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  1. Article ; Online: An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony.

    Humble, Emily / Paijmans, Anneke J / Forcada, Jaume / Hoffman, Joseph I

    G3 (Bethesda, Md.)

    2020  Volume 10, Issue 8, Page(s) 2787–2799

    Abstract: High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants ... ...

    Abstract High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (
    MeSH term(s) Animals ; Antarctic Regions ; Fur Seals/genetics ; Genome ; Genotype ; Humans ; Inbreeding
    Language English
    Publishing date 2020-08-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.120.401268
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): Implications for conservation amid climate-driven range shifts.

    Gose, Marc-Alexander / Humble, Emily / Brownlow, Andrew / Wall, Dave / Rogan, Emer / Sigurðsson, Guðjón Már / Kiszka, Jeremy J / Thøstesen, Charlotte Bie / IJsseldijk, Lonneke L / Ten Doeschate, Mariel / Davison, Nicholas J / Øien, Nils / Deaville, Rob / Siebert, Ursula / Ogden, Rob

    Heredity

    2024  Volume 132, Issue 4, Page(s) 192–201

    Abstract: Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate ... ...

    Abstract Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.
    MeSH term(s) Animals ; Dolphins/genetics ; Metagenomics ; Climate Change ; Temperature
    Language English
    Publishing date 2024-02-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2423-5
    ISSN 1365-2540 ; 0018-067X
    ISSN (online) 1365-2540
    ISSN 0018-067X
    DOI 10.1038/s41437-024-00672-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx.

    Humble, Emily / Stoffel, Martin A / Dicks, Kara / Ball, Alex D / Gooley, Rebecca M / Chuven, Justin / Pusey, Ricardo / Remeithi, Mohammed Al / Koepfli, Klaus-Peter / Pukazhenthi, Budhan / Senn, Helen / Ogden, Rob

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 18, Page(s) e2210756120

    Abstract: In an age of habitat loss and overexploitation, small populations, both captive and wild, are increasingly facing the effects of isolation and inbreeding. Genetic management has therefore become a vital tool for ensuring population viability. However, ... ...

    Abstract In an age of habitat loss and overexploitation, small populations, both captive and wild, are increasingly facing the effects of isolation and inbreeding. Genetic management has therefore become a vital tool for ensuring population viability. However, little is known about how the type and intensity of intervention shape the genomic landscape of inbreeding and mutation load. We address this using whole-genome sequence data of the scimitar-horned oryx (
    MeSH term(s) Animals ; Inbreeding ; Antelopes/genetics ; Genotype ; Homozygote ; Alleles ; Polymorphism, Single Nucleotide ; Mutation
    Language English
    Publishing date 2023-04-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2210756120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification.

    Vasiljevic, Nina / Lim, Marisa / Humble, Emily / Seah, Adeline / Kratzer, Adelgunde / Morf, Nadja V / Prost, Stefan / Ogden, Rob

    Forensic science international. Genetics

    2021  Volume 53, Page(s) 102493

    Abstract: Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this ...

    Abstract Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.
    MeSH term(s) Animals ; Birds/genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Deer/genetics ; Forensic Genetics ; High-Throughput Nucleotide Sequencing/instrumentation ; Humans ; Lynx/genetics ; Nanopores ; Panthera/genetics ; Reproducibility of Results ; Rupicapra/genetics ; Sequence Analysis, DNA/instrumentation ; Species Specificity ; Sus scrofa/genetics
    Chemical Substances DNA, Mitochondrial ; Cytochromes b (9035-37-4)
    Language English
    Publishing date 2021-03-12
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Validation Study
    ZDB-ID 2493339-9
    ISSN 1878-0326 ; 1872-4973
    ISSN (online) 1878-0326
    ISSN 1872-4973
    DOI 10.1016/j.fsigen.2021.102493
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Comparative population genomics of manta rays has global implications for management.

    Humble, Emily / Hosegood, Jane / Carvalho, Gary / de Bruyn, Mark / Creer, Simon / Stevens, Guy M W / Armstrong, Amelia / Bonfil, Ramon / Deakos, Mark / Fernando, Daniel / Froman, Niv / Peel, Lauren R / Pollett, Stephen / Ponzo, Alessandro / Stewart, Joshua D / Wintner, Sabine / Ogden, Rob

    Molecular ecology

    2023  

    Abstract: Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation ... ...

    Abstract Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonization, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.
    Language English
    Publishing date 2023-11-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.17220
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment.

    Pomerantz, Aaron / Sahlin, Kristoffer / Vasiljevic, Nina / Seah, Adeline / Lim, Marisa / Humble, Emily / Kennedy, Susan / Krehenwinkel, Henrik / Winter, Sven / Ogden, Rob / Prost, Stefan

    Nature protocols

    2022  Volume 17, Issue 6, Page(s) 1415–1443

    Abstract: In many parts of the world, human-mediated environmental change is depleting biodiversity faster than it can be characterized, while invasive species cause agricultural damage, threaten human health and disrupt native habitats. Consequently, the ... ...

    Abstract In many parts of the world, human-mediated environmental change is depleting biodiversity faster than it can be characterized, while invasive species cause agricultural damage, threaten human health and disrupt native habitats. Consequently, the application of effective approaches for rapid surveillance and identification of biological specimens is increasingly important to inform conservation and biosurveillance efforts. Taxonomic assignments have been greatly advanced using sequence-based applications, such as DNA barcoding, a diagnostic technique that utilizes PCR and DNA sequence analysis of standardized genetic regions. However, in many biodiversity hotspots, endeavors are often hindered by a lack of laboratory infrastructure, funding for biodiversity research and restrictions on the transport of biological samples. A promising development is the advent of low-cost, miniaturized scientific equipment. Such tools can be assembled into functional laboratories to carry out genetic analyses in situ, at local institutions, field stations or classrooms. Here, we outline the steps required to perform amplicon sequencing applications, from DNA isolation to nanopore sequencing and downstream data analysis, all of which can be conducted outside of a conventional laboratory environment using miniaturized scientific equipment, without reliance on Internet connectivity. Depending on sample type, the protocol (from DNA extraction to full bioinformatic analyses) can be completed within 10 h, and with appropriate quality controls can be used for diagnostic identification of samples independent of core genomic facilities that are required for alternative methods.
    MeSH term(s) Biodiversity ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Humans ; Nanopores ; Sequence Analysis, DNA/methods
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2022-04-11
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-022-00682-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible.

    Tebbe, Jonas / Humble, Emily / Stoffel, Martin Adam / Tewes, Lisa Johanna / Müller, Caroline / Forcada, Jaume / Caspers, Barbara / Hoffman, Joseph Ivan

    PeerJ

    2020  Volume 8, Page(s) e10131

    Abstract: Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the ... ...

    Abstract Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publication bias. Additionally, replication is often considered too difficult in field settings where many factors are beyond the investigator's control and where spatial and temporal dependencies may be strong. We investigated the feasibility of reproducing original research findings in the field of chemical ecology by performing an exact replication of a previous study of Antarctic fur seals (
    Language English
    Publishing date 2020-10-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.10131
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.

    Humble, Emily / Thorne, Michael A S / Forcada, Jaume / Hoffman, Joseph I

    BMC research notes

    2016  Volume 9, Issue 1, Page(s) 418

    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 ... ...

    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.
    MeSH term(s) Gene Frequency/genetics ; Genotyping Techniques/methods ; Humans ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide/genetics ; Probability ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Transcriptome/genetics
    Language English
    Publishing date 2016-08-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2413336-X
    ISSN 1756-0500 ; 1756-0500
    ISSN (online) 1756-0500
    ISSN 1756-0500
    DOI 10.1186/s13104-016-2209-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Born blonde: a recessive loss-of-function mutation in the melanocortin 1 receptor is associated with cream coat coloration in Antarctic fur seals.

    Peters, Lucy / Humble, Emily / Kröcker, Nicole / Fuchs, Birgit / Forcada, Jaume / Hoffman, Joseph I

    Ecology and evolution

    2016  Volume 6, Issue 16, Page(s) 5705–5717

    Abstract: Although the genetic basis of color variation has been extensively studied in humans and domestic animals, the genetic polymorphisms responsible for different color morphs remain to be elucidated in many wild vertebrate species. For example, ... ...

    Abstract Although the genetic basis of color variation has been extensively studied in humans and domestic animals, the genetic polymorphisms responsible for different color morphs remain to be elucidated in many wild vertebrate species. For example, hypopigmentation has been observed in numerous marine mammal species but the underlying mutations have not been identified. A particularly compelling candidate gene for explaining color polymorphism is the melanocortin 1 receptor (MC1R), which plays a key role in the regulation of pigment production. We therefore used Antarctic fur seals (Arctocephalus gazella) as a highly tractable marine mammal system with which to test for an association between nucleotide variation at the MC1R and melanin-based coat color phenotypes. By sequencing 70 wild-type individuals with dark-colored coats and 26 hypopigmented individuals with cream-colored coats, we identified a nonsynonymous mutation that results in the substitution of serine with phenylalanine at an evolutionarily highly conserved structural domain. All of the hypopigmented individuals were homozygous for the allele coding for phenylalanine, consistent with a recessive loss-of-function allele. In order to test for cryptic population structure, which can generate artefactual associations, and to evaluate whether homozygosity at the MC1R could be indicative of low genome-wide heterozygosity, we also genotyped all of the individuals at 50 polymorphic microsatellite loci. We were unable to detect any population structure and also found that wild-type and hypopigmented individuals did not differ significantly in their standardized multilocus heterozygosity. Such a lack of association implies that hypopigmented individuals are unlikely to suffer disproportionately from inbreeding depression, and hence, we have no reason to believe that they are at a selective disadvantage in the wider population.
    Language English
    Publishing date 2016-07-22
    Publishing country England
    Document type Journal Article
    ISSN 2045-7758
    ISSN 2045-7758
    DOI 10.1002/ece3.2290
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild.

    Humble, Emily / Dobrynin, Pavel / Senn, Helen / Chuven, Justin / Scott, Alan F / Mohr, David W / Dudchenko, Olga / Omer, Arina D / Colaric, Zane / Lieberman Aiden, Erez / Al Dhaheri, Shaikha Salem / Wildt, David / Oliaji, Shireen / Tamazian, Gaik / Pukazhenthi, Budhan / Ogden, Rob / Koepfli, Klaus-Peter

    Molecular ecology resources

    2020  Volume 20, Issue 6, Page(s) 1668–1681

    Abstract: Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation ... ...

    Abstract Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a large-scale and long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.
    MeSH term(s) Animals ; Antelopes/genetics ; Chromosomes ; Endangered Species ; Genome ; Inbreeding ; Synteny
    Language English
    Publishing date 2020-06-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406833-0
    ISSN 1755-0998 ; 1755-098X
    ISSN (online) 1755-0998
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13181
    Database MEDical Literature Analysis and Retrieval System OnLINE

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