lupus familiaris) and are often inapplicable for genotyping the DNA of the gray wolf (Canis lupus lupus). We propose a CPlex test system, including one hexa‐ and 12 tetranucleotide autosomal STR loci, as well as two sex loci, that is equally efficient in DNA identification of biological samples of the wolf and the dog. Analysis of molecular variance between samples revealed significant differentiation values (FST = 0.0784, p < 0.001), which allows to use the panel to differentiate wolf and dog samples. Population subdivision coefficients (θ‐values) were calculated for each of the 13 STR loci of the developed test system. It was shown that the values of the genotype frequency for dogs and wolves, without and with considering the θ‐value, differ by three orders of magnitude (for dogs 8.9 × 10⁻¹⁶ and 2.1 × 10⁻¹⁴ and for wolves 1.9 × 10⁻¹⁵ and 4.5 × 10⁻¹⁴, respectively). The use of population subdivision coefficients will allow to identify the most reliable results of an expert identification study and the power of exclusion provided by the STR loci of the CPlex test system makes it possible to achieve a reliable level of evidence in forensic DNA analysis of both wolves and dogs. The test system has been validated for use in forensic identification of the dog and wolf based on biological traces found at crime scenes, as well as for individual identification and establishing biological relationship of animals of these species.
... To assess genotyping error rates, genotyping of up to 10% of samples was conducted twice. All microsatellite data were tested in Micro-Checker for allelic dropout and the presence of null alleles, stutter bands, and genotyping inconsistencies (Van Oosterhout et al., 2004). ...
The present study aims at filling genetic structure gaps of grey seals ( Halichoerus grypus ) in the Northeast Atlantic, where effective Management Units (MUs) must be established to fulfil international obligations set by OSPAR and the EU’s MSFD. Mitochondrial and nuclear genetic markers were analysed for seals from the island of Ireland, southwest England and the German/ Danish North Sea coasts, whereby the integration of previously published data led to the largest genetic dataset analysed for this species to date. Results revealed that individuals from the island of Ireland are part of a single interbreeding population, with Southwest England being a source of migrants to the island of Ireland, and the southern North Sea (Germany, Denmark) being either a source or sharing a common source of migrants to the island of Ireland. Based on observed genetic structure within the Northeast Atlantic, two MUs are proposed: (i) the Faroe Islands, Scotland and the North Sea and (ii) the island of Ireland, southwestern UK (Cornwall) and France. Additionally, Northwest Scotland and the English Channel/Dutch North Sea are proposed as transition zones. Given the species’ high mobility, an adaptive management plan based on an ongoing regional/ European scale monitoring programme is recommended.
Understanding connectivity patterns in endangered species living in fragmented habitats is fundamental to improve management and conservation actions. Such improvements can be particularly pressing at trailing edges where populations are facing the greatest challenges of climate change, and appear all the more crucial if the species is commercially harvested. Seascape genetics have been increasingly used to meet these needs. In this study, we examined connectivity patterns among 32 populations located at the southern range limit of the oarweed kelp Laminaria digitata. Our populations were sampled in a roughly continuous manner, with the distance between neighboring populations ranging from a few km to about a few hundreds. By genotyping 11 microsatellite markers, our aim was to (1) refine analyses of population structure, (2) test whether on-shelf islands are genetically more differentiated compared to mainland populations, (3) evaluate the relative importance of various abiotic conditions in shaping the genetic structure and (4) evaluate if the relative importance of each environmental factor varied according to sampling schemes. Our analyses revealed a positive relation between connectivity links and genetic diversity: populations with high levels of connectivity were genetically enriched while isolated populations showed signs of genetic erosion. The genetically impoverished populations corresponded to the southernmost populations as well as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay) and the northernmost population in Pas-de-Calais. By performing db-RDA on various sampling schemes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor when analyzing continuously distributed populations.
Biodiversity patterns are shaped by the interplay between geodiversity and organismal characteristics. Superimposing genetic structure onto landscape heterogeneity (i.e., landscape genetics) can help to disentangle their interactions and better understand population dynamics. Previous studies on the sub‐Antarctic Prince Edward Islands (located midway between Antarctica and Africa) have highlighted the importance of landscape and climatic barriers in shaping spatial genetic patterns and have drawn attention to the value of these islands as natural laboratories for studying fundamental concepts in biology. Here, we assessed the fine‐scale spatial genetic structure of the springtail, Cryptopygus antarcticus travei, which is endemic to Marion Island, in tandem with high‐resolution geological data. Using a species‐specific suite of microsatellite markers, a fine‐scale sampling design incorporating landscape complexity and generalised linear models (GLMs), we examined genetic patterns overlaid onto high‐resolution digital surface models and surface geology data across two 1‐km sampling transects. The GLMs revealed that genetic patterns across the landscape closely track landscape resistance data in concert with landscape discontinuities and barriers to gene flow identified at a scale of a few metres. These results show that the island's geodiversity plays an important role in shaping biodiversity patterns and intraspecific genetic diversity. This study illustrates that fine‐scale genetic patterns in soil arthropods are markedly more structured than anticipated, given that previous studies have reported high levels of genetic diversity and evidence of genetic structing linked to landscape changes for springtail species and considering the homogeneity of the vegetation complexes characteristic of the island at the scale of tens to hundreds of metres. By incorporating fine‐scale and high‐resolution landscape features into our study, we were able to explain much of the observed spatial genetic patterns. Our study highlights geodiversity as a driver of spatial complexity. More widely, it holds important implications for the conservation and management of the sub‐Antarctic islands.
The blue shark, Prionace glauca, is the most abundant pelagic shark in the open ocean but its vulnerability remains poorly understood while being one of the most fecund sharks. In the Mediterranean Sea, the blue shark is listed as Critically Endangered (CR) by the International Union for Conservation of Nature. The species is facing a strong decline due to fishing, and scientific data regarding its genetic structure and vulnerability are still lacking. Here, we investigated the genetic diversity, demographic history, and population structure of the blue shark within the Mediterranean Sea, from samples of the Gulf of Lion and Malta, using sequences of the mtDNA control region and 22 microsatellite markers. We also compared our mitochondrial data to previous studies to examine the Atlantic-Mediterranean population structure. We assessed the blue shark’s genetic vulnerability in the Mediterranean basin by modelling its effective population size. Our results showed a genetic differentiation between the Atlantic and the Mediterranean basins, with limited gene flow between the two areas, and distinct demographic histories making the Mediterranean population an independent management unit. Within the Mediterranean Sea, no sign of population structure was detected, suggesting a single population across the Western and Central parts of the sea. The estimated effective population size was low and highlighted the high vulnerability of the Mediterranean blue shark population, as the estimated size we calculated might not be sufficient to ensure the long-term persistence of the population. Our data also provide additional evidence that the Gulf of Lion area acts as a nursery for P. glauca, where protection is essential for the conservation strategy of the species in the Mediterranean.
Cinnamomum parthenoxylon is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of C. parthenoxylon, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (C. parthenoxylon) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of C. parthenoxylon were analyzed via an Illumina HiSeqTM 4000 sequencing system. A total of 27,363,199 bases were generated for C. parthenoxylon. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG, GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of C. parthenoxylon. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of C. parthenoxylon was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in C. parthenoxylon. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of C. parthenoxylon.
Leptospirosis (caused by pathogenic bacteria in the genus Leptospira) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, such as rats, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus, is an important reservoir of leptospirosis in urban settings. We investigated leptospirosis among brown rats in Boston, Massachusetts and hypothesized that rat dispersal in this urban setting influences the movement, persistence, and diversity of Leptospira. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016-2022); 59 rats representing 12 of 17 sites were positive for Leptospira. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira isolates obtained from frozen and fresh tissue from some of the 59 Leptospira-positive rat kidneys. When isolates were not obtained, we attempted Leptospira genomic DNA capture and enrichment, which yielded 14 additional Leptospira genomes from rats. We also generated an enriched Leptospira genome from a 2018 human case in Boston. We found evidence of high genetic structure and limited dispersal among rat populations that is likely influenced by major roads and/or other unknown dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats, with specific clades tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and movement of leptospirosis in this urban rat community is driven by rat dispersal. Finally, our genomic analyses of the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other urban settings.
Forest and landscape restoration is one of the main strategies for overcoming the environmental crisis. This activity is particularly relevant for biodiversity-rich areas threatened by deforestation, such as tropical forests. Efficient long-term restoration requires understanding the composition and genetic structure of native populations, as well as the factors that influence these genetic components. This is because these populations serve as the seed sources and, therefore, the gene reservoirs for areas under restoration. In the present study, we investigated the influence of environmental, climatic and spatial distance factors on the genetic patterns of Plathymenia reticulata, aiming to support seed translocation strategies for restoration areas. We collected plant samples from nine populations of P. reticulata in the state of Bahia, Brazil, located in areas of Atlantic Forest and Savanna, across four climatic types, and genotyped them using nine nuclear and three chloroplast microsatellite markers. The populations of P. reticulata evaluated generally showed low to moderate genotypic variability and low haplotypic diversity. The populations within the Savanna phytophysiognomy showed values above average for six of the eight evaluated genetic diversity parameters. Using this classification based on phytophysiognomy demonstrated a high predictive power for genetic differentiation in P. reticulata. Furthermore, the interplay of climate, soil and geographic distance influenced the spread of alleles across the landscape. Based on our findings, we propose seed translocation, taking into account the biome, with restricted use of seed sources acquired or collected from the same environment as the areas to be restored (Savanna or Atlantic Forest).
The white-bellied pangolin is subject to intense trafficking, feeding both local and international trade networks. In order to assess its population genetics and trace its domestic trade, we genotyped 562 pangolins from local to large bushmeat markets in western central Africa. We show that the two lineages described from the study region (WCA and Gab) were overlapping in ranges, with limited introgression in southern Cameroon. There was a lack of genetic differentiation across WCA and a significant signature of isolation-by-distance possibly due to unsuspected dispersal capacities involving a Wahlund effect. We detected a c. 74.1–82.5% decline in the effective population size of WCA during the Middle Holocene. Private allele frequency tracing approach indicated up to 600 km sourcing distance by large urban markets from Cameroon, including Equatorial Guinea. The 20 species-specific microsatellite loci provided individual-level genotyping resolution and should be considered as valuable resources for future forensic applications. Because admixture was detected between lineages, we recommend a multi-locus approach for tracing the pangolin trade. The Yaoundé market was the main hub of the trade in the region, and thus should receive specific monitoring to mitigate pangolins’ domestic trafficking. Our study also highlighted the weak implementation of CITES regulations at European borders.
Captive breeding programs play an important role in preserving the genetic diversity of endangered species. It is of utmost importance to conduct genetic assessment for captive populations in order to develop scientific breeding plans and conservation management strategies. Here, we genotyped 10 microsatellite loci and sequenced 368 bp of mitochondrial DNA control region for the golden snub‐nosed monkey (Rhinopithecus roxellana) from eight captive populations in China, and compared the genetic indices of captive populations with a wild population. Meanwhile, we performed paternity tests to verify the genealogical records and established genetic lineages. A total of 157 individuals were identified from 161 fecal samples, including 135 captive individuals (approximately 25% of captive individuals in China). Microsatellite analysis showed that the nine populations had moderate levels of genetic diversity, with polymorphism information content (PIC) ranging from 0.43 to 0.542; the genetic diversity of captive populations (average PIC: 0.503) was slightly higher than that of the wild population (PIC: 0.438). The Structure analysis indicated that individuals of the eight captive populations contained two different genetic components. We conducted either single‐blind or double‐blind paternity testing on 40 offspring of captive individuals and found that five offspring from two zoos (Nanjing Hongshan Forest Zoo and Shanghai Wild Animal Park) showed discrepant kinships from their pedigree records, probably due to the inaccuracies in pedigree records. By constructing genetic pedigrees, inbred offspring were found in Beijing Zoo, Shanghai Zoo, Hangzhou Zoo, and Chengdu Zoo. Analysis based on mitochondrial DNA showed a high level of genetic diversity in the eight captive populations (mean nucleotide diversity: 0.047). However, no nucleotide diversity was found in the wild population. This study conducted a genetic survey for captive golden snub‐nosed monkeys and will significantly benefit the genetic conservation management for captive populations in the future.
Hybridization between the indigenous Japanese pond turtle, Mauremys japonica, and the exotic Reeves’ pond turtle, Mauremys reevesii, is widespread in Japan. In this study, we examined this hybridization using an analysis of mtDNA and 11 microsatellite markers (MS) combined with morphometry. In a Bayesian clustering analysis of MS, the admixture of two clusters equivalent to the two species was detected in the Seto Inland Sea and Ise Bay regions. While mtDNA showed reciprocal hybridization between the two species, their hybrids tended to possess the mtDNA of the rarer species at each locality. Contrary to preceding studies, F2/later generations outnumbered F1 generations. In addition, the admixture of two mtDNA lineages (Chinese and Korean) of M. reevesii was widely observed in all regions, together with the range expansion of the recently introduced Chinese lineage. A significant correlation was observed between plastron morph and assignment probability of MS, showing that plastron morphology reflects the degree of introgression by M. reevesii in M. japonica. This finding means that the reproductive interference of the dominant species on a rarer species is a major factor driving the hybridization of the two Mauremys species. In addition, the range expansion of the Chinese lineage of M. reevesii appears to enhance the introgression by M. reevesii in M. japonica.
Humans and wildlife experience complex interactions in urban ecosystems, favoring the presence of commensal species, among which invasive species are particularly successful. Rodents are the main vertebrate group introduced to oceanic islands, where the invasion process and dispersal patterns strongly influence their evolutionary and genetic patterns. We evaluated the house mouse Mus musculus and the black rat Rattus rattus on Cozumel Island, Mexico. We assessed genetic diversity and structure, connectivity, gene flow, relatedness and bottleneck signals based on microsatellite loci. Our genetic findings suggest that introduction of individuals of different geographic sources to the island promotes high allelic diversity and the effective establishment of migrants. We identified a clear genetic structure and low connectivity for the two species, tightly linked with anthropogenic and urban features. Notably, we found that the genetic structure of the house mouse sampled within the city of San Miguel Cozumel is associated with the historical human population growth pulses accompanying the urbanization of the city. At the fine-scale genetic level, the main urban drivers of connectivity of the house mouse were both the impervious land surfaces, i.e. the urban landscape, and the informal commerce across the city (a proxy of resources availability). Chances of a secondary invasion to natural environments have been relatively low, which is crucial for the endemic taxa of the island. Nonetheless, improving urban planning to regulate future expansions of San Miguel Cozumel is of the outmost importance to prevent these invasive species to disperse further.
Extra-pair paternity is widespread in passerine birds. The number of extra-pair young (EPY) varies among different species and populations of the same species. We tested if it is a case for a small passerine bird with poly-territorial behaviour, the Wood Warbler (Phylloscopus sibilatrix). The results are based on the microsatellite analysis of seven loci and revealed a high level of EPY in Central Russia population of Wood Warbler (EPY in 41% of all nests, 16 of 39 nests; 25% of all young were EPY, 52 of 212 young). We did not find relationship between relatedness among mates in the pair and the presence of EPY. There was no difference in heterozygosity and body mass between EPY and within pair young (WPY). Possible causes of extra-pair paternity are discussed.
Genetic diversity underpins evolutionary potential that is essential for the long‐term viability of wildlife populations. Captive populations harbor genetic diversity potentially lost in the wild, which could be valuable for release programs and genetic rescue. The Critically Endangered Arabian leopard (Panthera pardus nimr) has disappeared from most of its former range across the Arabian Peninsula, with fewer than 120 individuals left in the wild, and an additional 64 leopards in captivity. We (i) examine genetic diversity in the wild and captive populations to identify global patterns of genetic diversity and structure; (ii) estimate the size of the remaining leopard population across the Dhofar mountains of Oman using spatially explicit capture–recapture models on DNA and camera trap data, and (iii) explore the impact of genetic rescue using three complementary computer modeling approaches. We estimated a population size of 51 (95% CI 32–79) in the Dhofar mountains and found that 8 out of 25 microsatellite alleles present in eight loci in captive leopards were undetected in the wild. This includes two alleles present only in captive founders known to have been wild‐sourced from Yemen, which suggests that this captive population represents an important source for genetic rescue. We then assessed the benefits of reintroducing novel genetic diversity into the wild population as well as the risks of elevating the genetic load through the release of captive‐bred individuals. Simulations indicate that genetic rescue can improve the long‐term viability of the wild population by reducing its genetic load and realized load. The model also suggests that the genetic load has been partly purged in the captive population, potentially making it a valuable source population for genetic rescue. However, the greater loss of its genetic diversity could exacerbate genomic erosion of the wild population during a rescue program, and these risks and benefits should be carefully evaluated. An important next step in the recovery of the Arabian leopard is to empirically validate these conclusions, implement and monitor a genomics‐informed management plan, and optimize a strategy for genetic rescue as a tool to recover Arabia's last big cat.
Rice paddies are wetland ecosystems recognized as important habitats for many organisms; however, the hybridization‐related extinction risk of native plant species has not been investigated in this system so far. Eclipta L. (Compositae) is a common paddy weed in Japan; however, its genetic composition might be altered due to the hybridization between the native E. thermalis and the closely related exotic E. alba . We examined Eclipta 's genetic composition using 12 microsatellite markers (612 samples collected from 109 populations) and found (i) widespread geographical distribution of E. alba in Japan, (ii) hybridization with E. thermalis , and a large number of later‐generation hybrids, and (iii) widely varying situations among regions and populations. Eclipta alba appears to have invaded an open niche in northern Japan but has not yet reached southern Japan. Both E. alba and E. thermalis were found in central Japan; however, the latter had become rare due to hybridization‐mediated processes such as competition, and demographic and genetic swamping. Notably, endogenous and exogenous selection plays an important role in the invasion of E. alba , but to varying degrees among different areas. In summary, considering the genetic variability in E. thermalis , the genetic cluster of mainland Japan is in a highly critical situation due to the invasion of E. alba .
Forests help to reduce global warming by capturing and storing atmospheric carbon. Understanding the genetics of keystone species at a population level is vital for the management and sustainable utilization of forest genetic resources. A comprehensive population genetics study was carried out on Rubroshorea curtisii, an important widespread hill dipterocarp species in Peninsular Malaysia. A total of 41 populations across its distribution range in Peninsular Malaysia were collected to elucidate the genetic diversity and ultimately provide management guidelines for this species. The population samples were analysed using 10 polymorphic microsatellite loci and sequenced with three chloroplast DNA (cpDNA) regions. A total of 145 alleles were derived from the microsatellite loci, and 21 haplotypes were identified based on 1,113 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.627 for microsatellite gene diversity and HT = 0.574 for average haplotype diversity) but low genetic differentiation (FST = 0.036). Using Bayesian clustering, the studied populations can be divided into two groups, one of which shows further substructuring. Further sub-structuring in Cluster 1 led to sub-clustering of 1a and 1b. Bottleneck analysis did not detect any recent bottleneck events. Based on our findings, priority areas for in situ and ex situ conservation and minimum population size are recommended for the sustainable utilization of R. curtisii.
Better knowledge of genetic relationships between the Fortymile caribou herd and its neighbors is needed for conservation decision-making in Canada. Here, we contribute the first fine-scale analysis of genetic population structure in nine contiguous caribou herds at the geographic boundaries between Barren-ground and Northern Mountain caribou, and at the Alaska-Yukon border. Using pairwise differentiation metrics, STRUCTURE, and discriminant analysis of principal components (DAPC) to analyze 15 microsatellite loci in 379 caribou, we found complex patterns of genetic differentiation. The Fortymile was the only herd assigned to more than one genetic cluster, indicative of its history as a larger herd whose range expansions and gene flow to other herds were likely important to maintaining diversity across a functioning genetic metapopulation. Some small herds (Chisana, Klaza, and White Mountains) were genetically distinct, while others (Hart River, Clear Creek, Mentasta) exhibited little differentiation from herds they occasionally overlap, including herds assigned to different conservation units (DUs). This genetic connectivity does not result from demographic connectivity, as episodic contact during rut, rather than herd switching, is the likely mechanism. Unusually, one small herd (White Mountains) maintained genetic differentiation despite rut overlap with Fortymile. Our data reveal that some herds with different ecological and behavioral attributes are demographically independent but nonetheless genetically connected. Thus, we suggest that managing caribou for an appropriate level of genetic connectivity, while also supporting herd persistence, will be essential to conserve caribou genetic diversity in the region.
Arctic regions of northeastern Asia represent areas of secondary contact of the glacial phylogenetic lineages of charrs belonging to the genus Salvelinus (Salmoniformes: Salmonidae). However, the post‐glacial dispersion of charr across Arctic regions is poorly understood, as knowledge of populations from Chukotka and its neighbouring areas remains limited. Specifically, there is no clear understanding of which charr species inhabit significant regions of Chukotka from the sea coasts to the Kolyma drainage. In this study, we explored the affiliation of lacustrine charrs from the Chukotka area with (1) the Arctic lineage of Taranetz' charr ( Salvelinus taranetzi ); (2) the Bering lineage of Northern Dolly Varden ( Salvelinus malma malma ) and (3) the Siberia and Atlantic lineages of Arctic charr ( Salvelinus alpinus ). We analysed sequence variation of the mitochondrial DNA control region (mtDNA CR; 960 base pairs) and genotyped seven microsatellite loci of nuclear DNA from charr collected at 13 sampling sites. We found different consequences of secondary contact: (1) complete fixation of introgressed mtDNA (mitochondrial capture) and (2) preservation of several mtDNA lineages with the absence of contemporary gene flow between resident populations. Combining the distribution patterns, phylogenetic network topology and knowledge of the glaciation history of the region, we propose two zones of secondary contact of the glacial lineages in Chukotka–Kolima‐Chukotka River system and Paleo‐Amguema River–from where charrs with introgressed genomes spread throughout this range. However, in some cases, the process of foreign mtDNA capture likely occurs in a more localised manner.
Context
Elucidating how demography and contemporary landscape features regulate functional connectivity is crucial to implementing effective conservation strategies. We assessed the impacts of landscape features on the genetic variation of a locally endangered carnivore, the leopard cat ( Prionailurus bengalensis ) in Taiwan.
Objectives
We aim to evaluate the association between genetic structure and landscape features. We further predicted the changes in genetic diversity and suitable habitats in the future.
Methods
We genotyped 184 leopard cats in western Taiwan using 12 nuclear microsatellites and a mitochondrial marker. We applied a landscape optimization procedure with two genetic distances to identify major genetic barriers and employed ecological niche modeling to predict the future distribution of the leopard cat.
Results
Bayesian demographic inferences revealed a dramatic population decline for all leopard cat populations in Taiwan. Genetic clustering and resistance surface modeling supported that the population connectivity was influenced by highways and high elevation. Niche modeling indicated low temperature was one of the primary factors limiting the occurrence of leopard cats that may inhibit their movement in high elevations. We predicted the suitable habitats of leopard cats would shrink northward and towards higher altitudes with rugged topography in response to global warming.
Conclusions
Our study provided genetic evidence that leopard cats in Taiwan had undergone a dramatic population decline that may be associated with anthropogenic impacts. We also inferred the anthropogenic linear feature compromised the connectivity and persistence of leopard cats in human-mediated landscapes. Our finding serves as a model for landscape genetic studies of island carnivores in subtropical regions.
Genetic analyses were conducted to investigate the individual identification (and matching) of southern right whales (Eubalaena australis) from samples collected in the austral summer in the Indian Ocean sector of the Antarctic (between 80°–135°E, south of 60°S). The study was conducted to evaluate the utility of this approach for studies on site fidelity and range. In total, 157 skin biopsy samples were collected from free-ranging whales during fourteen summer surveys. The DNA was extracted from each biopsy sample, genotyped at fourteen microsatellite loci, sequenced for 381 nucleotides of the mtDNA control region, and the sex determined by the presence of a Y-chromosome specific locus. Eight matches were detected (four males and four females) using individual matching by multi-locus genotypes supported by mtDNA haplotype and sex determination. Where photographs were available, two matches were confirmed by photo-identification. These eight re-samples show that at least some males and females returned to the same feeding grounds across years. The average longitudinal dispersal ranges, latitudinal dispersal ranges and average direct distances between marks and recaptures were: 13°06′ and 7°15′; 1°23′ and 0°47′; and 361 n.miles and 199 n.miles for males and females, respectively. The time spans ranged from 3–13 years with an average of 6.7 and 7.8 years for males and females, respectively. Sampling and matching occurred in an area where visual surveys showed aggregations of southern right whales associated with high krill concentration. The study confirms the feasibility of the genetic approach, but more definitive inferences on site fidelity and movement ranges will require a large number of biopsy samples genotyped, from both south and north of 60°S.
Taxus baccata L. is a highly valuable species with wide distribution but scattered and locally rare occurrence. Human intervention, including forest management practices and fragmentation, can significantly impact the species’ genetic diversity, structure, and dynamics. In this study, we investigated these factors within T. baccata populations in the Bavarian Forest National Park (NP) in Germany and their implications for conservation. We used 13 EST-SSRs to assess the genetic diversity and structure of the population. Our analysis revealed a scarcity of small-diameter trees, indicating limited natural regeneration over time. However, conservation efforts, like selectively removing competitor species and using protective fencing, have improved growth conditions and promoted seedling emergence. The NP’s natural zone has no active management, which is confined to the development and management zones. Genetic diversity assessments revealed high genetic diversity (He: 0.612 and 0.614 for seedlings and adults, respectively) compared to other studies in Taxus baccata, dispelling concerns of significant inbreeding and showcasing a stable genetic structure. However, significant spatial clustering of related individuals (family structures) in both cohorts and low effective population size in the progeny hints at restricted gene flow, necessitating conservation efforts prioritizing safeguarding and promoting natural regeneration in development and management zones. Limited natural regeneration and the recent decrease in effective population size in the NP populations indicate habitat fragmentation and human interventions. Effective population size estimates emphasize the need for diverse conservation strategies. Conservation efforts should prioritize protecting natural regeneration and enhancing gene flow by actively promoting European yew, e.g., by shelterwood cutting, to ensure the long-term viability of T. baccata in the region outside the NP.
Landscape features can impede dispersal, gene flow, and population demography, resulting in the formation of many meta-populations within a continuous landscape. Understanding a species' ability to overcome these barriers is critical for predicting genetic connectivity and population persistence, and implementing effective conservation strategies. In the present study, we conducted a fine-scale analysis of spatial genetic analysis and contemporary gene flow within red panda populations in the Eastern Himalayas. Employing geometric aspects of reserve design, we delineated the critical core habitats for red pandas, which comprise 14.5 % of the landscape (12,189.75 Km2), with only a mere 443 Km2 falling within protected areas. We identified corridors among the core habitats, which may be vital for the species' long-term genetic viability. Furthermore, we identified substantial landscape barriers, including Sela Pass in the western region, Siang River in the central region, and the Dibang, Lohit rivers, along with Dihang, Dipher, and Kumjawng passes in the eastern region, which hinder gene flow. We suggest managing red panda populations through the creation of Community Conservation Reserves in the identified core habitats, following landscape-level management planning based on the core principles of geometric reserve design. This includes a specific emphasis on identified core habitats of red panda (CH-RP 5 and CH-RP 8) to facilitate corridors and implement meta-population dynamics. We envision the development of a comprehensive, long-term conservation and management plan for red pandas in the transboundary landscape, covering China, Nepal, and Bhutan.
We report the first field and genetic studies of the reproductive strategies of the Amazonian dart-poison frog Dendrobates ventrimaculatus, a species with biparental care. Neither males nor females are strictly monogamous. Males are aggressively territorial, but
some females interact without aggression. Monitoring of breeding pools revealed high rates of multiple clutch deposition and
high levels of larval cannibalism. Laboratory experiments confirmed larval cannibalism and suggested a benefit to cannibals
in increased growth rate. Genetic analyses indicate that offspring from different clutches in or above the same pool vary
in relatedness and are on average intermediate in relatedness between individuals from the same clutch and unrelated individuals
(from different pools). These data suggest that reproductive parasitism may be common in this species
In this study, we compared the genotypes obtained at a microsatellite locus using two methods of amplification and detection of variation in a set of individuals belonging to the red alga haplo-diploid species, Gracilaria gracilis. The methods varied in their capacity to detect longer alleles in heterozygotes, resulting in an apparent heterozygote deficiency. We attributed this bias in favour of short alleles to competition leading to the preferential amplification of shorter alleles (short allele dominance). To test this hypothesis, we created artificial heterozygotes (mixtures of two haploid DNA samples) and showed that long alleles already less intense than short alleles, ‘suffer’ more from being in association.
Note that an updated reference for Genepop is Rousset (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux (DOI: 10.1111/j.1471-8286.2007.01931.x)
Restriction fragment length polymorphisms (RFLP) analysis using the Southern blot technique can be used to recognize copy number variation of variable number of tandem repeats (VNTR) of conserved core sequences at several regions of the human genome. This new class of polymorphisms reveals a high degree of genetic variation, useful for individual identification purposes. Criticisms against forensic applications of such DNA typing data include the limitation of employing Hardy-Weinberg expectation of genotype frequencies, since several surveys indicate apparent deficiency of heterozygosity (or excess homozygosity) in comparison with Hardy-Weinberg expectations. This research postulates an alternative explanation of deficiency of apparent heterozygosity which is caused by the inability to detect extremely small-sized alleles (called 'non-detectable' alleles) due to the sensitivity of Southern gel electrophoresis. We show that the presence of 'non-detectable' alleles can produce pseudo-homozygosity and their frequencies can be predicted from the observed proportional heterozygote deficiency. Furthermore, in the covert presence of such 'non-detectable' alleles, we show that the gene-count method provides over-estimates of allele frequencies in the sample population, and hence the Hardy-Weinberg predictions of genotype frequencies avoid wrongful bias against suspects in forensic applications of DNA typing data. Applications of this theory to population data on six VNTR loci in US Caucasians and US Blacks suggest that the presence of 'non-detectable' alleles could be the major cause of apparent heterozygote deficiency, and the current approaches of predicting the population frequency of specific DNA phenotypes are practically free of the possible wrongful bias in courtroom applications of DNA typing data.
During microsatellite polymerase chain reaction (PCR), insertion-deletion mutations produce stutter products differing from the original template by multiples of the repeat unit length. We analyzed the PCR slippage products of (CA)n and (A)n tracts cloned in a pUC18 vector. Repeat numbers varied from two to 14 (CA)n and four to 12 (A)n. Data was generated on approximately 10 single molecules for each clone type using two rounds of nested PCR. The size and peak areas of the products were obtained by capillary electrophoresis. A quasi- likelihood approach to the analysis of the data estimated the mutation rate/repeat/PCR cycle. The rate for (CA)n tracts was 3.6 x 10(-3) with contractions 14 times greater than expansions. For (A)n tracts the rate was 1.5 x 10(-2) and contractions outnumbered expansions by 5-fold. The threshold for detecting 'stutter' products was computed to be four repeats for (CA)n and eight repeats for (A)n or approximately 8 bp in both cases. A comparison was made between the computationally and experimentally derived threshold values. The threshold and expansion to contraction ratios are explained on the basis of the active site structure of Taq DNA polymerase and models of the energetics of slippage events, respectively.
During microsatellite polymerase chain reaction (PCR), insertion–deletion mutations produce stutter products differing from
the original template by multiples of the repeat unit length. We analyzed the PCR slippage products of (CA)n and (A)n tracts cloned in a pUC18 vector. Repeat numbers varied from two to 14 (CA)n and four to 12 (A)n. Data was generated on approximately 10 single molecules for each clone type using two rounds of nested PCR. The size and
peak areas of the products were obtained by capillary electrophoresis. A quasi‐ likelihood approach to the analysis of the
data estimated the mutation rate/repeat/PCR cycle. The rate for (CA)n tracts was 3.6 × 10–3 with contractions 14 times greater than expansions. For (A)n tracts the rate was 1.5 × 10–2 and contractions outnumbered expansions by 5‐fold. The threshold for detecting ‘stutter’ products was computed to be four
repeats for (CA)n and eight repeats for (A)n or ∼8 bp in both cases. A comparison was made between the computationally and experimentally derived threshold values. The
threshold and expansion to contraction ratios are explained on the basis of the active site structure of Taq DNA polymerase and models of the energetics of slippage events, respectively.
Microsatellite DNA markers were applied for the first time in a population genetic study of a cephalopod and compared with previous estimates of genetic differentiation obtained using allozyme and mitochondrial DNA (mtDNA) markers. Levels of genetic variation detected with microsatellites were much higher than found with previous markers (mean number of alleles per locus=10.6, mean expected heterozygosity (HE)=0.79; allozyme HE=0.08; mtDNA restriction fragment length polymorphism (RFLP) HE=0.16). In agreement with previous studies, microsatellites demonstrated genetic uniformity across the population occupying the European shelf seas of the North East Atlantic, and extreme genetic differentiation of the Azores population (RST/FST=0.252/0.245; allozyme FST=0.536; mtDNA FST=0.789). In contrast to other markers, microsatellites detected more subtle, and significant, levels of differentiation between the populations of the North East Atlantic offshore banks (Rockall and Faroes) and the shelf population (RST=0.048 and 0.057). Breakdown of extensive gene flow among these populations is indicated, with hydrographic (water depth) and hydrodynamic (isolating current regimes) factors suggested as possible barriers to migration. The demonstration of genetic subdivision in an abundant, highly mobile marine invertebrate has implications for the interpretation of dispersal and population dynamics, and consequent management, of such a commercially exploited species. Relative levels of differentiation indicated by the three different marker systems, and the use of measures of differentiation (assuming different mutation models), are discussed.
Growing interest in microsatellite genotyping, combined with noninvasive genetic sampling has led to the increased production of data. New tools to analyse these data are required. gimlet is a user-friendly software package designed to perform several simple tasks: (i) construction of consensus genotypes from repeated genotyping; (ii) estimation of genotyping error rates; (iii) identification of identical genotypes; (iv) comparison of new genotypes to a set of reference genotypes; (v) determination of the kinship; and (vi) estimation of several population parameters such as allele frequencies, heterozygosity, probability of identity, and population size.
The unambiguous identification of Central Valley spring-run chinook salmon has become imperative since their proposed listing in 1998. The accuracy of methods used to assign individuals to their stock of origin is critical for understanding juvenile migration patterns and determining the success of protection measures. Existing microsatellites discriminate between the endangered winter-run and other chinook but are insufficient to characterize phylogenetically less distinct runs. Here, we isolated and developed highly variable tetranucleotide microsatellites for the specific goal of increasing discriminatory power among closely related populations, providing a new power towards the reliable differentiation of nonwinter runs
Keywords:DNA profiles;heterozygote deficiency;maximum likelihood estimation;null alleles
Paternity inference using highly polymorphic codominant markers is becoming common in the study of natural populations. However, multiple males are often found to be genetically compatible with each offspring tested, even when the probability of excluding an unrelated male is high. While various methods exist for evaluating the likelihood of paternity of each nonexcluded male, interpreting these likelihoods has hitherto been difficult, and no method takes account of the incomplete sampling and error-prone genetic data typical of large-scale studies of natural systems. We derive likelihood ratios for paternity inference with codominant markers taking account of typing error, and define a statistic delta for resolving paternity. Using allele frequencies from the study population in question, a simulation program generates criteria for delta that permit assignment of paternity to the most likely male with a known level of statistical confidence. The simulation takes account of the number of candidate males, the proportion of males that are sampled and gaps and errors in genetic data. We explore the potentially confounding effect of relatives and show that the method is robust to their presence under commonly encountered conditions. The method is demonstrated using genetic data from the intensively studied red deer (Cervus elaphus) population on the island of Rum, Scotland. The Windows-based computer program, CERVUS, described in this study is available from the authors. CERVUS can be used to calculate allele frequencies, run simulations and perform parentage analysis using data from all types of codominant markers.
Although it is clear that errors in genotyping data can lead to severe errors in linkage analysis, there is as yet no consensus strategy for identification of genotyping errors. Strategies include comparison of duplicate samples, independent calling of alleles, and Mendelian-inheritance-error checking. This study aimed to develop a better understanding of error types associated with microsatellite genotyping, as a first step toward development of a rational error-detection strategy. Two microsatellite marker sets (a commercial genomewide set and a custom-designed fine-resolution mapping set) were used to generate 118,420 and 22,500 initial genotypes and 10,088 and 8,328 duplicates, respectively. Mendelian-inheritance errors were identified by PedManager software, and concordance was determined for the duplicate samples. Concordance checking identifies only human errors, whereas Mendelian-inheritance-error checking is capable of detection of additional errors, such as mutations and null alleles. Neither strategy is able to detect all errors. Inheritance checking of the commercial marker data identified that the results contained 0.13% human errors and 0.12% other errors (0.25% total error), whereas concordance checking found 0.16% human errors. Similarly, Mendelian-inheritance-error checking of the custom-set data identified 1.37% errors, compared with 2.38% human errors identified by concordance checking. A greater variety of error types were detected by Mendelian-inheritance-error checking than by duplication of samples or by independent reanalysis of gels. These data suggest that Mendelian-inheritance-error checking is a worthwhile strategy for both types of genotyping data, whereas fine-mapping studies benefit more from concordance checking than do studies using commercial marker data. Maximization of error identification increases the likelihood of linkage when complex diseases are analyzed.
A growing number of population genetic studies utilize nuclear DNA microsatellite data from museum specimens and noninvasive sources. Genotyping errors are elevated in these low quantity DNA sources, potentially compromising the power and accuracy of the data. The most conservative method for addressing this problem is effective, but requires extensive replication of individual genotypes. In search of a more efficient method, we developed a maximum-likelihood approach that minimizes errors by estimating genotype reliability and strategically directing replication at loci most likely to harbor errors. The model assumes that false and contaminant alleles can be removed from the dataset and that the allelic dropout rate is even across loci. Simulations demonstrate that the proposed method marks a vast improvement in efficiency while maintaining accuracy. When allelic dropout rates are low (0-30%), the reduction in the number of PCR replicates is typically 40-50%. The model is robust to moderate violations of the even dropout rate assumption. For datasets that contain false and contaminant alleles, a replication strategy is proposed. Our current model addresses only allelic dropout, the most prevalent source of genotyping error. However, the developed likelihood framework can incorporate additional error-generating processes as they become more clearly understood.
Protein, mtDNA, and nuclear microsatellite DNA analyses have demonstrated that the Yellowstone grizzly bear has low levels of genetic variability compared with other Ursus arctos populations. Researchers have attributed this difference to inbreeding during a century of anthropogenic isolation and population size reduction. We test this hypothesis and assess the seriousness of genetic threats by generating microsatellite data for 110 museum specimens collected between 1912 and 1981. A loss of variability is detected, but it is much less severe than hypothesized. Variance in allele frequencies over time is used to estimate an effective population size of approximately 80 across the 20th century and >100 currently. The viability of the population is unlikely to be substantially reduced by genetic factors in the next several generations. However, gene flow from outside populations will be beneficial in avoiding inbreeding and the erosion of genetic diversity in the future.
The amount of nuclear DNA extracted from teeth of 279 individual red fox Vulpes vulpes collected over a period spanning the last three decades was determined by quantitative polymerase chain reaction (PCR). Although teeth were autoclaved during initial collection, 73.8% of extracts contained sufficient DNA concentration (> 5 pg/ micro L) suitable for reliable microsatellite genotyping but the quantity of nuclear DNA decayed significantly over time in a nonlinear pattern. The success of PCR amplification across four examined canine microsatellites over time was dependent on fragment size. By including data from two different tests for human contamination and from frequencies of allelic dropout and false alleles, the methodological constraints of population genetic studies using microsatellite loci amplified from historic DNA are discussed.
Despite increasing evidence that current exploitation rates can contribute to shifts in life-history traits and the collapse of marine fish stocks, few empirical studies have investigated the likely evolutionary impacts. Here, we used DNA recovered from a temporal series of archived North Sea cod (Gadus morhua) otoliths, to investigate genetic diversity within the Flamborough Head population between 1954 and 1998, during which time the population underwent two successive declines. Microsatellite data indicated a significant reduction in genetic diversity between 1954 and 1970 (total number of alleles: 1954, 46; 1960, 42; 1970, 37), and a subsequent recovery between 1970 and 1998 (total number of alleles: 1970, 37; 1981, 42; 1998, 45). Furthermore, estimates of genetic differentiation (F(ST) and R(ST)) showed a significant divergence between 1998 and earlier samples. Data are consistent with a period of prolonged genetic drift, accompanied by a replacement of the Flamborough Head population through an increased effective migration rate that occurred during a period of high exploitation and appreciable demographic and phenotypic change. Other studies indicate that diversity at neutral microsatellite loci may be correlated with variability at selected genes, thus compromising a population's subsequent recovery and adaptive potential. Such effects are especially pertinent to North Sea cod, which are threatened by continuing exploitation and rising sea temperatures.
Assessing allelic dropout and genotyping reliability using maximum likelihood
- Miller
- Joyce P Cr
- Lp
Miller CR, Joyce P, Waits LP (2002) Assessing allelic dropout and genotyping reliability using maximum likelihood. Genetics, 160, 357–366.
Apparent heterozygote deficiencies observed in DNA typing data and their implications in forensic applications
- R Chakraborty
- De Andrade
- M Daiger
- Sp Budowle
Chakraborty R, De Andrade M, Daiger SP, Budowle B (1992)
Apparent heterozygote deficiencies observed in DNA typing
data and their implications in forensic applications. Annals of
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Statistical confidence for likelihood-based paternity inference in natural populations
- Tc Marshall
- J Slate
- Leb Kruuk
- Jm Pemberton
Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical
confidence for likelihood-based paternity inference in natural
populations. Molecular Ecology, 7, 639 – 655.