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Utzeri VJ, Cilli E, Fontani F, Zoboli D, Orsini M, Ribani A, Latorre A, Lissovsky AA, Pillola GL, Bovo S, Gruppioni G, Luiselli D, Fontanesi L. Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph. Sci Rep 2023; 13:13635. [PMID: 37604894 PMCID: PMC10442435 DOI: 10.1038/s41598-023-40746-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.
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Affiliation(s)
- Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy.
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy.
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Daniel Zoboli
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria SS 554, 09042, Monserrato, Italy
| | - Massimiliano Orsini
- Laboratory of Microbial Ecology, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'università 10, 35120, Legnaro, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Adriana Latorre
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Andrey A Lissovsky
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Gian Luigi Pillola
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria SS 554, 09042, Monserrato, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Giorgio Gruppioni
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy.
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Ciucani MM, Ramos-Madrigal J, Hernández-Alonso G, Carmagnini A, Aninta SG, Sun X, Scharff-Olsen CH, Lanigan LT, Fracasso I, Clausen CG, Aspi J, Kojola I, Baltrūnaitė L, Balčiauskas L, Moore J, Åkesson M, Saarma U, Hindrikson M, Hulva P, Bolfíková BČ, Nowak C, Godinho R, Smith S, Paule L, Nowak S, Mysłajek RW, Lo Brutto S, Ciucci P, Boitani L, Vernesi C, Stenøien HK, Smith O, Frantz L, Rossi L, Angelici FM, Cilli E, Sinding MHS, Gilbert MTP, Gopalakrishnan S. The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs. iScience 2023; 26:107307. [PMID: 37559898 PMCID: PMC10407145 DOI: 10.1016/j.isci.2023.107307] [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: 06/22/2022] [Revised: 11/04/2022] [Accepted: 07/04/2023] [Indexed: 08/11/2023] Open
Abstract
The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.
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Affiliation(s)
- Marta Maria Ciucani
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Germán Hernández-Alonso
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Carmagnini
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sabhrina Gita Aninta
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Xin Sun
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Liam Thomas Lanigan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ilaria Fracasso
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Cecilie G. Clausen
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Finland
| | - Ilpo Kojola
- Natural Resources Institute Finland, Rovaniemi, Finland
| | | | | | - Jane Moore
- Società Amatori Cirneco dell’Etna, Modica (RG), Italy
| | - Mikael Åkesson
- Swedish University of Agricultural Sciences, Grimsö Wildlife Research Station, Department of Ecology, Riddarhyttan, Sweden
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Pavel Hulva
- Charles University, Department of Zoology, Faculty of Science, Prague 2, Czech Republic
| | | | - Carsten Nowak
- Center for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Raquel Godinho
- CIBIO/InBIO, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Steve Smith
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Ladislav Paule
- Faculty of Forestry, Technical University, Zvolen, Slovakia
| | - Sabina Nowak
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Robert W. Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Sabrina Lo Brutto
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technology (STEBICEF), University of Palermo, Palermo, Italy
- Museum of Zoology "P. Doderlein", SIMUA, University of Palermo, Palermo, Italy
| | - Paolo Ciucci
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Luigi Boitani
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Hans K. Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Oliver Smith
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Francesco Maria Angelici
- FIZV, Via Marco Aurelio 2, Roma, Italy
- National Center for Wildlife, Al Imam Faisal Ibn Turki Ibn Abdullah, Ulaishah, Saudi Arabia
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage (DBC), University of Bologna, Bologna, Italy
| | - Mikkel-Holger S. Sinding
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Martínez-Navarro B, Gossa T, Carotenuto F, Bartolini-Lucenti S, Palmqvist P, Asrat A, Figueirido B, Rook L, Niespolo EM, Renne PR, Herzlinger G, Hovers E. The earliest Ethiopian wolf: implications for the species evolution and its future survival. Commun Biol 2023; 6:530. [PMID: 37193884 DOI: 10.1038/s42003-023-04908-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/03/2023] [Indexed: 05/18/2023] Open
Abstract
In 2017, a hemimandible (MW5-B208), corresponding to the Ethiopian wolf (Canis simensis), was found in a stratigraphically-controlled and radio-isotopically-dated sequence of the Melka Wakena paleoanthropological site-complex, on the Southeastern Ethiopian Highlands, ~ 2300 m above sea level. The specimen is the first and unique Pleistocene fossil of this species. Our data provide an unambiguous minimum age of 1.6-1.4 Ma for the species' presence in Africa and constitutes the first empirical evidence that supports molecular interpretations. Currently, C. simensis is one of the most endangered carnivore species of Africa. Bioclimate niche modeling applied to the time frame indicated by the fossil suggests that the lineage of the Ethiopian wolf faced severe survival challenges in the past, with consecutive drastic geographic range contractions during warmer periods. These models help to describe future scenarios for the survival of the species. Projections ranging from most pessimistic to most optimistic future climatic scenarios indicate significant reduction of the already-deteriorating territories suitable for the Ethiopian Wolf, increasing the threat to the specie's future survival. Additionally, the recovery of the Melka Wakena fossil underscores the importance of work outside the East African Rift System in research of early human origins and associated biodiversity on the African continent.
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Affiliation(s)
- Bienvenido Martínez-Navarro
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES-CERCA), Zona Educacional 4, Campus Sescelades URV (Edifici W3), 43007, Tarragona, Spain.
- Universitat Rovira i Virgili, Departament d'Història i Història de l'Art, Avinguda de Catalunya 35, 43002, Tarragona, Spain.
| | - Tegenu Gossa
- Human Evolution Research Center (HERC), The University of California at Berkeley, Berkeley, CA, USA.
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Department of History and Heritage Management, Arba Minch University, Arba Minch, Ethiopia.
| | - Francesco Carotenuto
- Department of Earth, Environment and Resource Sciences, University of Naples "Federico II", Naples, Italy
| | - Saverio Bartolini-Lucenti
- Earth Science Department, Paleo[Fab]Lab, University of Florence, Via G. La Pira 4, Firenze, 50121, Italy
- Institut Català de Paleontogia M. Crusafont, Universitat Autònoma de Barcelona, E-08193, Cerdanyola del Vallès, Spain
| | - Paul Palmqvist
- Departamento de Ecología y Geología, Universidad de Málaga, Universidad de Málaga, Campus de Teatinos, 29071, Málaga, Spain
| | - Asfawossen Asrat
- Department of Mining and Geological Engineering, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
- School of Earth Sciences, Addis Ababa University, P. O. Box 1176, Addis Ababa, Ethiopia
| | - Borja Figueirido
- Departamento de Ecología y Geología, Universidad de Málaga, Universidad de Málaga, Campus de Teatinos, 29071, Málaga, Spain
| | - Lorenzo Rook
- Earth Science Department, Paleo[Fab]Lab, University of Florence, Via G. La Pira 4, Firenze, 50121, Italy
| | - Elizabeth M Niespolo
- Department of Geosciences, Princeton University, Princeton, NJ, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Berkeley Geochronology Center, Berkeley, CA, USA
| | - Paul R Renne
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Berkeley Geochronology Center, Berkeley, CA, USA
| | - Gadi Herzlinger
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Erella Hovers
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Institute of Human Origins, Arizona State University, Tempe, USA.
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Zedda M, Brunetti A, Palombo MR. First Attempt to Infer Sound Hearing and Its Paleoenvironmental Implications in the Extinct Insular Canid Cynotherium sardous Studiati, 1857 (Sardinia, Italy). Animals (Basel) 2022; 12:ani12070833. [PMID: 35405823 PMCID: PMC8996844 DOI: 10.3390/ani12070833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/10/2022] [Accepted: 03/13/2022] [Indexed: 11/25/2022] Open
Abstract
Simple Summary The microtomographic approach allows nondestructive acquisition of anatomical details of the bone labyrinth that houses the inner ear. The petrosal bone can be a gold mine of information for a variety of questions in different research fields, including taxonomic, behavioral, and genetic studies. The semicircular canals provide information on head posture and locomotor ability, whereas the cochlea provides data on hearing ability. The petrosal bone is the hardest structure in the skeleton and could be well preserved in fossil specimens. As a result, it is becoming more and more popular in current archaeological and paleontological studies. In this study, petrosal microtomographic analysis was applied for the first time to Cynotherium sardous, a highly modified endemic canid that inhabited Sardinia during the Middle to Late Pleistocene. Indications about its hearing ability may provide interesting insights to better understand the new lifestyle and behavior this canid acquired during the long evolutionary process it underwent in the peculiar insular ecosystem with a depleted fauna. The poor hearing and echolocalization capabilities of Cynotherium sardous would have been the outcome of reduced competition pressure due to the absence of predators and the abundance of prey, such as the large ochotonid Prolagus sardus, while the high-frequency hearing could be interpreted as an adaptation to detect sounds emitted by its preferred prey. Abstract This is the first study on the bony labyrinth of Cynotherium sardous, an intriguing extinct canid that inhabited Sardinia in the late Middle and Late Pleistocene. The morphological features of the cochlea indicate that C. sardous had a lower number of cochlear turns (2.25) than all extant canids. This feature, as well as the reduced length of the spiral canal, the cochlear curvature rate, and the narrow basal membrane, indicates that C. sardous had poor hearing abilities limited to high-frequency sounds with a low limit of 250 Hz and poor echolocalization skills. From the data available, it is not possible to infer whether C. sardous was unable to echolocalize its prey and relied on other senses (e.g., smell and sight) to locate them or whether the acoustic range of C. sardous was specialized for identifying the sounds produced by its most common prey to transmit signals for predator warnings or group communication. All things considered, the results obtained confirm the utility of cochlea morphological studies in reconstructing the hearing abilities of this species and in providing some suggestions about its ethology, but they fall short of providing any new sound evidence regarding the ecological role of C. sardous in the Late Pleistocene Sardinian ecosystem.
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Affiliation(s)
- Marco Zedda
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Correspondence: ; Tel.: +39-079-229-583
| | - Antonio Brunetti
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Maria Rita Palombo
- CNR-IGAG c/o Department of Earth Sciences, Sapienza University, 00185 Rome, Italy;
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