A simple and improved PCR-based technique for white-tailed deer (Odocoileus virginianus) sex identification

Epigenetic Measurement of Key Vertebrate Population Biology Parameters

The age, sex, and sexual maturity of individual animals are key parameters in assessing wild populations and informing conservation management strategies. These parameters represent the reproductive potential of a population and can indicate recovery rates or vulnerabilities. Natural populations of wild animals are difficult to study; logistically, economically, and due to the impacts of invasive biomonitoring. Genetic and epigenetic analyses offer a low impact, low cost, and information-rich alternative. As epigenetic mechanisms are intrinsically linked with both biological aging and reproductive processes, DNA methylation can be used as a suitable biomarker for population biology study. This review assesses published research utilizing DNA methylation analysis in relation to three key population parameters: age, sex, and sexual maturity. We review studies on wild vertebrates that investigate epigenetic age relationships, with successful age estimation assays designed for mammals, birds, and fish. For both determination of sex and identification of sexual maturity, very little has been explored regarding DNA methylation-based assays. Related research, however, confirms the links between DNA methylation and these processes. Future development of age estimation assays for underrepresented and key conservation taxa is suggested, as is the experimental development and design of DNA methylation-based assays for both sex and sexual maturity identification, further expanding the genomics toolkit for population biology studies.

Non-invasive genetic sexing technique for analysis of short-beaked echidna (Tachyglossus aculeatus) populations

Identifying male and female echidnas is challenging due to the lack of external genitalia or any other differing morphological features. This limits studies of wild populations and is a major problem for echidna captive management and breeding. Non-invasive genetic approaches to determine sex minimise the need for handling animals and are used extensively in other mammals. However, currently available approaches cannot be applied to monotremes because their sex chromosomes share no homology with sex chromosomes in other mammals. In this study we used recently identified X and Y chromosome-specific sequences to establish a non-invasive polymerase chain reaction-based technique to determine the sex of echidnas. Genomic DNA was extracted from echidna hair follicles followed by amplification of two Y chromosome (male-specific) genes (mediator complex subunit 26 Y-gametolog (CRSPY) and anti-Müllerian hormone Y-gametolog (AMHY)) and the X chromosome gene (anti-Müllerian hormone X-gametolog (AMHX)). Using this technique, we identified the sex of 10 juvenile echidnas born at Perth Zoo, revealing that eight of the 10 echidnas were female. Future use of the genetic sexing technique in echidnas will inform captive management, continue breeding success and can be used to investigate sex ratios and population dynamics in wild populations.

Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces)

Monitoring of wild animal populations is challenging, yet reliable information about population processes is important for both management and conservation efforts. Access to molecular markers, such as SNPs, enables population monitoring through genotyping of various DNA sources. We have developed 96 high quality SNP markers for individual identification of moose (Alces alces), an economically and ecologically important top-herbivore in boreal regions. Reduced representation libraries constructed from 34 moose were high-throughput de novo sequenced, generating nearly 50 million read pairs. About 50 000 stacks of aligned reads containing one or more SNPs were discovered with the Stacks pipeline. Several quality criteria were applied on the candidate SNPs to find markers informative on the individual level and well representative for the population. An empirical validation by genotyping of sequenced individuals and additional moose, resulted in the selection of a final panel of 86 high quality autosomal SNPs. Additionally, five sex-specific SNPs and five SNPs for sympatric species diagnostics are included in the panel. The genotyping error rate was 0.002 for the total panel and probability of identities were low enough to separate individuals with high confidence. Moreover, the autosomal SNPs were highly informative also for population level analyses. The potential applications of this SNP panel are thus many including investigations of population size, sex ratios, relatedness, reproductive success and population structure. Ideally, SNP-based studies could improve today’s population monitoring and increase our knowledge about moose population dynamics.

Identification of Lyme borreliae proteins promoting vertebrate host blood-specific spirochete survival in Ixodes scapularis nymphs using artificial feeding chambers

Lyme borreliosis, the most common vector-borne illness in Europe and the United States, is caused by spirochetes of the Borrelia burgdorferi sensu lato complex and transmitted by Ixodes ticks. In humans, the spirochetes disseminate from the tick bite site to multiple tissues, leading to serious clinical manifestations. The ability of spirochetes to survive in ticks during blood feeding is thought to be essential for Lyme borreliae to be transmitted to different vertebrate hosts. This ability is partly attributed to several B. burgdorferi proteins, including BBA52 and Lp6.6, which promote spirochete survival in nymphal ticks feeding on mice. One of the strategies to identify such proteins without using live animals is to feed B. burgdorferi-infected ticks on blood via artificial feeding chambers. In previous studies, ticks were only fed on bovine blood in the feeding chambers. In this study, we used this chamber model and showed that I. scapularis ticks will not only acquire bovine blood but human and quail blood as well. The latter two are the incidental host and an avian host of Lyme borreliae, respectively. We also investigated the roles that BBA52 and Lp6.6 play in promoting spirochete survival in nymphal ticks fed on human or quail blood. After feeding on human blood, spirochete burdens in ticks infected with an lp6.6-deficient B. burgdorferi were significantly reduced, while bba52-deficient spirochete burdens in ticks remained unchanged, similar to the wild-type strain. No strain showed a change in spirochete burdens in ticks fed on quail blood. These results indicate that Lp6.6 plays a role for B. burgdorferi in nymphs fed on human but not quail blood. Such information also demonstrates that the artificial feeding chamber is a powerful tool to identify B. burgdorferi proteins that promote vertebrate host blood-specific spirochete survival in I. scapularis ticks.

Intestinal Microbial Community Dynamics of White-Tailed Deer (Odocoileus virginianus) in an Agroecosystem

The intestinal microbiota has important functions that contribute to host health. The compositional dynamics of microbial communities are affected by many factors, including diet and presence of pathogens. In contrast to humans and domestic mammals, the composition and seasonal dynamics of intestinal microbiota of wildlife species remain comparatively understudied. White-tailed deer (Odocoileus virginianus) is an ecologically and economically important wildlife species that inhabits agricultural ecosystems and is known to be a reservoir of enteric pathogens. Nevertheless, there is a lack of knowledge of white-tailed deer intestinal microbiota diversity and taxonomic composition. This study's first objective was to characterize and compare the intestinal microbiota of 66 fecal samples from white-tailed deer collected during two sampling periods (March and June) using 16S rDNA pyrosequencing. Associations between community diversity and composition and factors including season, sex, host genetic relatedness, and spatial location were quantified. Results revealed that white-tailed deer intestinal microbiota was predominantly comprised of phyla Firmicutes and Proteobacteria, whose relative frequencies varied significantly between sampling periods. The second objective was to examine the associations between the presence of Escherichia coli and Salmonella, and microbiota composition and diversity. Results indicated that relative abundance of some microbial taxa varied when a pathogen was present. This study provides insights into microbial compositional dynamics of a wildlife species inhabiting coupled natural and agricultural landscapes. Data focus attention on the high prevalence of Proteobacteria particularly during the summer and highlight the need for future research regarding the role of white-tailed deer as a natural pathogen reservoir in agroecosystems.

Characterization of enteropathogenic and Shiga toxin-producing Escherichia coli in cattle and deer in a shared agroecosystem

Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen. Cattle are suggested to be an important reservoir for STEC; however, these pathogens have also been isolated from other livestock and wildlife. In this study we sought to investigate transmission of STEC, enterohemorrhagic E. coli (EHEC) and enteropathogenic E. coli (EPEC) between cattle and white-tailed deer in a shared agroecosystem. Cattle feces were collected from 100 animals in a Michigan dairy farm in July 2012, while 163 deer fecal samples were collected during two sampling periods (March and June). The locations of deer fecal pellets were recorded via geographic information system mapping and microsatellite multi-locus genotyping was used to link the fecal samples to individual deer at both time points. Following subculture to sorbitol MacConkey agar and STEC CHROMagar, the pathogens were characterized by serotyping, stx profiling, and PCR-based fingerprinting; multilocus sequence typing (MLST) was performed on a subset. STEC and EHEC were cultured from 12 to 16% of cattle, respectively, and EPEC was found in 36%. Deer were significantly less likely to have a pathogen in March vs. June where the frequency of STEC, EHEC, and EPEC was 1, 6, and 22%, respectively. PCR fingerprinting and MLST clustered the cattle- and deer-derived strains together in a phylogenetic tree. Two STEC strains recovered from both animal species shared MLST and fingerprinting profiles, thereby providing evidence of interspecies transmission and highlighting the importance of wildlife species in pathogen shedding dynamics and persistence in the environment and cattle herds.

Determination of sex origin of meat and meat products on the DNA basis: a review

Sex determination of domestic animal's meat is of potential value in meat authentication and quality control studies. Methods aiming at determining the sex origin of meat may be based either on the analysis of hormone or on the analysis of nucleic acids. At the present time, sex determination of meat and meat products based on hormone analysis employ gas chromatography-mass spectrometry (GC-MS), high-performance liquid chromatography-mass spectrometry/mass spectrometry (HPLC-MS/MS), and enzyme-linked immunosorbent assay (ELISA). Most of the hormone-based methods proved to be highly specific and sensitive but were not performed on a regular basis for meat sexing due to the technical limitations or the expensive equipments required. On the other hand, the most common methodology to determine the sex of meat is unquestionably traditional polymerase chain reaction (PCR) that involves gel electrophoresis of DNA amplicons. This review is intended to provide an overview of the DNA-based methods for sex determination of meat and meat products.

A minimally invasive method for gender determination in the prehensile-tailed porcupine (Coendou prehensilis)

Prehensile-tailed porcupines (Coendou prehensilis), like other rodents, lack external sexual traits, making it difficult to non-invasively determine their gender. By exploiting genetic differences between the X and the Y chromosome, we developed a simple genetic test to determine the gender of Coendous from shed quills. We Sanger sequenced a short portion (195 bp) of the zinc finger protein gene of known male (XY) Coendous to identify positions that are polymorphic between the X and Y chromosomes at this locus. By directly sequencing this fragment, we were able to correctly determine (confirmed via anatomical sexing) the gender of male and female Coendous by the presences or absence of polymorphisms in the resulting chromatograms. This assay is simple, quick and is applicable to other porcupine species.

Sex determination of sika deer (Cervus nippon yesoensis) using nested PCR from feces collected in the field

We describe a method for determining the sex of sika deer (Cervus nippon yesoensis) from feces collected in the field. Using a nested polymerase chain reaction (nested PCR), partial sequences of the sex determination region of the Y chromosome (SRY) gene and X zinc finger protein (ZFX) gene were amplified. In 19 individuals with sex information, the correct sex was successfully detected and sequences of target amplicons were completely matched between muscle and feces from the rectum. Among 75 fecal samples collected noninvasively in the field, 68-71 samples (90.7-94.7%) yielded successful sex determinations. Using this technique, feces collected in the field would enhance the utility of genetic analysis. As a result, instead of biomaterials, these samples can serve as new or alternative materials. Finally, it can be expected that this technique will contribute to reveal in advanced detail of the population dynamics and genetic diversity that needed to carry out effective population control and to reduce the extinction risk of sika deer.

Species and sex identification of Formosa landlocked salmon using loop-mediated isothermal amplification

Species and sex identification are among the most important parameters for conservation management. However, it is extremely difficult to perform such identification in Formosa landlocked salmon (Oncorhynchus masou formosanus). Both sexual dimorphism in landlocked dwarf form Formosa landlocked salmon and morphological difference among cherry salmon complex are minimal. We developed a simple, rapid and noninvasive method for identifying sex and species of this critically endangered species using a loop-mediated isothermal amplification (LAMP) technique. The LAMP assay showed the advantage of simple detection (evaluated by visual inspection), rapid reaction time (< 1 h), isothermal condition (less equipment required) and high efficiency (only 0.5-5 pg of DNA was required in the reaction mixture). Therefore, the method is more economical and practical than PCR. The LAMP assay can be easily performed in the field and is a valuable tool for detecting sex ratios in wild populations and identifying species in commercial imports. This is the first application of LAMP in identifying species and sex of salmonids as far as we know and clearly shows the potential application of LAMP in molecular ecology and conservation efforts.

Zinc-finger intron 7: a new locus for sex identification of giant panda (Ailuropoda melanoleuca)

We developed a single-reaction test for identifying the sex of giant panda (Ailuropoda melanoleuca) targeted to co-amplify homologous fragments with size polymorphism that located at zinc-finger (ZF) intron 7 by using one pair of primers. This assay produced one sex-specific fragment in females (XX genotypes) whereas two fragments were produced in males (XY genotypes). Indels (insertion/deletion) in intron 7 of Y-linked allele provide a significant discrimination between ZFX and ZFY, thus the amplification products can be simply distinguished by agarose gel electrophoresis, exhibiting sex-specific banding patterns (female, 354 bp; male, 354 bp, 135 bp). The new primer set was successfully tested on known-sex giant pandas by using template DNA extracted from both blood and fecal samples. Cross-species test was also performed, revealing that this assay could be applied to other Ursidae species.