Biology subjects

Rey-Iglesia, A.

Publications and source records attributed to Rey-Iglesia, A..

12 recordsLinked to original sources

bioRxiv2026

Habitat discontinuity and fidelity to migratory routes shape narwhal genetic structure and diversity

Rapid Arctic warming is reshaping marine ecosystems and altering the evolutionary trajectories of ice-associated species. Narwhals (Monodon monoceros) are Arctic endemics that are thought to be vulnerable to climate change. We present the first nuclear genomic assessment of narwhals across their distribution to evaluate population structure, demographic history, local adaptation, inbreeding and genetic load. Using genomes from 117 individuals, we identified three populations: Canadian Arctic Archipelago/West Greenland, Northeast Greenland/Svalbard and Southeast Greenland. Demographic reconstructions indicated low effective population size over at least 600,000 years, followed by population growth during the last glacial period. Our results suggest that population structure is maintained by habitat discontinuities and fidelity to migration routes. The latter may promote local adaptation, as genes related to long-term memory were found in regions putatively under selection in Canadian Arctic Archipelago/West Greenland narwhals, which undertake the longest migrations. Genome-wide diversity was uniformly low across populations. Inbreeding levels were inversely related to estimated population sizes. The small and rapidly declining Southeast Greenland population exhibited elevated recent inbreeding. Deleterious mutations were primarily masked in heterozygous genotypes, raising concerns for this population. Together, our results demonstrate that past climate, habitat discontinuities and migration fidelity jointly structure narwhal populations.

evolutionary biology↗

bioRxiv2025

Impact of tusk anomalies on the long-term foraging ecology of narwhals

Male narwhals are unique in having one long, spiralled tusk, while females of the species do not have a tusk. However, a small number of individuals develop tusk anomalies, including two-tusked males or females with a tusk. In this study, we combine genetic sexing and bone collagen stable isotope ({delta}13C and {delta}15N) analysis to evaluate whether these tooth anomalies impact foraging ecology. Our analysis of individuals collected in the waters around Greenland showed no systematic impacts; nine of ten two-tusked male narwhals, and all three one-tusked female narwhals were within the normal range of known isotopic diversity from the sampled geographic regions. Two specimens with other forms of unusual dentition both showed stable isotope values outside the range of narwhals, suggesting their diet was different. Our findings underscore how DNA data retrieved from museum specimens can elucidate biological questions of interest, such as the sex of anomalous individuals. They also show how stable isotope analysis can be used to assign individuals with unknown provenance to their geographic region of origin.

zoology↗

bioRxiv2024

Ancient biomolecular analysis of 39 mammoth individuals from Kostenki 11-Ia elucidates Upper Palaeolithic human resource use

Circular structures made from woolly mammoth bones are found across Ukraine and west Russia, yet the origin of the bones remains uncertain. We present ten new mammoth radiocarbon dates from the largest circular structure at Kostenki 11-Ia, identifying two mammoth mandibles [~]200-1,200 years older than the other dated materials from the site, suggesting skeletal material from long-dead individuals was scavenged and used in the site construction. Biomolecular sexing of 30 individuals showed a predominance of females, suggesting the Kostenki mammoths are primarily from herds. We identify six mitochondrial lineages across 16 samples, showing they are not all from the same matriline. Integrating biomolecular sexing with stable{delta} 13C and{delta} 15N isotope analysis, we find no isotopically-differentiated resource use by females and males, providing the first analysis of foraging differences between sexes in any Late Pleistocene megafauna. Our study highlights the significance of integrating ancient biomolecular approaches in archaeological inference. TeaserIntegrating 14C dating, ancient DNA, palaeoproteomics, and stable isotopes improves our understanding of Kostenki 11-Ia

evolutionary biology↗

bioRxiv2024

Four centuries of commercial whaling eroded 11,000 years of population stability in bowhead whales

The bowhead whale, an Arctic endemic, was heavily overexploited during commercial whaling between the 16th-20th centuries1. Current climate warming, with Arctic amplification of average global temperatures, poses a new threat to the species2. Assessing the vulnerability of bowhead whales to near-future predictions of climate change remains challenging, due to lacking data on population dynamics prior to commercial whaling and responses to past climatic change. Here, we integrate palaeogenomics and stable isotope ({delta}13C and{delta} 15N) analysis of 201 bowhead whale fossils from the Atlantic Arctic with palaeoclimate and ecological modelling based on 823 radiocarbon dated fossils, 151 of which are new to this study. We find long-term resilience of bowhead whales to Holocene environmental perturbations, with no obvious changes in genetic diversity or population structure, despite large environmental shifts and centuries of whaling by Indigenous peoples prior to commercial harvests. Leveraging our empirical data, we simulated a time-series model to quantify population losses associated with commercial whaling. Our results indicate that commercial exploitation induced population subdivision and losses of genetic diversity that are yet to be fully realised; declines in genetic diversity will continue, even without future population size reductions, compromising the species resilience to near-future predictions of Arctic warming.

evolutionary biology↗

bioRxiv2023

Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent

Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species dispersal ability and leads to small effective population sizes, making species susceptible to environmental change. The giant root-rat (Tachyoryctes macrocephalus) is a highly fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its whole [~]1,000 km2 range. Our data revealed a distinct division into a northern and southern subpopulation, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial genomes indicated that population subdivision was driven by steep slopes and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene ([~]42,000 to 16,000 years ago). Despite the pronounced subdivision observed at the range-wide scale, weak geographic structuring of sampling localities within subpopulations indicated gene flow across distances of at least 16 km, suggesting aboveground dispersal and high mobility for relatively long distances. Our study highlights how topographic barriers can lead to the genetic subdivision of fossorial species, despite their potential to maintain gene flow at the local scale. These factors can reduce genetic variability, which should be considered when developing conservation strategies.

evolutionary biology↗

bioRxiv2023

The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations

The brown bear (Ursus arctos) is one of the survivors of the Late Quaternary megafauna extinctions. However, despite being widely distributed across the Holarctic, brown bears have experienced extensive range reductions, and even extirpations in some geographic regions. Previous research efforts utilising genetic data have provided valuable insights into their evolutionary history. However, most studies have been limited to contemporary individuals or mitochondrial DNA, limiting insights into population processes that preceded the present. Here we present genomic data from two Late Pleistocene brown bears from Honshu, Japan, and eastern Siberia, and combine them with published contemporary and ancient genomes from across the Holarctic range of brown bears to investigate the evolutionary relationships among brown bear populations through time and space. By including genomic data from Late Pleistocene and Holocene individuals sampled outside the current distribution range we uncover diversity not present in the contemporary populations. Notably, although contemporary individuals display geographically structured populations most likely driven by isolation-by-distance, this pattern varies among the ancient samples across different regions. The inclusion of ancient brown bears in our analysis provides novel insights into the evolutionary history of brown bears and contributes to understanding the populations and diversity lost during the Late Quaternary.

evolutionary biology↗

bioRxiv2021

Combining δ13C and δ15N from bone and dentine in marine mammal palaeoecological research: insights from toothed whales

Stable carbon ({delta}13C) and nitrogen ({delta}15N) isotope compositions of bone and dentine collagen extracted from museum specimens have been widely used to study the paleoecology of past populations. Due to possible systematic differences in stable isotope values between bone and dentine, dentine values need to be transformed into bone-collagen equivalent using a correction factor to allow comparisons between the two collagen sources. Here, we provide correction factors to transform dentine{delta} 13C and{delta} 15N values into bone-collagen equivalent for two toothed whales: narwhal and beluga. We sampled bone and tooth dentine from the skulls of 11 narwhals and 26 belugas. In narwhals, dentine was sampled from tusk and embedded tooth; in beluga, dentine was sampled from tooth.{delta} 13C and{delta} 15N were measured and intraindividual bone and dentine isotopic compositions were used to calculate correction factors for each species. We detected differences in{delta} 13C and{delta} 15N. In narwhals, we found (i) lower average{delta} 13C and{delta} 15N in bone compared with dentine; (ii) no difference in dentine{delta} 13C between tusk and embedded tooth. For belugas, we also detected lower{delta} 13C and{delta} 15N in bone compared with tooth dentine. The correction factors provided by the study enable the combined analysis of stable isotope data from bone and dentine in these species.

ecology↗

bioRxiv2021

How low can you go: sex identification from sequencing data of species lacking assembled sex chromosomes

Accurate sex identification is crucial for elucidating the biology of a species. In the absence of directly observable sexual characteristics, sex identification of wild fauna can be challenging, if not impossible. Molecular sexing offers a powerful alternative to morphological sexing approaches. Here, we present SeXY, a novel sex-identification pipeline, for very low-coverage shotgun sequencing data from a single individual. SeXY was designed to utilise low-effort screening data for sex identification and does not require a conspecific sex-chromosome assembly as reference. We assess the accuracy of our pipeline to data quantity by downsampling sequencing data from 100,000 to 1,000 mapped reads, and to reference genome selection by mapping to a variety of reference genomes of various qualities and phylogenetic distance. We show that our method is 100% accurate when mapping to a high-quality (highly contiguous N50 > 30 Mb) conspecific genome, even down to 1,000 mapped reads. For lower-quality reference assemblies (N50 < 30 Mb), our method is 100% accurate with 50,000 mapped reads, regardless of reference assembly quality or phylogenetic distance. The SeXY pipeline provides several advantages over previously implemented methods; SeXY (i) requires sequencing data from only a single individual, (ii) does not require assembled conspecific sex-chromosomes, or even a conspecific reference assembly, (iii) takes into account variation in coverage across the genome, and (iv) is accurate with only 1,000 mapped reads in many cases.

genomics↗

bioRxiv2021

Late Pleistocene palaeoecology and phylogeography of woolly rhinoceroses

The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted herbivore, widely distributed from western Europe to north-east Siberia during the Late Pleistocene. Previous studies associate the extinction of the species ~14,000 years before present to climatic and vegetational changes, and suggest that later survival of populations in north-east Siberia may relate to the later persistence of open vegetation in that region. Here, we analyzed carbon ({delta}13C) and nitrogen ({delta}15N) stable isotopes and mitochondrial DNA sequences to elucidate the evolutionary ecology of the species. Our dataset comprised 286 woolly rhinoceros isotopic records, including 192 unpublished records, from across the species range, dating from >58,600 14C years to ~14,000 years before present. Crucially, we present the first 71 isotopic records available to date of the 15,000 years preceding woolly rhinoceros extinction. The data reveal ecological flexibility and geographical variation in woolly rhinoceros stable isotope compositions through time. In north-east Siberia, we detected{delta} 15N stability through time. This could reflect long-term environmental stability, and might have enabled the later survival of the species in the region. To further investigate the palaeoecology of woolly rhinoceroses, we compared their isotopic compositions with that of other contemporary herbivores. This analysis suggests possible niche partitioning between woolly rhinoceros and both horse (Equus spp.) and woolly mammoth (Mammuthus primigenius), and isotopic similarities between woolly rhinoceros and both musk ox (Ovibos moschatus) and saiga (Saiga tatarica) at different points in time. To provide phylogeographical context to the isotopic data, we analyzed 61 published mitochondrial control region sequences. The data show a lack of geographic structuring; we found three haplogroups with overlapping distributions, all of which show a signal of expansion during the Last Glacial Maximum. Furthermore, our genetic findings support the notion that environmental stability in Siberia had an impact on the paleoecology of woolly rhinoceroses in the region. Our study highlights the utility of combining stable isotopic records with ancient DNA to advance our knowledge of the evolutionary ecology of past populations and extinct species.

evolutionary biology↗

bioRxiv2020

Speciation in the face of gene flow within the toothed whale superfamily Delphinoidea

AO_SCPLOWBSTRACTC_SCPLOWThe importance of post-divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide-ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae, Monodontidae). To investigate the role of post-divergence gene flow in the speciation process, we used a multifaceted approach, including: (i) phylogenomics, (ii) the distribution of shared derived alleles, and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding-window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D-statistics, D-foil, and f-branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggests that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species gene pools.

evolutionary biology↗

bioRxiv2019

Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the ancestral sub-Saharan African intestinal microbiome

The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. Our results indicate that the distal IM of the Neolithic Middle Iron Age (c. AD 1485) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Otzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians, reveals that this IM precedes recent adaptation to Western diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago.

microbiology↗

bioRxiv2018

MobiSeq: De Novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements

In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular, the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site-associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted-enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.), and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome, and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms - enabling the exploration of diverse evolutionary and conservation questions.

genomics↗