Editorial: Polar Genomics in a Changing World.

Polar regions play critical roles in the function of the Earth's climate system, many of which are underpinned by their endemic biota [...].

The genetic consequences of captive breeding, environmental change and human exploitation in the endangered peninsular pronghorn.

Endangered species with small population sizes are susceptible to genetic erosion, which can be detrimental to long-term persistence. Consequently, monitoring and mitigating the loss of genetic diversity are essential for conservation. The Peninsular pronghorn (Antilocapra americana peninsularis) is an endangered pronghorn subspecies that is almost entirely held in captivity. Captive breeding has increased the number of pronghorns from 25 founders in 1997 to around 700 individuals today, but it is unclear how the genetic diversity of the captive herd may have changed over time. We therefore generated and analysed data for 16 microsatellites spanning 2009-2021. We detected a decline in heterozygosity and an increase in the proportion of inbred individuals over time. However, these trends appear to have been partially mitigated by a genetically informed breeding management attempt that was implemented in 2018. We also reconstructed the recent demographic history of the Peninsular pronghorn, revealing two sequential population declines putatively linked to the desertification of the Baja California peninsula around 6000 years ago, and hunting and habitat loss around 500 years ago, respectively. Our results provide insights into the genetic diversity of an endangered antelope and indicate the potential for genetically informed management to have positive conservation outcomes.

Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible.

Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publication bias. Additionally, replication is often considered too difficult in field settings where many factors are beyond the investigator's control and where spatial and temporal dependencies may be strong. We investigated the feasibility of reproducing original research findings in the field of chemical ecology by performing an exact replication of a previous study of Antarctic fur seals (Arctocephalus gazella). In the original study, skin swabs from 41 mother-offspring pairs from two adjacent breeding colonies on Bird Island, South Georgia, were analyzed using gas chromatography-mass spectrometry. Seals from the two colonies differed significantly in their chemical fingerprints, suggesting that colony membership may be chemically encoded, and mothers were also chemically similar to their pups, hinting at the possible involvement of phenotype matching in mother-offspring recognition. In the current study, we generated and analyzed chemical data from a non-overlapping sample of 50 mother-offspring pairs from the same two colonies 5 years later. The original results were corroborated in both hypothesis testing and estimation contexts, with p-values remaining highly significant and effect sizes, standardized between studies by bootstrapping the chemical data over individuals, being of comparable magnitude. However, exact replication studies are only capable of showing whether a given effect can be replicated in a specific setting. We therefore investigated whether chemical signatures are colony-specific in general by expanding the geographic coverage of our study to include pups from a total of six colonies around Bird Island. We detected significant chemical differences in all but a handful of pairwise comparisons between colonies. This finding adds weight to our original conclusion that colony membership is chemically encoded, and suggests that chemical patterns of colony membership not only persist over time but can also be generalized over space. Our study systematically confirms and extends our previous findings, while also implying more broadly that spatial and temporal heterogeneity need not necessarily negate the reproduction and generalization of ecological research findings.

Extremely low Plasmodium prevalence in wild plovers and coursers from Cape Verde and Madagascar.

BACKGROUND: Relatively little is known about the prevalence of blood parasites in shorebirds, especially those breeding in the tropics. The prevalence of blood parasites of the genera Plasmodium, Haemoproteus and Leucocytozoon was assessed in blood samples from Kentish plovers and cream-coloured coursers in Cape Verde, and samples of Kittlitz's plovers, Madagascar plovers and white-fronted plovers in Madagascar. RESULTS: Only two of these samples were positive for Plasmodium: a Kittlitz's plover was infected by a generalist lineage of Plasmodium that has already been reported in Europe and Africa, while in a white-fronted plover direct sequencing revealed a previously un-described Plasmodium lineage. CONCLUSION: Potential explanations for the low prevalence of blood parasites include the scarcity of vectors in habitats used by these bird species and their resistance to parasitic infections.

Offspring Hormones Reflect the Maternal Prenatal Social Environment: Potential for Foetal Programming?

Females of many species adaptively program their offspring to predictable environmental conditions, a process that is often mediated by hormones. Laboratory studies have shown, for instance, that social density affects levels of maternal cortisol and testosterone, leading to fitness-relevant changes in offspring physiology and behaviour. However, the effects of social density remain poorly understood in natural populations due to the difficulty of disentangling confounding influences such as climatic variation and food availability. Colonially breeding marine mammals offer a unique opportunity to study maternal effects in response to variable colony densities under similar ecological conditions. We therefore quantified maternal and offspring hormone levels in 84 Antarctic fur seals (Arctocephalus gazella) from two closely neighbouring colonies of contrasting density. Hair samples were used as they integrate hormone levels over several weeks or months and therefore represent in utero conditions during foetal development. We found significantly higher levels of cortisol and testosterone (both P < 0.001) in mothers from the high density colony, reflecting a more stressful and competitive environment. In addition, offspring testosterone showed a significant positive correlation with maternal cortisol (P < 0.05). Although further work is needed to elucidate the potential consequences for offspring fitness, these findings raise the intriguing possibility that adaptive foetal programming might occur in fur seals in response to the maternal social environment. They also lend support to the idea that hormonally mediated maternal effects may depend more strongly on the maternal regulation of androgen rather than cortisol levels.

De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite.

BACKGROUND: Studies of non-model species are important for understanding the molecular processes underpinning phenotypic variation under natural ecological conditions. The common buzzard (Buteo buteo; Aves: Accipitriformes) is a widespread and common Eurasian raptor with three distinct plumage morphs that differ in several fitness-related traits, including parasite infestation. To provide a genomic resource for plumage polymorphic birds in general and to search for candidate genes relating to fitness, we generated a transcriptome from a single dead buzzard specimen plus easily accessible, minimally invasive samples from live chicks. RESULTS: We not only de novo assembled a near-complete buzzard transcriptome, but also obtained a significant fraction of the transcriptome of its malaria-like parasite, Leucocytozoon buteonis. By identifying melanogenesis-related transcripts that are differentially expressed in light ventral and dark dorsal feathers, but which are also expressed in other regions of the body, we also identified a suite of candidate genes that could be associated with fitness differences among the morphs. These include several immune-related genes, providing a plausible link between melanisation and parasite load. qPCR analysis of a subset of these genes revealed significant differences between ventral and dorsal feathers and an additional effect of morph. CONCLUSION: This new resource provides preliminary insights into genes that could be involved in fitness differences between the buzzard colour morphs, and should facilitate future studies of raptors and their malaria-like parasites.

Climate change selects for heterozygosity in a declining fur seal population.

Global environmental change is expected to alter selection pressures in many biological systems, but the long-term molecular and life history data required to quantify changes in selection are rare. An unusual opportunity is afforded by three decades of individual-based data collected from a declining population of Antarctic fur seals in the South Atlantic. Here, climate change has reduced prey availability and caused a significant decline in seal birth weight. However, the mean age and size of females recruiting into the breeding population are increasing. We show that such females have significantly higher heterozygosity (a measure of within-individual genetic variation) than their non-recruiting siblings and their own mothers. Thus, breeding female heterozygosity has increased by 8.5% per generation over the last two decades. Nonetheless, as heterozygosity is not inherited from mothers to daughters, substantial heterozygote advantage is not transmitted from one generation to the next and the decreasing viability of homozygous individuals causes the population to decline. Our results provide compelling evidence that selection due to climate change is intensifying, with far-reaching consequences for demography as well as phenotypic and genetic variation.