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Owen K, Carlström J, Eriksson P, Andersson M, Nordström R, Lalander E, Sveegaard S, Kyhn LA, Griffiths ET, Cosentino M, Tougaard J. Rerouting of a major shipping lane through important harbour porpoise habitat caused no detectable change in annual occurrence or foraging patterns. Mar Pollut Bull 2024; 202:116294. [PMID: 38537499 DOI: 10.1016/j.marpolbul.2024.116294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 05/08/2024]
Abstract
Shipping is one of the largest industries globally, with well-known negative impacts on the marine environment. Despite the known negative short-term (minutes to hours) impact of shipping on individual animal behavioural responses, very little is understood about the long-term (months to years) impact on marine species presence and area use. This study took advantage of a planned rerouting of a major shipping lane leading into the Baltic Sea, to investigate the impact on the presence and foraging behaviour of a marine species known to be sensitive to underwater noise, the harbour porpoise (Phocoena phocoena). Passive acoustic monitoring data were collected from 15 stations over two years. Against predictions, no clear change occurred in monthly presence or foraging behaviour of the porpoises, despite the observed changes in noise and vessel traffic. However, long-term heightened noise levels may still impact communication, echolocation, or stress levels of individuals, and needs further investigation.
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Affiliation(s)
- Kylie Owen
- Department of Population Analysis and Monitoring, Swedish Museum of Natural History, Frescativägen 40, Stockholm 104 05, Sweden.
| | - Julia Carlström
- Department of Population Analysis and Monitoring, Swedish Museum of Natural History, Frescativägen 40, Stockholm 104 05, Sweden
| | - Pia Eriksson
- Department of Population Analysis and Monitoring, Swedish Museum of Natural History, Frescativägen 40, Stockholm 104 05, Sweden
| | - Mathias Andersson
- Department of Defence Technology, FOI-Swedish Defence Research Agency, Stockholm, Sweden
| | - Robin Nordström
- Department of Defence Technology, FOI-Swedish Defence Research Agency, Stockholm, Sweden
| | - Emilia Lalander
- Department of Defence Technology, FOI-Swedish Defence Research Agency, Stockholm, Sweden
| | - Signe Sveegaard
- Section for Marine Mammal Research, Department of Ecoscience, Aarhus University, DK-4000 Roskilde, Denmark
| | - Line A Kyhn
- Section for Marine Mammal Research, Department of Ecoscience, Aarhus University, DK-4000 Roskilde, Denmark
| | - Emily T Griffiths
- Section for Marine Mammal Research, Department of Ecoscience, Aarhus University, DK-4000 Roskilde, Denmark
| | - Mel Cosentino
- Section for Marine Mammal Research, Department of Ecoscience, Aarhus University, DK-4000 Roskilde, Denmark
| | - Jakob Tougaard
- Section for Marine Mammal Research, Department of Ecoscience, Aarhus University, DK-4000 Roskilde, Denmark
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2
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Tengstedt ANB, Liu S, Jacobsen MW, Gundlund C, Møller PR, Berg S, Bekkevold D, Hansen MM. Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.). Mol Ecol 2024:e17367. [PMID: 38686435 DOI: 10.1111/mec.17367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Population genomics analysis holds great potential for informing conservation of endangered populations. We focused on a controversial case of European whitefish (Coregonus spp.) populations. The endangered North Sea houting is the only coregonid fish that tolerates oceanic salinities and was previously considered a species (C. oxyrhinchus) distinct from European lake whitefish (C. lavaretus). However, no firm evidence for genetic-based salinity adaptation has been available. Also, studies based on microsatellite and mitogenome data suggested surprisingly recent divergence (c. 2500 years bp) between houting and lake whitefish. These data types furthermore have provided no evidence for possible inbreeding. Finally, a controversial taxonomic revision recently classified all whitefish in the region as C. maraena, calling conservation priorities of houting into question. We used whole-genome and ddRAD sequencing to analyse six lake whitefish populations and the only extant indigenous houting population. Demographic inference indicated post-glacial expansion and divergence between lake whitefish and houting occurring not long after the Last Glaciation, implying deeper population histories than previous analyses. Runs of homozygosity analysis suggested not only high inbreeding (FROH up to 30.6%) in some freshwater populations but also FROH up to 10.6% in the houting prompting conservation concerns. Finally, outlier scans provided evidence for adaptation to high salinities in the houting. Applying a framework for defining conservation units based on current and historical reproductive isolation and adaptive divergence led us to recommend that the houting be treated as a separate conservation unit regardless of species status. In total, the results underscore the potential of genomics to inform conservation practices, in this case clarifying conservation units and highlighting populations of concern.
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Affiliation(s)
| | - Shenglin Liu
- Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Magnus W Jacobsen
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Peter Rask Møller
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Søren Berg
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
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3
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O'Mahony ÉN, Sremba AL, Keen EM, Robinson N, Dundas A, Steel D, Wray J, Baker CS, Gaggiotti OE. Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics. Mol Ecol Resour 2024:e13957. [PMID: 38576153 DOI: 10.1111/1755-0998.13957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory 'blow' samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS-collected whale blow for conservation genetics from a remote location.
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Affiliation(s)
- Éadin N O'Mahony
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, UK
- North Coast Cetacean Society, Alert Bay, British Columbia, Canada
| | - Angela L Sremba
- Marine Mammal Institute, Hatfield Marine Science Centre, Oregon State University, Newport, Oregon, USA
- Cooperative Institute for Marine Ecosystem Resources, Oregon State University, Newport, Oregon, USA
| | - Eric M Keen
- North Coast Cetacean Society, Alert Bay, British Columbia, Canada
- Sewanee: The University of the South, Sewanee, Tennessee, USA
| | - Nicole Robinson
- Gitga'at Oceans and Lands Department, Hartley Bay, British Columbia, Canada
| | - Archie Dundas
- Gitga'at Oceans and Lands Department, Hartley Bay, British Columbia, Canada
| | - Debbie Steel
- Marine Mammal Institute, Hatfield Marine Science Centre, Oregon State University, Newport, Oregon, USA
| | - Janie Wray
- North Coast Cetacean Society, Alert Bay, British Columbia, Canada
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Centre, Oregon State University, Newport, Oregon, USA
| | - Oscar E Gaggiotti
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, UK
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du Plessis SJ, Blaxter M, Koepfli KP, Chadwick EA, Hailer F. Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods. Mol Biol Evol 2023; 40:msad207. [PMID: 37713621 PMCID: PMC10630326 DOI: 10.1093/molbev/msad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/04/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023] Open
Abstract
Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated "stronghold" populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s-1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.
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Affiliation(s)
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Centre for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | | | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, UK
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Martins AB, Valença-Montenegro MM, Lima MGM, Lynch JW, Svoboda WK, Silva-Júnior JDSE, Röhe F, Boubli JP, Fiore AD. A New Assessment of Robust Capuchin Monkey ( Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation. Genes (Basel) 2023; 14:genes14050970. [PMID: 37239330 DOI: 10.3390/genes14050970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Robust capuchin monkeys, Sapajus genus, are among the most phenotypically diverse and widespread groups of primates in South America, with one of the most confusing and often shifting taxonomies. We used a ddRADseq approach to generate genome-wide SNP markers for 171 individuals from all putative extant species of Sapajus to access their evolutionary history. Using maximum likelihood, multispecies coalescent phylogenetic inference, and a Bayes Factor method to test for alternative hypotheses of species delimitation, we inferred the phylogenetic history of the Sapajus radiation, evaluating the number of discrete species supported. Our results support the recognition of three species from the Atlantic Forest south of the São Francisco River, with these species being the first splits in the robust capuchin radiation. Our results were congruent in recovering the Pantanal and Amazonian Sapajus as structured into three monophyletic clades, though new morphological assessments are necessary, as the Amazonian clades do not agree with previous morphology-based taxonomic distributions. Phylogenetic reconstructions for Sapajus occurring in the Cerrado, Caatinga, and northeastern Atlantic Forest were less congruent with morphology-based phylogenetic reconstructions, as the bearded capuchin was recovered as a paraphyletic clade, with samples from the Caatinga biome being either a monophyletic clade or nested with the blond capuchin monkey.
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Affiliation(s)
- Amely Branquinho Martins
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mônica Mafra Valença-Montenegro
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
| | - Marcela Guimarães Moreira Lima
- Laboratório de Biogeografia da Conservação e Macroecologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66077-530, PA, Brazil
| | - Jessica W Lynch
- Institute for Society and Genetics, Department of Anthropology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Walfrido Kühl Svoboda
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Centro Interdisciplinar de Ciências da Vida, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu 85870-650, PR, Brazil
| | - José de Sousa E Silva-Júnior
- Museu Paraense Emílio Goeldi, Ministério da Ciência, Tecnologia, Inovações e Comunicações, Coordenação de Zoologia, Campus de Pesquisa, Setor de Mastozoologia, Belém 66077-830, PA, Brazil
| | - Fábio Röhe
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus 69067-005, AM, Brazil
| | - Jean Philippe Boubli
- School of Science, Engineering and the Environment, University of Salford, Salford M5 4WT, UK
| | - Anthony Di Fiore
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
- Tiputini Biodiversity Station, Universidad San Francisco de Quito, Quito 170901, Ecuador
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Siebert U, Grilo ML, Kesselring T, Lehnert K, Ronnenberg K, Pawliczka I, Galatius A, Kyhn LA, Dähne M, Gilles A. Variation of blubber thickness for three marine mammal species in the southern Baltic Sea. Front Physiol 2022; 13:880465. [PMID: 36505079 PMCID: PMC9726720 DOI: 10.3389/fphys.2022.880465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
Evaluating populational trends of health condition has become an important topic for marine mammal populations under the Marine Strategy Framework Directive (MSFD). In the Baltic Sea, under the recommendation of Helsinki Commission (HELCOM), efforts have been undertaken to use blubber thickness as an indicator of energy reserves in marine mammals. Current values lack geographical representation from the entire Baltic Sea area and a large dataset is only available for grey seals (Halichoerus grypus) from Sweden and Finland. Knowledge on variation of blubber thickness related to geography throughout the Baltic Sea is important for its usage as an indicator. Such evaluation can provide important information about the energy reserves, and hence, food availability. It is expected that methodological standardization under HELCOM should include relevant datasets with good geographical coverage that can also account for natural variability in the resident marine mammal populations. In this study, seasonal and temporal trends of blubber thickness were evaluated for three marine mammal species-harbor seal (Phoca vitulina), grey seal (Halichoerus grypus) and harbor porpoise (Phocoena phocoena)-resident in the southern Baltic Sea collected and investigated under stranding networks. Additionally, the effects of age, season and sex were analyzed. Seasonal variation of blubber thickness was evident for all species, with harbor seals presenting more pronounced effects in adults and grey seals and harbor porpoises presenting more pronounced effects in juveniles. For harbor seals and porpoises, fluctuations were present over the years included in the analysis. In the seal species, blubber thickness values were generally higher in males. In harbor seals and porpoises, blubber thickness values differed between the age classes: while adult harbor seals displayed thicker blubber layers than juveniles, the opposite was observed for harbor porpoises. Furthermore, while an important initial screening tool, blubber thickness assessment cannot be considered a valid methodology for overall health assessment in marine mammals and should be complemented with data on specific health parameters developed for each species.
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Affiliation(s)
- Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover Foundation, Büsum, Germany,*Correspondence: Ursula Siebert,
| | - Miguel L. Grilo
- MARE—Marine and Environmental Sciences Centre, ISPA—Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Tina Kesselring
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover Foundation, Büsum, Germany
| | - Kristina Lehnert
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover Foundation, Büsum, Germany
| | - Katrin Ronnenberg
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover Foundation, Büsum, Germany
| | - Iwona Pawliczka
- Department of Oceanography and Geography, Krzysztof Skóra Hel Marine Station, University of Gdansk, Hel, Poland
| | - Anders Galatius
- Marine Mammal Research, Institute of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Line A. Kyhn
- Marine Mammal Research, Institute of Ecoscience, Aarhus University, Roskilde, Denmark
| | | | - Anita Gilles
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover Foundation, Büsum, Germany
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Amarilla-Stevens HN, Stevens RD, Phillips CD, Bradley RD. Temporal rate of postmortem DNA degradation in archived tissue samples: evidence from liver and muscle. J Mammal 2022. [DOI: 10.1093/jmammal/gyac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Guidelines identifying best practices for harvesting tissues that lead to optimal DNA preservation are few but are important curatorial concerns for genetic resource collections. We conducted a temporal study to establish rate of DNA degradation of tissue samples extracted from field-caught museum specimens. Five individuals of Sigmodon hispidus were collected and their liver and muscle tissues were harvested. Each tissue type was sectioned into 15 subsamples, and each was preserved in liquid nitrogen at different time intervals (2, 4, 8, 16, and 32 min; 1, 2, 4, 8, and 16 h; and 1, 2, 4, 8, and 16 days) following death. DNA was extracted using an automated robotic instrument and molecular mass profiles were determined fluorometrically. Postmortem DNA degradation was continuous and dependent on time, but also was significantly affected by differences among individual cotton rats. DNA fragments of ≥10,000 base pairs in length were present in muscle samples across all time intervals, whereas DNA fragments of this size in liver samples were no longer present after 8–16 h postmortem. DNA molecular mass profiles showed that muscle samples retained 80% of their longest fragments (≥10,000 base pairs) until 1 day postmortem, whereas liver samples retained the same percentage only until 8 min after death. Although rates of decay were measured from samples in a laboratory (not field) setting, rates of decay presented here can guide field and museum workers in best practices. Results suggest that opportunistic samples, such as those from roadkill specimens, are more likely to be of use for a variety of molecular methods when muscle is preserved. Considerations of differences in rates of degradation may also guide selection of tissue types housed in genetic resource collections, especially under space-limited circumstances.
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Affiliation(s)
- Heidi N Amarilla-Stevens
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
| | - Richard D Stevens
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
- Department of Natural Resources Management, Texas Tech University , Lubbock, Texas 79409-3131 , USA
| | - Caleb D Phillips
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
- Department of Biological Sciences, Texas Tech University , Lubbock, Texas 79409-3131 , USA
| | - Robert D Bradley
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
- Department of Biological Sciences, Texas Tech University , Lubbock, Texas 79409-3131 , USA
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Gross S, Müller A, Seinige D, Wohlsein P, Oliveira M, Steinhagen D, Kehrenberg C, Siebert U. Occurrence of Antimicrobial-Resistant Escherichia coli in Marine Mammals of the North and Baltic Seas: Sentinels for Human Health. Antibiotics (Basel) 2022; 11:antibiotics11091248. [PMID: 36140027 PMCID: PMC9495373 DOI: 10.3390/antibiotics11091248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance is a global health threat that involves complex, opaque transmission processes in the environment. In particular, wildlife appears to function as a reservoir and vector for antimicrobial-resistant bacteria as well as resistance genes. In the present study, the occurrence of antimicrobial-resistant Escherichia coli was determined in marine mammals and various fish species of the North and Baltic Seas. Rectal or faecal swabs were collected from 66 live-caught or stranded marine mammals and 40 fish specimens. The antimicrobial resistance phenotypes and genotypes of isolated E. coli were determined using disk diffusion tests and PCR assays. Furthermore, isolates were assigned to the four major phylogenetic groups of E. coli. Additionally, post mortem examinations were performed on 41 of the sampled marine mammals. The investigations revealed resistant E. coli in 39.4% of the marine mammal samples, while no resistant isolates were obtained from any of the fish samples. The obtained isolates most frequently exhibited resistance against aminoglycosides, followed by β-lactams. Of the isolates, 37.2% showed multidrug resistance. Harbour porpoises (Phocoena phocoena) mainly carried E. coli isolates belonging to the phylogenetic group B1, while seal isolates were most frequently assigned to group B2. Regarding antimicrobial resistance, no significant differences were seen between the two sampling areas or different health parameters, but multidrug-resistant isolates were more frequent in harbour porpoises than in the sampled seals. The presented results provide information on the distribution of antimicrobial-resistant bacteria in the North and Baltic Seas, and highlight the role of these resident marine mammal species as sentinels from a One Health perspective.
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Affiliation(s)
- Stephanie Gross
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstraße 6, 25761 Büsum, Germany
| | - Anja Müller
- Institute for Veterinary Food Science, Justus Liebig University Giessen, Frankfurter Str. 92, 35392 Giessen, Germany
| | - Diana Seinige
- Office for Veterinary Affairs and Consumer Protection, Ministry of Lower Saxony for Food, Agriculture and Consumer Protection, Alte Grenze 7, 29221 Celle, Germany
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Manuela Oliveira
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Dieter Steinhagen
- Fish Disease Research Unit, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Justus Liebig University Giessen, Frankfurter Str. 92, 35392 Giessen, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstraße 6, 25761 Büsum, Germany
- Correspondence:
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Knipler ML, Dowton M, Clulow J, Meyer N, Mikac KM. Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis. CONSERV GENET. [DOI: 10.1007/s10592-022-01435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAustralian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.
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12
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Amundin M, Carlström J, Thomas L, Carlén I, Teilmann J, Tougaard J, Loisa O, Kyhn LA, Sveegaard S, Burt ML, Pawliczka I, Koza R, Arciszewski B, Galatius A, Laaksonlaita J, MacAuley J, Wright AJ, Gallus A, Dähne M, Acevedo‐Gutiérrez A, Benke H, Koblitz J, Tregenza N, Wennerberg D, Brundiers K, Kosecka M, Tiberi Ljungqvist C, Jussi I, Jabbusch M, Lyytinen S, Šaškov A, Blankett P. Estimating the abundance of the critically endangered Baltic Proper harbour porpoise ( Phocoena phocoena) population using passive acoustic monitoring. Ecol Evol 2022; 12:e8554. [PMID: 35222950 PMCID: PMC8858216 DOI: 10.1002/ece3.8554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/18/2022] Open
Abstract
Knowing the abundance of a population is a crucial component to assess its conservation status and develop effective conservation plans. For most cetaceans, abundance estimation is difficult given their cryptic and mobile nature, especially when the population is small and has a transnational distribution. In the Baltic Sea, the number of harbour porpoises (Phocoena phocoena) has collapsed since the mid-20th century and the Baltic Proper harbour porpoise is listed as Critically Endangered by the IUCN and HELCOM; however, its abundance remains unknown. Here, one of the largest ever passive acoustic monitoring studies was carried out by eight Baltic Sea nations to estimate the abundance of the Baltic Proper harbour porpoise for the first time. By logging porpoise echolocation signals at 298 stations during May 2011-April 2013, calibrating the loggers' spatial detection performance at sea, and measuring the click rate of tagged individuals, we estimated an abundance of 71-1105 individuals (95% CI, point estimate 491) during May-October within the population's proposed management border. The small abundance estimate strongly supports that the Baltic Proper harbour porpoise is facing an extremely high risk of extinction, and highlights the need for immediate and efficient conservation actions through international cooperation. It also provides a starting point in monitoring the trend of the population abundance to evaluate the effectiveness of management measures and determine its interactions with the larger neighboring Belt Sea population. Further, we offer evidence that design-based passive acoustic monitoring can generate reliable estimates of the abundance of rare and cryptic animal populations across large spatial scales.
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Affiliation(s)
| | - Julia Carlström
- AquaBiota Water ResearchStockholmSweden
- Present address:
Department of Environmental Research and MonitoringSwedish Museum of Natural HistoryStockholmSweden
| | - Len Thomas
- Centre for Research into Ecological and Environmental ModellingUniversity of St AndrewsSt AndrewsUK
| | - Ida Carlén
- AquaBiota Water ResearchStockholmSweden
- Present address:
Department of ZoologyStockholm UniversityStockholmSweden
| | - Jonas Teilmann
- Marine Mammal ResearchDepartment of BioscienceAarhus UniversityRoskildeDenmark
| | - Jakob Tougaard
- Marine Mammal ResearchDepartment of BioscienceAarhus UniversityRoskildeDenmark
| | - Olli Loisa
- Turku University of Applied SciencesTurkuFinland
| | - Line A. Kyhn
- Marine Mammal ResearchDepartment of BioscienceAarhus UniversityRoskildeDenmark
| | - Signe Sveegaard
- Marine Mammal ResearchDepartment of BioscienceAarhus UniversityRoskildeDenmark
| | - M. Louise Burt
- Centre for Research into Ecological and Environmental ModellingUniversity of St AndrewsSt AndrewsUK
| | - Iwona Pawliczka
- Prof. Krzysztof Skóra Hel Marine StationDepartment of Oceanography and GeographyUniversity of GdańskHelPoland
| | - Radomil Koza
- Prof. Krzysztof Skóra Hel Marine StationDepartment of Oceanography and GeographyUniversity of GdańskHelPoland
| | - Bartlomiej Arciszewski
- Prof. Krzysztof Skóra Hel Marine StationDepartment of Oceanography and GeographyUniversity of GdańskHelPoland
| | - Anders Galatius
- Marine Mammal ResearchDepartment of BioscienceAarhus UniversityRoskildeDenmark
| | | | - Jamie MacAuley
- School of BiologyBute BuildingUniversity of St AndrewsSt AndrewsUK
- Present address:
Department of Biology ‐ ZoophysiologyAarhus UniversityAarhusDenmark
| | - Andrew J. Wright
- Marine Mammal ResearchDepartment of BioscienceAarhus UniversityRoskildeDenmark
- Present address:
Fisheries and Oceans CanadaMaritimes, DartmouthNova ScotiaCanada
| | | | | | | | | | - Jens Koblitz
- German Oceanographic MuseumStralsundGermany
- Present address:
Max Planck Institute of Animal BehaviorKonstanzGermany
- Present address:
Centre for the Advanced Study of Collective BehaviourUniversity of KonstanzKonstanzGermany
- Present address:
Department of BiologyUniversity of KonstanzKonstanzGermany
| | | | - Daniel Wennerberg
- Kolmarden Wildlife ParkKolmårdenSweden
- Present address:
Swedish Meteorological and Hydrological Institute, Core ServicesNorrköpingSweden
| | | | - Monika Kosecka
- Prof. Krzysztof Skóra Hel Marine StationDepartment of Oceanography and GeographyUniversity of GdańskHelPoland
- Present address:
Scottish Association for Marine ScienceUniversity of Highlands and IslandsObanUK
| | - Cinthia Tiberi Ljungqvist
- Kolmarden Wildlife ParkKolmårdenSweden
- Present address:
County Administrative Board of StockholmStockholmSweden
| | - Ivar Jussi
- ProMare NPOVintriku Saula küla, Kose valdHarjumaaEstonia
| | | | | | - Aleksej Šaškov
- Marine Research instituteKlaipėda UniversityKlaipėdaLithuania
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13
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Siebert U, Stürznickel J, Schaffeld T, Oheim R, Rolvien T, Prenger-Berninghoff E, Wohlsein P, Lakemeyer J, Rohner S, Aroha Schick L, Gross S, Nachtsheim D, Ewers C, Becher P, Amling M, Morell M. Blast injury on harbour porpoises (Phocoena phocoena) from the Baltic Sea after explosions of deposits of World War II ammunition. Environ Int 2022; 159:107014. [PMID: 34883460 DOI: 10.1016/j.envint.2021.107014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 05/21/2023]
Abstract
Harbour porpoises are under pressure from increasing human activities. This includes the detonation of ammunition that was dumped in large amounts into the sea during and after World War II. In this context, forty-two British ground mines from World War II were cleared by means of blasting in the period from 28 to 31 August 2019 by a NATO unit in the German Exclusive Economic Zone within the marine protected area of Fehmarn Belt in the Baltic Sea, Germany. Between September and November 2019, 24 harbour porpoises were found dead in the period after those clearing events along the coastline of the federal state of Schleswig-Holstein and were investigated for direct and indirect effects of blast injury. Health evaluations were conducted including examinations of the brain, the air-filled (lungs and gastrointestinal tract) and acoustic organs (melon, acoustic fat in the lower jaw, ears and their surrounding tissues). The bone structure of the tympano-periotic complexes was examined using high-resolution peripheral quantitative computed tomography (HR-pQCT). In 8/24 harbour porpoises, microfractures of the malleus, dislocation of middle ear bones, bleeding, and haemorrhages in the melon, lower jaw and peribullar acoustic fat were detected, suggesting blast injury. In addition, one bycaught animal and another porpoise with signs of blunt force trauma also showed evidence of blast injury. The cause of death of the other 14 animals varied and remained unclear in two individuals. Due to the vulnerability and the conservation status of harbour porpoise populations in the Baltic Sea, noise mitigation measures must be improved to prevent any risk of injury. The data presented here highlight the importance of systematic investigations into the acute and chronic effects of blast and acoustic trauma in harbour porpoises, improving the understanding of underwater noise effects and herewith develop effective measures to protect the population level.
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Affiliation(s)
- Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany.
| | - Julian Stürznickel
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529 Hamburg, Germany; Department of Trauma and Orthopaedic Surgery, Division of Orthopaedics, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Tobias Schaffeld
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany
| | - Ralf Oheim
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529 Hamburg, Germany
| | - Tim Rolvien
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529 Hamburg, Germany; Department of Trauma and Orthopaedic Surgery, Division of Orthopaedics, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Ellen Prenger-Berninghoff
- Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Frankfurter Str. 85-87, 35392 Giessen, Germany
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Jan Lakemeyer
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany
| | - Simon Rohner
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany
| | - Luca Aroha Schick
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany
| | - Stephanie Gross
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany
| | - Dominik Nachtsheim
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany
| | - Christa Ewers
- Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Frankfurter Str. 85-87, 35392 Giessen, Germany
| | - Paul Becher
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Michael Amling
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Lottestr. 59, 22529 Hamburg, Germany
| | - Maria Morell
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany
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14
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Graham CF, Boreham DR, Manzon RG, Wilson JY, Somers CM. Population structure of lake whitefish ( Coregonus clupeaformis) from the Mississippian lineage in North America. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The lake whitefish ( Coregonus clupeaformis) is a commercially valuable freshwater species with a broad distribution in North America. Some phylogeographic work has been done on this species, but little is known about genetic population subdivision among populations of the widely dispersed Mississippian lineage. We used 3,173 single nucleotide polymorphisms in 508 lake whitefish from 22 different lakes to examine population structure across central Canada and the United States. Bayesian clustering, ordination, and fixation indices identified population subdivision that largely reflected geographic distance and hydrological connectivity, with greater differentiation between lakes that are farther apart. Population subdivision was hierarchical, with greater differentiation between Canadian provinces and less differentiation based on river basins within provincial boundaries. Interestingly, isolation by distance alone was not sufficient to account for all of the observed genetic differentiation among populations. We conclude that important components of lake whitefish genetic diversity are present at different spatial scales, and that populations within the Mississippian lineage have differentiated widely across their range.
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Affiliation(s)
- Carly F. Graham
- Department of Biology, University of Regina, Regina, SK, Canada
| | - Douglas R. Boreham
- Medical Sciences, Northern Ontario School of Medicine, Greater Sudbury, ON, Canada
| | | | - Joanna Y. Wilson
- Department of Biology, McMaster University, Hamilton, ON, Canada
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15
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Gallego-García N, Caballero S, Shaffer HB. Are genomic updates of well-studied species worth the investment for conservation? A case study of the Critically Endangered Magdalena River turtle. J Hered 2021; 112:575-589. [PMID: 34628509 DOI: 10.1093/jhered/esab063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
As genomic-scale data sets become economically feasible for most organisms, a key question for conservation biology is whether the increased resolution offered by new genomic approaches justifies repeating earlier studies based on traditional markers, rather than investing those same time and monetary resources in less-known species. Genomic studies offer clear advantages when the objective is to identify adaptive loci that may be critical to conservation policy-makers. However, the answer is far less certain for the population and landscape studies based on neutral loci that dominate the conservation genetics research agenda. We used RADseq to revisit earlier molecular studies of the IUCN Critically Endangered Magdalena River turtle (Podocnemis lewyana), documenting the conservation insights gained by increasing the number of neutral markers by several orders of magnitude. Earlier research indicated that P. lewyana has the lowest genetic diversity known for any chelonian, and little or no population differentiation among independent rivers. In contrast, the RADseq data revealed discrete population structure with isolation-by-distance within river segments and identified precise population breaks clearly delineating management units. It also confirmed that the species does not have extremely low heterozygosity and that effective population sizes are probably sufficient to maintain long-term evolutionary potential. Contrary to earlier inferences from more limited population genetic markers, our genomic data suggest that management strategies should shift from active genetic rescue to more passive protection without extreme interventions. We conclude with a list of examples of conservation studies in other vertebrates indicating that for many systems a genomic update is worth the investment.
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Affiliation(s)
- Natalia Gallego-García
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Departamento de Ciencias Biológicas, Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Universidad de los Andes, Bogotá, Colombia
| | - Susana Caballero
- Departamento de Ciencias Biológicas, Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Universidad de los Andes, Bogotá, Colombia
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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16
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Owen K, Sköld M, Carlström J. An increase in detection rates of the critically endangered Baltic Proper harbor porpoise in Swedish waters in recent years. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Kylie Owen
- Department of Environmental Research and Monitoring Swedish Museum of Natural History Stockholm Sweden
| | - Martin Sköld
- Department of Environmental Research and Monitoring Swedish Museum of Natural History Stockholm Sweden
- Department of Mathematics Stockholm University Stockholm Sweden
| | - Julia Carlström
- Department of Environmental Research and Monitoring Swedish Museum of Natural History Stockholm Sweden
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17
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Morin PA, Forester BR, Forney KA, Crossman CA, Hancock-Hanser BL, Robertson KM, Barrett-Lennard LG, Baird RW, Calambokidis J, Gearin P, Hanson MB, Schumacher C, Harkins T, Fontaine MC, Taylor BL, Parsons KM. Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor-quality samples. Mol Ecol 2021; 30:1457-1476. [PMID: 33544423 DOI: 10.1111/mec.15827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 12/24/2022]
Abstract
Harbor porpoise in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of single nucleotide polymoirphisms as microhaplotypes (N = 271 samples) in addition to mitochondrial (mtDNA) sequence data (N = 413 samples) to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We confirmed an overall pattern of strong isolation-by-distance, suggesting that individual dispersal is restricted. We also found evidence of regions where genetic differences are larger than expected based on geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct (FST = 0.02 [microhaplotypes]; 0.31 [mtDNA]), with both reduced genetic variability and high frequency of an otherwise rare mtDNA haplotype. At the northern end of our study range, we found significant genetic differentiation of samples from the Strait of Georgia, previously identified as a potential biogeographical boundary or secondary contact zone between harbor porpoise populations. Association of microhaplotypes with remotely sensed environmental variables indicated potential local adaptation, especially at the southern end of the species' range. These results inform conservation and management for this nearshore species, illustrate the value of genomic methods for detecting patterns of genetic structure within a continuously distributed marine species, and highlight the power of microhaplotype genotyping for detecting genetic structure in harbor porpoises despite reliance on poor-quality samples.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Karin A Forney
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Moss Landing, CA, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA, USA
| | - Carla A Crossman
- Biology Department, Saint Mary's University, Halifax, NS, Canada.,Cetacean Research Program, Vancouver Aquarium, Vancouver, BC, Canada
| | | | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | | | | | | | - Pat Gearin
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | - M Bradley Hanson
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | | | | | - Michael C Fontaine
- MIVEGEC Research Unit (Université de Montpellier, CNRS, IRD) & Centre for Research on the Ecology and Evolution of Diseases (CREES), Centre IRD de Montpellier, Montpellier, France.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Kim M Parsons
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA.,Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
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18
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Benestan LM, Rougemont Q, Senay C, Normandeau E, Parent E, Rideout R, Bernatchez L, Lambert Y, Audet C, Parent GJ. Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus). Evol Appl 2021; 14:588-606. [PMID: 33664797 PMCID: PMC7896722 DOI: 10.1111/eva.13143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.
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Affiliation(s)
- Laura M. Benestan
- CEFEUniv Montpellier, CNRS, EPHE‐PSL UniversityIRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Caroline Senay
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Eric Parent
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Rick Rideout
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreN.L.St. John’sCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Yvan Lambert
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Céline Audet
- Institut des sciences de la mer de RimouskiUniversité du Québec à RimouskiRimouskiQCCanada
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19
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O'Toole B, Simmons NB, Hekkala E. Reconstructing the Genomic Diversity of a Widespread Sub-Saharan Bat (Pteropodidae: Eidolon helvum) Using Archival Museum Collections. Acta Chiropterologica 2020. [DOI: 10.3161/15081109acc2020.22.2.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Brian O'Toole
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Evon Hekkala
- Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
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20
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Gross S, Roller M, Haslob H, Grilo M, Lakemeyer J, Reckendorf A, Wohlsein P, Siebert U. Spatiotemporal accumulation of fatal pharyngeal entrapment of flatfish in harbour porpoises ( Phocoena phocoena) in the German North Sea. PeerJ 2020; 8:e10160. [PMID: 33150078 PMCID: PMC7583609 DOI: 10.7717/peerj.10160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/21/2020] [Indexed: 11/20/2022] Open
Abstract
The evolution of a permanent separation of the upper respiratory and digestive tract is one of the adaptions cetaceans evolved for their aquatic life. Generally, it prevents odontocetes from choking on either saltwater or foreign bodies during ingestion under water. Nevertheless, several sporadic single case reports from different parts of the world show that this separation can be reversed especially by overly large items of prey. This incident can have a fatal outcome for the odontocetes. The German federal state of Schleswig-Holstein has a year-round, permanent and systematic stranding network that retrieves stranded marine mammals from its shorelines and constantly enables post-mortem examinations. In 2016, with nine affected animals, a high incidence of fatal pharyngeal entrapment of flatfish in harbour porpoises (Phocoena phocoena) occurred during spring and early summer on the German North Sea island of Sylt. All flatfish were identified as common sole (Solea solea). A retrospective post-mortem data analysis over a 30-year period from the North and Baltic Sea revealed similar yearly and seasonally case accumulations on the same island in the 1990s as well as several single case events over the whole timespan. All cases except one were caused by flatfish. When flatfish speciation was performed, only common sole was identified. From 1990 to 2019, of all examined harbour porpoises, 0.3% (2/713) from the Baltic Sea and 5.5% (45/820) from the North Sea died due to fish entrapped in the pharynx. On the North Sea coast, the occurrence of fatal obstruction shows high yearly variations from 0 to 33.3%. Years that stand out are especially 1990 to 1992, 1995, as well as 2016. The majority of all cases generally occurred between April and July, indicating also a seasonality of cases. This study evaluates the occurrence of fatal pharyngeal entrapment of fish in two geographically separated harbour porpoise populations. Additionally, common sole is clearly identified as a potentially risky item of prey for these small odontocetes.
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Affiliation(s)
- Stephanie Gross
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Büsum, Germany
| | - Marco Roller
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Büsum, Germany
| | - Holger Haslob
- Thünen-Institute of Sea Fisheries, Bremerhaven, Germany
| | - Miguel Grilo
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Büsum, Germany.,CIISA-Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Lisbon, Portugal
| | - Jan Lakemeyer
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Büsum, Germany
| | - Anja Reckendorf
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Büsum, Germany
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Büsum, Germany
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21
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Siebert U, Pawliczka I, Benke H, von Vietinghoff V, Wolf P, Pilāts V, Kesselring T, Lehnert K, Prenger-Berninghoff E, Galatius A, Anker Kyhn L, Teilmann J, Hansen MS, Sonne C, Wohlsein P. Health assessment of harbour porpoises (PHOCOENA PHOCOENA) from Baltic area of Denmark, Germany, Poland and Latvia. Environ Int 2020; 143:105904. [PMID: 32615352 DOI: 10.1016/j.envint.2020.105904] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Harbour porpoise (Phocoena phocoena), the only resident cetacean species of the Baltic Sea is formed of two subpopulations populations, occurring in the western Baltic, Belt Seas and Kattegat and the Baltic Proper, respectively. Harbour porpoises throughout these areas are exposed to a large number of human activities causing direct and indirect effects on individuals, that might also harm this species on a population level. From Latvia, Poland, Germany and Denmark 385 out of 1769 collected dead harbour porpoises were suitable for extensive necropsy. The animals were collected between 1990 and 2015 and were either by-caught or found dead on the coastline. Following necropsies, histopathological, microbiological, virological and parasitological investigations were conducted. Females and males were equally distributed among the 385 animals. Most animals from the different countries were juveniles between 3 months and 3 years old (varying between 46.5 and 100% of 385 animals per country). The respiratory tract had the highest number of morphological lesions, including lungworms in 25 to 58% and pneumonia in 21 to 58% of the investigated animals. Of those with pneumonia 8 to 33% were moderate or severe. The alimentary, hearing, and haematopoietic systems had inflammatory lesions and parasitic infections with limited health impact. 45.5 to 100% of the animals from the different countries were known by-caught individuals, of which 20 to 100% varying between countries had netmarks. Inflammatory lesions, especially in the respiratory tract were found in higher numbers when compared to control populations in areas with less human activities such as arctic waters. The high number of morphological changes in the respiratory tract and of bycatches especially among immature animals before reaching sexual maturity is of serious concern, as well as the low number of adult animals among the material. Data on health status and the causes of death are valuable for management. A next step in this regard will combine data from health and genetic investigations in order to detect differences between the two populations of the Baltic.
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Affiliation(s)
- U Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany; Marine Mammal Research, Institute of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - I Pawliczka
- Prof. Krzysztof Skóra Hel Marine Station, Department of Oceanography and Geography, University of Gdansk, Morska 2, 84-150 Hel, Poland
| | - H Benke
- German Oceanographic Museum, Katharinenberg 14/20, 18347 Stralsund, Germany
| | - V von Vietinghoff
- German Oceanographic Museum, Katharinenberg 14/20, 18347 Stralsund, Germany
| | - P Wolf
- Landesveterinär- und Lebensmitteluntersuchungsamt Rostock, Thierfelder Str. 18, 18059 Rostock, Germany
| | - V Pilāts
- Nature Conservation Agency, Baznīcas iela 7, Sigulda LV-2150, Latvia
| | - T Kesselring
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany
| | - K Lehnert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstr. 6, 25761 Büsum, Germany
| | - E Prenger-Berninghoff
- Institute for Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Frankfurter Str. 85-87, 35392 Giessen, Germany
| | - A Galatius
- Marine Mammal Research, Institute of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - L Anker Kyhn
- Marine Mammal Research, Institute of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - J Teilmann
- Marine Mammal Research, Institute of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - M S Hansen
- Section of Pathology, Department of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 3, 1870 Frederiksberg C, Denmark
| | - C Sonne
- Marine Mammal Research, Institute of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - P Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
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22
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Lakemeyer J, Siebert U, Abdulmawjood A, Ryeng KA, IJsseldijk LL, Lehnert K. Anisakid nematode species identification in harbour porpoises ( Phocoena phocoena) from the North Sea, Baltic Sea and North Atlantic using RFLP analysis. Int J Parasitol Parasites Wildl 2020; 12:93-98. [PMID: 32489854 PMCID: PMC7260678 DOI: 10.1016/j.ijppaw.2020.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 10/26/2022]
Abstract
Harbour porpoises (Phocoena phocoena) are the only native cetacean species in the German North and Baltic Seas and the final host of Anisakis (A.) simplex, which infects their first and second gastric compartments and may cause chronic ulcerative gastritis. Anisakis simplex belongs to the family Anisakidae (Ascaridoidea, Rhabditida) as well as the phocine gastric nematode species Pseudoterranova (P.) decipiens and Contracaecum (C.) osculatum. These nematode species are the main causative agents for the zoonosis anisakidosis. The taxonomy of these genus with life cycles including crustaceans and commercially important fish is complex because of the formation of sibling species. Little is known about anisakid species infecting porpoises in the study area. Mature nematodes and larval stages are often identifiable only by molecular methods due to high morphological and genetic similarity. The restriction fragment length polymorphism (RFLP) method is an alternative to sequencing and was applied to identify anisakid nematodes found in harbour porpoises from the North Sea, Baltic Sea and North Atlantic to species level for the first time. In the study areas, five gastric nematodes from different harbour porpoise hosts were selected to be investigated with restriction enzymes HinfI, RsaI and HaeIII, which were able to differentiate several anisakid nematode species by characteristic banding patterns. Anisakis simplex s. s. was the dominant species found in the North Sea and Baltic porpoises, identified by all three restriction enzymes. Additionally, a hybrid of A. simplex s. s. and A. pegreffii was determined by HinfI in the North Sea samples. Within the North Atlantic specimens, A. simplex s. s., P. decipiens s. s. and Hysterothylacium (H.) aduncum were identified by all enzymes. This demonstrates the value of the RFLP method and the chosen restriction enzymes for the species identification of a broad variety of anisakid nematodes affecting the health of marine mammals.
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Affiliation(s)
- Jan Lakemeyer
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine, Foundation, Hannover, Werftstrasse 6, 25761, Büsum, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine, Foundation, Hannover, Werftstrasse 6, 25761, Büsum, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine, Foundation, Hannover, Bünteweg 17, 30559, Hannover, Germany
| | - Kathrine A. Ryeng
- Institute of Marine Research, Fram Centre, P.O. Box 6606 Langnes, NO, 9296, Tromsø, Norway
| | - Lonneke L. IJsseldijk
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division of Pathology, Utrecht University, Yalelaan 1, 3584, CL, Utrecht, the Netherlands
| | - Kristina Lehnert
- Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine, Foundation, Hannover, Werftstrasse 6, 25761, Büsum, Germany
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23
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LaCava MEF, Gagne RB, Stowell SML, Gustafson KD, Buerkle CA, Knox L, Ernest HB. Pronghorn population genomics show connectivity in the core of their range. J Mammal 2020; 101:1061-1071. [PMID: 33100929 DOI: 10.1093/jmammal/gyaa054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/21/2020] [Indexed: 01/17/2023] Open
Abstract
Preserving connectivity in the core of a species' range is crucial for long-term persistence. However, a combination of ecological characteristics, social behavior, and landscape features can reduce connectivity among wildlife populations and lead to genetic structure. Pronghorn (Antilocapra americana), for example, exhibit fluctuating herd dynamics and variable seasonal migration strategies, but GPS tracking studies show that landscape features such as highways impede their movements, leading to conflicting hypotheses about expected levels of genetic structure. Given that pronghorn populations declined significantly in the early 1900s, have only partially recovered, and are experiencing modern threats from landscape modification, conserving connectivity among populations is important for their long-term persistence in North America. To assess the genetic structure and diversity of pronghorn in the core of their range, we genotyped 4,949 genome-wide single-nucleotide polymorphisms and 11 microsatellites from 398 individuals throughout the state of Wyoming. We found no evidence of genetic subdivision and minimal evidence of isolation by distance despite a range that spans hundreds of kilometers, multiple mountain ranges, and three interstate highways. In addition, a rare variant analysis using putatively recent mutations found no genetic division between pronghorn on either side of a major highway corridor. Although we found no evidence that barriers to daily and seasonal movements of pronghorn impede gene flow, we suggest periodic monitoring of genetic structure and diversity as a part of management strategies to identify changes in connectivity.
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Affiliation(s)
- Melanie E F LaCava
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Roderick B Gagne
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Sierra M Love Stowell
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Kyle D Gustafson
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Department of Biology and Environmental Health, Missouri Southern State University, Joplin, MO, USA
| | - C Alex Buerkle
- Program in Ecology, University of Wyoming, Laramie, WY, USA.,Department of Botany, University of Wyoming, Laramie, WY, USA
| | - Lee Knox
- Wyoming Game and Fish Department, Laramie, WY, USA
| | - Holly B Ernest
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
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24
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Schlägel UE, Grimm V, Blaum N, Colangeli P, Dammhahn M, Eccard JA, Hausmann SL, Herde A, Hofer H, Joshi J, Kramer-Schadt S, Litwin M, Lozada-Gobilard SD, Müller MEH, Müller T, Nathan R, Petermann JS, Pirhofer-Walzl K, Radchuk V, Rillig MC, Roeleke M, Schäfer M, Scherer C, Schiro G, Scholz C, Teckentrup L, Tiedemann R, Ullmann W, Voigt CC, Weithoff G, Jeltsch F. Movement-mediated community assembly and coexistence. Biol Rev Camb Philos Soc 2020; 95:1073-1096. [PMID: 32627362 DOI: 10.1111/brv.12600] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 01/11/2023]
Abstract
Organismal movement is ubiquitous and facilitates important ecological mechanisms that drive community and metacommunity composition and hence biodiversity. In most existing ecological theories and models in biodiversity research, movement is represented simplistically, ignoring the behavioural basis of movement and consequently the variation in behaviour at species and individual levels. However, as human endeavours modify climate and land use, the behavioural processes of organisms in response to these changes, including movement, become critical to understanding the resulting biodiversity loss. Here, we draw together research from different subdisciplines in ecology to understand the impact of individual-level movement processes on community-level patterns in species composition and coexistence. We join the movement ecology framework with the key concepts from metacommunity theory, community assembly and modern coexistence theory using the idea of micro-macro links, where various aspects of emergent movement behaviour scale up to local and regional patterns in species mobility and mobile-link-generated patterns in abiotic and biotic environmental conditions. These in turn influence both individual movement and, at ecological timescales, mechanisms such as dispersal limitation, environmental filtering, and niche partitioning. We conclude by highlighting challenges to and promising future avenues for data generation, data analysis and complementary modelling approaches and provide a brief outlook on how a new behaviour-based view on movement becomes important in understanding the responses of communities under ongoing environmental change.
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Affiliation(s)
- Ulrike E Schlägel
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany
| | - Volker Grimm
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.,Department of Ecological Modelling, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Niels Blaum
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany
| | - Pierluigi Colangeli
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Department of Ecology and Ecosystem Modelling, University of Potsdam, Maulbeerallee 2, 14469, Potsdam, Germany
| | - Melanie Dammhahn
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Animal Ecology, University of Potsdam, Maulbeerallee 1, 14469, Potsdam, Germany
| | - Jana A Eccard
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Animal Ecology, University of Potsdam, Maulbeerallee 1, 14469, Potsdam, Germany
| | - Sebastian L Hausmann
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Plant Ecology, Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Antje Herde
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615, Bielefeld, Germany
| | - Heribert Hofer
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Jasmin Joshi
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Biodiversity Research and Systematic Botany, University of Potsdam, Maulbeerallee 2, 14469, Potsdam, Germany.,Institute for Landscape and Open Space, Hochschule für Technik HSR Rapperswil, Seestrasse 10, 8640 Rapperswil, Switzerland
| | - Stephanie Kramer-Schadt
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany.,Department of Ecology, Technische Universität Berlin, Rothenburgstr. 12, 12165, Berlin, Germany
| | - Magdalena Litwin
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Evolutionary Biology/Systematic Zoology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Sissi D Lozada-Gobilard
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Biodiversity Research and Systematic Botany, University of Potsdam, Maulbeerallee 2, 14469, Potsdam, Germany
| | - Marina E H Müller
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz-Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374, Müncheberg, Germany
| | - Thomas Müller
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz-Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374, Müncheberg, Germany
| | - Ran Nathan
- Department of Ecology, Evolution and Behavior, Movement Ecology Laboratory, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jana S Petermann
- Department of Biosciences, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - Karin Pirhofer-Walzl
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Plant Ecology, Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany.,Leibniz-Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374, Müncheberg, Germany
| | - Viktoriia Radchuk
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Matthias C Rillig
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Plant Ecology, Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Manuel Roeleke
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Merlin Schäfer
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz-Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374, Müncheberg, Germany
| | - Cédric Scherer
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Gabriele Schiro
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz-Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374, Müncheberg, Germany
| | - Carolin Scholz
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Lisa Teckentrup
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany
| | - Ralph Tiedemann
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Evolutionary Biology/Systematic Zoology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Wiebke Ullmann
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz-Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374, Müncheberg, Germany
| | - Christian C Voigt
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany.,Behavioral Biology, Institute of Biology, Freie Universität Berlin, Takustr. 6, 14195, Berlin, Germany
| | - Guntram Weithoff
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany.,Department of Ecology and Ecosystem Modelling, University of Potsdam, Maulbeerallee 2, 14469, Potsdam, Germany
| | - Florian Jeltsch
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, 14476, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195, Berlin, Germany
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25
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Graham CF, Boreham DR, Manzon RG, Stott W, Wilson JY, Somers CM. How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: A case study using the lake whitefish. PLoS One 2020; 15:e0226608. [PMID: 31978053 PMCID: PMC6980518 DOI: 10.1371/journal.pone.0226608] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 12/01/2019] [Indexed: 12/30/2022] Open
Abstract
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth, as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these “simple” methodological decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) a larger number of loci at low sequencing depth based on a 9mer (library A); and (2) fewer loci at higher sequencing depth based on a 10mer (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters, largely due to retention of more loci in analyses. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. When detecting fine population differentiation, the population map influenced the number of loci and missing data, which generated artefacts in all downstream analyses tested. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library construction and bioinformatics parameters can have important impacts on the interpretation of population subdivision. Although potentially more costly on a per-locus basis, early investment in striking a balance between the number of loci and sequencing effort is well worth the reduced genomic coverage for population genetics studies. More conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation. Overall, we recommend that researchers approach “simple” methodological decisions with caution, especially when working on non-model species for the first time.
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Affiliation(s)
- Carly F. Graham
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Douglas R. Boreham
- Medical Sciences, Northern Ontario School of Medicine, Greater Sudbury, Ontario, Canada
| | - Richard G. Manzon
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Wendylee Stott
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Joanna Y. Wilson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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26
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Mynhardt S, Bennett NC, Bloomer P. New insights from RADseq data on differentiation in the Hottentot golden mole species complex from South Africa. Mol Phylogenet Evol 2019; 143:106667. [PMID: 31676418 DOI: 10.1016/j.ympev.2019.106667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/28/2019] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
Abstract
Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub-Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have relatively wide ranges. We recently uncovered cryptic diversity within A. hottentotus, through a phylogeographic analysis of this taxon using two mitochondrial gene regions and a nuclear intron. To further investigate this cryptic diversity, we generated nuclear SNP data from across the genome of A. hottentotus, by means of double-digest restriction-site associated DNA sequencing (ddRADSeq), and mapped reads to the Cape golden mole genome. We conducted a phylogenetic analysis and investigated population differentiation. Our results support the distinctiveness of A. h. meesteri. Furthermore, we provide evidence from nuclear SNPs in support of our previous finding that Central coastal samples represent a unique cryptic lineage that is highly divergent from A. h. pondoliae farther south. Although mtDNA suggests that Umtata may represent a unique lineage sister to A. h. longiceps, mito-nuclear discordance from our RADseq data indicate that these samples may instead be closer to A. h. pondoliae, and therefore may not represent a distinct lineage. We stress the importance of recognizing that understudied populations, such as that of Umtata, may represent populations or ESUs under threat and in need of conservation attention. We present a high-quality filtered SNP dataset, comprising thousands of SNPs, which may serve as a useful resource for future golden mole studies. We have thus added to the growing body of research demonstrating the power and utility of RADseq to investigate population differentiation.
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Affiliation(s)
- Samantha Mynhardt
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa; Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa.
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27
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Affiliation(s)
- Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
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28
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Rey-Iglesia A, Gopalakrishan S, Carøe C, Alquezar-Planas DE, Ahlmann Nielsen A, Röder T, Bruhn Pedersen L, Naesborg-Nielsen C, Sinding MHS, Fredensborg Rath M, Li Z, Petersen B, Gilbert MTP, Bunce M, Mourier T, Hansen AJ. MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. Mol Ecol Resour 2019; 19:512-525. [PMID: 30575257 DOI: 10.1111/1755-0998.12984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Abstract
In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site-associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms-enabling the exploration of diverse evolutionary and conservation questions.
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Affiliation(s)
- Alba Rey-Iglesia
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Shyam Gopalakrishan
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David E Alquezar-Planas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Anne Ahlmann Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Timo Röder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lene Bruhn Pedersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Mikkel-Holger S Sinding
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | | | - Zhipeng Li
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Kedah, Malaysia
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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29
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Rekdahl ML, Garland EC, Carvajal GA, King CD, Collins T, Razafindrakoto Y, Rosenbaum H. Culturally transmitted song exchange between humpback whales ( Megaptera novaeangliae) in the southeast Atlantic and southwest Indian Ocean basins. R Soc Open Sci 2018; 5:172305. [PMID: 30564382 PMCID: PMC6281946 DOI: 10.1098/rsos.172305] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
In migratory marine species, investigating population connectivity and structure can be challenging given barriers to dispersal are less evident and multiple factors may influence individual movement patterns. Male humpback whales sing a song display that can provide insights into contemporary connectivity patterns, as there can be a cultural exchange of a single, population-wide shared song type with neighbouring populations in acoustic contact. Here, we investigated song exchange between populations located on the east and west coasts of Africa using 5 years of concurrent data (2001-2005). Songs were qualitatively and quantitatively transcribed by measuring acoustic features of all song units and then compared using both Dice's similarity index and the Levenshtein distance similarity index (LSI) to quantitatively calculate song similarity. Song similarity varied among individuals and potentially between populations depending on the year (Dice: 36-100%, LSI: 21-100%), suggesting varying levels of population connectivity and/or interchange among years. The high degree of song sharing indicated in this study further supports genetic studies that demonstrate interchange between these two populations and reinforces the emerging picture of broad-scale connectivity in Southern Hemisphere populations. Further research incorporating additional populations and years would be invaluable for better understanding of fine-scale, song interchange patterns between Southern Hemisphere male humpback whales.
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Affiliation(s)
- Melinda L. Rekdahl
- Wildlife Conservation Society, Ocean Giants Program, Global Conservation Program, 2300 Southern Boulevard, Bronx, NY 10460-1099, USA
| | - Ellen C. Garland
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
| | - Gabriella A. Carvajal
- Wildlife Conservation Society, Ocean Giants Program, Global Conservation Program, 2300 Southern Boulevard, Bronx, NY 10460-1099, USA
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
| | - Carissa D. King
- Wildlife Conservation Society, Ocean Giants Program, Global Conservation Program, 2300 Southern Boulevard, Bronx, NY 10460-1099, USA
| | - Tim Collins
- Wildlife Conservation Society, Ocean Giants Program, Global Conservation Program, 2300 Southern Boulevard, Bronx, NY 10460-1099, USA
| | - Yvette Razafindrakoto
- COSAP Sahamalaza Miaro Dugong C/O Madagascar National Parks Sahamalaza, Analalava, Maromandia, Madagascar
| | - Howard Rosenbaum
- Wildlife Conservation Society, Ocean Giants Program, Global Conservation Program, 2300 Southern Boulevard, Bronx, NY 10460-1099, USA
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30
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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31
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Flanagan SP, Forester BR, Latch EK, Aitken SN, Hoban S. Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation. Evol Appl 2018; 11:1035-1052. [PMID: 30026796 PMCID: PMC6050180 DOI: 10.1111/eva.12569] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/20/2017] [Indexed: 12/14/2022] Open
Abstract
Identifying and monitoring locally adaptive genetic variation can have direct utility for conserving species at risk, especially when management may include actions such as translocations for restoration, genetic rescue, or assisted gene flow. However, genomic studies of local adaptation require careful planning to be successful, and in some cases may not be a worthwhile use of resources. Here, we offer an adaptive management framework to help conservation biologists and managers decide when genomics is likely to be effective in detecting local adaptation, and how to plan assessment and monitoring of adaptive variation to address conservation objectives. Studies of adaptive variation using genomic tools will inform conservation actions in many cases, including applications such as assisted gene flow and identifying conservation units. In others, assessing genetic diversity, inbreeding, and demographics using selectively neutral genetic markers may be most useful. And in some cases, local adaptation may be assessed more efficiently using alternative approaches such as common garden experiments. Here, we identify key considerations of genomics studies of locally adaptive variation, provide a road map for successful collaborations with genomics experts including key issues for study design and data analysis, and offer guidelines for interpreting and using results from genomic assessments to inform monitoring programs and conservation actions.
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Affiliation(s)
- Sarah P. Flanagan
- National Institute for Mathematical and Biological SynthesisUniversity of TennesseeKnoxvilleTNUSA
| | - Brenna R. Forester
- Duke University, Nicholas School of the EnvironmentDurhamNCUSA
- Present address:
Department of BiologyColorado State UniversityFort CollinsCOUSA
| | - Emily K. Latch
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWIUSA
| | - Sally N. Aitken
- Faculty of ForestryUniversity of British ColumbiaVancouverBCCanada
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32
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Jahnke M, Jonsson PR, Moksnes P, Loo L, Nilsson Jacobi M, Olsen JL. Seascape genetics and biophysical connectivity modelling support conservation of the seagrass Zostera marina in the Skagerrak-Kattegat region of the eastern North Sea. Evol Appl 2018; 11:645-661. [PMID: 29875808 PMCID: PMC5979629 DOI: 10.1111/eva.12589] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 12/08/2017] [Indexed: 01/02/2023] Open
Abstract
Maintaining and enabling evolutionary processes within meta-populations are critical to resistance, resilience and adaptive potential. Knowledge about which populations act as sources or sinks, and the direction of gene flow, can help to focus conservation efforts more effectively and forecast how populations might respond to future anthropogenic and environmental pressures. As a foundation species and habitat provider, Zostera marina (eelgrass) is of critical importance to ecosystem functions including fisheries. Here, we estimate connectivity of Z. marina in the Skagerrak-Kattegat region of the North Sea based on genetic and biophysical modelling. Genetic diversity, population structure and migration were analysed at 23 locations using 20 microsatellite loci and a suite of analytical approaches. Oceanographic connectivity was analysed using Lagrangian dispersal simulations based on contemporary and historical distribution data dating back to the late 19th century. Population clusters, barriers and networks of connectivity were found to be very similar based on either genetic or oceanographic analyses. A single-generation model of dispersal was not realistic, whereas multigeneration models that integrate stepping-stone dispersal and extant and historic distribution data were able to capture and model genetic connectivity patterns well. Passive rafting of flowering shoots along oceanographic currents is the main driver of gene flow at this spatial-temporal scale, and extant genetic connectivity strongly reflects the "ghost of dispersal past" sensu Benzie, 1999. The identification of distinct clusters, connectivity hotspots and areas where connectivity has become limited over the last century is critical information for spatial management, conservation and restoration of eelgrass.
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Affiliation(s)
- Marlene Jahnke
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
- Groningen Institute for Evolutionary Life SciencesSection: Ecology and Evolutionary Genomics in Nature (GREEN)University of GroningenGroningenThe Netherlands
| | - Per R. Jonsson
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | - Per‐Olav Moksnes
- Department of Marine ScienceUniversity of GothenburgGothenburgSweden
| | - Lars‐Ove Loo
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | - Martin Nilsson Jacobi
- Complex Systems GroupDepartment of Energy and EnvironmentChalmers University of TechnologyGothenburgSweden
| | - Jeanine L. Olsen
- Groningen Institute for Evolutionary Life SciencesSection: Ecology and Evolutionary Genomics in Nature (GREEN)University of GroningenGroningenThe Netherlands
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33
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Teske PR, Golla TR, Sandoval-Castillo J, Emami-Khoyi A, van der Lingen CD, von der Heyden S, Chiazzari B, Jansen van Vuuren B, Beheregaray LB. Mitochondrial DNA is unsuitable to test for isolation by distance. Sci Rep 2018; 8:8448. [PMID: 29855482 PMCID: PMC5981212 DOI: 10.1038/s41598-018-25138-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/16/2018] [Indexed: 12/04/2022] Open
Abstract
Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species' true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.
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Affiliation(s)
- Peter R Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa.
| | - Tirupathi Rao Golla
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Carl D van der Lingen
- Branch: Fisheries Management, Department of Agriculture, Forestry and Fisheries, Private Bag X2, Vlaeberg, 8012, South Africa
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Private Bag X3, Rondebosch, 7700, South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, 7602, Matieland, South Africa
| | - Brent Chiazzari
- School of Life Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Luciano B Beheregaray
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
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