An accurate assignment test for extremely low-coverage whole-genome sequence data

Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. In ancient DNA research, such characters can provide further information on population continuity, evolution, climate change, species migration, or trade, depending on archaeological context. Yet, assignment tests often rely on moderate- to high-coverage sequence data, which can be difficult to obtain for many ancient specimens and in ecological studies, which often use sequencing techniques such as ddRAD to bypass the need for costly whole-genome sequencing. We have developed a novel approach that efficiently assigns biologically relevant information (such as population identity or structural variants) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic Single Nucleotide Polymorphisms (SNPs) associated with a biological characteristic. Low coverage alignment files from ancient specimens are subsequently compared to these databases to ascertain allelic state yielding a joint probability for each association. To assess the efficacy of this approach, we assigned inversion haplotypes and population identity in several species including Heliconius butterflies, Atlantic herring, and Atlantic cod. We used both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage (e.g. 0.0001x fold) based on genome-wide SNPs. This approach will therefore increase the number of ancient samples in ecological and bioarchaeological research for which relevant biological information can be obtained.

Genetic Assignment Tests to Identify the Probable Geographic Origin of a Captive Specimen of Military Macaw (Ara militaris) in Mexico: Implications for Conservation

The Military Macaw (Ara militaris) faces a number of serious conservation threats. The use of genetic markers and assignment tests may help to identify the geographic origin of captive individuals and improve conservation and management programs. The purpose of this study was to identify the possible geographic origin of a captive individual using genetic markers. We used a reference database of genotypes of 86 individuals previously shown to belong to two different genetic groups to determine the genetic assignment of the captive individual of unknown origin (captive specimen) and five individuals of known geographic origin (as positive controls). We evaluated the accuracy of three assignment/exclusion criteria to determine the success of correct assignment of the individual of unknown origin and the five positive control individuals. WICHLOCI estimated that eight loci were required to achieve an assignment success of 83%. The correct geographic origin of positive controls was identified with 83% confidence. All of the analyses assigned the captive individual to the genetic group from the Sierra Madre Oriental. Bayesian assignment tests, tests for genetic distance and allele frequency tests assigned the unknown individual to the locations from the Sierra Madre Oriental with a probability of 71.2–82.4%. We show that the use of genetic markers provides a promising tool for determining the origin of pets and individuals seized from the illegal animal trade to better inform decisions on reintroduction and improve conservation programs.

Hydrogen isotopes reveal evidence of migration of Miniopterus schreibersii in Europe

Background The Schreiber’s bat, Miniopterus schreibersii, is adapted to long-distance flight, yet long distance movements have only been recorded sporadically using capture-mark-recapture. In this study, we used the hydrogen isotopic composition of 208 wing and 335 fur specimens from across the species' European range to test the hypothesis that the species migrates over long distances. Results After obtaining the hydrogen isotopic composition (δ2H) of each sample, we performed geographic assignment tests by comparing the δ2H of samples with the δ2H of sampling sites. We found that 95 bats out of 325 showed evidence of long-distance movement, based on the analysis of either fur or wing samples. The eastern European part of the species range (Greece, Bulgaria and Serbia) had the highest numbers of bats that had moved. The assignment tests also helped identify possible migratory routes, such as movement between the Alps and the Balkans. Conclusions This is the first continental-scale study to provide evidence of migratory behaviour of M. schreibersii throughout its European range. The work highlights the need for further investigation of this behaviour to provide appropriate conservation strategies.

Disentangling the relative merits and disadvantages of parentage analysis and assignment tests for inferring population connectivity

Accurately estimating patterns of population connectivity in marine systems remains an elusive goal. Current genetic approaches have focused on assigning individuals back to their natal populations using one of two methods: parentage analyses and assignment tests. Each of these approaches has their relative merits and weaknesses. Here, we illustrate these tradeoffs using a forward-time agent-based model that incorporates relevant natural history and physical oceanography for 135 Kellet’s whelk (Kelletia kelletii) populations from Southern California. Like most marine organisms, Kellet’s whelks live in large meta-populations where local populations are connected by dispersive larvae. For estimating population connectivity, we found parentage analyses to be relatively insensitive to the amount of genetic differentiation among local populations, but highly sensitive to the proportion of the meta-population sampled. Assignment tests, on the other hand, were relatively insensitive to the proportion of the meta-population sampled, but highly sensitive to the amount of genetic differentiation found among local populations. Comparisons between the true connectivity matrices (generated by using the true origin of all sampled individuals) and those obtained via parentage analyses and assignment tests reveal that neither approach can explain >26% of the variation in true connectivity. Furthermore, even with perfect assignment of all sampled individuals, sampling error alone can introduce noise into the estimated population connectivity matrix. Future work should aim to improve the number of correct assignments without the expense of additional incorrect assignments, perhaps by using dispersal information obtained from related individuals as priors in a Bayesian framework. These analyses dispel a number of common misconceptions in the field and highlight areas for both future research and methodological improvements.

Evaluation of molecular variability in germplasm of vanilla (Vanilla planifoliaG. Jackson in Andrews) in Southeast Mexico: implications for genetic improvement and conservation

Molecular variability of vanilla (Vanilla planifolia) and three wild species was assessed to explore the possible sources of variation that can be used for crop improvement. A total of 154 ISSR loci were analysed by the UPGMA, assignment tests of individuals (STRUCTURE) and indices of genetic diversity. The assignment tests were done at two levels: first considering the four species and then only the accessions ofV. planifolia. The molecular analysis indicated 99.3% polymorphism among all species and 70.45% withinV. planifolia. The UPGMA showed the separation of these four species into three groups and groupedV. planifoliaaccessions into three subgroups. The more genetically differentiated accessions were of the Rayada morphotype and a wild accession was from Oaxaca, followed by a wild accession from Quintana Roo; all the commercial accessions ofV. planifolia(Mansa morphotype) were grouped together. The STRUCTURE analysis differentiated betweenV. planifoliaand the three wild species, and among the accessions of the Mansa and Rayada morphotypes and the wild accessions. The STRUCTURE analysis also indicated the presence of mixed individuals. These results are of great importance since the accessions ofV. planifoliathat are genetically more differentiated are the most threatened due to the scarcity of these individuals, the destruction of habitat and replacement by the commercial morphotype. These individuals should be salvaged and used to expand the genetic background of vanilla.