Causes and consequences of an unusually male-biased adult sex ratio in an unmanaged feral horse population

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses

Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.

Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed jay population

Sex-biased demography, including sex-biased survival or migration, can alter allele frequency changes across the genome. In particular, we can expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well as differences in effective population size, transmission modes, and the strength and mode of selection. Here, we demonstrate the role that sex differences in life history played in shaping short-term evolutionary dynamics across the genome. We used a 25-year pedigree and genomic dataset from a long-studied population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of sex-biased demography and inheritance in shaping genome-wide allele frequency trajectories. We used gene dropping simulations to estimate individual genetic contributions to future generations and to model drift and immigration on the known pedigree. We quantified differential expected genetic contributions of males and females over time, showing the impact of sex-biased dispersal in a monogamous system. Due to female-biased dispersal, more autosomal variation is introduced by female immigrants. However, due to male-biased transmission, more Z variation is introduced by male immigrants. Finally, we partitioned the proportion of variance in allele frequency change through time due to male and female contributions. Overall, most allele frequency change is due to variance in survival and births. Males and females make similar contributions to autosomal allele frequency change, but males make higher contributions to allele frequency change on the Z chromosome. Our work shows the importance of understanding sex-specific demographic processes in characterizing genome-wide allele frequency change in wild populations.

Sex ratios and gender norms: why both are needed to understand sexual conflict in humans

Sexual conflict theory has been successfully applied to predict how in non-human animal populations, sex ratios can lead to conflicting reproductive interests of females and males and affect their bargaining positions in resolving such conflicts of interests. Recently this theory has been extended to understand the resolution of sexual conflict in humans, but with mixed success. We argue that an underappreciation of the complex relationship between gender norms and sex ratios has hampered a successful understanding of sexual conflict in humans. In this paper, we review and expand upon existing theory to increase its applicability to humans, where gender norms regulate sex ratio effects on sexual conflict. Gender norms constrain who is on the marriage market and how they are valued, and may affect reproductive decision-making power. Gender norms can also directly affect sex ratios, and we hypothesize that they structure how individuals respond to market value gained or lost through biased sex ratios. Importantly, gender norms are in part a product of women's and men's sometimes conflicting reproductive interests, but these norms are also subject to other evolutionary processes. An integration of sexual conflict theory and cultural evolutionary theory is required to allow for a full understanding of sexual conflict in humans.

The semi-arid ecosystem of Asiatic Lion Landscape in Saurashtra, Gujarat: Population density, biomass and conservation of nine wild prey species

The present study aimed to assess the population density, structure, and population change of nine wild prey species in the semi-arid landscape of Saurashtra, Gujarat, India. A total of eight sites, representing a gradient from highly protected woodlands and grasslands to unreserved grasslands, were selected for sampling. We employed the road transect methodology under a distance sampling framework to achieve our objectives. We evaluated the realized growth rate of the Gir ungulate population through linear regression analysis. Our findings revealed that deer species exhibited higher density and biomass in woodlands compared to grasslands and coastal forests. On the other hand, antelopes showed higher density and biomass in grasslands and coastal forests compared to woodlands. The density gradient of wild prey species was influenced by various factors, including habitat structure, social organization, grouping tendencies, and topography. Over the last four decades, the population of wild prey species in Gir showed minimal changes. Our study provides a comprehensive understanding of wild prey species' density and biomass patterns at the landscape level. The inclusion of findings from ecologically significant and unique areas, such as coastal forests, further enhances the importance of this study. The implications of this study extend beyond the conservation of wild prey species alone; they also contribute to the conservation of the large carnivore guild in the Saurashtra landscape.

Hair Cortisol Concentrations in Feral Horses and the Influence of Physiological and Social Factors

Cortisol is a glucocorticoid hormone produced during activation of the hypothalamic-pituitary-adrenal axis (HPA) in response to psychological or physiological demands. High amounts of circulating cortisol can be found in individuals experiencing energetically demanding physiological events, such as pregnancy, lactation, injury, or starvation, but, also, in individuals who may have less obvious HPA activation from social situations. The feral horse population on Sable Island (Nova Scotia, Canada) provides an opportunity to look at hair cortisol concentration (HCC) as a proxy for circulating cortisol concentration to better understand physiological correlates. The horse's complex social structure also allows us to look at how the population and group structure may influence HPA activation. Hair samples (n = 282) were analyzed from 113 females and 135 males. Females with dependent offspring (foals) had higher HCC than those females without dependent offspring (p = 0.005). Horses in poor body condition were also more likely to have higher HCC (females: p < 0.001, males: p = 0.028); females had greater variation in the body condition index (BCI), which also correlated with foal production. In general, the top-ranked models describing female cortisol levels included age, BCI, presence of a foal, as well as social measures such as harem size and the number of bachelors in the vicinity. The top model describing male cortisol levels included age, BCI, and year of collection only, and the number of bachelors in the home range appeared in subsequent, though still high-ranked, models. Among the variables not of direct interest, we found some significant results relating to hair color and hair texture. Differences in HCC patterns between feral and domestically kept horses (e.g., age and sex) are likely linked to periods of resource limitations, particularly for individuals experiencing energetically demanding processes such as reproduction, illness/parasitism, or related to experiencing the full range of social and reproductive behaviors.

Sex roles and sex ratios in animals

In species with separate sexes, females and males often differ in their morphology, physiology and behaviour. Such sex-specific traits are functionally linked to variation in reproductive competition, mate choice and parental care, which have all been linked to sex roles. At the 150th anniversary of Darwin's theory on sexual selection, the question of why patterns of sex roles vary within and across species remains a key topic in behavioural and evolutionary ecology. New theoretical, experimental and comparative evidence suggests that variation in the adult sex ratio (ASR) is a key driver of variation in sex roles. Here, we first define and discuss the historical emergence of the sex role concept, including recent criticisms and rebuttals. Second, we review the various sex ratios with a focus on ASR, and explore its theoretical links to sex roles. Third, we explore the causes, and especially the consequences, of biased ASRs, focusing on the results of correlational and experimental studies of the effect of ASR variation on mate choice, sexual conflict, parental care and mating systems, social behaviour, hormone physiology and fitness. We present evidence that animals in diverse societies are sensitive to variation in local ASR, even on short timescales, and propose explanations for conflicting results. We conclude with an overview of open questions in this field integrating demography, life history and behaviour.

A paleolimnological context of ecological vulnerability for the freshwater ecosystems of Sable Island National Park Reserve, Canada

Protected areas require long-term monitoring to understand the influence and extent of ecosystem stress to inform management and conservation decisions. As long-term data are not always available, paleolimnological methods offer a way of extending our knowledge of past environmental conditions necessary to use as context for remediation. Here, we examine four sediment cores and additional surface sediments from 14 ponds located on Sable Island National Park Reserve Canada (SINPR), where long-term ecological changes and vulnerability to disturbance are not well defined. We develop a paleolimnological approach to assessing environmental vulnerability through the use of biological indicators (Diptera: Chironomidae), where shifts in the environment are inferred by shifts in chironomid assemblages over time. Analysis of surface sediments show four distinct assemblage types reflecting four different habitat conditions; primarily represented by the presence of Glyptotendipes, Chironomus, Microtendipes, and Dicrotendipes. Differences in habitat conditions through time based on these results are then compared to biostratigraphic analysis of sediment cores from four of the ponds. We found that two ponds had large shifts in chironomids assemblages that were associated with changes in habitat over time, while two others that were not as exposed to the influence of erosion and influx of sand dunes did not. Our findings established a baseline of historical change in SINPR, broadening the scope of long-term monitoring, which is essential for defining goals for management and conservation of the ecological integrity of Sable Island.

Drivers of a temporal change in the adult sex ratio of a Roosevelt elk (Cervus canadensis roosevelti) population

Ecological processes driving female-skewed adult sex ratios (ASRs; males:females) in populations with polygynous mating systems have been addressed theoretically, but empirical support is scarce. The theoretical framework of the female substitution hypothesis (FSH) asserts that a female-skewed ASR at carrying capacity reflects an overall fitness benefit for females and for males competitive in acquiring access to reproductive females. The FSH predicts that as population abundance increases females should acquire forage more efficiently than males, thereby leading to passive displacement of males. The result is declining ASR associated with differential habitat use by both sexes as food resources are depleted by female scramble competition. We characterized the temporal variation in ASR in a Roosevelt elk population inhabiting the Redwood National and State Parks, California, across 24 years, and determined which of two possible ecological mechanisms was the driver of a declining ASR. The first mechanism explored was that increasing female abundance associated with declining forage in the study area led to the passive displacement of males into the study periphery over time. The second mechanism explored was that a declining ASR was precipitated by a lack of males within the study area and the study periphery. Systematic population surveys from a vehicle were done to estimate abundance and ASR as well as assess male abundance in the study periphery. Forage biomass was estimated in quarter-m2 plots randomly placed in meadows inhabited by female elk. Our multiple regression analysis revealed an inverse relationship between abundance and ASR indicating density dependence. We found numerous males in the study periphery when females were abundant. Our least squares models indicated declining food resources across years when female abundance increased. Our results showed that the first, and not the second, ecological mechanism examined was responsible for a female-skewed ASR. Our findings provide empirical support for the theoretical framework of the FSH in a nonmigratory population protected from hunting.

Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs

The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of single nucleotide polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics’ Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10 ng of host DNA (ATG’s recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 88.8% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.

Long-term storage of feces at -80 °C versus -20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome

The development of next-generation sequencing technologies has spurred a surge of research on bacterial microbiome diversity and function. But despite the rapid growth of the field, many uncertainties remain regarding the impact of differing methodologies on downstream results. Sample storage temperature is conventionally thought to be among the most important factors for ensuring reproducibility across marker gene studies, but to date much of the research on this topic has focused on short-term storage in the context of clinical applications. Consequently, it has remained unclear if storage at −80 °C, widely viewed as the gold standard for long-term archival of feces, is truly required for maintaining sample integrity in amplicon-based studies. A better understanding of the impacts of long-term storage conditions is important given the substantial cost and limited availability of ultra-low temperature freezers. To this end, we compared bacterial microbiome profiles inferred from 16S V3–V4 amplicon sequencing for paired fecal samples obtained from a feral horse population from Sable Island, Nova Scotia, Canada, stored at either −80 °C or −20 °C for 4 years. We found that storage temperature did not significantly affect alpha diversity measures, including amplicon sequence variant (ASV) richness and evenness, and abundance of rare sequence variants, nor presence/absence, relative abundances and phylogenetic diversity weighted measures of beta diversity. These results indicate that storage of equine feces at −20 °C for periods ranging from a few months to a few years is equivalent to storage at −80 °C for amplicon-based microbiome studies, adding to accumulating evidence indicating that standard domestic freezers are both economical and effective for microbiome research.