1
|
Ouled-Cheikh J, March D, Borras-Chavez R, Drago M, Goebel ME, Fariña JM, Gazo M, Coll M, Cardona L. Future climate-induced distribution shifts in a sexually dimorphic key predator of the Southern Ocean. Glob Chang Biol 2024; 30:e17191. [PMID: 38433338 DOI: 10.1111/gcb.17191] [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] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 03/05/2024]
Abstract
The response to climate change in highly dimorphic species can be hindered by differences between sexes in habitat preferences and movement patterns. The Antarctic fur seal, Arctocephalus gazella, is the most abundant pinniped in the Southern Hemisphere, and one of the main consumers of Antarctic krill, Euphausia superba, in the Southern Ocean. However, the populations breeding in the Atlantic Southern Ocean are decreasing, partly due to global warming. Male and female Antarctic fur seals differ greatly in body size and foraging ecology, and little is known about their sex-specific responses to climate change. We used satellite tracking data and Earth System Models to predict changes in habitat suitability for male and female Antarctic fur seals from the Western Antarctic Peninsula under different climate change scenarios. Under the most extreme scenario (SSP5-8.5; global average temperature +4.4°C projected by 2100), suitable habitat patches will shift southward during the non-breeding season, leading to a minor overall habitat loss. The impact will be more pronounced for females than for males. The reduction of winter foraging grounds might decrease the survival of post-weaned females, reducing recruitment and jeopardizing population viability. During the breeding season, when males fast on land, suitable foraging grounds for females off the South Shetland Islands will remain largely unmodified, and new ones will emerge in the Bellingshausen Sea. As Antarctic fur seals are income breeders, the foraging grounds of females should be reasonably close to the breeding colony. As a result, the new suitable foraging grounds will be useful for females only if nearby beaches currently covered by sea ice emerge by the end of the century. Furthermore, the colonization of these new, ice-free breeding locations might be limited by strong female philopatry. These results should be considered when managing the fisheries of Antarctic krill in the Southern Ocean.
Collapse
Affiliation(s)
- Jazel Ouled-Cheikh
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- iMARES group, Departament de Recursos Marins Renovables, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - David March
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Paterna, València, Spain
- Centre for Ecology and Conservation, College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, UK
| | - Renato Borras-Chavez
- Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Biology, Baylor University, Waco, Texas, USA
| | - Massimiliano Drago
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Michael E Goebel
- Institute of Marine Sciences, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
- Antarctic Ecosystem Research Division, SWFSC, NMFS, NOAA, La Jolla, California, USA
| | - José M Fariña
- Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manel Gazo
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Marta Coll
- iMARES group, Departament de Recursos Marins Renovables, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
- Ecopath International Initiative (EII), Barcelona, Spain
| | - Luis Cardona
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
2
|
Forcada J, Hoffman JI, Gimenez O, Staniland IJ, Bucktrout P, Wood AG. Ninety years of change, from commercial extinction to recovery, range expansion and decline for Antarctic fur seals at South Georgia. Glob Chang Biol 2023; 29:6867-6887. [PMID: 37839801 DOI: 10.1111/gcb.16947] [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] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023]
Abstract
With environmental change, understanding how species recover from overharvesting and maintain viable populations is central to ecosystem restoration. Here, we reconstruct 90 years of recovery trajectory of the Antarctic fur seal at South Georgia (S.W. Atlantic), a key indicator species in the krill-based food webs of the Southern Ocean. After being harvested to commercial extinction by 1907, this population rebounded and now constitutes the most abundant otariid in the World. However, its status remains uncertain due to insufficient and conflicting data, and anthropogenic pressures affecting Antarctic krill, an essential staple for millions of fur seals and other predators. Using integrated population models, we estimated simultaneously the long-term abundance for Bird Island, northwest South Georgia, epicentre of recovery of the species after sealing, and population adjustments for survey counts with spatiotemporal applicability. Applied to the latest comprehensive survey data, we estimated the population at South Georgia in 2007-2009 as 3,510,283 fur seals [95% CI: 3,140,548-3,919,604] (ca. 98% of global population), after 40 years of maximum growth and range expansion owing to an abundant krill supply. At Bird Island, after 50 years of exponential growth followed by 25 years of slow stable growth, the population collapsed in 2009 and has thereafter declined by -7.2% [-5.2, -9.1] per annum, to levels of the 1970s. For the instrumental record, this trajectory correlates with a time-varying relationship between coupled climate and sea surface temperature cycles associated with low regional krill availability, although the effects of increasing krill extraction by commercial fishing and natural competitors remain uncertain. Since 2015, fur seal longevity and recruitment have dropped, sexual maturation has retarded, and population growth is expected to remain mostly negative and highly variable. Our analysis documents the rise and fall of a key Southern Ocean predator over a century of profound environmental and ecosystem change.
Collapse
Affiliation(s)
- Jaume Forcada
- British Antarctic Survey, Natural Environment Research Council, UKRI, Cambridge, UK
| | - Joseph I Hoffman
- British Antarctic Survey, Natural Environment Research Council, UKRI, Cambridge, UK
- Department of Animal Behavior, University of Bielefeld, Bielefeld, Germany
| | - Olivier Gimenez
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | | | - Pete Bucktrout
- British Antarctic Survey, Natural Environment Research Council, UKRI, Cambridge, UK
| | - Andrew G Wood
- British Antarctic Survey, Natural Environment Research Council, UKRI, Cambridge, UK
| |
Collapse
|
3
|
Convey P, Hughes KA. Untangling unexpected terrestrial conservation challenges arising from the historical human exploitation of marine mammals in the Atlantic sector of the Southern Ocean. Ambio 2023; 52:357-375. [PMID: 36048407 PMCID: PMC9755428 DOI: 10.1007/s13280-022-01782-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Intensive human exploitation of the Antarctic fur seal (Arctocephalus gazella) in its primary population centre on sub-Antarctic South Georgia, as well as on other sub-Antarctic islands and parts of the South Shetland Islands, in the eighteenth and nineteenth centuries rapidly brought populations to the brink of extinction. The species has now recovered throughout its original distribution. Non-breeding and yearling seals, almost entirely males, from the South Georgia population now disperse in the summer months far more widely and in higher numbers than there is evidence for taking place in the pre-exploitation era. Large numbers now haul out in coastal terrestrial habitats in the South Orkney Islands and also along the north-east and west coast of the Antarctic Peninsula to at least Marguerite Bay. In these previously less- or non-visited areas, the seals cause levels of damage likely never to have been experienced previously to fragile terrestrial habitats through trampling and over-fertilisation, as well as eutrophication of sensitive freshwater ecosystems. This increased area of summer impact is likely to have further synergies with aspects of regional climate change, including reduction in extent and duration of sea ice permitting seals access farther south, and changes in krill abundance and distribution. The extent and conservation value of terrestrial habitats and biodiversity now threatened by fur seal distribution expansion, and the multiple anthropogenic factors acting in synergy both historically and to the present day, present a new and as yet unaddressed challenge to the agencies charged with ensuring the protection and conservation of Antarctica's unique ecosystems.
Collapse
Affiliation(s)
- Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
- Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa.
| | - Kevin A Hughes
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| |
Collapse
|
4
|
Pretorius LE, Bester MN, Connan M, Hofmeyr GJG. Canine morphometrics as a tool for distinguishing species, sex, and age class in Southern Ocean fur seals. J Morphol 2022; 283:1546-1560. [PMID: 36223543 PMCID: PMC9828835 DOI: 10.1002/jmor.21521] [Citation(s) in RCA: 1] [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: 02/28/2022] [Revised: 09/14/2022] [Accepted: 10/07/2022] [Indexed: 01/19/2023]
Abstract
Carcasses resulting from natural mortalities are invaluable for use in scientific studies, provided species, sex, and age class are known. When such data are unavailable, identifying skeletal remains is necessary if one is to use the information contained within samples. Teeth are amongst the best preserved skeletal remains owing to the durability of enamel and dentine. Here, we tested whether external measurements of canines could be used to distinguish two partially sympatric species of Southern Ocean fur seals, the Antarctic Arctocephalus gazella and Sub-Antarctic A. tropicalis fur seals. We also investigated whether the external measurements of canines could be used to determine the age, sex, as well as island of origin of the animals. Eight morphological variables (crown length, root length, crown width, root width, crown thickness, root thickness, total canine length, and count of external surface annular ridges) were recorded from canines of 340 individuals of known species, sex, and island of origin. The count of external annular ridges provided a good estimate of age, which was confirmed by counting the growth layer groups of sectioned teeth, especially for older animals (> 9 years old). External canine measurements proved useful in distinguishing species, as well as sex within and between species, particularly in adult animals. Species were more difficult to distinguish in females than in males. The islands of origin could only be inferred in male Antarctic fur seals. This study indicates that fur seal teeth of unknown provenance, found either in breeding colonies or as vagrants, provide evidence on species, sex, and age of the animal, which increases the value of associated samples. It further highlights the importance of external measurements of skeletal remains such as canine teeth in separating closely related species.
Collapse
Affiliation(s)
- Liezl E. Pretorius
- Department of Zoology and Entomology, Mammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
| | - Marthán N. Bester
- Department of Zoology and Entomology, Mammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
| | - Maëlle Connan
- Marine Apex Predator Research Unit, Department of Zoology, Institute for Coastal and Marine ResearchNelson Mandela UniversityGqeberhaSouth Africa
| | - G. J. Greg Hofmeyr
- Marine Apex Predator Research Unit, Department of Zoology, Institute for Coastal and Marine ResearchNelson Mandela UniversityGqeberhaSouth Africa,Port Elizabeth Museum at BayworldGqeberhaSouth Africa
| |
Collapse
|
5
|
Vendrami DLJ, Gossmann TI, Chakarov N, Paijmans AJ, Eyre-Walker A, Forcada J, Hoffman JI. Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biol Evol 2022; 14:6637498. [PMID: 35809042 PMCID: PMC9338431 DOI: 10.1093/gbe/evac104] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2022] [Indexed: 11/13/2022] Open
Abstract
Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared to their mitochondrial homologs to characterize synonymous to non-synonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterise 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to non-canonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation.
Collapse
Affiliation(s)
- David L J Vendrami
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Toni I Gossmann
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Anneke J Paijmans
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Adam Eyre-Walker
- School of Life Science, University of Sussex, Brighton, BN1 9QG, UK
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| |
Collapse
|
6
|
Foley CM, Lynch HJ. A method to estimate pre-exploitation population size. Conserv Biol 2020; 34:256-265. [PMID: 31460682 DOI: 10.1111/cobi.13416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/26/2018] [Revised: 03/15/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
Antarctic fur seals (Arctocephalus gazella) were commercially exploited on the subantarctic island of South Georgia for over 100 years and nearly driven to extinction. Since the cessation of harvesting, however, their populations have rebounded, and they are now often considered a nuisance species whose impact on the terrestrial landscape should be mitigated. Any evaluation of their current population requires the context provided by their historic, pre-exploitation abundance, lest ecologists fall prey to shifting baseline syndrome in which their perspective on current abundance is compared only with an altered state resulting from past anthropogenic disturbance. Estimating pre-exploitation abundance is critical to defining species recovery and setting recovery targets, both of which are needed for the International Union for the Conservation of Nature's recent efforts to develop a green list of recovering species. To address this issue, we reconstructed the South Georgia fur seal harvest from 1786 to 1908 from ship logbooks and other historical records and interpolated missing harvest data as necessary with a generalized linear model fit to the historical record. Using an approximate Bayesian computation framework, harvest data, and a stochastic age-structured population model, we estimated the pre-exploitation abundance of Antarctic fur seals on South Georgia was 2.5 million females (95% CI 1.5-3.5 million). This estimate is similar to recent abundance estimates, and suggests current populations, and the ecological consequences of so many fur seals on the island, may be similar to conditions prior to human harvest. Although the historic archive on the fur sealing era is unavoidably patchy, the use of archival records is essential for reconstructing the past and, correspondingly, to understanding the present. Article impact statement: Defining species recovery requires an understanding of baseline population state, which can be estimated through statistical methods.
Collapse
Affiliation(s)
- Catherine M Foley
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, P.O. Box 1346, Kāne'ohe, HI 96744, USA
| | - Heather J Lynch
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY, 11794, U.S.A
| |
Collapse
|
7
|
Abstract
The Antarctic fur seal (Arctocephalus gazella) is an abundant Antarctic otariid. Here, we present the complete mitochondrial DNA sequence of this species, which includes 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and the control region for a total length of 16,156 bp. A phylogenetic analysis including all 25 publically available pinniped mitogenomes nested the Antarctic fur seal within the Otariid clade, which was clearly resolved from the Phocidae and Odobenidae.
Collapse
Affiliation(s)
- Rebecca Nagel
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | | | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.,British Antarctic Survey, Cambridge, UK
| |
Collapse
|
8
|
Vendrami DLJ, Forcada J, Hoffman JI. Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal. BMC Genomics 2019; 20:72. [PMID: 30669975 DOI: 10.1186/s12864-019-5440-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 01/08/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Restriction site-associated DNA sequencing (RADseq) has revolutionized the study of wild organisms by allowing cost-effective genotyping of thousands of loci. However, for species lacking reference genomes, it can be challenging to select the restriction enzyme that offers the best balance between the number of obtained RAD loci and depth of coverage, which is crucial for a successful outcome. To address this issue, PredRAD was recently developed, which uses probabilistic models to predict restriction site frequencies from a transcriptome assembly or other sequence resource based on either GC content or mono-, di- or trinucleotide composition. This program generates predictions that are broadly consistent with estimates of the true number of restriction sites obtained through in silico digestion of available reference genome assemblies. However, in practice the actual number of loci obtained could potentially differ as incomplete enzymatic digestion or patchy sequence coverage across the genome might lead to some loci not being represented in a RAD dataset, while erroneous assembly could potentially inflate the number of loci. To investigate this, we used genome and transcriptome assemblies together with RADseq data from the Antarctic fur seal (Arctocephalus gazella) to compare PredRAD predictions with empirical estimates of the number of loci obtained via in silico digestion and from de novo assemblies. RESULTS PredRAD yielded consistently higher predicted numbers of restriction sites for the transcriptome assembly relative to the genome assembly. The trinucleotide and dinucleotide models also predicted higher frequencies than the mononucleotide or GC content models. Overall, the dinucleotide and trinucleotide models applied to the transcriptome and the genome assemblies respectively generated predictions that were closest to the number of restriction sites estimated by in silico digestion. Furthermore, the number of de novo assembled RAD loci mapping to restriction sites was similar to the expectation based on in silico digestion. CONCLUSIONS Our study reveals generally high concordance between PredRAD predictions and empirical estimates of the number of RAD loci. This further supports the utility of PredRAD, while also suggesting that it may be feasible to sequence and assemble the majority of RAD loci present in an organism's genome.
Collapse
|
9
|
Jeanniard-du-Dot T, Trites AW, Arnould JPY, Speakman JR, Guinet C. Activity-specific metabolic rates for diving, transiting, and resting at sea can be estimated from time-activity budgets in free-ranging marine mammals. Ecol Evol 2017; 7:2969-2976. [PMID: 28479996 PMCID: PMC5415512 DOI: 10.1002/ece3.2546] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 05/09/2016] [Revised: 08/12/2016] [Accepted: 09/22/2016] [Indexed: 11/07/2022] Open
Abstract
Time and energy are the two most important currencies in animal bioenergetics. How much time animals spend engaged in different activities with specific energetic costs ultimately defines their likelihood of surviving and successfully reproducing. However, it is extremely difficult to determine the energetic costs of independent activities for free-ranging animals. In this study, we developed a new method to calculate activity-specific metabolic rates, and applied it to female fur seals. We attached biologgers (that recorded GPS locations, depth profiles, and triaxial acceleration) to 12 northern (Callorhinus ursinus) and 13 Antarctic fur seals (Arctocephalus gazella), and used a hierarchical decision tree algorithm to determine time allocation between diving, transiting, resting, and performing slow movements at the surface (grooming, etc.). We concomitantly measured the total energy expenditure using the doubly-labelled water method. We used a general least-square model to establish the relationship between time-activity budgets and the total energy spent by each individual during their foraging trip to predict activity-specific metabolic rates. Results show that both species allocated similar time to diving (~29%), transiting to and from their foraging grounds (~26-30%), and resting (~8-11%). However, Antarctic fur seals spent significantly more time grooming and moving slowly at the surface than northern fur seals (36% vs. 29%). Diving was the most expensive activity (~30 MJ/day if done non-stop for 24 hr), followed by transiting at the surface (~21 MJ/day). Interestingly, metabolic rates were similar between species while on land or while slowly moving at the surface (~13 MJ/day). Overall, the average field metabolic rate was ~20 MJ/day (for all activities combined). The method we developed to calculate activity-specific metabolic rates can be applied to terrestrial and marine species to determine the energetic costs of daily activities, as well as to predict the energetic consequences for animals forced to change their time allocations in response to environmental shifts.
Collapse
Affiliation(s)
- Tiphaine Jeanniard-du-Dot
- Marine Mammal Research UnitInstitute for the Oceans and Fisheries University of British Columbia Vancouver BC Canada.,Centre d'Etudes Biologiques de Chizé CNRS Villiers en Bois France
| | - Andrew W Trites
- Marine Mammal Research UnitInstitute for the Oceans and Fisheries University of British Columbia Vancouver BC Canada
| | - John P Y Arnould
- School of Life and Environmental Sciences (Burwood Campus) Deakin University Geelong Australia
| | - John R Speakman
- The Institute of Biological and Environmental Sciences Aberdeen UK
| | | |
Collapse
|
10
|
Humble E, Thorne MAS, Forcada J, Hoffman JI. Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success. BMC Res Notes 2016; 9:418. [PMID: 27562535 PMCID: PMC5000416 DOI: 10.1186/s13104-016-2209-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 03/31/2016] [Accepted: 08/06/2016] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. RESULTS Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. CONCLUSIONS Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future studies of non-model organisms.
Collapse
Affiliation(s)
- Emily Humble
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501, Bielefeld, Germany. .,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
| | - Michael A S Thorne
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501, Bielefeld, Germany
| |
Collapse
|
11
|
Waluda CM, Staniland IJ. Entanglement of Antarctic fur seals at Bird Island, South Georgia. Mar Pollut Bull 2013; 74:244-252. [PMID: 23915979 DOI: 10.1016/j.marpolbul.2013.06.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 04/25/2013] [Revised: 06/19/2013] [Accepted: 06/23/2013] [Indexed: 06/02/2023]
Abstract
Between November 1989 and March 2013, 1033 Antarctic fur seals Arctocephalus gazella were observed entangled in marine debris at Bird Island, South Georgia. The majority of entanglements involved plastic packaging bands (43%), synthetic line (25%) or fishing net (17%). Juvenile male seals were the most commonly entangled (44%). A piecewise regression analysis showed that a single breakpoint at 1994 gave the best description of inter-annual variability in the data, with higher levels of entanglements prior to 1994 (mean=110±28) followed by persistent lower levels (mean=28±4). Records of entanglements from other sites monitored in the Scotia Sea are also presented. Legislation imposed by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) has, to a certain extent, been effective, but persistent low levels of seal entanglements are still a cause for concern at South Georgia.
Collapse
Affiliation(s)
- Claire M Waluda
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK.
| | | |
Collapse
|