Reliability assessment of null allele detection: inconsistencies between and within different methods

Traces of past reintroduction in genetic diversity: The case of the Balkan chamois (Mammalia, Artiodactyla)

The translocation of wild animal species became a common practice worldwide to re-establish local populations threatened with extinction. Archaeological data confirm that chamois once lived in the Biokovo Mountain but, prior to their reintroduction in the 1960s, there was no written evidence of their recent existence in the area. The population was reintroduced in the period 1964-1969, when 48 individuals of Balkan chamois from the neighbouring mountains in Bosnia and Herzegovina were released. The main objective of this study was to determine the accuracy of the existing historical data on the origin of the Balkan chamois population from the Biokovo Mountain and to assess the genetic diversity and population structure of the source and translocated populations 56 years after reintroduction. Sixteen microsatellite loci were used to analyse the genetic structure of three source chamois populations from Prenj, Čvrsnica and Čabulja Mountains and from Biokovo Mountain. Both STRUCTURE and GENELAND analyses showed a clear separation of the reintroduced population on Biokovo from Prenj's chamois and considerable genetic similarity between the Biokovo population and the Čvrsnica-Čabulja population. This suggests that the current genetic composition of the Biokovo population does not derive exclusively from Prenj, as suggested by the available literature and personal interviews, but also from Čvrsnica and Čabulja. GENELAND analysis recognised the Balkan chamois from Prenj as a separate cluster, distinct from the populations of Čvrsnica and Čabulja. Our results thus highlight the need to implement genetic monitoring of both reintroduced and source populations of endangered Balkan chamois to inform sustainable management and conservation strategies in order to maximise the chances of population persistence.

Conservation genetics of the European fallow deer: a reply to Marchesini et al

In this letter, we revisit a study we published in 2017, following comment in a paper by Marchesini et al. published in this volume. We provide some further analyses that help us to reinforce the original conclusions of our earlier paper, and to address the points raised by Marchesini et al. We conclude that the concerns raised in their review do not alter the inference we presented earlier, and we identify issues with analyses presented by Marchesini et al. that limit their utility. The key points of inference remain that this species in Europe shows remarkably low levels of diversity within populations and strong structure among populations which can be explained by a combination of natural and anthropogenic processes.

Genetic patterns in Mugil cephalus and implications for fisheries and aquaculture management

Exploitation of fisheries and aquaculture practices are exposing marine fish populations to increasing genetic risks. Therefore, the integration of genetic information into fisheries and aquaculture management is becoming crucial to ensure species' long-term persistence. The raising commercial value of grey mullet (Mugil cephalus) and its roe represents a growing challenge to the sustainable management of this economically important fishery resource. Here, microsatellites were used to investigate patterns of genetic variation in a Mediterranean area that harbor flourishing fisheries and practice semi-intensive farming of grey mullet. Genetic diversity within populations is smaller than values reported in previous studies as a result of the lower polymorphism displayed by the new microsatellite loci. Lack of genetic structuring points to the existence of a unique genetic stock, which is consistent with the species' high dispersal capabilities. Nonetheless, differences in local population effective size as well as the excess of related individuals do not completely fit the picture of a large panmictic population. Baseline genetic information here gathered will allow to set up the genetic monitoring of regional fish stocks, which is needed to assess the impact of both harvesting and aquaculture on the genetic integrity of Mugil cephalus wild populations.

Locality, time and heterozygosity affect chytrid infection in yellow-bellied toads

The chytrid fungus Batrachochytrium dendrobatidis (Bd) infects numerous amphibian species worldwide and is suggested to drive population declines and extinction events. We report a study of Bd infection at the northernmost distribution of the European yellow-bellied toad Bombina variegata. A total of 577 individuals from ponds in 16 study sites were sampled for DNA and Bd throughout the breeding season. Microsatellite genotyping revealed 3 genetic clusters for the host B. variegata with an overall low genetic diversity. One of the clusters displayed a low microsatellite heterozygosity, a high inbreeding coefficient as well as high Bd infection prevalence and intensities. Multi-model estimates identified site, time of sampling, and heterozygosity to be important predictors of an individual's Bd infection status, and identified a strong effect of site on individual Bd infection intensity. The study site effects are suggestive of localized infection peaks, and the increase of individual Bd infection probabilities towards the end of the sampling period suggests cumulative infection during the breeding season. This study highlights the need for regular monitoring of Bd infection variables at multiple localities and times to gain insights into Bd dynamics. Due to the detected relationship between individual Bd infection status and heterozygosity, conservation measures should focus on the maintenance of high genetic diversity and connectivity within and among amphibian populations.

Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: Effect of null alleles

Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self-fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1,010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro-Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79, and He from 0.53 to 0.80. All loci were in H-W disequilibrium. The null allele frequencies values were high, with lower estimations using segregation analysis than estimated using Micro-Checker. The present results show high levels of population genetic diversity and indicate that null alleles were not the only cause of deviation from H-W equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlund effect.

Long-term stocking practices threaten the original genetic diversity of the southernmost European populations of Atlantic salmon Salmo salar

Many Atlantic salmon Salmo salar populations in Europe are threatened by previous stocking with foreign hatchery strains. Temporal patterns of genetic characteristics of salmon from northern Spain, the southernmost European populations, were compared before and after species decline and heavy stocking with specimens from northern Europe. Eleven microsatellite loci were analysed in archival (scales from 1958-1960) and contemporary (2007-2008) samples from the River Sella. Temporal analyses revealed a similar heterozygosity between archival and contemporary samples, despite a drastic decrease in population abundance, while the contemporary sample showed a higher allelic richness due to the occurrence of foreign alleles. Considering only the alleles with at least 4% frequency in the archival sample, 2 alleles exclusive to the River Sella were absent in the contemporary sample, and 14 alleles showed a decrease of at least 4% frequency. Four alleles common in Scotland showed a high occurrence in the contemporary sample, so they are good candidates as markers of introgression of foreign genes. The heavy stocking with non-native Scottish broodstocks between 1970 and 1990 caused the introgression found in the contemporary sample when compared with the pristine population. An abrupt decrease was evident when the estimates of effective number of breeders were adjusted to take into account overlapping generations (NbAdj), effective population size (NeAdj) estimated from NbAdj, and number of breeders estimated using the sibship assignment method (NbSIB). The very low effective size values found in the contemporary sample, together with the detrimental synergy between genetic drift and high rates of introgression, represent a severe risk for the conservation of native salmon.

Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula

The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA, is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on the data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from approximate Bayesian computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately five effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. five individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.

Influence of genetic drift on patterns of genetic variation: The footprint of aquaculture practices in Sparus aurata (Teleostei: Sparidae)

Aquaculture finfish production based on floating cage technology has raised increasing concerns regarding the genetic integrity of natural populations. Accidental mass escapes can induce the loss of genetic diversity in wild populations by increasing genetic drift and inbreeding. Farm escapes probably represent an important issue in the gilthead sea bream (Sparus aurata), which accounted for 76.4% of total escapees recorded in Europe during a 3-year survey. Here, we investigated patterns of genetic variation in farmed and wild populations of gilthead sea bream from the Western Mediterranean, a region of long gilthead sea bream farming. We focused on the role that genetic drift may play in shaping these patterns. Results based on microsatellite markers matched those observed in previous studies. Farmed populations showed lower levels of genetic diversity than wild populations and were genetically divergent from their wild counterparts. Overall, farmed populations showed the smallest effective population size and increased levels of relatedness compared to wild populations. The small broodstock size coupled with breeding practices that may favour the variance in individual reproductive success probably boosted genetic drift. This factor appeared to be a major driver of the genetic patterns observed in the gilthead sea bream populations analysed in the present study. These results further stress the importance of recommendations aimed at maintaining broodstock sizes as large as possible and equal sex-ratios among breeders, as well as avoiding unequal contributions among parents.

Kinship influences sperm whale social organization within, but generally not among, social units

Sperm whales have a multi-level social structure based upon long-term, cooperative social units. What role kinship plays in structuring this society is poorly understood. We combined extensive association data (518 days, during 2005-2016) and genetic data (18 microsatellites and 346 bp mitochondrial DNA (mtDNA) control region sequences) for 65 individuals from 12 social units from the Eastern Caribbean to examine patterns of kinship and social behaviour. Social units were clearly matrilineally based, evidenced by greater relatedness within social units (mean r = 0.14) than between them (mean r = 0.00) and uniform mtDNA haplotypes within social units. Additionally, most individuals (82.5%) had a first-degree relative in their social unit, while we found no first-degree relatives between social units. Generally and within social units, individuals associated more with their closer relatives (matrix correlations: 0.18-0.25). However, excepting a highly related pair of social units that merged over the study period, associations between social units were not correlated with kinship (p > 0.1). These results are the first to robustly demonstrate kinship's contribution to social unit composition and association preferences, though they also reveal variability in association preferences that is unexplained by kinship. Comparisons with other matrilineal species highlight the range of possible matrilineal societies and how they can vary between and even within species.

Genetic and ecological insights into glacial refugia of walnut (Juglans regia L.)

The distribution and survival of trees during the last glacial maximum (LGM) has been of interest to paleoecologists, biogeographers, and geneticists. Ecological niche models that associate species occurrence and abundance with climatic variables are widely used to gain ecological and evolutionary insights and to predict species distributions over space and time. The present study deals with the glacial history of walnut to address questions related to past distributions through genetic analysis and ecological modeling of the present, LGM and Last Interglacial (LIG) periods. A maximum entropy method was used to project the current walnut distribution model on to the LGM (21–18 kyr BP) and LIG (130–116 kyr BP) climatic conditions. Model tuning identified the walnut data set filtered at 10 km spatial resolution as the best for modeling the current distribution and to hindcast past (LGM and LIG) distributions of walnut. The current distribution model predicted southern Caucasus, parts of West and Central Asia extending into South Asia encompassing northern Afghanistan, Pakistan, northwestern Himalayan region, and southwestern Tibet, as the favorable climatic niche matching the modern distribution of walnut. The hindcast of distributions suggested the occurrence of walnut during LGM was somewhat limited to southern latitudes from southern Caucasus, Central and South Asian regions extending into southwestern Tibet, northeastern India, Himalayan region of Sikkim and Bhutan, and southeastern China. Both CCSM and MIROC projections overlapped, except that MIROC projected a significant presence of walnut in the Balkan Peninsula during the LGM. In contrast, genetic analysis of the current walnut distribution suggested a much narrower area in northern Pakistan and the surrounding areas of Afghanistan, northwestern India, and southern Tajikistan as a plausible hotspot of diversity where walnut may have survived glaciations. Overall, the findings suggest that walnut perhaps survived the last glaciations in several refugia across a wide geographic area between 30° and 45° North latitude. However, humans probably played a significant role in the recent history and modern distribution of walnut.

Lock-picks: fungal infection facilitates the intrusion of strangers into ant colonies

Studies investigating host-parasite systems rarely deal with multispecies interactions, and mostly explore impacts on hosts as individuals. Much less is known about the effects at colony level, when parasitism involves host organisms that form societies. We surveyed the effect of an ectoparasitic fungus, Rickia wasmannii, on kin-discrimination abilities of its host ant, Myrmica scabrinodis, identifying potential consequences at social level and subsequent changes in colony infiltration success of other organisms. Analyses of cuticular hydrocarbons (CHCs), known to be involved in insects' discrimination processes, revealed variations in chemical profiles correlated with the infection status of the ants, that could not be explained by genetic variation tested by microsatellites. In behavioural assays, fungus-infected workers were less aggressive towards both non-nestmates and unrelated queens, enhancing the probability of polygyny. Likewise, parasitic larvae of Maculinea butterflies had a higher chance of adoption by infected colonies. Our study indicates that pathogens can modify host recognition abilities, making the society more prone to accept both conspecific and allospecific organisms.

Polygamy slows down population divergence in shorebirds

Sexual selection may act as a promotor of speciation since divergent mate choice and competition for mates can rapidly lead to reproductive isolation. Alternatively, sexual selection may also retard speciation since polygamous individuals can access additional mates by increased breeding dispersal. High breeding dispersal should hence increase gene flow and reduce diversification in polygamous species. Here, we test how polygamy predicts diversification in shorebirds using genetic differentiation and subspecies richness as proxies for population divergence. Examining microsatellite data from 79 populations in 10 plover species (Genus: Charadrius) we found that polygamous species display significantly less genetic structure and weaker isolation-by-distance effects than monogamous species. Consistent with this result, a comparative analysis including 136 shorebird species showed significantly fewer subspecies for polygamous than for monogamous species. By contrast, migratory behavior neither predicted genetic differentiation nor subspecies richness. Taken together, our results suggest that dispersal associated with polygamy may facilitate gene flow and limit population divergence. Therefore, intense sexual selection, as occurs in polygamous species, may act as a brake rather than an engine of speciation in shorebirds. We discuss alternative explanations for these results and call for further studies to understand the relationships between sexual selection, dispersal, and diversification.

Population structure of Purple Sandpipers (Calidris maritima) as revealed by mitochondrial DNA and microsatellites

The Purple Sandpiper (Calidris maritima) is a medium‐sized shorebird that breeds in the Arctic and winters along northern Atlantic coastlines. Migration routes and affiliations between breeding grounds and wintering grounds are incompletely understood. Some populations appear to be declining, and future management policies for this species will benefit from understanding their migration patterns. This study used two mitochondrial DNA markers and 10 microsatellite loci to analyze current population structure and historical demographic trends. Samples were obtained from breeding locations in Nunavut (Canada), Iceland, and Svalbard (Norway) and from wintering locations along the coast of Maine (USA), Nova Scotia, New Brunswick, and Newfoundland (Canada), and Scotland (UK). Mitochondrial haplotypes displayed low genetic diversity, and a shallow phylogeny indicating recent divergence. With the exception of the two Canadian breeding populations from Nunavut, there was significant genetic differentiation among samples from all breeding locations; however, none of the breeding populations was a monophyletic group. We also found differentiation between both Iceland and Svalbard breeding populations and North American wintering populations. This pattern of divergence is consistent with a previously proposed migratory pathway between Canadian breeding locations and wintering grounds in the United Kingdom, but argues against migration between breeding grounds in Iceland and Svalbard and wintering grounds in North America. Breeding birds from Svalbard also showed a genetic signature intermediate between Canadian breeders and Icelandic breeders. Our results extend current knowledge of Purple Sandpiper population genetic structure and present new information regarding migration routes to wintering grounds in North America.

Unexpectedly complex gradation of coral population structure in the Nansei Islands, Japan

To establish effective locations and sizes of potential protected areas for reef ecosystems, detailed information about source and sink relationships between populations is critical, especially in archipelagic regions. Therefore, we assessed population structure and genetic diversity of Acropora tenuis, one of the dominant stony coral species in the Pacific, using 13 microsatellite markers to investigate 298 colonies from 15 locations across the Nansei Islands in southwestern Japan. Genetic diversity was not significant among sampling locations, even in possibly peripheral locations. In addition, our results showed that there are at least two populations of A. tenuis in the study area. The level of genetic differentiation between these populations was relatively low, but significant between many pairs of sampling locations. Directions of gene flow, which were estimated using a coalescence-based approach, suggest that gene flow not only occurs from south to north, but also from north to south in various locations. Consequently, the Yaeyama Islands and the Amami Islands are potential northern and southern sources of corals. On the other hand, the Miyako Islands and west central Okinawa Island are potential sink populations. The Kerama Islands and the vicinity of Taketomi Island are potential contact points of genetic subdivision of coral populations in the Nansei Islands. We found that genetic population structure of A. tenuis in the Nansei Islands is more complex than previously thought. These cryptic populations are very important for preserving genetic diversity and should be maintained.

A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection approach to examine the potential for genotypic and phenotypic evolution in Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs. 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that these bottlenecks may have occurred prior to 2003. A greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. However, populations differed significantly between sampling years for resistance: some populations maintained high resistance between the sampling years whereas others exhibited increased or decreased resistance. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We probably uncovered only modest increases in resistance on average between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that nonresistant migrants germinate from the seed bank.

Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera

Population genomic investigations on highly dispersive marine organisms typically require thousands of genome-wide SNP loci to resolve fine-scale population structure and detect signatures of selection. This information is important for species conservation efforts and stock management in both wild and captive populations, as well as genome mapping and genome wide association studies. Double digest Restriction site-Associated DNA Sequencing (ddRADseq) is a recent tool for delivering genome wide SNPs for non-model organisms. However, its application to marine invertebrate taxa has been limited, particularly given the complex and highly repetitive nature of many of these organisms' genomes. This study develops and evaluates an optimised ddRADseq technique together with associated analyses for generating genome-wide SNP data, and performs population genomic analyses to inform aquaculture and fishery management of a marine bivalve, the black-lip pearl oyster Pinctada margaritifera. A total of 5243 high-quality genome-wide SNP markers were detected, and used to assess population structure, genome diversity, detect Fst outliers and perform association testing in 156 individuals belonging to three wild and one hatchery produced populations from the Fiji Islands. Shallow but significant population structure was revealed among all wild populations (average pairwise Fst=0.046) when visualised with DAPC and an individual network analysis (NetView P), with clear evidence of a genetic bottleneck in the hatchery population (NeLD=6.1), compared to wild populations (NeLD>192.5). Fst outlier detection revealed 42-62 highly differentiated SNPs (p<0.02), while case-control association discovered up to 152 SNPs (p<0.001). Both analyses were able to successfully differentiate individuals between the orange and black tissue colour morphotypes characteristic of this species. BLAST searches revealed that five of these SNPs were associated with a melanin biosynthesis pathway, demonstrating their biological relevance. This study has produced highly informative SNP and population genomic data in P. margaritifera, and using the same approach promises to be of substantial value to a range of other non-model, broadcast-spawning or marine invertebrate taxa.

Estimating Relatedness in the Presence of Null Alleles

Studies of genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. However, with the presence of null alleles, an observed genotype can represent one of several possible true genotypes. This results in biased estimates of relatedness. As the numbers of marker loci are often limited, loci with null alleles cannot be abandoned without substantial loss of statistical power. Here, we show how loci with null alleles can be incorporated into six estimators of relatedness (two novel). We evaluate the performance of various estimators before and after correction for null alleles. If the frequency of a null allele is <0.1, some estimators can be used directly without adjustment; if it is >0.5, the potency of estimation is too low and such a locus should be excluded. We make available a software package entitled PolyRelatedness v1.6, which enables researchers to optimize these estimators to best fit a particular data set.

Population genetics and the effects of a severe bottleneck in an ex situ population of critically endangered Hawaiian tree snails

As wild populations decline, ex situ propagation provides a potential bank of genetic diversity and a hedge against extinction. These programs are unlikely to succeed if captive populations do not recover from the severe bottleneck imposed when they are founded with a limited number of individuals from remnant populations. In small captive populations allelic richness may be lost due to genetic drift, leading to a decline in fitness. Wild populations of the Hawaiian tree snail Achatinella lila, a hermaphroditic snail with a long life history, have declined precipitously due to introduced predators and other human impacts. A captive population initially thrived after its founding with seven snails, exceeding 600 captive individuals in 2009, but drastically declined in the last five years. Measures of fitness were examined from 2,018 captive snails that died between 1998 and 2012, and compared with genotypic data for six microsatellite loci from a subset of these deceased snails (N = 335), as well as live captive snails (N = 198) and wild snails (N = 92). Surprisingly, the inbreeding coefficient (F_is) declined over time in the captive population, and is now approaching values observed in the 2013 wild population, despite a significant decrease in allelic richness. However, adult annual survival and fecundity significantly declined in the second generation. These measures of fitness were positively correlated with heterozygosity. Snails with higher measures of heterozygosity had more offspring, and third generation offspring with higher measures of heterozygosity were more likely to reach maturity. These results highlight the importance of maintaining genetic diversity in captive populations, particularly those initiated with a small number of individuals from wild remnant populations. Genetic rescue may allow for an increase in genetic diversity in the captive population, as measures of heterozygosity and rarified allelic richness were higher in wild tree snails.

Challenges in analysis and interpretation of microsatellite data for population genetic studies

Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (F ST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.

'True' null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements

Null alleles are alleles that for various reasons fail to amplify in a PCR assay. The presence of null alleles in microsatellite data is known to bias the genetic parameter estimates. Thus, efficient detection of null alleles is crucial, but the methods available for indirect null allele detection return inconsistent results. Here, our aim was to compare different methods for null allele detection, to explain their respective performance and to provide improvements. We applied several approaches to identify the 'true' null alleles based on the predictions made by five different methods, used either individually or in combination. First, we introduced simulated 'true' null alleles into 240 population data sets and applied the methods to measure their success in detecting the simulated null alleles. The single best-performing method was ML-NullFreq_frequency. Furthermore, we applied different noise reduction approaches to improve the results. For instance, by combining the results of several methods, we obtained more reliable results than using a single one. Rule-based classification was applied to identify population properties linked to the false discovery rate. Rules obtained from the classifier described which population genetic estimates and loci characteristics were linked to the success of each method. We have shown that by simulating 'true' null alleles into a population data set, we may define a null allele frequency threshold, related to a desired true or false discovery rate. Moreover, using such simulated data sets, the expected null allele homozygote frequency may be estimated independently of the equilibrium state of the population.

Genetic variability of the grey wolf Canis lupus in the Caucasus in comparison with Europe and the Middle East: distinct or intermediary population?

Despite continuous historical distribution of the grey wolf (Canis lupus) throughout Eurasia, the species displays considerable morphological differentiation that resulted in delimitation of a number of subspecies. However, these morphological discontinuities are not always consistent with patterns of genetic differentiation. Here we assess genetic distinctiveness of grey wolves from the Caucasus (a region at the border between Europe and West Asia) that have been classified as a distinct subspecies C. l. cubanensis. We analysed their genetic variability based on mtDNA control region, microsatellite loci and genome-wide SNP genotypes (obtained for a subset of the samples), and found similar or higher levels of genetic diversity at all these types of loci as compared with other Eurasian populations. Although we found no evidence for a recent genetic bottleneck, genome-wide linkage disequilibrium patterns suggest a long-term demographic decline in the Caucasian population--a trend consistent with other Eurasian populations. Caucasian wolves share mtDNA haplotypes with both Eastern European and West Asian wolves, suggesting past or ongoing gene flow. Microsatellite data also suggest gene flow between the Caucasus and Eastern Europe. We found evidence for moderate admixture between the Caucasian wolves and domestic dogs, at a level comparable with other Eurasian populations. Taken together, our results show that Caucasian wolves are not genetically isolated from other Eurasian populations, share with them the same demographic trends, and are affected by similar conservation problems.