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Kotli P, Morgenstern D, Bocquentin F, Khalaily H, Horwitz LK, Boaretto E. A label-free quantification method for assessing sex from modern and ancient bovine tooth enamel. Sci Rep 2024; 14:18195. [PMID: 39107380 PMCID: PMC11303769 DOI: 10.1038/s41598-024-68603-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Identification of the sex of modern, fossil and archaeological animal remains offers many insights into their demography, mortality profiles and domestication pathways. However, due to many-factors, sex determination of osteological remains is often problematic. To overcome this, we have developed an innovative protocol to determine an animal's sex from tooth enamel, by applying label-free quantification (LFQ) of two unique AmelY peptides 'LRYPYP' (AmelY;[M+2]2 + 404.7212 m/z) and 'LRYPYPSY' (AmelY;[M+2]2 + 529.7689 m/z) that are only present in the enamel of males. We applied this method to eight modern cattle (Bos taurus) of known sex, and correctly assigned them to sex. We then applied the same protocol to twelve archaeological Bos teeth from the Neolithic site of Beisamoun, Israel (8-th-7-th millennium BC) and determined the sex of the archaeological samples. Since teeth are usually better preserved than bones, this innovative protocol has potential to facilitate sex determination in ancient and modern bovine remains that currently cannot be sexed.
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Affiliation(s)
- Paula Kotli
- Scientific Archaeology and D-REAMS Radiocarbon Dating Laboratory, Weizmann Institute of Science, 760001, Rehovot, Israel.
| | - David Morgenstern
- Nancy and Stephen Grand Israel National Center for Personalized Medicine G-INCPM, Weizmann Institute of Science, 760001, Rehovot, Israel
| | - Fanny Bocquentin
- CNRS, UMR 8068 TEMPS, MSH Mondes-Bâtiment Ginouvès, 21 allée de l'université, 92023, Nanterre Cedex, France
| | | | - Liora Kolska Horwitz
- National Natural History Collections, E. Safra-Givat Ram Campus, The Hebrew University of Jerusalem, 96194, Jerusalem, Israel
| | - Elisabetta Boaretto
- Scientific Archaeology and D-REAMS Radiocarbon Dating Laboratory, Weizmann Institute of Science, 760001, Rehovot, Israel.
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2
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Caduff M, Eckel R, Leuenberger C, Wegmann D. Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data. Mol Ecol Resour 2024; 24:e13913. [PMID: 38173222 DOI: 10.1111/1755-0998.13913] [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: 09/16/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non-model organisms.
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Affiliation(s)
- Madleina Caduff
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Raphael Eckel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Christoph Leuenberger
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
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3
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MacRoberts RA, Liberato M, Roca-Rada X, Valente MJ, Relvado C, Matos Fernandes T, Barrocas Dias C, Llamas B, Vasconcelos Vilar H, Schöne BR, Ribeiro S, Santos JF, Teixeira JC, Maurer AF. Shrouded in history: Unveiling the ways of life of an early Muslim population in Santarém, Portugal (8th- 10th century AD). PLoS One 2024; 19:e0299958. [PMID: 38446809 PMCID: PMC10917335 DOI: 10.1371/journal.pone.0299958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
In around 716 AD, the city of Santarém, Portugal, was conquered by the Berber and Arab armies that swept the Iberian Peninsula and went on to rule the region until the 12th century. Archaeological excavations in 2007/08 discovered an Islamic necropolis (Avenida 5 de Outubro #2-8) that appears to contain the remains of an early Muslim population in Santarém (8th- 10th century). In this study, skeletal material from 58 adult individuals was analysed for stable carbon (δ13Ccol; δ13Cap), nitrogen (δ15N) and sulphur (δ34S) isotope ratios in bones, and stable oxygen (δ18O), carbon (δ13Cen) and radiogenic strontium (87Sr/86Sr) isotopes in tooth enamel. The results of this study revealed a dietary pattern of predominantly C3-plant and domestic C3-fed herbivore consumption during adulthood (δ13Ccol and δ15N, respectively) but a higher proportion of C4-plant input during childhood (δ13Cen) for some individuals-interpreted as possible childhood consumption of millet porridge, a common practice in North Africa-in those with unorthodox burial types (Groups 1 and 2) that was not practiced in the individuals with canonical burials (Group 3). In this first mobility study of a medieval Muslim population in Portugal, δ18ODW values revealed greater heterogeneity in Groups 1 and 2, consistent with diverse origins, some in more humid regions than Santarém when compared to regional precipitation δ18O data, contrasting the more homogenous Group 3, consistent with the local precipitation δ18O range. Ancient DNA analysis conducted on three individuals revealed maternal (mtDNA) and paternal (Y-chromosome) lineages compatible with a North African origin for (at least) some of the individuals. Additionally, mobility of females in this population was higher than males, potentially resulting from a patrilocal social system, practiced in Berber and Arab communities. These results serve to offer a more detailed insight into the ancestry and cultural practices of early Muslim populations in Iberia.
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Affiliation(s)
| | - Marco Liberato
- Centro de Estudos de Arqueologia, Artes e Ciências do Património (CEAACP), Universidade de Coimbra, Coimbra, Portugal
| | - Xavier Roca-Rada
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- Faculdade de Letras, University of Coimbra, Coimbra, Portugal
| | - Maria João Valente
- Faculdade de Ciências Humanas e Sociais (FCHS), Universidade do Algarve, Faro, Portugal
| | - Claudia Relvado
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), University of Algarve, Faro, Portugal
| | - Teresa Matos Fernandes
- School of Technology Sciences, Department of Biology, University of Évora, Évora, Portugal
- Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal
| | - Cristina Barrocas Dias
- HERCULES Laboratory and IN2PAST, University of Évora, Évora, Portugal
- School of Technology Sciences, Department of Chemistry and Biochemistry, University of Évora, Évora, Portugal
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | | | - Bernd R. Schöne
- Institute of Geosciences, University of Mainz, Mainz, Germany
| | - Sara Ribeiro
- Geobiotec, Department of Geosciences, University of Aveiro, Aveiro, Portugal
| | | | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, Australia
- Centre for Interdisciplinary Studies (CEIS20), University of Coimbra, Coimbra, Portugal
- Evolution of Cultural Diversity Initiative, The Australian National University, Canberra, Australia
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4
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Delezene LK, Scott JE, Irish JD, Villaseñor A, Skinner MM, Hawks J, Berger LR. Sex-biased sampling may influence Homo naledi tooth size variation. J Hum Evol 2024; 187:103490. [PMID: 38266614 DOI: 10.1016/j.jhevol.2023.103490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
A frequent source of debate in paleoanthropology concerns the taxonomic unity of fossil assemblages, with many hominin samples exhibiting elevated levels of variation that can be interpreted as indicating the presence of multiple species. By contrast, the large assemblage of hominin fossils from the Rising Star cave system, assigned to Homo naledi, exhibits a remarkably low degree of variation for most skeletal elements. Many factors can contribute to low sample variation, including genetic drift, strong natural selection, biased sex ratios, and sampling of closely related individuals. In this study, we tested for potential sex-biased sampling in the Rising Star dental sample. We compared coefficients of variation for the H. naledi teeth to those for eight extant hominoid samples. We used a resampling procedure that generated samples from the extant taxa that matched the sample size of the fossil sample for each possible Rising Star dental sex ratio. We found that variation at four H. naledi tooth positions-I2, M1, P4, M1-is so low that the possibility that one sex is represented by few or no individuals in the sample cannot be excluded. Additional evidence is needed to corroborate this inference, such as ancient DNA or enamel proteome data, and our study design does not address other potential factors that would account for low sample variation. Nevertheless, our results highlight the importance of considering the taphonomic history of a hominin assemblage and suggest that sex-biased sampling is a plausible explanation for the low level of phenotypic variation found in some aspects of the current H. naledi assemblage.
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Affiliation(s)
- Lucas K Delezene
- Department of Anthropology, University of Arkansas, Fayetteville, AR, 72701, USA; Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Private Bag 3, WITS, 2050, South Africa.
| | - Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Joel D Irish
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Private Bag 3, WITS, 2050, South Africa; School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Amelia Villaseñor
- Department of Anthropology, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Matthew M Skinner
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Private Bag 3, WITS, 2050, South Africa; Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - John Hawks
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Private Bag 3, WITS, 2050, South Africa; Department of Anthropology, University of Wisconsin-Madison. Madison, WI, 53706, USA
| | - Lee R Berger
- Centre for the Exploration of the Deep Human Journey, University of the Witwatersrand, Private Bag 3, WITS, 2050, South Africa; National Geographic Society, 1145 17th Street NW, Washington DC, 20036, USA
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5
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Chen N, Zhang Z, Hou J, Chen J, Gao X, Tang L, Wangdue S, Zhang X, Sinding MHS, Liu X, Han J, Lü H, Lei C, Marshall F, Liu X. Evidence for early domestic yak, taurine cattle, and their hybrids on the Tibetan Plateau. SCIENCE ADVANCES 2023; 9:eadi6857. [PMID: 38091398 PMCID: PMC10848728 DOI: 10.1126/sciadv.adi6857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023]
Abstract
Domestic yak, cattle, and their hybrids are fundamental to herder survival at high altitudes on the Tibetan Plateau. However, little is known about their history. Bos remains are uncommon in this region, and ancient domestic yak have not been securely identified. To identify Bos taxa and investigate their initial management, we conducted zooarchaeological analyses of 193 Bos specimens and sequenced five nuclear genomes from recently excavated assemblages at Bangga. Morphological data indicated that more cattle than yak were present. Ancient mitochondrial DNA and nuclear genome sequences identified taurine cattle and provided evidence for domestic yak and yak-cattle hybridization ~2500 years ago. Reliance on diverse Bos species and their hybrid has increased cattle adaptation and herder resilience to plateau conditions. Ancient cattle and yak at Bangga were closely related to contemporary livestock, indicating early herder legacies and the continuity of cattle and yak husbandry on the Tibetan Plateau.
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Affiliation(s)
- Ningbo Chen
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Zhengwei Zhang
- Center for Archaeological Science, Sichuan University, Chengdu 610065, P. R. China
| | - Jiawen Hou
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Jialei Chen
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Xuan Gao
- Center for Archaeological Science, Sichuan University, Chengdu 610065, P. R. China
| | - Li Tang
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena 07745, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, Jena 07745, Germany
| | - Shargan Wangdue
- Institute for Conservation and Research of Cultural Relics of Tibet Autonomous Region, Lhasa 850000, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming 650201, P. R. China
| | - Mikkel-Holger S. Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen DK-1350, Denmark
| | - Xuexue Liu
- National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse 31000, France
| | - Jianlin Han
- Yazhouwan National Laboratory, Sanya 572024, P. R. China
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, P. R. China
| | - Hongliang Lü
- Center for Archaeological Science, Sichuan University, Chengdu 610065, P. R. China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P. R. China
| | - Fiona Marshall
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xinyi Liu
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
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6
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Jones ME, Sheard C. The macroevolutionary dynamics of mammalian sexual size dimorphism. Proc Biol Sci 2023; 290:20231211. [PMID: 37964522 PMCID: PMC10646455 DOI: 10.1098/rspb.2023.1211] [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: 05/31/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
Sexual size dimorphism (SSD) is a common phenomenon across the animal kingdom. Mammals are unusual in primarily displaying male-biased SSD, where males of a species are typically larger than females. The driving factors behind the evolution of this SSD have been much debated, with popular hypotheses invoking the influence of mating system and social organization via sexual selection, dietary niche divergence and broad-scale correlations with body size (Rensch's rule). Here, we investigate the macroevolutionary origins and maintenance of SSD among mammals, using phylogenetic general mixed linear models and a comprehensive global dataset to evaluate correlations of diet, body mass, seasonality, social organization and mating system with SSD type. We find that SSD as a whole is lost at a greater rate than it is gained, with female-biased SSD being particularly unstable. Non-monogamous mating systems, vertebrate prey consumption and temperature seasonality correlate with male-biased SSD, while polyandry correlates with female-biased SSD, and both types of SSD are positively correlated with body mass. This is in partial contrast to the predictions of Rensch's rule, which predicts that female-biased SSD would correlate negatively with body size. Taken together, our results highlight the importance of considering multiple ecological and social drivers when evaluating the macroevolutionary trajectory of sex differences in body size.
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Affiliation(s)
- Megan E. Jones
- Department of Earth and Environmental Sciences, University of Manchester, 176 Oxford Road, Manchester M13 9QQ, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Catherine Sheard
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biological Sciences, University of Aberdeen, Tillydrone Ave, Aberdeen, AB24 2TZ, UK
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7
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Wereszczuk A, Fedotova A, Marciszak A, Popiołek M, Zharova A, Zalewski A. Various responses of pine marten morphology and demography to temporal climate changes and primary productivity. J Zool (1987) 2022. [DOI: 10.1111/jzo.13022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- A. Wereszczuk
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - A. Fedotova
- Universitetskaya naberezhnaya 5/2 Saint Petersburg Russia
| | - A. Marciszak
- Department of Palaeozoology Institute of Environmental Biology University of Wrocław Wrocław Poland
| | - M. Popiołek
- Department of Parasitology University of Wrocław Wrocław Poland
| | - A. Zharova
- Clinical Hospital named after St. Luke the Blessed Surgeon Saint Petersburg Russia
| | - A. Zalewski
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
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8
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Cabrera AA, Rey-Iglesia A, Louis M, Skovrind M, Westbury MV, Lorenzen ED. How low can you go? Introducing SeXY: sex identification from low-quantity sequencing data despite lacking assembled sex chromosomes. Ecol Evol 2022; 12:e9185. [PMID: 36035270 PMCID: PMC9405501 DOI: 10.1002/ece3.9185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/19/2022] [Indexed: 12/01/2022] Open
Abstract
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 utilize 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 1000 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 1000 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 1000 mapped reads in many cases.
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Affiliation(s)
| | | | - Marie Louis
- Globe Institute University of Copenhagen Copenhagen K Denmark.,Greenland Institute of Natural Resources Nuuk Greenland
| | - Mikkel Skovrind
- Globe Institute University of Copenhagen Copenhagen K Denmark
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9
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Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MHS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs. Nature 2022; 607:313-320. [PMID: 35768506 PMCID: PMC9279150 DOI: 10.1038/s41586-022-04824-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/28/2022] [Indexed: 01/01/2023]
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) lived1–8. 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. DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Molly Cassatt-Johnstone
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ophélie Lebrasseur
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Morgane Ollivier
- University of Rennes, CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution)-UMR 6553, Rennes, France
| | - Leo Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.,Genetics Institute, University College London, London, UK
| | | | - Michael V Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Joscha Gretzinger
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Susanne C Münzel
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pooja Swali
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden.,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Texas A&M University, College Station, TX, USA.,Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | | | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris Baumann
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | | | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Ruth F Carden
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | | | | | | | - Pam Groves
- University of Alaska, Fairbanks, AK, USA
| | - Stefan T Hertwig
- Naturhistorisches Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | | | - Richard P Jennings
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Irina V Kirillova
- Ice Age Museum, Shidlovskiy National Alliance 'Ice Age', Moscow, Russian Federation
| | - Islam Kurmaniyazov
- Department of Archaeology, Ethnology and Museology, Al-Farabi Kazakh State University, Almaty, Kazakhstan
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | | | | | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Cóilín O'Drisceoil
- National Monuments Service, Department of Housing, Local Government and Heritage, Dublin, Ireland
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Elena Y Pavlova
- Arctic & Antarctic Research Institute, St Petersburg, Russian Federation
| | - Angela R Perri
- PaleoWest, Henderson, NV, USA.,Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Małgorzata Pilot
- Museum & Institute of Zoology, Polish Academy of Sciences, Gdańsk, Poland
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | | | | | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - Victor F Zaibert
- Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Grant Zazula
- Yukon Palaeontology Program, Whitehorse, Yukon Territories, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | | | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Stockholm University, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - 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
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
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10
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Scarsbrook L, Verry AJF, Walton K, Hitchmough RA, Rawlence NJ. Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: phylogeography of the New Zealand gecko genus
Hoplodactylus. Mol Ecol 2022; 32:2964-2984. [DOI: 10.1111/mec.16434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/04/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Lachie Scarsbrook
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Alexander J. F. Verry
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | - Kerry Walton
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
| | | | - Nicolas J. Rawlence
- Otago Paleogenetics Laboratory Department of Zoology University of Otago Dunedin New Zealand
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11
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Meineke EK, Daru BH. Bias assessments to expand research harnessing biological collections. Trends Ecol Evol 2021; 36:1071-1082. [PMID: 34489117 DOI: 10.1016/j.tree.2021.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/22/2022]
Abstract
Biological collections are arguably the most important resources for investigations into the impacts of human activities on biodiversity. However, the apparent opportunities presented by museum-derived datasets have not resulted in consistent or widespread use of specimens in ecology outside phenological research and species distribution modeling. We attribute this gap between opportunity and application to biases introduced by collectors, curators, and preservation practices and an imperfect understanding of these biases and how to mitigate them. To facilitate broader use of specimen-based data, we characterize collection biases across key axes and explore interactions among them. We then present a framework for determining the bias assessments needed when extracting data from biological collections. We show that bias assessments required by particular ecological studies will depend on the response variables being measured and the predictor axes of interest. We argue that quantification of biases in specimen-derived datasets is needed to facilitate the widespread application of these data.
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Affiliation(s)
- Emily K Meineke
- Department of Entomology and Nematology, University of California, Davis 95616, CA, USA.
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA.
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12
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Onley IR, Austin JJ, Mitchell KJ, Moseby KE. Understanding dispersal patterns can inform future translocation strategies: A case study of the threatened greater stick‐nest rat (
Leporillus conditor
). AUSTRAL ECOL 2021. [DOI: 10.1111/aec.13100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Isabelle R. Onley
- School of Biological Sciences Australian Centre for Ancient DNA (ACAD) University of Adelaide Adelaide South Australia 5005Australia
| | - Jeremy J. Austin
- School of Biological Sciences Australian Centre for Ancient DNA (ACAD) University of Adelaide Adelaide South Australia 5005Australia
| | - Kieren J. Mitchell
- School of Biological Sciences Australian Centre for Ancient DNA (ACAD) University of Adelaide Adelaide South Australia 5005Australia
- School of Biological Sciences ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH) University of Adelaide Adelaide South AustraliaAustralia
| | - Katherine E. Moseby
- Centre for Ecosystem Sciences, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
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13
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The ultimate database to (re)set the evolutionary history of primate genital bones. Sci Rep 2021; 11:11245. [PMID: 34045627 PMCID: PMC8160331 DOI: 10.1038/s41598-021-90787-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/17/2021] [Indexed: 02/04/2023] Open
Abstract
Scientific literature concerning genital bones in primates consists of both ancient works (dating back to the nineteenth century) and more recent revisions/meta-analyses, which, however, are not always so detailed or exhaustive. Based on a thorough analysis, several conflicting data, inaccurate references, and questionable claims have emerged. We generated a binary matrix of genital bone occurrence data, considering only data at the species level, based on (1) a rigorous literature search protocol, (2) raw data (collected exclusively from primary literature), (3) an updated taxonomy (often tracing back to the species taxonomic history) and (4) new occurrence data from scanned genitals of fresh and museum specimens (using micro-computed tomography-micro-CT). Thanks to this methodological approach, we almost doubled available occurrence data so far, avoiding any arbitrary extension of generic data to conspecific species. This practice, in fact, has been recently responsible for an overestimation of the occurrence data, definitively flattening the interspecific variability. We performed the ancestral state reconstruction analysis of genital bone occurrence and results were mapped onto the most updated phylogeny of primates. As for baculum, we definitively demonstrated its simplesiomorphy for the entire order. As for baubellum, we interpreted all scattered absences as losses, actually proposing (for the first time) a simplesiomorphic state for the clitoral bone as well. The occurrence data obtained, while indirectly confirming the baculum/baubellum homology (i.e., for each baubellum a baculum was invariably present), could also directly demonstrate an intra-specific variability affecting ossa genitalia occurrence. With our results, we established a radically improved and updated database about the occurrence of genital bones in primates, available for further comparative analyses.
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14
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Duffy MA, García-Robledo C, Gordon SP, Grant NA, Green DA, Kamath A, Penczykowski RM, Rebolleda-Gómez M, Wale N, Zaman L. Model Systems in Ecology, Evolution, and Behavior: A Call for Diversity in Our Model Systems and Discipline. Am Nat 2021; 198:53-68. [PMID: 34143717 DOI: 10.1086/714574] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractEcologists and evolutionary biologists are fascinated by life's variation but also seek to understand phenomena and mechanisms that apply broadly across taxa. Model systems can help us extract generalities from amid all the wondrous diversity, but only if we choose and develop them carefully, use them wisely, and have a range of model systems from which to choose. In this introduction to the Special Feature on Model Systems in Ecology, Evolution, and Behavior (EEB), we begin by grappling with the question, What is a model system? We then explore where our model systems come from, in terms of the skills and other attributes required to develop them and the historical biases that influence traditional model systems in EEB. We emphasize the importance of communities of scientists in the success of model systems-narrow scientific communities can restrict the model organisms themselves. We also consider how our discipline was built around one type of "model scientist"-a history still reflected in the field. This lack of diversity in EEB is unjust and also narrows the field's perspective, including by restricting the questions asked and talents used to answer them. Increasing diversity, equity, and inclusion will require acting at many levels, including structural changes. Diversity in EEB, in both model systems and the scientists who use them, strengthens our discipline.
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15
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Bradshaw CJ, Johnson CN, Llewelyn J, Weisbecker V, Strona G, Saltré F. Relative demographic susceptibility does not explain the extinction chronology of Sahul's megafauna. eLife 2021; 10:63870. [PMID: 33783356 PMCID: PMC8043753 DOI: 10.7554/elife.63870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/29/2021] [Indexed: 11/17/2022] Open
Abstract
The causes of Sahul’s megafauna extinctions remain uncertain, although several interacting factors were likely responsible. To examine the relative support for hypotheses regarding plausible ecological mechanisms underlying these extinctions, we constructed the first stochastic, age-structured models for 13 extinct megafauna species from five functional/taxonomic groups, as well as 8 extant species within these groups for comparison. Perturbing specific demographic rates individually, we tested which species were more demographically susceptible to extinction, and then compared these relative sensitivities to the fossil-derived extinction chronology. Our models show that the macropodiformes were the least demographically susceptible to extinction, followed by carnivores, monotremes, vombatiform herbivores, and large birds. Five of the eight extant species were as or more susceptible than the extinct species. There was no clear relationship between extinction susceptibility and the extinction chronology for any perturbation scenario, while body mass and generation length explained much of the variation in relative risk. Our results reveal that the actual mechanisms leading to the observed extinction chronology were unlikely related to variation in demographic susceptibility per se, but were possibly driven instead by finer-scale variation in climate change and/or human prey choice and relative hunting success.
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Affiliation(s)
- Corey Ja Bradshaw
- Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Tarndanya (Adelaide), Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
| | - Christopher N Johnson
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia.,Dynamics of Eco-Evolutionary Pattern, University of Tasmania, Hobart, Australia
| | - John Llewelyn
- Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Tarndanya (Adelaide), Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
| | - Vera Weisbecker
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia.,College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Giovanni Strona
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Frédérik Saltré
- Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Tarndanya (Adelaide), Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
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16
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Sex assignment in a non-model organism in the absence of field records using Diversity Arrays Technology (DArT) data. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01203-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Davidson R, Fehren-Schmitz L, Llamas B. A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations. Genes (Basel) 2021; 12:215. [PMID: 33540755 PMCID: PMC7913103 DOI: 10.3390/genes12020215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 01/10/2023] Open
Abstract
The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.
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Affiliation(s)
- Roberta Davidson
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics (NCIG), Australian National University, Canberra, ACT 0200, Australia
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18
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Mitchell KJ, Rawlence NJ. Examining Natural History through the Lens of Palaeogenomics. Trends Ecol Evol 2021; 36:258-267. [PMID: 33455740 DOI: 10.1016/j.tree.2020.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.
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Affiliation(s)
- Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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19
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Bergström A, Frantz L, Schmidt R, Ersmark E, Lebrasseur O, Girdland-Flink L, Lin AT, Storå J, Sjögren KG, Anthony D, Antipina E, Amiri S, Bar-Oz G, Bazaliiskii VI, Bulatović J, Brown D, Carmagnini A, Davy T, Fedorov S, Fiore I, Fulton D, Germonpré M, Haile J, Irving-Pease EK, Jamieson A, Janssens L, Kirillova I, Horwitz LK, Kuzmanovic-Cvetković J, Kuzmin Y, Losey RJ, Dizdar DL, Mashkour M, Novak M, Onar V, Orton D, Pasarić M, Radivojević M, Rajković D, Roberts B, Ryan H, Sablin M, Shidlovskiy F, Stojanović I, Tagliacozzo A, Trantalidou K, Ullén I, Villaluenga A, Wapnish P, Dobney K, Götherström A, Linderholm A, Dalén L, Pinhasi R, Larson G, Skoglund P. Origins and genetic legacy of prehistoric dogs. Science 2020; 370:557-564. [PMID: 33122379 PMCID: PMC7116352 DOI: 10.1126/science.aba9572] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022]
Abstract
Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Ryan Schmidt
- School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland
- CIBIO-InBIO, University of Porto, Campus de Vairão, Portugal
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 18C, Stockholm, Sweden
| | - Ophelie Lebrasseur
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Linus Girdland-Flink
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
- Liverpool John Moores University, Liverpool, UK
| | - Audrey T Lin
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - David Anthony
- Hartwick College, Oneonta, NY, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ekaterina Antipina
- Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Sarieh Amiri
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | | | | | | | | | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Tom Davy
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | - Ivana Fiore
- Bioarchaeology Service, Museo delle Civiltà, Rome, Italy
- Environmental and Evolutionary Biology Doctoral Program, Sapienza University of Rome, Rome, Italy
| | | | | | - James Haile
- University of Copenhagen, Copenhagen, Denmark
| | - Evan K Irving-Pease
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Lundbeck GeoGenetics Centre, The Globe Institute, Copenhagen, Denmark
| | - Alexandra Jamieson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | | | | | | | | | - Yaroslav Kuzmin
- Sobolev Institute of Geology and Mineralogy of the Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
- Tomsk State University, Tomsk, Russian Federation
| | | | | | - Marjan Mashkour
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Paris, France
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Vedat Onar
- Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | | | - Maja Pasarić
- Institute of Ethnology and Folklore Research, Zagreb, Croatia
| | | | | | | | - Hannah Ryan
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | | | | | | | - Katerina Trantalidou
- Hellenic Ministry of Culture & Sports, Athens, Greece
- University of Thessaly, Argonauton & Philellinon, Volos, Greece
| | - Inga Ullén
- National Historical Museums, Stockholm, Sweden
| | - Aritza Villaluenga
- Consolidated Research Group on Prehistory (IT-1223-19), University of the Basque Country (UPV-EHU), Vitoria-Gasteiz, Spain
| | - Paula Wapnish
- Pennsylvania State University, University Park, PA, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
- Department of Archaeology, University of Aberdeen, Aberdeen, UK
- Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada
- School of Philosophical and Historical Inquiry, Faculty of Arts and Social Sciences, University of Sydney, Sydney, NSW, Australia
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 18C, Stockholm, Sweden
- Stockholm University, Stockholm, Sweden
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 18C, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
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20
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Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass. Commun Biol 2020; 3:84. [PMID: 32081985 PMCID: PMC7035339 DOI: 10.1038/s42003-020-0806-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/31/2020] [Indexed: 11/18/2022] Open
Abstract
Ancient remains found in permafrost represent a rare opportunity to study past ecosystems. Here, we present an exceptionally well-preserved ancient bird carcass found in the Siberian permafrost, along with a radiocarbon date and a reconstruction of its complete mitochondrial genome. The carcass was radiocarbon dated to approximately 44–49 ka BP, and was genetically identified as a female horned lark. This is a species that usually inhabits open habitat, such as the steppe environment that existed in Siberia at the time. This near-intact carcass highlights the potential of permafrost remains for evolutionary studies that combine both morphology and ancient nucleic acids. Nicolas Dussex et al. identify a 44,000–49,000 year old bird found in Siberian permafrost as a female horned lark using ancient DNA. This exceptionally well-preserved specimen illustrates the potential contribution to science of permafrost deposits, such as the study of ecology and evolution of ancient ecosystems, calibration of molecular clocks, and furthering our understanding of processes such as biological regulation and gene expression in relation to climate change.
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Martin JM, Barboza PS. Decadal heat and drought drive body size of North American bison ( Bison bison) along the Great Plains. Ecol Evol 2020; 10:336-349. [PMID: 31988731 PMCID: PMC6972834 DOI: 10.1002/ece3.5898] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/07/2019] [Accepted: 11/15/2019] [Indexed: 11/29/2022] Open
Abstract
Large grazers are visible and valuable indicators of the effects of projected changes in temperature and drought on grasslands. The grasslands of the Great Plains have supported the greatest number of bison (Bison bison; Linnaeus, 1758) since prehistoric times. We tested the hypothesis that body mass (BM, kg) and asymptotic body mass (ABM, kg) of Bison decline with rising temperature and increasing drought over both temporal and spatial scales along the Great Plains. Temporally, we modeled the relationship of annual measures of BM and height (H, m) of 5,781 Bison at Wind Cave National Park (WICA) from 1966 to 2015. We used Gompertz equations of BM against age to estimate ABM in decadal cohorts; both females and males decreased from the 1960s to the 2010s. Male ABM was variable but consistently larger (699 vs. 441 kg) than female ABM. We used local mean decadal temperature (MDT) and local mean decadal Palmer Drought Severity Index (dPDSI) to model the effects of climate on ABM. Drought decreased ABM temporally (-16 kg/local dPDSI) at WICA. Spatially, we used photogrammetry to measure body height (HE ) of 773 Bison to estimate BME in 19 herds from Saskatchewan to Texas, including WICA. Drought also decreased ABM spatially (-16 kg/local dPDSI) along the Great Plains. Temperature decreased ABM both temporally at WICA (-115 kg/°C local MDT) and spatially (-1 kg/°C local MDT) along the Great Plains. Our data indicate that temperature and drought drive Bison ABM presumably by affecting seasonal mass gain. Bison body size is likely to decline over the next five decades throughout the Great Plains due to projected increases in temperatures and both the frequency and intensity of drought.
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Affiliation(s)
- Jeff M. Martin
- Department of Wildlife and Fisheries SciencesTexas A&M UniversityCollege StationTXUSA
| | - Perry S. Barboza
- Department of Wildlife and Fisheries SciencesTexas A&M UniversityCollege StationTXUSA
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