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Heimeier D, Garland EC, Eichenberger F, Garrigue C, Vella A, Baker CS, Carroll EL. A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Mol Ecol Resour 2024; 24:e13955. [PMID: 38520161 DOI: 10.1111/1755-0998.13955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 03/25/2024]
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.
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Affiliation(s)
- Dorothea Heimeier
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
| | - Ellen C Garland
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Franca Eichenberger
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Claire Garrigue
- UMR ENTROPIE, (IRD, Université de La Réunion, Université de la Nouvelle-Calédonie, IFREMER, CNRS, Laboratoire d'Excellence-CORAIL), Nouméa, New Caledonia
- Opération Cétacés, Nouméa, New Caledonia
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, Malta
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Corvallis, Oregon, USA
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
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2
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Yang Z, Liang L, Xiang W, Wang L, Ma Q, Wang Z. Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis. PLANT DIVERSITY 2024; 46:294-308. [PMID: 38798732 PMCID: PMC11119545 DOI: 10.1016/j.pld.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 05/29/2024]
Abstract
Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis-C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis-C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis-C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis-C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis-C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.
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Affiliation(s)
- Zhen Yang
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Weibo Xiang
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, China Three Gorges Corporation, Beijing 100083, China
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang 443133, China
| | - Lujun Wang
- Research Institute of Economic Forest Cultivation and Processing, Anhui Academy of Forestry, Hefei 230031, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhaoshan Wang
- Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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3
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Buss DL, Atmore LM, Zicos MH, Goodall-Copestake WP, Brace S, Archer FI, Baker CS, Barnes I, Carroll EL, Hart T, Kitchener AC, Sabin R, Sremba AL, Weir CR, Jackson JA. Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales. Genes (Basel) 2023; 14:1038. [PMID: 37239398 PMCID: PMC10218396 DOI: 10.3390/genes14051038] [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: 03/31/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.
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Affiliation(s)
- Danielle L. Buss
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Lane M. Atmore
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Maria H. Zicos
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - William P. Goodall-Copestake
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
- Scottish Association for Marine Science, Oban PA37 1QA, UK
| | - Selina Brace
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Frederick I. Archer
- National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - C. Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Ian Barnes
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Emma L. Carroll
- Te Kura Mātauranga Koiora—School of Biological Sciences, University of Auckland Waipapa Taumata Rau, Auckland 1010, New Zealand
| | - Tom Hart
- Department of Zoology, University of Oxford, Mansfield Road, Oxford OX1 3SZ, UK
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Richard Sabin
- The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Angela L. Sremba
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
| | - Caroline R. Weir
- Falklands Conservation, Ross Road, Stanley F1QQ 1ZZ, Falkland Islands
| | - Jennifer A. Jackson
- British Antarctic Survey, National Environment Research Council, Cambridge CB3 0ET, UK
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4
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Chambers EA, Tarvin RD, Santos JC, Ron SR, Betancourth-Cundar M, Hillis DM, Matz MV, Cannatella DC. 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics. Ecol Evol 2023; 13:e9842. [PMID: 36911313 PMCID: PMC9994478 DOI: 10.1002/ece3.9842] [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: 01/24/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 03/10/2023] Open
Abstract
Restriction-site-associated DNA sequencing (RADseq) has become an accessible way to obtain genome-wide data in the form of single-nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non-model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well-supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony-informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA.,Department of Environmental Science, Policy, and Management and Museum of Vertebrate Zoology University of California Berkeley Berkeley California USA
| | - Rebecca D Tarvin
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA.,Department of Integrative Biology and Museum of Vertebrate Zoology University of California Berkeley Berkeley California USA
| | - Juan C Santos
- Department of Biological Sciences St John's University New York New York USA
| | - Santiago R Ron
- Museo de Zoología, Escuela de Ciencias Biológicas Pontificia Universidad Católica del Ecuador Quito Ecuador
| | | | - David M Hillis
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
| | - David C Cannatella
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
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5
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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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6
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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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7
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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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8
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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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9
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Meza Cerda MI, Gray R, Thomson PC, Butcher L, Simpson K, Cameron A, Marcus AD, Higgins DP. Developing Immune Profiles of Endangered Australian Sea Lion ( Neophoca cinerea) Pups Within the Context of Endemic Hookworm ( Uncinaria sanguinis) Infection. Front Vet Sci 2022; 9:824584. [PMID: 35529837 PMCID: PMC9069138 DOI: 10.3389/fvets.2022.824584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
As a top predator, the endangered Australian sea lion (Neophoca cinerea) is a sentinel of ecosystem change, where population trends can reflect broader shifts in the marine environment. The population of this endemic pinniped was historically diminished by commercial sealing, and recovery has been slowed by fishery interactions, disease and, potentially, pollutants. Hookworm infects 100% of neonatal pups and has been identified as a contributor to population decline. Here, a multivariable approach using traditional serological and novel molecular tools such as qPCR and ddPCR was used to examine immune phenotypes of developing Australian sea lion pups infected with the endemic hookworm (Uncinaria sanguinis) from two South Australian colonies. Results show changing immunophenotypes throughout the patent period of infection represented by pro-inflammatory cytokines (IL-6), IgG and acute-phase proteins. Although cytokines may prove useful as markers of resistance, in this study, IL-6 is determined to be an early biomarker of inflammation in Australian sea lion pups, excluding the alternative hypothesis. Additionally, immunological differences between animals from high- and low-intensity hookworm seasons, as well as ivermectin-treated animals, indicate hookworm infection modulation of the host immune response, as evidenced by a lower IL-6 mRNA expression in the non-treated groups. This study of the Australian sea lion is an example of an ecoimmunological approach to disease investigation, which can be applied to evaluate the impact of environmental and anthropogenic factors on susceptibility to infectious diseases in free-ranging species
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Affiliation(s)
- María-Ignacia Meza Cerda
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Rachael Gray
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Peter C Thomson
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Loreena Butcher
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Kelly Simpson
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Abby Cameron
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Alan D Marcus
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Damien P Higgins
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
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10
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Noh HJ, Turner-Maier J, Schulberg SA, Fitzgerald ML, Johnson J, Allen KN, Hückstädt LA, Batten AJ, Alfoldi J, Costa DP, Karlsson EK, Zapol WM, Buys ES, Lindblad-Toh K, Hindle AG. The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling. Commun Biol 2022; 5:140. [PMID: 35177770 PMCID: PMC8854659 DOI: 10.1038/s42003-022-03089-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
AbstractThe Weddell seal (Leptonychotes weddellii) thrives in its extreme Antarctic environment. We generated the Weddell seal genome assembly and a high-quality annotation to investigate genome-wide evolutionary pressures that underlie its phenotype and to study genes implicated in hypoxia tolerance and a lipid-based metabolism. Genome-wide analyses included gene family expansion/contraction, positive selection, and diverged sequence (acceleration) compared to other placental mammals, identifying selection in coding and non-coding sequence in five pathways that may shape cardiovascular phenotype. Lipid metabolism as well as hypoxia genes contained more accelerated regions in the Weddell seal compared to genomic background. Top-significant genes were SUMO2 and EP300; both regulate hypoxia inducible factor signaling. Liver expression of four genes with the strongest acceleration signals differ between Weddell seals and a terrestrial mammal, sheep. We also report a high-density lipoprotein-like particle in Weddell seal serum not present in other mammals, including the shallow-diving harbor seal.
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11
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Bubac CM, Cullingham CI, Fox JA, Bowen WD, den Heyer CE, Coltman DW. Genetic association with boldness and maternal performance in a free-ranging population of grey seals (Halichoerus grypus). Heredity (Edinb) 2021; 127:35-51. [PMID: 33927365 PMCID: PMC8249389 DOI: 10.1038/s41437-021-00439-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 02/03/2023] Open
Abstract
Individual variation in quantitative traits clearly influence many ecological and evolutionary processes. Moderate to high heritability estimates of personality and life-history traits suggest some level of genetic control over these traits. Yet, we know very little of the underlying genetic architecture of phenotypic variation in the wild. In this study, we used a candidate gene approach to investigate the association of genetic variants with repeated measures of boldness and maternal performance traits (weaning mass and lactation duration) collected over an 11- and 28-year period, respectively, in a free-ranging population of grey seals on Sable Island National Park Reserve, Canada. We isolated and re-sequenced five genes: dopamine receptor D4 (DRD4), serotonin transporter (SERT), oxytocin receptor (OXTR), and melanocortin receptors 1 (MC1R) and 5 (MC5R). We discovered single nucleotide polymorphisms (SNPs) in each gene; and, after accounting for loci in linkage disequilibrium and filtering due to missing data, we were able to test for genotype-phenotype relationships at seven loci in three genes (DRD4, SERT, and MC1R). We tested for association between these loci and traits of 180 females having extreme shy-bold phenotypes using mixed-effects models. One locus within SERT was significantly associated with boldness (effect size = 0.189) and a second locus within DRD4 with weaning mass (effect size = 0.232). Altogether, genotypes explained 6.52-13.66% of total trait variation. Our study substantiates SERT and DRD4 as important determinants of behaviour, and provides unique insight into the molecular mechanisms underlying maternal performance variation in a marine predator.
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Affiliation(s)
- Christine M. Bubac
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB Canada
| | - Catherine I. Cullingham
- grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, ON Canada
| | - Janay A. Fox
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB Canada ,grid.14709.3b0000 0004 1936 8649Redpath Museum and Department of Biology, McGill University, Montreal, QC Canada
| | - W. Don Bowen
- grid.418256.c0000 0001 2173 5688Population Ecology Division, Bedford Institute of Oceanography, Dartmouth, NS Canada ,grid.55602.340000 0004 1936 8200Biology Department, Dalhousie University, Halifax, NS Canada
| | - Cornelia E. den Heyer
- grid.418256.c0000 0001 2173 5688Population Ecology Division, Bedford Institute of Oceanography, Dartmouth, NS Canada
| | - David W. Coltman
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB Canada
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12
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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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13
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Ierardi JL, Veloso A, Mancia A. Transcriptome analysis of cadmium exposure in kidney fibroblast cells of the North Atlantic Right Whale (Eubalaena glacialis). Comp Biochem Physiol C Toxicol Pharmacol 2021; 242:108946. [PMID: 33285320 DOI: 10.1016/j.cbpc.2020.108946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/20/2020] [Accepted: 11/29/2020] [Indexed: 11/16/2022]
Abstract
An 8X15k oligonucleotide microarray was developed consisting of 2334 Eubalaena glacialis probes and 2166 Tursiops truncatus probes and used to measure the effects, at transcriptomic level, of cadmium exposure in right whale kidney fibroblast cells. Cells were exposed to three concentrations (1 μM, 0.1 μM, and 0.01 μM) of cadmium chloride (CdCl2) for three exposure times (1, 4, and 24 h). Cells exposed to 1 μM CdCl2 for 4 h and 24 h showed upregulated genes involved in protection from metal toxicity and oxidative stress, protein renaturation, apoptosis inhibition, as well as several regulators of cellular processes. Downregulated genes represented a suite of functions including cell proliferation, transcription regulation, actin polymerization, and stress fiber synthesis. The collection of differentially expressed genes in this study support proposed mechanisms of cadmium-induced apoptosis such as ubiquitin proteasome system disruption, Ca2+ homeostasis interference, mitochondrial membrane potential collapse, reactive oxygen species (ROS) production, and cell cycle arrest. The results also have confirmed the right whale microarray as a reproducible tool in measuring differentiated gene expression that could be a valuable asset for transcriptome analysis of other baleen whales and potential health assessment protocols.
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Affiliation(s)
- Jessalyn L Ierardi
- Graduate Program of Marine Biology, College of Charleston, 205 Fort Johnson Rd, Charleston, SC 29412, USA
| | - Artur Veloso
- Graduate Program of Marine Biology, College of Charleston, 205 Fort Johnson Rd, Charleston, SC 29412, USA
| | - Annalaura Mancia
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 171 Ashley Ave, Charleston, SC 29425, USA; Marine Biomedicine and Environmental Sciences Center, Medical University of South Carolina, 331 Fort Johnson Rd, Charleston, SC 29412, USA; Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, Ferrara 44121, Italy.
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14
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Nelms SE, Alfaro-Shigueto J, Arnould JPY, Avila IC, Bengtson Nash S, Campbell E, Carter MID, Collins T, Currey RJC, Domit C, Franco-Trecu V, Fuentes MMPB, Gilman E, Harcourt RG, Hines EM, Hoelzel AR, Hooker SK, Johnston DW, Kelkar N, Kiszka JJ, Laidre KL, Mangel JC, Marsh H, Maxwell SM, Onoufriou AB, Palacios DM, Pierce GJ, Ponnampalam LS, Porter LJ, Russell DJF, Stockin KA, Sutaria D, Wambiji N, Weir CR, Wilson B, Godley BJ. Marine mammal conservation: over the horizon. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01115] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Marine mammals can play important ecological roles in aquatic ecosystems, and their presence can be key to community structure and function. Consequently, marine mammals are often considered indicators of ecosystem health and flagship species. Yet, historical population declines caused by exploitation, and additional current threats, such as climate change, fisheries bycatch, pollution and maritime development, continue to impact many marine mammal species, and at least 25% are classified as threatened (Critically Endangered, Endangered or Vulnerable) on the IUCN Red List. Conversely, some species have experienced population increases/recoveries in recent decades, reflecting management interventions, and are heralded as conservation successes. To continue these successes and reverse the downward trajectories of at-risk species, it is necessary to evaluate the threats faced by marine mammals and the conservation mechanisms available to address them. Additionally, there is a need to identify evidence-based priorities of both research and conservation needs across a range of settings and taxa. To that effect we: (1) outline the key threats to marine mammals and their impacts, identify the associated knowledge gaps and recommend actions needed; (2) discuss the merits and downfalls of established and emerging conservation mechanisms; (3) outline the application of research and monitoring techniques; and (4) highlight particular taxa/populations that are in urgent need of focus.
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Affiliation(s)
- SE Nelms
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
| | - J Alfaro-Shigueto
- ProDelphinus, Jose Galvez 780e, Miraflores, Perú
- Facultad de Biologia Marina, Universidad Cientifica del Sur, Lima, Perú
| | - JPY Arnould
- School of Life and Environmental Sciences, Deakin University, Burwood, VIC 3125, Australia
| | - IC Avila
- Grupo de Ecología Animal, Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Cali, Colombia
| | - S Bengtson Nash
- Environmental Futures Research Institute (EFRI), Griffith University, Nathan Campus, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - E Campbell
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
- ProDelphinus, Jose Galvez 780e, Miraflores, Perú
| | - MID Carter
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, KY16 8LB, UK
| | - T Collins
- Wildlife Conservation Society, 2300 Southern Blvd., Bronx, NY 10460, USA
| | - RJC Currey
- Marine Stewardship Council, 1 Snow Hill, London, EC1A 2DH, UK
| | - C Domit
- Laboratory of Ecology and Conservation, Marine Study Center, Universidade Federal do Paraná, Brazil
| | - V Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Uruguay
| | - MMPB Fuentes
- Marine Turtle Research, Ecology and Conservation Group, Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - E Gilman
- Pelagic Ecosystems Research Group, Honolulu, HI 96822, USA
| | - RG Harcourt
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - EM Hines
- Estuary & Ocean Science Center, San Francisco State University, 3150 Paradise Dr. Tiburon, CA 94920, USA
| | - AR Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - SK Hooker
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, KY16 8LB, UK
| | - DW Johnston
- Duke Marine Lab, 135 Duke Marine Lab Road, Beaufort, NC 28516, USA
| | - N Kelkar
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, Karnataka, India
| | - JJ Kiszka
- Department of Biological Sciences, Coastlines and Oceans Division, Institute of Environment, Florida International University, Miami, FL 33199, USA
| | - KL Laidre
- Polar Science Center, APL, University of Washington, 1013 NE 40th Street, Seattle, WA 98105, USA
| | - JC Mangel
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
- ProDelphinus, Jose Galvez 780e, Miraflores, Perú
| | - H Marsh
- James Cook University, Townsville, QLD 48111, Australia
| | - SM Maxwell
- School of Interdisciplinary Arts and Sciences, University of Washington Bothell, Bothell WA 98011, USA
| | - AB Onoufriou
- School of Biology, University of St Andrews, Fife, KY16 8LB, UK
- Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - DM Palacios
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97330, USA
| | - GJ Pierce
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Cientificas, Eduardo Cabello 6, 36208 Vigo, Pontevedra, Spain
| | - LS Ponnampalam
- The MareCet Research Organization, 40460 Shah Alam, Malaysia
| | - LJ Porter
- SMRU Hong Kong, University of St. Andrews, Hong Kong
| | - DJF Russell
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, KY16 8LB, UK
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - KA Stockin
- Animal Welfare Science and Bioethics Centre, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - D Sutaria
- School of Interdisciplinary Arts and Sciences, University of Washington Bothell, Bothell WA 98011, USA
| | - N Wambiji
- Kenya Marine and Fisheries Research Institute, P.O. Box 81651, Mombasa-80100, Kenya
| | - CR Weir
- Ketos Ecology, 4 Compton Road, Kingsbridge, Devon, TQ7 2BP, UK
| | - B Wilson
- Scottish Association for Marine Science, Oban, Argyll, PA37 1QA, UK
| | - BJ Godley
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
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15
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Tarlinton RE, Fabijan J, Hemmatzadeh F, Meers J, Owen H, Sarker N, Seddon JM, Simmons G, Speight N, Trott DJ, Woolford L, Emes RD. Transcriptomic and genomic variants between koala populations reveals underlying genetic components to disorders in a bottlenecked population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01340-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AbstractHistorical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future.
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16
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McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S, Polanowski A, Morin PA, Rossiter SJ. Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Syst Biol 2020; 69:479-501. [PMID: 31633766 PMCID: PMC7164366 DOI: 10.1093/sysbio/syz068] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022] Open
Abstract
The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal}
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}{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]
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Affiliation(s)
- Michael R McGowen
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.,Department of Vertebrate Zoology, Smithsonian Museum of Natural History, 10th & Constitution Ave. NW, Washington DC 20560, USA
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Sandra Álvarez-Carretero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Robert Deaville
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Paul D Jepson
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Simon Jarman
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Andrea Polanowski
- Australian Antarctic Division, 203 Channel Highway, Kingston TAS 7050, Australia
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla CA 92037 USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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17
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Lam EK, Allen KN, Torres-Velarde JM, Vázquez-Medina JP. Functional Studies with Primary Cells Provide a System for Genome-to-Phenome Investigations in Marine Mammals. Integr Comp Biol 2020; 60:348-360. [PMID: 32516367 DOI: 10.1093/icb/icaa065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Marine mammals exhibit some of the most dramatic physiological adaptations in their clade and offer unparalleled insights into the mechanisms driving convergent evolution on relatively short time scales. Some of these adaptations, such as extreme tolerance to hypoxia and prolonged food deprivation, are uncommon among most terrestrial mammals and challenge established metabolic principles of supply and demand balance. Non-targeted omics studies are starting to uncover the genetic foundations of such adaptations, but tools for testing functional significance in these animals are currently lacking. Cellular modeling with primary cells represents a powerful approach for elucidating the molecular etiology of physiological adaptation, a critical step in accelerating genome-to-phenome studies in organisms in which transgenesis is impossible (e.g., large-bodied, long-lived, fully aquatic, federally protected species). Gene perturbation studies in primary cells can directly evaluate whether specific mutations, gene loss, or duplication confer functional advantages such as hypoxia or stress tolerance in marine mammals. Here, we summarize how genetic and pharmacological manipulation approaches in primary cells have advanced mechanistic investigations in other non-traditional mammalian species, and highlight the need for such investigations in marine mammals. We also provide key considerations for isolating, culturing, and conducting experiments with marine mammal cells under conditions that mimic in vivo states. We propose that primary cell culture is a critical tool for conducting functional mechanistic studies (e.g., gene knockdown, over-expression, or editing) that can provide the missing link between genome- and organismal-level understanding of physiological adaptations in marine mammals.
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Affiliation(s)
- Emily K Lam
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kaitlin N Allen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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18
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Van Cise AM, Baird RW, Baker CS, Cerchio S, Claridge D, Fielding R, Hancock-Hanser B, Marrero J, Martien KK, Mignucci-Giannoni AA, Oleson EM, Oremus M, Poole MM, Rosel PE, Taylor BL, Morin PA. Oceanographic barriers, divergence, and admixture: Phylogeography and taxonomy of two putative subspecies of short-finned pilot whale. Mol Ecol 2019; 28:2886-2902. [PMID: 31002212 DOI: 10.1111/mec.15107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/10/2019] [Indexed: 12/11/2022]
Abstract
Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short-finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the "Naisa" and "Shiho" forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short-finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short-finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally-distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.
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Affiliation(s)
- Amy M Van Cise
- Scripps Institution of Oceanography, La Jolla, California.,Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California.,Woods Hole Oceanographic Institution, Woods Hole, Massachusetts
| | | | - Charles Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, Oregon
| | | | - Diane Claridge
- Bahamas Marine Mammal Research Organisation, Abaco, Bahamas
| | - Russell Fielding
- Department of Earth & Environmental Systems, University of the South, Sewanee, Tennessee
| | - Brittany Hancock-Hanser
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
| | - Jacobo Marrero
- Asociación Tonina, Investigación y Divulgación del medio natural Marino, San Cristóbal de La Laguna, Spain.,BIOECOMAC, Department of Animal Biology, La Laguna University, La Laguna, Tenerife, Canary Islands, Spain
| | - Karen K Martien
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
| | | | - Erin M Oleson
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, Honolulu, Hawaii
| | - Marc Oremus
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, Oregon
| | | | - Patricia E Rosel
- Southeast Fisheries Science Center, National Marine Fisheries Service, NOAA, Lafayette, Louisiana
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, California
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19
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Ramirez-Flores O, Birtles A, Pazmino D, Zenger KR, Van-Herwerden L. Dwarf minke whales from the South Pacific share a matrilineal lineage distinct from Balaenoptera acutorostrata acutorostrata and B. a. scammoni. AUSTRALIAN MAMMALOGY 2019. [DOI: 10.1071/am18015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Dwarf minke whales are regarded as an undescribed subspecies of common minke whales (Balaenoptera acutorostrata), but appropriate conservation action requires taxonomic confirmation. The relationship of the Australian Great Barrier Reef (GBR) dwarf minke whale aggregation to other minke whales is unknown. This study aims to clarify the phylogenetic relationship of GBR dwarf minke whales, using partial mitochondrial DNA sequence data from 23 GBR dwarf minke whales, compared with other available minke whale sequences. GBR dwarf minke whales share haplotypes with other West South Pacific (WSP) dwarf minke whales. Satellite tagging studies corroborate these findings, indicating that GBR dwarf minke whales migrate south along the east Australian coast towards the Southern Ocean. Despite nuclear data not being available, GBR and WSP dwarf minke whales share a distinctive mitochondrial lineage compared with other common minke whales and should be managed independently of North Pacific and Atlantic Ocean common minke whale populations.
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20
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Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour 2018; 18:1469-1481. [PMID: 30035363 DOI: 10.1111/1755-0998.12932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 11/27/2022]
Abstract
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.
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Affiliation(s)
- Marijke Autenrieth
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Ljerka Lah
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Anna Roos
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Alice B Dennis
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
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21
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Ferrante JA, Giles MR, Benzie E, Hunter ME. A novel technique for isolating DNA from Tempus™ blood RNA tubes after RNA isolation. BMC Res Notes 2018; 11:563. [PMID: 30081941 PMCID: PMC6080204 DOI: 10.1186/s13104-018-3671-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/01/2018] [Indexed: 11/10/2022] Open
Abstract
Objective We use Tempus blood RNA tubes (Applied Biosystems) during health assessments of American moose (Alces alces spp.) as a minimally invasive means to obtain RNA. Here we describe a novel protocol to additionally isolate high-quality DNA from the supernatant remaining after the RNA isolation methodology. Metrics used to qualify DNA quality included measuring the concentration, obtaining a DNA integrity number from a genomic DNA ScreenTape assay (Agilent), and running the isolated DNA on an agarose gel. Results Of the 23 samples analyzed, the average DNA concentration was 121 ng/µl (range 4–337 ng/µl) and a genomic DNA ScreenTape assay of seven samples indicated high DNA integrity values for 6 of the 7 samples (range 9.1–9.4 out of 10). Of the DNA sent for genotyping by sequencing, all proved to be of sufficient integrity to yield high-quality next-generation sequence results. We recommend this simple procedure to maximize the yield of both RNA and DNA from blood samples.
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Affiliation(s)
- Jason A Ferrante
- Cherokee Nation Technologies contracted to the U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA.
| | - Michelle R Giles
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Emily Benzie
- University of California-Davis, 1 Shields Ave, Davis, CA, 95616, USA
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
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22
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Martinez B, Khudyakov J, Rutherford K, Crocker DE, Gemmell N, Ortiz RM. Adipose transcriptome analysis provides novel insights into molecular regulation of prolonged fasting in northern elephant seal pups. Physiol Genomics 2018; 50:495-503. [PMID: 29625017 DOI: 10.1152/physiolgenomics.00002.2018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The physiological and cellular adaptations to extreme fasting in northern elephant seals ( Mirounga angustirostris, NES) are remarkable and may help to elucidate endocrine mechanisms that regulate lipid metabolism and energy homeostasis in mammals. Recent studies have highlighted the importance of thyroid hormones in the maintenance of a lipid-based metabolism during prolonged fasting in weaned NES pups. To identify additional molecular regulators of fasting, we used a transcriptomics approach to examine changes in global gene expression profiles before and after 6-8 wk of fasting in weaned NES pups. We produced a de novo assembly and identified 98 unique protein-coding genes that were differentially expressed between early and late fasting. Most of the downregulated genes were associated with lipid, carbohydrate, and protein metabolism. A number of downregulated genes were also associated with maintenance of the extracellular matrix, consistent with tissue remodeling during weight loss and the multifunctional nature of blubber tissue, which plays both metabolic and structural roles in marine mammals. Using this data set, we predict potential mechanisms by which NES pups sustain metabolism and regulate adipose stores throughout the fast, and provide a valuable resource for additional studies of extreme metabolic adaptations in mammals.
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Affiliation(s)
- Bridget Martinez
- Department of Molecular & Cellular Biology, University of California, Merced, California.,Department of Medicine, St. George's University School of Medicine, St. George, Grenada.,Department of Anatomy, University of Otago , Dunedin , New Zealand.,Department of Physics and Engineering, Los Alamos National Laboratory , Los Alamos, New Mexico
| | - Jane Khudyakov
- Department of Biological Sciences, University of the Pacific , Stockton, California
| | - Kim Rutherford
- Department of Anatomy, University of Otago , Dunedin , New Zealand
| | - Daniel E Crocker
- Department of Biology, Sonoma State University , Rohnert Park, California
| | - Neil Gemmell
- Department of Anatomy, University of Otago , Dunedin , New Zealand
| | - Rudy M Ortiz
- Department of Molecular & Cellular Biology, University of California, Merced, California
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23
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Schell CJ. Urban Evolutionary Ecology and the Potential Benefits of Implementing Genomics. J Hered 2018; 109:138-151. [DOI: 10.1093/jhered/esy001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/06/2018] [Indexed: 01/01/2023] Open
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24
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Attard CRM, Beheregaray LB, Sandoval-Castillo J, Jenner KCS, Gill PC, Jenner MNM, Morrice MG, Möller LM. From conservation genetics to conservation genomics: a genome-wide assessment of blue whales ( Balaenoptera musculus) in Australian feeding aggregations. ROYAL SOCIETY OPEN SCIENCE 2018; 5:170925. [PMID: 29410806 PMCID: PMC5792883 DOI: 10.1098/rsos.170925] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/02/2018] [Indexed: 06/08/2023]
Abstract
Genetic datasets of tens of markers have been superseded through next-generation sequencing technology with genome-wide datasets of thousands of markers. Genomic datasets improve our power to detect low population structure and identify adaptive divergence. The increased population-level knowledge can inform the conservation management of endangered species, such as the blue whale (Balaenoptera musculus). In Australia, there are two known feeding aggregations of the pygmy blue whale (B. m. brevicauda) which have shown no evidence of genetic structure based on a small dataset of 10 microsatellites and mtDNA. Here, we develop and implement a high-resolution dataset of 8294 genome-wide filtered single nucleotide polymorphisms, the first of its kind for blue whales. We use these data to assess whether the Australian feeding aggregations constitute one population and to test for the first time whether there is adaptive divergence between the feeding aggregations. We found no evidence of neutral population structure and negligible evidence of adaptive divergence. We propose that individuals likely travel widely between feeding areas and to breeding areas, which would require them to be adapted to a wide range of environmental conditions. This has important implications for their conservation as this blue whale population is likely vulnerable to a range of anthropogenic threats both off Australia and elsewhere.
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Affiliation(s)
- Catherine R. M. Attard
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Cetacean Ecology, Behaviour and Evolution Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - K. Curt S. Jenner
- Centre for Whale Research, PO Box 1622, Fremantle, Western Australia 6959, Australia
| | - Peter C. Gill
- Blue Whale Study, C/- Post Office, Narrawong, Victoria 3285, Australia
- School of Life and Environmental Sciences, Deakin University, PO Box 423, Warrnambool, Victoria 3280, Australia
| | | | - Margaret G. Morrice
- School of Life and Environmental Sciences, Deakin University, PO Box 423, Warrnambool, Victoria 3280, Australia
| | - Luciana M. Möller
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Cetacean Ecology, Behaviour and Evolution Lab, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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Morin PA, Foote AD, Hill CM, Simon-Bouhet B, Lang AR, Louis M. SNP Discovery from Single and Multiplex Genome Assemblies of Non-model Organisms. Methods Mol Biol 2018; 1712:113-144. [PMID: 29224072 DOI: 10.1007/978-1-4939-7514-3_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. "Hancock-Hanser et al., Mol Ecol Resour 13:254-268, 2013") can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA.
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Christopher M Hill
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Benoit Simon-Bouhet
- Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, 79360, Villiers-en-Bois, France
| | - Aimee R Lang
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Marie Louis
- Scottish Oceans Institute, University of St Andrews, East Sands, KY16 8LB, St Andrews, UK
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Andruszkiewicz EA, Sassoubre LM, Boehm AB. Persistence of marine fish environmental DNA and the influence of sunlight. PLoS One 2017; 12:e0185043. [PMID: 28915253 PMCID: PMC5600408 DOI: 10.1371/journal.pone.0185043] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/04/2017] [Indexed: 11/23/2022] Open
Abstract
Harnessing information encoded in environmental DNA (eDNA) in marine waters has the potential to revolutionize marine biomonitoring. Whether using organism-specific quantitative PCR assays or metabarcoding in conjunction with amplicon sequencing, scientists have illustrated that realistic organism censuses can be inferred from eDNA. The next step is establishing ways to link information obtained from eDNA analyses to actual organism abundance. This is only possible by understanding the processes that control eDNA concentrations. The present study uses mesocosm experiments to study the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence. We seeded solute-permeable dialysis bags with water containing indigenous eDNA and suspended them in a large tank containing seawater. Bags were subjected to two treatments: half the bags were suspended near the water surface where they received high doses of sunlight, and half at depth where they received lower doses of sunlight. Bags were destructively sampled over the course of 87 hours. eDNA was extracted from water samples and used as template for a Scomber japonicus qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. S. japonicus eDNA, as measured by qPCR, exhibited first order decay with a rate constant ~0.01 hr -1 with no difference in decay rate constants between the two experimental treatments. eDNA metabarcoding identified 190 organizational taxonomic units (OTUs) assigned to varying taxonomic ranks. There was no difference in marine fish communities as measured by eDNA metabarcoding between the two experimental treatments, but there was an effect of time. Given the differences in UVA and UVB fluence received by the two experimental treatments, we conclude that sunlight is not the main driver of fish eDNA decay in the experiments. However, there are clearly temporal effects that need to be considered when interpreting information obtained using eDNA approaches.
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Affiliation(s)
- Elizabeth A. Andruszkiewicz
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Lauren M. Sassoubre
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States of America
- * E-mail:
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Abstract
Whales and dolphins (Cetacea) have excellent social learning skills as well as a long and strong mother-calf bond. These features produce stable cultures, and, in some species, sympatric groups with different cultures. There is evidence and speculation that this cultural transmission of behavior has affected gene distributions. Culture seems to have driven killer whales into distinct ecotypes, which may be incipient species or subspecies. There are ecotype-specific signals of selection in functional genes that correspond to cultural foraging behavior and habitat use by the different ecotypes. The five species of whale with matrilineal social systems have remarkably low diversity of mtDNA. Cultural hitchhiking, the transmission of functionally neutral genes in parallel with selective cultural traits, is a plausible hypothesis for this low diversity, especially in sperm whales. In killer whales the ecotype divisions, together with founding bottlenecks, selection, and cultural hitchhiking, likely explain the low mtDNA diversity. Several cetacean species show habitat-specific distributions of mtDNA haplotypes, probably the result of mother-offspring cultural transmission of migration routes or destinations. In bottlenose dolphins, remarkable small-scale differences in haplotype distribution result from maternal cultural transmission of foraging methods, and large-scale redistributions of sperm whale cultural clans in the Pacific have likely changed mitochondrial genetic geography. With the acceleration of genomics new results should come fast, but understanding gene-culture coevolution will be hampered by the measured pace of research on the socio-cultural side of cetacean biology.
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Affiliation(s)
- Hal Whitehead
- Department of Biology, Dalhousie University, Halifax, NS, Canada B3H 4R2
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28
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Whitehead H, Vachon F, Frasier TR. Cultural Hitchhiking in the Matrilineal Whales. Behav Genet 2017; 47:324-334. [PMID: 28275880 DOI: 10.1007/s10519-017-9840-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/13/2017] [Indexed: 11/25/2022]
Abstract
Five species of whale with matrilineal social systems (daughters remain with mothers) have remarkably low levels of mitochondrial DNA diversity. Non-heritable matriline-level demography could reduce genetic diversity but the required conditions are not consistent with the natural histories of the matrilineal whales. The diversity of nuclear microsatellites is little reduced in the matrilineal whales arguing against bottlenecks. Selective sweeps of the mitochondrial genome are feasible causes but it is not clear why these only occurred in the matrilineal species. Cultural hitchhiking (cultural selection reducing diversity at neutral genetic loci transmitted in parallel to the culture) is supported in sperm whales which possess suitable matrilineal socio-cultural groups (coda clans). Killer whales are delineated into ecotypes which likely originated culturally. Culture, bottlenecks and selection, as well as their interactions, operating between- or within-ecotypes, may have reduced their mitochondrial diversity. The societies, cultures and genetics of false killer and two pilot whale species are insufficiently known to assess drivers of low mitochondrial diversity.
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Affiliation(s)
- Hal Whitehead
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada.
| | - Felicia Vachon
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4J1, Canada
| | - Timothy R Frasier
- Department of Biology & Forensic Sciences Programme, Saint Mary's University, Halifax, Canada
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29
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Kershaw F, Carvalho I, Loo J, Pomilla C, Best PB, Findlay KP, Cerchio S, Collins T, Engel MH, Minton G, Ersts P, Barendse J, Kotze PGH, Razafindrakoto Y, Ngouessono S, Meÿer M, Thornton M, Rosenbaum HC. Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales. Mol Ecol 2017; 26:977-994. [DOI: 10.1111/mec.13943] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/01/2016] [Accepted: 11/16/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Francine Kershaw
- Columbia University; 116th Street and Broadway New York NY 10027 USA
| | - Inês Carvalho
- Population and Conservation Genetics Group; Instituto Gulbenkian de Ciência; Rua da Quinta Grande, 6 2780-156 Oeiras Portugal
- Centre for Environmental and Marine Studies (CESAM); Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Jacqueline Loo
- Department of Biology; New York University; 100 Washington Square New York NY 10012 USA
| | - Cristina Pomilla
- Wellcome Trust Sanger Institute; Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA UK
| | - Peter B. Best
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - Ken P. Findlay
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - Salvatore Cerchio
- Wildlife Conservation Society; Ocean Giants Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
| | - Tim Collins
- Wildlife Conservation Society; Ocean Giants Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
- Environment Society of Oman; P.O. Box 3955 PC 112 Ruwi Sultanate of Oman
| | - Marcia H. Engel
- Humpback Whale Project/Humpback Whale Institute; Rua Barão do Rio Branco, 125 Caravelas Bahia Brazil
| | - Gianna Minton
- Environment Society of Oman; P.O. Box 3955 PC 112 Ruwi Sultanate of Oman
| | - Peter Ersts
- Center for Biodiversity and Conservation; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
| | - Jaco Barendse
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - P. G. H. Kotze
- Department of Environmental Affairs; Branch Oceans and Coasts; Private Bag x2, Roggebaai 8012 Cape Town South Africa
| | - Yvette Razafindrakoto
- Wildlife Conservation Society-Madagascar Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
| | - Solange Ngouessono
- Agence Nationale des Parcs Nationaux; Batterie 4 BP 20379 Libreville Gabon
| | - Michael Meÿer
- Department of Environmental Affairs; Branch Oceans and Coasts; Private Bag x2, Roggebaai 8012 Cape Town South Africa
| | - Meredith Thornton
- Mammal Research Institute; University of Pretoria; c/o Iziko South African Museum, P.O. Box 61 Cape Town 8000 South Africa
| | - Howard C. Rosenbaum
- Wildlife Conservation Society; Ocean Giants Program; 2300 Southern Blvd. Bronx NY 10460-1099 USA
- Sackler Institute for Comparative Genomics; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
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Fontaine MC. Harbour Porpoises, Phocoena phocoena, in the Mediterranean Sea and Adjacent Regions: Biogeographic Relicts of the Last Glacial Period. ADVANCES IN MARINE BIOLOGY 2016; 75:333-358. [PMID: 27770989 DOI: 10.1016/bs.amb.2016.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The harbour porpoise, Phocoena phocoena, is one of the best studied cetacean species owing to its common distribution along the coastal waters of the Northern Hemisphere. In European waters, strandings are common and bycatch mortalities in commercial fisheries reach alarming numbers. Lethal interactions resulting from human activities together with ongoing environmental changes raise serious concerns about population viability throughout the species' range. These concerns foster the need to fill critical gaps in knowledge of harbour porpoise biology, including population structure, feeding ecology, habitat preference and evolutionary history, that are critical information for planning effective management and conservation efforts. While the species is distributed fairly continuously in the North Atlantic Ocean, it becomes fragmented in the south-eastern part with isolated populations occurring along the Atlantic coasts of the Iberian Peninsula, Northwest Africa and the Black Sea. The latter population is separated from Atlantic populations by the Mediterranean Sea, where the species is almost entirely absent. Understanding the evolutionary history of these populations occurring in marginal habitats holds the potential to reveal fundamental aspects of the species' biology such as the factors determining its distribution, ecological niche, and how past and recent environmental variation have shaped the current population structure. This information can be critical for understanding the future evolution of the species in consideration of ongoing environmental changes. This chapter summarizes the recent advances in our knowledge regarding the populations bordering the Mediterranean Sea with a special emphasis on their ecological and evolutionary history, which has recently been reconstructed from genetic analyses.
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Affiliation(s)
- M C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands.
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