Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis)

Captive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.

Bill Variation of Captive and Wild Chukar Partridge Populations: Shape or Size

Traditionally, morphological characters are widely used to distinguish between interspecies and intraspecies. In addition to the size of morphological characters, shape has also been used as an indicator in the last decades. We evaluated the geometric morphometry and morphometric of the bill of Chukar Partridge, Alectoris chukar from captive and wild populations to determine the bill variation and population relationships. Although there was a size difference between the sexes, no shape difference was found. However, captive populations differed from wild populations in both size and shape. Although there was no difference in shape among wild populations, some differences were found in size. Moreover, bill sizes of captive populations were statistically longer than western, centre, and eastern wild populations. It was also shown that the western populations had the most significant variation among the wild populations. The results revealed that using the size and shape together was more effective in comparing populations.

Phylogeography of the Mauremys mutica complex and the implications for conservation management.

For more than three decades, the Asian turtle crisis has resulted in the decline of every native species in China. For some species, such as the yellow pond turtle (Mauremys mutica), wild populations have dwindled to near functional extinction. Previous studies show there is deep genetic divergence of M. mutica sensu lato between populations north and south of the Pearl River Drainage but no data to show if phylogeographic structure occurs within these two main types. In this study, we found clear phylogeographic structure. In northern types, we found two main clades, corresponding to mainland China and island clades (Taiwan and Yaeyema Islands) with uncorrected p values of 0.00-2.0% divergence in our 2353 bp concatenated mtDNA data set. For the southern types, we found three main clades corresponding to Hainan, Mainland (Vietnam/Guangxi) and the Annam pond turtle (Mauremys annamensis) with divergence ranging from 1.0-1.8% among these three groups. Moreover, the identification of northern and southern types by phenotype was roughly 98% accurate, which, coupling with the deep genetic divergence in mtDNA (5.5-6.7%) and in the 6056 bp nuDNA data set (0.16-0.37%) provide sufficient evidence for northern M. mutica to be an independent species, and individuals from the southern clade should be regarded as subspecies of M. annamensis. Finally, we provide the most comprehensive database to date which can be used to determine the region of origin for captive stock. Making the large captive populations of M. mutica, under the right conditions, potentially valuable for restocking or augmentation of wild populations.

Transposon-induced epigenetic silencing in the X chromosome as a novel form of dmrt1 expression regulation during sex determination in the fighting fish

Background Fishes are the one of the most diverse groups of animals with respect to their modes of sex determination, providing unique models for uncovering the evolutionary and molecular mechanisms underlying sex determination and reversal. Here, we have investigated how sex is determined in a species of both commercial and ecological importance, the Siamese fighting fish Betta splendens. Results We conducted association mapping on four commercial and two wild populations of B. splendens. In three of the four commercial populations, the master sex determining (MSD) locus was found to be located in a region of ~ 80 kb on LG2 which harbours five protein coding genes, including dmrt1, a gene involved in male sex determination in different animal taxa. In these fish, dmrt1 shows a male-biased gonadal expression from undifferentiated stages to adult organs and the knockout of this gene resulted in ovarian development in XY genotypes. Genome sequencing of XX and YY genotypes identified a transposon, drbx1, inserted into the fourth intron of the X-linked dmrt1 allele. Methylation assays revealed that epigenetic changes induced by drbx1 spread out to the promoter region of dmrt1. In addition, drbx1 being inserted between two closely linked cis-regulatory elements reduced their enhancer activities. Thus, epigenetic changes, induced by drbx1, contribute to the reduced expression of the X-linked dmrt1 allele, leading to female development. This represents a previously undescribed solution in animals relying on dmrt1 function for sex determination. Differentiation between the X and Y chromosomes is limited to a small region of ~ 200 kb surrounding the MSD gene. Recombination suppression spread slightly out of the SD locus. However, this mechanism was not found in the fourth commercial stock we studied, or in the two wild populations analysed, suggesting that it originated recently during domestication. Conclusions Taken together, our data provide novel insights into the role of epigenetic regulation of dmrt1 in sex determination and turnover of SD systems and suggest that fighting fish are a suitable model to study the initial stages of sex chromosome evolution.

Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations

In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.

Haemagogus leucocelaenus (Diptera: Culicidae), the potential wild vector of yellow fever in the border zone of northern Misiones, Argentina

Haemagogus leucocelaenus (Diptera: Culicidae) is considered the primary vector of yellow fever virus (Flaviviridae) in wild environments in South America. Previous research has defined Hg. leucocelaenus as a wild species with phytotelmata-type breeding sites. The objective of this study was to report the temporal and space occurrence of Hg. leucocelaenus at the microscale in the wild-periurban fringe through a systematic and spatially stratified sampling using 81 ovitraps between April 2019 and February 2 020 in the locality of Puerto Iguazú, Argentina. Of the total ovitraps, eight were positive for Hg. leucocelaenus, six in the wild environment and two in the periurban environment. Regarding the time distribution, 98.5% of the occurrence was concentrated in November and December 2019 towards the beginning of the rainy season. The results confirm the habitat plasticity of Hg. leucocelaenus and establish the aptitude of artificial containers as a methodology in monitoring studies, since they illustrate the potential of wild populations to deposit fertile eggs in them at least up to 300 m from the wild-periurban fringe. This work is a contribution to determine the temporal and space risk of yellow fever virus transmission in the region, based on the distribution patterns of this species as a function to the ecotone associated with forest borders and climatic variables.

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

Understanding the genetic mechanisms leading to new traits is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different stickleback fish species to alter the length and number of bony dorsal spines. In Gasterosteus aculeatus, a variant HOXDB allele is genetically linked to shortening an existing spine and adding a spine. In Apeltes quadracus, a variant allele is associated with lengthening an existing spine and adding a spine. The alleles alter the same conserved non-coding HOXDB enhancer by diverse molecular mechanisms, including SNPs, deletions, and transposable element insertions. The independent cis-acting regulatory changes are linked to anterior expansion or contraction of HOXDB expression. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key morphological patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.

RECORD OF A LEUCISTIC PAMPAS FOX LYCALOPEX GYMNOCERCUS (CARNIVORA: CANIDAE) IN NORTHEASTERN OF ARGENTINA

Leucism is a frequent chromatic mutation in mammals that causes partial or complete fur depigmentation. This type of mutation is interesting because they have physiological and ecological implications. We report here the first record of leucism in a pampas fox Lycalopex gymnocercus (Carnivora: Canidae), photographed using a camera trap in the northeast of the province of Corrientes, Argentina. Although cases of hypopigmentation are apparently very rare among pampas foxes, they could actually be more frequent than previously assumed. Given the ecological and physiological importance of these anomalies, researchers should report all records of this type in order to understand the degree to which these genetic variants are present in wild populations of different species of vertebrates.