Browsing by Author "Miller, Joshua M."
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- ItemA new lineage of Galapagos giant tortoises identified from museum samples(2022) Jensen, Evelyn L.; Quinzin, Maud C.; Miller, Joshua M.; Russello, Michael A.; Garrick, Ryan C.; Edwards, Danielle L.; Glaberman, Scott; Chiari, Ylenia; Poulakakis, Nikos; Tapia, Washington; Gibbs, James P.; Caccone, AdalgisaThe Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased individuals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave are from a clade that is distinct among known Galapagos giant tortoises but closely related to the species from Española and Pinta Islands. The haplotype of the individual collected alive in 1906 is in the same clade as the haplotype in the contemporary population. To search for traces of a second lineage in the contemporary population on San Cristóbal, we closely examined the population by sequencing the mitochondrial control region for 129 individuals and genotyping 70 of these for both 21 microsatellite loci and >12,000 genome-wide single nucleotide polymorphisms [SNPs]. Only a single mitochondrial haplotype was found, with no evidence to suggest substructure based on the nuclear markers. Given the geographic and temporal proximity of the two deeply divergent mitochondrial lineages in the historical samples, they were likely sympatric, raising the possibility that the lineages coexisted. Without the museum samples, this important discovery of an additional lineage of Galapagos giant tortoise would not have been possible, underscoring the value of such collections and providing insights into the early evolution of this iconic radiation.
- ItemA phylogeographic contact zone for Arctic grayling (Thymallus arcticus) in Alberta, Canada(2021) Reilly, Jessica R.; Miller, Joshua M.Arctic Grayling Thymallus arcticus are a salmonid with a Holarctic distribution, extending from north-eastern Eurasia through north-western North America. Throughout their range, Arctic Grayling face a number of threats including angling mortality, habitat fragmentation and loss and climate change. Thus, there is a need to protect the species through targeted management actions. Genetic information can assist in determining the appropriate scale for these actions through description of Designatable Units (DUs). Here we use newly collected mitochondrial DNA sequence data to assess the phylogeographic structure of Arctic Grayling in Alberta, Canada and link these with previously collected mitochondrial and microsatellite data to determine how many DUs may exist across Canada. Our assessment of 831 base pairs of sequence data in 96 individuals found two deeply divergent lineages in Alberta. When combined with 22 previously collected sequences our results highlight that Alberta is a contact zone for the observed lineages of Arctic Grayling in North America. Reassessment of nine microsatellites genotyped in 1,116 individuals further highlighted inter-basin divergence, likely the result of historical processes. Given the divergence and geographic distribution of the genetic diversity, Arctic Grayling in Canada merit consideration for separate DUs in future species status assessments and management plans. Continuing research should aim to expand sampling geographically (e.g. regions east of Great Slave Lake and along the Arctic coastline) to clarify possible colonization routes, and add to or synthesize work on Arctic Grayling behaviour, morphology, and life-history to address the limited understanding of local adaptions within this species.
- ItemAncient hybridization patterns between bighorn and thinhorn sheep(2021) Santos, Sarah H. D.; Peery, Rhiannon M.; Miller, Joshua M.; Dao, Anh; Lyu, Feng-Hua; Li, Xin; Li, Meng-Hua; Coltman, David W.Whole-genome sequencing has advanced the study of species evolution, including the detection of genealogical discordant events such as ancient hybridization and incomplete lineage sorting (ILS). The evolutionary history of bighorn (Ovis canadensis) and thinhorn (Ovis dalli) sheep present an ideal system to investigate evolutionary discordance due to their recent and rapid radiation and putative secondary contact between bighorn and thinhorn sheep subspecies, specifically the dark pelage Stone sheep (O. dalli stonei) and predominately white Dall sheep (O. dalli dalli), during the last ice age. Here, we used multiple genomes of bighorn and thinhorn sheep, together with snow (O. nivicola) and the domestic sheep (O. aries) as outgroups, to assess their phylogenomic history, potential introgression patterns and their adaptive consequences. Among the Pachyceriforms (snow, bighorn and thinhorn sheep) a consistent monophyletic species tree was retrieved; however, many genealogical discordance patterns were observed. Alternative phylogenies frequently placed Stone and bighorn as sister clades. This relationship occurred more often and was less divergent than that between Dall and bighorn. We also observed many blocks containing introgression signal between Stone and bighorn genomes in which coat colour genes were present. Introgression signals observed between Dall and bighorn were more random and less frequent, and therefore probably due to ILS or intermediary secondary contact. These results strongly suggest that Stone sheep originated from a complex series of events, characterized by multiple, ancient periods of secondary contact with bighorn sheep.
- ItemEwe are what ewe wear: bigger horns, better ewes and the potential consequence of trophy hunting on female fitness in bighorn sheep(2022) Deakin, Samuel; Festa-Bianchet, Marco; Miller, Joshua M.; Pelletier, Fanie; Coltman, David W.In polygynous species, secondary sexual traits such as weapons or elaborate ornaments have evolved through intrasexual competition for mates. In some species, these traits are present in both sexes but are underdeveloped in the sex facing lower intrasexual competition for mates. It is often assumed that these underdeveloped sexually selected traits are a vestige of strong sexual selection on the other sex. Here, we challenge this assumption and investigate whether the expression of secondary sexual traits is associated with fitness in female bighorn sheep. Analyses of 45 years of data revealed that female horn length at 2 years, while accounting for mass and environmental variables, is associated with younger age at primiparity, younger age of first offspring weaned, greater reproductive lifespan and higher lifetime reproductive success. There was no association between horn length and fecundity. These findings highlight a potential conservation issue. In this population, trophy hunting selects against males with fast-growing horns. Intersexual genetic correlations imply that intense selective hunting of large-horned males before they can reproduce can decrease female horn size. Therefore, intense trophy hunting of males based on horn size could reduce female reproductive performance through the associations identified here, and ultimately reduce population growth and viability.
- ItemGlobal genetic diversity status and trends:towards a suite of Essential BiodiversityVariables (EBVs) for genetic composition(2022) Hoban, Sean; Archer, Frederick I.; Bertola, Laura D.; Bragg, Jason G.; Breed, Martin F.; Bruford, Michael W.; Coleman, Melinda A.; Ekblom, Robert; Funk, W. Chris; Grueber, Catherine E.; Hand, Brian K.; Jaffé, Rodolfo; Jensen, Evelyn L.; Johnson, Jeremy S.; Kershaw, Francine; Liggins, Libby; MacDonald, Anna J.; Mergeay, Joachim; Miller, Joshua M.; Muller-Karger, Frank; O'Brien, David; Paz-Vinas, Ivan; Potter, Kevin M.; Razgour, Orly; Vernesi, Cristiano; Hunter, Margaret E.Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well-being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within-species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv)Effective Population Size (Ne). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the GeneticEBVs and review advances and needs in archiving genetic composition data and metadata. We discuss how GeneticEBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVsbeyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large-scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species’ long-term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policymakers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.
- ItemIdentifying unknown soft coral species of Anthelia (Octocorallia) with multilocus DNA barcoding(2023) Pataria, Mannraj; Shaw, Ross; Miller, Joshua M.There are an estimated 1-9 million species of corals yet to be discovered. Anthelia is a species of soft coral that belongs to the Xeniid ae family within Octocorallia. The Xeniidae family of soft corals are of interest due to their ability to rapidly recolonize disturbed reefs, which have become more prevalent with global warming. Octocorallia also contains some of the most valuable corals used in jewelry. Identifying corals not only contributes to its conservation and our knowledge of its evolution, but also prevents fraudulent coral jewelry and the overharvesting of coral beds. However, morphologically identifying corals is very difficult and is further exacerbated with global warming or when it is polished and carved into jewelry. Instead, multilocus DNA barcoding can utilize the genetic material of corals to reveal an accurate classification of species and prevent its exploitation. Specifically, genetic loci in the mitochondrial or nuclear genes can be used to tag and classify corals, with referencing done to genetic databases such as GenBank or NCBI. We identified the soft corals Anthelia glauca, Sarcophtyon tro cheliophorum, and a Sinularia spp. that was mistaken for a species of Nepthea.
- ItemLinking genetic, morphological, and behavioural divergence between inland island and mainland deer mice(2022) Miller, Joshua M.; Garant, Dany; Perrier, Charles; Juette, Tristan; Jameson, Joël W.; Normandeau, Eric; Bernatchez, Louis; Réale, DenisThe island syndrome hypothesis (ISH) stipulates that, as a result of local selection pressures and restricted gene flow, individuals from island populations should differ from individuals within mainland populations. Specifically, island populations are predicted to contain individuals that are larger, less aggressive, more sociable, and that invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here, using a novel set of genome-wide SNP markers in wild deer mice (Peromyscus maniculatus) we conducted a genomic assessment of predictions underlying the ISH in an inland riverine island system: analysing island-mainland population structure, and quantifying heritability of phenotypes thought to underlie the ISH. We found clear genomic differentiation between island and mainland populations and moderate to high marker based heritability estimates for overall variation in traits previously found to differ in line with the ISH between mainland and island locations. FST outlier analyses highlighted 12 loci associated with differentiation between mainland and island populations. Together these results suggest that the island populations examined are on independent evolutionary trajectories, the traits considered have a genetic basis (rather than phenotypic variation being solely due to phenotypic plasticity). Coupled with the previous results showing significant phenotypic differentiation between island and mainland groups in this system, this study suggests that the ISH can hold even on a small spatial scale.
- ItemThe crucial role of genome-wide genetic variation in conservation(2021) Kardos, Marty; Armstrong, Ellie E.; Fitzpatrick, Sarah; Hauser, Samantha; Hedrick, Philip W.; Miller, Joshua M.; Tallmon, David A.; Funk, W. ChrisThe unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations towards extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.