Development and validation of a novel forensic STR multiplex assay for blue (Anthropoides paradiseus), wattled (Bugeranus carunculatus), and grey-crowned crane (Balearica regulorum)

The blue crane (Anthropoides paradiseus), wattled crane (Bugeranus carunculatus), and grey-crowned crane (Balearica regulorum) are species of concern as their populations are declining and they face several threats including habitat loss, disturbance and illegal trade. In South Africa, these species are bred in captivity for trade purposes which is permitted and regulated globally under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Legal sustainable trade through captive breeding of endangered wildlife species such as cranes has been promoted to counteract the illegal trade of individuals from the wild. Captive breeding independent of wild populations may reduce the harvest pressures on wild bird populations which in turn benefit the recovery of exploited species. This approach is considered to be controversial by some individuals. Although captive breeding of endangered species, for both population sustainability and commercial purposes, is promoted to aid in conserving species, concerns have been raised with regards to breeding facilities being used for laundering of animals. To monitor the legal trade of cranes in South Africa a short tandem repeat (STR) assay following recommendations of the International Society for Forensic Genetics (ISFG) was developed and validated. An STR assay comprising of four multiplexes that include 16 STR markers and two gender determination markers was proven to be highly informative with average polymorphic information content (PIC) values of 0.806, 0.646 and 0.725 for A. paradiseus, B. regulorum and B. carunculatus respectively. In addition, the assay showed sufficient discriminatory power for parentage assignment of closely related individuals in all three species (A. paradiseus: PI = 1.7×10-24, PIsibs = 4.7×10-08, and B. carunculatus: PI = 1.4×10-19, PIsibs = 2.9×10-07 and B. regulorum: PI = 1.7×10-12, PIsibs = 5.0×10-05). Analysis of 251 samples suggested that the validated multiplex assay ensures reliability, reproducibility, and repeatability for applications in forensic case work where illegal trade of offspring is suspected through verifying parentage of captive birds in breeding facilities.

A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales

The rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e., southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.

A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium

A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo's range were evaluated in this study. Using available microsatellite data (2-17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.

Construction of an in-house allelic ladder for Canine Genotypes™ Panel 2.1 Kit

Dogs (Canis lupus familiaris) are among the most common companion animals in the Republic of Korea. Recently, there have been many criminal cases of dog cruelty, injury, and theft, among others. This has increased the importance of dog-related biological evidence at crime scenes. The National Forensic Service of the Republic of Korea conducts short tandem repeat (STR) analysis using the Thermo Scientific Canine Genotypes™ Panel 2.1 Kit (Canine Kit) to identify individual dogs through forensic analysis. The Canine Kit was developed as a forensic STR kit for the identification of individual dogs. However, an allelic ladder was neither developed nor included in the commercial kit, leaving an issue of accurate genotyping. Primer details for the 18 markers used in the Canine Kit are proprietary information, and thus, unavailable to end-users. In this study, an allelic ladder was constructed with 160 fragments by combining 158 fragments of STR alleles obtained by nested PCR and two fragments artificially obtained from the sex-determination marker. By including the new allelic ladder in analysis of samples amplified with the Canine Kit, the accuracy and reliability of data analysis were improved. Application of this allelic ladder would be helpful for interlaboratory data sharing and standardization of canine genotype databases.

Mapping the geographic origin of captive and confiscated Hermann's tortoises: A genetic toolkit for conservation and forensic analyses

The illegal trade has been threatening tortoise populations worldwide for decades. Nowadays, however, DNA typing and forensic genetic approaches allow us to investigate the geographic origin of confiscated animals and to relocate them into the wild, providing that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land tortoise Testudo hermanni hermanni. Specific allelic ladders were created for each locus and tested on several reference samples. We used the microsatellite panel to (i) increase our understanding of the population genetic structure in wild populations with new data from previously unsampled geographic areas (overall 461 wild individuals from 28 sampling sites); (ii) detect the presence of non-native individuals in wild populations; and (iii) identify the most likely geographic area of origin of 458 confiscated individuals hosted in Italian seizure and recovery centers. Our analysis initially identified six major genetic clusters corresponding to different geographic macro-areas along the Mediterranean range. Long-distance migrants among wild populations, due to translocations, were found and removed from the reference database. Assignment tests allowed us to allocate approximately 70 % of confiscated individuals of unknown origin to one of the six Mediterranean macro-areas. Most of the assigned tortoises belonged to the genetic cluster corresponding to the area where the respective captivity center was located. However, we also found evidence of long-distance origins of confiscated individuals, especially in centers along the Adriatic coast and facing the Balkan regions, a well-known source of illegally traded individuals. Our results clearly show that the microsatellite panel and the reference dataset can play a beneficial role in reintroduction and repatriation projects when confiscated individuals need to be re-assigned to their respective macro-area of origin before release, and can assist future forensic genetic applications in detecting the illegal trade and possession of Testudo hermanni individuals.

A reference allelic ladder for Western Capercaillie (Tetrao urogallus) and Black Grouse (Tetrao tetrix) enables linking grouse genetic data across studies

Rapid anthropogenic climate change and progressing habitat degradation are considered top threats to biodiversity. The employment of demanding umbrella species as indicators for ecosystem health is a popular and cost-effective strategy that facilitates continuous monitoring and evaluation within a long-term conservation management scheme. The Western Capercaillie (Tetrao urogallus) and the Black Grouse (Tetrao tetrix) are both considered viable candidates due to their extensive habitat requirements, the possibility for conservative, non-invasive sampling, and their broad popular appeal. Regional population surveys based on genetic data from Short Sequence Repeat (SSR) analysis are being conducted throughout the Palearctic. However, to ensure reliable comparability among laboratories, standardization is required. Here, we report a catalogue of fifty fully characterized reference alleles from twelve SSR loci and the construction of a customizable allelic ladder for genotyping and individualization in Western Capercaillie and Black Grouse. This methodological improvement will help to cost-efficiently generate and collate supraregional data from different grouse surveys and thereby contribute to conservation management. Reference alleles and ladders can be obtained on demand.

An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern

BACKGROUND

Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted.

RESULTS

Here we used microsatellite and SNP data generated from Gunnison sage-grouse (Centrocercus minimus) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity (HO, HE, FIS, AR) and differentiation (FST, GST, DJost). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for HE, FIS, AR, and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data.

CONCLUSION

We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.

Range-wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod

Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range-wide examinations suggest significant transatlantic divergence, although the fine-scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data-synthesis approach, integrating multiple genome-wide single-nucleotide polymorphism (SNP) datasets representative of different regions to create a single range-wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post-glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability.

Estimating seed and pollen dispersal kernels from genetic data demonstrates a high pollen dispersal capacity for an endangered palm species

PREMISE OF THE STUDY

Seed and pollen dispersal are key processes shaping plant population dynamics and maintaining genetic diversity. The essence of these processes is the movement of propagules from a parental tree to the site of propagule establishment. The estimation of plant dispersal kernels has remained challenging due to the difficulty of making direct observations. We estimated the dispersal capacity of the endangered palm Euterpe edulis, whose seeds are dispersed by vertebrates and pollen by insects.

METHODS

We used a hierarchical Bayesian model with genetic data from reproductive plants, juveniles, and embryos to estimate dispersal kernels. Our analyses account for genotyping error and uncertainty in parental assignment.

KEY RESULTS

We found that seeds were dispersed at most a few hundred meters, but pollen was dispersed up to several kilometers. We hypothesize that this long-distance pollen dispersal is generated mainly by euglossine bees, whereas the main dispersal vectors for short-distance seed dispersal are thrushes. The long-distance dispersal of pollen suggests a high level of gene flow that should maintain genetic diversity of E. edulis. Despite the relation between long-distance dispersal and genetic diversity, we observed low genetic diversity and inbreeding within the local population, which are probably due to restricted gene flow due to the low density of this population and its aggregated spatial distribution.

CONCLUSIONS

We conclude that if conservation actions are able to restore the population density of E. edulis, the recovery of its genetic diversity will be facilitated because of its high dispersal capacity, especially with regard to pollen.

Current trends in microsatellite genotyping

Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost-effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next-generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non-model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatic tools, from primer design to allele calling.

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.)

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size (‘size shifts’), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Normalization and binning of historical and multi-source microsatellite data: overcoming the problems of allele size shift with allelogram

Microsatellite allele data have long been plagued by size shifts that can at best make it difficult to accurately assign genotypes to allele products, and at worse can cause whole batches of data from different instruments, dates or laboratories to be incorrectly assigned. Although modern genotyping technology (capillary electrophoresis) has overcome many of these problems, concern remains regarding the consistency of scores within a laboratory over time and between laboratories when combining data from multiple sources into a single analysis. There remain a large number of laboratories using older technologies or combining data from multiple sources. In addition, thousands of data sets that could potentially be expanded as samples become available are generally regarded as unusable because of the effort that would be required to validate congruence of genotypes from old and new data sets. We present methods to normalize and bin alleles from multiple data sources using a relatively small set of controls and the freely available program allelogram.

Significant deviations from Hardy-Weinberg equilibrium caused by low levels of microsatellite genotyping errors

Microsatellite genotyping from samples with varying quality can result in an uneven distribution of errors. Previous studies reporting error rates have focused on estimating the effects of both randomly distributed and locus-specific errors. Sample-specific errors, however, can also significantly affect results in population studies despite a large sample size. From two studies including six microsatellite markers genotyped from 272 sperm whale DNA samples, and 33 microsatellites genotyped from 213 bowhead whales, we investigated the effects of sample- and locus-specific errors on calculations of Hardy-Weinberg equilibrium. The results of a jackknife analysis in these two studies identified seven individuals that were highly influential on estimates of Hardy-Weinberg equilibrium for six different markers. In each case, the influential individual was homozygous for a rare allele. Our results demonstrate that Hardy-Weinberg P values are very sensitive to homozygosity in rare alleles for single individuals, and that > 50% of these cases involved genotype errors likely due to low sample quality. This raises the possibility that even small, normal levels of laboratory errors can result in an overestimate of the degree to which markers are out of Hardy-Weinberg equilibrium and hence overestimate population structure. To avoid such bias, we recommend routine identification of influential individuals and multiple replications of those samples.

A cautionary tale: Lack of consistency in allele sizes between two laboratories for a published multilocus microsatellite typing system

For species with low genetic diversity, typing using the differences in PCR fragment length resulting from variations in numbers of short tandem repeats has been shown to provide a high level of discrimination. This technique has been called multilocus microsatellite typing (MLMT) or multiple-locus variable-number tandem repeat analysis, and studies usually employ genetic or sequence analyzers to size PCR fragments to a high degree of precision. We set out to validate one such system that has been developed for Aspergillus fumigatus (H. A. de Valk, J. F. G. M. Meis, I. M. Curfs, K. Muehlethaler, J. W. Mouton, and C. H. W. Klaassen, J. Clin. Microbiol. 43:4112-4120, 2005). The sizes of the alleles were compared both by sequencing and from two genotyping laboratories, where they used capillary electrophoresis (CE) for sizing. Size differences of up to 6 bases were found between the actual sizes reported by sequencing and the sizes reported by CE. In addition, because the two genotyping laboratories used different machines and running conditions, differences of up to 3 bases were identified between them. As the microsatellite markers used differ by repeat units of 3 or 4 bases, it was not possible to assign PCR fragments to the correct alleles without confirming the sizes of a range of alleles by direct sequencing. Lines of best fit were plotted for each CE machine against actual sizes and will therefore enable unsequenced PCR fragments to be assigned to the correct alleles. This study highlights the care required to ensure that an MLMT system undergoes a suitable correction procedure before data can be merged between different laboratories involved in the typing of individual species.