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Meier R, Hartop E, Pylatiuk C, Srivathsan A. Towards holistic insect monitoring: species discovery, description, identification and traits for all insects. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230120. [PMID: 38705187 PMCID: PMC11070263 DOI: 10.1098/rstb.2023.0120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/25/2024] [Indexed: 05/07/2024] Open
Abstract
Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Rudolf Meier
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Institute of Biology, Humboldt University, 10115 Berlin, Germany
| | - Emily Hartop
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Christian Pylatiuk
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
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2
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Sueur C, Huffman MA. Co-cultures: exploring interspecies culture among humans and other animals. Trends Ecol Evol 2024:S0169-5347(24)00122-8. [PMID: 38902164 DOI: 10.1016/j.tree.2024.05.011] [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: 01/25/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
The concept of 'co-culture' is introduced as a novel framework for understanding the mutual cultural evolution between animal species, including, but not only, humans. It explores the dynamics of interspecies interactions, particularly in how different species influence each other's behavioural and cognitive adaptations. Various instances of interspecies cultural exchange are highlighted, such as the acquisition of medicinal plants from animals resulting in a shared medicinal culture, adaptive behaviours of urban wildlife, and cooperative behaviours between animal species. Co-culture challenges the notion of species-specific culture, underscoring the complexity and interconnectedness of human and animal societies, and between animal societies. Further research into co-culture is advocating and emphasising its implications for conservation, urban planning, and a deeper understanding of animal cognition and behaviour.
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Affiliation(s)
- Cédric Sueur
- Université de Strasbourg, IPHC UMR7178, CNRS, Strasbourg, France; Anthropo-lab, ETHICS EA 7446, Université Catholique de Lille, Lille, France; Institut Universitaire de France, Paris, France.
| | - Michael A Huffman
- Wildlife Research Center, Kyoto University, Inuyama, Japan; Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
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3
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Garroway CJ, de Greef E, Lefort KJ, Thorstensen MJ, Foote AD, Matthews CJD, Higdon JW, Kucheravy CE, Petersen SD, Rosing-Asvid A, Ugarte F, Dietz R, Ferguson SH. Climate change introduces threatened killer whale populations and conservation challenges to the Arctic. GLOBAL CHANGE BIOLOGY 2024; 30:e17352. [PMID: 38822670 DOI: 10.1111/gcb.17352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
The Arctic is the fastest-warming region on the planet, and the lengthening ice-free season is opening Arctic waters to sub-Arctic species such as the killer whale (Orcinus orca). As apex predators, killer whales can cause significant ecosystem-scale changes. Setting conservation priorities for killer whales and their Arctic prey species requires knowledge of their evolutionary history and demographic trajectory. Using whole-genome resequencing of 24 killer whales sampled in the northwest Atlantic, we first explored the population structure and demographic history of Arctic killer whales. To better understand the broader geographic relationship of these Arctic killer whales to other populations, we compared them to a globally sampled dataset. Finally, we assessed threats to Arctic killer whales due to anthropogenic harvest by reviewing the peer-reviewed and gray literature. We found that there are two highly genetically distinct, non-interbreeding populations of killer whales using the eastern Canadian Arctic. These populations appear to be as genetically different from each other as are ecotypes described elsewhere in the killer whale range; however, our data cannot speak to ecological differences between these populations. One population is newly identified as globally genetically distinct, and the second is genetically similar to individuals sampled from Greenland. The effective sizes of both populations recently declined, and both appear vulnerable to inbreeding and reduced adaptive potential. Our survey of human-caused mortalities suggests that harvest poses an ongoing threat to both populations. The dynamic Arctic environment complicates conservation and management efforts, with killer whales adding top-down pressure on Arctic food webs crucial to northern communities' social and economic well-being. While killer whales represent a conservation priority, they also complicate decisions surrounding wildlife conservation and resource management in the Arctic amid the effects of climate change.
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Affiliation(s)
- Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Evelien de Greef
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kyle J Lefort
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
| | - Matt J Thorstensen
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew D Foote
- Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Cory J D Matthews
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
| | - Jeff W Higdon
- Higdon Wildlife Consulting, Winnipeg, Manitoba, Canada
| | - Caila E Kucheravy
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
| | - Stephen D Petersen
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Conservation and Research Department, Assiniboine Park Zoo, Winnipeg, Manitoba, Canada
| | | | | | - Rune Dietz
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Steven H Ferguson
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
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4
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Jourdain E, Karoliussen R, Fordyce Martin SL, Langangen Ø, Robeck T, Borgå K, Ruus A, Foote AD. Social and genetic connectivity despite ecological variation in a killer whale network. Proc Biol Sci 2024; 291:20240524. [PMID: 38628123 PMCID: PMC11022014 DOI: 10.1098/rspb.2024.0524] [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: 03/03/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Philopatric kin-based societies encourage a narrow breadth of conservative behaviours owing to individuals primarily learning from close kin, promoting behavioural homogeneity. However, weaker social ties beyond kin, and across a behaviourally diverse social landscape, could be sufficient to induce variation and a greater ecological niche breadth. We investigated a network of 457 photo-identified killer whales from Norway (548 encounters in 2008-2021) with diet data available (46 mixed-diet individuals feeding on both fish and mammals, and 411 exclusive fish-eaters) to quantify patterns of association within and between diet groups, and to identify underlying correlates. We genotyped a subset of 106 whales to assess patterns of genetic differentiation. Our results suggested kinship as main driver of social bonds within and among cohesive social units, while diet was most likely a consequence reflective of cultural diffusion, rather than a driver. Flexible associations within and between ecologically diverse social units led to a highly connected network, reducing social and genetic differentiation between diet groups. Our study points to a role of social connectivity, in combination with individual behavioural variation, in influencing population ecology in killer whales.
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Affiliation(s)
- Eve Jourdain
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Norwegian Orca Survey, 8480 Andenes, Norway
| | | | - Sarah L. Fordyce Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technologies (NTNU), 7491 Trondheim, Norway
| | | | - Todd Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL 32819, USA
| | - Katrine Borgå
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Anders Ruus
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Norwegian Institute of Water Research, 32821 Oslo, Norway
| | - Andrew D. Foote
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technologies (NTNU), 7491 Trondheim, Norway
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5
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Morin PA, McCarthy ML, Fung CW, Durban JW, Parsons KM, Perrin WF, Taylor BL, Jefferson TA, Archer FI. Revised taxonomy of eastern North Pacific killer whales ( Orcinus orca): Bigg's and resident ecotypes deserve species status. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231368. [PMID: 38545612 PMCID: PMC10966402 DOI: 10.1098/rsos.231368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 04/26/2024]
Abstract
Killer whales (Orcinus orca) are currently recognized as a single ecologically and morphologically diverse, globally distributed species. Multiple morphotypes or ecotypes have been described, often associated with feeding specialization, and several studies have suggested taxonomic revision to include multiple subspecies or species in the genus. We review the ecological, morphological and genetic data for the well-studied 'resident' and Bigg's (aka 'transient') ecotypes in the eastern North Pacific and use quantitative taxonomic guidelines and standards to determine whether the taxonomic status of these killer whale ecotypes should be revised. Our review and new analyses indicate that species-level status is justified in both cases, and we conclude that eastern North Pacific Bigg's killer whales should be recognized as Orcinus rectipinnus (Cope in Scammon, 1869) and resident killer whales should be recognized as Orcinus ater (Cope in Scammon, 1869).
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Affiliation(s)
- Phillip A. Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Morgan L. McCarthy
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Charissa W. Fung
- University of British Columbia, Vancouver, British ColumbiaV6T 1Z4, Canada
| | - John W. Durban
- Marine Mammal Institute, Oregon State University, Newport, OR97365, USA
| | - Kim M. Parsons
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA98112, USA
| | - William F. Perrin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Barbara L. Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Thomas A. Jefferson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
| | - Frederick I. Archer
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA92037, USA
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6
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Teixeira H, Le Corre M, Michon L, Nicoll MAC, Jaeger A, Nikolic N, Pinet P, Couzi FX, Humeau L. Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts. Sci Rep 2024; 14:1960. [PMID: 38263429 PMCID: PMC10805739 DOI: 10.1038/s41598-024-52556-9] [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: 10/04/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.
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Affiliation(s)
- Helena Teixeira
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France.
| | - Matthieu Le Corre
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | - Laurent Michon
- Université de La Réunion, Laboratoire Géosciences Réunion, 97744, Saint Denis, France
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, 75005, Paris, France
| | - Malcolm A C Nicoll
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Audrey Jaeger
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | | | - Patrick Pinet
- Parc National de La Réunion, Life+ Pétrels, 258 Rue de la République, 97431, Plaine des Palmistes, Réunion Island, France
| | - François-Xavier Couzi
- Société d'Etudes Ornithologiques de La Réunion (SEOR), 13 ruelle des Orchidées, 97440, Saint André, Réunion Island, France
| | - Laurence Humeau
- UMR PVBMT (Université de La Réunion, CIRAD), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
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7
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Whitehead H. Sperm whale clans and human societies. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231353. [PMID: 38204796 PMCID: PMC10776220 DOI: 10.1098/rsos.231353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
Sperm whale society is structured into clans that are primarily distinguished by vocal dialects, which may be symbolic markers of clan identity. However, clans also differ in non-vocal behaviour. These distinctive behaviours, as well as clan membership itself, are learned socially, largely within matrilines. The clans can contain thousands of whales and span thousands of kilometres. Two or more clans typically use an area, but the whales only socialize with members of their own clan. In many respects the closest parallel may be the ethno-linguistic groups of humans. Patterns and processes of human prehistory that may be instructive in studying sperm whale clans include: the extreme variability of human societies; no clear link between modes of resource acquisition and social structure; that patterns of vocalizations may not map well onto other behavioural distinctions; and that interacting societies may deliberately distinguish their behaviour (schismogenesis). Conversely, while the two species and their societies are very different, the existence of very large-scale social structures in both sperm whales and humans supports some primary drivers of the phenomenon that are common to both species (such as cognition, cooperation, culture and mobility) and contraindicates others (e.g. tool-making and syntactic language).
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Affiliation(s)
- Hal Whitehead
- Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
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8
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Morin PA, Martien KK, Lang AR, Hancock-Hanser BL, Pease VL, Robertson KM, Sattler M, Slikas E, Rosel PE, Baker CS, Taylor BL, Archer FI. Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes. J Hered 2023; 114:612-624. [PMID: 37647537 DOI: 10.1093/jhered/esad049] [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: 01/31/2023] [Accepted: 08/28/2023] [Indexed: 09/01/2023] Open
Abstract
In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic decisions relative to conventional use of the control region or other gene fragments of the mitochondrial genome. To improve quantitative guidelines for taxonomic decisions in cetaceans, we build on a previous effort targeting the control region and evaluate, for whole mitogenome sequences, a suite of divergence and diagnosability estimates for pairs of recognized cetacean populations, subspecies, and species. From this overview, we recommend new guidelines based on complete mitogenomes, combined with other types of evidence for isolation and divergence, which will improve resolution for taxonomic decisions, especially in the face of small sample sizes or low levels of genetic diversity. We further use simulated data to assist interpretations of divergence in the context of varying forms of historical demography, culture, and ecology.
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Affiliation(s)
- Phillip A Morin
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Karen K Martien
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Aimee R Lang
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Brittany L Hancock-Hanser
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Victoria L Pease
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Maya Sattler
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Elizabeth Slikas
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Patricia E Rosel
- Marine Mammal and Turtle Division, Southeast Fisheries Science Center, National Marine Fisheries Service, NOAA, Lafayette, LA, United States
| | - C Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, United States
| | - Barbara L Taylor
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
| | - Frederick I Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, United States
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9
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Pratt EAL, Beheregaray LB, Fruet P, Tezanos-Pinto G, Bilgmann K, Zanardo N, Diaz-Aguirre F, Secchi ER, Freitas TRO, Möller LM. Genomic Divergence and the Evolution of Ecotypes in Bottlenose Dolphins (Genus Tursiops). Genome Biol Evol 2023; 15:evad199. [PMID: 37935115 PMCID: PMC10655200 DOI: 10.1093/gbe/evad199] [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: 10/27/2023] [Revised: 10/03/2023] [Accepted: 10/14/2023] [Indexed: 11/09/2023] Open
Abstract
Climatic changes have caused major environmental restructuring throughout the world's oceans. Marine organisms have responded to novel conditions through various biological systems, including genomic adaptation. Growing accessibility of next-generation DNA sequencing methods to study nonmodel species has recently allowed genomic changes underlying environmental adaptations to be investigated. This study used double-digest restriction-site associated DNA (ddRAD) sequence data to investigate the genomic basis of ecotype formation across currently recognized species and subspecies of bottlenose dolphins (genus Tursiops) in the Southern Hemisphere. Subspecies-level genomic divergence was confirmed between the offshore common bottlenose dolphin (T. truncatus truncatus) and the inshore Lahille's bottlenose dolphin (T. t. gephyreus) from the southwestern Atlantic Ocean (SWAO). Similarly, subspecies-level divergence is suggested between inshore (eastern Australia) Indo-Pacific bottlenose dolphin (T. aduncus) and the proposed Burrunan dolphin (T. australis) from southern Australia. Inshore bottlenose dolphin lineages generally had lower genomic diversity than offshore lineages, a pattern particularly evident for T. t. gephyreus, which showed exceptionally low diversity. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems appear to have undergone repeated adaptive evolution in inshore lineages across the Southern Hemisphere. We hypothesize that comparable selective pressures in the inshore environment drove similar adaptive responses in each lineage, supporting parallel evolution of inshore bottlenose dolphins. With climate change altering marine ecosystems worldwide, it is crucial to gain an understanding of the adaptive capacity of local species and populations. Our study provides insights into key adaptive pathways that may be important for the long-term survival of cetaceans and other organisms in a changing marine environment.
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Affiliation(s)
- Eleanor A L Pratt
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Pedro Fruet
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Kaosa, Rio Grande, Brazil
| | | | - Kerstin Bilgmann
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Department of Environment and Water, Adelaide, South Australia, Australia
| | - Fernando Diaz-Aguirre
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Eduardo R Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
| | - Thales R O Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
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10
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Wang D, Sun Y, Lei W, Zhu H, Wang J, Bi H, Feng S, Liu J, Ru D. Backcrossing to different parents produced two distinct hybrid species. Heredity (Edinb) 2023; 131:145-155. [PMID: 37264213 PMCID: PMC10382510 DOI: 10.1038/s41437-023-00630-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
Repeated homoploid hybrid speciation (HHS) events with the same parental species have rarely been reported. In this study, we used population transcriptome data to test paraphyly and HHS events in the conifer Picea brachytyla. Our analyses revealed non-sister relationships for two lineages of P. brachytyla, with the southern lineage being placed within the re-circumscribed P. likiangensis species complex (PLSC) and P. brachytyla sensu stricto (s.s.) consisted solely of the northern lineage, forming a distinct clade that is paratactic to both the PLSC and P. wilsonii. Our phylogenetic and coalescent analyses suggested that P. brachytyla s.s. arose from HHS between the ancestor of the PLSC before its diversification and P. wilsonii through an intermediate hybrid lineage at an early stage and backcrossing to the ancestral PLSC. Additionally, P. purpurea shares the same parents and an extinct lineage with P. brachytyla s.s. but backcrossing to the other parent, P. wilsonii at a later stage. We reveal the first case that backcrossing to different parents of the same extinct hybrid lineage produced two different hybrid species. Our results highlight the existence of more reticulate evolution during species diversification in the spruce genus and more complex homoploid hybrid events than previously identified.
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Affiliation(s)
- Donglei Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Yongshuai Sun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Weixiao Lei
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hui Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Ji Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Hao Bi
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai, China
| | - Jianquan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China.
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Dafu Ru
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China.
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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11
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Rutz C, Bronstein M, Raskin A, Vernes SC, Zacarian K, Blasi DE. Using machine learning to decode animal communication. Science 2023; 381:152-155. [PMID: 37440653 DOI: 10.1126/science.adg7314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
New methods promise transformative insights and conservation benefits.
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Affiliation(s)
- Christian Rutz
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
| | - Michael Bronstein
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
| | - Aza Raskin
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
| | - Sonja C Vernes
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
| | | | - Damián E Blasi
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
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12
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Weiss MN, Croft DP. Killer whales. Curr Biol 2023; 33:R668-R670. [PMID: 37339590 DOI: 10.1016/j.cub.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Michael Weiss and Darren Croft introduce Orcas (Orcinus orca) also known as killer whales.
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Affiliation(s)
- Michael N Weiss
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK; Center for Whale Research, Friday Harbor, WA, USA
| | - Darren P Croft
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK.
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13
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Wittwer S, Gerber L, Allen SJ, Willems EP, Marfurt SM, Krützen M. Reconstructing the colonization history of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in Northwestern Australia. Mol Ecol 2023. [PMID: 37173858 DOI: 10.1111/mec.16984] [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] [Received: 11/24/2022] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Bottlenose dolphins (Tursiops spp.) are found in waters around Australia, with T. truncatus typically occupying deeper, more oceanic habitat, while T. aduncus occur in shallower, coastal waters. Little is known about the colonization history of T. aduncus along the Western Australian coastline; however, it has been hypothesized that extant populations are the result of an expansion along the coastline originating from a source in the north of Australia. To investigate the history of coastal T. aduncus populations in the area, we generated a genomic SNP dataset using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach. The resulting dataset consisted of 103,201 biallelic SNPs for 112 individuals which were sampled from eleven coastal and two offshore sites between Shark Bay and Cygnet Bay, Western Australia. Our population genomic analyses showed a pattern consistent with the proposed source in the north with significant isolation by distance along the coastline, as well as a reduction in genomic diversity measures along the coastline with Shark Bay showing the most pronounced reduction. Our demographic analysis indicated that the expansion of T. aduncus along the coastline began around the last glacial maximum and progressed southwards with the Shark Bay population being founded only 13 kya. Our results are in line with coastal colonization histories inferred for Tursiops globally, highlighting the ability of delphinids to rapidly colonize novel coastal niches as habitat is released during glacial cycle-related global sea level and temperature changes.
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Affiliation(s)
- Samuel Wittwer
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - Livia Gerber
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australian Capital Territory, Australia
| | - Simon J Allen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Erik P Willems
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - Svenja M Marfurt
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
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14
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Wang C, Wu DD, Yuan YH, Yao MC, Han JL, Wu YJ, Shan F, Li WP, Zhai JQ, Huang M, Peng SM, Cai QH, Yu JY, Liu QX, Liu ZY, Li LX, Teng MS, Huang W, Zhou JY, Zhang C, Chen W, Tu XL. Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation. BMC Biol 2023; 21:64. [PMID: 37069598 PMCID: PMC10111772 DOI: 10.1186/s12915-023-01552-y] [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] [Received: 03/29/2022] [Accepted: 02/21/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Among six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers. RESULTS In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher FROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records. CONCLUSIONS The identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.
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Affiliation(s)
- Chen Wang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
| | | | - Meng-Cheng Yao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | - Ya-Jiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Fen Shan
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Wan-Ping Li
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Jun-Qiong Zhai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Mian Huang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Shi-Ming Peng
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Qin-Hui Cai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | | | | | | | - Lin-Xiang Li
- Suzhou Shangfangshan Forest Zoo, Suzhou, 215009, China
| | | | - Wei Huang
- Nanchang Zoo, Nanchang, 330025, China
| | - Jun-Ying Zhou
- Chinese Association of Zoological Gardens, Beijing, 100037, China
| | - Chi Zhang
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China.
| | - Xiao-Long Tu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, 650204, China.
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15
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Suzuki M, Ohno K, Sawayama E, Morinaga SI, Kishida T, Matsumoto T, Kato H. Genomics reveals a genetically isolated population of the Pacific white-sided dolphin (Lagenorhynchus obliquidens) distributed in the Sea of Japan. Mol Ecol 2023; 32:881-891. [PMID: 36440502 DOI: 10.1111/mec.16797] [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: 07/21/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]
Abstract
The processes by which animals become genetically isolated in an open environment such as the ocean have not yet been fully elucidated. Morphologically different populations of Pacific white-sided dolphin Lagenorhynchus obliquidens are observed sympatrically in the Sea of Japan. However, genetic studies that exclusively used limited mitochondrial loci or microsatellite DNA have failed to demonstrate the existence of genetically distinct populations. Here, to reveal the population structure, we analysed genome-wide population genetic data using single nucleotide polymorphisms (SNPs) gathered in 2018-2021 from all domestic captive individuals in aquaria, the majority of which originated from the wild, as well as from some stranded individuals, together covering a wide area of coastal water around Japan (n = 123). Multiplexed intersimple sequence repeat genotyping-by-sequencing analysis was performed to obtain the SNP data. Principal coordinate analysis and the clustering method structure indicated that two genetically-distinct populations exist, with little interpopulation gene flow revealed. In addition, the genotypic segregation was reflected in differences in external morphotype. Furthermore, a population demographic analysis based on the whole-genome sequences of an individual from each population indicated that sea-level changes during the Last Glacial Period probably led to allopatric divergence of this species in a limited area of the Sea of Japan, with that group subsequently sharing a distribution area with the other population. These findings yield insights into the formation of genetically isolated sympatric populations in the ocean.
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Affiliation(s)
- Miwa Suzuki
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Kaho Ohno
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Eitaro Sawayama
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Shin-Ichi Morinaga
- Department of Natural & Environmental Science, Teikyo University of Science, Tokyo, Japan
| | - Takushi Kishida
- Museum of Natural and Environmental History, Shizuoka, Japan
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16
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Zamorano-Abramson J, Michon M, Hernández-Lloreda MV, Aboitiz F. Multimodal imitative learning and synchrony in cetaceans: A model for speech and singing evolution. Front Psychol 2023; 14:1061381. [PMID: 37138983 PMCID: PMC10150787 DOI: 10.3389/fpsyg.2023.1061381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/13/2023] [Indexed: 05/05/2023] Open
Abstract
Multimodal imitation of actions, gestures and vocal production is a hallmark of the evolution of human communication, as both, vocal learning and visual-gestural imitation, were crucial factors that facilitated the evolution of speech and singing. Comparative evidence has revealed that humans are an odd case in this respect, as the case for multimodal imitation is barely documented in non-human animals. While there is evidence of vocal learning in birds and in mammals like bats, elephants and marine mammals, evidence in both domains, vocal and gestural, exists for two Psittacine birds (budgerigars and grey parrots) and cetaceans only. Moreover, it draws attention to the apparent absence of vocal imitation (with just a few cases reported for vocal fold control in an orangutan and a gorilla and a prolonged development of vocal plasticity in marmosets) and even for imitation of intransitive actions (not object related) in monkeys and apes in the wild. Even after training, the evidence for productive or "true imitation" (copy of a novel behavior, i.e., not pre-existent in the observer's behavioral repertoire) in both domains is scarce. Here we review the evidence of multimodal imitation in cetaceans, one of the few living mammalian species that have been reported to display multimodal imitative learning besides humans, and their role in sociality, communication and group cultures. We propose that cetacean multimodal imitation was acquired in parallel with the evolution and development of behavioral synchrony and multimodal organization of sensorimotor information, supporting volitional motor control of their vocal system and audio-echoic-visual voices, body posture and movement integration.
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Affiliation(s)
- José Zamorano-Abramson
- Centro de Investigación en Complejidad Social, Facultad de Gobierno, Universidad del Desarrollo, Santiago, Chile
- Grupo UCM de Psicobiología Social, Evolutiva y Comparada, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: José Zamorano-Abramson,
| | - Maëva Michon
- Centro de Estudios en Neurociencia Humana y Neuropsicología, Facultad de Psicología, Universidad Diego Portales, Santiago, Chile
- Laboratory for Cognitive and Evolutionary Neuroscience, Department of Psychiatry, Faculty of Medicine, Interdisciplinary Center for Neuroscience, Pontificia Universidad Católica de, Santiago, Chile
- Maëva Michon,
| | - Ma Victoria Hernández-Lloreda
- Grupo UCM de Psicobiología Social, Evolutiva y Comparada, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Psicobiología y Metodología de las Ciencias del Comportamiento, Facultad de Psicología, Campus de Somosaguas, Universidad Complutense de Madrid, Madrid, Spain
| | - Francisco Aboitiz
- Laboratory for Cognitive and Evolutionary Neuroscience, Department of Psychiatry, Faculty of Medicine, Interdisciplinary Center for Neuroscience, Pontificia Universidad Católica de, Santiago, Chile
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17
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Tigano A, Russello MA. The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid. Mol Ecol 2022; 31:6588-6604. [PMID: 36208020 DOI: 10.1111/mec.16724] [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: 06/20/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.
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Affiliation(s)
- Anna Tigano
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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18
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Seascape genomics of common dolphins (Delphinus delphis) reveals adaptive diversity linked to regional and local oceanography. BMC Ecol Evol 2022; 22:88. [PMID: 35818031 PMCID: PMC9275043 DOI: 10.1186/s12862-022-02038-1] [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: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
High levels of standing genomic variation in wide-ranging marine species may enhance prospects for their long-term persistence. Patterns of connectivity and adaptation in such species are often thought to be influenced by spatial factors, environmental heterogeneity, and oceanographic and geomorphological features. Population-level studies that analytically integrate genome-wide data with environmental information (i.e., seascape genomics) have the potential to inform the spatial distribution of adaptive diversity in wide-ranging marine species, such as many marine mammals. We assessed genotype-environment associations (GEAs) in 214 common dolphins (Delphinus delphis) along > 3000 km of the southern coast of Australia.
Results
We identified 747 candidate adaptive SNPs out of a filtered panel of 17,327 SNPs, and five putatively locally-adapted populations with high levels of standing genomic variation were disclosed along environmentally heterogeneous coasts. Current velocity, sea surface temperature, salinity, and primary productivity were the key environmental variables associated with genomic variation. These environmental variables are in turn related to three main oceanographic phenomena that are likely affecting the dispersal of common dolphins: (1) regional oceanographic circulation, (2) localised and seasonal upwellings, and (3) seasonal on-shelf circulation in protected coastal habitats. Signals of selection at exonic gene regions suggest that adaptive divergence is related to important metabolic traits.
Conclusion
To the best of our knowledge, this represents the first seascape genomics study for common dolphins (genus Delphinus). Information from the associations between populations and their environment can assist population management in forecasting the adaptive capacity of common dolphins to climate change and other anthropogenic impacts.
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19
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Onoufriou AB, Gaggiotti OE, Aguilar de Soto N, McCarthy ML, Morin PA, Rosso M, Dalebout M, Davison N, Baird RW, Baker CS, Berrow S, Brownlow A, Burns D, Caurant F, Claridge D, Constantine R, Demaret F, Dreyer S, Ðuras M, Durban JW, Frantzis A, Freitas L, Genty G, Galov A, Hansen SS, Kitchener AC, Martin V, Mignucci-Giannoni AA, Montano V, Moulins A, Olavarría C, Poole MM, Reyes Suárez C, Rogan E, Ryan C, Schiavi A, Tepsich P, Urban R. J, West K, Olsen MT, Carroll EL. Biogeography in the deep: Hierarchical population genomic structure of two beaked whale species. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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20
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Foote A, Bunskoek P. The genome sequence of the killer whale, Orcinus orca (Linnaeus, 1758). Wellcome Open Res 2022; 7:250. [PMID: 36974126 PMCID: PMC10039322 DOI: 10.12688/wellcomeopenres.18278.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly from an individual female Orcinus orca (the killer whale; Chordata; Mammalia; Artiodactyla; Delphinidae). The genome sequence is 2.65 gigabases in span. The majority of the assembly (93.76%) is scaffolded into 22 chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.4 kilobases in length.
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Affiliation(s)
- Andrew Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | | | | | - Tree of Life Core Informatics collective
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Dolfinarium Harderwijk, Harderwijk, Netherlands Antilles
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21
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de Greef E, Einfeldt AL, Miller PJO, Ferguson SH, Garroway CJ, Lefort KJ, Paterson IG, Bentzen P, Feyrer LJ. Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus. Mol Ecol 2022; 31:4919-4931. [PMID: 35947506 PMCID: PMC9804413 DOI: 10.1111/mec.16643] [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: 03/17/2022] [Revised: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 01/05/2023]
Abstract
Information on wildlife population structure, demographic history, and adaptations are fundamental to understanding species evolution and informing conservation strategies. To study this ecological context for a cetacean of conservation concern, we conducted the first genomic assessment of the northern bottlenose whale, Hyperoodon ampullatus, using whole-genome resequencing data (n = 37) from five regions across the North Atlantic Ocean. We found a range-wide pattern of isolation-by-distance with a genetic subdivision distinguishing three subgroups: the Scotian Shelf, western North Atlantic, and Jan Mayen regions. Signals of elevated levels of inbreeding in the Endangered Scotian Shelf population indicate this population may be more vulnerable than the other two subgroups. In addition to signatures of inbreeding, evidence of local adaptation in the Scotian Shelf was detected across the genome. We found a long-term decline in effective population size for the species, which poses risks to their genetic diversity and may be exacerbated by the isolating effects of population subdivision. Protecting important habitat and migratory corridors should be prioritized to rebuild population sizes that were diminished by commercial whaling, strengthen gene flow, and ensure animals can move across regions in response to environmental changes.
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Affiliation(s)
- Evelien de Greef
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada,Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | | | | | | | - Colin J. Garroway
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Kyle J. Lefort
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Ian G. Paterson
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Paul Bentzen
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Laura J. Feyrer
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada,Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
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22
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Tiley GP, van Elst T, Teixeira H, Schüßler D, Salmona J, Blanco MB, Ralison JM, Randrianambinina B, Rasoloarison RM, Stahlke AR, Hohenlohe PA, Chikhi L, Louis EE, Radespiel U, Yoder AD. Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests. Mol Ecol 2022; 31:4901-4918. [PMID: 35880414 DOI: 10.1111/mec.16632] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 06/25/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component of the pre-human Central Highlands vegetation. Consequently, there is now vigorous debate regarding the extent to which these grasslands have expanded due to anthropogenic pressures. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, making them a valuable indicator species. Population divergences among forest-dwelling mammals will reflect changes to their habitat, including fragmentation, whereas patterns of post-divergence gene flow can reveal formerly wooded migration corridors. To explore these patterns, we used RADseq data to infer population genetic structure, demographic models of post-divergence gene flow, and population size change through time. The results offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread forest fragmentation occurred naturally during a period of decreased precipitation near the Last Glacial Maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may already be vulnerable from paleoclimatic conditions.
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Affiliation(s)
- George P Tiley
- Department of Biology, Duke University, Durham, NC, USA.,Royal Botanic Gardens Kew, Richmond, UK
| | - Tobias van Elst
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Helena Teixeira
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Dominik Schüßler
- Research Group Vegetation Ecology and Nature Conservation, Institute of Biology and Chemistry, University of Hildesheim, Hildesheim, Germany
| | - Jordi Salmona
- CNRS, Université Paul Sabatier, IRD; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | | | - José M Ralison
- Département de Biologie Animale, Université d'Antananarivo, Antananarivo, Madagascar
| | - Blanchard Randrianambinina
- Group d'Etude et de Recherche sur les Primates de Madagascar (GERP), Antananarivo, Madagascar.,Faculté des Sciences, University of Mahajanga, Mahajanga, Madagascar
| | - Rodin M Rasoloarison
- Département de Biologie Animale, Université d'Antananarivo, Antananarivo, Madagascar.,Group d'Etude et de Recherche sur les Primates de Madagascar (GERP), Antananarivo, Madagascar
| | - Amanda R Stahlke
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Lounès Chikhi
- CNRS, Université Paul Sabatier, IRD; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA
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23
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Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
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Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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24
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Servheen C, Gunther KA. Conservation and management of the culture of bears. Ecol Evol 2022; 12:e8840. [PMID: 35462976 PMCID: PMC9019140 DOI: 10.1002/ece3.8840] [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: 12/04/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 11/10/2022] Open
Abstract
Culture is widely accepted as an important social factor present across a wide range of species. Bears have a culture as defined as behavioral traditions inherited through social learning usually from mothers to offspring. Successful bear cultures can enhance fitness and resource exploitation benefits. In contrast, some bear cultures related to response to humans and human‐related foods can be maladaptive and result in reduced fitness and direct mortality. In environments with minimal human influence most bear culture has evolved over generations to be beneficial and well adapted to enhance fitness. However, most bears across the world do not live in areas with minimal human influence and in these areas, bear culture is often changed by bear interactions with humans, usually to the detriment of bear survival. We highlight the importance of identifying unique bear cultural traits that allow efficient use of local resources and the value of careful management to preserve these adaptive cultural behaviors. It is also important to select against maladaptive cultural behaviors that are usually related to humans in order to reduce human–bear conflicts and high bear mortality. We use examples from Yellowstone National Park to demonstrate how long‐term management to reduce maladaptive bear cultures related to humans has resulted in healthy bear populations and a low level of human–bear conflict in spite of a high number of Yellowstone National Park visitors in close association with bears.
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Affiliation(s)
- Christopher Servheen
- W.A. Franke College of Forestry and Conservation University of Montana Missoula Montana USA
| | - Kerry A. Gunther
- Bear Management Office Yellowstone Center for Resources Yellowstone National Park Wyoming USA
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25
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Berta A, Kienle SS, Lanzetti A. Evolution: Killer whale bites and appetites. Curr Biol 2022; 32:R375-R377. [DOI: 10.1016/j.cub.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Neveceralova P, Carroll EL, Steel D, Vermeulen E, Elwen S, Zidek J, Stafford JK, Chivell W, Hulva P. Population Changes in a Whale Breeding Ground Revealed by Citizen Science Noninvasive Genetics. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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27
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Palma-Vera SE, Reyer H, Langhammer M, Reinsch N, Derezanin L, Fickel J, Qanbari S, Weitzel JM, Franzenburg S, Hemmrich-Stanisak G, Schoen J. Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. BMC Biol 2022; 20:52. [PMID: 35189878 PMCID: PMC8862358 DOI: 10.1186/s12915-022-01248-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits. RESULTS Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits. CONCLUSIONS The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.
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Affiliation(s)
- Sergio E Palma-Vera
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
| | - Henry Reyer
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Martina Langhammer
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Norbert Reinsch
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Lorena Derezanin
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Joerns Fickel
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- University of Potsdam, Institute for Biochemistry and Biology, Potsdam, Germany
| | - Saber Qanbari
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Joachim M Weitzel
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | | | | | - Jennifer Schoen
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Department of Reproduction Biology, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
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28
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Anderson SJ, Côté SD, Richard JH, Shafer ABA. Genomic architecture of phenotypic extremes in a wild cervid. BMC Genomics 2022; 23:126. [PMID: 35151275 PMCID: PMC8841092 DOI: 10.1186/s12864-022-08333-x] [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: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 12/30/2022] Open
Abstract
Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.
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29
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Pratt EAL, Beheregaray LB, Bilgmann K, Zanardo N, Diaz-Aguirre F, Brauer C, Sandoval-Castillo J, Möller LM. Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity. Mol Ecol 2022; 31:2223-2241. [PMID: 35146819 DOI: 10.1111/mec.16389] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/30/2022]
Abstract
Heterogeneous seascapes and strong environmental gradients in coastal waters are expected to influence adaptive divergence, particularly in species with large population sizes where selection is expected to be highly efficient. However, these influences might also extend to species characterized by strong social structure, natal philopatry and small home ranges. We implemented a seascape genomic study to test this hypothesis in Indo-Pacific bottlenose dolphins (Tursiops aduncus) distributed along the environmentally heterogeneous coast of southern Australia. The datasets included oceanographic and environmental variables thought to be good predictors of local adaptation in dolphins and 8,081 filtered single nucleotide polymorphisms (SNPs) genotyped for individuals sampled from seven different bioregions. From a neutral perspective, population structure and connectivity of the dolphins were generally influenced by habitat type and social structuring. Genotype-environment association analysis identified 241 candidate adaptive loci and revealed that sea surface temperature and salinity gradients influenced adaptive divergence in these animals at both large- (1,000s km) and fine-scales (<100 km). Enrichment analysis and annotation of candidate genes revealed functions related to sodium-activated ion transport, kidney development, adipogenesis and thermogenesis. The findings of spatial adaptive divergence and inferences of putative physiological adaptations challenge previous suggestions that marine megafauna is most likely to be affected by environmental and climatic changes via indirect, trophic effects. Our work contributes to conservation management of coastal bottlenose dolphins subjected to anthropogenic disturbance and to efforts of clarifying how seascape heterogeneity influences adaptive diversity and evolution in small cetaceans.
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Affiliation(s)
- Eleanor A L Pratt
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Kerstin Bilgmann
- Department of Biological Sciences, Macquarie University, 2109, New South Wales, Australia
| | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Department of Environment and Water, Adelaide, 5000, South Australia, Australia
| | - Fernando Diaz-Aguirre
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Chris Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
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30
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Chen C, Parejo M, Momeni J, Langa J, Nielsen RO, Shi W, Vingborg R, Kryger P, Bouga M, Estonba A, Meixner M. Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing. Genes (Basel) 2022; 13:genes13020182. [PMID: 35205227 PMCID: PMC8872436 DOI: 10.3390/genes13020182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 01/27/2023] Open
Abstract
Background: Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera). Methods: We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches. Results: Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers. Conclusions: If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory.
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Affiliation(s)
- Chao Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China;
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing 100093, China
- Correspondence: (C.C.); (M.P.)
| | - Melanie Parejo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.L.); (A.E.)
- Swiss Bee Research Center, Agroscope, 3003 Bern, Switzerland
- Correspondence: (C.C.); (M.P.)
| | - Jamal Momeni
- Eurofins Genomics, 8200 Aarhus, Denmark; (J.M.); (R.O.N.); (R.V.)
| | - Jorge Langa
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.L.); (A.E.)
| | | | - Wei Shi
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China;
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing 100093, China
| | | | - Rikke Vingborg
- Eurofins Genomics, 8200 Aarhus, Denmark; (J.M.); (R.O.N.); (R.V.)
| | - Per Kryger
- Department of Agroecology, Aarhus University, 4200 Slagelse, Denmark;
| | - Maria Bouga
- Lab of Agricultural Zoology and Entomology, Agricultural University of Athens, 11855 Athens, Greece;
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.L.); (A.E.)
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31
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Stronen AV, Norman AJ, Vander Wal E, Paquet PC. The relevance of genetic structure in ecotype designation and conservation management. Evol Appl 2022; 15:185-202. [PMID: 35233242 PMCID: PMC8867706 DOI: 10.1111/eva.13339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome‐enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.
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Affiliation(s)
- Astrid V. Stronen
- Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
- Department of Biotechnology and Life Sciences Insubria University Varese Italy
- Department of Chemistry and Bioscience Aalborg University Aalborg Denmark
| | - Anita J. Norman
- Department of Fish, Wildlife and Environmental Studies Swedish University of Agricultural Sciences Umeå Sweden
| | - Eric Vander Wal
- Department of Biology Memorial University of Newfoundland St. John’s NL Canada
| | - Paul C. Paquet
- Department of Geography University of Victoria Victoria BC Canada
- Raincoast Conservation Foundation Sidney BC Canada
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32
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do Amaral KB, Barragán-Barrera DC, Mesa-Gutiérrez RA, Farías-Curtidor N, Caballero Gaitán SJ, Méndez-Fernandez P, Santos MCO, Rinaldi C, Rinaldi R, Siciliano S, Martín V, Carrillo M, de Meirelles ACO, Franco-Trecu V, Fagundes NJR, Moreno IB, Lacey Knowles L, Amaral AR. Seascape Genetics of the Atlantic Spotted Dolphin (Stenella frontalis) Based on Mitochondrial DNA. J Hered 2021; 112:646-662. [PMID: 34453543 DOI: 10.1093/jhered/esab050] [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: 12/21/2020] [Accepted: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
The Atlantic spotted dolphin (Stenella frontalis) is endemic to tropical, subtropical, and warm temperate waters of the Atlantic Ocean. Throughout its distribution, both geographic distance and environmental variation may contribute to population structure of the species. In this study, we follow a seascape genetics approach to investigate population differentiation of Atlantic spotted dolphins based on a large worldwide dataset and the relationship with marine environmental variables. The results revealed that the Atlantic spotted dolphin exhibits population genetic structure across its distribution based on mitochondrial DNA control region (mtDNA-CR) data. Analyses based on the contemporary landscape suggested, at both the individual and population level, that the population genetic structure is consistent with the isolation-by-distance model. However, because geography and environmental matrices were correlated, and because in some, but not all analyses, we found a significant effect for the environment, we cannot rule out the addition contribution of environmental factors in structuring genetic variation. Future analyses based on nuclear data are needed to evaluate whether local processes, such as social structure and some level of philopatry within populations, may be contributing to the associations among genetic structure, geographic, and environmental distance.
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Affiliation(s)
- Karina Bohrer do Amaral
- Laboratório de Sistemática e Ecologia de Aves e Mamíferos Marinhos (LABSMAR), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-70 Porto Alegre, RS, Brazil
| | - Dalia C Barragán-Barrera
- Centro de Investigaciones Oceanográficas de Hidrográficas del Caribe CIOH-DIMAR, Barrio Bosque, Sector Manzanillo Escuela Naval de Cadetes "Almirante Padilla," Cartagena, Colombia.,Fundación Macuáticos Colombia, Colombia, Medellín, Colombia.,Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departmento de Ciencias Biológicas, Universidad de los Andes, Carrera 1E No 18A-12, Bogotá, Colombia
| | | | | | - Susana Josefina Caballero Gaitán
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos (LEMVA), Departmento de Ciencias Biológicas, Universidad de los Andes, Carrera 1E No 18A-12, Bogotá, Colombia
| | - Paula Méndez-Fernandez
- Observatoire PELAGIS, UMS 3462 La Rochelle Université / CNRS, Pôle Analytique, 5 allées de l'Océan, 17000 La Rochelle, France
| | - Marcos C Oliveira Santos
- Laboratório de Biologia da Conservação de Mamíferos Aquáticos (LABCMA), Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico, 191, Sala 145-A, 05508-120 São Paulo, SP, Brazil
| | - Caroline Rinaldi
- Association Evasion Tropicale (AET), 1 Rue des Palétuviers, Pigeon Bouillante, 97125 Guadeloupe, France
| | - Renato Rinaldi
- Association Evasion Tropicale (AET), 1 Rue des Palétuviers, Pigeon Bouillante, 97125 Guadeloupe, France
| | - Salvatore Siciliano
- Fundação Oswaldo Cruz (Fiocruz), Av. Brasil 4.365, Manguinhos, Rio de Janeiro, RJ 21040-360, Brazil
| | - Vidal Martín
- Sociedad para el Estudio de Cetáceos del Archipélago Canario (SECAC), Casa de los Arroyo, Avda. Coll n.6, 35500 Arrecife, Lanzarote, Spain
| | - Manuel Carrillo
- Tenerife Conservación, C/Maya No. 8, La Laguna, Tenerife, Canary Islands, Spain
| | - Ana Carolina O de Meirelles
- AQUASIS-Associação de Pesquisa e Preservação de Ecossistemas Aquáticos, Praia de Iparana, s/no, SESC Iparana, 61600-000 Caucaia, CE, Brazil
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, UdelaR, Iguá 4225, 11400, Montevideo, Uruguay
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-70 Porto Alegre, RS, Brazil.,Laboratório de Genética Médica e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul. Avenida Bento Gonçalves 9500, Prédio 43312, sala 113, Agronomia, 91501-970 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco III, Prédio 43312, 91501-970 Porto Alegre, RS, Brazil
| | - Ignacio Benites Moreno
- Laboratório de Sistemática e Ecologia de Aves e Mamíferos Marinhos (LABSMAR), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Bloco IV, Prédio 43435, 91501-70 Porto Alegre, RS, Brazil.,Centro de Estudos Costeiros, Limnológicos e Marinhos (CECLIMAR), Campus Litoral Norte, Universidade Federal do Rio Grande do Sul, Avenida Tramandaí, 976, Imbé, Rio Grande do Sul, 95625-000, Brazil
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, MI
| | - Ana Rita Amaral
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY 10024
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33
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Hämäläinen L, M. Rowland H, Mappes J, Thorogood R. Social information use by predators: expanding the information ecology of prey defences. OIKOS 2021. [DOI: 10.1111/oik.08743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Hannah M. Rowland
- Max Planck Inst. for Chemical Ecology Jena Germany
- Dept of Zoology, Univ. of Cambridge Cambridge UK
| | - Johanna Mappes
- Research Programme in Organismal&Evolutionary Biology, Faculty of Biological and Environmental Sciences, Univ. of Helsinki Helsinki Finland
- Dept of Biological and Environmental Sciences, Univ. of Jyväskylä Jyväskylä Finland
| | - Rose Thorogood
- Research Programme in Organismal&Evolutionary Biology, Faculty of Biological and Environmental Sciences, Univ. of Helsinki Helsinki Finland
- HiLIFE Helsinki Inst. of Life Science, Univ. of Helsinki Helsinki Finland
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Miao J, Farhat P, Wang W, Ruhsam M, Milne R, Yang H, Tso S, Li J, Xu J, Opgenoorth L, Miehe G, Mao K. Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau. ANNALS OF BOTANY 2021; 128:903-918. [PMID: 34472580 PMCID: PMC8577208 DOI: 10.1093/aob/mcab114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP). METHODS The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow-endemic junipers from the QTP that are sister to each other, was surveyed using RNA-sequencing data. Coalescent-based analyses were used to test speciation, migration and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species. KEY RESULTS Analyses of 149 052 single nucleotide polymorphisms showed that the two species are well differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma but only one for J. erectopatens. The identified positively selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter. CONCLUSIONS This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in understanding the current distribution pattern and genetic diversity of threatened species in mountainous regions.
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Affiliation(s)
- Jibin Miao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Perla Farhat
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Wentao Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Richard Milne
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Heng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Sonam Tso
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Jingjing Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Lars Opgenoorth
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Georg Miehe
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
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Teixeira H, Salmona J, Arredondo A, Mourato B, Manzi S, Rakotondravony R, Mazet O, Chikhi L, Metzger J, Radespiel U. Impact of model assumptions on demographic inferences: the case study of two sympatric mouse lemurs in northwestern Madagascar. BMC Ecol Evol 2021; 21:197. [PMID: 34727890 PMCID: PMC8561976 DOI: 10.1186/s12862-021-01929-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Quaternary climate fluctuations have been acknowledged as major drivers of the geographical distribution of the extraordinary biodiversity observed in tropical biomes, including Madagascar. The main existing framework for Pleistocene Malagasy diversification assumes that forest cover was strongly shaped by warmer Interglacials (leading to forest expansion) and by cooler and arid glacials (leading to forest contraction), but predictions derived from this scenario for forest-dwelling animals have rarely been tested with genomic datasets. RESULTS We generated genomic data and applied three complementary demographic approaches (Stairway Plot, PSMC and IICR-simulations) to infer population size and connectivity changes for two forest-dependent primate species (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. The analyses suggested major demographic changes in both species that could be interpreted in two ways, depending on underlying model assumptions (i.e., panmixia or population structure). Under panmixia, the two species exhibited larger population sizes across the Last Glacial Maximum (LGM) and towards the African Humid Period (AHP). This peak was followed by a population decline in M. ravelobensis until the present, while M. murinus may have experienced a second population expansion that was followed by a sharp decline starting 3000 years ago. In contrast, simulations under population structure suggested decreasing population connectivity between the Last Interglacial and the LGM for both species, but increased connectivity during the AHP exclusively for M. murinus. CONCLUSION Our study shows that closely related species may differ in their responses to climatic events. Assuming that Pleistocene climatic conditions in the lowlands were similar to those in the Malagasy highlands, some demographic dynamics would be better explained by changes in population connectivity than in population size. However, changes in connectivity alone cannot be easily reconciled with a founder effect that was shown for M. murinus during its colonization of the northwestern Madagascar in the late Pleistocene. To decide between the two alternative models, more knowledge about historic forest dynamics in lowland habitats is necessary. Altogether, our study stresses that demographic inferences strongly depend on the underlying model assumptions. Final conclusions should therefore be based on a comparative evaluation of multiple approaches.
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Affiliation(s)
- Helena Teixeira
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
| | - Jordi Salmona
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Armando Arredondo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Beatriz Mourato
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Sophie Manzi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Romule Rakotondravony
- Ecole Doctorale Ecosystèmes Naturels (EDEN), University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
| | - Olivier Mazet
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Lounès Chikhi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Julia Metzger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, 30559, Hannover, Germany
- Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
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Louis M, Galimberti M, Archer F, Berrow S, Brownlow A, Fallon R, Nykänen M, O'Brien J, Roberston KM, Rosel PE, Simon-Bouhet B, Wegmann D, Fontaine MC, Foote AD, Gaggiotti OE. Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. SCIENCE ADVANCES 2021; 7:eabg1245. [PMID: 34705499 PMCID: PMC8550227 DOI: 10.1126/sciadv.abg1245] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 09/08/2021] [Indexed: 05/27/2023]
Abstract
Studying repeated adaptation can provide insights into the mechanisms allowing species to adapt to novel environments. Here, we investigate repeated evolution driven by habitat specialization in the common bottlenose dolphin. Parapatric pelagic and coastal ecotypes of common bottlenose dolphins have repeatedly formed across the oceans. Analyzing whole genomes of 57 individuals, we find that ecotype evolution involved a complex reticulated evolutionary history. We find parallel linked selection acted upon ancient alleles in geographically distant coastal populations, which were present as standing genetic variation in the pelagic populations. Candidate loci evolving under parallel linked selection were found in ancient tracts, suggesting recurrent bouts of selection through time. Therefore, despite the constraints of small effective population size and long generation time on the efficacy of selection, repeated adaptation in long-lived social species can be driven by a combination of ecological opportunities and selection acting on ancestral standing genetic variation.
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Affiliation(s)
- Marie Louis
- Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews KY16 8LB, Scotland, UK
- Centre d'Etudes Biologiques de Chize, La Rochelle Université, 17000 La Rochelle, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
- Globe Institute, University of Copenhagen, Øster Voldgade 5, 1350 Copenhagen, Denmark
| | - Marco Galimberti
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Frederick Archer
- National Marine Fisheries Service, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
- Scripps Institution of Oceanography, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Galway-Mayo Institute of Technology, Dublin Road, H91 T8NW Galway, Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ramon Fallon
- School of Medicine, University of St Andrews, North Haugh, St Andrews, Fife KY16 9TF, Scotland, UK
| | | | - Joanne O'Brien
- Irish Whale and Dolphin Group, Kilrush, Co Clare, Ireland
- Marine and Freshwater Research Centre, Department of Natural Sciences, School of Science and Computing, Galway-Mayo Institute of Technology, Dublin Road, H91 T8NW Galway, Ireland
| | - Kelly M Roberston
- National Marine Fisheries Service, Southwest Fisheries Science Center, NOAA, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
| | - Patricia E Rosel
- National Marine Fisheries Service, Southeast Fisheries Science Center, NOAA, 646 Cajundome Boulevard, Lafayette, LA 70506, USA
| | - Benoit Simon-Bouhet
- Centre d'Etudes Biologiques de Chize, La Rochelle Université, 17000 La Rochelle, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France
| | - Andrew D Foote
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, UK
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim 7012, Norway
| | - Oscar E Gaggiotti
- Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews KY16 8LB, Scotland, UK
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Carroll EL, McGowen MR, McCarthy ML, Marx FG, Aguilar N, Dalebout ML, Dreyer S, Gaggiotti OE, Hansen SS, van Helden A, Onoufriou AB, Baird RW, Baker CS, Berrow S, Cholewiak D, Claridge D, Constantine R, Davison NJ, Eira C, Fordyce RE, Gatesy J, Hofmeyr GJG, Martín V, Mead JG, Mignucci-Giannoni AA, Morin PA, Reyes C, Rogan E, Rosso M, Silva MA, Springer MS, Steel D, Olsen MT. Speciation in the deep: genomics and morphology reveal a new species of beaked whale Mesoplodon eueu. Proc Biol Sci 2021; 288:20211213. [PMID: 34702078 PMCID: PMC8548795 DOI: 10.1098/rspb.2021.1213] [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: 05/28/2021] [Accepted: 09/30/2021] [Indexed: 11/12/2022] Open
Abstract
The deep sea has been described as the last major ecological frontier, as much of its biodiversity is yet to be discovered and described. Beaked whales (ziphiids) are among the most visible inhabitants of the deep sea, due to their large size and worldwide distribution, and their taxonomic diversity and much about their natural history remain poorly understood. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari's beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous peoples of the lands from which the species holotype and paratypes were recovered. Mitogenome and ddRAD-derived phylogenies demonstrate reciprocally monophyletic divergence between M. eueu and True's beaked whale (M. mirus) from the North Atlantic, with which it was previously subsumed. Morphometric analyses of skulls also distinguish the two species. A time-calibrated mitogenome phylogeny and analysis of two nuclear genomes indicate divergence began circa 2 million years ago (Ma), with geneflow ceasing 0.35-0.55 Ma. This is an example of how deep sea biodiversity can be unravelled through increasing international collaboration and genome sequencing of archival specimens. Our consultation and involvement with Indigenous peoples offers a model for broadening the cultural scope of the scientific naming process.
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Affiliation(s)
- Emma L. Carroll
- School of Biological Sciences Te Kura Mātauranga Koiora, University of Auckland Waipapa Taumata Rau, Auckland 1010, Aotearoa New Zealand
| | - Michael R. McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC 20560, USA
| | - Morgan L. McCarthy
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
| | - Felix G. Marx
- Museum of New Zealand Te Papa Tongarewa, Wellington, Aotearoa New Zealand
- Department of Geology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Natacha Aguilar
- BIOECOMAC, Department of Animal Biology, Edaphology and Geology, University of La Laguna, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Merel L. Dalebout
- School of Biological, Earth, and Environmental Sciences, University of New South Wales, Kensington 2052, Australia
| | - Sascha Dreyer
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
| | | | - Sabine S. Hansen
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
| | - Anton van Helden
- School of Biological Sciences Te Kura Mātauranga Koiora, University of Auckland Waipapa Taumata Rau, Auckland 1010, Aotearoa New Zealand
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC 20560, USA
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
- Museum of New Zealand Te Papa Tongarewa, Wellington, Aotearoa New Zealand
- Department of Geology, University of Otago, Dunedin, Aotearoa New Zealand
- BIOECOMAC, Department of Animal Biology, Edaphology and Geology, University of La Laguna, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
- School of Biological, Earth, and Environmental Sciences, University of New South Wales, Kensington 2052, Australia
- School of Biology, University of St Andrews, St Andrews KY16 8LB, UK
- Cascadia Research Collective, 218 1/2 W. 4th Avenue, Olympia, WA 98501, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI 96744, USA
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
- Irish Whale and Dolphin Group, Merchants Quay, Kilrush, Co Clare, Ireland/Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Ireland
- Northeast Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration (NOAA), 166 Waters Street, Woods Hole, MA 02543, USA
- Bahamas Marine Mammal Research Organisation (BMMRO), Sandy Point, Abaco, Bahamas
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
- Departamento de Biologia, CESAM and ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
- Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Rua das Matas nacionais, Figueira da Foz 3080-530, Portugal
- Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
- Port Elizabeth Museum at Bayworld, Gqeberha 6013, South Africa
- Department of Zoology, Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha 6031, South Africa
- Study of the Cetaceans in the Canary Archipelago (SECAC) Casa de Los Arroyo, Arrecife de Lanzarote, Canary Islands, Spain
- Caribbean Manatee Conservation Center, Inter American University of Puerto Rico, 500 Carretera Dr John Will Harris, Bayamón 00957, Puerto Rico
- Center for Conservation Medicine and Ecosystem Health, Ross University School of Veterinary Medicine, PO Box 334, Basseterre, St Kitts
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA 92037, USA
- School of Biological, Earth and Environmental Sciences, University College Cork, Ireland
- CIMA Research Foundation, Via Magliotto 2, Savona 17100, Italy
- Okeanos—Instituto de Investigação em Ciências do Mar & IMAR—Instituto do MAR, Universidade dos Açores, Horta, Portugal
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - Aubrie B. Onoufriou
- BIOECOMAC, Department of Animal Biology, Edaphology and Geology, University of La Laguna, San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
- School of Biology, University of St Andrews, St Andrews KY16 8LB, UK
| | - Robin W. Baird
- Cascadia Research Collective, 218 1/2 W. 4th Avenue, Olympia, WA 98501, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI 96744, USA
| | - C. Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Simon Berrow
- Irish Whale and Dolphin Group, Merchants Quay, Kilrush, Co Clare, Ireland/Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Ireland
| | - Danielle Cholewiak
- Northeast Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration (NOAA), 166 Waters Street, Woods Hole, MA 02543, USA
| | - Diane Claridge
- Bahamas Marine Mammal Research Organisation (BMMRO), Sandy Point, Abaco, Bahamas
| | - Rochelle Constantine
- School of Biological Sciences Te Kura Mātauranga Koiora, University of Auckland Waipapa Taumata Rau, Auckland 1010, Aotearoa New Zealand
| | - Nicholas J. Davison
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Catarina Eira
- Departamento de Biologia, CESAM and ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
- Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Rua das Matas nacionais, Figueira da Foz 3080-530, Portugal
| | - R. Ewan Fordyce
- Museum of New Zealand Te Papa Tongarewa, Wellington, Aotearoa New Zealand
- Department of Geology, University of Otago, Dunedin, Aotearoa New Zealand
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - G. J. Greg Hofmeyr
- Port Elizabeth Museum at Bayworld, Gqeberha 6013, South Africa
- Department of Zoology, Institute for Coastal and Marine Research, Nelson Mandela University, Gqeberha 6031, South Africa
| | - Vidal Martín
- Study of the Cetaceans in the Canary Archipelago (SECAC) Casa de Los Arroyo, Arrecife de Lanzarote, Canary Islands, Spain
| | - James G. Mead
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC 20560, USA
| | - Antonio A. Mignucci-Giannoni
- Caribbean Manatee Conservation Center, Inter American University of Puerto Rico, 500 Carretera Dr John Will Harris, Bayamón 00957, Puerto Rico
- Center for Conservation Medicine and Ecosystem Health, Ross University School of Veterinary Medicine, PO Box 334, Basseterre, St Kitts
| | - Phillip A. Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA 92037, USA
| | - Cristel Reyes
- School of Biology, University of St Andrews, St Andrews KY16 8LB, UK
| | - Emer Rogan
- School of Biological, Earth and Environmental Sciences, University College Cork, Ireland
| | | | - Mónica A. Silva
- Okeanos—Instituto de Investigação em Ciências do Mar & IMAR—Instituto do MAR, Universidade dos Açores, Horta, Portugal
| | - Mark S. Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - Debbie Steel
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K DK-1353, Denmark
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Myers HJ, Olsen DW, Matkin CO, Horstmann LA, Konar B. Passive acoustic monitoring of killer whales (Orcinus orca) reveals year-round distribution and residency patterns in the Gulf of Alaska. Sci Rep 2021; 11:20284. [PMID: 34645878 PMCID: PMC8514554 DOI: 10.1038/s41598-021-99668-0] [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: 05/27/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Killer whales (Orcinus orca) are top predators throughout the world's oceans. In the North Pacific, the species is divided into three ecotypes-resident (fish-eating), transient (mammal-eating), and offshore (largely shark-eating)-that are genetically and acoustically distinct and have unique roles in the marine ecosystem. In this study, we examined the year-round distribution of killer whales in the northern Gulf of Alaska from 2016 to 2020 using passive acoustic monitoring. We further described the daily acoustic residency patterns of three killer whale populations (southern Alaska residents, Gulf of Alaska transients, and AT1 transients) for one year of these data. Highest year-round acoustic presence occurred in Montague Strait, with strong seasonal patterns in Hinchinbrook Entrance and Resurrection Bay. Daily acoustic residency times for the southern Alaska residents paralleled seasonal distribution patterns. The majority of Gulf of Alaska transient detections occurred in Hinchinbrook Entrance in spring. The depleted AT1 transient killer whale population was most often identified in Montague Strait. Passive acoustic monitoring revealed that both resident and transient killer whales used these areas much more extensively than previously known and provided novel insights into high use locations and times for each population. These results may be driven by seasonal foraging opportunities and social factors and have management implications for this species.
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Affiliation(s)
- Hannah J Myers
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Dr., Fairbanks, AK, 99775, USA.
| | - Daniel W Olsen
- North Gulf Oceanic Society, 3430 Main St., Suite B1, Homer, AK, 99603, USA
| | - Craig O Matkin
- North Gulf Oceanic Society, 3430 Main St., Suite B1, Homer, AK, 99603, USA
| | - Lara A Horstmann
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Dr., Fairbanks, AK, 99775, USA
| | - Brenda Konar
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Dr., Fairbanks, AK, 99775, USA
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Fitak RR. OptM: estimating the optimal number of migration edges on population trees using Treemix. Biol Methods Protoc 2021; 6:bpab017. [PMID: 34595352 PMCID: PMC8476930 DOI: 10.1093/biomethods/bpab017] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022] Open
Abstract
The software Treemix has become extensively used to estimate the number of migration events, or edges (m), on population trees from genome-wide allele frequency data. However, the appropriate number of edges to include remains unclear. Here, I show that an optimal value of m can be inferred from the second-order rate of change in likelihood (Δm) across incremental values of m. Repurposed from its original use to estimate the number of population clusters in the software Structure (ΔK), I show using simulated populations that Δm performs equally as well as current recommendations for Treemix. A demonstration of an empirical dataset from domestic dogs indicates that this method may be preferable in large, complex population histories and can prioritize migration events for subsequent investigation. The method has been implemented in a freely available R package called “OptM” and as a web application (https://rfitak.shinyapps.io/OptM/) to interface directly with the output files of Treemix.
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Affiliation(s)
- Robert R Fitak
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA
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41
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Benítez-Burraco A, Pörtl D, Jung C. Did Dog Domestication Contribute to Language Evolution? Front Psychol 2021; 12:695116. [PMID: 34589022 PMCID: PMC8473740 DOI: 10.3389/fpsyg.2021.695116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022] Open
Abstract
Different factors seemingly account for the emergence of present-day languages in our species. Human self-domestication has been recently invoked as one important force favoring language complexity mostly via a cultural mechanism. Because our self-domestication ultimately resulted from selection for less aggressive behavior and increased prosocial behavior, any evolutionary or cultural change impacting on aggression levels is expected to have fostered this process. Here, we hypothesize about a parallel domestication of humans and dogs, and more specifically, about a positive effect of our interaction with dogs on human self-domestication, and ultimately, on aspects of language evolution, through the mechanisms involved in the control of aggression. We review evidence of diverse sort (ethological mostly, but also archeological, genetic, and physiological) supporting such an effect and propose some ways of testing our hypothesis.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
| | - Daniela Pörtl
- Psychiatric Department, Saale-Unstrut Klinikum, Teaching Hospital Leipzig and Jena Universities, Naumburg, Germany
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42
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Taylor RS, Manseau M, Klütsch CFC, Polfus JL, Steedman A, Hervieux D, Kelly A, Larter NC, Gamberg M, Schwantje H, Wilson PJ. Population dynamics of caribou shaped by glacial cycles before the last glacial maximum. Mol Ecol 2021; 30:6121-6143. [PMID: 34482596 PMCID: PMC9293238 DOI: 10.1111/mec.16166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/04/2022]
Abstract
Pleistocene glacial cycles influenced the diversification of high‐latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. We investigate population size changes and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 whole genome sequences coupled with larger‐scale mitochondrial data. We found that a major population expansion of caribou occurred starting around 110,000 years ago (kya), the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20–30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results have implications for other whole genome analyses using pairwise sequentially Markovian coalescent (PSMC) analyses, as well as highlighting the need to investigate pre‐LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high‐latitude species.
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Affiliation(s)
- Rebecca S Taylor
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Micheline Manseau
- Biology Department, Trent University, Peterborough, Ontario, Canada.,Landscape Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | | | - Jean L Polfus
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Audrey Steedman
- Parks Canada, Government of Canada, Winnipeg, Manitoba, Canada
| | - Dave Hervieux
- Department of Environment and Parks, Government of Alberta, Grande Prairie, Alberta, Canada
| | - Allicia Kelly
- Department of Environment and Natural Resources, Government of the Northwest Territories, Fort Smith, Northwest Territories, Canada
| | - Nicholas C Larter
- Department of Environment and Natural Resources, Government of the Northwest Territories, Fort Simpson, Northwest Territories, Canada
| | | | - Helen Schwantje
- BC Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Nanaimo, British Columbia, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, Ontario, Canada
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43
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The information continuum model of evolution. Biosystems 2021; 209:104510. [PMID: 34416317 DOI: 10.1016/j.biosystems.2021.104510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022]
Abstract
Most biologists agree that evolution is contingent on inherited information shaped by natural selection. This apparent consensus could be taken to indicate agreement on the forces shaping evolution, but vivid discussions reveal divergences on how evolution is perceived. The predominant Modern Synthesis (MS) paradigm holds the position that evolution occurs through random changes acting on genomic inheritance. However, studies from recent decades have revealed that evolutionary inheritance also includes DNA-methylation, RNA, symbionts, and culture, among other factors. This has fueled a demand of a broader evolutionary perspective, for example from the proponents of the Extended Evolutionary Synthesis (EES). Despite fundamental disagreements the different views agree that natural selection happens through dissimilar perpetuation of inheritable information. Yet, neither the MS, nor the ESS dwell extensively on the nature of hereditary information. We do - and conclude that information in and of itself is immaterial. We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems.
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Foote AD, Hooper R, Alexander A, Baird RW, Baker CS, Ballance L, Barlow J, Brownlow A, Collins T, Constantine R, Dalla Rosa L, Davison NJ, Durban JW, Esteban R, Excoffier L, Martin SLF, Forney KA, Gerrodette T, Gilbert MTP, Guinet C, Hanson MB, Li S, Martin MD, Robertson KM, Samarra FIP, de Stephanis R, Tavares SB, Tixier P, Totterdell JA, Wade P, Wolf JBW, Fan G, Zhang Y, Morin PA. Runs of homozygosity in killer whale genomes provide a global record of demographic histories. Mol Ecol 2021; 30:6162-6177. [PMID: 34416064 DOI: 10.1111/mec.16137] [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: 01/12/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023]
Abstract
Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
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Affiliation(s)
- Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK.,CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Rebecca Hooper
- University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Alana Alexander
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Charles Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lisa Ballance
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Jay Barlow
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, New York City, New York
| | | | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - John W Durban
- Marine Mammal Institute, Oregon State University, Newport, Oregon, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Ruth Esteban
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Sarah L Fordyce Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway
| | - Karin A Forney
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Moss Landing, California, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, California, USA
| | - Tim Gerrodette
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway.,Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christophe Guinet
- UMR 7372 La Rochelle Université - CNRS, Centre d'Etudes Biologiques de Chizé (CEBC), Villiers-en-Bois, France
| | - M Bradley Hanson
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington, USA
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, China
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU, Trondheim, Norway
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
| | - Filipa I P Samarra
- University of Iceland's Institute of Research Centres, Vestmannaeyjar, Iceland
| | - Renaud de Stephanis
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Sara B Tavares
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK.,Cetacean Research Program, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, Canada
| | - Paul Tixier
- UMR 7372 La Rochelle Université - CNRS, Centre d'Etudes Biologiques de Chizé (CEBC), Villiers-en-Bois, France.,MARBEC Université de Montpellier-CNRS-IFREMER-IRD, Sète, France
| | | | - Paul Wade
- National Marine Mammal Laboratory, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Alaska Fisheries Science Center, Seattle, Washington, USA
| | - Jochen B W Wolf
- Section of Evolutionary Biology, Department of Biology II, Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Translational Immunology group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Phillip A Morin
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, La Jolla, California, USA
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45
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Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. J Evol Biol 2021; 34:4-15. [PMID: 33460491 DOI: 10.1111/jeb.13756] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 12/28/2022]
Abstract
Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model-based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.
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Affiliation(s)
- Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Portugal.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Kerstin Johannesson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,IST Austria, Klosterneuburg, Austria
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Patil AB, Vijay N. Repetitive genomic regions and the inference of demographic history. Heredity (Edinb) 2021; 127:151-166. [PMID: 34002046 PMCID: PMC8322061 DOI: 10.1038/s41437-021-00443-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Inference of demographic histories using whole-genome datasets has provided insights into diversification, adaptation, hybridization, and plant-pathogen interactions, and stimulated debate on the impact of anthropogenic interventions and past climate on species demography. However, the impact of repetitive genomic regions on these inferences has mostly been ignored by masking of repeats. We use the Populus trichocarpa genome (Pop_tri_v3) to show that masking of repeat regions leads to lower estimates of effective population size (Ne) in the distant past in contrast to an increase in Ne estimates in recent times. However, in human datasets, masking of repeats resulted in lower estimates of Ne at all time points. We demonstrate that repeats affect demographic inferences using diverse methods like PSMC, MSMC, SMC++, and the Stairway plot. Our genomic analysis revealed that the biases in Ne estimates were dependent on the repeat class type and its abundance in each atomic interval. Notably, we observed a weak, yet consistently significant negative correlation between the repeat abundance of an atomic interval and the Ne estimates for that interval, which potentially reflects the recombination rate variation within the genome. The rationale for the masking of repeats has been that variants identified within these regions are erroneous. We find that polymorphisms in some repeat classes occur in callable regions and reflect reliable coalescence histories (e.g., LTR Gypsy, LTR Copia). The current demography inference methods do not handle repeats explicitly, and hence the effect of individual repeat classes needs careful consideration in comparative analysis. Deciphering the repeat demographic histories might provide a clear understanding of the processes involved in repeat accumulation.
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Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India.
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Lou RN, Jacobs A, Wilder A, Therkildsen NO. A beginner's guide to low-coverage whole genome sequencing for population genomics. Mol Ecol 2021; 30:5966-5993. [PMID: 34250668 DOI: 10.1111/mec.16077] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/26/2022]
Abstract
Low-coverage whole genome sequencing (lcWGS) has emerged as a powerful and cost-effective approach for population genomic studies in both model and non-model species. However, with read depths too low to confidently call individual genotypes, lcWGS requires specialized analysis tools that explicitly account for genotype uncertainty. A growing number of such tools have become available, but it can be difficult to get an overview of what types of analyses can be performed reliably with lcWGS data, and how the distribution of sequencing effort between the number of samples analyzed and per-sample sequencing depths affects inference accuracy. In this introductory guide to lcWGS, we first illustrate how the per-sample cost for lcWGS is now comparable to RAD-seq and Pool-seq in many systems. We then provide an overview of software packages that explicitly account for genotype uncertainty in different types of population genomic inference. Next, we use both simulated and empirical data to assess the accuracy of allele frequency and genetic diversity estimation, detection of population structure, and selection scans under different sequencing strategies. Our results show that spreading a given amount of sequencing effort across more samples with lower depth per sample consistently improves the accuracy of most types of inference, with a few notable exceptions. Finally, we assess the potential for using imputation to bolster inference from lcWGS data in non-model species, and discuss current limitations and future perspectives for lcWGS-based population genomics research. With this overview, we hope to make lcWGS more approachable and stimulate its broader adoption.
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Affiliation(s)
- Runyang Nicolas Lou
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
| | - Arne Jacobs
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Aryn Wilder
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027, USA
| | - Nina O Therkildsen
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
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Insights from comparative research on social and cultural learning. PROGRESS IN BRAIN RESEARCH 2021; 254:247-270. [PMID: 32859290 DOI: 10.1016/bs.pbr.2020.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Social cognitive skills play a crucial role in human life, and have allowed us to reach a unique level of behavioral and cultural complexity. However, many nonhuman species also show a complex understanding of the social world. Building on theories of human social development, we will follow the emergence of cultural learning skills across taxa, discussing similarities and differences between humans and other species. We will first review literature on social learning, including enhancement, emulation and imitation. Then, we will discuss existing studies on the evolution of teaching, and finally, we will critically review literature on the social transmission of skills and knowledge across generations. By adopting a comparative perspective, we will be able to identify the unique characteristics of social transmission in humans, and the social skills that are instead shared with other species, to gain a deeper understanding of the role of cultural learning in social cognitive development.
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49
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Ben Chehida Y, Loughnane R, Thumloup J, Kaschner K, Garilao C, Rosel PE, Fontaine MC. No leading-edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications. Evol Appl 2021; 14:1588-1611. [PMID: 34178106 PMCID: PMC8210799 DOI: 10.1111/eva.13227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 01/12/2023] Open
Abstract
Understanding species responses to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three subspecies. Despite major impacts of fisheries on natural populations, little is known about population connectivity and dispersal, how they reacted to the Pleistocene changes, and how they will evolve in the future. Here, we used phylogenetics, population genetics, and predictive habitat modeling to investigate population structure and phylogeographic history of the North Atlantic porpoises. A total of 925 porpoises were characterized at 10 microsatellite loci and one quarter of the mitogenome (mtDNA). A highly divergent mtDNA lineage was uncovered in one porpoise off Western Greenland, suggesting that a cryptic group may occur and could belong to a recently discovered mesopelagic ecotype off Greenland. Aside from it and the southern subspecies, spatial genetic variation showed that porpoises from both sides of the North Atlantic form a continuous system belonging to the same subspecies (Phocoena phocoena phocoena). Yet, we identified important departures from random mating and restricted dispersal forming a highly significant isolation by distance (IBD) at both mtDNA and nuclear markers. A ten times stronger IBD at mtDNA compared with nuclear loci supported previous evidence of female philopatry. Together with the lack of spatial trends in genetic diversity, this IBD suggests that migration-drift equilibrium has been reached, erasing any genetic signal of a leading-edge effect that accompanied the predicted recolonization of the northern habitats freed from Pleistocene ice. These results illuminate the processes shaping porpoise population structure and provide a framework for designing conservation strategies and forecasting future population evolution.
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Affiliation(s)
- Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Roisin Loughnane
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Julie Thumloup
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Kristin Kaschner
- Department of Biometry and Environmental System AnalysisFaculty of Environment and Natural ResourcesUniversity of FreiburgFreiburgGermany
| | | | - Patricia E. Rosel
- Southeast Fisheries Science CenterNational Marine Fisheries ServiceNOAALafayetteLAUSA
| | - Michael C. Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
- Laboratoire MIVEGEC (Université de Montpellier, CNRS, IRD)Montpellier Cedex 5France
- Centre de Recherche en Écologie et Évolution de la Santé (CREESMontpellier Cedex 5France
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50
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Jones MR, Winkler DE, Massatti R. The demographic and ecological factors shaping diversification among rare
Astragalus
species. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Matthew R. Jones
- Southwest Biological Science Center U.S. Geological Survey Flagstaff AZ USA
| | - Daniel E. Winkler
- Southwest Biological Science Center U.S. Geological Survey Moab UT USA
| | - Rob Massatti
- Southwest Biological Science Center U.S. Geological Survey Flagstaff AZ USA
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