1
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Voelker G, Wogan GOU, Huntley JW, Kaliba PM, DE Swardt DH, Bowie RCK. Climate cycling did not affect haplotype distribution in an abundant Southern African avian habitat generalist species, the familiar chat (Oenanthe familiaris). Integr Zool 2024. [PMID: 39075951 DOI: 10.1111/1749-4877.12879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Avian species diversity in Southern Africa is remarkably high, yet the mechanisms responsible for that diversity are poorly understood. While this is particularly true with respect to species endemic to the subregion, it is unclear as to how more broadly distributed African species may have colonized southern Africa. One process that may in part account for the high bird species diversity in southern Africa is a "species pump" model, wherein the region was repeatedly colonized by lineages from areas further north: a pattern related to climate cycling and the eastern African arid corridor. Once occupying southern Africa, with its many varied biomes, it is possible that climate cycling further affected lineages by generating genetic diversity in multiple refugia, a pattern recently shown for several southern African bird species. Here, we used mtDNA to address these questions in a widespread, sedentary habitat generalist bird species, the familiar chat (Oenanthe familiaris). The phylogenetic structure suggests a north-to-south colonization pattern, supporting the "species pump" model. Haplotype diversity was partitioned into two distinct clusters: southern Africa and Malawi (East Africa). Southern African haplotypes were not geographically partitioned, and we hypothesize that this pattern has arisen because this species is a habitat generalist, and as such resilient to habitat-altering climate perturbations. Based on our phylogenetic results, we discuss the validity of currently recognized subspecies.
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Affiliation(s)
- Gary Voelker
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, Texas, USA
| | - Guinevere O U Wogan
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
| | - Jerry W Huntley
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, Texas, USA
| | | | - Dawie H DE Swardt
- Department of Ornithology, National Museum, Bloemfontein, South Africa
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, California, USA
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute, University of Cape Town, Rondebosch, South Africa
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2
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Rowan J, Du A, Lundgren EJ, Faith JT, Beaudrot L, Campisano CJ, Joordens JC, Lazagabaster IA, Locke EM, Smail IE, Reed KE, Kamilar JM. Long-term biotic homogenization in the East African Rift System over the last 6 million years of hominin evolution. Nat Ecol Evol 2024:10.1038/s41559-024-02462-0. [PMID: 39009848 DOI: 10.1038/s41559-024-02462-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/05/2024] [Indexed: 07/17/2024]
Abstract
Eastern Africa preserves the most complete record of human evolution anywhere in the world but we have little knowledge of how long-term biogeographic dynamics in the region influenced hominin diversity and distributions. Here, we use spatial beta diversity analyses of mammal fossil records from the East African Rift System to reveal long-term biotic homogenization (increasing compositional similarity of faunas) over the last 6 Myr. Late Miocene and Pliocene faunas (~6-3 million years ago (Ma)) were largely composed of endemic species, with the shift towards biotic homogenization after ~3 Ma being driven by the loss of endemic species across functional groups and a growing number of shared grazing species. This major biogeographic transition closely tracks the regional expansion of grass-dominated ecosystems. Although grazers exhibit low beta diversity in open environments of the Early Pleistocene, the high beta diversity of Mio-Pliocene browsers and frugivores occurred in the context of extensive woody vegetation. We identify other key aspects of the Late Cenozoic biogeographic development of eastern Africa, their likely drivers and place the hominin fossil record in this context. Because hominins were undoubtedly influenced by many of the same factors as other eastern African mammals, this provides a new perspective on the links between environmental and human evolutionary histories.
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Affiliation(s)
- John Rowan
- Department of Archaeology, University of Cambridge, Cambridge, UK.
| | - Andrew Du
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - Erick J Lundgren
- Centre for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, Aarhus, Denmark
| | - J Tyler Faith
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
- Natural History Museum of Utah, University of Utah, Salt Lake City, UT, USA
- Origins Centre, University of the Witwatersrand, Johannesburg, South Africa
| | - Lydia Beaudrot
- Department of Biosciences, Rice University, Houston, TX, USA
- Program in Ecology and Evolutionary Biology, Rice University, Houston, TX, USA
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Christopher J Campisano
- Institute of Human Origins, Arizona State University, Tempe, AZ, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Josephine C Joordens
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Faculty of Archaeology, Leiden University, Leiden, the Netherlands
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Faculty of Science and Engineering, Maastricht University, Maastricht, the Netherlands
| | - Ignacio A Lazagabaster
- CENIEH (National Research Center on Human Evolution), Burgos, Spain
- Department of Evolution, Ecology & Behaviour, University of Liverpool, Liverpool, UK
| | - Ellis M Locke
- Department of Anatomy, Idaho College of Osteopathic Medicine, Idaho, ID, USA
| | - Irene E Smail
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, Lewisburg, WV, USA
| | - Kaye E Reed
- Institute of Human Origins, Arizona State University, Tempe, AZ, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Jason M Kamilar
- Department of Anthropology, University of Massachusetts Amherst, Amherst, MA, USA
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, USA
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3
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Liu X, Lin L, Sinding MHS, Bertola LD, Hanghøj K, Quinn L, Garcia-Erill G, Rasmussen MS, Schubert M, Pečnerová P, Balboa RF, Li Z, Heaton MP, Smith TPL, Pinto RR, Wang X, Kuja J, Brüniche-Olsen A, Meisner J, Santander CG, Ogutu JO, Masembe C, da Fonseca RR, Muwanika V, Siegismund HR, Albrechtsen A, Moltke I, Heller R. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations. Nat Commun 2024; 15:2921. [PMID: 38609362 PMCID: PMC11014984 DOI: 10.1038/s41467-024-47015-y] [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: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024] Open
Abstract
The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus' range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.
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Affiliation(s)
- Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Rui Resende Pinto
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jonas Meisner
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Research Centre for Mental Health, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph O Ogutu
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Rute R da Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vincent Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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4
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Bertola LD, Quinn L, Hanghøj K, Garcia-Erill G, Rasmussen MS, Balboa RF, Meisner J, Bøggild T, Wang X, Lin L, Nursyifa C, Liu X, Li Z, Chege M, Moodley Y, Brüniche-Olsen A, Kuja J, Schubert M, Agaba M, Santander CG, Sinding MHS, Muwanika V, Masembe C, Siegismund HR, Moltke I, Albrechtsen A, Heller R. Giraffe lineages are shaped by major ancient admixture events. Curr Biol 2024; 34:1576-1586.e5. [PMID: 38479386 DOI: 10.1016/j.cub.2024.02.051] [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: 06/11/2023] [Revised: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.
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Affiliation(s)
- Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bøggild
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mumbi Chege
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands; Wildlife Research and Training Institute, Naivasha, Kenya
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Morris Agaba
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road, Arusha, Tanzania
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, P O. Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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5
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Mirzaee Z, Sadeghi S, Ballarin F, Schmitt T, Simões M, Wiemers M. Life history and biogeography of the enigmatic mantid Nilomantisfloweri (Mantodea, Nanomantidae). Zookeys 2023; 1173:275-295. [PMID: 37577153 PMCID: PMC10422127 DOI: 10.3897/zookeys.1173.107204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
The biology and distribution patterns of the Sahelian mantid species Nilomantisfloweri are still insufficiently known. For the first time, records are confirmed of this species from Iran and the distribution map of its native range is updated. Records are compiled from the Sahel zone of North Africa, the Arabian Peninsula, and Iran. Detailed information on its biology, oothecal characteristics, male genitalia variation, and intraspecific molecular diversity in the mitochondrial gene cytochrome c oxidase are provided, and ecological niche modelling was used to gain insight into the overall species distribution and understand its climatic niche limits. Genetic analysis revealed only one haplotype shared between Iran and Oman. The Iranian populations likely represent two distinct clusters, both more related to the diverse Oman haplotypes than to each other. Based on new data, N.floweri appears to be mostly associated with coastal areas in southwestern Asia, with the vast majority of records found along the Red Sea, Persian Gulf, and Oman Gulf coasts. This distribution contrasts markedly with N.floweri records in the Sahel, where most collections have been reported in the transitional zone between the southern Sahara and arid thorn savannah, far off the coast. This study contributes to a comprehensive understanding of this still enigmatic mantid species.
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Affiliation(s)
- Zohreh Mirzaee
- Senckenberg German Entomological Institute, Eberswalder Str. 90, 15374 Müncheberg, GermanySenckenberg German Entomological InstituteMünchebergGermany
- Biology Department, Faculty of Sciences, Shiraz University, Shiraz, IranShiraz UniversityShirazIran
- Entomology and Biogeography, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, D-14476 Potsdam, GermanyTokyo Metropolitan UniversityTokyoJapan
| | - Saber Sadeghi
- Biology Department, Faculty of Sciences, Shiraz University, Shiraz, IranShiraz UniversityShirazIran
| | - Francesco Ballarin
- Entomology and Biogeography, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, D-14476 Potsdam, GermanyTokyo Metropolitan UniversityTokyoJapan
| | - Thomas Schmitt
- Senckenberg German Entomological Institute, Eberswalder Str. 90, 15374 Müncheberg, GermanySenckenberg German Entomological InstituteMünchebergGermany
- Systematic Zoology Laboratory, Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-shi, 192-0397, Tokyo, JapanTokyo Metropolitan UniversityTokyoGermany
| | - Marianna Simões
- Senckenberg Research Institute and Natural History Museum, Frankfurt, GermanySenckenberg Research Institute and Natural History MuseumFrankfurtGermany
| | - Martin Wiemers
- Senckenberg German Entomological Institute, Eberswalder Str. 90, 15374 Müncheberg, GermanySenckenberg German Entomological InstituteMünchebergGermany
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6
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Russo IM, de Jager D, van Wyk AM, Klopper AW, Uiseb K, Birss C, Rushworth I, Bloomer P. The Contribution of Digital Sequence Information to Conservation Biology: A Southern African Perspective. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2200032. [PMID: 37288168 PMCID: PMC10242406 DOI: 10.1002/ggn2.202200032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Indexed: 06/09/2023]
Abstract
Many recent contributions have made a compelling case that genetic diversity is not adequately reflected in international frameworks and policies, as well as in local governmental processes implementing such frameworks. Using digital sequence information (DSI) and other publicly available data is supported to assess genetic diversity, toward formulation of practical actions for long-term conservation of biodiversity, with the particular goal of maintaining ecological and evolutionary processes. Given the inclusion of specific goals and targets regarding DSI in the latest draft of the Global Biodiversity Framework negotiated at the 15th Conference of the Parties (COP15) in Montreal in December 2022 and the crucial decisions on access and benefit sharing to DSI that will be taken in the coming months and future COP meetings, a southern African perspective on how and why open access to DSI is essential for the conservation of intraspecific biodiversity (genetic diversity and structure) across country borders is provided.
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Affiliation(s)
| | - Deon de Jager
- Section of Molecular Ecology and EvolutionGlobe InstituteUniversity of CopenhagenCopenhagen1353Denmark
| | - Anna M. van Wyk
- Department of BiochemistryGenetics and MicrobiologyUniversity of PretoriaPretoria0002South Africa
| | - Arrie W. Klopper
- Department of BiochemistryGenetics and MicrobiologyUniversity of PretoriaPretoria0002South Africa
| | - Kenneth Uiseb
- Ministry of Environment, Forestry and TourismWindhoek13306Namibia
| | | | - Ian Rushworth
- Ezemvelo KZN WildlifePietermaritzburg3201South Africa
| | - Paulette Bloomer
- Department of BiochemistryGenetics and MicrobiologyUniversity of PretoriaPretoria0002South Africa
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7
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Alemseged Z. Reappraising the palaeobiology of Australopithecus. Nature 2023; 617:45-54. [PMID: 37138108 DOI: 10.1038/s41586-023-05957-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/14/2023] [Indexed: 05/05/2023]
Abstract
The naming of Australopithecus africanus in 1925, based on the Taung Child, heralded a new era in human evolutionary studies and turned the attention of the then Eurasian-centric palaeoanthropologists to Africa, albeit with reluctance. Almost one hundred years later, Africa is recognized as the cradle of humanity, where the entire evolutionary history of our lineage prior to two million years ago took place-after the Homo-Pan split. This Review examines data from diverse sources and offers a revised depiction of the genus and characterizes its role in human evolution. For a long time, our knowledge of Australopithecus came from both A. africanus and Australopithecus afarensis, and the members of this genus were portrayed as bipedal creatures that did not use stone tools, with a largely chimpanzee-like cranium, a prognathic face and a brain slightly larger than that of chimpanzees. Subsequent field and laboratory discoveries, however, have altered this portrayal, showing that Australopithecus species were habitual bipeds but also practised arboreality; that they occasionally used stone tools to supplement their diet with animal resources; and that their infants probably depended on adults to a greater extent than what is seen in apes. The genus gave rise to several taxa, including Homo, but its direct ancestor remains elusive. In sum, Australopithecus had a pivotal bridging role in our evolutionary history owing to its morphological, behavioural and temporal placement between the earliest archaic putative hominins and later hominins-including the genus Homo.
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8
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Edwards TR, Pickering R, Mallett TL, Herries AIR. Challenging the antiquity of the Cradle of Humankind, South Africa: Geochronological evidence restricts the age of Eurotomys bolti and Parapapio to less than 2.3 Ma at Waypoint 160, Bolt's Farm. J Hum Evol 2023; 178:103334. [PMID: 36931115 DOI: 10.1016/j.jhevol.2023.103334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 03/17/2023]
Abstract
Waypoint 160 is a paleocave at Bolt's Farm in the 'Cradle of Humankind,' South Africa. It is known for the novel murid taxa Eurotomys bolti, argued to be morphologically intermediate between Eurotomys pelomyoides from Langebaanweg (∼5.1 Ma) and the earliest Otomyinae from Makapansgat Limeworks (∼3.0-2.6 Ma). Based on the presence of this specimen, an age of ∼4.5 Ma was inferred for Waypoint 160, making it far older than other Cradle sites. This biochronological age was used to argue that Parapapio and Cercopithecoides fossils from Waypoint 160 were the oldest in the region. Here, we provide a detailed sedimentological context for the in-situ deposits at Waypoint 160. We have identified interior cave deposits, in contrast to other sites at Bolt's Farm. Petrography confirms that one unit (facies D) contains in-situ microfaunal fossils, indicating the likely provenience of the E. bolti specimen. Palaeomagnetic analysis shows four periods of magnetic polarity in the sequence. Using U-Pb ages as chronological pins, we argue that the upper part of the sequence records a polarity change at the end of the Olduvai subChron (1.78 Ma). The lower part of the sequence records a polarity shift from normal to reversed that likely relates to the Feni subChron (2.16-2.12 Ma), based on a basal flowstone U-Pb age of 2.269 ± 0.075 Ma. Together this points to a depositional window of ∼500 ka, with the Parapapio and E. bolti tentatively attributed to the micromammal fossil-bearing layers dating to ∼2.27-2.07 Ma. This has significant implications for other biochronological dates in South Africa, as E. bolti is now less than ∼2.27 Ma, younger than the oldest Otomyinae at Makapansgat Limeworks and thus not ancestral to them. This chronology for Waypoint 160 challenges the presence of older, early to mid-Pliocene deposits >3.20 Ma in the Gauteng portion of the Cradle.
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Affiliation(s)
- Tara R Edwards
- Department of Geological Sciences, Human Evolution Research Institute, University of Cape Town, Rondebosch, 7700, South Africa; Human Evolution Research Institute, University of Cape Town, Rondebosch, 7700, South Africa.
| | - Robyn Pickering
- Department of Geological Sciences, Human Evolution Research Institute, University of Cape Town, Rondebosch, 7700, South Africa; Human Evolution Research Institute, University of Cape Town, Rondebosch, 7700, South Africa
| | - Tom L Mallett
- The Australian Archaeomagnetism Laboratory, Dept. Archaeology and History, La Trobe University, Melbourne Campus, Bundoora, 3086, Australia
| | - Andy I R Herries
- The Australian Archaeomagnetism Laboratory, Dept. Archaeology and History, La Trobe University, Melbourne Campus, Bundoora, 3086, Australia; Palaeo-Research Institute, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa
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9
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Dianat M, Voet I, Ortiz D, Goüy de Bellocq J, Cuypers LN, Kryštufek B, Bureš M, Čížková D, Bryjová A, Bryja J, Nicolas V, Konečný A. Cryptic diversity of Crocidura shrews in the savannahs of Eastern and Southern Africa. Mol Phylogenet Evol 2023; 180:107708. [PMID: 36657626 DOI: 10.1016/j.ympev.2023.107708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023]
Abstract
Crocidura (Eulipotyphla, Soricidae) is the most species-rich genus among mammals, with high cryptic diversity and complicated taxonomy. The hirta-flavescens group of Crocidura represents the most abundant and widespread shrews in savannahs of eastern and southern Africa, making them a suitable phylogeographical model for assessing the role of paleoclimatic changes on current biodiversity in open African habitats. We present the first comprehensive study on the phylogeography, evolutionary history, geographical distribution, systematics, and taxonomy of the group, using the integration of mitochondrial, genome-wide (ddRAD sequencing), morphological and morphometrical data collected from specimens over most of the known geographic distribution. Our genomic data confirmed the monophyly of this group and its sister relationship with the olivieri group of Crocidura. There is a substantial genetic variation within the hirta-flavescens group, with three highly supported clades showing parapatric distribution and which can be distinguished morphologically: C. hirta, distributed in both the Zambezian and Somali-Masai bioregions, C. flavescens, known from South Africa and south-western Zambia, and C. cf. flavescens, which is known to occur only in central and western Tanzania. Morphometric data revealed relatively minor differences between C. hirta and C. cf. flavescens, but they differ in the colouration of the pelage. Diversification of the hirta-flavescens group has most likely happened during phases of grassland expansion and contraction during Plio-Pleistocene climatic cycles. Eastern African Rift system, rivers, and the distinctiveness of Zambezian and Somali-Masai bioregions seem to have also shaped the pattern of their diversity, which is very similar to sympatric rodent species living in open habitats. Finally, we review the group's taxonomy and propose to revalidate C. bloyeti, currently a synonym of C. hirta, including the specimens treated as C. cf. flavescens.
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Affiliation(s)
- Malahat Dianat
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic.
| | - Inessa Voet
- Institut de Systematique, Evolution, Biodiversite (ISYEB), Museum national d'Histoire naturelle, CNRS, Sorbonne Universite, EPHE, Universite des Antilles, CP51, 75005 Paris, France
| | - David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic
| | - Laura N Cuypers
- Evolutionary Ecology Group, Department of Biology, University of Antwerp,Universiteitsplein 1, 2610 Antwerp, Belgium
| | | | - Michal Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Dagmar Čížková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Violaine Nicolas
- Institut de Systematique, Evolution, Biodiversite (ISYEB), Museum national d'Histoire naturelle, CNRS, Sorbonne Universite, EPHE, Universite des Antilles, CP51, 75005 Paris, France
| | - Adam Konečný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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10
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Kopp GH, Sithaldeen R, Trede F, Grathwol F, Roos C, Zinner D. A Comprehensive Overview of Baboon Phylogenetic History. Genes (Basel) 2023; 14:genes14030614. [PMID: 36980887 PMCID: PMC10048742 DOI: 10.3390/genes14030614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
Baboons (genus Papio) are an intriguing study system to investigate complex evolutionary processes and the evolution of social systems. An increasing number of studies over the last 20 years has shown that considerable incongruences exist between phylogenies based on morphology, mitochondrial, and nuclear sequence data of modern baboons, and hybridization and introgression have been suggested as the main drivers of these patterns. Baboons, therefore, present an excellent opportunity to study these phenomena and their impact on speciation. Advances both in geographic and genomic coverage provide increasing details on the complexity of the phylogeography of baboons. Here, we compile the georeferenced genetic data of baboons and review the current knowledge on baboon phylogeny, discuss the evolutionary processes that may have shaped the patterns that we observe today, and propose future avenues for research.
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Affiliation(s)
- Gisela H. Kopp
- Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78457 Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
- Correspondence:
| | - Riashna Sithaldeen
- Academic Development Programme, Centre for Higher Education and Development, University of Cape Town, Cape Town 7700, South Africa
| | - Franziska Trede
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Franziska Grathwol
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-University, 37073 Göttingen, Germany
- Leibniz-ScienceCampus Primate Cognition, 37077 Göttingen, Germany
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11
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Mas-Coma S, Valero MA, Bargues MD. Human and Animal Fascioliasis: Origins and Worldwide Evolving Scenario. Clin Microbiol Rev 2022; 35:e0008819. [PMID: 36468877 PMCID: PMC9769525 DOI: 10.1128/cmr.00088-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fascioliasis is a plant- and waterborne zoonotic parasitic disease caused by two trematode species: (i) Fasciola hepatica in Europe, Asia, Africa, the Americas, and Oceania and (ii) F. gigantica, which is restricted to Africa and Asia. Fasciolid liver flukes infect mainly herbivores as ruminants, equids, and camelids but also omnivore mammals as humans and swine and are transmitted by freshwater Lymnaeidae snail vectors. Two phases may be distinguished in fasciolid evolution. The long predomestication period includes the F. gigantica origin in east-southern Africa around the mid-Miocene, the F. hepatica origin in the Near-Middle East of Asia around the latest Miocene to Early Pliocene, and their subsequent local spread. The short postdomestication period includes the worldwide spread by human-guided movements of animals in the last 12,000 years and the more recent transoceanic anthropogenic introductions of F. hepatica into the Americas and Oceania and of F. gigantica into several large islands of the Pacific with ships transporting livestock in the last 500 years. The routes and chronology of the spreading waves followed by both fasciolids into the five continents are redefined on the basis of recently generated knowledge of human-guided movements of domesticated hosts. No local, zonal, or regional situation showing disagreement with historical records was found, although in a few world zones the available knowledge is still insufficient. The anthropogenically accelerated evolution of fasciolids allows us to call them "peridomestic endoparasites." The multidisciplinary implications for crucial aspects of the disease should therefore lead the present baseline update to be taken into account in future research studies.
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Affiliation(s)
- Santiago Mas-Coma
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - M. Adela Valero
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - M. Dolores Bargues
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
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12
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Rasmussen MS, Garcia-Erill G, Korneliussen TS, Wiuf C, Albrechtsen A. Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage. Genetics 2022; 222:iyac148. [PMID: 36173322 PMCID: PMC9713400 DOI: 10.1093/genetics/iyac148] [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: 08/22/2022] [Accepted: 09/14/2022] [Indexed: 12/13/2022] Open
Abstract
The site frequency spectrum is an important summary statistic in population genetics used for inference on demographic history and selection. However, estimation of the site frequency spectrum from called genotypes introduces bias when working with low-coverage sequencing data. Methods exist for addressing this issue but sometimes suffer from 2 problems. First, they can have very high computational demands, to the point that it may not be possible to run estimation for genome-scale data. Second, existing methods are prone to overfitting, especially for multidimensional site frequency spectrum estimation. In this article, we present a stochastic expectation-maximization algorithm for inferring the site frequency spectrum from NGS data that address these challenges. We show that this algorithm greatly reduces runtime and enables estimation with constant, trivial RAM usage. Furthermore, the algorithm reduces overfitting and thereby improves downstream inference. An implementation is available at github.com/malthesr/winsfs.
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Affiliation(s)
| | - Genís Garcia-Erill
- Department of Biology, University of Copenhagen, 2200 København N, Denmark
| | | | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, 2100 København Ø, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, 2200 København N, Denmark
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13
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Odili JB, Noraziah A, Alkazemi B, Zarina M. Stochastic process and tutorial of the African buffalo optimization. Sci Rep 2022; 12:17319. [PMID: 36243886 PMCID: PMC9569383 DOI: 10.1038/s41598-022-22242-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/12/2022] [Indexed: 01/10/2023] Open
Abstract
This paper presents the data description of the African buffalo optimization algorithm (ABO). ABO is a recently-designed optimization algorithm that is inspired by the migrant behaviour of African buffalos in the vast African landscape. Organizing their large herds that could be over a thousand buffalos using just two principal sounds, the /maaa/ and the /waaa/ calls present a good foundation for the development of an optimization algorithm. Since elaborate descriptions of the manual workings of optimization algorithms are rare in literature, this paper aims at solving this problem, hence it is our main contribution. It is our belief that elaborate manual description of the workings of optimization algorithms make it user-friendly and encourage reproducibility of the experimental procedures performed using this algorithm. Again, our ability to describe the algorithm's basic flow, stochastic and data generation processes in a language so simple that any non-expert can appreciate and use as well as the practical implementation of the popular benchmark Rosenbrock and Shekel Foxhole functions with the novel algorithm will assist the research community in benefiting maximally from the contributions of this novel algorithm. Finally, benchmarking the good experimental output of the ABO with those of the popular, highly effective and efficient Cuckoo Search and Flower Pollination Algorithm underscores the ABO as a worthy contribution to the existing body of population-based optimization algorithms.
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Affiliation(s)
- Julius Beneoluchi Odili
- grid.411782.90000 0004 1803 1817Faculty of Science and Science Education, Anchor University Lagos, Lagos, Nigeria
| | - A. Noraziah
- grid.440438.f0000 0004 1798 1407Faculty of Computing, Universiti Malaysia Pahang, Pekan, Kuantan Malaysia ,grid.440438.f0000 0004 1798 1407Centre for Software Development and Integrated Computing, University Malaysia Pahang, 26600 Pekan,, Pahang Malaysia
| | - Basem Alkazemi
- grid.412832.e0000 0000 9137 6644Department of Computer Science, Umm al-Qura University, Makkah al Mukarramah, Saudi Arabia
| | - M. Zarina
- grid.449643.80000 0000 9358 3479Faculty of Informatics and Computing, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia
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14
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Veron G, Daniel C, Pagani P, Do Linh San E, Kitchener AC, Hassanin A. A tale of two African mongooses (Carnivora: Herpestidae): differing genetic diversity and geographical structure across a continent. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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15
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Bargues MD, Halajian A, Artigas P, Luus-Powell WJ, Valero MA, Mas-Coma S. Paleobiogeographical origins of Fasciola hepatica and F. gigantica in light of new DNA sequence characteristics of F. nyanzae from hippopotamus. Front Vet Sci 2022; 9:990872. [PMID: 36157179 PMCID: PMC9500510 DOI: 10.3389/fvets.2022.990872] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Fascioliasis is a highly pathogenic disease affecting humans and livestock worldwide. It is caused by the liver flukes Fasciola hepatica transmitted by Galba/Fossaria lymnaeid snails in Europe, Asia, Africa, the Americas and Oceania, and F. gigantica transmitted by Radix lymnaeids in Africa and Asia. An evident founder effect appears in genetic studies as the consequence of their spread by human-guided movements of domestic ruminants, equines and Old World camelids in the post-domestication period from the beginning of the Neolithic. Establishing the geographical origins of fasciolid expansion is multidisciplinary crucial for disease assessment. Sequencing of selected nuclear ribosomal and mitochondrial DNA markers of F. nyanzae infecting hippopotamuses (Hippopotamus amphibius) in South Africa and their comparative analyses with F. hepatica and F. gigantica, and the two Fascioloides species, Fs. jacksoni from Asian elephants and Fs. magna from Holarctic cervids, allow to draw a tuned-up evolutionary scenario during the pre-domestication period. Close sequence similarities indicate a direct derivation of F. hepatica and F. gigantica from F. nyanzae by speciation after host capture phenomena. Phylogenetic reconstruction, genetic distances and divergence estimates fully fit fossil knowledge, past interconnecting bridges between continents, present fasciolid infection in the wild fauna, and lymnaeid distribution. The paleobiogeographical analyses suggest an origin for F. gigantica by transfer from primitive hippopotamuses to grazing bovid ancestors of Reduncinae, Bovinae and Alcelaphinae, by keeping the same vector Radix natalensis in warm lowlands of southeastern Africa in the mid-Miocene, around 13.5 mya. The origin of F. hepatica should have occurred after capture from primitive, less amphibious Hexaprotodon hippopotamuses to mid-sized ovicaprines as the wild bezoar Capra aegagrus and the wild mouflon Ovis gmelini, and from R. natalensis to Galba truncatula in cooler areas and mountainous foothills of Asian Near East in the latest Miocene to Early Pliocene, around 6.0 to 4.0 mya and perhaps shortly afterwards.
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Affiliation(s)
- María Dolores Bargues
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
- *Correspondence: María Dolores Bargues
| | - Ali Halajian
- DSI-NRF SARChi Chair (Ecosystem Health), Department of Biodiversity, University of Limpopo, Sovenga, South Africa
- Research Administration and Development, University of Limpopo, Sovenga, South Africa
| | - Patricio Artigas
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - Wilmien J. Luus-Powell
- DSI-NRF SARChi Chair (Ecosystem Health), Department of Biodiversity, University of Limpopo, Sovenga, South Africa
| | - M. Adela Valero
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - Santiago Mas-Coma
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
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16
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Akomo-Okoue EF, Inoue E, Atteke C, Nakashima Y, Hongo S, Inoue-Murayama M, Yamagiwa J. Effect of landscape features on the genetic structure of forest duikers (Cephalophinae) in Moukalaba forest, Gabon. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00301-y] [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]
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17
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Garcia-Erill G, Jørgensen CHF, Muwanika VB, Wang X, Rasmussen MS, de Jong YA, Gaubert P, Olayemi A, Salmona J, Butynski TM, Bertola LD, Siegismund HR, Albrechtsen A, Heller R. Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes. Mol Biol Evol 2022; 39:6627297. [PMID: 35779009 PMCID: PMC9250280 DOI: 10.1093/molbev/msac134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
African wild pigs have a contentious evolutionary and biogeographic history. Until recently, desert warthog (Phacochoerus aethiopicus) and common warthog (P. africanus) were considered a single species. Molecular evidence surprisingly suggested they diverged at least 4.4 million years ago, and possibly outside of Africa. We sequenced the first whole-genomes of four desert warthogs and 35 common warthogs from throughout their range. We show that these two species diverged much later than previously estimated, 400,000–1,700,000 years ago depending on assumptions of gene flow. This brings it into agreement with the paleontological record. We found that the common warthog originated in western Africa and subsequently colonized eastern and southern Africa. During this range expansion, the common warthog interbred with the desert warthog, presumably in eastern Africa, underlining this region’s importance in African biogeography. We found that immune system–related genes may have adaptively introgressed into common warthogs, indicating that resistance to novel diseases was one of the most potent drivers of evolution as common warthogs expanded their range. Hence, we solve some of the key controversies surrounding warthog evolution and reveal a complex evolutionary history involving range expansion, introgression, and adaptation to new diseases.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Christian H F Jørgensen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Vincent B Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Xi Wang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Malthe S Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Yvonne A de Jong
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Philippe Gaubert
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria
| | - Jordi Salmona
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Thomas M Butynski
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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18
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Meneganzin A, Pievani T, Manzi G. Pan-Africanism vs. single-origin of Homo sapiens: Putting the debate in the light of evolutionary biology. Evol Anthropol 2022; 31:199-212. [PMID: 35848454 PMCID: PMC9540121 DOI: 10.1002/evan.21955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 02/23/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022]
Abstract
The scenario of Homo sapiens origin/s within Africa has become increasingly complex, with a pan-African perspective currently challenging the long-established single-origin hypothesis. In this paper, we review the lines of evidence employed in support of each model, highlighting inferential limitations and possible terminological misunderstandings. We argue that the metapopulation scenario envisaged by pan-African proponents well describes a mosaic diversification among late Middle Pleistocene groups. However, this does not rule out a major contribution that emerged from a single population where crucial derived features-notably, a globular braincase-appeared as the result of a punctuated, cladogenetic event. Thus, we suggest that a synthesis is possible and propose a scenario that, in our view, better reconciles with consolidated expectations in evolutionary theory. These indicate cladogenesis in allopatry as an ordinary pattern for the origin of a new species, particularly during phases of marked climatic and environmental instability.
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Affiliation(s)
| | | | - Giorgio Manzi
- Department of Environmental BiologySapienza University of RomeRomeItaly
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19
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Blinkhorn J, Timbrell L, Grove M, Scerri EML. Evaluating refugia in recent human evolution in Africa. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200485. [PMID: 35249393 PMCID: PMC8899617 DOI: 10.1098/rstb.2020.0485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/21/2022] [Indexed: 11/12/2022] Open
Abstract
Homo sapiens have adapted to an incredible diversity of habitats around the globe. This capacity to adapt to different landscapes is clearly expressed within Africa, with Late Pleistocene Homo sapiens populations occupying savannahs, woodlands, coastlines and mountainous terrain. As the only area of the world where Homo sapiens have clearly persisted through multiple glacial-interglacial cycles, Africa is the only continent where classic refugia models can be formulated and tested to examine and describe changing patterns of past distributions and human phylogeographies. The potential role of refugia has frequently been acknowledged in the Late Pleistocene palaeoanthropological literature, yet explicit identification of potential refugia has been limited by the patchy nature of palaeoenvironmental and archaeological records, and the low temporal resolution of climate or ecological models. Here, we apply potential climatic thresholds on human habitation, rooted in ethnographic studies, in combination with high-resolution model datasets for precipitation and biome distributions to identify persistent refugia spanning the Late Pleistocene (130-10 ka). We present two alternate models suggesting that between 27% and 66% of Africa may have provided refugia to Late Pleistocene human populations, and examine variability in precipitation, biome and ecotone distributions within these refugial zones. This article is part of the theme issue 'Tropical forests in the deep human past'.
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Affiliation(s)
- James Blinkhorn
- Pan-African Evolution Research Group, Max Planck Institute for the Science of Human History, Jena, Germany
- Centre for Quaternary Research, Department of Geography, Royal Holloway, University of London, Egham, UK
| | - Lucy Timbrell
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Matt Grove
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Eleanor M. L. Scerri
- Pan-African Evolution Research Group, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Classics and Archaeology, University of Malta, Msida, Malta
- Institute of Prehistoric Archaeology, University of Cologne, Cologne, Germany
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20
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Bertola LD, Vermaat M, Lesilau F, Chege M, Tumenta PN, Sogbohossou EA, Schaap OD, Bauer H, Patterson BD, White PA, de Iongh HH, Laros JFJ, Vrieling K. Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo). BMC Genomics 2022; 23:321. [PMID: 35459090 PMCID: PMC9027350 DOI: 10.1186/s12864-022-08510-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/29/2022] [Indexed: 11/23/2022] Open
Abstract
Background Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. Results In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. Conclusions The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08510-y.
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Affiliation(s)
- L D Bertola
- City University of New York, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA. .,Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands. .,Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.
| | - M Vermaat
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - F Lesilau
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.,Kenya Wildlife Service, Nairobi, Kenya
| | - M Chege
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.,Kenya Wildlife Service, Nairobi, Kenya
| | - P N Tumenta
- Centre for Environment and Developmental Studies, Cameroon (CEDC), Yaounde, Cameroon.,Regional Training Centre Specialized in Agriculture, Forest and Wood, University of Dschang, BP 138, Yaounde, Cameroon
| | - E A Sogbohossou
- Laboratoire d'Ecologie Appliquée, Université d'Abomey-Calavi, 03 BP 294, Cotonou, Benin
| | - O D Schaap
- Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
| | - H Bauer
- Wildlife Conservation Research Unit, Zoology, University of Oxford Recanati-Kaplan Centre, Tubney, OX13 5QL, UK
| | - B D Patterson
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
| | - P A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095-1496, USA
| | - H H de Iongh
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.,Department of Biology, Evolutionary Ecology Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - J F J Laros
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - K Vrieling
- Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
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21
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Rocha JL, Vaz Pinto P, Siegismund HR, Meyer M, Jansen van Vuuren B, Veríssimo L, Ferrand N, Godinho R. African climate and geomorphology drive evolution and ghost introgression in sable antelope. Mol Ecol 2022; 31:2968-2984. [PMID: 35305042 DOI: 10.1111/mec.16427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/13/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022]
Abstract
The evolutionary history of African ungulates has been largely explained in the light of Pleistocene climatic oscillations and the way these influenced the distribution of vegetation types, leading to range expansions and/or isolation in refugia. In contrast, comparatively fewer studies have addressed the continent's environmental heterogeneity and the role played by its geomorphological barriers. In this study, we performed a range-wide analysis of complete mitogenomes of sable antelope (Hippotragus niger) to explore how these different factors may have contributed as drivers of evolution in South-Central Africa. Our results supported two sympatric and deeply divergent mitochondrial lineages in west Tanzanian sables, which can be explained as the result of introgressive hybridization of a mitochondrial ghost lineage from an archaic, as-yet-undefined, congener. Phylogeographic subdivisions into three main lineages suggest that sable diversification may not have been solely driven by climatic events affecting populations differently across a continental scale. Often in interplay with climate, geomorphological features have also clearly shaped the species' patterns of vicariance, where the East Africa Rift System and the Eastern Arc Mountains acted as geological barriers. Subsequent splits among southern populations may be linked to rearrangements in the Zambezi system, possibly framing the most recent time when the river attained its current drainage profile. This work underscores how the use of comprehensive mitogenomic datasets on a model species with a wide geographic distribution can contribute to a much-enhanced understanding of environmental, geomorphological, and evolutionary patterns in Africa throughout the Quaternary.
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Affiliation(s)
- Joana L Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Pedro Vaz Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Fundação Kissama, Rua Joaquim Capango 49, Luanda, Angola
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bettine Jansen van Vuuren
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Luís Veríssimo
- Fundação Kissama, Rua Joaquim Capango 49, Luanda, Angola
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
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22
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Coyotee Howard C, Crowl AA, Harvey TS, Cellinese N. Peeling Back the Layers: First Phylogenomic Insights into the Ledebouriinae (Scilloideae, Asparagaceae). Mol Phylogenet Evol 2022; 169:107430. [DOI: 10.1016/j.ympev.2022.107430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/11/2022] [Accepted: 01/25/2022] [Indexed: 11/26/2022]
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23
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Cuypers LN, Sabuni C, Šumbera R, Aghová T, Lišková E, Leirs H, Baird SJE, Goüy de Bellocq J, Bryja J. Biogeographical Importance of the Livingstone Mountains in Southern Tanzania: Comparative Genetic Structure of Small Non-volant Mammals. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.742851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Livingstone Mountains (LM; also known as the Kipengere Range) found in south-western Tanzania at the northern end of Lake Nyasa are an important region for understanding the biogeography of Eastern Africa. The two branches of the East African Rift Valley meet here and the mountains might represent stepping stones for colonization and migration between different parts of the Eastern Afromontane Biodiversity Hotspot (especially the link between the Eastern Arc Mountains, EAM, and the Southern Rift Mountains, SRM), as well as an efficient barrier to gene flow for taxa living in drier savannahs in lower elevations. Here we combine new mitochondrial sequence data from 610 recently sampled rodents and shrews with available georeferenced genetic data (3538 specimens) from southern Tanzania, northern Malawi/Zambia and northern Mozambique and compare the spatial genetic structure among different taxa. There is no universal phylogeographic pattern in taxa preferring humid montane habitats. For some of them, the Makambako Gap acts as a barrier between the SRM and the EAM, but other taxa can bridge this gap. Barriers within the EAM (frequently) and within the SRM (sometimes) appear more important. The Rukwa rift between the SRM and the ARM is an important barrier that perhaps can only be crossed by taxa that are not that strictly tied to humid montane environments. For mammals living in lower-elevation savannah-like habitats, the LM can act as a strict barrier to gene flow, and together with the Ufipa Plateau, Lake Nyasa and the EAM create a very similar phylogeographic pattern with three recognizable genetic groups in most savannah-dwellers. The Livingstone Mountains thus appear to be one of the most important biogeographic crossroads in Eastern Africa.
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24
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Kitchener AC, Hoffmann M, Yamaguchi N, Breitenmoser-Würsten C, Wilting A. A system for designating taxonomic certainty in mammals and other taxa. Mamm Biol 2022. [DOI: 10.1007/s42991-021-00205-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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25
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Bertola LD, Miller SM, Williams VL, Naude VN, Coals P, Dures SG, Henschel P, Chege M, Sogbohossou EA, Ndiaye A, Kiki M, Gaylard A, Ikanda DK, Becker MS, Lindsey P. Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion ( Panthera leo). Evol Appl 2022; 15:22-39. [PMID: 35126646 PMCID: PMC8792481 DOI: 10.1111/eva.13318] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
Conservation translocations have become an important management tool, particularly for large wildlife species such as the lion (Panthera leo). When planning translocations, the genetic background of populations needs to be taken into account; failure to do so risks disrupting existing patterns of genetic variation, ultimately leading to genetic homogenization, and thereby reducing resilience and adaptability of the species. We urge wildlife managers to include knowledge of the genetic background of source/target populations, as well as species-wide patterns, in any management intervention. We present a hierarchical decision-making tool in which we list 132 lion populations/lion conservation units and provide information on genetic assignment, uncertainty and suitability for translocation for each source/target combination. By including four levels of suitability, from 'first choice' to 'no option', we provide managers with a range of options. To illustrate the extent of international trade of lions, and the potential disruption of natural patterns of intraspecific diversity, we mined the CITES Trade Database for estimated trade quantities of live individuals imported into lion range states during the past 4 decades. We identified 1056 recorded individuals with a potential risk of interbreeding with wild lions, 772 being captive-sourced. Scoring each of the records with our decision-making tool illustrates that only 7% of the translocated individuals were 'first choice' and 73% were 'no option'. We acknowledge that other, nongenetic factors are important in the decision-making process, and hence a pragmatic approach is needed. A framework in which source/target populations are scored based on suitability is not only relevant to lion, but also to other species of wildlife that are frequently translocated. We hope that the presented overview supports managers to include genetics in future management decisions and contributes towards conservation of the lion in its full diversity.
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Affiliation(s)
- Laura D. Bertola
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- City College of New YorkNew YorkNew YorkUSA
| | - Susan M. Miller
- FitzPatrick Institute of African OrnithologyDSI‐NRF Centre of ExcellenceUniversity of Cape TownCape TownSouth Africa
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Vivienne L. Williams
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Vincent N. Naude
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Peter Coals
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Wildlife Conservation Research UnitUniversity of OxfordOxfordUK
| | | | | | - Monica Chege
- Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
- Kenya Wildlife ServiceNairobiKenya
| | | | | | - Martial Kiki
- Département de Génie de l’EnvironnementUniversité d’Abomey‐CalaviCotonouBenin
| | - Angela Gaylard
- Conservation Development & Assurance DepartmentAfrican Parks NetworkJohannesburgSouth Africa
| | | | | | - Peter Lindsey
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
- Environmental Futures Research InstituteGriffith UniversityNathanQueenslandAustralia
- Wildlife Conservation NetworkSan FranciscoCaliforniaUSA
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26
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Hánová A, Konečný A, Mikula O, Bryjová A, Šumbera R, Bryja J. Diversity, distribution, and evolutionary history of the most studied African rodents, multimammate mice of the genus
Mastomys
: An overview after a quarter of century of using DNA sequencing. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Alexandra Hánová
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Brno Czech Republic
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Adam Konečný
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Ondřej Mikula
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Brno Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Brno Czech Republic
| | - Radim Šumbera
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Brno Czech Republic
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
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27
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Taft JM, Maritz B, Tolley KA. Stable climate corridors promote gene flow in the Cape sand snake species complex (Psammophiidae). ZOOL SCR 2021. [DOI: 10.1111/zsc.12514] [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)
- Jody M. Taft
- Department of Biodiversity and Conservation Biology University of the Western Cape Private Bag X17 Bellville South Africa
- Kirstenbosch Research Center South African National Biodiversity Institute Cape Town South Africa
| | - Bryan Maritz
- Department of Biodiversity and Conservation Biology University of the Western Cape Private Bag X17 Bellville South Africa
| | - Krystal A. Tolley
- Kirstenbosch Research Center South African National Biodiversity Institute Cape Town South Africa
- School of Animal, Plant and Environmental Sciences University of the Witwatersrand Johannesburg South Africa
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28
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Engelbrecht HM, Branch WR, Tolley KA. Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae). PeerJ 2021; 9:e11728. [PMID: 34434643 PMCID: PMC8351568 DOI: 10.7717/peerj.11728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/15/2021] [Indexed: 11/20/2022] Open
Abstract
Background The African continent is comprised of several different biomes, although savanna is the most prevalent. The current heterogeneous landscape was formed through long-term vegetation shifts as a result of the global cooling trend since the Oligocene epoch. The overwhelming trend was a shift from primarily forest, to primarily savanna. As such, faunal groups that emerged during the Paleogene/Neogene period and have species distributed in both forest and savanna habitat should show a genetic signature of the possible evolutionary impact of these biome developments. Crotaphopeltis and Philothamnus (Colubridae) are excellent taxa to investigate the evolutionary impact of these biome developments on widespread African colubrid snakes, and whether timing and patterns of radiation are synchronous with biome reorganisation. Methods A phylogenetic framework was used to investigate timing of lineage diversification. Phylogenetic analysis included both genera as well as other Colubridae to construct a temporal framework in order to estimate radiation times for Crotaphopeltis and Philothamnus. Lineage diversification was estimated in Bayesian Evolutionary Analysis Sampling Trees (BEAST), using two mitochondrial markers (cyt–b, ND4), one nuclear marker (c–mos), and incorporating one fossil and two biogeographical calibration points. Vegetation layers were used to classify and confirm species association with broad biome types (‘closed’ = forest, ‘open’ = savanna/other), and the ancestral habitat state for each genus was estimated. Results Philothamnus showed an ancestral state of closed habitat, but the ancestral habitat type for Crotaphopeltis was equivocal. Both genera showed similar timing of lineage diversification diverging from their sister genera during the Oligocene/Miocene transition (ca. 25 Mya), with subsequent species radiation in the Mid-Miocene. Philothamnus appeared to have undergone allopatric speciation during Mid-Miocene forest fragmentation. Habitat generalist and open habitat specialist species emerged as savanna became more prevalent, while at least two forest associated lineages within Crotaphopeltis moved into Afromontane forest habitat secondarily and independently. Discussion With similar diversification times, but contrasting ancestral habitat reconstructions, we show that these genera have responded very differently to the same broad biome shifts. Differences in biogeographical patterns for the two African colubrid genera is likely an effect of distinct life-history traits, such as the arboreous habits of Philothamnus compared to the terrestrial lifestyle of Crotaphopeltis.
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Affiliation(s)
- Hanlie M Engelbrecht
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa.,Kirstenbosch Research Centre, South African National Biodiversity Institute, Cape Town, Western Cape, South Africa.,Department of Botany & Zoology, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - William R Branch
- Herpetology, Port Elizabeth Museum (Bayworld), Port Elizabeth, Eastern Cape, South Africa.,Department of Zoology, Nelson Mandela Metropolitan University, Port Elizabeth, Eastern Cape, South Africa
| | - Krystal A Tolley
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa.,Kirstenbosch Research Centre, South African National Biodiversity Institute, Cape Town, Western Cape, South Africa
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29
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Hempel E, Westbury MV, Grau JH, Trinks A, Paijmans JLA, Kliver S, Barlow A, Mayer F, Müller J, Chen L, Koepfli KP, Hofreiter M, Bibi F. Diversity and Paleodemography of the Addax ( Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction. Genes (Basel) 2021; 12:genes12081236. [PMID: 34440410 PMCID: PMC8394336 DOI: 10.3390/genes12081236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 12/18/2022] Open
Abstract
Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.
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Affiliation(s)
- Elisabeth Hempel
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
- Correspondence:
| | - Michael V. Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark;
| | - José H. Grau
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
| | - Alexandra Trinks
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Institute of Pathology, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany;
| | - Johanna L. A. Paijmans
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK;
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia;
| | - Axel Barlow
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK;
| | - Frieder Mayer
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
| | - Johannes Müller
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China;
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA;
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA 22630, USA
- Computer Technologies Laboratory, ITMO University, 197101 Saint Petersburg, Russia
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
| | - Faysal Bibi
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
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30
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Edwards SV, Robin V, Ferrand N, Moritz C. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 2021; 14:6339579. [PMID: 34347070 PMCID: PMC8743039 DOI: 10.1093/gbe/evab176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Vv Robin
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati, Andhra Pradesh, 517507, India
| | - Nuno Ferrand
- CIBIO/InBIO, Laboratório Associado, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Portugal
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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Abstract
In this study, we synthesize terrestrial and marine proxy records, spanning the past 620 ky, to decipher pan-African climate variability and its drivers and potential linkages to hominin evolution. We find a tight correlation between moisture availability across Africa to El Niño Southern Ocean oscillation (ENSO) variability, a manifestation of the Walker Circulation, that was most likely driven by changes in Earth's eccentricity. Our results demonstrate that low-latitude insolation was a prominent driver of pan-African climate change during the Middle to Late Pleistocene. We argue that these low-latitude climate processes governed the dispersion and evolution of vegetation as well as mammals in eastern and western Africa by increasing resource-rich and stable ecotonal settings thought to have been important to early modern humans.
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32
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Myers EA, Folly H, Ragalzi E, Feio RN, Santana DJ. Late Pliocene population divergence and persistence despite Pleistocene climatic fluctuations in the Rio Doce snouted Treefrog ( Ololygon carnevallii). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Edward A. Myers
- Department of Vertebrate Zoology National Museum of Natural HistorySmithsonian Institution Washington DC USA
| | - Henrique Folly
- Departamento de Biologia Animal Museu de Zoologia João MoojenUniverisdade Federal de Viçosa Viçosa MG Brazil
- Instituto de Biociências Laboratório de Zoologia Universidade Federal de Mato Grosso do Sul Campo Grande MS Brazil
| | - Eric Ragalzi
- Instituto de Biociências Laboratório de Zoologia Universidade Federal de Mato Grosso do Sul Campo Grande MS Brazil
| | - Renato Neves Feio
- Departamento de Biologia Animal Museu de Zoologia João MoojenUniverisdade Federal de Viçosa Viçosa MG Brazil
| | - Diego José Santana
- Instituto de Biociências Laboratório de Zoologia Universidade Federal de Mato Grosso do Sul Campo Grande MS Brazil
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33
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Pečnerová P, Garcia-Erill G, Liu X, Nursyifa C, Waples RK, Santander CG, Quinn L, Frandsen P, Meisner J, Stæger FF, Rasmussen MS, Brüniche-Olsen A, Hviid Friis Jørgensen C, da Fonseca RR, Siegismund HR, Albrechtsen A, Heller R, Moltke I, Hanghøj K. High genetic diversity and low differentiation reflect the ecological versatility of the African leopard. Curr Biol 2021; 31:1862-1871.e5. [PMID: 33636121 DOI: 10.1016/j.cub.2021.01.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/13/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022]
Abstract
Large carnivores are generally sensitive to ecosystem changes because their specialized diet and position at the top of the trophic pyramid is associated with small population sizes. Accordingly, low genetic diversity at the whole-genome level has been reported for all big cat species, including the widely distributed leopard. However, all previous whole-genome analyses of leopards are based on the Far Eastern Amur leopards that live at the extremity of the species' distribution and therefore are not necessarily representative of the whole species. We sequenced 53 whole genomes of African leopards. Strikingly, we found that the genomic diversity in the African leopard is 2- to 5-fold higher than in other big cats, including the Amur leopard, likely because of an exceptionally high effective population size maintained by the African leopard throughout the Pleistocene. Furthermore, we detected ongoing gene flow and very low population differentiation within African leopards compared with those of other big cats. We corroborated this by showing a complete absence of an otherwise ubiquitous equatorial forest barrier to gene flow. This sets the leopard apart from most other widely distributed large African mammals, including lions. These results revise our understanding of trophic sensitivity and highlight the remarkable resilience of the African leopard, likely because of its extraordinary habitat versatility and broad dietary niche.
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Affiliation(s)
- Patrícia Pečnerová
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Ryan K Waples
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark; Copenhagen Zoo, Research and Conservation, Roskildevej 32, 2000 Frederiksberg, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Frederik Filip Stæger
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Malthe Sebro Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anna Brüniche-Olsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark; Department of Forestry and Natural Resources, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | | | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
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34
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de Jager D, Glanzmann B, Möller M, Hoal E, van Helden P, Harper C, Bloomer P. High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes. Sci Rep 2021; 11:4540. [PMID: 33633171 PMCID: PMC7907399 DOI: 10.1038/s41598-021-83823-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 02/04/2021] [Indexed: 12/30/2022] Open
Abstract
Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.
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Affiliation(s)
- Deon de Jager
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa.
| | - Brigitte Glanzmann
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eileen Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Paul van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa.,Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Cindy Harper
- Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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35
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Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021; 10:e63167. [PMID: 33599612 PMCID: PMC7963486 DOI: 10.7554/elife.63167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Nico L Avenant
- National Museum and Centre for Environmental Management, University of the Free StateBloemfonteinSouth Africa
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums ScotlandEdinburghUnited Kingdom
| | - Erwan Corre
- CNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de RoscoffRoscoffFrance
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
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36
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Cooper DM, Dugmore AJ, Kitchener AC, Metzger MJ, Trabucco A. A kingdom in decline: Holocene range contraction of the lion ( Panthera leo) modelled with global environmental stratification. PeerJ 2021; 9:e10504. [PMID: 33628628 PMCID: PMC7891088 DOI: 10.7717/peerj.10504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/15/2020] [Indexed: 12/02/2022] Open
Abstract
Aim We use ecological niche models and environmental stratification of palaeoclimate to reconstruct the changing range of the lion (Panthera leo) during the late Pleistocene and Holocene. Location The modern (early 21st century) range of the lion extends from southern Africa to the western Indian Subcontinent, yet through the 20th century this range has been drastically reduced in extent and become increasingly fragmented as a result of human impacts. Methods We use Global Environmental Stratification with MaxEnt ecological niche models to map environmental suitability of the lion under current and palaeoclimatic scenarios. By examining modelled lion range in terms of categorical environmental strata, we characterise suitable bioclimatic conditions for the lion in a descriptive manner. Results We find that lion habitat suitability has reduced throughout the Holocene, controlled by pluvial/interpluvial cycles. The aridification of the Sahara 6ka dramatically reduced lion range throughout North Africa. The association of Saharan aridification with the development of pastoralism and the growth of sedentary communities, who practised animal husbandry, would have placed additional and lasting anthropogenic pressures on the lion. Main Conclusions This research highlights the need to integrate the full effects of the fluctuating vegetation and desiccation of the Sahara into palaeoclimatic models, and provides a starting point for further continental-scale analyses of shifting faunal ranges through North Africa and the Near East during the Holocene. This scale of ecological niche modelling does not explain the current pattern of genetic variation in the lion, and we conclude that narrow but substantial physical barriers, such as rivers, have likely played a major role in population vicariance throughout the Late Pleistocene.
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Affiliation(s)
- David M Cooper
- Institute of Geography, University of Edinburgh, School of Geosciences,, Edinburgh, United Kingdom.,Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
| | - Andrew J Dugmore
- Institute of Geography, University of Edinburgh, School of Geosciences,, Edinburgh, United Kingdom.,Human Ecodynamics Research Center and Doctoral Program in Anthropology, City University of New York (CUNY), NY, United States of America
| | - Andrew C Kitchener
- Institute of Geography, University of Edinburgh, School of Geosciences,, Edinburgh, United Kingdom.,Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
| | - Marc J Metzger
- Institute of Geography, University of Edinburgh, School of Geosciences,, Edinburgh, United Kingdom
| | - Antonio Trabucco
- Euro-Mediterranean Center on Climate Change, IAFES Division, Sassari, Italy
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37
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Chromosomal evolution in Raphicerus antelope suggests divergent X chromosomes may drive speciation through females, rather than males, contrary to Haldane's rule. Sci Rep 2021; 11:3152. [PMID: 33542477 PMCID: PMC7862234 DOI: 10.1038/s41598-021-82859-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/19/2021] [Indexed: 01/17/2023] Open
Abstract
Chromosome structural change has long been considered important in the evolution of post-zygotic reproductive isolation. The premise that karyotypic variation can serve as a possible barrier to gene flow is founded on the expectation that heterozygotes for structurally distinct chromosomal forms would be partially sterile (negatively heterotic) or show reduced recombination. We report the outcome of a detailed comparative molecular cytogenetic study of three antelope species, genus Raphicerus, that have undergone a rapid radiation. The species are largely conserved with respect to their euchromatic regions but the X chromosomes, in marked contrast, show distinct patterns of heterochromatic amplification and localization of repeats that have occurred independently in each lineage. We argue a novel hypothesis that postulates that the expansion of heterochromatic blocks in the homogametic sex can, with certain conditions, contribute to post-zygotic isolation. i.e., female hybrid incompatibility, the converse of Haldane’s rule. This is based on the expectation that hybrids incur a selective disadvantage due to impaired meiosis resulting from the meiotic checkpoint network’s surveillance of the asymmetric expansions of heterochromatic blocks in the homogametic sex. Asynapsis of these heterochromatic regions would result in meiotic silencing of unsynapsed chromatin and, if this persists, germline apoptosis and female infertility.
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38
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Couvreur TL, Dauby G, Blach‐Overgaard A, Deblauwe V, Dessein S, Droissart V, Hardy OJ, Harris DJ, Janssens SB, Ley AC, Mackinder BA, Sonké B, Sosef MS, Stévart T, Svenning J, Wieringa JJ, Faye A, Missoup AD, Tolley KA, Nicolas V, Ntie S, Fluteau F, Robin C, Guillocheau F, Barboni D, Sepulchre P. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna. Biol Rev Camb Philos Soc 2021; 96:16-51. [PMID: 32924323 PMCID: PMC7821006 DOI: 10.1111/brv.12644] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/30/2022]
Abstract
Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.
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Affiliation(s)
| | - Gilles Dauby
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - Anne Blach‐Overgaard
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Vincent Deblauwe
- Center for Tropical Research (CTR), Institute of the Environment and SustainabilityUniversity of California, Los Angeles (UCLA)Los AngelesCA90095U.S.A.
- International Institute of Tropical Agriculture (IITA)YaoundéCameroon
| | | | - Vincent Droissart
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Oliver J. Hardy
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - David J. Harris
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghU.K.
| | | | - Alexandra C. Ley
- Institut für Geobotanik und Botanischer GartenUniversity Halle‐WittenbergNeuwerk 21Halle06108Germany
| | | | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
| | | | - Tariq Stévart
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Jan J. Wieringa
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333 CRThe Netherlands
| | - Adama Faye
- Laboratoire National de Recherches sur les Productions Végétales (LNRPV)Institut Sénégalais de Recherches Agricoles (ISRA)Route des Hydrocarbures, Bel Air BP 1386‐ CP18524DakarSenegal
| | - Alain D. Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of ScienceUniversity of DoualaPO Box 24157DoualaCameroon
| | - Krystal A. Tolley
- South African National Biodiversity InstituteKirstenbosch Research CentrePrivate Bag X7, ClaremontCape Town7735South Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandPrivate Bag 3Wits2050South Africa
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesCP51, 57 rue CuvierParis75005France
| | - Stéphan Ntie
- Département de Biologie, Faculté des SciencesUniversité des Sciences et Techniques de MasukuFrancevilleBP 941Gabon
| | - Frédiéric Fluteau
- Institut de Physique du Globe de Paris, CNRSUniversité de ParisParisF‐75005France
| | - Cécile Robin
- CNRS, Géosciences Rennes, UMR6118University of RennesRennes35042France
| | | | - Doris Barboni
- CEREGE, Aix‐Marseille University, CNRS, IRD, Collège de France, INRA, Technopole Arbois MéditerranéeBP80Aix‐en‐Provence cedex413545France
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteF‐91191France
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Sarabia C, vonHoldt B, Larrasoaña JC, Uríos V, Leonard JA. Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster). Mol Ecol 2020; 30:6101-6120. [PMID: 33372365 DOI: 10.1111/mec.15784] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022]
Abstract
Pleistocene climate change impacted entire ecosystems throughout the world. In the northern hemisphere, the distribution of Arctic species expanded during glacial periods, while more temperate and mesic species contracted into climatic refugia, where isolation drove genetic divergence. Cycles of local cooling and warming in the Sahara region of northern Africa caused repeated contractions and expansions of savannah-like environments which connected mesic species isolated in refugia during interglacial times, possibly driving population expansions and contractions; divergence and geneflow in the associated fauna. Here, we use whole genome sequences of African golden wolves (Canis lupaster), a generalist mesopredator with a wide distribution in northern Africa to estimate their demographic history and past episodes of geneflow. We detect a correlation between divergence times and cycles of increased aridity-associated Pleistocene glacial cycles. A complex demographic history with responses to local climate change in different lineages was found, including a relict lineage north of the High Atlas Mountains of Morocco that has been isolated for more than 18,000 years, possibly a distinct ecotype.
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Affiliation(s)
- Carlos Sarabia
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC, Seville, Spain
| | - Bridgett vonHoldt
- Faculty of Ecology and Evolutionary Biology, University of Princeton, Princeton, NJ, USA
| | | | - Vicente Uríos
- Vertebrate Zoology Research Group, University of Alicante, Alicante, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC, Seville, Spain
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40
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Ludington AJ, Sanders KL. Demographic analyses of marine and terrestrial snakes (Elapidae) using whole genome sequences. Mol Ecol 2020; 30:545-554. [PMID: 33170980 DOI: 10.1111/mec.15726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/13/2020] [Accepted: 11/03/2020] [Indexed: 11/27/2022]
Abstract
The question of whether spatial aspects of evolution differ in marine versus terrestrial realms has endured since Ernst Mayr's 1954 essay on marine speciation. Marine systems are often suggested to support larger and more highly connected populations, but quantitative comparisons with terrestrial systems have been lacking. Here, we compared the population histories of marine and terrestrial elapid snakes using the pairwise sequentially Markovian coalescent (PSMC) model to track historical fluctuations in species' effective population sizes (Ne ) from individual whole-genome sequences. To do this we generated a draft genome for the olive sea snake (Aiysurus laevis) and analysed this alongside six published elapid genomes and their sequence reads (marine species Hydrophis curtus, H. melanocephalus and Laticauda laticaudata; terrestrial species Pseudonaja textilis, Naja Naja and Notechis scutatus). Counter to the expectation that marine species should show higher overall Ne and less pronounced fluctuations in Ne , our analyses reveal demographic patterns that are highly variable among species and do not clearly correspond to major ecological divisions. At deeper time intervals, the four marine elapids appear to have experienced relatively stable Ne , while each terrestrial species shows a prominent upturn in Ne starting at ~4 million years ago (Ma) followed by an equally strong decline. However, over the last million years, all seven species show strong and divergent fluctuations. Estimates of Ne in the most recent intervals (~10 kya) are lowest in two of four marine species (H. melanocephalus and Laticauda), and do not correspond to contemporary range sizes in marine or terrestrial taxa.
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Affiliation(s)
- Alastair J Ludington
- School of Biological Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kate L Sanders
- School of Biological Science, The University of Adelaide, Adelaide, South Australia, Australia
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41
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Garcia-Erill G, Kjaer MM, Albrechtsen A, Siegismund HR, Heller R. Vicariance followed by secondary gene flow in a young gazelle species complex. Mol Ecol 2020; 30:528-544. [PMID: 33226701 PMCID: PMC7898927 DOI: 10.1111/mec.15738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 01/03/2023]
Abstract
Grant's gazelles have recently been proposed to be a species complex comprising three highly divergent mtDNA lineages (Nanger granti, N. notata and N. petersii). The three lineages have nonoverlapping distributions in East Africa, but without any obvious geographical divisions, making them an interesting model for studying the early‐stage evolutionary dynamics of allopatric speciation in detail. Here, we use genomic data obtained by restriction site‐associated (RAD) sequencing of 106 gazelle individuals to shed light on the evolutionary processes underlying Grant's gazelle divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex. We date the species divergence to 134,000 years ago, which is recent in evolutionary terms. We find population subdivision within N. granti, which coincides with the previously suggested two subspecies, N. g. granti and N. g. robertsii. Moreover, these two lineages seem to have hybridized in Masai Mara. Perhaps more surprisingly given their extreme genetic differentiation, N. granti and N. petersii also show signs of prolonged admixture in Mkomazi, which we identified as a hybrid population most likely founded by allopatric lineages coming into secondary contact. Despite the admixed composition of this population, elevated X chromosomal differentiation suggests that selection may be shaping the outcome of hybridization in this population. Our results therefore provide detailed insights into the processes of allopatric speciation and secondary contact in a recently radiated species complex.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Michael Munkholm Kjaer
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark.,Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anders Albrechtsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Hans Redlef Siegismund
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
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Larison B, Kaelin CB, Harrigan R, Henegar C, Rubenstein DI, Kamath P, Aschenborn O, Smith TB, Barsh GS. Population structure, inbreeding and stripe pattern abnormalities in plains zebras. Mol Ecol 2020; 30:379-390. [PMID: 33174253 DOI: 10.1111/mec.15728] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 01/14/2023]
Abstract
One of the most iconic wild equids, the plains zebra occupies a broad region of sub-Saharan Africa and exhibits a wide range of phenotypic diversity in stripe patterns that have been used to classify multiple subspecies. After decades of relative stability, albeit with a loss of at least one recognized subspecies, the total population of plains zebras has undergone an approximate 25% decline since 2002. Individuals with abnormal stripe patterns have been recognized in recent years but the extent to which their appearance is related to demography and/or genetics is unclear. Investigating population genetic health and genetic structure are essential for developing effective strategies for plains zebra conservation. We collected DNA from 140 plains zebra, including seven with abnormal stripe patterns, from nine locations across the range of plains zebra, and analyzed data from restriction site-associated and whole genome sequencing (RAD-seq, WGS) libraries to better understand the relationships between population structure, genetic diversity, inbreeding, and abnormal phenotypes. We found that genetic structure did not coincide with described subspecific variation, but did distinguish geographic regions in which anthropogenic habitat fragmentation is associated with reduced gene flow and increased evidence of inbreeding, especially in certain parts of East Africa. Further, zebras with abnormal striping exhibited increased levels of inbreeding relative to normally striped individuals from the same populations. Our results point to a genetic cause of stripe pattern abnormalities, and dramatic evidence of the consequences of habitat fragmentation.
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Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA.,Center for Tropical Research, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ryan Harrigan
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA.,Center for Tropical Research, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | | | - Daniel I Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Pauline Kamath
- School of Food and Agriculture, University of Maine, Orono, ME, USA
| | - Ortwin Aschenborn
- School of Veterinary Medicine, University of Namibia, Neudamm Windhoek, Namibia
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA.,Center for Tropical Research, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
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43
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Wang B, Wang Z, Zhou J, Liu W, Lin Z, Zhang C, Liu G, Zhou B, Wan W, Zhao R, Wang W, Heller R, Chen L. The Draft Genome of Red Lechwe, Kobus leche leche. Front Genet 2020; 11:582638. [PMID: 33250921 PMCID: PMC7674670 DOI: 10.3389/fgene.2020.582638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/02/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Bao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jiong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Wei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zeshan Lin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Chenzhou Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Guichun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Botong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Wenting Wan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
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44
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Abstract
Advances in genomics have led to an appreciation that introgression is common, but its evolutionary consequences are poorly understood. In recent species radiations the sharing of genetic variation across porous species boundaries can facilitate adaptation to new environments and generate novel phenotypes, which may contribute to further diversification. Most Anopheles mosquito species that are of major importance as human malaria vectors have evolved within recent and rapid radiations of largely nonvector species. Here, we focus on one of the most medically important yet understudied anopheline radiations, the Afrotropical Anopheles funestus complex (AFC), to investigate the role of introgression in its diversification and the possible link between introgression and vector potential. The AFC comprises at least seven morphologically similar species, yet only An. funestus sensu stricto is a highly efficient malaria vector with a pan-African distribution. Based on de novo genome assemblies and additional whole-genome resequencing, we use phylogenomic and population genomic analyses to establish species relationships. We show that extensive interspecific gene flow involving multiple species pairs has shaped the evolutionary history of the AFC since its diversification. The most recent introgression event involved a massive and asymmetrical movement of genes from a distantly related AFC lineage into An. funestus, an event that predated and plausibly facilitated its subsequent dramatic geographic range expansion across most of tropical Africa. We propose that introgression may be a common mechanism facilitating adaptation to new environments and enhancing vectorial capacity in Anopheles mosquitoes.
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45
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Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon. DIVERSITY 2020. [DOI: 10.3390/d12110428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.
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46
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Hánová A, Konečný A, Nicolas V, Denys C, Granjon L, Lavrenchenko LA, Šumbera R, Mikula O, Bryja J. Multilocus phylogeny of African striped grass mice (Lemniscomys): Stripe pattern only partly reflects evolutionary relationships. Mol Phylogenet Evol 2020; 155:107007. [PMID: 33160039 DOI: 10.1016/j.ympev.2020.107007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/20/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Murine rodents are one of the most evolutionary successful groups of extant mammals. They are also important for human as vectors and reservoirs of zoonoses and agricultural pests. Unfortunately, their fast and relatively recent diversification impedes our understanding of phylogenetic relationships and species limits of many murine taxa, including those with very conspicuous phenotype that has been frequently used for taxonomic purposes. One of such groups are the striped grass mice (genus Lemniscomys), distributed across sub-Saharan Africa in 11 currently recognized species. These are traditionally classified into three morphological groups according to different pelage colouration on the back: (a) L. barbarus group (three species) with several continuous pale longitudinal stripes; (b) L. striatus group (four species) with pale stripes diffused into short lines or dots; and (c) L. griselda group (four species) with a single mid-dorsal black stripe. Here we reconstructed the most comprehensive molecular phylogeny of the genus Lemniscomys to date, using the largest currently available multi-locus genetic dataset of all but two species. The results show four main lineages (=species complexes) with the distribution corresponding to the major biogeographical regions of Africa. Surprisingly, the four phylogenetic lineages are only in partial agreement with the morphological classification, suggesting that the single-stripe and/or multi-striped phenotypes evolved independently in multiple lineages. Divergence dating showed the split of Lemniscomys and Arvicanthis genera at the beginning of Pleistocene; most of subsequent speciation processes within Lemniscomys were affected by Pleistocene climate oscillations, with predominantly allopatric diversification in fragmented savanna biome. We propose taxonomic suggestions and directions for future research of this striking group of African rodents.
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Affiliation(s)
- Alexandra Hánová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| | - Adam Konečný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France.
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France.
| | - Laurent Granjon
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, 755 avenue du Campus Agropolis, CS 30016, 34988 Montferrier-sur-Lez cedex, France.
| | - Leonid A Lavrenchenko
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia.
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic.
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic.
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
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47
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Chapuis M, Raynal L, Plantamp C, Meynard CN, Blondin L, Marin J, Estoup A. A young age of subspecific divergence in the desert locust inferred by ABC random forest. Mol Ecol 2020; 29:4542-4558. [DOI: 10.1111/mec.15663] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 02/04/2023]
Affiliation(s)
- Marie‐Pierre Chapuis
- CBGP CIRAD Montpellier France
- CBGP CIRAD INRAE IRD Montpellier SupAgro University of Montpellier Montpellier France
| | - Louis Raynal
- IMAG CNRS University of Montpellier Montpellier France
| | | | - Christine N. Meynard
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
| | | | | | - Arnaud Estoup
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
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48
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Molecular characterization of Acomys louisae from Somaliland: a deep divergence and contrasting genetic patterns in a rift zone. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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49
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Humble E, Dobrynin P, Senn H, Chuven J, Scott AF, Mohr DW, Dudchenko O, Omer AD, Colaric Z, Lieberman Aiden E, Al Dhaheri SS, Wildt D, Oliaji S, Tamazian G, Pukazhenthi B, Ogden R, Koepfli KP. Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild. Mol Ecol Resour 2020; 20:1668-1681. [PMID: 32365406 DOI: 10.1111/1755-0998.13181] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 01/04/2023]
Abstract
Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a large-scale and long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.
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Affiliation(s)
- Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Pavel Dobrynin
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA.,Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Helen Senn
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Justin Chuven
- Terrestrial & Marine Biodiversity Sector, Environment Agency, Abu Dhabi, United Arab Emirates
| | - Alan F Scott
- Genetic Resources Core Facility, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David W Mohr
- Genetic Resources Core Facility, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | | | - David Wildt
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Shireen Oliaji
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gaik Tamazian
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia
| | - Budhan Pukazhenthi
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
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50
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Matthee CA. The influence of host dispersal on the gene flow and genetic diversity of generalist and specialist ectoparasites. AFRICAN ZOOLOGY 2020. [DOI: 10.1080/15627020.2020.1762512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Conrad A Matthee
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
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