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Grathwol F, Roos C, Zinner D, Hume B, Porcier SM, Berthet D, Cuisin J, Merker S, Ottoni C, Van Neer W, Dominy NJ, Kopp GH. Adulis and the transshipment of baboons during classical antiquity. eLife 2023; 12:e87513. [PMID: 37767965 PMCID: PMC10597581 DOI: 10.7554/elife.87513] [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: 03/07/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Adulis, located on the Red Sea coast in present-day Eritrea, was a bustling trading centre between the first and seventh centuries CE. Several classical geographers-Agatharchides of Cnidus, Pliny the Elder, Strabo-noted the value of Adulis to Greco-Roman Egypt, particularly as an emporium for living animals, including baboons (Papio spp.). Though fragmentary, these accounts predict the Adulite origins of mummified baboons in Ptolemaic catacombs, while inviting questions on the geoprovenance of older (Late Period) baboons recovered from Gabbanat el-Qurud ('Valley of the Monkeys'), Egypt. Dated to ca. 800-540 BCE, these animals could extend the antiquity of Egyptian-Adulite trade by as much as five centuries. Previously, Dominy et al. (2020) used stable isotope analysis to show that two New Kingdom specimens of Papio hamadryas originate from the Horn of Africa. Here, we report the complete mitochondrial genomes from a mummified baboon from Gabbanat el-Qurud and 14 museum specimens with known provenance together with published georeferenced mitochondrial sequence data. Phylogenetic assignment connects the mummified baboon to modern populations of P. hamadryas in Eritrea, Ethiopia, and eastern Sudan. This result, assuming geographical stability of phylogenetic clades, corroborates Greco-Roman historiographies by pointing toward present-day Eritrea, and by extension Adulis, as a source of baboons for Late Period Egyptians. It also establishes geographic continuity with baboons from the fabled Land of Punt (Dominy et al., 2020), giving weight to speculation that Punt and Adulis were essentially the same trading centres separated by a thousand years of history.
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Affiliation(s)
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate ResearchGöttingenGermany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate ResearchGöttingenGermany
- Department of Primate Cognition, Georg-August-University of GöttingenGöttingenGermany
- Leibniz-ScienceCampus Primate CognitionGöttingenGermany
| | - Benjamin Hume
- Department of Biology, University of KonstanzKonstanzGermany
- SequAna – Sequencing Analysis Core Facility, University of KonstanzKonstanzGermany
| | - Stéphanie M Porcier
- Laboratoire CNRS ASM « Archéologie des Sociétés Méditerranéennes » (UMR 5140), Université Paul-Valéry, LabEx ArchimedeMontpellierFrance
| | | | | | - Stefan Merker
- Department of Zoology, State Museum of Natural History StuttgartStuttgartGermany
| | - Claudio Ottoni
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor VergataRomeItaly
| | - Wim Van Neer
- Royal Belgian Institute of Natural SciencesBrusselsBelgium
- Department of Biology, KU LeuvenLeuvenBelgium
| | - Nathaniel J Dominy
- Departments of Anthropology and Biological Sciences, Dartmouth CollegeHanoverUnited States
- Zukunftskolleg, University of KonstanzKonstanzGermany
| | - Gisela H Kopp
- Department of Biology, University of KonstanzKonstanzGermany
- Zukunftskolleg, University of KonstanzKonstanzGermany
- Department of Migration, Max Planck Institute of Animal BehaviorKonstanzGermany
- Centre for the Advanced Study of Collective Behaviour, University of KonstanzKonstanzGermany
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2
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Hempel E, Bibi F, Faith JT, Koepfli KP, Klittich AM, Duchêne DA, Brink JS, Kalthoff DC, Dalén L, Hofreiter M, Westbury MV. Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus). Mol Biol Evol 2022; 39:msac241. [PMID: 36322483 PMCID: PMC9750129 DOI: 10.1093/molbev/msac241] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/25/2022] [Accepted: 10/31/2022] [Indexed: 11/07/2022] Open
Abstract
The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.
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Affiliation(s)
- Elisabeth Hempel
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108
- Department of Anthropology, University of Utah, 260 South Central Campus Drive, Salt Lake City, UT 84112
- Origins Centre, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Achim M Klittich
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - David A Duchêne
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
- Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1352, Denmark
| | - James S Brink
- National Museum Bloemfontein, Florisbad Quaternary Research Station and Department, PO Box 266, Bloemfontein 9031, Republic of South Africa
- Centre for Environmental Management, University of the Free State, PO Box 339, Bloemfontein 9300, Republic of South Africa
| | - Daniela C Kalthoff
- Swedish Museum of Natural History, Department of Zoology, Box 50007, 10405 Stockholm, Sweden
| | - Love Dalén
- Swedish Museum of Natural History, Department of Bioinformatics and Genetics, Box 50007, 10405 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20c, 10691 Stockholm, Sweden
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Michael V Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
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3
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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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4
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Santander C, Molinaro L, Mutti G, Martínez FI, Mathe J, Ferreira da Silva MJ, Caldon M, Oteo-Garcia G, Aldeias V, Archer W, Bamford M, Biro D, Bobe R, Braun DR, Hammond P, Lüdecke T, Pinto MJ, Meira Paulo L, Stalmans M, Regala FT, Bertolini F, Moltke I, Raveane A, Pagani L, Carvalho S, Capelli C. Genomic variation in baboons from central Mozambique unveils complex evolutionary relationships with other Papio species. BMC Ecol Evol 2022; 22:44. [PMID: 35410131 PMCID: PMC8996594 DOI: 10.1186/s12862-022-01999-7] [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: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/11/2022] Open
Abstract
Background Gorongosa National Park in Mozambique hosts a large population of baboons, numbering over 200 troops. Gorongosa baboons have been tentatively identified as part of Papio ursinus on the basis of previous limited morphological analysis and a handful of mitochondrial DNA sequences. However, a recent morphological and morphometric analysis of Gorongosa baboons pinpointed the occurrence of several traits intermediate between P. ursinus and P. cynocephalus, leaving open the possibility of past and/or ongoing gene flow in the baboon population of Gorongosa National Park. In order to investigate the evolutionary history of baboons in Gorongosa, we generated high and low coverage whole genome sequence data of Gorongosa baboons and compared it to available Papio genomes. Results We confirmed that P. ursinus is the species closest to Gorongosa baboons. However, the Gorongosa baboon genomes share more derived alleles with P. cynocephalus than P. ursinus does, but no recent gene flow between P. ursinus and P. cynocephalus was detected when available Papio genomes were analyzed. Our results, based on the analysis of autosomal, mitochondrial and Y chromosome data, suggest complex, possibly male-biased, gene flow between Gorongosa baboons and P. cynocephalus, hinting to direct or indirect contributions from baboons belonging to the “northern” Papio clade, and signal the presence of population structure within P. ursinus. Conclusions The analysis of genome data generated from baboon samples collected in central Mozambique highlighted a complex set of evolutionary relationships with other baboons. Our results provided new insights in the population dynamics that have shaped baboon diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01999-7.
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Affiliation(s)
- Cindy Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Oxford, Oxford, UK.
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Giacomo Mutti
- Department of Biosciences, University of Milan, Milan, Italy.,Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Felipe I Martínez
- Escuela de Antropología, Facultad de Ciencias Sociales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jacinto Mathe
- School of Anthropology, University of Oxford, Oxford, UK
| | - Maria Joana Ferreira da Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,ONE - Organisms and Environment Group, School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, UK
| | - Matteo Caldon
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gonzalo Oteo-Garcia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Vera Aldeias
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
| | - Will Archer
- Department of Archaeology, National Museum, Bloemfontein, South Africa
| | - Marion Bamford
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Dora Biro
- Department of Zoology, University of Oxford, Oxford, UK
| | - René Bobe
- School of Anthropology, University of Oxford, Oxford, UK.,Gorongosa National Park, Sofala, Mozambique
| | - David R Braun
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, USA
| | | | - Tina Lüdecke
- School of Anthropology, University of Oxford, Oxford, UK.,Emmy Noether Group for Hominin Meat Consumption, Max Planck Institute for Chemistry, Mainz, Germany
| | - Maria José Pinto
- AESDA - Associação de Estudos Subterrâneos e Defesa do Ambiente, Lisbon, Portugal
| | - Luis Meira Paulo
- AESDA - Associação de Estudos Subterrâneos e Defesa do Ambiente, Lisbon, Portugal
| | - Marc Stalmans
- Department of Scientific Services, Gorongosa National Park, Chitengo, Sofala Province, Mozambique
| | - Frederico Tátá Regala
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biology, University of Padua, Padua, Italy
| | - Susana Carvalho
- School of Anthropology, University of Oxford, Oxford, UK. .,Gorongosa National Park, Sofala, Mozambique.
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, UK. .,Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
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5
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Ancient DNA from the koala lemur puts Madagascar on the paleogenomic map. Proc Natl Acad Sci U S A 2021; 118:2110218118. [PMID: 34301878 DOI: 10.1073/pnas.2110218118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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6
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Marciniak S, Mughal MR, Godfrey LR, Bankoff RJ, Randrianatoandro H, Crowley BE, Bergey CM, Muldoon KM, Randrianasy J, Raharivololona BM, Schuster SC, Malhi RS, Yoder AD, Louis EE, Kistler L, Perry GH. Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi. Proc Natl Acad Sci U S A 2021; 118:e2022117118. [PMID: 34162703 PMCID: PMC8255780 DOI: 10.1073/pnas.2022117118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal "subfossil" remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ∼160 kg) and other extraordinary Malagasy megafauna that survived into the past millennium. Yet, much about the evolutionary biology of these now-extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and subtropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here, we present a nuclear genome sequence (∼2× coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (∼85 kg). To support the testing of key phylogenetic and evolutionary hypotheses, we also generated high-coverage nuclear genomes for two extant lemurs, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemurs and 47 nonlemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and an extant folivore (a colobine monkey) and an herbivore (horse) in genes encoding proteins that function in plant toxin biodegradation and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.
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Affiliation(s)
- Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Mehreen R Mughal
- Bioinformatics and Genomics Intercollege Graduate Program, Pennsylvania State University, University Park, PA 16082
| | - Laurie R Godfrey
- Department of Anthropology, University of Massachusetts, Amherst, MA 01003
| | - Richard J Bankoff
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Heritiana Randrianatoandro
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Brooke E Crowley
- Department of Geology, University of Cincinnati, Cincinnati, OH 45220
- Department of Anthropology, University of Cincinnati, Cincinnati, OH 45220
| | - Christina M Bergey
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Department of Genetics, Rutgers University, New Brunswick, NJ 08854
| | | | - Jeannot Randrianasy
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Brigitte M Raharivololona
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 639798
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801
- Department of Ecology, Evolution and Behavior, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708
| | - Edward E Louis
- Department of Conservation Genetics, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107;
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560;
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802;
- Bioinformatics and Genomics Intercollege Graduate Program, Pennsylvania State University, University Park, PA 16082
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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7
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Roos C, Knauf S, Chuma IS, Maille A, Callou C, Sabin R, Portela Miguez R, Zinner D. New mitogenomic lineages in Papio baboons and their phylogeographic implications. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 174:407-417. [PMID: 33244782 DOI: 10.1002/ajpa.24186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/01/2020] [Accepted: 11/09/2020] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Incomplete and/or biased sampling either on a taxonomic or geographic level can lead to delusive phylogenetic and phylogeographic inferences. However, a complete taxonomic and geographical sampling is often and for various reasons impossible, particularly for widespread taxa such as baboons (Papio spp.). Previous studies on baboon phylogeography identified several sampling gaps, some of which we fill by investigating additional material including samples from museum specimens. MATERIALS AND METHODS We generated 10 new mitochondrial genomes either via conventional PCR and subsequent Sanger sequencing from two blood samples or via high-throughput shotgun sequencing from degraded DNA extracted from eight museum specimens. Phylogenetic relationships and divergence times among baboon lineages were determined using maximum-likelihood and Bayesian inferences. RESULTS We identified new mitochondrial lineages in baboons from Central Africa (Chad, the Central African Republic), from the Mahale, and the Udzungwa Mountains (Tanzania), with the latter likely representing a case of mitochondrial capture from sympatric kipunjis (Rungwecebus kipunji). We also found that the mitochondrial clades of olive baboons found in Ivory Coast and Tanzania extend into Niger and the Democratic Republic of Congo, respectively. Moreover, an olive baboon from Sierra Leone carries a mitochondrial haplotype usually found in Guinea baboons, suggesting gene flow between these two species. DISCUSSION The extension of the geographic sampling by including samples from areas difficult to visit or from populations that are most likely extirpated has improved the geographic and temporal resolution of the mitochondrial phylogeny of baboons considerably. Our study also shows the great value of museum material for genetic analyses even when DNA is highly degraded.
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Affiliation(s)
- Christian Roos
- Primate Genetics Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany.,Gene Bank of Primates, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany.,Department for Animal Sciences, Georg-August-University, Göttingen, Germany
| | - Idrissa S Chuma
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Audrey Maille
- Unité Eco-Anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Musée de l'Homme, Université de Paris, Paris, France
| | - Cécile Callou
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | | | | | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center (DPZ), Leibniz Institute for Primate Research, Göttingen, Germany.,Leibniz Science Campus Primate Cognition, Göttingen, Germany.,Department of Primate Cognition, Georg-August-University, Göttingen, Germany
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8
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Orkin JD, Kuderna LFK, Marques-Bonet T. The Diversity of Primates: From Biomedicine to Conservation Genomics. Annu Rev Anim Biosci 2020; 9:103-124. [PMID: 33197208 DOI: 10.1146/annurev-animal-061220-023138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.
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Affiliation(s)
- Joseph D Orkin
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , ,
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , ,
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , , .,Sequencing Unit, National Genomic Analysis Center, Centre for Genomic Regulation, Barcelona Institute of Science, 08036 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autónoma de Barcelona, 08193 Barcelona, Spain
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9
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Branching out: what omics can tell us about primate evolution. Curr Opin Genet Dev 2020; 62:65-71. [DOI: 10.1016/j.gde.2020.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/25/2022]
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