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Browsing by Author "Barrett, Craig F."

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    Ancient Polyploidy and Genome Evolution in Palms
    (Oxford University Press, 2019) Barrett, Craig F.; McKain, Michael R.; Sinn, Brandon T.; Ge, Xue-Jun; Zhang, Yuqu; Antonelli, Alexandre; Bacon, Christine D.; West Virginia University; University of Alabama Tuscaloosa; Chinese Academy of Sciences; South China Botanical Garden, CAS; University of Gothenburg; Royal Botanic Gardens, Kew
    Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
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    Digitized collections elucidate invasion history and patterns of awn polymorphism in Microstegium vimineum
    (Wiley, 2022) Barrett, Craig F.; Huebner, Cynthia D.; Bender, Zoe A.; Budinsky, Trezalka A.; Corbett, Cameron W.; Latvis, Maribeth; McKain, Michael R.; Motley, M'Kayla; Skibicki, Samuel V.; Thixton, Hana L.; Santee, Mathilda V.; Cumberledge, Aubrey N.; West Virginia University; United States Department of Agriculture (USDA); United States Forest Service; Gettysburg College; University of Pittsburgh; South Dakota State University; University of Alabama Tuscaloosa
    Premise Digitized collections can help illuminate the mechanisms behind the establishment and spread of invasive plants. These databases provide a record of traits in space and time that allows for investigation of abiotic and biotic factors that influence invasive species. Methods Over 1100 digitized herbarium records were examined to investigate the invasion history and trait variation of Microstegium vimineum. Presence-absence of awns was investigated to quantify geographic patterns of this polymorphic trait, which serves several functions in grasses, including diaspore burial and dispersal to germination sites. Floret traits were further quantified, and genomic analyses of contemporary samples were conducted to investigate the history of M. vimineum's introduction and spread into North America. Results Herbarium records revealed similar patterns of awn polymorphism in native and invaded ranges of M. vimineum, with awned forms predominating at higher latitudes and awnless forms at lower latitudes. Herbarium records and genomic data suggested initial introduction and spread of the awnless form in the southeastern United States, followed by a putative secondary invasion and spread of the awned form from eastern Pennsylvania. Awned forms have longer florets, and floret size varies significantly with latitude. There is evidence of a transition zone with short-awned specimens at mid-latitudes. Genomic analyses revealed two distinct clusters corresponding to awnless and awned forms, with evidence of admixture. Conclusions Our results demonstrate the power of herbarium data to elucidate the invasion history of a problematic weed in North America and, together with genomic data, reveal a possible key trait in introduction success: presence or absence of an awn.
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    Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes
    (Frontiers, 2022) Timilsena, Prakash Raj; Wafula, Eric K.; Barrett, Craig F.; Ayyampalayam, Saravanaraj; McNeal, Joel R.; Rentsch, Jeremy D.; McKain, Michael R.; Heyduk, Karolina; Harkess, Alex; Villegente, Matthieu; Conran, John G.; Illing, Nicola; Fogliani, Bruno; Ane, Cecile; Pires, J. Chris; Davis, Jerrold, I; Zomlefer, Wendy B.; Stevenson, Dennis W.; Graham, Sean W.; Givnish, Thomas J.; Leebens-Mack, James; DePamphilis, Claude W.; Pennsylvania State University; Pennsylvania State University - University Park; West Virginia University; University of Georgia; Kennesaw State University; University of Alabama Tuscaloosa; University of Hawaii Manoa; HudsonAlpha Institute for Biotechnology; Universite Nouvelle Caledonie; University of Adelaide; University of Cape Town; University of Wisconsin Madison; University of Missouri Columbia; Cornell University; University of British Columbia; New York Botanical Garden; Virginia Polytechnic Institute & State University
    We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.