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Sun Y, Lorenzen ED, Westbury MV. Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation. BMC Genomics 2024; 25:826. [PMID: 39278943 PMCID: PMC11403954 DOI: 10.1186/s12864-024-10617-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 07/12/2024] [Indexed: 09/18/2024] Open
Abstract
The polar bear (Ursus maritimus) occupies a relatively narrow ecological niche, with many traits 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 twelve key genes that are highly differentiated between polar and brown bears, show signatures of selection in the polar bear lineage, and are associated with polar bear adaptation to the Arctic environment. Further research suggested fixed derived 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 based on a larger and geographically more representative dataset of 119 polar bears and 135 brown bears, and assess the timing of derived allele fixation in polar bears by incorporating the genomes of two Late Pleistocene individuals (aged 130-100,000 years old and 100-70,000 years old). In contrast with previous results, we found no evidence of derived alleles fixed in present-day polar bears within the key genes arising from de novo mutation. Most derived alleles fixed in present-day polar bears were also fixed in the Late Pleistocene polar bears, suggesting selection occurred prior to 70,000 years ago. However, some derived alleles fixed in present-day polar bears were not fixed in the two Late Pleistocene polar bears, including at sites within APOB, LYST, and TTN. These three genes are associated with cardiovascular function, metabolism, and pigmentation, suggesting selection may have acted on different loci at different times.
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Affiliation(s)
- Yulin Sun
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- School of The Environment, The University of Queensland, Brisbane, QLD, Australia
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Cueva DF, Zug R, Pozo MJ, Molina S, Cisneros R, Bustamante MR, Torres MDL. Evidence of population genetic structure in Ecuadorian Andean bears. Sci Rep 2024; 14:2834. [PMID: 38310153 PMCID: PMC10838292 DOI: 10.1038/s41598-024-53003-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024] Open
Abstract
Wildlife conservation in Andean countries is a global priority because of the high levels of biodiversity and endemism. Historically, these countries have had limited resources to monitor wildlife (e.g., through genetic tools) and establish conservation programs. Focusing on the study and emblematic use of a few charismatic species has been a strategic approach to direct efforts for conservation and development planning. Consequently, the Andean bear is a flagship and umbrella species for highly biodiverse Andean countries like Ecuador. The few studies exploring the population genetics of this species have concluded that it has low genetic diversity and few units for conservation as populations appear to be well connected. However, these results might be attributed to ascertainment bias as studies have been performed with heterologous molecular markers. Here, using both mtDNA sequences and species-specific microsatellite markers, we show that Andean bears in Ecuador have population structure. Additionally, we found through the study of three Ecuadorian populations that the species might have a higher genetic diversity than we previously thought. These results could support the revision of research priorities, conservation, and planning strategies to improve connectivity for this species which occurs in crucial biodiversity hotspots.
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Affiliation(s)
- Dario F Cueva
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador
| | - Rebecca Zug
- Laboratorio de Carnívoros, Universidad San Francisco de Quito USFQ, Diego de Robles y Vía Interoceanica s/n, Quito, 170157, Ecuador
| | - María José Pozo
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador
| | - Santiago Molina
- Laboratorio de Carnívoros, Universidad San Francisco de Quito USFQ, Diego de Robles y Vía Interoceanica s/n, Quito, 170157, Ecuador
- Fundación Zoológica del Ecuador, Pircapamaba s/n y Rumichupa, Guayllabamba, Quito, Ecuador
| | - Rodrigo Cisneros
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto, C/París s/n., 1101608, Loja, Ecuador
| | - Martín R Bustamante
- Fundación Zoológica del Ecuador, Pircapamaba s/n y Rumichupa, Guayllabamba, Quito, Ecuador
| | - María de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador.
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Westbury MV, Brown SC, Lorenzen J, O’Neill S, Scott MB, McCuaig J, Cheung C, Armstrong E, Valdes PJ, Samaniego Castruita JA, Cabrera AA, Blom SK, Dietz R, Sonne C, Louis M, Galatius A, Fordham DA, Ribeiro S, Szpak P, Lorenzen ED. Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator. SCIENCE ADVANCES 2023; 9:eadf3326. [PMID: 37939193 PMCID: PMC10631739 DOI: 10.1126/sciadv.adf3326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/09/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
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 modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide 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.
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Affiliation(s)
- Michael V. Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen DK-1350, Denmark
| | - Stuart C. Brown
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen DK-1350, Denmark
- Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Department for Environment and Water, Adelaide, South Australia, Australia
| | - Julie Lorenzen
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen DK-1350, Denmark
| | - Stuart O’Neill
- Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Michael B. Scott
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, Ontario K9L0G2, Canada
| | - Julia McCuaig
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, Ontario K9L0G2, Canada
| | - Christina Cheung
- Department of Anthropology, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Edward Armstrong
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Paul J. Valdes
- School of Geographical Sciences, University of Bristol, Bristol, UK
| | | | - Andrea A. Cabrera
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen DK-1350, Denmark
| | - Stine Keibel Blom
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen DK-1350, Denmark
| | - Rune Dietz
- Arctic Research Centre (ARC), Department of Ecoscience, Aarhus University, Frederiksborgvej 399, PO Box 358, Roskilde DK-4000, Denmark
- Section for Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, Roskilde DK-4000, Denmark
| | - Christian Sonne
- Arctic Research Centre (ARC), Department of Ecoscience, Aarhus University, Frederiksborgvej 399, PO Box 358, Roskilde DK-4000, Denmark
- Section for Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, Roskilde DK-4000, Denmark
| | - Marie Louis
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen DK-1350, Denmark
- Greenland Institute of Natural Resources, Kivioq 2, PO Box 570, Nuuk 3900, Denmark
| | - Anders Galatius
- Section for Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, Roskilde DK-4000, Denmark
| | - Damien A. Fordham
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen DK-1350, Denmark
- Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Sofia Ribeiro
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen DK-1350, Denmark
- Glaciology and Climate Department, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, Copenhagen DK-1350, Denmark
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, Ontario K9L0G2, Canada
| | - Eline D. Lorenzen
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen DK-1350, Denmark
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Whole-Genome Sequencing of Six Neglected Arboviruses Circulating in Africa Using Sequence-Independent Single Primer Amplification (SISPA) and MinION Nanopore Technologies. Pathogens 2022; 11:pathogens11121502. [PMID: 36558837 PMCID: PMC9781818 DOI: 10.3390/pathogens11121502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
On the African continent, a large number of arthropod-borne viruses (arboviruses) with zoonotic potential have been described, and yet little is known of most of these pathogens, including their actual distribution or genetic diversity. In this study, we evaluated as a proof-of-concept the effectiveness of the nonspecific sequencing technique sequence-independent single primer amplification (SISPA) on third-generation sequencing techniques (MinION sequencing, Oxford Nanopore Technologies, Oxford, UK) by comparing the sequencing results from six different samples of arboviruses known to be circulating in Africa (Crimean-Congo hemorrhagic fever virus (CCHFV), Rift Valley fever virus (RVFV), Dugbe virus (DUGV), Nairobi sheep disease virus (NSDV), Middleburg virus (MIDV) and Wesselsbron virus (WSLV)). All sequenced samples were derived either from previous field studies or animal infection trials. Using this approach, we were able to generate complete genomes for all six viruses without the need for virus-specific whole-genome PCRs. Higher Cq values in diagnostic RT-qPCRs and the origin of the samples (from cell culture or animal origin) along with their quality were found to be factors affecting the success of the sequencing run. The results of this study may stimulate the use of metagenomic sequencing approaches, contributing to a better understanding of the genetic diversity of neglected arboviruses.
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Willey C, Korstanje R. Sequencing and assembling bear genomes: the bare necessities. Front Zool 2022; 19:30. [PMID: 36451195 PMCID: PMC9710173 DOI: 10.1186/s12983-022-00475-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Unique genetic adaptations are present in bears of every species across the world. From (nearly) shutting down important organs during hibernation to preventing harm from lifestyles that could easily cause metabolic diseases in humans, bears may hold the answer to various human ailments. However, only a few of these unique traits are currently being investigated at the molecular level, partly because of the lack of necessary tools. One of these tools is well-annotated genome assemblies from the different, extant bear species. These reference genomes are needed to allow us to identify differences in genetic variants, isoforms, gene expression, and genomic features such as transposons and identify those that are associated with biomedical-relevant traits. In this review we assess the current state of the genome assemblies of the eight different bear species, discuss current gaps, and the future benefits these reference genomes may have in informing human biomedical applications, while at the same time improving bear conservation efforts.
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Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z, Moon KL, Kapp JD, Vinner L, Vardanyan Z, Ardelean CF, Arroyo-Cabrales J, Cahill JA, Heintzman PD, Zazula G, MacPhee RDE, Shapiro B, Durbin R, Willerslev E. Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Curr Biol 2021; 31:2728-2736.e8. [PMID: 33878301 DOI: 10.1016/j.cub.2021.04.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.
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Affiliation(s)
- Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily E Puckett
- Department of Biological Sciences, University of Memphis, 3770 Walker Avenue, Ellington Hall, Memphis, TN 38152, USA
| | - Zhenquan Gu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Beijing 100101, China
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zaruhi Vardanyan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ciprian F Ardelean
- Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Campus II, Col. Progreso, 98066 Zacatecas, Mexico; The Archaeology Centre, Department of Anthropology, University of Toronto, 19 Ursula Franklin Street, Toronto, ON M5S 2S2, Canada
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoologia, Subdireccion de Laboratorios y Apoyo Academico, Instituto Nacional de Antropologia e Historia, Moneda 16, Col. Centro, 06060 Mexico, CdMx, Mexico
| | - James A Cahill
- Laboratory of the Neurogenetics of Language, Rockefeller University, New York, NY, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, PO Box 6050, Langnes, N-9037 Tromsø, Norway
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism & Culture, Government of Yukon, Whitehorse, YT Y1A 2C6, Canada
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 12484, USA; American Museum of Natural History, New York, NY, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany.
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