ORCID Profile
0000-0003-1371-219X
Current Organisation
IT University of Copenhagen
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Publisher: The Royal Society
Date: 07-10-2013
Abstract: Niche variation owing to in idual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue s les of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina . Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-in idual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-in idual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish.
Publisher: Springer Science and Business Media LLC
Date: 26-04-2021
DOI: 10.1038/S41467-021-22386-8
Abstract: Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 08-12-2017
Abstract: Animals tend to respond to threats with the well-known behaviors of fight, flee, or freeze, each of which requires a different suite of physiological responses. Marine mammals face particular challenges because they may flee into an environment where oxygen is not available and pressure must be accommodated. Williams et al. placed a submersible electrocardiograph, depth, and acceleration recorder on narwhals after they were freed from entanglement. The animals displayed contrary cardiovascular responses simultaneously, which placed extreme stress on the cardiovascular system and the tissues that it protects. Science , this issue p. 1328
Publisher: Elsevier BV
Date: 09-2020
Publisher: Wiley
Date: 06-2021
DOI: 10.1002/GGN2.10051
Abstract: Enigmatic phenomena have sparked the imagination of people around the globe into creating folkloric creatures. One prime ex le is Zana of Abkhazia (South Caucasus), a well‐documented 19th century female who was captured living wild in the forest. Zana's appearance was sufficiently unusual, that she was referred to by locals as an Almasty—the analog of Bigfoot in the Caucasus. Although the exact location of Zana's burial site was unknown, the grave of her son, Khwit, was identified in 1971. The genomes of Khwit and the alleged Zana skeleton were sequenced to an average depth of ca. 3× using ancient DNA techniques. The identical mtDNA and parent‐offspring relationship between the two indicated that the unknown woman was indeed Zana. Population genomic analyses demonstrated that Zana's immediate genetic ancestry can likely be traced to present‐day East‐African populations. We speculate that Zana might have had a genetic disorder such as congenital generalized hypertrichosis which could partially explain her strange behavior, lack of speech, and long body hair. Our findings elucidate Zana's unfortunate story and provide a clear ex le of how prejudices of the time led to notions of cryptic hominids that are still held and transmitted by some today.
Publisher: Wiley
Date: 10-10-2017
Publisher: Springer Science and Business Media LLC
Date: 16-04-2014
Publisher: Cold Spring Harbor Laboratory
Date: 23-06-2020
DOI: 10.1101/2020.06.22.164178
Abstract: Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. Here we analyzed 19 parent-offspring trios of rhesus macaques ( Macaca mulatta ) at high sequencing coverage of ca. 76X per in idual, and estimated an average rate of 0.77 × 10 −8 de novo mutations per site per generation (95 % CI: 0.69 × 10 −8 - 0.85 × 10 −8 ). By phasing 50 % of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed an average of 81 % of the de novo mutations, with a trend of an increasing male contribution for older fathers. About 3.5 % of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the ergence times between closely related primates calculated based on the yearly mutation rate of rhesus macaque generally reconcile with ergence estimated with molecular clock methods, except for the Cercopithecidae/Hominoidea molecular ergence dated at 52 Mya using our new estimate of the yearly mutation rate.
Publisher: The Royal Society
Date: 27-11-2019
Abstract: Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
Publisher: Springer Science and Business Media LLC
Date: 20-09-2022
DOI: 10.1186/S12862-022-02062-1
Abstract: The banteng ( Bos javanicus ) is an endangered species within the wild Asian Bos complex, that has traditionally been sub ided into three geographically isolated subspecies based on (i) mainland Southeast Asia ( B. j. birmanicus ), (ii) Java ( B. j. javanicus ), and (iii) Borneo ( B. j. lowi ). However, analysis of a single Bornean banteng mitochondrial genome generated through a genome skimming approach was used to suggest that it may actually represent a distinct species (Ishige et al. in Mitochondrial DNA A DNA Mapp Seq Anal 27(4):2453–4. 0.3109/19401736.2015.1033694 , 2016). To explore this hypothesis further, we leveraged on the GenBank (NCBI) raw read sequencing data originally used to construct the mitochondrial genome and reconstructed its nuclear genome at low (0.2×) coverage. When analysed in the context of nuclear genomic data representing a broad reference panel of Asian Bos species, we find the Bornean banteng affiliates strongly with the Javan banteng, in contradiction to the expectation if the separate species hypothesis was correct. Thus, despite the Bornean banteng’s unusual mitochondrial lineage, we argue there is no genomic evidence that the Bornean banteng is a distinct species.
Publisher: Oxford University Press (OUP)
Date: 26-06-2017
Publisher: Springer Science and Business Media LLC
Date: 11-11-2020
Publisher: Cold Spring Harbor Laboratory
Date: 14-08-2018
DOI: 10.1101/391680
Abstract: An aerial line transect survey of whales in West and East Greenland was conducted in August-September 2015. The survey covered the area between the coast of West Greenland and offshore (up to 100 km) to the shelf break. In East Greenland, the survey lines covered the area from the coast up to 50 km offshore crossing the shelf break. A total of 423 sightings of 12 cetacean species were obtained and abundance estimates were developed for common minke whale, from now on called minke whale, ( Balaenoptera acutorostrata) (32 sightings), fin whale ( Balaenoptera physalus ) (129 sightings), humpback whale ( Megaptera novaeangliae) (84 sightings), harbour porpoise ( Phocoena phocoena) (55 sightings), long-finned pilot whale, from now on called pilot whale, ( Globicephala melas) (42 sightings) and white-beaked dolphins ( Lagenorhynchus albirostri) (50 sightings). The developed at-surface abundance estimates were corrected for both perception bias and availability bias if possible. Data on surface corrections for minke whales and harbour porpoises were collected from whales instrumented with satellite-linked time-depth-recorders. Options for estimation methods are presented and the preferred estimates are: Minke whales: 5,095 (95% CI: 2,171-11,961) in West Greenland and 2,762 (95% CI: 1,160-6,574) in East Greenland, fin whales: 2,215 (95% CI: 1,017-4,823) in West Greenland and 6,440 (95% CI: 3,901-10,632) in East Greenland, humpback whales: 993 (95% CI: 434-2,272) in West Greenland and 4,223 (95%CI: 1,845-9,666) in East Greenland, harbour porpoise: 83,321 (95% CI: 43,377-160,047) in West Greenland and 1,642 (95% CI: 319-8,464) in East Greenland, pilot whales: 9,190 (95% CI: 3,635-23,234) in West Greenland and 258 (95% CI: 50-1,354) in East Greenland, white-beaked dolphins 15,261 (95% CI: 7,048-33,046) in West Greenland and 11,889 (95% CI: 4,710-30,008) in East Greenland. The abundance of cetaceans in coastal areas of East Greenland has not been estimated before, but the limited historical information from the area indicate that the achieved abundance estimates were remarkably high. When comparing the abundance estimates from 2015 in West Greenland with a similar survey conducted in 2007 there is a clear trend towards lower densities in 2015 for the three baleen whale species and white-beaked dolphins. Harbour porpoises and pilot whales however, did not show a similar decline. The decline in baleen whale and white-beaked dolphin abundance is likely due to emigration to the East Greenland shelf areas where recent climate driven changes in pelagic productivity may have accelerated favourable conditions for these species.
Publisher: Cold Spring Harbor Laboratory
Date: 11-02-2019
DOI: 10.1101/546820
Abstract: While sequencing ancient DNA from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but also shows evidence of biologically relevant tissue-specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA-seq data such as exon-exon junction presence and high endogenous ribosomal RNA content confirms our data’s authenticity. By performing independent technical replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues, but also that it has potential for tissue identification, and possibly further uses such as in vivo genome activity and adaptation, when sequenced using this technology.
Publisher: Cold Spring Harbor Laboratory
Date: 24-08-2023
DOI: 10.1101/2023.08.23.553838
Abstract: Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs ( Potamochoerus larvatus ) and red river hogs ( P. porcus ) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old ergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable F ST values, and a recent ergence time ( ,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs erged from southern African populations and underwent a limited bottleneck 1,000-5,000 years ago, concurrent with human arrival in Madagascar. These results shed new light on the evolutionary history of an iconic and widespread African genus and provide insight into the longstanding biogeographic puzzle surrounding the bushpig’s presence in Madagascar.
Publisher: Springer Science and Business Media LLC
Date: 18-07-2023
DOI: 10.1038/S41467-023-39532-Z
Abstract: Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient s les to coastal populations increases as the age of the s les decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.
Publisher: F1000 Research Ltd
Date: 12-11-2021
DOI: 10.12688/WELLCOMEOPENRES.17332.1
Abstract: We present a genome assembly from an in idual male Canis lupus orion (the grey wolf, subspecies: Greenland wolf Chordata Mammalia Carnivora Canidae). The genome sequence is 2,447 megabases in span. The majority of the assembly (98.91%) is scaffolded into 40 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.
Publisher: Wiley
Date: 22-07-2020
DOI: 10.1002/ECE3.6464
Publisher: Oxford University Press (OUP)
Date: 03-2020
Publisher: Elsevier BV
Date: 12-2019
Publisher: Springer Science and Business Media LLC
Date: 13-01-2021
Publisher: American Association for the Advancement of Science (AAAS)
Date: 06-07-2018
Abstract: Dogs have been present in North America for at least 9000 years. To better understand how present-day breeds and populations reflect their introduction to the New World, Ní Leathlobhair et al. sequenced the mitochondrial and nuclear genomes of ancient dogs (see the Perspective by Goodman and Karlsson). The earliest New World dogs were not domesticated from North American wolves but likely originated from a Siberian ancestor. Furthermore, these lineages date back to a common ancestor that coincides with the first human migrations across Beringia. This lineage appears to have been mostly replaced by dogs introduced by Europeans, with the primary extant lineage remaining as a canine transmissible venereal tumor. Science , this issue p. 81 see also p. 27
Publisher: Springer Science and Business Media LLC
Date: 19-07-2022
DOI: 10.1038/S41467-022-31508-9
Abstract: Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin ersification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, ing, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth.
Publisher: Springer Science and Business Media LLC
Date: 29-06-2017
Publisher: Proceedings of the National Academy of Sciences
Date: 04-05-2020
Abstract: Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions ( Panthera leo spelaea ), 12 historic lions ( Panthera leo leo/Panthera leo melanochaita ) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their ergence. Within modern lions, we found 2 main lineages that erged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic ersity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the ersity of this vulnerable species.
Publisher: Ubiquity Press, Ltd.
Date: 08-05-2017
DOI: 10.5334/OQ.33
Publisher: Wiley
Date: 27-05-2019
DOI: 10.1111/MEC.15099
Abstract: Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic s ling and genome-wide data to s le the variation in ancestry within in iduals.
Publisher: MDPI AG
Date: 15-06-2017
DOI: 10.3390/GENES8060164
Publisher: Springer Science and Business Media LLC
Date: 14-06-2013
Publisher: Springer International Publishing
Date: 12-2019
Publisher: Oxford University Press (OUP)
Date: 03-2023
Abstract: Genome sequences can reveal the extent of inbreeding in small populations. Here, we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (FROH ≥ 0.65). Detected recombination cross-over events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with 3 modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among geographically dispersed social groups within this morphotype. Limitations to the insights gained in this study stem from the nonindependence of the 3 closely related modern genomes, the recent coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for both the distinctive morphology, and the coupling of genetic barriers to gene flow with other killer whale populations.
Publisher: Elsevier BV
Date: 10-2020
Publisher: Oxford University Press (OUP)
Date: 10-10-2017
Abstract: Natural selection in domestic dogs is of great interest in evolutionary biology since dogs have migrated to every inhabited continent of the world alongside humans, and adapted to erse environments. Here, we explored their demographic history and genetic basis of adaptation to the tropical African environment using whole genome analyses of 19 African indigenous dogs from Nigeria. Demographic analysis suggests that the ancestors of these dogs migrated into Africa from Eurasia 14,000 years ago and underwent a severe founder effect before population expansion. Admixture analysis further reveals that African dog genomes contain about 1.88-3.50% introgression from African golden wolves (Canis anthus). Population genetic analysis identifies 50 positively selected genes linked with immunity, angiogenesis, ultraviolet protection, as well as insulin secretion and sensitivity that may contribute to adaptation to tropical conditions. One of the positively selected genes, adhesion G protein-coupled receptor E1 (ADGRE1), has also been found to be association with severe malaria resistance in African human populations. Functional assessments showed that ADGRE1 provides protective host defense against Plasmodium infections. This result, together with the fact that the inflammatory response to canine babesiosis is similar to complicated falciparum malaria in humans, support the dogs as a model for the study of malaria control and treatment.
Publisher: Springer Science and Business Media LLC
Date: 17-12-2019
DOI: 10.1038/S41467-019-13549-9
Abstract: The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable s les. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the in idual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.
Publisher: Frontiers Media SA
Date: 02-12-2016
Publisher: Oxford University Press (OUP)
Date: 10-03-2020
DOI: 10.1093/ZOOLINNEAN/ZLAA004
Abstract: The Javan rhinoceros (Rhinoceros sondaicus) is one of five extant rhinoceros species and among the rarest large mammals on Earth. Once widespread across Southeast Asia, it is now on the verge of extinction, with only one wild population remaining (estimated at ~60 in iduals) on the island of Java, Indonesia. To assess the past genetic ersity of the female lineage of R. sondaicus, we generated mitochondrial genome data from eight museum specimens dating back to the 19th century, before the range of the Javan rhinoceros was dramatically reduced, for comparison against mitochondrial DNA (mtDNA) sequences of current R. sondaicus and other rhinoceros species. We succeeded in reconstructing five full and three partial ancient mitogenomes from the eight s les. We used BEAST to assess the phylogenetic relationship of the five extant rhinoceros species and the historical s les. The results show that the oldest and most erse mtDNA lineages of R. sondaicus are found in historical s les, indicating a significant reduction of mtDNA ersity in modern Javan rhinos. We anticipate that the newly sequenced data will represent a useful resource for improving our understanding of evolutionary history of this species, should future studies be able to increase the available dataset. We hope this information may help in conservation efforts for this species.
Publisher: Wiley
Date: 05-07-2018
Abstract: The use of environmental DNA (eDNA) has become an applicable noninvasive tool with which to obtain information about bio ersity. A subdiscipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterize the bio ersity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of s les from only a single or a few different locations. In this study, we investigate the suitability of iDNA extracted from more than 3,000 haematophagous terrestrial leeches as a tool for detecting a wide range of terrestrial vertebrates across five different geographical regions on three different continents. These regions cover almost the full geographical range of haematophagous terrestrial leeches, thus representing all parts of the world where this method might apply. We identify host taxa through metabarcoding coupled with high-throughput sequencing on Illumina and IonTorrent sequencing platforms to decrease economic costs and workload and thereby make the approach attractive for practitioners in conservation management. We identified hosts in four different taxonomic vertebrate classes: mammals, birds, reptiles and hibians, belonging to at least 42 different taxonomic families. We find that vertebrate blood ingested by haematophagous terrestrial leeches throughout their distribution is a viable source of DNA with which to examine a wide range of vertebrates. Thus, this study provides encouraging support for the potential of haematophagous terrestrial leeches as a tool for detecting and monitoring terrestrial vertebrate bio ersity.
Publisher: Springer Science and Business Media LLC
Date: 02-2018
Publisher: Wiley
Date: 27-09-2016
DOI: 10.1111/ZSC.12212
Publisher: UiT The Arctic University of Norway
Date: 10-2018
DOI: 10.7557/3.4689
Abstract: An aerial line transect survey of whales in West and East Greenland was conducted in August-September 2015. The survey covered the area between the coast of West Greenland and offshore (up to 100 km) to the shelf break. In East Greenland, the survey lines covered the area from the coast up to 50 km offshore crossing the shelf break. A total of 423 sightings of 12 cetacean species were obtained and abundance estimates were developed for common minke whale, (Balaenoptera acutorostrata) (32 sightings), fin whale (Balaenoptera physalus) (129 sightings), humpback whale (Megaptera novaeangliae) (84 sightings), harbour porpoise (Phocoena phocoena) (55 sightings), long-finned pilot whale, (Globicephala melas) (42 sightings) and white-beaked dolphin (Lagenorhynchus albirostri) (50 sightings). The developed at-surface abundance estimates were corrected for both perception bias and availability bias if possible. Data on surface corrections for minke whales and harbour porpoises were collected from whales instrumented with satellite-linked time-depth-recorders. Options for estimation methods are presented and the preferred estimates are: minke whales: 5,095 (95% CI: 2,171-11,961) in West Greenland and 2,762 (95% CI: 1,160-6,574) in East Greenland, fin whales: 2,215 (95% CI: 1,017-4,823) in West Greenland and 6,440 (95% CI: 3,901-10,632) in East Greenland, humpback whales: 993 (95% CI: 434-2,272) in West Greenland and 4,223 (95% CI: 1,845-9,666) in East Greenland, harbour porpoises: 83,321 (95% CI: 43,377-160,047) in West Greenland and 1,642 (95% CI: 319-8,464) in East Greenland, pilot whales: 9,190 (95% CI: 3,635-23,234) in West Greenland and 258 (95% CI: 50-1,354) in East Greenland, white-beaked dolphins 15,261 (95% CI: 7,048-33,046) in West Greenland and 11,889 (95% CI: 4,710-30,008) in East Greenland. The abundance of cetaceans in coastal areas of East Greenland has not been estimated before, but the limited historical information from the area indicates that the achieved abundance estimates were remarkably high. When comparing the abundance estimates from 2015 in West Greenland with a similar survey conducted in 2007, there is a clear trend towards lower densities in 2015 for the three baleen whale species and white-beaked dolphins. Harbour porpoises and pilot whales, however, did not show a similar decline. The decline in baleen whale and white-beaked dolphin abundance is likely due to emigration to the East Greenland shelf areas where recent climate driven changes in pelagic productivity may have accelerated favourable conditions for these species.
Publisher: Elsevier BV
Date: 2015
Publisher: Ubiquity Press, Ltd.
Date: 27-09-2016
DOI: 10.5334/OQ.25
Publisher: Elsevier BV
Date: 2021
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-10-2020
Publisher: Wiley
Date: 03-02-2023
DOI: 10.1111/MEC.16851
Abstract: The iconic Cape buffalo has experienced several documented population declines in recent history. These declines have been largely attributed to the late 19th century rinderpest pandemic. However, the effect of the rinderpest pandemic on their genetic ersity remains contentious, and other factors that have potentially affected this ersity include environmental changes during the Pleistocene, range expansions and recent human activity. Motivated by this, we present analyses of whole genome sequencing data from 59 in iduals from across the Cape buffalo range to assess present‐day levels of genome‐wide genetic ersity and what factors have influenced these levels. We found that the Cape buffalo has high average heterozygosity overall (0.40%), with the two southernmost populations having significantly lower heterozygosity levels (0.33% and 0.29%) on par with that of the domesticated water buffalo (0.29%). Interestingly, we found that these lower levels are probably due to recent inbreeding (average fraction of runs of homozygosity 23.7% and 19.9%) rather than factors further back in time during the Pleistocene. Moreover, detailed investigations of recent demographic history show that events across the past three centuries were the main drivers of the exceptional loss of genetic ersity in the southernmost populations, coincident with the onset of colonialism in the southern extreme of the Cape buffalo range. Hence, our results add to the growing body of studies suggesting that multiple recent human‐mediated impacts during the colonial period caused massive losses of large mammal abundance in southern Africa.
Publisher: Cold Spring Harbor Laboratory
Date: 27-02-2021
DOI: 10.1101/2021.02.26.432714
Abstract: The Sardinian dhole ( Cynotherium sardous ) 1 was an iconic and unique canid species of canid that was endemic of Sardinia and Corsica until it became extinct at the end of the Late Pleistocene 2–5 . Given its peculiar dental morphology, small body size and high level of endemism, several canids have been proposed as possible ancestors of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor 3,6–9 . Morphometric analyses 3,6,8–12 have failed to clarify the evolutionary relationship with other canids. We sequenced the genome of a ca 21,100 year old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found it represents a separate taxon from all other living canids from Eurasia, Africa and North America, and that the Sardinian and Asian dhole lineages erged ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, that ended approximately 500-300 ka, when the landbridge between Sardinia and mainland Italy was broken, severing their population connectivity. Our s le showed low genome-wide ersity compared to other extant canids - probably a result of the long-term isolation - that could have contributed to the subsequent extinction of the Sardinian dhole.
Publisher: Springer Science and Business Media LLC
Date: 08-01-2016
Publisher: Wiley
Date: 06-02-2019
Abstract: 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 in iduals 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 s les, 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 erse evolutionary and conservation questions.
Publisher: Wiley
Date: 02-02-2023
DOI: 10.1111/MEC.16858
Abstract: Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white‐tailed eagle ( Haliaeetus albicilla ) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white‐tailed eagles, from both historical and contemporary s les, clear signatures of ancient biogeographic substructure across Europe and the North‐East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other s led mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All s led populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: (1) Isolation of refugia during the last glacial period 110–115,000 years ago, (2) population ergence following the colonization of the deglaciated areas ~10,000 years ago, (3) human population expansion, which led to the settlement in Iceland ~1100 years ago, and (4) human persecution and exposure to toxic pollutants during the last two centuries.
Publisher: Wiley
Date: 02-01-2020
DOI: 10.1111/MEC.15329
Publisher: Proceedings of the National Academy of Sciences
Date: 20-09-2021
Abstract: The Siberian Arctic has witnessed numerous societal changes since the first known appearance of dogs in the region ∼10,000 years ago. These changes include the introduction of ironworking ∼2,000 years ago and the emergence of reindeer pastoralism ∼800 years ago. The analysis of 49 ancient dog genomes reveals that the ancestry of Arctic Siberia dogs shifted over the last 2,000 years due to an influx of dogs from the Eurasian Steppe and Europe. Combined with genomic data from humans and archaeological evidence, our results suggest that though the ancestry of human populations in Arctic Siberia did not change over this period, people there participated in trade with distant communities that involved both dogs and material culture.
Publisher: Springer Science and Business Media LLC
Date: 29-06-2022
DOI: 10.1038/S41586-022-04824-9
Abstract: The grey wolf ( Canis lupus ) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage ( Canis familiaris ) lived 1–8 . Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
Publisher: Cold Spring Harbor Laboratory
Date: 18-07-2018
DOI: 10.1101/370122
Abstract: Grey wolves ( Canis lupus ) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.
Publisher: Public Library of Science (PLoS)
Date: 13-06-2018
Publisher: Elsevier BV
Date: 08-2017
Publisher: American Association for the Advancement of Science (AAAS)
Date: 26-06-2020
Abstract: Dogs have been used for sledding in the Arctic as far back as ∼9500 years ago. However, the relationships among the earliest sled dogs, other dog populations, and wolves are unknown. Sinding et al. sequenced an ancient sled dog, 10 modern sled dogs, and an ancient wolf and analyzed their genetic relationships with other modern dogs. This analysis indicates that sled dogs represent an ancient lineage going back at least 9500 years and that wolves bred with the ancestors of sled dogs and precontact American dogs. However, gene flow between sled dogs and wolves likely stopped before ∼9500 years ago. Science , this issue p. 1495
Publisher: American Association for the Advancement of Science (AAAS)
Date: 08-06-2018
Publisher: Oxford University Press (OUP)
Date: 12-2018
Publisher: Public Library of Science (PLoS)
Date: 30-07-2019
Publisher: Cold Spring Harbor Laboratory
Date: 10-09-2018
DOI: 10.1101/407692
Abstract: Ancient DNA (aDNA) sequencing has enabled unprecedented reconstruction of speciation, migration, and admixture events for extinct taxa 1 . Outside the permafrost, however, irreversible aDNA post-mortem degradation 2 has so far limited aDNA recovery within the ˜0.5 million years (Ma) time range 3 . Tandem mass spectrometry (MS)-based collagen type I (COL1) sequencing provides direct access to older biomolecular information 4 , though with limited phylogenetic use. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae 5-7 using ˜1.77 million years (Ma) old dental enamel proteome sequences of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus) 8 . Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly ( Coelodonta antiquitatis ) and Merck’s rhinoceros ( S. kirchbergensis ) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that this genus includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference, and also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.
Publisher: Authorea, Inc.
Date: 13-12-2022
DOI: 10.22541/AU.167092760.05022662/V1
Abstract: Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary s les, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other s led mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All s led populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: I) isolation of refugia during the last glacial period 110-115,000 years ago, II) population ergence following the colonization of the deglaciated areas ~10,000 years ago, III) human population expansion, which led to the settlement in Iceland ~1,100 years ago, and IV) human persecution and exposure to toxic pollutants during the last two centuries.
Publisher: Elsevier BV
Date: 11-2021
Publisher: Springer Science and Business Media LLC
Date: 11-09-2019
Publisher: Inter-Research Science Center
Date: 11-06-2018
DOI: 10.3354/MEPS12588
Publisher: Springer Science and Business Media LLC
Date: 29-10-2020
DOI: 10.1038/S41598-020-75658-6
Abstract: Arctic top predators are expected to be impacted by increasing temperatures associated with climate change, but the relationship between increasing sea temperatures and population dynamics of Arctic cetaceans remains largely unexplored. Narwhals ( Monodon monoceros ) are considered to be among the most sensitive of Arctic endemic marine mammals to climate change due to their limited prey selection, strict migratory patterns and high site fidelity. In the context of climate change, we assume that the population dynamics of narwhals are partly influenced by changes in environmental conditions, with warm areas of increasing sea temperatures having lower abundance of narwhals. Using a unique large dataset of 144 satellite tracked narwhals, sea surface temperature (SST) data spanning 25 years (1993–2018) and narwhal abundance estimates from 17 localities, we (1) assessed the thermal exposure of this species, (2) investigated the SST trends at the summer foraging grounds, and (3) assessed the relationship between SST and abundance of narwhals. We showed a sharp SST increase in Northwest, Mideast and Southeast Greenland, whereas no change could be detected in the Canadian Arctic Archipelago (CAA) and in the Greenland Sea. The rising sea temperatures were correlated with the smallest narwhal abundance observed in the Mideast and Southeast Greenland ( 2000 in iduals), where the mean summer sea temperatures were the highest (6.3 °C) compared to the cold waters of the CAA (0.7 °C) that were associated with the largest narwhal populations ( 40,000 in iduals). These results support the hypothesis that warming ocean waters will restrict the habitat range of the narwhal, further suggesting that narwhals from Mideast and Southeast Greenland may be under pressure to abandon their traditional habitats due to ocean warming, and consequently either migrate further North or locally go extinct.
Publisher: Oxford University Press (OUP)
Date: 20-03-2019
Abstract: Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands (SGs), for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproofing, immunity, and thermoregulation, through the secretion of sebum, a complex mixture of various neutral lipids such as triacylglycerol, free fatty acids, wax esters, cholesterol, and squalene. Remarkably, SGs are absent in a few mammalian lineages, including the iconic Cetacea. We investigated the evolution of the key molecular components responsible for skin sebum production: Dgat2l6, Awat1, Awat2, Elovl3, Mogat3, and Fabp9. We show that all analyzed genes have been rendered nonfunctional in Cetacea species (toothed and baleen whales). Transcriptomic analysis, including a novel skin transcriptome from blue whale, supports gene inactivation. The conserved mutational pattern found in most analyzed genes, indicates that pseudogenization events took place prior to the ersification of modern Cetacea lineages. Genome and skin transcriptome analysis of the common hippopotamus highlighted the convergent loss of a subset of sebum-producing genes, notably Awat1 and Mogat3. Partial loss profiles were also detected in non-Cetacea aquatic mammals, such as the Florida manatee, and in terrestrial mammals displaying specialized skin phenotypes such as the African elephant, white rhinoceros and pig. Our findings reveal a unique landscape of “gene vestiges” in the Cetacea sebum-producing compartment, with limited gene loss observed in other mammalian lineages: suggestive of specific adaptations or specializations of skin lipids.
Publisher: Wiley
Date: 07-07-2021
DOI: 10.1111/MEC.16048
Abstract: The red wolf ( Canis rufus ) of the eastern US was driven to near‐extinction by colonial‐era persecution and habitat conversion, which facilitated coyote ( C . latrans ) range expansion and widespread hybridization with red wolves. The observation of some grey wolf ( C . lupus ) ancestry within red wolves sparked controversy over whether it was historically a subspecies of grey wolf with its predominant “coyote‐like” ancestry obtained from post‐colonial coyote hybridization (2‐species hypothesis) versus a distinct species closely related to the coyote that hybridized with grey wolf (3‐species hypothesis). We analysed mitogenomes sourced from before the 20th century bottleneck and coyote invasion, along with hundreds of modern licons, which led us to reject the 2‐species model and to investigate a broader phylogeographic 3‐species model suggested by the fossil record. Our findings broadly support this model, in which red wolves ranged the width of the American continent prior to arrival of the grey wolf to the mid‐continent 60–80 ka red wolves subsequently disappeared from the mid‐continent, relegated to California and the eastern forests, which ushered in emergence of the coyote in their place (50–30 ka) by the early Holocene (12–10 ka), coyotes had expanded into California, where they admixed with and phenotypically replaced western red wolves in a process analogous to the 20th century coyote invasion of the eastern forests. Findings indicate that the red wolf pre‐dated not only European colonization but human, and possibly coyote, presence in North America. These findings highlight the urgency of expanding conservation efforts for the red wolf.
Publisher: Elsevier BV
Date: 11-2018
Publisher: Cold Spring Harbor Laboratory
Date: 13-12-2018
DOI: 10.1101/493882
Abstract: We present a complete ancient human genome and oral microbiome sequenced from a piece of resinous "chewing gum" recovered from a Stone Age site on the island of Lolland, Denmark, and directly dated to 5,858-5,661 cal. BP (GrM-13305 5,007+/-11). We sequenced the genome to an average depth-of-coverage of 2.3x and find that the in idual who chewed the resin was female and genetically more closely related to western hunter-gatherers from mainland Europe, than hunter-gatherers from central Scandinavia. We use imputed genotypes to predict physical characteristics and find that she had dark skin and hair, and blue eyes. Lastly, we also recovered microbial DNA that is characteristic of an oral microbiome and faunal reads that likely associate with diet. The results highlight the potential for this type of s le material as a new source of ancient human and microbial DNA.
Publisher: Springer Science and Business Media LLC
Date: 08-04-2021
DOI: 10.1038/S41586-021-03473-8
Abstract: A Correction to this paper has been published: 0.1038/s41586-021-03473-8.
Publisher: Elsevier BV
Date: 2021
Publisher: Elsevier BV
Date: 11-2018
Publisher: Cold Spring Harbor Laboratory
Date: 04-11-2022
DOI: 10.1101/2022.11.03.515020
Abstract: Parallel evolution provides among the strongest evidence of the role of natural selection in shaping adaptation to the local environment. Yet, the chronology, mode and tempo of the process of parallel evolution remains broadly debated and discussed in the field of evolutionary biology. In this study, we harness the temporal resolution of paleogenomics to understand the tempo and independence of parallel coastal ecotype adaptation in common bottlenose dolphins ( Tursiops truncatus ). For this, we generated whole genome resequencing data from subfossil dolphins (8,610-5,626 years BP) originating from around the formation time of new coastal habitat and compared them with data from contemporary populations. Genomic data revealed a shift in genetic affinity, with the oldest ancient s le being closer to the pelagic populations, while the younger s les had intermediate ancestry that showed greater affinity with the local contemporary coastal populations. We found coastal-associated genotypes in the genome of our highest coverage ancient s le, SP1060, providing rare evidence of rapid adaptation from standing genetic variation. Lastly, using admixture graph analyses, we found a reticulate evolutionary history between pelagic and coastal populations. Ancestral gene flow from coastal populations was the probable source of standing genetic variation present in the pelagic populations that enabled rapid adaptation to newly emerged coastal habitat. The genetic response to past climatic warming provides an understanding of how bottlenose dolphins will respond to ongoing directional climate change and shifting coastlines.
Publisher: Elsevier BV
Date: 12-2019
Publisher: Public Library of Science (PLoS)
Date: 12-11-2018
Publisher: Public Library of Science (PLoS)
Date: 27-07-2022
DOI: 10.1371/JOURNAL.PONE.0270040
Abstract: Fur is known from contemporary written sources to have been a key commodity in the Viking Age. Nevertheless, the fur trade has been notoriously difficult to study archaeologically as fur rarely survives in the archaeological record. In Denmark, fur finds are rare and fur in clothing has been limited to a few reports and not recorded systematically. We were therefore given access to fur from six Danish high status graves dated to the Viking Age. The fur was analysed by aDNA and palaeoproteomics methods to identify the species of origin in order to explore the Viking Age fur trade. Endogenous aDNA was not recovered, but fur proteins (keratins) were analysed by MALDI-TOF-MS and LC-MS/MS. We show that Viking Age skin clothing were often composites of several species, showing highly developed manufacturing and material knowledge. For ex le, fur was produced from wild animals while leather was made of domesticates. Several ex les of beaver fur were identified, a species which is not native to Denmark, and therefore indicative of trade. We argue that beaver fur was a luxury commodity, limited to the elite and worn as an easily recognisable indicator of social status.
Publisher: Oxford University Press (OUP)
Date: 09-2019
DOI: 10.1093/GIGASCIENCE/GIZ117
Abstract: Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled ing seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their ing capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such erse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of in idual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.
Publisher: eLife Sciences Publications, Ltd
Date: 26-11-2019
DOI: 10.7554/ELIFE.47509
Abstract: The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 in iduals from across the species’ geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
Publisher: The Royal Society
Date: 02-2020
Abstract: Jetsam ambergris, found on beaches worldwide, has always been assumed to originate as a natural product of sperm whales (Physeteroidea). However, only indirect evidence has ever been produced for this, such as the presence of whale prey remains in ambergris. Here, we extracted and analysed DNA sequences from jetsam ambergris from beaches in New Zealand and Sri Lanka, and sequences from ambergris of a sperm whale beached in The Netherlands. The lipid-rich composition of ambergris facilitated high preservation-quality of endogenous DNA, upon which we performed shotgun Illumina sequencing. Alignment of mitochondrial and nuclear genome sequences with open-access reference data for multiple whale species confirms that all three jetsam s les derived originally from sperm whales ( Physeter macrocephalus ). Shotgun sequencing here also provides implications for metagenomic insights into ambergris-preserved DNA. These results demonstrate significant implications for elucidating the origins of jetsam ambergris as a prized natural product, and also for the understanding of sperm whale metabolism and diet, and the ecological mechanisms underlying these coproliths.
Publisher: Oxford University Press (OUP)
Date: 13-07-2017
Publisher: Elsevier BV
Date: 2015
Location: Australia
No related grants have been discovered for Mikkel Holger Strander Sinding.