Abstract Detail

Phylogenomics

Webb, Campbell O [1], Burleigh, J Gordon [2], Ickert-Bond, Steffi [3].

Phylogenomics of willow (Salix L.) species in Alaska.

In order to discover the evolutionary relationships among Alaskan willow species and to contribute to the understanding of higher-level classification of Salix, we conducted a phylogenomic analysis of 122 willow individuals from 43 taxa sampled from herbarium specimens at ALA (University of Alaska Museum of the North). Almost all specimens had been annotated by George Argus. A small amount of leaf material from each herbarium sheet was processed at the University of Florida, and sequenced using target-enrichment methods and the GoFlag angiosperm 408 probe set, which covers the same set of conserved exons as the GoFlag 408 flagellate land plant probe set described in Breinholt et al. (2021, doi:10.1002/aps3.11406). Samples were sequenced on an Illumina HiSeq 3000 and contigs were assembled by iterative bait assembly using Bridger (Chang et al. 2015; doi:10.1186/s13059-015-0596-2). We will report results based on the full sequences (probe target plus flanking regions), although similar results were produced using only target regions. An average of 1.09 haplotypes were recovered for each locus across all samples and loci. However in subsequent analyses we conservatively dropped any locus for each sample for which variants had been found for that sample. Phylogenetic analysis was performed using i) maximum likelihood in IQTree2 (Nguyen et al. 2015; doi:10.1093/molbev/msu300) on a concatenated, partitioned supermatrix, with bootstrapping, and ii) maximum likelihood in IQTree2 to generate locus-specific phylogenies, for which a consensus was then produced with Astral (Mirarab et al. 2015; doi:10.1093/bioinformatics/btv234). Gene and Site Concordance Factors were then calculated for the best tree from each method using IQTree2. The resulting phylogenies from these two approaches did not differ significantly. Bootstrap values and posterior probabilities of nearly 100% supported clades of individuals identified to the same species in all cases except for a clade of mixed individuals of S. glauca, S. arctica, S. polaris, S. rotundifolia, and S. sphenophylla. The resulting phylogenies support the emerging molecular phylogeny-based classification of Salix, with two subgenera, Salix and Vertix Dumort. Differences in the arrangement of clades in this study and the section-level classification of Argus (1997; doi:10.2307/25096638) will be discussed, as will the alignment of morphological character states to these clades.

1 - University of Alaska Fairbanks, Museum of the North, Fairbanks, AK, 99775, USA
2 - University of Florida, Department of Biology, Gainesville, FL, 32611, USA
3 - University of Alaska Fairbanks, Herbarium (ALA) and Dept of Biology and Wildlife, Fairbanks, AK, 99775, USA

Keywords:
Salix L.
willow
molecular phylogenetics
Classification 
GoFlag 408.

Presentation Type: Poster
Number: PPL008
Abstract ID:510
Candidate for Awards:None