The Relevance of Pedigrees in the Conservation Genomics Era

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome-wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well-informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities

Exploring the Evolutionary History of North American Prairie Grouse (Genus: Tympanuchus) Using Multi-locus Coalescent Analyses

Conservation biologists are increasingly using phylogenetics as a tool to understand evolutionary relationships and taxonomic classification. The taxonomy of North American prairie grouse (sharp-tailed grouse, T. phasianellus; lesser prairie-chicken, T. pallidicinctus; greater prairie-chicken, T. cupido; including multiple subspecies) has been designated based on physical characteristics, geography, and behavior. However, previous studies have been inconclusive in determining the evolutionary history of prairie grouse based on genetic data. Therefore, additional research investigating the evolutionary history of prairie grouse is warranted. In this study, ten loci (including mitochondrial, autosomal, and Z-linked markers) were sequenced across multiple populations of prairie grouse, and both traditional and coalescent-based phylogenetic analyses were used to address the evolutionary history of this genus. Results from this study indicate that North American prairie grouse diverged in the last 200,000 years, with species-level taxa forming well-supported monophyletic clades in species tree analyses. With these results, managers of the critically endangered Attwater's prairie-chicken (T. c. attwateri) can better evaluate whether outcrossing Attwater's with greater prairie-chickens would be a viable management tool for Attwater's conservation

Contribución de las danzas folklóricas al fortalecimiento en el respeto de normas de convivencia en niños de 4 años en un centro educativo particular de Pueblo Libre

La presente investigación, tiene como objetivo contribuir al fortalecimiento del respeto de las normas de convivencia mediante danzas folklóricas en los niños de 4 años de un centro educativo particular en el distrito de Pueblo Libre. Se trata de una investigación-acción en el aula, que es una investigación con enfoque cualitativo, de nivel descriptivo. En este caso en particular, se detectó un problema que ocurre en el aula y con la convivencia de los niños, por lo que se propuso una serie de actividades que buscaron solucionar este problema en el mismo lugar donde se desarrollan y desenvuelven los participantes. En la investigación participaron 20 niños de un aula de cuatro años en una institución educativa de Educación Inicial. Se realizaron listas de cotejo al inicio de las sesiones, tanto por la investigadora como por la tutora de aula. Se desarrollaron nueve sesiones de danza folklórica, tratando también las normas de convivencia antes de iniciar cada sesión y durante su desarrollo. Se registraron las observaciones en un diario de campo y al finalizar se volvieron a aplicar las listas de cotejo para comparar si había una mejora en el respeto a las normas de convivencia en el aula. Con respecto a los resultados, se registró un progreso muy discreto en el fortalecimiento de las normas de convivencia al trabajarlo a través de las danzas folklóricas. Por lo que se considera que el trabajo constante a lo largo de todo el año escolar podría arrojar resultados más positivos, puesto que, si en nueve sesiones se pudo lograr un mínimo avance, trabajar las danzas folklóricas a lo largo del año fortalecería la interiorización de las normas de convivencia.Tesi

Conservation of Sharp-Tailed Grouse (\u3cem\u3eTympanuchus phasianellus columbianus\u3c/em\u3e) Through Fecal DNA Extraction

Columbian Sharp-tailed Grouse (Tympanuchus phasianellus columbianus) are the rarest of the six extant Sharp-tailed Grouse subspecies. This subspecies experienced a 90% range contraction over the last century and have been extirpated from several states (Figure 1). In Washington alone, populations that once numbered hundreds of thousands of individuals now consist of fewer than 1,000 birds. Conservation efforts—including conservation translocations and habitat management—are underway to help bolster this imperiled subspecies across their range. However, little is known about the ecology of this charismatic species and the factors that may be contributing towards higher rates of decline. The collection of fecal pellets presents an opportunity to better understand Columbian Sharp-tailed Grouse across their range, by providing information on their diet and host ID. As a HERC Fellow in the Conservation Genetics Lab at Boise State University, I have been exploring the potential to use non-invasively collected fecal samples to understand how we can best capture different DNA types, which can be used to better inform the conservation and management of this charismatic grouse

Pedigree Validation Using Genetic Markers in an Intensively-Managed Taonga Species, the Critically Endangered Kakī (\u3cem\u3eHimantopus novaezelandiae\u3c/em\u3e)

Many species recovery programmes use pedigrees to understand the genetic ancestry of individuals to inform conservation management. However, incorrect parentage assignment may limit the accuracy of these pedigrees and subsequent management decisions. This is especially relevant for pedigrees that include wild individuals, where misassignment may not only be attributed to human error, but also promiscuity (i.e. extra-pair parentage) or egg-dumping (i.e. brood parasitism). Here, we evaluate pedigree accuracy in the socially monogamous and critically endangered kakī (black stilt, Himantopus novaezelandiae) using microsatellite allele-exclusion analyses for 56 wild family groups across three breeding seasons (2014–2016, n= 340). We identified 16 offspring where parentage was incorrectly assigned, representing 5.9% of all offspring. Of the 16 misassigned offspring, three can be attributed to non-kakī brood parasitism, one can be assigned to human error, but others cannot be readily distinguished between non-monogamous mating behaviours and human error. In the short term, we advise the continued use of microsatellites to identify misassigned offspring in the kakī pedigree, and to verify non-kakī brood parasitism. We also recommend the Department of Conservation’s Kakī Recovery Programme further evaluate the implications of pedigree error to the management of this critically endangered taonga species

Meta-Analysis Reveals Challenges and Gaps for Genome-to-Phenome Research Underpinning Plant Drought Response

Severe drought conditions and extreme weather events are increasing worldwide with climate change, threatening the persistence of native plant communities and ecosystems. Many studies have investigated the genomic basis of plant responses to drought. However, the extent of this research throughout the plant kingdom is unclear, particularly among species critical for the sustainability of natural ecosystems. This study aimed to broaden our understanding of genome-to-phenome (G2P) connections in drought-stressed plants and identify focal taxa for future research. Bioinformatics pipelines were developed to mine and link information from databases and abstracts from 7730 publications. This approach identified 1634 genes involved in drought responses among 497 plant taxa. Most (83.30%) of these species have been classified for human use, and most G2P interactions have been described within model organisms or crop species. Our analysis identifies several gaps in G2P research literature and database connectivity, with 21% of abstracts being linked to gene and taxonomy data in NCBI. Abstract text mining was more successful at identifying potential G2P pathways, with 34% of abstracts containing gene, taxa, and phenotype information. Expanding G2P studies to include non-model plants, especially those that are adapted to drought stress, will help advance our understanding of drought responsive G2P pathways

Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management

Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance species recovery. However, a lack of readily available genomic resources, including conspecific reference genomes, often limits the inclusion of genomic data. Here, we investigate the utility of closely related high-quality reference genomes for single nucleotide polymorphism (SNP) discovery using the critically endangered kakī/black stilt (Himantopus novaezelandiae) and four Charadriiform reference genomes as proof of concept. We compare diversity estimates (i.e., nucleotide diversity, individual heterozygosity, and relatedness) based on kakī SNPs discovered from genotyping-by-sequencing and whole genome resequencing reads mapped to conordinal (killdeer, Charadrius vociferus), confamilial (pied avocet, Recurvirostra avosetta), congeneric (pied stilt, Himantopus himantopus) and conspecific reference genomes. Results indicate that diversity estimates calculated from SNPs discovered using closely related reference genomes correlate significantly with estimates calculated from SNPs discovered using a conspecific genome. Congeneric and confamilial references provide higher correlations and more similar measures of nucleotide diversity, individual heterozygosity, and relatedness. While conspecific genomes may be necessary to address other questions in conservation, SNP discovery using high-quality reference genomes of closely related species is a cost-effective approach for estimating diversity measures in threatened species

A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide

Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kakī/ black stilt (Himantopus novaezelandiae) and kākāriki karaka/orange-fronted parakeet (Cyanoramphus malherbi). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent–offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using PMx are most similar between pedigree and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide

Conservation genomic management of two critically endangered New Zealand birds.

In order to conserve global biodiversity, a multifaceted approach is needed to address complex conservation issues. One valuable tool in this approach is the use of genetic data to inform management (i.e., conservation genetics). For intensively managed threatened populations, genetic diversity can be managed through a conservation breeding approach, where relatively unrelated individuals are paired together to minimise inbreeding and maximise diversity in an effort to maximise evolutionary potential. For many, the pedigree has been the tool of choice for making pairing recommendations in conservation breeding programmes, as it relies on available ancestry data to estimate kinship —a measure of coancestry or pairwise relatedness— between individuals. However, threatened species recovery programmes often struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can measure relatedness for pairing recommendations, emerging evidence indicates this approach lacks precision in genetically depauperate species and more precise measures may be obtained from genomic data (i.e., thousands of single nucleotide polymorphisms, or SNPs). The field of conservation genetics is currently transitioning from using relatively few genetic markers to using thousands of genome-wide SNPs using high throughput sequencing (HTS) technologies. While the emerging field of conservation genomics promises greater precision for population diversity measures, relatively few studies to date have used these technologies, and exemplars are needed to demonstrate how to effectively and efficiently navigate from genetic to genomic technologies for use in conservation genetic management. This thesis serves as one such exemplar, using two critically endangered birds as Proof-of-Concept: the kakī/black stilt (Himantopus novaezelandiae) and kākāriki karaka/orange-fronted parakeet (Cyanoramphus malherbi). Both species are endemic to Aotearoa New Zealand and part of their management includes conservation breeding programmes, where individuals are bred in captivity with their offspring translocated to predator-controlled wild habitats. Pairing recommendations for captive kakī and kākāriki karaka have been based loosely on visualised pedigree diagrams, but no studies to date have formally analysed either pedigree. In order to establish the capabilities and limitations of existing tools for genetic/genomic management, in Chapter 2 I developed multigenerational pedigrees for both species to investigate founder representation, relatedness, and mean kinship. This chapter highlights limitations of pedigrees for species with conservation breeding programmes that are routinely augmented by individuals of unknown ancestry, and underscores the value in incorporating empirical data (i.e., genetics and genomics) into management. In the form of a Molecular Ecology opinion piece lead by me, Chapter 3 provides an overview of the gap between the availability of genomic tools and their use for conservation (i.e., the ‘conservation genomics gap’) and provides a pathway for people to transition and upskill in bioinformatic capacity. This piece describes how interdisciplinary relationships are enabling advances in both conservation genomics and primary industry research (e.g., agriculture, fisheries, forestry and horticulture), given the shared goals and applied nature of both disciplines. While conservation geneticists can learn about genomic approaches for aligned questions from primary industry, conservation geneticists can lend biodiversity expertise to primary industry for improved primary production output. In Chapter 4, in an invited submission for the Genes “Conservation Genetics and Genomics” Special Issue, my co-authors (including co-first author Natalie Forsdick) and I explore the capacity for using readily available closely-related reference genomes for conservation management. In this chapter, we compare diversity estimates (i.e., nucleotide diversity, individual heterozygosity, and relatedness) derived from SNPs discovered using genotyping-by-sequencing and whole genome resequencing reads mapped to conordinal (killdeer, Charadrius vociferus), confamilial (pied avocet, Recurvirostra avosetta), congeneric (pied stilt, Himantopus himantopus) and conspecific reference genomes. Results indicate that diversity and individual heterozygosity estimates calculated from SNPs discovered using closely related reference genomes correlate significantly with estimates calculated from SNPs discovered using a conspecific genome, with congeneric and confamilial references provide higher correlations and more similar measures. While conspecific genomes may be necessary to address other questions in conservation, SNP discovery in birds using high-quality reference genomes of closely related species is a cost-effective approach for estimating diversity measures in threatened species. In Chapter 5, in a manuscript submitted to Evolutionary Applications, my co- authors and I compare relatedness measures using pedigree, genetic, and genomic approaches for making pairing decisions in two critically endangered birds from Aotearoa with conservation breeding programmes: kakī and kākāriki karaka. This study uses family groups (i.e., parents, offspring, and siblings) to assess methods of estimating relatedness, as first order relationships between parents & offspring and siblings in these conservation breeding programmes are known. Our findings indicate genetic measures of relatedness are indeed the least precise when assessing known parent-offspring and sibling relationships, with SNPs providing more precision. Our results also show that pairing recommendations are most similar when using pedigrees and SNPs. Overall, these results indicate that in lieu of robust pedigrees, SNPs are the most effective measure of relatedness, which has exciting implications for poorly pedigreed populations worldwide. Beyond using putatively independent SNPs for estimating relatedness, many researchers are looking to discover the genomic basis underlying maladaptive traits in small populations (e.g., inbreeding depression). While outside the scope of this thesis, Chapter 6 discusses new avenues for research given rich genomic and pedigree data sets now available for both kakī and kākāriki karaka. We anticipate that population genomic management simulations that balance selection for genome-wide diversity while penalising individuals for carrying maladaptive traits will allow researchers the ability to assess whether this approach enhances recovery in threatened populations. Overall, these combined chapters provide a toolbox for conservation geneticists who are transitioning to genomic technologies, especially for conservation breeding programmes. While this research project uses kakī and kākāriki karaka as focal species, it sits under the umbrella of a forward-thinking conservation genomics initiative that seeks to maximise the genetic diversity of a wide range of threatened species and enhance recovery efforts for species worldwide

Expanding the Conservation Genomics Toolbox: Incorporating Structural Variants to Enhance Genomic Studies for Species of Conservation Concern

Structural variants (SVs) are large rearrangements (\u3e50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature–predominantly in human health, agriculture and ecoevolutionary biology–to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world\u27s most threatened species