Browsing by Author "Hohenlohe PA"

Now showing 1 - 3 of 3
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    Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD
    (Springer Nature BV, 2021-08) Laikre L; Hohenlohe PA; Allendorf FW; Bertola LD; Breed MF; Bruford MW; Funk WC; Gajardo G; González-Rodríguez A; Grueber CE; Hedrick PW; Heuertz M; Hunter ME; Johannesson K; Liggins L; MacDonald AJ; Mergeay J; Moharrek F; O’Brien D; Ogden R; Orozco-terWengel P; Palma-Silva C; Pierson J; Paz-Vinas I; Russo I-RM; Ryman N; Segelbacher G; Sjögren-Gulve P; Waits LP; Vernesi C; Hoban S
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    Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved
    (Elsevier Ltd, 2020-08) Hoban S; Bruford M; D'Urban Jackson J; Lopes-Fernandes M; Heuertz M; Hohenlohe PA; Paz-Vinas I; Sjögren-Gulve P; Segelbacher G; Vernesi C; Aitken S; Bertola LD; Bloomer P; Breed M; Rodríguez-Correa H; Funk WC; Grueber CE; Hunter ME; Jaffe R; Liggins L; Mergeay J; Moharrek F; O'Brien D; Ogden R; Palma-Silva C; Pierson J; Ramakrishnan U; Simo-Droissart M; Tani N; Waits L; Laikre L
    The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics. Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.
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    Leveraging an existing whole-genome resequencing population data set to characterize toll-like receptor gene diversity in a threatened bird
    (John Wiley and Sons, Ltd, 2022-10) Magid M; Wold JR; Moraga R; Cubrinovska I; Houston DM; Gartrell BD; Steeves TE; Hohenlohe PA
    Species recovery programs are increasingly using genomic data to measure neutral genetic diversity and calculate metrics like relatedness. While these measures can inform conservation management, determining the mechanisms underlying inbreeding depression requires information about functional genes associated with adaptive or maladaptive traits. Toll-like receptors (TLRs) are one family of functional genes, which play a crucial role in recognition of pathogens and activation of the immune system. Previously, these genes have been analysed using species-specific primers and PCR. Here, we leverage an existing short-read reference genome, whole-genome resequencing population data set, and bioinformatic tools to characterize TLR gene diversity in captive and wild tchūriwat'/tūturuatu/shore plover (Thinornis novaeseelandiae), a threatened bird endemic to Aotearoa New Zealand. Our results show that TLR gene diversity in tchūriwat'/tūturuatu is low, and forms two distinct captive and wild genetic clusters. The bioinformatic approach presented here has broad applicability to other threatened species with existing genomic resources in Aotearoa New Zealand and beyond.