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  • 1
    Online Resource
    Online Resource
    Generating continuous maps of genetic diversity using moving windows
    Wiley ; 2023
    In:  Methods in Ecology and Evolution Vol. 14, No. 5 ( 2023-05), p. 1175-1181
    Details
    In: Methods in Ecology and Evolution, Wiley, Vol. 14, No. 5 ( 2023-05), p. 1175-1181
    Abstract: Genetic diversity plays a key role in maintaining population viability by preventing inbreeding depression and providing the building blocks for adaptation. Understanding how genetic diversity varies across space is, therefore, of key interest in conservation and population genetics. Here, we introduce wingen , an r package for calculating continuous maps of genetic diversity, including nucleotide diversity, allelic richness, and heterozygosity, from standard genotypic and spatial data using a spatial moving window approach. We provide functions to account for variation in sample size across space using rarefaction, to create kriging‐interpolated maps of genetic diversity, and to mask any areas that are outside the area of interest. Tests with simulated and empirical datasets demonstrate that wingen can successfully capture variation in genetic diversity across landscapes from both reduced‐representation and whole genome sequencing datasets. For reduced‐representation datasets, wingen 's functions can be run easily on a standard laptop computer, and we provide options for parallelization to increase the efficiency of running larger whole genome datasets. wingen provides novel and computationally tractable tools for creating informative maps of genetic diversity with applications for conservation prioritization as well as population and landscape genetic analyses.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    URL: Article
    DOI: 10.1111/mee3.v14.5
    DOI: 10.1111/2041-210X.14090
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2528492-7
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  • 2
    Online Resource
    Online Resource
    Prevalence and Risk Factors of Hypothyroidism: Findings from the Canadian Study of Health and Aging
    Cambridge University Press (CUP) ; 2001
    In:  Canadian Journal on Aging / La Revue canadienne du vieillissement Vol. 20, No. 1 ( 2001), p. 127-135
    Details
    In: Canadian Journal on Aging / La Revue canadienne du vieillissement, Cambridge University Press (CUP), Vol. 20, No. 1 ( 2001), p. 127-135
    Abstract: The objective of this research is to determine the prevalence and risk factors for primary hypothyroidism in a sample of Canadian seniors. The Canadian Study of Health and Aging (CSHA) was a prevalence survey of seniors living at home and in long-term care facilities ( n = 10,263). Detailed clinical examinations were conducted on 2,914 seniors, of which 1,415 had serum TSH levels measured.The ten Canadian Provinces were grouped into five geographic regions (Atlantic, Quebec, Ontario, Prairies and British Columbia). Only seniors who underwent detailed clinical examinations ( n = 2,914) are included. Hypothyroidism was defined as seniors taking thyroid hormone replacement or seniors having a serum TSH level greater than 10 mU/L. An estimated 9.6 per cent of seniors had hypothyroidism, 5.1 per cent were inadequately treated and 2.1 per cent were untreated. Age, gender, cultural background, geographic region and place of residence were potential risk factors for hypothyroidism. Hypothyroidism was found to be a prevalent problem in this population.
    Type of Medium: Online Resource
    ISSN: 0714-9808 , 1710-1107
    URL: Article
    DOI: 10.1017/S0714980800012174
    Language: English
    Publisher: Cambridge University Press (CUP)
    Publication Date: 2001
    detail.hit.zdb_id: 2166531-X
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  • 3
    Online Resource
    Online Resource
    The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation
    Oxford University Press (OUP) ; 2023
    In:  Systematic Biology Vol. 72, No. 2 ( 2023-06-16), p. 357-371
    Details
    In: Systematic Biology, Oxford University Press (OUP), Vol. 72, No. 2 ( 2023-06-16), p. 357-371
    Abstract: With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability to draw accurate species boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa can determine if assortative mating or selection against hybrids exists (supporting the presence of two distinct species), or alternatively if mating is random among genotypes and admixture among adjacent populations is gradual and continuous (supporting geographic variation within a single species). Here, we test two alternative hypotheses for two pairs of named taxa at contact zones within the American milksnake (Lampropeltis triangulum) complex. A prior morphological analysis found areas of gradual intergradation among named taxa, and concluded that the taxa represented geographical races of a single polytypic species. In contrast, a subsequent analysis of gene sequence data, but with limited sampling near the contact zones, hypothesized distinct boundaries between species at the contact zones. At the contact zone between proposed species L. triangulum and Lampropeltis gentilis, we examined a $\sim$700 km-wide transect across the states of Kansas and Missouri, with thorough sampling and reduced-representation genomic-level sequencing, to test the two opposing taxonomic hypotheses. Our transect analyses included examinations of population structure, fixed differences, cline-fitting, and an admixture index analysis. These analyses all supported a gradual and continuous geographic cline across a broad intergrade zone between two geographic forms of L. triangulum, thus providing strong support for a single species in this region (and no support for the recognition of L. gentilis as a distinct species). At a second contact zone between proposed species L. triangulum and Lampropeltis elapsoides (but variously treated as species or subspecies by different researchers) in Kentucky and Tennessee, we re-evaluated morphological data. In this case, the contact zone analysis indicated sympatry and reproductive isolation of the two taxa, and thus strongly supported L. triangulum and L. elapsoides as distinct species. We conclude that detailed studies of contact zones, based on either genetic or morphological data, are essential for distinguishing intraspecific from interspecific variation in the case of widely and continuously distributed taxa. [Contact zones; speciation; species concepts; species delimitation; taxonomy.]
    Type of Medium: Online Resource
    ISSN: 1063-5157 , 1076-836X
    URL: Article
    DOI: 10.1093/sysbio/syac056
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1482572-7
    detail.hit.zdb_id: 1123455-6
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Contemporary Methods and Evidence for Species Delimitation
    American Society of Ichthyologists and Herpetologists (ASIH) ; 2021
    In:  Ichthyology & Herpetology Vol. 109, No. 3 ( 2021-9-29)
    Details
    In: Ichthyology & Herpetology, American Society of Ichthyologists and Herpetologists (ASIH), Vol. 109, No. 3 ( 2021-9-29)
    Type of Medium: Online Resource
    ISSN: 2766-1512
    URL: Article
    DOI: 10.1643/h2021082
    Language: Unknown
    Publisher: American Society of Ichthyologists and Herpetologists (ASIH)
    Publication Date: 2021
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  • 5
    Online Resource
    Online Resource
    Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections
    Public Library of Science (PLoS) ; 2016
    In:  PLOS ONE Vol. 11, No. 4 ( 2016-4-26), p. e0154363-
    Details
    In: PLOS ONE, Public Library of Science (PLoS), Vol. 11, No. 4 ( 2016-4-26), p. e0154363-
    Type of Medium: Online Resource
    ISSN: 1932-6203
    URL: Article
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    DOI: 10.1371/journal.pone.0154363
    DOI: 10.1371/journal.pone.0154363.g001
    DOI: 10.1371/journal.pone.0154363.g002
    DOI: 10.1371/journal.pone.0154363.g003
    DOI: 10.1371/journal.pone.0154363.g004
    DOI: 10.1371/journal.pone.0154363.t001
    DOI: 10.1371/journal.pone.0154363.t002
    DOI: 10.1371/journal.pone.0154363.s001
    DOI: 10.1371/journal.pone.0154363.s002
    DOI: 10.1371/journal.pone.0154363.s003
    DOI: 10.1371/journal.pone.0154363.s004
    DOI: 10.1371/journal.pone.0154363.s005
    DOI: 10.1371/journal.pone.0154363.s006
    DOI: 10.1371/journal.pone.0154363.s007
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2016
    detail.hit.zdb_id: 2267670-3
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  • 6
    Online Resource
    Online Resource
    The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa
    Oxford University Press (OUP) ; 2020
    In:  Systematic Biology Vol. 69, No. 1 ( 2020-01-01), p. 184-193
    Details
    In: Systematic Biology, Oxford University Press (OUP), Vol. 69, No. 1 ( 2020-01-01), p. 184-193
    Abstract: Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic–nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.
    Type of Medium: Online Resource
    ISSN: 1063-5157 , 1076-836X
    URL: Article
    DOI: 10.1093/sysbio/syz042
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1482572-7
    detail.hit.zdb_id: 1123455-6
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs
    Wiley ; 2023
    In:  Molecular Ecology Resources Vol. 23, No. 5 ( 2023-07), p. 1124-1141
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 23, No. 5 ( 2023-07), p. 1124-1141
    Abstract: DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I ( COI ) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species‐delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty‐eight other named species share OTUs, such as Azemiops feae and A. kharini , Gloydius halys , G. shedaoensis , and G. intermedius , and Bungarus multicinctus and B. candidus , representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v23.5
    DOI: 10.1111/1755-0998.13784
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Species Persistence with Hybridization in Toad-Headed Lizards Driven by Divergent Selection and Low Recombination
    Oxford University Press (OUP) ; 2022
    In:  Molecular Biology and Evolution Vol. 39, No. 4 ( 2022-04-10)
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 39, No. 4 ( 2022-04-10)
    Abstract: Speciation plays a central role in evolutionary studies, and particularly how reproductive isolation (RI) evolves. The origins and persistence of RI are distinct processes that require separate evaluations. Treating them separately clarifies the drivers of speciation and then it is possible to link the processes to understand large-scale patterns of diversity. Recent genomic studies have focused predominantly on how species or RI originate. However, we know little about how species persist in face of gene flow. Here, we evaluate a contact zone of two closely related toad-headed lizards (Phrynocephalus) using a chromosome-level genome assembly and population genomics. To some extent, recent asymmetric introgression from Phrynocephalus putjatai to P. vlangalii reduces their genomic differences. However, their highly divergent regions (HDRs) have heterogeneous distributions across the genomes. Functional gene annotation indicates that many genes within HDRs are involved in reproduction and RI. Compared with allopatric populations, contact areas exhibit recent divergent selection on the HDRs and a lower population recombination rate. Taken together, this implies that divergent selection and low genetic recombination help maintain RI. This study provides insights into the genomic mechanisms that drive RI and two species persistence in the face of gene flow during the late stage of speciation.
    Type of Medium: Online Resource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msac064
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2024221-9
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    COI barcoding provides reliable species identification and pinpoints cryptic diversity in Western Palearctic amphibians
    Brill ; 2023
    In:  Amphibia-Reptilia ( 2023-07-11), p. 1-15
    Details
    In: Amphibia-Reptilia, Brill, ( 2023-07-11), p. 1-15
    Abstract: Assembling DNA barcode reference libraries for various taxonomic groups allows researchers to use metabarcoding or environmental DNA approaches to gain a rapid understanding of diversity in given environments. However, our ability to use reference libraries depends on how accurately DNA barcodes are able to recover taxonomic boundaries and identify species, which is rarely considered. We constructed an extensive COI barcoding library for amphibians of the Western Palearctic and successfully recovered barcodes from 60 urodele and 73 anuran species (representing 94% and 98% of the nominal anuran and urodele species in the Western Palearctic, respectively), covering the intraspecific diversity of the majority of species in this region. We tested the effectiveness of our assembled DNA barcode dataset for species identification using barcoding gap, efficiency analyses, and two phylogenetic species delimitation methods. We obtained DNA barcodes for 1251 specimens (691 anurans and 560 urodeles) with a high success rate (92-96%) of species identification. The absence of a barcoding gap in a number of samples was linked to species misidentifications, which suggest incipient speciation or cryptic diversity, or previously described mitochondrial introgression events. The phylogenetic species delimitation methods resulted in substantial oversplitting of currently accepted taxonomy. This COI barcoding library provides an almost complete and reliable reference library for Western Palearctic amphibians. We highlight the importance of generating comprehensive and well curated reference libraries that include intra- and interspecific genetic variability and the need of detailed taxonomic revision when ambiguous or incorrect DNA barcodes exist.
    Type of Medium: Online Resource
    ISSN: 0173-5373 , 1568-5381
    URL: Article
    DOI: 10.1163/15685381-bja10148
    Language: Unknown
    Publisher: Brill
    Publication Date: 2023
    detail.hit.zdb_id: 2036962-1
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics
    Wiley ; 2023
    In:  Ecology and Evolution Vol. 13, No. 3 ( 2023-03)
    Details
    In: Ecology and Evolution, Wiley, Vol. 13, No. 3 ( 2023-03)
    Abstract: Restriction‐site‐associated DNA sequencing (RADseq) has become an accessible way to obtain genome‐wide data in the form of single‐nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non‐model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well‐supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony‐informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    URL: Article
    DOI: 10.1002/ece3.v13.3
    DOI: 10.1002/ece3.9842
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2635675-2
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