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Kitchener, A. C.

Publications and source records attributed to Kitchener, A. C..

13 recordsLinked to original sources
bioRxiv2026

Shared and genus-specific impact of domestication on mammal oral microbiomes revealed through museomics

Animal domestication involves genetic, behavioural and ecological changes, all of which also impact the host-associated microbial communities. Early studies reported diversity loss in the gut microbiomes of domestic and captive animals, but comparisons across a wider diversity of host species showed that loss of microbiota does not always occur. For microbial communities other than the gut, comparisons of multiple domestic-wild pairs are lacking. Here, we use dental calculus metagenomics to investigate the impact of a domesticated lifestyle on the oral microbiome of three pairs of wild and domestic mammals from the genera Equus (plains zebra, horse), Ovis (argali, sheep) and Sus (wild boar, pig). We find that the oral microbiome of the three domesticates differs both in terms of taxonomic composition and functional capacity from their wild counterparts, but the change is smaller in Sus than the other two pairs. While the microbiomes of sheep and horses bear increased resemblance to those of humans compared to their wild relatives, this is unlikely to be due to colonisation by human-derived microbes, as our results suggest that ancestral lineages are mostly retained. Overall, the oral microbiome shows both a consistent signal of domestication, found across all three clades, and a host genus-dependent effect, which likely results from specific changes that underpinned each domestication event.

evolutionary biology↗
bioRxiv2026

Museum specimens reveal evolutionary drivers and functions of oral microbiome in mammals

The microbiomes of wild animals, despite being integral to host survival, remain largely unexplored, particularly beyond the gut. Here, using > 450 museum-preserved dental calculus samples from 34 ecologically and phylogenetically diverse mammalian species, most of them previously unstudied, we determine the main drivers of oral microbiome evolution. We show that, similar to the gut, the oral microbiome is shaped by host ecology, particularly diet, and to a lesser extent host phylogenetic relationships. It may contribute to host adaptation, by synthesising essential micronutrients and degrading potentially harmful compounds. We also find that some oral microorganisms consistently associated with mammals throughout over evolutionary time scales and provide evidence for a likely oral origin of some rumen taxa. Together our findings demonstrate the importance of this mostly overlooked microbial community for mammalian biology.

evolutionary biology↗
bioRxiv2025

Genomic and morphometric evidence for Austronesian-mediated pig translocation in the Pacific

Human mediated translocation of non-native pig species (genus Sus) to the islands of Wallacea and Oceania has significantly altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 714 modern and ancient dental remains. Our analyses demonstrate that feral and domestic pigs in Wallacea and Oceania possess diverse ancestries resulting from the introduction of multiple, sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry these pigs all possess a distinct tooth morphology, and a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers [~]4,000-3,000 years ago via Taiwan and the Philippines.

evolutionary biology↗
bioRxiv2025

Host traits impact the outcome of metagenomic library preparation from dental calculus samples across diverse mammals

Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. While we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly due to both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing, and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.

genomics↗
bioRxiv2024

Characterisation of the historic demographic decline of the British European polecat population

The European polecat (Mustela putorius) has a widespread distribution across many countries of mainland Europe but is documented to be declining within these ranges. In Britain, direct persecution led to a severe decline of the polecat population during the 19th century. Unlike European mainland populations, it is now recovering across much of its former British range. The genomic and conservation implications of such a severe demographic decline, followed by the current recovery, have still to be characterised in the European polecat in Britain. Here we carry out population-level whole-genome analyses of 65 polecats from Britain (Wales and England) and the European mainland. Our analyses reveal that Welsh polecats show genetic variability from both English and European polecats, while British polecats as a whole exhibit signs of genetic isolation from mainland European populations. We also reconstructed the demographic history of the Welsh polecat to quantify the magnitude of the bottleneck. Our analyses confirmed the drastic decline of the Welsh polecats effective population size, with a severe genetic bottleneck around 30-40 generations ago (1854-1894). We investigated whether whole genome diversity reflected this demographic event and found that Welsh polecats had significantly less genetic diversity than English polecats, but not European polecats. Runs of homozygosity and genetic load present in Welsh and English polecat genomes also indicated recent historic inbreeding. Our findings suggest that the increase in the British polecat population size may be attributed to admixture events. Additionally, we demonstrate that the Welsh polecat constitutes a genetically distinct population, which could be crucial for the overall conservation of European polecats by preserving unique genetic diversity.

evolutionary biology↗
bioRxiv2024

Genomic insights into red squirrels in Scotland reveals loss of heterozygosity associated with extreme founder effects

Remnant populations of endangered species often have complex demographic histories associated with human impact. This can present challenges for conservation as the genetic status of these populations are often a-typical of natural populations, and may require bespoke management. The Eurasian red squirrel, Sciurus vulgaris (L., 1758), is endangered in the UK. Scotland represents a key stronghold, but Scottish populations have been subjected to intense anthropogenic influence, including wide-spread extirpations, reintroductions and competition from an invasive species. This study examined the genetic legacy of these events through whole genome resequencing of 106 red squirrels. Using SNP and genotype likelihood datasets, previously undetected population structure and patterns of gene-flow were uncovered. One off-shore island, three mainland Scottish populations, and a key east-coast migration corridor were observed. An abrupt historical population bottleneck related to extreme founder effects has led to a severe and prolonged depression in genome-wide heterozygosity, which is amongst the lowest reported for any species. Current designated red squirrel conservation stronghold locations do not encompass all existing diversity. These findings highlight the genetic legacies of past anthropogenic influence on long-term diversity in endangered taxa. Continuing management interventions and regular genetic monitoring are recommended to safeguard and improve future diversity.

genomics↗
bioRxiv2023

Large-scale phylogenomics uncovers a complex evolutionary history and extensive ancestral gene flow in an African primate radiation

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as a potential facilitator of adaptive radiations. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the worlds largest primate radiations, we show that rampant gene flow characterizes their evolutionary history, and identify ancient hybridization across deeply divergent lineages differing in ecology, morphology and karyotypes. Lineages experiencing gene flow tend to be more species-rich than non-admixed lineages. Mitochondrial transfers between distant lineages were likely facilitated by co-introgression of co-adapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. This study provides important insights into the prevalence, role and outcomes of ancestral hybridization in a large mammalian radiation.

evolutionary biology↗
bioRxiv2023

Not one, but multiple radiations underlie the biodiversity of Madagascar's endangered lemurs

Lemurs are often cited as an example of adaptive radiation. Since colonizing Madagascar, more than 100 extant lemur species have evolved to fill a variety of ecological niches on the island. However, recent work suggests that lemurs do not exhibit one of the hallmarks of other adaptive radiations: explosive speciation rates that decline over time. Thus, characterizing the tempo and mode of evolution in lemurs can help us understand alternative ways that hyperdiverse clades arise over time, which might differ from traditional models. We explore the evolution of lemurs using a phylogenomic dataset with broad taxonomic sampling that includes the lemurs sister group, the lorisiforms of Asia and continental Africa. Our analyses reveal multiple bursts of diversification (without subsequent declines) that explain much of todays lemur diversity. We also find higher rates of speciation in Madagascars lemurs compared to lorisiforms, and we demonstrate that the lemur clades with exceptionally high diversification rates have higher rates of genomic introgression. This suggests that hybridization in these primates is not an evolutionary dead-end, but a driving force for diversification. Considering the conservation crisis affecting strepsirrhine primates, with approximately 95% of species being threatened with extinction, this phylogenomic study offers a new perspective for explaining Madagascars exceptional primate diversity and reveals patterns of speciation, extinction, and gene flow that will help inform future conservation decisions.

evolutionary biology↗
bioRxiv2021

Abnormal (hydroxy)prolines deuterium content redefines hydrogen chemical mass

Analysing the {delta}2H in individual amino acids of proteins extracted from vertebrates, we unexpectedly found in some samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than in seawater. This corresponds to at least four times higher {delta}2H than in any previously reported biogenic sample. We ruled out diet as a plausible mechanism for such anomalous enrichment. This finding puts into question the old adage that you are what you eat. SUMMARYThe chemical mass of hydrogen is defined as an interval from the lowest to the highest content of deuterium 2H, hydrogens heavy stable isotope. Measurements of the deviations {delta}2H in the deuterium content from the standard (ocean water, {delta}2H = 0{per thousand}) are used to characterise biological samples, such as animal bone collagen. The results are often interpreted in terms of the trophic level and diet of the animal as well as prevailing climate during its lifetime. The majority of the published bone collagen {delta}2H data fall into a narrow {delta}2H range limited to {+/-}100{per thousand}. Using novel analysis method, we unexpectedly found greatly higher {delta}2H values, up to 1500{per thousand}, in seal bone collagen. Such anomalous deuterium enrichment is detected only in two amino acid residues, proline and its derivative hydroxyproline, while other residues show much smaller {delta}2H values. Anomalously high {delta}2H values, albeit of lower magnitudes, are also found for these residues in other biological sources. This finding substantially expands the upper bound of the hydrogen chemical mass for biogenic sources. Since neither diet nor environment explain these mysteriously high enrichment levels amounting to more than twice deuterium content in sea water, our understanding of stable isotopes in nature, as well as the old adage "you are what you eat", are put in question.

biochemistry↗
bioRxiv2021

Variation in predicted COVID-19 risk among lemurs and lorises

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

genetics↗
bioRxiv2020

Macroscopic digestive anatomy of ring-tailed lemurs (Lemur catta), including a comparison of frozen and formalin-stored specimens

Digestive tract measurements are often considered species-specific, but little information exists on the degree to which they change during ontogeny within species. Additionally, access to anatomical material from nondomestic species is often limited, with fixed tissues possibly representing the only available source, though the degree at which this material is representative in terms of dimensions and weight is debatable. In the present study, the macroscopic digestive tract anatomy (length of intestinal portions, and tissue weights of stomach and intestines) of n=58 Lemur catta (from neonates to 25 years of age) was quantified, of which 27 had been stored frozen and 31 fixed in formalin. Particular attention was paid to the caecum and the possible presence of an appendix. The intraspecific allometric scaling of body mass (BM)0.46[0.40;0.51] for total intestine length and BM0.48[0.41;0.54] for small intestine length was higher than the expected geometric scaling of BM0.33, similar to literature results on interspecific scaling. This difference in scaling is usually explained by the hypothesis that the diameter of the intestinal tube cannot increase geometrically, to maintain optimal absorption. Therefore, geometric volume gain of increasing body mass is accommodated by more-than-geometric length scaling. Literature describes L. catta as being variable with respect to the presence of an appendix. No appendix was found in specimens of the present study. The proportions of length measurements did not change markedly during ontogeny, indicating that proportions developed in the foetus are already representative for the adult animal. By contrast, width and tissue-mass scaling of the caecum indicated a disproportionate growth of this organ during ontogeny that was not reflected in its length. Compared to overall intraspecific variation, the method of storage (frozen vs. formalin) had no relevant impact on length or weight measurements.

zoology↗
bioRxiv2019

Population fragmentation leads to morpho-functional variation in British red squirrels (Sciurus vulgaris)

It is well-known that population fragmentation and isolation can lead to rapid morphological and functional divergence, with the effect being particularly well-documented in rodents. Here, we investigated whether such a phenomenon could be identified in the Eurasian red squirrel (Sciurus vulgaris), which was once widespread across the majority of Great Britain, but suffered a severe population decline across the 20th century, leaving a highly fragmented distribution. The aim was to test for morphological and biomechanical variation of the mandible between the remaining British red squirrel populations. Linear and geometric morphometric methods were used to analyse shape in a sample of over 250 squirrel mandibles from across the UK and Germany. Canonical variates analysis identified significant shape differences between most British red squirrel populations, but particularly between squirrels from Formby and those from other populations. Linear measurements showed that Formby red squirrels have a significantly lower mechanical advantage of the temporalis muscle, indicating that they are less efficient at gnawing. We suggest that this difference may be related to past supplemental feeding of Formby squirrels with peanuts, which are less mechanically resistant than food items that occur naturally in the diet of British red squirrels.

evolutionary biology↗