Development of a targeted forensic test for the identification of Eurasian beaver DNA

Eurasian beaver (Castor fiber) has recently been reintroduced in Scotland after more than 400 years of extinction and in 2019 received legal protection; deliberate killing or disturbing beavers without a license is therefore now an offense. We present a validated polymerase chain reaction (PCR)-based Eurasian beaver identification test for use in forensic casework where persecution of Eurasian beaver is suspected. Primers were designed to target a 271 base pair region of the mitochondrial cytochrome b (Cytb) gene in Eurasian beavers, and positive amplicons were confirmed by sequence analysis. Validation was carried out across two laboratories in Scotland, and included studies on sensitivity, specificity, reproducibility, and robustness. The developed test reliably detects Eurasian beaver DNA to the lower limit of 0.1 pg DNA input and differentiates Castor fiber from other species, including congeners. In conclusion, the developed test was successfully optimized and validated to identify Eurasian beaver DNA and will be a valuable tool in wildlife forensic laboratories in cases of suspected persecution of Eurasian beavers

Splitting or Lumping? A Conservation Dilemma Exemplified by the Critically Endangered Dama Gazelle (Nanger dama)

Managers of threatened species often face the dilemma of whether to keep populations separate to conserve local adaptations and minimize the risk of outbreeding, or whether to manage populations jointly to reduce loss of genetic diversity and minimise inbreeding. In this study we examine genetic relatedness and diversity in three of the five last remaining wild populations of dama gazelle and a number of captive populations, using mtDNA control region and cytochrome b data. Despite the sampled populations belonging to the three putative subspecies, which are delineated according to phenotypes and geographical location, we find limited evidence for phylogeographical structure within the data and no genetic support for the putative subspecies. In the light of these data we discuss the relevance of inbreeding depression, outbreeding depression, adaptive variation, genetic drift, and phenotypic variation to the conservation of the dama gazelle and make some recommendations for its future conservation management. The genetic data suggest that the best conservation approach is to view the dama gazelle as a single species without subspecific divisions

Distinguishing the victim from the threat: SNP‐based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration

The degree of introgressive hybridization between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here, we use a 35‐SNP‐marker test, designed to assess hybridization between wildcat and domestic cat populations in Scotland, to assess a database of 295 wild‐living and captive cat samples, and test the assumptions of the test using 3,097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic resolution provided by these methods, wild‐living cats in Scotland show a complete genetic continuum or hybrid swarm structure when judged against reference data. The historical population of wildcats, although hybridized, clearly groups at one end of this continuum, as does the captive population of wildcats. The interpretation of pelage scores against nuclear genetic data continues to be problematic. This is probably because of a breakdown in linkage equilibrium between wildcat pelage genes as the two populations have become increasingly mixed, meaning that pelage score or SNP score alone is poor diagnostic predictors of hybrid status. Until better tools become available, both should be used jointly, where possible, when making management decisions about individual cats. We recommend that the conservation community in Scotland must now define clearly what measures are to be used to diagnose a wildcat in the wild in Scotland, if future conservation action is to be effective

Phylogenomics and species delimitation for effective conservation of manta and devil rays

Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome‐wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide‐ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies

Splitting or lumping? A conservation dilemma exemplified by the critically endangered Dama Gazelle (Nanger dama)

Managers of threatened species often face the dilemma of whether to keep populations separate to conserve local adaptations and minimize the risk of outbreeding, or whether to manage populations jointly to reduce loss of genetic diversity and minimise inbreeding. In this study we examine genetic relatedness and diversity in three of the five last remaining wild populations of dama gazelle and a number of captive populations, using mtDNA control region and cytochrome b data. Despite the sampled populations belonging to the three putative subspecies, which are delineated according to phenotypes and geographical location, we find limited evidence for phylogeographical structure within the data and no genetic support for the putative subspecies. In the light of these data we discuss the relevance of inbreeding depression, outbreeding depression, adaptive variation, genetic drift, and phenotypic variation to the conservation of the dama gazelle and make some recommendations for its future conservation management. The genetic data suggest that the best conservation approach is to view the dama gazelle as a single species without subspecific divisions

Method for producing micro heat panels

Flat or curved micro heat pipe panels are fabricated by arranging essentially parallel filaments in the shape of the desired panel. The configuration of the filaments corresponds to the desired configuration of the tubes that will constitute the heat pipes. A thermally conductive material is then deposited on and around the filaments to fill in the desired shape of the panel. The filaments are then removed, leaving tubular passageways of the desired configuration and surface texture in the material. The tubes are then filled with a working fluid and sealed. Composite micro heat pipe laminates are formed by layering individual micro heat pipe panels and bonding them to each other to form a single structure. The layering sequence of the micro heat pipe panels can be tailored to transport heat preferentially in specific directions as desired for a particular application.U

3097SNP_dataset

For a subset of 68 of the cats typed at 35SNPs and an additional eight cats collected from across the UK, ddRAD analysis of the samples was conducted using a modification of the protocol by (Peterson et al., 2012), which is described in (Bourgeois et al., 2018). A list of all used samples can be found in Supplementary Material 2. In short, DNA quality was assessed via agarose gel electrophoresis on a 1% gel and only non-degraded DNA (as judged by a tight high molecular weight band against a lambda standard) was selected for the library preparation stage. It should be noted here that DNA quality requirements for this protocol preclude running the analysis on poor quality or degraded samples (e.g. most historical or non-invasive sample types). DNA was quantified using a Qubit Broad Range dsDNA Assay (Thermofisher Scientific) and normalised to 7 ng µl-1. Each sample was processed in triplicate or quadruplet to enhance evenness of coverage of samples within the library. Individual genomic DNA was restriction-digested using both SbfI and SphI enzymes and Illumina specific sequencing adaptors (P1 & P2) were then ligated to fragment ends. The pooled samples were size selected (320-590bp fragments) by gel electrophoresis, PCR amplified (15 cycles) and the resultant amplicons (ddRAD library) were purified and quantified. Combinatorial inline barcodes (5 or 7 bases long), included in the P1 &P2 adaptors, allowed each sample replicate to be identified post sequencing. The ddRAD library was sequenced on the Illumina MiSeq Platform (a single paired-end run; v2 chemistry, 2 x 160 bases). Positive control samples were run on all libraries. The sequence data were quality assessed using FastQC (Andrew, 2010) and the reads demultiplexed by barcode and quality filtered using the process_radtags module (default parameters) of the stacks bioinformatics pipeline (Catchen et al. 2013). The retained reads were then trimmed to a standard 135 bases in length. Demultiplexed read files were concatenated into read files for each individual (three or four barcode combinations per individual, see above). Read 1 and Read 2 files were then joined into a single file per individual. The individual data files were then processed using the denovo_map.pl module of Stacks (-M 2, -n 1) to assemble and create a catalogue of genetic loci contained in the data. The Stacks scripts export_sql.pl (snps_l=1, -F snps_u=1, -F pare_l=10, -F alle_u=2) was then used to create a whitelist of all loci, which contained exactly one SNP with two alleles, where the minor variant was present in at least 10 samples. This whitelist was then used to filter the data with the populations function (-r 0.75, -m 10) to create a final dataset, where at each locus a minimum of 75% of individuals had been typed with a depth of at least 10 reads. Further filtering was then conducted in PLINK to remove any loci at which there was >33% missing data. This generated a final data matrix, which consisted of a list of 3097 variable SNPs typed in 76 cats: 20 captive, five domestic and 51 wild-living. The overall % missingness in the data matrix was 6.4%. This data set is referred to as the 3097SNP_dataset. We consider this dataset to represent the most unbiased genetic data for the Scottish wildcat so far. The 35 SNP test was derived from European wildcat data, and thus although effort was made to minimise any impact of bias in subsequent re-design of the test for Scotland (Senn & Ogden 2015), there is the potential that hidden issues with reference data or sub-structuring within the wildcat or domestic cat populations could have biasing consequences on this relatively small panel of markers. The purpose of this dataset here is primarily to the verify the performance 35SNP syste

Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2-fucosyllactose utilization can be facilitated by coexisting species.

The early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2-fucosyllactose (2FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2FL breakdown, thus critical for B. breves growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individuals microbiome

Data from: Cooperative investment in public goods is kin directed in communal nests of social birds

The tragedy of the commons predicts social collapse when public goods are jointly exploited by individuals attempting to maximise their fitness at the expense of other social group members. However, animal societies have evolved many times despite this vulnerability to exploitation by selfish individuals. Kin selection offers a solution to this social dilemma, but in large social groups mean relatedness is often low. Sociable weavers (Philetairus socius) live in large colonies that share the benefits of a massive communal nest, which requires individual investment for construction and maintenance. Here, we show that despite low mean kinship within colonies, relatives are spatially and socially clustered and that nest-building males have higher local relatedness to other colony members than do non-building males. Alternative hypotheses received little support, so we conclude that the benefits of the public good are shared with kin and that cooperative investment is, despite the large size and low relatedness of these communities, kin-directed