Phylogenetics, Population Genetics, and Evolution of the Mallard Complex

Speciation is primarily regarded as an ancestral split that results in two distinct taxonomic units, and proceeds in stages along a continuum from initiation (i.e., population divergence) to completion (i.e., reproductively isolated species). Establishing how and why populations diverge, including the primary mechanisms influencing these events is a major objective for evolutionary scientists. Focusing on incipient forms, researchers attempt to disentangle the antagonistic nature of selection, genetic drift, and gene flow in the speciation process. In chapter 1, I investigate the phylogenetic relationships of 14 closely related taxa within the mallard complex (Anas spp.) that underwent a radiation within the past one million years. Using mitochondrial DNA (mtDNA) and 20 nuclear loci for one to five individuals per taxon, I further examine how recombination and hybridization affect species tree reconstructions. In general, relationships within major clades were robust to treatment of recombination (i.e., ignoring or filtering) and inclusion or exclusion of hybridizing taxa, but branch lengths and posterior support were sensitive to both treatments. Of the 14 taxa, the most confounded relationships were those within the New World (NW) group comprising the sexually dichromatic mallard (Anas platyrhynchos) and the monochromatic American black duck (A. rubripes; black duck ), mottled duck (A. fulvigula), and Mexican duck (A. [p.] diazi). Finally, I address discordance between nuclear, morphometric, and mitochondrial trees, particularly with regard to the placement of the Hawaiian duck (A. wyvilliana), Philippine duck (A. luzonica), and two spot-billed ducks (A. zonorhyncha and A. poecilorhyncha) and discuss how alternative modes of speciation (i.e., hybrid speciation) may lead to variance in these relationships. In Chapter 2, I attempt to disentangle the evolutionary relationships of the New World (NW) group using mtDNA and 17 nuclear loci for a larger per taxon sample size (24-25 individuals per taxon). In general, whereas both Florida and Gulf Coast mottled ducks were differentiated from one another and from the other taxa (mean ΦST = 0.024 - 0.064), mallards, American black ducks, and Mexican duck were not significantly differentiated among nuclear markers (mean ΦST \u3c 0.020). Using coalescent methods to estimate rates of gene flow between mallards and each of the monochromatic taxa generally supported hybridization, but I could not reject complete isolation for any pairwise comparison. Furthermore, species tree reconstructions revealed that phylogenetic relationships were sensitive to stochastic sampling of individuals likely due to incomplete lineage sorting or hybridization. I conclude that members of the NW Mallard group appear to be adaptive incipient morphs, and that future work should focus on genomic regions under selection to better understand the stage and process of speciation in this group. In Chapter 3, I use restriction site associated DNA (RAD) sequencing methods to generate a pseudorandom sampling of 3,563 autosomal and 172 sex-linked (Z chromosome) markers scattered across the genome to more rigorously test the mechanism of speciation between Mexican ducks (N = 105 individuals from six Mexican states and two US states) and mallards (N = 17). Specifically, I aim to determine the stage of speciation and whether speciation has been driven by few loci with large effects versus many loci with small effects, plumage associated differentiation, or genetic drift. Marker comparisons between mallards and Mexican ducks revealed strong discordance among autosomal ΦST = 0.014), sex-linked (mean ΦST = 0.091), and mtDNA (ΦST = 0.12) markers. In general, divergence at autosomal loci followed a stepping stone model, with a gradual transition in genotypic frequencies from North to South

Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini)

Insight into complex evolutionary histories continues to build through broad comparative phylogenomic and population genomic studies. In particular, there is a need to understand the extent and scale that gene flow contributes to standing genomic diversity and the role introgression has played in evolutionary processes such as hybrid speciation. Here, we investigate the evolutionary history of the Mergini tribe (sea ducks) by coupling multi-species comparisons with phylogenomic analyses of thousands of nuclear ddRAD-seq loci, including Z-sex chromosome and autosomal linked loci, and the mitogenome assayed across all extant sea duck species in North America. All sea duck species are strongly structured across all sampled marker types (pair-wise species ΦST \u3e 0.2), with clear genetic assignments of individuals to their respective species, and phylogenetic relationships recapitulate known relationships. Despite strong species integrity, we identify at least 18 putative hybrids; with all but one being late generational backcrosses. Most interesting, we provide the first evidence that an ancestral gene flow event between long-tailed ducks (Clangula hyemalis) and true Eiders (Somateria spp.) not only moved genetic material into the former species, but likely generated a novel species — the Steller’s eider (Polysticta stelleri) — via hybrid speciation. Despite generally low contemporary levels of gene flow, we conclude that hybridization has and continues to be an important process that shifts novel genetic variation between species within the tribe Mergini. Finally, we outline methods that permit researchers to contrast genomic patterns of contemporary versus ancestral gene flow when attempting to reconstruct potentially complex evolutionary histories

New Primers Reveal the Presence of a Duplicate Histone H3 in the Marine Turtle Leech Ozobranchus branchiatus

Marine leeches, specific to sea turtles, have been implicated as potential vector organisms in the spread of fibropapillomatosis (FP), a pandemic neoplastic disease with green turtles (Chelonia mydas) having the highest affliction rate. Polymerase chain reaction identified two independent, seemingly functional histone H3 loci for marine turtle leeches Ozobranchus branchiatus collected from C. mydas in Florida and Hawaii. Primers were developed to amplify each product separately. These novel markers will be useful in identifying ectoparasites in FP research, evaluating other histone variants, and chromatin dynamics regulation studies. This poster was created and presented by Triet M. Truong at the Wright State University Chemistry Department posters in the hall event on June 1, 2012 and the results were published in Conservation Genetics Resources (2012), 4, 487-490

Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum0

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stunz, E., Fetcher, N., Lavretsky, P., Mohl, J., Tang, J., & Moody, M. Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum. Frontiers in Plant Science, 13, (2022): 860439, https://doi.org/10.3389/fpls.2022.860439.Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth’s land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass (Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum, including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum, which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity.This research was made possible by funding provided by NSF/PLR-1417645 to MM. The Botanical Society of America Graduate Student Research Award and the Dodson Research Grant from the Graduate School of the University of Texas at El Paso provided assistance to ES. The grant 5U54MD007592 from the National Institute on Minority Health and Health Disparities (NIMHD), a component of the National Institutes of Health (NIH) provided bioinformatics resources and support of JM

Consistent changes in muscle metabolism underlie dive performance across multiple lineages of diving ducks

Diving animals must sustain high activity with limited O₂ stores to successfully capture prey. Studies suggest that increasing body O₂ stores supports breath-hold diving, but less is known about metabolic specializations that underlie underwater locomotion. We measured maximal activities of 10 key enzymes in locomotory muscles (gastrocnemius and pectoralis) to identify biochemical changes associated with diving in pathways of oxidative and substrate-level phosphorylation and compared them across three groups of ducks—the longest diving sea ducks (eight spp.), the mid-tier diving pochards (three spp.) and the non-diving dabblers (five spp.). Relative to dabblers, both diving groups had increased activities of succinate dehydrogenase and cytochrome c oxidase, and sea ducks further showed increases in citrate synthase (CS) and hydroxyacyl-CoA dehydrogenase (HOAD). Both diving groups had relative decreases in capacity for anaerobic metabolism (lower ratio of lactate dehydrogenase to CS), with sea ducks also showing a greater capacity for oxidative phosphorylation and lipid oxidation (lower ratio of pyruvate kinase to CS, higher ratio of HOAD to hexokinase). These data suggest that the locomotory muscles of diving ducks are specialized for sustaining high rates of aerobic metabolism, emphasizing the importance of body O₂ stores for dive performance in these species

simRestore:A decision‐making tool for adaptive management of the native genetic status of wild populations

Anthropogenic hybridization, or higher and non-natural rates of gene flow directly and indirectly induced by human activities, is considered a significant threat to biodiversity. The primary concern for conservation is the potential for genomic extinction and loss of adaptiveness for native species due to the extensive introgression of non-native genes. To alleviate or reverse trends for such scenarios requires the direct integration of genomic data within a model framework for effective management. Towards this end, we developed the simRestore R program as a decision-making tool that integrates ecological and genomic information to simulate ancestry outcomes from optimized conservation strategies. In short, the program optimizes supplementation and removal strategies across generations until a set native genetic threshold is reached within the studied population. Importantly, in addition to helping with initial decision-making, simulations can be updated with the outcomes of ongoing efforts, allowing for the adaptive management of populations. After demonstrating functionality, we apply and optimize among actionable management strategies for the endangered Hawaiian duck for which the current primary threat is genetic extinction through ongoing anthropogenic hybridization with feral mallards. Simulations demonstrate that supplemental and removal efforts can be strategically tailored to move the genetic ancestry of Hawaii's hybrid populations towards Hawaiian duck without the need to completely start over. Further, we discuss ecological parameter sensitivity, including which factors are most important to ensure genetic outcomes (i.e. number of offspring). Finally, to facilitate use, the program is also available online as a Shiny Web application

FASTA, ADMIXTURE/SIMULATIONS, PCA, HAPLOTYPE BLOCK/ANCESTRY_HHM INPUT FILES

(1) Individual and concatenated fasta files for 3,037 Autosomal and 163 Z linked markers identified using ddRAD-seq protocols for 290 Mallards, American black ducks, and hybrids. Concatenated fasta files are provided by chromosome, as well as a fasta file with mitochondrial sequences. (2) Run-ready ped/map input files of 163 Z-linked and 3,037 autosomal ddRAD-seq markers for PCA and ADMIXTURE analyses for 290 Mallards, American black ducks, and hybrids. Additionally, simulation code and run-ready ped/map ADMIXTURE files are provided. (3) Run-ready input files for BAYESCAN are provided. (4) Simulation code and steps to take for haplotype block and ANCESTRY_HHM analyses

simRestore:A decision‐making tool for adaptive management of the native genetic status of wild populations

Anthropogenic hybridization, or higher and non-natural rates of gene flow directly and indirectly induced by human activities, is considered a significant threat to biodiversity. The primary concern for conservation is the potential for genomic extinction and loss of adaptiveness for native species due to the extensive introgression of non-native genes. To alleviate or reverse trends for such scenarios requires the direct integration of genomic data within a model framework for effective management. Towards this end, we developed the simRestore R program as a decision-making tool that integrates ecological and genomic information to simulate ancestry outcomes from optimized conservation strategies. In short, the program optimizes supplementation and removal strategies across generations until a set native genetic threshold is reached within the studied population. Importantly, in addition to helping with initial decision-making, simulations can be updated with the outcomes of ongoing efforts, allowing for the adaptive management of populations. After demonstrating functionality, we apply and optimize among actionable management strategies for the endangered Hawaiian duck for which the current primary threat is genetic extinction through ongoing anthropogenic hybridization with feral mallards. Simulations demonstrate that supplemental and removal efforts can be strategically tailored to move the genetic ancestry of Hawaii's hybrid populations towards Hawaiian duck without the need to completely start over. Further, we discuss ecological parameter sensitivity, including which factors are most important to ensure genetic outcomes (i.e. number of offspring). Finally, to facilitate use, the program is also available online as a Shiny Web application

simRestore:A decision‐making tool for adaptive management of the native genetic status of wild populations

Anthropogenic hybridization, or higher and non-natural rates of gene flow directly and indirectly induced by human activities, is considered a significant threat to biodiversity. The primary concern for conservation is the potential for genomic extinction and loss of adaptiveness for native species due to the extensive introgression of non-native genes. To alleviate or reverse trends for such scenarios requires the direct integration of genomic data within a model framework for effective management. Towards this end, we developed the simRestore R program as a decision-making tool that integrates ecological and genomic information to simulate ancestry outcomes from optimized conservation strategies. In short, the program optimizes supplementation and removal strategies across generations until a set native genetic threshold is reached within the studied population. Importantly, in addition to helping with initial decision-making, simulations can be updated with the outcomes of ongoing efforts, allowing for the adaptive management of populations. After demonstrating functionality, we apply and optimize among actionable management strategies for the endangered Hawaiian duck for which the current primary threat is genetic extinction through ongoing anthropogenic hybridization with feral mallards. Simulations demonstrate that supplemental and removal efforts can be strategically tailored to move the genetic ancestry of Hawaii's hybrid populations towards Hawaiian duck without the need to completely start over. Further, we discuss ecological parameter sensitivity, including which factors are most important to ensure genetic outcomes (i.e. number of offspring). Finally, to facilitate use, the program is also available online as a Shiny Web application

simRestore:A decision‐making tool for adaptive management of the native genetic status of wild populations

Anthropogenic hybridization, or higher and non-natural rates of gene flow directly and indirectly induced by human activities, is considered a significant threat to biodiversity. The primary concern for conservation is the potential for genomic extinction and loss of adaptiveness for native species due to the extensive introgression of non-native genes. To alleviate or reverse trends for such scenarios requires the direct integration of genomic data within a model framework for effective management. Towards this end, we developed the simRestore R program as a decision-making tool that integrates ecological and genomic information to simulate ancestry outcomes from optimized conservation strategies. In short, the program optimizes supplementation and removal strategies across generations until a set native genetic threshold is reached within the studied population. Importantly, in addition to helping with initial decision-making, simulations can be updated with the outcomes of ongoing efforts, allowing for the adaptive management of populations. After demonstrating functionality, we apply and optimize among actionable management strategies for the endangered Hawaiian duck for which the current primary threat is genetic extinction through ongoing anthropogenic hybridization with feral mallards. Simulations demonstrate that supplemental and removal efforts can be strategically tailored to move the genetic ancestry of Hawaii's hybrid populations towards Hawaiian duck without the need to completely start over. Further, we discuss ecological parameter sensitivity, including which factors are most important to ensure genetic outcomes (i.e. number of offspring). Finally, to facilitate use, the program is also available online as a Shiny Web application