Journal Articles
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Item Comparative analysis of plastid genomes from allopolyploid Tragopogon miscellus and its diploid parents(John Wiley and Sons Ltd on behalf of German Society for Plant Sciences, Royal Botanical Society of the Netherlands, 2025-09-15) Mukhtar U; Newmarch SC; Winkworth RC; Soltis PS; Soltis DE; Tate JA; Wang X-QTragopogon is a model system for the study of recent, recurrent, and reciprocal allopolyploid formation. Recent research has focused on the fates of nuclear genes duplicated in the allopolyploid T. miscellus relative to the parental diploids, T. dubius and T. pratensis. In contrast, little attention has been given to organellar genomes, which interact with the duplicated nuclear genomes via their gene products. Here we reconstructed plastid genomes (plastomes) for representatives of these three species to investigate their structure and variability among natural and synthetic allopolyploids. Genomic libraries were Illumina-sequenced for several individuals of the allopolyploid T. miscellus and its diploid parents. Whole plastomes were assembled from skimmed data with comparative analyses used to quantify structural and nucleotide variation. Tragopogon plastomes have a typical quadripartite structure and are similar in size to those of other Asteraceae. The 12 plastomes were highly similar, sharing ~99.5%–100% identity. In all but one case, the plastome sequence for each of the polyploids was most similar to that of its expected maternal parent. The exception involved a polyploid that unexpectedly had a T. dubius plastome type, likely as the result of backcrossing with its presumed paternal parent. Such backcrossing events may have contributed to the demise of this polyploid population. Plastome sequences can be used to infer the maternal origins of polyploids as well as investigate ongoing population-level dynamics. More fully assessing plastome variation across the geographic distribution of polyploids and their diploid progenitors may provide additional insights into polyploid formation, population dynamics, and subsequent evolution.Item Admixture Increases Genetic Diversity and Adaptive Potential in Australasian Killer Whales(John Wiley and Sons Ltd, 2025-02-28) Reeves IM; Totterdell JA; Sandoval-Castillo J; Betty EL; Stockin KA; Oliphant Stewart R; Johnstone M; Foote AD; Kardos MAdmixture is the exchange of genetic variation between differentiated demes, resulting in ancestry within a population coalescing in multiple ancestral source populations. Low-latitude killer whales (Orcinus orca) populations typically have higher genetic diversity than those in more densely populated, high productivity and high-latitude regions. This has been hypothesized to be due to episodic admixture between populations with distinct genetic backgrounds. We test this hypothesis by estimating variation in local ancestry of whole genome sequences from three genetically differentiated, low-latitude killer whale populations and comparing them to global genetic variation. We find 'Antarctic-like' ancestry tracts in the genomes of southwestern Australia (SWA) population including recent (within the last 2-4 generations) admixture. Admixed individuals had, on average, shorter and fewer runs of homozygosity than unadmixed individuals and increased effective population size (Ne). Thus, connectivity between demes results in the maintenance of Ne of relatively small demes at a level comparable to the sum of Ne across demes. A subset of the admixed regions was inferred to be evolving under selection in the SWA population, suggesting that this admixed variation may be contributing to the population's adaptive potential. This study provides important and rare empirical evidence that small populations can maintain genetic diversity due to sporadic admixture between different genetic backgrounds and that admixed ancestry can promote the long-term stability of Ne.Item Genome Evolution and Introgression in the New Zealand mud Snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa(Oxford University Press on behalf of Society for Molecular Biology and Evolution, 2024-05-22) Fields PD; Jalinsky JR; Bankers L; McElroy KE; Sharbrough J; Higgins C; Morgan-Richards M; Boore JL; Neiman M; Logsdon JMWe have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species Potamopyrgus antipodarum-a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness-and thus provide key evolutionary context for understanding its unusual biology. The P. estuarinus and P. kaitunuparaoa genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of P. antipodarum-a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that P. kaitunuparaoa is likely the closest relative to P. antipodarum. We nevertheless show that there has been considerable introgression between P. estuarinus and P. kaitunuparaoa. That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between P. estuarinus and P. kaitunuparaoa. Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of nonintrogression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species.