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Westbury, M. V.

Publications and source records attributed to Westbury, M. V..

At least 19 recordsLinked to original sources

Reference mapping and whole-genome alignment yield comparable phylogenomic inferences

Reference-genome choice can introduce mapping bias when sequencing data are analysed against a heterospecific genome, but it remains unclear how strongly this bias affects species-level phylogenomic inference. We tested this across Ursidae using nine species spanning approximately 20 million years of divergence, including the extinct giant short-faced bear (Arctodus simus). We independently mapped the same sequencing datasets to four reference genomes spanning a broad range of evolutionary distances and compared these with two assembly-based whole-genome-alignment approaches. We developed PhyloSlide to analyse all treatments consistently, offering a streamlined pipeline for sliding-window phylogenomics. Using this approach, we found that mapping reference choice strongly affected sequence recovery, with missing data generally increasing with evolutionary distance. Nonetheless, all six treatments recovered an identical species-tree topology and highly similar gene and site concordance factors. Relative divergence-time estimates were also largely consistent between approaches. Together, these findings demonstrate that mapping sequencing reads from multiple species to a shared reference genome can yield phylogenomic inferences comparable to whole-genome alignment, despite substantial reference-dependent sequence loss across millions of years of evolutionary divergence.

evolutionary biology↗

SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences

Summary: Controlled modification of sequencing data is important for reproducible benchmarking, particularly when evaluating analyses affected by read fragmentation, divergent reference genomes and ancient DNA damage. SCAR introduces controlled mutations, fragmentation and position-specific damage into FASTA and FASTQ data. All features can be used separately or in combination, and empirical fragment-length and mismatch profiles can be supplied to closely reproduce the properties of targeted datasets. Validation analyses showed the successful implementation of the requested sequence changes, and their impact on read mapping and heterozygosity analyses. Availability and Implementation: SCAR is implemented in C++ and the latest code is available at https://github.com/Madshartmann1/SCAR. The version described in this article is archived at Zenodo at https://doi.org/10.5281/zenodo.22789736 , with validation material available at https://doi.org/10.5281/zenodo.21915766.

genomics↗

Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteus

The extinct giant deer (Megaloceros giganteus) was one of the most striking megafaunal species of the Late Quaternary, distinguished by its enormous palmated antlers reaching up to 3.5 m across, the largest known among both living and extinct cervids. Despite its iconic status, little is known about its genomic history prior to extinction [~]8 thousand years ago (kya). We generated the first nuclear palaeogenomes for Megaloceros, represented by nine individuals from Germany ([~]40 kya) and Ireland ([~]11 kya), mapped to a new chromosome-level reference genome of the fallow deer (Dama dama). Phylogenomic analyses placed Megaloceros as sister to Dama (divergence [~]3.5 Ma) and revealed evidence of gene flow with ancestral Cervus lineages. Population analyses identified clear differentiation between German and Irish lineages, with higher genetic diversity in the German individuals. Two genes under strong positive selection, BNIPL and SLC10A7, are associated with apoptosis regulation and skeletal development/bone mineralisation, respectively, and may relate to the species large body and antler size. Demographic reconstructions indicate a long-term decline in effective population size, extremely low heterozygosity, little evidence of extensive runs of homozygosity, and an elevated burden of predicted deleterious alleles. Together, these results suggest that Megaloceros entered the terminal Pleistocene in a genomically fragile state, offering new insight into the biology and evolutionary legacy of one of the largest and most distinctive cervids that ever lived.

evolutionary biology↗

Ancient DNA reveals early use of melons in China's Song Dynasty

Melon (Cucumis melo L.) domestication is thought to have occurred independently once in Northeast Africa and twice in India, but archaeobotanical seed remains point to a possible additional domestication in China. Because Cucumis seeds are difficult to diagnose morphologically, genomic data from archaeological material are needed to evaluate these scenarios and reconstruct ancient melon traits. We sequenced two Song Dynasty melon seeds from Shuomen Gugang (China), recovering 4.6x and 1.7x nuclear genome coverage. Nuclear and chloroplast analyses place both seeds within cultivated C. melo from China, supporting introduction from the broader Asian domestication pool rather than independent Chinese domestication. To assess whether these seeds carried traits associated with sweet dessert melons, we examined loci underlying fruit phenotypes. Neither seed carried alleles for orange flesh; one harbored an allele linked to yellow/orange peel, the other possessed alleles associated with green flesh and reduced acidity. Since wild melons are monoecious, the presence of the derived andromonoecy allele in one seed, associated with rounder fruit shape, suggests early selection on fruit morphology. Together, these findings indicate that Song Dynasty melons were likely consumed as fresh or culinary fruits rather than as sweet dessert melons. Their flesh coloration resonates with Song-period aesthetic sensibilities, exemplified by jade-green celadon ceramics frequently crafted in melon-shaped forms. By anchoring East Asian archaeobotanical remains within modern melon genomic variation, this study provides a temporal framework for melon dispersal into China and shows how ancient genomics can illuminate past crop use.

evolutionary biology↗

Tracing the drivers of range-wide bowhead whale genomic structure and diversity

Understanding how past environmental and anthropogenic factors shaped contemporary genetic patterns is essential for assessing the vulnerability of species in the face of ongoing climate change. The bowhead whale (Balaena mysticetus) - the only baleen whale found in the Arctic year-round - has a strong association with sea ice, long history of human exploitation, and a circumpolar distribution, making it a valuable model for investigating how these factors have shaped population structure in the marine Arctic. We analysed both nuclear and mitochondrial genomes from bowhead whale individuals sampled across the species circumpolar range, encompassing all four recognized management stocks. Our results reveal three not four genetically differentiated populations: the Sea of Okhotsk stock; the East Greenland-Svalbard-Barents Sea stock; and a combined population containing the Bering-Chukchi-Beaufort Seas and East Canada-West Greenland stocks. We utilised ecological niche modeling and bowhead whale telemetry data to model stock connectivity over the past 11,700 years, and identify past habitat connectivity as a key driver of current population structure. Despite centuries of intensive commercial whaling, the three bowhead whale populations exhibit little-to-no evidence of recent inbreeding and retain high genetic diversity relative to other mammalian species. The lowest genetic diversity, most inbreeding, and highest realised genetic load being in the Sea of Okhotsk population. Collectively, our findings shed light on the recent population history and dynamics of bowhead whales, and offer valuable baseline data on present-day genetic structure and diversity to support effective conservation and management strategies.

evolutionary biology↗

Paleogenomics unveil domesticated camelid herding and wild camelid hunting in early pastoralist societies in the Atacama Desert

The domestication of camelids played a significant role in the development of Andean societies. Although South American camelids can be osteometrically classified as large (putatively Lama), or small (putatively Vicugna), it is difficult to differentiate between wild or domesticated. Here we utilise palaeogenomic data to reveal the sex and ancestry of camelids from archaeological sites from the Tulan ravine, a key area for understanding the transition from hunter-gatherer to pastoral societies in the South-Central Andes. We inferred the ancestry of 49 individuals with genome-wide coverages >0.001x and found evidence for both Vicugna and Lama. Investigations into 26 individuals of >0.01x showed that all individuals, except one male llama, represented ancestry not found in modern individuals. Similar male-to-female sex ratios suggest hunting rather than herding. Moreover, while intergeneric admixture is widespread in modern domesticated individuals, we find limited evidence of this in our dataset. Overall, our findings suggest that lost early domesticate lineages and/or wild camelids, not the direct ancestors of contemporary domesticates, were the primary source of camelids in both domestic and ritual contexts in the Tulan ravine during the Early Formative period (3,360-2,370 cal. yr BP).

evolutionary biology↗

A multidisciplinary investigation into whether Andean caravans reached the southern lowlands of the Parana-Plata basin during pre-Columbian times

The expansion of llama caravans and the dispersal of domesticated camelids to extra-Andean regions is one of the key topics in South American archaeology, as it reflects the degree of connection between Andean societies and the surrounding lowland societies, as well as the extent of pre-Columbian pastoralism. One of the primary indicators of both processes is the presence of domesticated camelids in the archaeological record, particularly the llama (Lama glama). Based on somewhat ambiguous historical evidence, it has been suggested that llama caravanning may have reached the northern Pampean region and the southern Parana River valley from an unspecified time until historical times. While the archaeological sites in these two regions have abundant camelid remains that have thus far been identified as guanaco (Lama guanicoe), the possibility of misidentification due to the osteometric similarity between the domestic and wild camelids could mask the presence of llamas in the record, undermining evidence of this potential major expansion of llama caravans. To clarify this issue, we applied a multidisciplinary approach combining archaeological, isotopic, and paleogenomic analyses to determine the taxonomic status of camelids recovered from archaeological sites in both areas. Our findings demonstrate that all the individuals analyzed correspond to guanacos, whose survival extended into early historical times. There is no regional evidence to support the presence of llama caravanning or domesticated camelids in the northern Pampean region or the lower Parana River valley.

genomics↗

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↗

Elucidating the sustainability of 700 years of Inuvialuit beluga whale hunting in the Mackenzie River Delta, Northwest Territories, Canada

Beluga whales play a critical role in the subsistence economies and cultural heritage of Indigenous communities across the Arctic, yet the effects of Indigenous hunting on beluga whales remains unknown. Here, we integrate paleogenomics and stable{delta} 13C and{delta} 15N isotope analysis to investigate 700 years of beluga subsistence hunting in the Mackenzie Delta area of northwestern Canada. Genetic identification of the zooarchaeological remains, which based on radiocarbon dating span three time periods (1290-1440 CE; 1450-1650 CE; 1800-1870 CE), indicate shifts across time in the sex ratio of the harvested belugas. The equal number of females and males harvested in 1450-1650 CE versus more males harvested in the two other time periods may reflect changes in hunting practices or temporal shifts in beluga availability. We find temporal shifts and sex-based differences in {delta}13C of the harvested belugas across time, suggesting historical adaptability in the foraging ecology of the whales. Although we uncovered novel mitochondrial diversity in the Mackenzie Delta belugas, we found no changes in nuclear genomic diversity nor any substructuring across time. Our findings indicate the genomic stability and continuity of the Mackenzie Delta beluga population across the 700 years surveyed, indicating the impact of Inuvialuit subsistence harvests on the genetic diversity of contemporary beluga individuals has been negligible. Significance StatementSince colonizing the Mackenzie Delta in northwestern Canada [~]1200 CE, Inuvialuit have been heavily reliant on belugas for their livelihoods and cultural heritage. However, little is known of the impact of centuries of sustained Inuvialuit subsistence hunting on the beluga population inhabiting the Mackenzie Delta. Using palaeogenomic and stable isotope analysis of zooarchaeological remains, and comparing the findings with contemporary data, we investigate temporal changes in beluga diversity, structuring, and foraging ecology. We show Inuvialuit harvests had a negligible impact on the genetic diversity of contemporary Mackenzie belugas, and highlight the applicability of combining genomic sexing and isotope analysis of zooarchaeological remains for advancing our understanding of past hunting practices and faunal ecologies.

genomics↗

Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation

The polar bear (Ursus maritimus) occupies a relatively narrow ecological niche, with many characteristics adapted for cold temperatures, movement across snow, ice and open water, and for consuming highly lipid-dense prey species. The divergence of polar bears from brown bears (Ursus arctos) and their adaptation to their Arctic lifestyle is a well-known example of rapid evolution. Previous research investigating whole genomes uncovered genomic regions containing an array of key genes highly differentiated between polar and brown bears, many of which were linked to the novel Arctic environment. Further research suggested fixed alleles in these genes arose from selection on both standing variation and de novo mutations in the evolution of polar bears. Here, we reevaluate these findings by incorporating more genomic data from previously unavailable polar and brown bear populations, and assess the timing of allele fixation by utilising the genomes of two Late Pleistocene polar bears (aged 130-100,000 years old and 100-70,000 years old). Contrary to previous results, we found no evidence for alleles fixed in all polar bears within these key genes arising from de novo mutation. Most alleles fixed in modern polar bears were also fixed in the Late Pleistocene bears, suggesting selection occurred prior to 70,000 years ago. However, some sites fixed in modern polar bears were not fixed in the Late Pleistocene bears, including at sites within APOB, LYST, and TTN. The functions of these three genes are associated with the cardiovascular functions, metabolism, and pigmentation, suggesting that selection may have acted on different loci at different times.

evolutionary biology↗

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↗

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↗

Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea-ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modelling, we investigate how Holocene environmental changes affected the evolutionary ecology of polar bears around Greenland. We show that throughout the last [~]11,000 years, Greenlandic polar bears have been heavily influenced by changes in sea-surface temperature (SST) and sea-ice cover. Most notable are major reductions in effective population size at the beginning of the Holocene and during the Holocene Thermal Maximum [~]6 kya, which coincide with increases in annual mean SST, reduction in sea-ice covers, declines in suitable habitat, and shifts in suitable habitat northwards. Furthermore, we show how individuals sampled from west and east Greenland are genetically, morphologically, and ecologically distinct. We find bears sampled in west Greenland to be larger, more genetically diverse and have diets dominated by ringed seals, whereas bears from east Greenland are smaller and less diverse with more varied diets, putatively driven by regional biotic differences. Taken together, we provide novel insights into the vulnerability of polar bears to environmental change, and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants. TeaserMultivariate investigations of the environments role in the evolutionary ecology of Greenlandic polar bears.

evolutionary biology↗

When blue turns to grey - Paleogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus)

The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (H. equinus) or sable (H. niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are unfavourable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4x mean coverage from a historical specimen (~200 years old) and one at 2.1x mean coverage from a fossil specimen dating to 9,800-9,300 cal BP, making it currently the oldest palaeogenome from Africa. Phylogenomics show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelopes, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely a decisive factor in the blue antelopes extinction.

evolutionary biology↗

Genomic insights into the evolutionary relationships and demographic history of kiwi

Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events among them. Here, we utilise single representative nuclear genomes of all extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species with available reference assemblies show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we uncover similarities and differences in the demographic histories of the five kiwi species over the past million years, and suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the evolutionary history of the group.

evolutionary biology↗

Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference

O_LIWithin evolutionary biology, mitochondrial genomes (mitogenomes) provide useful insights at both population and species level. Several approaches are available to assemble mitogenomes. However, most are not suitable for divergent, extinct species, due to the requirement of a reference mitogenome from a conspecific or close relative, and relatively high-quality DNA. C_LIO_LIIterative mapping can overcome the lack of a close reference sequence, and has been applied to an array of extinct species. Despite its widespread use, the accuracy of the reconstructed assemblies are yet to be comprehensively assessed. Here, we investigated the influence of mapping software (BWA or MITObim), parameters, and bait reference phylogenetic distance on the accuracy of the reconstructed assembly using two simulated datasets: (i) spotted hyena and various mammalian bait references, and (ii) southern cassowary and various avian bait references. Specifically, we assessed the accuracy of results through pairwise distance (PWD) to the reference conspecific mitogenome, number of incorrectly inserted base pairs (bp), and total length of the reconstructed assembly. C_LIO_LIWe found large discrepancies in the accuracy of reconstructed assemblies using different mapping software, parameters, and bait references. PWD to the reference conspecific mitogenome, which reflected the level of incorrect base calls, was consistently higher with BWA than MITObim. The same was observed for the number of incorrectly inserted bp. In contrast, the total sequence length was lower. Overall, the most accurate results were obtained with MITObim using mismatch values of 3 or 5, and the phylogenetically closest bait reference sequence. Accuracy could be further improved by combining results from multiple bait references. C_LIO_LIWe present the first comprehensive investigation of how mapping software, parameters, and bait reference influence mitogenome reconstruction from ancient DNA through iterative mapping. Our study provides information on how mitogenomes are best reconstructed from divergent, short-read data. By obtaining the most accurate reconstruction possible, one can be more confident as to the reliability of downstream analyses, and the evolutionary inferences made from them. C_LI

bioinformatics↗

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↗

Palaeogenomics reveal a hybrid origin of the world's largest Camelus species

The extinct Camelus knoblochi is known as the largest camel in genus Camelus, but its relationship to modern Camelus species remains unclear. In this study, we reported the first mitochondrial and nuclear analyses of seven Late Pleistocene C. knoblochi samples from Northeastern China. We found that they are inseparable to wild Bactrian camel on the matrilineal side, but belong to a distinct cluster on the biparental nuclear side. Further admixture proportion analyses suggested hybrid ancestry between both the ancestors of the modern wild and domesticated Bactrian camels, with ~65% contribution from the former and ~35% from the later. By calculating the coalescence time for three Camelus species above, we estimated the hybridization event occurred between approximately 0.8 and 0.33 Ma. We also used Bayesian skyline to reconstruct the maternal demographic trajectories for different Camelus to better compare their evolutionary histories. Our results provide molecular insights into C. knoblochi and fill in a vital piece in understanding the genus Camelus.

molecular biology↗