DNA extraction from keratin and chitin

Genetic diversity of the endangered Mongolian saiga antelope Saiga tatarica mongolica (Artiodactyla: Bovidae) provides insights into conservation

The Saiga antelope (Saiga tatarica) is one of the few megafauna species from the mammoth steppe still living today. Currently, saiga are classified as critically endangered, persisting only in small areas of Central Asian steppe and desert ecosystems. The species is divided into two subspecies: Saiga tatarica mongolica and Saiga tatarica tatarica. In this study, we have for the first time characterized the genetic diversity of the Mongolian saiga (S. t. mongolica) using both mitochondrial DNA and microsatellite markers. We also analysed S. t. tatarica specimens in order to genetically compare both subspecies. The mitochondrial control region was sequenced for a total of 89 individuals: 20 skin, 53 umbilical cord, three placentae and a muscle sample from S. t. mongolica, and a total of 12 hair samples from S. t. tatarica. Additionally, 19 microsatellites developed for saiga antelope were also screened. Our results revealed that the Mongolian saiga presents very low genetic diversity at the mitochondrial level, with no shared mitochondrial haplotype between the two subspecies. Low genetic diversity is also present at the autosomal level, with most loci having low heterozygosity (Ho/He) and a low number of alleles per locus. Despite the low genetic diversity, we found no separation between the subpopulations in Mongolia, indicating that conservation corridors are actually promoting contact between different herds. Our results validate current conservation efforts and inform the implementation of new measures to increase the viability of the S. t. mongolica subspecies.

Application of Loop-Mediated Isothermal Amplification (LAMP) in Sex Identification of Parrots Bred in Egypt

Over 400 of the 3800 tropical avian species are endangered or threatened. One of many solutions to conserve animal biodiversity is breeding animals in zoos or private animal farms. Animal breeding programs are difficult to implement in species with sexual monomorphism, such as parrots. Molecular biology methods offer a solution to determine the sex of these species. Therefore, in this study, we aimed to test the performance of PCR and LAMP techniques on sex identification for 21 parrot species belonging to three families, i.e., Psittacidae, Cacatuidae, and Psittaculidae. We established a protocol for DNA isolation from feathers in our laboratory and found optimal conditions for PCR and LAMP. We showed that the LAMP method with the use of the PSI-W primers set, developed by Centeno-Cuadros, functions in 17 previously untested species. Moreover, we found that further improvements are required in universal LAMP primers for the detection of parrot DNA, which are necessary for confirmation of the male sex. The LAMP method also proved to be more sensitive for female sex identification in contrast to the reference PCR test. Therefore, we conclude that LAMP is a suitable method for the routine diagnostic sex identification of parrots.

Comparison of DNA extraction techniques for the recovery of bovine DNA from fly larvae crops

Forensic entomology aids investigations using insects and is primarily associated with the estimation of post-mortem interval (PMI). Studies have shown that human DNA can be recovered from the crops of fly larvae. While several factors regarding the recovery of human DNA from crops have been studied, DNA extraction methods have not been thoroughly assessed. Determining a method for optimal extraction could aid crime laboratories in implementing DNA extraction from larvae and streamlining future research. Bovine DNA was used as a substitute for human DNA to test several DNA extractions kits. Four DNA extraction kits (Chelex®, PDQeX forensicGEM, EZ1® DNA Investigator, DNeasy® Powersoil® Pro Kit) were evaluated based on the quantity and quality of bovine DNA extracted. Extractions were performed on whole fly larvae and dissected crops. Quantification was performed using real-time PCR (qPCR) on a StepOne™ Real-Time PCR System with SYBR® Green using bovine-specific cytochrome b primers. The quality of extracts was determined by checking for inhibition using commercial qPCR chemistries with an internal PCR control (IPC). When using whole fly larvae, Powersoil® Pro yielded the highest average DNA yield (n = 10, 0.668 ± 0.458 ng/μl), while EZ1® DNA Investigator yielded the highest average with crops (n = 10, 0.605 ± 0.403 ng/μl). Chelex and forensicGEM yielded low amounts of bovine DNA, and its extracts were inhibited, unlike EZ1® and Powersoil® Pro, which have purification steps. Therefore, it is recommended to use EZ1® DNA Investigator coupled with automation on EZ1® Advanced XL to recover DNA from fly larvae crops.

OUP accepted manuscript

The woodrats or packrats of the genus Neotoma have been the subject of a wide array of research including paleoecology, physiology, morphological evolution, systematics, speciation, and hybridization. In recent years, much work has been done to elucidate evolutionary relationships within and between closely related species of the genus; in particular the addition of newly collected specimens from critical geographic regions has provided new opportunities for taxonomic assessment. Given these new data and their potential, parsimony (PARS), maximum likelihood (ML), and Bayesian inference (BI) analyses were conducted on DNA sequences obtained from nine individual genes (four mitochondrial loci: 12S, 16S, CoII, and Cytb; five nuclear loci: AdhI2, BfibI7, En2, Mlr, and Myh6) to estimate the phylogenetic relationships among 23 species of Neotoma. Results of these analyses depicted a wide array of phylogenetic relationships among taxa; with substantial nodal support recovered in both the ML and PARS analyses at some mid-level and terminal positions. Several individual genes, particularly 12S, AdhI2, BfibI7, CoII, and Cytb, provided support at several basal positions; however, phylogenetic resolution was limited in the other genes. A final BI analysis where the nine genes were concatenated into a single data set produced several supported clades that corresponded to previously recognized species groups (floridana, micropus, mexicana, and lepida) and the subgenus Homodontomys. Levels of genetic divergence for within-species comparisons (estimated from the Cytb data set) ranged from 0.88% (N. magister) to 6.82% (N. fuscipes); for between sister species comparisons ranged from 4.68% (N. devia and N. lepida) to 12.70% (N. angustapalata and N. nelsoni); and for members within closely related clades ranged from 8.70% (N. bryanti and N. lepida) to 12.57% (N. goldmani and N. magister). Evaluations of generic, subgeneric, and species group boundaries were explored using phylogenetic principles on the DNA sequence data presented herein, as well as morphological findings from previous studies. Results obtained suggest that the most conservative taxonomic interpretation involves the abandonment of subgeneric delineations and relies on the recognition of eight species groups (cinerea, floridana, fuscipes, lepida, mexicana, micropus, phenax, and stephensi) as the backbone of the woodrat classification.

Varying Intensities of Introgression Obscure Incipient Venom-Associated Speciation in the Timber Rattlesnake (Crotalus horridus)

Ecologically divergent selection can lead to the evolution of reproductive isolation through the process of ecological speciation, but the balance of responsible evolutionary forces is often obscured by an inadequate assessment of demographic history and the genetics of traits under selection. Snake venoms have emerged as a system for studying the genetic basis of adaptation because of their genetic tractability and contributions to fitness, and speciation in venomous snakes can be associated with ecological diversification such as dietary shifts and corresponding venom changes. Here, we explored the neurotoxic (type A)–hemotoxic (type B) venom dichotomy and the potential for ecological speciation among Timber Rattlesnake (Crotalus horridus) populations. Previous work identified the genetic basis of this phenotypic difference, enabling us to characterize the roles geography, history, ecology, selection, and chance play in determining when and why new species emerge or are absorbed. We identified significant genetic, proteomic, morphological, and ecological/environmental differences at smaller spatial scales, suggestive of incipient ecological speciation between type A and type B C. horridus. Range-wide analyses, however, rejected the reciprocal monophyly of venom type, indicative of varying intensities of introgression and a lack of reproductive isolation across the range. Given that we have now established the phenotypic distributions and ecological niche models of type A and B populations, genome-wide data are needed and capable of determining whether type A and type B C. horridus represent distinct, reproductively isolated lineages due to incipient ecological speciation or differentiated populations within a single species.

Declining genetic diversity of European honeybees along the twentieth century

The European honeybee (Apis mellifera) is a key pollinator and has in the last decades suffered significant population decline. A combination of factors, including decrease in genetic diversity and introduction of Varroa mites, have been suggested to be responsible for these losses, but no definitive cause has yet been appointed. In Europe not only have wild colonies been severely affected, but managed hives have had a massive decline in numbers. To test the hypothesis that honeybees’ genetic diversity has decreased in the recent past, we used reduced representation genome sequencing of 40 historical honeybee specimens collected in Natural History collections across Europe and compared them to genomic data from 40 individuals from extant populations (collected post 2006). Our results are consistent with the existence of five evolutionary lineages as previously described, and show a decrease in genetic diversity between historical and extant individuals of the same lineage, as well as high levels of admixture in historical specimens. Our data confirm that a loss of genetic diversity has occurred during the last century, potentially increasing honeybees’ vulnerability to contemporary ecological and anthropogenic stressors.

Rarity is a more reliable indicator of land-use impacts on soil invertebrate communities than other diversity metrics

The effects of land use on soil invertebrates - an important ecosystem component - are poorly understood. We investigated land-use impacts on a comprehensive range of soil invertebrates across New Zealand, measured using DNA metabarcoding and six biodiversity metrics. Rarity and phylogenetic rarity - direct measures of the number of species or the portion of a phylogeny unique to a site - showed stronger, more consistent responses across taxa to land use than widely used metrics of species richness, effective species numbers, and phylogenetic diversity. Overall, phylogenetic rarity explained the highest proportion of land use-related variance. Rarity declined from natural forest to planted forest, grassland, and perennial cropland for most soil invertebrate taxa, demonstrating pervasive impacts of agricultural land use on soil invertebrate communities. Commonly used diversity metrics may underestimate the impacts of land use on soil invertebrates, whereas rarity provides clearer and more consistent evidence of these impacts.

The Sicilian Wolf: Genetic Identity of a Recently Extinct Insular Population

Historically, many local grey wolf (Canis lupus) populations have undergone substantial reductions in size or become extinct. Among these, the wolf population once living in Sicily, the largest island in the Mediterranean Sea, was completely eradicated by human activity in the early decades of the 20th century. To gain a better understanding of the genetic identity of the Sicilian wolf, we used techniques for the study of ancient DNA to analyze the mitochondrial (mt) variability of six specimens stored in Italian museums. We were able to amplify a diagnostic mtDNA fragment of the control region (CR) in four of the samples. Two of the samples shared the same haplotype, differing by two substitutions from the currently most diffused Italian wolf haplotype (W14) and one substitution from the only other Italian haplotype (W16). The third sample showed a previously unreported wolf-like haplotype, and the fourth a haplotype commonly found in dogs. All of the wolf haplotypes analyzed in this study belonged to the mitochondrial haplogroup that includes haplotypes detected in all the known European Pleistocene wolves and in several modern southern European populations. Unfortunately, this endemic island population, which exhibited unique mtDNA variability, was definitively lost before it was possible to understand its taxonomic uniqueness and conservational value.

An ‛Aukward' Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks

One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller’s candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars’ minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.

Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus

Molecular approaches to prey identification are increasingly useful in elucidating predator-prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons.

Molecular data indicate a cryptic species in Neotoma albigula (Cricetidae: Neotominae) from northwestern México

DNA sequences from the mitochondrial cytochrome- b gene were obtained from 41 specimens of Neotoma albigula from the southwestern United States and northwestern México. Phylogenetic analyses depicted that samples of N. a. melanura from southern Sonora and northern Sinaloa formed a clade separate from representatives of the other sampled subspecies of N. albigula ( albigula , laplataensis , mearnsi , seri , sheldoni , and venusta ). Genetic distances detected between these clades (7.41%) approached divergence levels reported for other sister species of woodrats and indicated that N. a. melanura is presumably a cryptic and genetically differentiated species relative to N . albigula . Analyses of DNA sequences from a nuclear gene (intron 2 of the alcohol dehydrogenase gene, Adh 1-I2) indicated that samples of N. a. melanura formed a separate, monophyletic clade relative to the remainder of N. albigula . Further, habitat, geographic distinctions, and morphological differences were apparent between members of the 2 clades. Together, those data support the elevation of N. a. melanura to species status.

Secuencias de ADN del gen mitocondrial citocromo- b se obtuvieron de 41 especímenes de Neotoma albigula provenientes del suroeste de los Estados Unidos y del noroeste de México. Análisis filogenéticos revelaron que las muestras de N. a. melanura del sureste de Sonora y del norte de Sinaloa formaron un clado separado de especímenes que representan a las otras subspecies de N. albigula (albigula, laplataensis, mearnsi, seri, sheldoni , y venusta ). Las distancias genéticas detectadas entre estos clados (7.41%) se aproximan a los valores de divergencia reportados para otras especies de ratas magueyeras, indicando que N. a. melanura es presumiblemente una especie críptica y relativamente diferenciada genéticamente de N. albigula . Los análisis de secuencias de ADN de un gen nuclear (intron 2 del gen alcohol deshidrogenasa, Adh -I2) indicaron que las muestras de N. a. melanura formaron un clado separado relativamente a especímenes de N. albigula . Adicionalmente, hábitat, distinciones geográficas, y diferencias morfológicas fueron aparentes entre miembros de los dos clados. Todos estos datos soportan la elevación de N. a. melanura al estatus de especie.