Males and females contribute unequally to offspring genetic diversity in the polygynandrous mating system of wild boar

Joint identification of sex and sex-linked scaffolds in non-model organisms using low depth sequencing data

Being able to assign sex to individuals and identify autosomal and sex-linked scaffolds are essential in most population genomic analyses. Non-model organisms often have genome assemblies at scaffold-level and lack characterization of sex-linked scaffolds. Previous methods to identify sex and sex-linked scaffolds have relied on synteny between the non-model organism and a closely related species or prior knowledge about the sex of the samples to identify sex-linked scaffolds. In the latter case, the difference in depth of coverage between the autosomes and the sex chromosomes are used. Here, we present "sex assignment through coverage" (SATC), a method to assign sex to samples and identify sex-linked scaffolds from next generation sequencing (NGS) data. The method works for species with a homogametic/heterogametic sex determination system and only requires a scaffold-level reference assembly and sampling of both sexes with whole genome sequencing (WGS) data. We use the sequencing depth distribution across scaffolds to jointly identify: (i) male and female individuals, and (ii) sex-linked scaffolds. This is achieved through projecting the scaffold depths into a low-dimensional space using principal component analysis (PCA) and subsequent Gaussian mixture clustering. We demonstrate the applicability of our method using data from five mammal species and a bird species complex. The method is freely available at https://github.com/popgenDK/SATC as R code and a graphical user interface (GUI).

Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis

Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.

Reproductive characteristics of wild boar males (Sus scrofa) under different environmental conditions

The wild boar population has been on a permanent increase over the last decades, causing conflicts with the requirements of modern human society. Existing effort to stabilize wild boar numbers generally fails with one of the causes being the high reproductive potential of wild boar. The aim of this study was to assess the onset of sexual maturity in wild boar males with regard to age, physical frame and environmental conditions on the basis of testicle development and sperm production. This study assessed the dimensions of gonads and the occurrence of sperm in boars caught during common hunts. Environmental conditions were found as an important factor for growth and sexual maturity of wild boar males. The body weight was a more important factor for sperm production than the age of young wild boar males. The weight threshold for sperm production in the testes was 29 kg of live weight, which corresponds to 6 months of age on average. This study has proven that environmental conditions are a significant factor affecting the physical development of male wild boars, more specifically the growth rate of their body frames and the onset of sexual maturity. In a better quality environment boars grow faster and enter puberty at an earlier age. Poor food supply and/or high hunting pressure result in slower body and testicular growth, as well as the production of sperm at a later age (approx. 2-3 months later).

Multiple paternity: A compensation mechanism of the Chinese alligator for inbreeding

The Chinese alligator Alligator sinensis is a critically endangered species endemic to China. Knowledge about reproductive strategies of a species contributes to their conservation. Little is, however, known about the reproductive strategies and its impact on the population. In the present study, an easy and non-invasive genetic method was used to improve the understanding of mating system of Chinese alligators and its effect on the population genetic diversity by nine polymorphic microsatellite loci. There was a high incidence of multiple paternity among 50 clutches, with a total 60% of the clutches having multiple paternity and up to three males contributing to single clutches. In addition, polyandry females choose to mate with males that are more distant in relatedness compared with monogamy females. Multiple paternity can decrease the inbreeding coefficient, while there is no significant difference between single and multiple paternity (P>0.05). Furthermore, there was an increased allelic diversity (though not heterozygosity) in multiple paternity sired offspring compared with the single paternity sired offspring in F2 generations (P<0.05), as predicted by the genetic diversity hypothesis. Multiple paternity may function as an important inbreeding avoidance compensation mechanism leading to the potential of the species to avoid extinction. These findings will not only enhance the understanding of the mating system and the biological traits of the Chinese alligator, but also improve the captive breeding program management and conservation strategies of the endangered species.