1
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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] [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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2
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Hayes KRR, Ylitalo GM, Anderson TA, Urbán
R. J, Jacobsen JK, Scordino JJ, Lang AR, Baugh KA, Bolton JL, Brüniche-Olsen A, Calambokidis J, Martínez-Aguilar S, Subbiah S, Gribble MO, Godard-Codding CAJ. Influence of Life-History Parameters on Persistent Organic Pollutant Concentrations in Blubber of Eastern North Pacific Gray Whales ( Eschrichtius robustus). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17119-17130. [PMID: 36346717 PMCID: PMC9730851 DOI: 10.1021/acs.est.2c05998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/12/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Exposure to persistent organic pollutants (POPs) can significantly impact marine mammal health, reproduction, and fitness. This study addresses a significant 20-year gap in gray whale contaminant monitoring through analysis of POPs in 120 blubber biopsies. The scope of this substantial sample set is noteworthy in its range and diversity with collection between 2003 and 2017 along North America's west coast and across diverse sex, age, and reproductive parameters, including paired mothers and calves. Mean blubber concentrations of polychlorinated biphenyls (∑PCBs), dichlorodiphenyltrichloroethanes (∑DDTs), and chlordanes (∑CHLs) generally decreased since previous reports (1968-1999). This is the first report of polybrominated diphenyl ethers (PBDEs) and select hexachlorocyclohexanes (HCHs) in this species. Statistical modeling of the 19 most frequently detected compounds in this dataset revealed sex-, age-, and reproductive status-related patterns, predominantly attributed to maternal offloading. Mean POP concentrations differed significantly by sex in adults (17 compounds, up to 3-fold higher in males) but not in immatures (all 19 compounds). Mean POP concentrations were significantly greater in adults versus immatures in both males (17 compounds, up to 12-fold) and females (13 compounds, up to 3-fold). POP concentrations were detected with compound-specific patterns in nursing calves, confirming maternal offloading for the first time in this species.
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Affiliation(s)
- Kia R. R. Hayes
- The
Institute of Environmental and Human Health, Texas Tech University, Lubbock, Texas 79409, United States
- Environmental
and Fisheries Sciences Division, Northwest Fisheries Science Center,
National Marine Fisheries Service, National
Oceanic and Atmospheric Administration, Seattle, Washington 98112, United States
- Ocean
Associates, Inc., Arlington, Virginia 22207, United States
| | - Gina M. Ylitalo
- Environmental
and Fisheries Sciences Division, Northwest Fisheries Science Center,
National Marine Fisheries Service, National
Oceanic and Atmospheric Administration, Seattle, Washington 98112, United States
| | - Todd A. Anderson
- The
Institute of Environmental and Human Health, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jorge Urbán
R.
- Departamento
de Ciencias Marinas y Costeras, Universidad
Autónoma de Baja California Sur, La Paz, BCS 23085, Mexico
| | | | - Jonathan J. Scordino
- Marine Mammal
Program, Makah Fisheries Management, Makah Tribe, Neah Bay, Washington 98357, United States
| | - Aimee R. Lang
- Ocean
Associates, Inc., Arlington, Virginia 22207, United States
- Southwest
Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California 92037, United States
| | - Keri A. Baugh
- Environmental
and Fisheries Sciences Division, Northwest Fisheries Science Center,
National Marine Fisheries Service, National
Oceanic and Atmospheric Administration, Seattle, Washington 98112, United States
| | - Jennie L. Bolton
- Environmental
and Fisheries Sciences Division, Northwest Fisheries Science Center,
National Marine Fisheries Service, National
Oceanic and Atmospheric Administration, Seattle, Washington 98112, United States
| | - Anna Brüniche-Olsen
- Department
of Forestry and Natural Resources, Purdue
University, West Lafayette, Indiana 47907, United States
| | - John Calambokidis
- Cascadia
Research Collective, Olympia, Washington 98501, United States
| | - Sergio Martínez-Aguilar
- Departamento
de Ciencias Marinas y Costeras, Universidad
Autónoma de Baja California Sur, La Paz, BCS 23085, Mexico
| | - Seenivasan Subbiah
- The
Institute of Environmental and Human Health, Texas Tech University, Lubbock, Texas 79409, United States
| | - Matthew O. Gribble
- Department
of Epidemiology, University of Alabama at
Birmingham, Birmingham, Alabama 35294, United
States
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3
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Muller-Girard M, Fowles G, Duchamp J, Kouneski S, Mollohan C, Smyser TJ, Turner GG, Westrich B, Doyle JM. A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population. BMC Ecol Evol 2022; 22:137. [PMID: 36418951 PMCID: PMC9686018 DOI: 10.1186/s12862-022-02083-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 10/19/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species' range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population. RESULTS We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population. CONCLUSIONS Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.
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Affiliation(s)
- Megan Muller-Girard
- grid.265122.00000 0001 0719 7561Department of Environmental Science and Studies, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | - Gretchen Fowles
- Endangered and Nongame Species Program, New Jersey DEP Fish and Wildlife, 1255 County Rd 629, Lebanon, NJ 08833 USA
| | - Joseph Duchamp
- grid.257427.10000000088740847Department of Biology, Indiana University of Pennsylvania, 975 Oakland Avenue, Indiana, PA 15705-1081 USA
| | - Samantha Kouneski
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | | | - Timothy J. Smyser
- grid.413759.d0000 0001 0725 8379USDA-APHIS-WS National Wildlife Research Center, Fort Collins, CO USA
| | - Gregory G. Turner
- Pennsylvania Game Commission, 2001 Elmerton Avenue, Harrisburg, PA 17110 USA
| | - Bradford Westrich
- grid.448453.a0000 0004 1130 5264Indiana Department of Natural Resources, 5596 East State Road 46, Bloomington, IN 47401 USA
| | - Jacqueline M. Doyle
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
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4
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Nursyifa C, Brüniche-Olsen A, Garcia-Erill G, Heller R, Albrechtsen A. Joint identification of sex and sex-linked scaffolds in non-model organisms using low depth sequencing data. Mol Ecol Resour 2021; 22:458-467. [PMID: 34431216 DOI: 10.1111/1755-0998.13491] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/23/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022]
Abstract
Being able to assign sex to individuals and identify autosomal and sex-linked scaffolds are essential in most population genomic analyses. Non-model organisms often have genome assemblies at scaffold-level and lack characterization of sex-linked scaffolds. Previous methods to identify sex and sex-linked scaffolds have relied on synteny between the non-model organism and a closely related species or prior knowledge about the sex of the samples to identify sex-linked scaffolds. In the latter case, the difference in depth of coverage between the autosomes and the sex chromosomes are used. Here, we present "sex assignment through coverage" (SATC), a method to assign sex to samples and identify sex-linked scaffolds from next generation sequencing (NGS) data. The method works for species with a homogametic/heterogametic sex determination system and only requires a scaffold-level reference assembly and sampling of both sexes with whole genome sequencing (WGS) data. We use the sequencing depth distribution across scaffolds to jointly identify: (i) male and female individuals, and (ii) sex-linked scaffolds. This is achieved through projecting the scaffold depths into a low-dimensional space using principal component analysis (PCA) and subsequent Gaussian mixture clustering. We demonstrate the applicability of our method using data from five mammal species and a bird species complex. The method is freely available at https://github.com/popgenDK/SATC as R code and a graphical user interface (GUI).
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Affiliation(s)
- Casia Nursyifa
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anna Brüniche-Olsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Genis Garcia-Erill
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Anders Albrechtsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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5
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Brüniche-Olsen A, Bickham JW, Godard-Codding CA, Brykov VA, Kellner KF, Urban J, DeWoody JA. Influence of Holocene habitat availability on Pacific gray whale ( Eschrichtius robustus) population dynamics as inferred from whole mitochondrial genome sequences and environmental niche modeling. J Mammal 2021. [DOI: 10.1093/jmammal/gyab032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Environmental changes since the Pleistocene and commercial whaling in the last few centuries have drastically reduced many whale populations, including gray whales in the North Pacific. Herein we use complete mitogenome sequences from 74 individuals to evaluate gray whale phylogeography and historical demography, then use environmental niche modeling to assess how habitat availability has changed through time for Pacific gray whales. We identify a large degree of haplotype sharing between gray whales sampled in Russian and Mexican waters, coupled with very limited matrilineal population structure. Confirming previous studies, our environmental niche models showed a decrease in available habitat during the Last Glacial Maximum, but we find no genetic signals of recent population declines in mitochondrial genomes despite both sustained habitat loss and a commercial whaling bottleneck. Our results illustrate the complex dynamics of baleen whale biogeography since the Holocene as well as the difficulty in detecting recent demographic bottlenecks from mitochondrial DNA sequences.
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Affiliation(s)
- Anna Brüniche-Olsen
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| | - John W Bickham
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Celine A Godard-Codding
- Institute of Environmental and Human Health, Texas Tech University (TTU) and TTU Health Sciences Center, Lubbock, TX, USA
| | - Vladimir A Brykov
- National Scientific Center for Marine Biology, Russian Academy of Sciences, Far Eastern Branch, Vladivostok, Russia
| | - Kenneth F Kellner
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Jorge Urban
- Departamento Academico de Ciencias Marinas y Costeras, Universidad Autonoma de Baja California Sur, Km 5.5 Carretera al Sur, Mezquitito, La Paz, BCS, Mexico
| | - J Andrew DeWoody
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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6
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Hoelzel AR, Sarigol F, Gridley T, Elwen SH. Natal origin of Namibian grey whale implies new distance record for in-water migration. Biol Lett 2021; 17:20210136. [PMID: 34102070 DOI: 10.1098/rsbl.2021.0136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We use genomics to identify the natal origin of a grey whale found in the South Atlantic, at least 20 000 km from the species core range (halfway around the world). The data indicate an origin in the North Pacific, possibly from the endangered western North Pacific population, thought to include only approximately 200 individuals. This contributes to our understanding of Atlantic sightings of this species known primarily from the North Pacific, and could have conservation implications if grey whales have the potential for essentially global dispersion. More broadly, documenting and understanding rare extreme migration events have potential implications for the understanding of how a species may be able to respond to global change.
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Affiliation(s)
- A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Fatih Sarigol
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Tess Gridley
- Sea Search Research and Conservation NPC, Cape Town, South Africa.,Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Simon H Elwen
- Sea Search Research and Conservation NPC, Cape Town, South Africa.,Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
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7
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Reproductive success of captive-reared Allegheny Woodrats (Neotoma magister) released into genetically depauperate populations. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01372-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Bröker KCA, Gailey G, Tyurneva OY, Yakovlev YM, Sychenko O, Dupont JM, Vertyankin VV, Shevtsov E, Drozdov KA. Site-fidelity and spatial movements of western North Pacific gray whales on their summer range off Sakhalin, Russia. PLoS One 2020; 15:e0236649. [PMID: 32797058 PMCID: PMC7428188 DOI: 10.1371/journal.pone.0236649] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 07/09/2020] [Indexed: 11/18/2022] Open
Abstract
The Western North-Pacific (WNP) gray whale feeding grounds are off the northeastern coast of Sakhalin Island, Russia and is comprised of a nearshore and offshore component that can be distinguished by both depth and location. Spatial movements of gray whales within their foraging grounds were examined based on 13 years of opportunistic vessel and shore-based photo-identification surveys. Site fidelity was assessed by examining annual return and resighting rates. Lagged Identification Rates (LIR) analyses were conducted to estimate the residency and transitional movement patterns within the two components of their feeding grounds. In total 243 individuals were identified from 2002-2014, among these were 94 calves. The annual return rate over the period 2002-2014 was 72%, excluding 35 calves only seen one year. Approximately 20% of the individuals identified from 2002-2010 were seen every year after their initial sighting (including eight individuals that returned for 13 consecutive years). The majority (239) of the WNP whales were observed in the nearshore area while only half (122) were found in the deeper offshore area. Within a foraging season, there was a significantly higher probability of gray whales moving from the nearshore to the offshore area. No mother-calf pairs, calves or yearlings were observed in the offshore area, which was increasingly used by mature animals. The annual return rates, and population growth rates that are primarily a result of calf production with little evidence of immigration, suggest that this population is demographically self-contained and that both the nearshore and offshore Sakhalin feeding grounds are critically important areas for their summer annual foraging activities. The nearshore habitat is also important for mother-calf pairs, younger individuals, and recently weaned calves. Nearshore feeding could also be energetically less costly compared to foraging in the deeper offshore habitat and provide more protection from predators, such as killer whales.
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Affiliation(s)
- Koen C. A. Bröker
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
- Shell Global Solutions International B.V., the Hague, The Netherlands
| | - Glenn Gailey
- Cetacean EcoSystem Research, Washington, Olympia, United States of America
| | - Olga Yu. Tyurneva
- A.V. Zhirmunsky National Scientific Center of Marine Biology of the Far Eastern Branch of the Russian Academy of Sciences (NSCMB FEB RAS), Vladivostok, Russian Federation
| | - Yuri M. Yakovlev
- A.V. Zhirmunsky National Scientific Center of Marine Biology of the Far Eastern Branch of the Russian Academy of Sciences (NSCMB FEB RAS), Vladivostok, Russian Federation
| | - Olga Sychenko
- Cetacean EcoSystem Research, Washington, Olympia, United States of America
| | - Jennifer M. Dupont
- ExxonMobil Upstream Research Company, Houston, Texas, United States of America
| | | | - Evgeny Shevtsov
- A.V. Zhirmunsky National Scientific Center of Marine Biology of the Far Eastern Branch of the Russian Academy of Sciences (NSCMB FEB RAS), Vladivostok, Russian Federation
| | - Konstantin A. Drozdov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far Eastern Branch of the Russian Academy of Sciences (PIBOC FEB RAS), Vladivostok, Russian Federation
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9
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von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020. [PMID: 31925943 DOI: 10.1111/1755-0998.13136.applying] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
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Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
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10
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von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020; 20. [PMID: 31925943 DOI: 10.1111/1755-0998.13136] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/24/2019] [Accepted: 01/05/2020] [Indexed: 01/16/2023]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
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Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
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11
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Mathur S, Tomeček JM, Heniff A, Luna R, DeWoody JA. Evidence of genetic erosion in a peripheral population of a North American game bird: the Montezuma quail (Cyrtonyx montezumae). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01218-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Lopes-Marques M, Machado AM, Alves LQ, Fonseca MM, Barbosa S, Sinding MHS, Rasmussen MH, Iversen MR, Frost Bertelsen M, Campos PF, da Fonseca R, Ruivo R, Castro LFC. Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea. Mol Biol Evol 2019; 36:1270-1280. [PMID: 30895322 PMCID: PMC6526905 DOI: 10.1093/molbev/msz068] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genomes are dynamic biological units, with processes of gene duplication and loss triggering evolutionary novelty. The mammalian skin provides a remarkable case study on the occurrence of adaptive morphological innovations. Skin sebaceous glands (SGs), for instance, emerged in the ancestor of mammals serving pivotal roles, such as lubrication, waterproofing, immunity, and thermoregulation, through the secretion of sebum, a complex mixture of various neutral lipids such as triacylglycerol, free fatty acids, wax esters, cholesterol, and squalene. Remarkably, SGs are absent in a few mammalian lineages, including the iconic Cetacea. We investigated the evolution of the key molecular components responsible for skin sebum production: Dgat2l6, Awat1, Awat2, Elovl3, Mogat3, and Fabp9. We show that all analyzed genes have been rendered nonfunctional in Cetacea species (toothed and baleen whales). Transcriptomic analysis, including a novel skin transcriptome from blue whale, supports gene inactivation. The conserved mutational pattern found in most analyzed genes, indicates that pseudogenization events took place prior to the diversification of modern Cetacea lineages. Genome and skin transcriptome analysis of the common hippopotamus highlighted the convergent loss of a subset of sebum-producing genes, notably Awat1 and Mogat3. Partial loss profiles were also detected in non-Cetacea aquatic mammals, such as the Florida manatee, and in terrestrial mammals displaying specialized skin phenotypes such as the African elephant, white rhinoceros and pig. Our findings reveal a unique landscape of “gene vestiges” in the Cetacea sebum-producing compartment, with limited gene loss observed in other mammalian lineages: suggestive of specific adaptations or specializations of skin lipids.
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Affiliation(s)
- Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - André M Machado
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Luís Q Alves
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
| | - Miguel M Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - Susana Barbosa
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | | | | | | | | | - Paula F Campos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Raquel Ruivo
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal
| | - L Filipe C Castro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, U. Porto-University of Porto, Porto, Portugal
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13
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The Singularity of Cetacea Behavior Parallels the Complete Inactivation of Melatonin Gene Modules. Genes (Basel) 2019; 10:genes10020121. [PMID: 30736361 PMCID: PMC6410235 DOI: 10.3390/genes10020121] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 12/26/2022] Open
Abstract
Melatonin, the hormone of darkness, is a peculiar molecule found in most living organisms. Emerging as a potent broad-spectrum antioxidant, melatonin was repurposed into extra roles such as the modulation of circadian and seasonal rhythmicity, affecting numerous aspects of physiology and behaviour, including sleep entrainment and locomotor activity. Interestingly, the pineal gland—the melatonin synthesising organ in vertebrates—was suggested to be absent or rudimentary in some mammalian lineages, including Cetacea. In Cetacea, pineal regression is paralleled by their unique bio-rhythmicity, as illustrated by the unihemispheric sleeping behaviour and long-term vigilance. Here, we examined the genes responsible for melatonin synthesis (Aanat and Asmt) and signalling (Mtnr1a and Mtnr1b) in 12 toothed and baleen whale genomes. Based on an ample genomic comparison, we deduce that melatonin-related gene modules are eroded in Cetacea.
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14
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Lammers F, Blumer M, Rücklé C, Nilsson MA. Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation. Mob DNA 2019; 10:5. [PMID: 30679961 PMCID: PMC6340175 DOI: 10.1186/s13100-018-0143-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/18/2018] [Indexed: 02/03/2023] Open
Abstract
Background Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs. Baleen whales exhibit the slowest nucleotide substitution rate among mammals, hence we additionally examined the evolutionary insertion rates of TE insertions across the genomes. Results In eleven whole-genome sequences representing the extant radiation of baleen whales, we identified 91,859 CHR-SINE insertions that were used to reconstruct the phylogeny with different approaches as well as perform evolutionary network analyses and a quantification of conflicting phylogenetic signals. Our results indicate that the radiation of rorquals and gray whales might not be bifurcating. The morphologically derived gray whales are placed inside the rorqual group, as the sister-species to humpback and fin whales. Detailed investigation of TE insertion rates confirm that a mutational slow down in the whale lineage is present but less pronounced for TEs than for nucleotide substitutions. Conclusions Whole genome sequencing based detection of TE insertions showed that the speciation processes in baleen whales represent a rapid radiation. Large genome-scale TE data sets in addition allow to understand retrotransposition rates in non-model organisms and show the potential for TE calling methods to study the evolutionary history of species. Electronic supplementary material The online version of this article (10.1186/s13100-018-0143-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fritjof Lammers
- 1Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,3Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Biologicum, Max-von-Laue-Straße 13, 60439 Frankfurt am Main, Germany
| | - Moritz Blumer
- 1Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Cornelia Rücklé
- 1Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Maria A Nilsson
- 1Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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15
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Brüniche-Olsen A, Urban RJ, Vertyankin VV, Godard-Codding CAJ, Bickham JW, DeWoody JA. Genetic data reveal mixed-stock aggregations of gray whales in the North Pacific Ocean. Biol Lett 2018; 14:rsbl.2018.0399. [PMID: 30305459 DOI: 10.1098/rsbl.2018.0399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/11/2018] [Indexed: 11/12/2022] Open
Abstract
Gray whales (Eschrichtius robustus) in the Western Pacific are critically endangered, whereas in the Eastern Pacific, they are relatively common. Holocene environmental changes and commercial whaling reduced their numbers, but gray whales in the Eastern Pacific now outnumber their Western counterparts by more than 100-fold. Herein, we investigate the genetic diversity and population structure within the species using a panel of genic single nucleotide polymorphisms. Results indicate the gray whale gene pool is differentiated into two substocks containing similar levels of genetic diversity, and that both our Eastern and Western geographical samples represent mixed-stock aggregations. Ongoing or future gene flow between the stocks may conserve genetic diversity overall, but admixture has implications for conservation of the critically endangered Western gray whale.
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Affiliation(s)
- Anna Brüniche-Olsen
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47905, USA
| | - R Jorge Urban
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Km 5.5 Carretera al Sur, Mezquitito, La Paz, BCS 23080, México
| | | | - Céline A J Godard-Codding
- Institute of Environmental and Human Health, Texas Tech University (TTU) and TTU Health Sciences Center, Lubbock, TX 79409, USA
| | - John W Bickham
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77845, USA
| | - J Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47905, USA.,Department of Biological Sciences, Purdue University, West Lafayette, IN 47905, USA
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16
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Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour 2018; 18:1469-1481. [PMID: 30035363 DOI: 10.1111/1755-0998.12932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 11/27/2022]
Abstract
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.
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Affiliation(s)
- Marijke Autenrieth
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Ljerka Lah
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Anna Roos
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Alice B Dennis
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
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17
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Leroy G, Carroll EL, Bruford MW, DeWoody JA, Strand A, Waits L, Wang J. Next-generation metrics for monitoring genetic erosion within populations of conservation concern. Evol Appl 2018; 11:1066-1083. [PMID: 30026798 PMCID: PMC6050182 DOI: 10.1111/eva.12564] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/11/2017] [Indexed: 12/26/2022] Open
Abstract
Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large-effect detrimental alleles, maladaptation and loss of adaptability). Technological advances in genomics now allow the production of data the can be measured by new metrics with improved precision, increased efficiency and the potential to discriminate between neutral diversity (shaped mainly by population size and gene flow) and functional/adaptive diversity (shaped mainly by selection), allowing the assessment of management-relevant genetic markers. The requirements of such studies in terms of sample size and marker density largely depend on the kind of population monitored, the questions to be answered and the metrics employed. We discuss prospects for the integration of this new information and metrics into conservation monitoring programmes.
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Affiliation(s)
- Gregoire Leroy
- Food and Agriculture Organization (FAO) of the United Nations, Animal Production and Health DivisionRomeItaly
| | - Emma L. Carroll
- Scottish Oceans Institute and School of BiologyUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places InstituteCardiff UniversityCardiffUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteINUSA
- Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Allan Strand
- Department of BiologyGrice Marine Laboratory, College of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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18
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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19
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Brüniche-Olsen A, Westerman R, Kazmierczyk Z, Vertyankin VV, Godard-Codding C, Bickham JW, DeWoody JA. The inference of gray whale (Eschrichtius robustus) historical population attributes from whole-genome sequences. BMC Evol Biol 2018; 18:87. [PMID: 29879895 PMCID: PMC5992727 DOI: 10.1186/s12862-018-1204-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 05/29/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Commercial whaling caused extensive demographic declines in many great whale species, including gray whales that were extirpated from the Atlantic Ocean and dramatically reduced in the Pacific Ocean. The Eastern Pacific gray whale has recovered since the 1982 ban on commercial whaling, but the Western Pacific gray whale-once considered possibly extinct-consists of only about 200 individuals and is considered critically endangered by some international authorities. Herein, we use whole-genome sequencing to investigate the demographic history of gray whales from the Pacific and use environmental niche modelling to make predictions about future gene flow. RESULTS Our sequencing efforts and habitat niche modelling indicate that: i) western gray whale effective population sizes have declined since the last glacial maximum; ii) contemporary gray whale genomes, both eastern and western, harbor less autosomal nucleotide diversity than most other marine mammals and megafauna; iii) the extent of inbreeding, as measured by autozygosity, is greater in the Western Pacific than in the Eastern Pacific populations; and iv) future climate change is expected to open new migratory routes for gray whales. CONCLUSION Our results indicate that gray whale genomes contain low nucleotide diversity and have been subject to both historical and recent inbreeding. Population sizes over the last million years likely peaked about 25,000 years before present and have declined since then. Our niche modelling suggests that novel migratory routes may develop within the next century and if so this could help retain overall genetic diversity, which is essential for adaption and successful recovery in light of global environmental change and past exploitation.
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Affiliation(s)
- Anna Brüniche-Olsen
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN, 47905, USA.
| | - Rick Westerman
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Zuzanna Kazmierczyk
- School of Forensic and Applied Sciences, University of Central Lancashire Preston, Preston, PR1 2HE, UK
| | | | - Celine Godard-Codding
- The Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, 1207 Gilbert Drive, Lubbock, TX, 79409, USA
| | - John W Bickham
- Department of Wildlife & Fisheries Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - J Andrew DeWoody
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN, 47905, USA
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20
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Doyle JM, Bell DA, Bloom PH, Emmons G, Fesnock A, Katzner TE, LaPré L, Leonard K, SanMiguel P, Westerman R, Andrew DeWoody J. New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus). BMC Genomics 2018; 19:233. [PMID: 29618317 PMCID: PMC5885362 DOI: 10.1186/s12864-018-4615-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/22/2018] [Indexed: 12/30/2022] Open
Abstract
Background Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge. Results We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population. Conclusions Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California’s prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole. Electronic supplementary material The online version of this article (10.1186/s12864-018-4615-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jacqueline M Doyle
- Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD, 21212, USA. .,Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN, 47907, USA.
| | - Douglas A Bell
- East Bay Regional Park District, 2950 Peralta Oaks Court, Oakland, CA, 94605, USA.,Department of Ornithology and Mammalogy, California Academy of Sciences, 55 Concourse Drive, Golden Gate Park, San Francisco, CA, 94118, USA
| | - Peter H Bloom
- Bloom Research Inc., 1820 S. Dunsmuir, Los Angeles, CA, 90019, USA
| | - Gavin Emmons
- National Park Service, Pinnacles National Park, 5000 Highway 146, Paicines, CA, 95043, USA
| | - Amy Fesnock
- California State Office, Bureau of Land Management, 2800 Cottage Way, Suite W-1928, Sacramento, CA, 95825, USA
| | - Todd E Katzner
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, 970 Lusk Street, Boise, ID, 83706, USA
| | - Larry LaPré
- Bureau of Land Management, California Desert District, 22835 Calle San Juan De Los Lagos, Moreno Valley, CA, 92553, USA
| | - Kolbe Leonard
- Department of Computer and Information Sciences, Towson University, 8000 York Rd, Baltimore, MD, 21212, USA
| | - Phillip SanMiguel
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Rick Westerman
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - J Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN, 47907, USA.,Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
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