Biology subjects

Hemmings, N.

Publications and source records attributed to Hemmings, N..

9 recordsLinked to original sources

bioRxiv2026

Genomic status of the Eurasian curlew Numenius arquata : estimating Essential Biodiversity Variables and selection signals for a declining migratory bird

Understanding how contemporary population declines affect the genomic diversity and structure of threatened species is important for effective conservation. The Eurasian curlew (Numenius arquata) is experiencing severe population declines across Europe, with Ireland among the most extreme, showing declines exceeding 90% over 40 years. Genomic data are increasingly incorporated into policy and used to assess conservation status by estimating genetic diversity, differentiation, inbreeding, effective population size, and adaptive divergence. Such data for curlew is scarce, and the population structure among northern and north-western European breeding populations remains unclear. To address this, we generated whole-genome resequencing data for 56 curlews across Ireland, Britain and Sweden. Irish and British populations showed minimal interpopulation differentiation, but both were substantially differentiated from Sweden. This was apparent from principal component analysis, and admixture and FST analyses. Measures of genetic diversity (nucleotide diversity, heterozygosity, Watterson's{theta} ) were similar across populations. A slightly elevated Tajima's D in Ireland, along with elevated FROH in Ireland and Britain relative to Sweden, may be the early genomic signs of recent population declines. We identified locally selected candidate genes. These had putative roles in metabolic processes, the immune response, and were potentially associated with distinct migratory behaviours and environmental conditions. We find a potential lag in genomic effects of decline being detectable following population contraction. We also show highly migratory species can exhibit differentiation in ecologically relevant traits, potentially driven by high site fidelity. These findings warrant consideration in translocation planning and broader conservation strategies.

genomics↗

bioRxiv2025

The illusion of stability in long-lived species: Poor early-life survival threatens the persistence of Giant Aldabra tortoise populations.

In long-lived species, logistical constraints often limit monitoring to adult population censuses, potentially generating data that is biased towards older, more discernible individuals, and obscuring problems occurring at early life stages. Since adult populations of long-lived species can persist for decades despite reduced productivity, declines driven by reproductive failure may remain undetected until sudden population collapses occur. We present preliminary data on fertilisation success, early embryo survival, and hatching success, across one natural and five translocated populations of Aldabra giant tortoises (Aldabrachelys gigantea) in the Seychelles. Of 317 eggs from 24 clutches, only 16% successfully hatched. Most failed eggs (97%) were undeveloped, and using recently developed microscopic methods to assess egg fertility, we provide the first population-level comparisons of fertilisation and hatching outcomes for this species. Although sample sizes are limited, our results consistently indicate low and variable hatching success across populations, driven primarily by embryo mortality. Complete clutch failure was common (67%), and among clutches that did experience some degree of hatching success, early embryo mortality was still prevalent. Hatching rates were markedly reduced in translocated populations (0-26%) compared to the natural Aldabra Atoll population (46%) and consistently fell below historical hatching rate estimates (60-80%) reported [~]50 years ago. Although preliminary, these data provide the most accurate estimates of fertility available for Aldabra giant tortoises, as well as the first reproductive success data for any translocated population and the first for Aldabra in the last five decades. Our findings highlight the limitations of relying solely on adult census data for threat assessments in long-lived species. We argue that it is essential to incorporate productivity metrics into monitoring frameworks to improve population vulnerability predictions and inform effective conservation management.

zoology↗

bioRxiv2025

Proteomic characterisation of Japanese quails unique seminal foam

Male Japanese quail (Coturnix japonica) produce a unique proctodeal foam upon ejaculation which is thought to enhance fertilisation success. However, the precise function and proteomic characterisation of this foam remain largely unexplored. Using high throughput LC-MS/MS proteomics analysis, we characterised the proteome of the quail seminal foam for the first time. Our analysis confidently identified 224 proteins in the foam using 32 pooled samples from 96 males. 96.4% of proteins had orthologs in the closely related (diverged 35 million years ago) chicken (Gallus gallus) which generated 40 Gene Ontology terms. Further interrogation revealed proteins involved in sperm motility, maturation and DNA protection, suggesting the foam plays a role in fertilisation success. Proteins linked to immune defence and inflammation modulation were identified, indicating the foam may protect sperm from antigens and reduce female immunogenic responses. This work advances our understanding of the function and evolution of Japanese quail unique seminal foam and directs future experiments to investigate the role of key seminal foam proteins in post-copulatory sexual selection. Significance of the StudySeminal fluid plays an important role in fertilisation success, yet the molecular components of seminal fluid and their function remain poorly understood in most species. This study provides the first comprehensive proteomic characterisation of a unique seminal foam produced by the Japanese quail (Coturnix japonica), revealing its potential mechanistic function in sperm regulation, sperm motility, immune protection, and fertilisation success. By identifying key proteins associated with energy production, membrane fluidity, and sperm maturation, our findings suggest the foam may influence post-ejaculatory sperm function. Additionally, the identification of immunity proteins indicates a role in sperm protection and modulation of female immune responses. This study advances our understanding of avian reproductive biology and opens new avenues for investigating the specific role of seminal foam proteins in fertilisation dynamics and post-copulatory sexual selection.

evolutionary biology↗

bioRxiv2023

Including the Invisible Fraction in Whole Population Studies: a Guide to the Genetic Sampling of Unhatched Bird Eggs

Early embryo mortality has recently been proven to be a significant component of avian reproductive failure. Due to the difficulty in distinguishing eggs which have suffered early embryo mortality from unfertilised eggs, this cause of reproductive failure has historically been underestimated and overlooked. We describe methods for recognising and collecting undeveloped, unhatched eggs from wild bird populations, identifying and isolating embryonic material in unhatched eggs, and efficiently extracting DNA from those samples. We test these methods on unhatched eggs collected from the field which have undergone post-mortem incubation. We obtained DNA yields from early-stage embryos that are sufficient for a wide range of molecular techniques, including microsatellite genotyping for parentage analysis and sex-typing. The type of tissue sample taken from the egg affected downstream DNA yields and microsatellite amplification rates. Species-specific microsatellite markers had higher amplification success rates than cross-species markers. We make key recommendations for each stage of the sampling and extraction process and suggest improvements potential and protocol modifications. Genetic and possibly genomic analysis of embryos that die early in development has the potential to advance many fields. The methods described here will allow a more in-depth exploration of the previously overlooked causes of early embryo mortality in wild populations of birds, including threatened species.

genetics↗

bioRxiv2023

Understanding early reproductive failure in turtles and tortoises

Turtles and tortoises (Order Testudines) are facing an extinction crisis, and ecosystems are at risk of collapsing with the loss of key roles they play. Hatching failure is a crucial barrier to population growth and persistence, but its causes are poorly understood, and it is unknown whether fertilisation rates are declining as many populations become smaller and more female-biased. Here, we first show that fertilisation rates are considered in only a very small proportion of studies of turtle and tortoise hatching success, and those studies that do attempt to measure fertilisation rates use unreliable methods. We also show that studies of hatching success are biased towards marine turtles, as opposed to freshwater and terrestrial species, and wild rather than captive populations. We address the lack of reliable methods for assessing fertilisation rates in turtles and tortoises by developing and testing a microscopy-based method for detecting perivitelline membrane (PVM) bound sperm and embryonic nuclei in the germinal disc of unhatched eggs. We demonstrate that this method can provide unequivocal evidence of egg fertilisation in three different turtle and tortoise species from both captive and wild populations, even after eggs have been left in the nest for the full incubation period. This approach therefore represents a valuable new tool for monitoring egg fertility and embryo survival rates in turtles and tortoises, with the potential to provide important insights into the underlying drivers of reproductive failure in threatened populations.

zoology↗

bioRxiv2020

Low hatching success in the critically endangered kakapo (Strigops habroptilus) is driven by early embryo mortality not infertility

In many endangered species, reproductive failure is a major barrier to recovery. The critically endangered k[a]k[a]p[o] (Strigops habroptilus) exemplifies this challenge: 61% of their eggs fail to hatch, and of these 73% show no sign of development. Undeveloped eggs have previously been attributed to male infertility, but recent studies of non-threatened bird species suggest fertilisation failure is rare in the wild. The underlying causes of fertilisation failure and embryo death differ, so distinguishing between them is essential for effective conservation management. Here we show that the majority (72%, n=124) of undeveloped k[a]k[a]p[o] eggs are fertilised, and combine this with conservation programme data on natural copulations, artificial inseminations, and paternity of developed eggs, to generate the most precise estimate to date of fertility in a wild population. We also demonstrate, for the first time in a wild bird, that artificial insemination results in greater numbers of sperm reaching the egg.

zoology↗

bioRxiv2019

Ecology, phylogeny, and the evolution of developmental duration in birds

The duration of the developmental period represents a fundamental axis of life history variation in animals, yet broad insights regarding the drivers of this diversity are currently lacking. Here using embryological data combined with information on incubation and fledging periods for 3096 species, we test key mechanistic and adaptive explanations for the evolutionary diversification of developmental durations in birds. First, using data on embryonic development for 20 model species, we show that developmental phases associated primarily with growth are longer and more variable than earlier phases, consistent with a role for allometric constraint in determining the duration of development. Second, using phylogenetic comparative methods, we find that avian developmental durations retain a strong imprint of deep evolutionary history, and that after accounting for these effects, body size differences among species explain less variation (5-22%) in developmental period lengths than previously thought. Finally, by collecting data for a suite of potential explanatory variables, our analyses reveal broad-scale ecological correlates of developmental durations, including variables associated with the relative safety of the developmental environment (e.g. nest height, insularity) and pressures of breeding phenology (e.g. migration). Overall, our results reveal that the combined effects of species body size, ecology, and phylogenetic history can account for 62-93% of the variation in developmental durations across birds, providing broad-scale quantitative insight into the relative importance of mechanistic constraints, adaptive evolution and evolutionary constraints in shaping the diversification of this key life-history trait.

evolutionary biology↗

bioRxiv2018

Sperm gatekeeping: 3D imaging reveals a constricted entrance to zebra finch sperm storage tubules

Females across many internally fertilising taxa store sperm, often in specialised storage organs in their reproductive tracts. In birds, several hundred sperm storage tubules exist in the utero-vaginal junction of the oviduct and there is growing evidence that sperm storage in these tubules is selective. The mechanisms underlying female sperm storage in birds remain unknown due to our limited ability to make three dimensional, live observations inside the large, muscular avian oviduct. Here, we describe a new application of fluorescence selective plane illumination microscopy to optically section oviduct tissue from zebra finch Taeniopygia guttata females label-free, by harnessing tissue autofluorescence. Our data provide the first description of the 3D structure of sperm storage organs in any vertebrate and reveal the presence of gate-like constricted openings that may play a role in sperm selection.\n\nStatement of SignificanceFemale birds can store sperm in microscopic tubular structures in their reproductive tract for up to several months, depending on species. Studying these sperm storage tubules has been a major challenge due to the muscular and opaque nature of reproductive tracts in birds. We have developed a new method for imaging live reproductive tract tissue using selective plane illumination microscopy, a fluorescence microscopy technique. From these images, we could extract three-dimensional measurements of sperm storage tubules and found these structures to have a gate-like constriction, providing evidence that females can actively select sperm at storage and ultimately influence the paternity of her offspring. Understanding these reproductive adaptations can help improve captive breeding programs and similar conservation strategies.

evolutionary biology↗

bioRxiv2018

Programmed DNA elimination of germline development genes in songbirds

Genomes can vary within individual organisms. Programmed DNA elimination leads to dramatic changes in genome organisation during the germline-soma differentiation of ciliates1, lampreys2, nematodes3,4, and various other eukaryotes5. A particularly remarkable example of tissue-specific genome differentiation is the germline-restricted chromosome (GRC) in the zebra finch which is consistently absent from somatic cells6. Although the zebra finch is an important animal model system7, molecular evidence from its large GRC (>150 megabases) is limited to a short intergenic region8 and a single mRNA9. Here, we combined cytogenetic, genomic, transcriptomic, and proteomic evidence to resolve the evolutionary origin and functional significance of the GRC. First, by generating tissue-specific de-novo linked-read genome assemblies and re-sequencing two additional germline and soma samples, we found that the GRC contains at least 115 genes which are paralogous to single-copy genes on 18 autosomes and the Z chromosome. We detected an amplification of [≥]38 GRC-linked genes into high copy numbers (up to 308 copies) but, surprisingly, no enrichment of transposable elements on the GRC. Second, transcriptome and proteome data provided evidence for functional expression of GRC genes at the RNA and protein levels in testes and ovaries. Interestingly, the GRC is enriched for genes with highly expressed orthologs in chicken gonads and gene ontologies involved in female gonad development. Third, we detected evolutionary strata of GRC-linked genes. Developmental genes such as bicc1 and trim71 have resided on the GRC for tens of millions of years, whereas dozens have become GRC-linked very recently. The GRC is thus likely widespread in songbirds (half of all bird species) and its rapid evolution may have contributed to their diversification. Together, our results demonstrate a highly dynamic evolutionary history of the songbird GRC leading to dramatic germline-soma genome differences as a novel mechanism to minimise genetic conflict between germline and soma.

evolutionary biology↗