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  1. Article ; Online: Individual-based landscape genomics for conservation: An analysis pipeline.

    Chambers, E Anne / Bishop, Anusha P / Wang, Ian J

    Molecular ecology resources

    2023  

    Abstract: Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional ... ...

    Abstract Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non-model systems has also enabled a shift away from population-based sampling to individual-based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual-based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population-based sampling to individual-based sampling schemes. Here, we discuss the benefits of individual-based sampling for conservation and describe how landscape genomic methods, paired with individual-based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user-friendly, open-source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). The algatr package includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.
    Language English
    Publishing date 2023-10-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2406833-0
    ISSN 1755-0998 ; 1755-098X
    ISSN (online) 1755-0998
    ISSN 1755-098X
    DOI 10.1111/1755-0998.13884
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Corrigendum to: Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations.

    Terasaki Hart, Drew E / Bishop, Anusha P / Wang, Ian J

    Molecular biology and evolution

    2021  Volume 38, Issue 11, Page(s) 5209

    Language English
    Publishing date 2021-10-04
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msab250
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2137: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  3. Article ; Online: Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations.

    Terasaki Hart, Drew E / Bishop, Anusha P / Wang, Ian J

    Molecular biology and evolution

    2021  Volume 38, Issue 10, Page(s) 4634–4646

    Abstract: Understanding the drivers of spatial patterns of genomic diversity has emerged as a major goal of evolutionary genetics. The flexibility of forward-time simulation makes it especially valuable for these efforts, allowing for the simulation of arbitrarily ...

    Abstract Understanding the drivers of spatial patterns of genomic diversity has emerged as a major goal of evolutionary genetics. The flexibility of forward-time simulation makes it especially valuable for these efforts, allowing for the simulation of arbitrarily complex scenarios in a way that mimics how real populations evolve. Here, we present Geonomics, a Python package for performing complex, spatially explicit, landscape genomic simulations with full spatial pedigrees that dramatically reduces user workload yet remains customizable and extensible because it is embedded within a popular, general-purpose language. We show that Geonomics results are consistent with expectations for a variety of validation tests based on classic models in population genetics and then demonstrate its utility and flexibility with a trio of more complex simulation scenarios that feature polygenic selection, selection on multiple traits, simulation on complex landscapes, and nonstationary environmental change. We then discuss runtime, which is primarily sensitive to landscape raster size, memory usage, which is primarily sensitive to maximum population size and recombination rate, and other caveats related to the model's methods for approximating recombination and movement. Taken together, our tests and demonstrations show that Geonomics provides an efficient and robust platform for population genomic simulations that capture complex spatial and evolutionary dynamics.
    MeSH term(s) Biological Evolution ; Computer Simulation ; Genetics, Population ; Genomics ; Metagenomics
    Language English
    Publishing date 2021-06-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msab175
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2137: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis.

    Bishop, Anusha P / Westeen, Erin P / Yuan, Michael L / Escalona, Merly / Beraut, Eric / Fairbairn, Colin / Marimuthu, Mohan P A / Nguyen, Oanh / Chumchim, Noravit / Toffelmier, Erin / Fisher, Robert N / Shaffer, H Bradley / Wang, Ian J

    The Journal of heredity

    2023  Volume 114, Issue 5, Page(s) 521–528

    Abstract: Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of ... ...

    Abstract Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.
    MeSH term(s) Animals ; Mexico ; Genome ; Ecosystem ; Genomics ; Lizards/genetics
    Language English
    Publishing date 2023-06-11
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 3044-2
    ISSN 1465-7333 ; 0022-1503
    ISSN (online) 1465-7333
    ISSN 0022-1503
    DOI 10.1093/jhered/esad037
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1824: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article: A machine learning approach to integrating genetic and ecological data in tsetse flies (

    Bishop, Anusha P / Amatulli, Giuseppe / Hyseni, Chaz / Pless, Evlyn / Bateta, Rosemary / Okeyo, Winnie A / Mireji, Paul O / Okoth, Sylvance / Malele, Imna / Murilla, Grace / Aksoy, Serap / Caccone, Adalgisa / Saarman, Norah P

    Evolutionary applications

    2021  Volume 14, Issue 7, Page(s) 1762–1777

    Abstract: Vector control is an effective strategy for reducing vector-borne disease transmission, but requires knowledge of vector habitat use and dispersal patterns. Our goal was to improve this knowledge for the tsetse ... ...

    Abstract Vector control is an effective strategy for reducing vector-borne disease transmission, but requires knowledge of vector habitat use and dispersal patterns. Our goal was to improve this knowledge for the tsetse species
    Language English
    Publishing date 2021-05-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2405496-3
    ISSN 1752-4563 ; 1752-4571
    ISSN (online) 1752-4563
    ISSN 1752-4571
    DOI 10.1111/eva.13237
    Database MEDical Literature Analysis and Retrieval System OnLINE

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