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1. Ordinal level phylogenomics of Odonata based on anchored hybrid enrichment

   Newton, Lacie G ; Abbott, John C ; Bybee, Seth M ; Frandsen, Paul B ; Goodman, Aaron ; Guralnick, Robert ; Kalkman, Vincent J ; Lontchi, Judicael F ; Lupiyanigdyah, Pungki ; Sanchez-Herrera, Melissa ; et al ( June 2023 , ICO 2023 program)

   Sparrow, David (Ed.)

   Odonata comprise approximately 6400 species with extensive morphological and ecological diversity, specifically their colour variation, flight behaviour patterns, and breadth of ecological niches. Additionally, their phylogenetic placement within Insecta as descendants of the first winged insects make them ideal candidates for exploring evolutionary forces that have shaped diversity patterns (e.g., diversification rate shifts) as well as character evolution (e.g., flight behaviour, colour). Even though morphological and ecological traits are relatively well known for most of odonate taxa, the lack of well-supported phylogenetic hypothesis across Odonata have limited the capability of evaluating evolutionary phenomena in a comparative context. Previous studies using various taxon sampling schemes and data types (i.e. morphology, targeted locus approaches) to reconstruct odonate relationships failed to resolve several interfamilial relationships, specifically in groups with likely incomplete lineage sorting and/or introgression. Even though a recent study by Bybee et al. (2021) incorporated genomic-scale anchored hybrid enrichment (AHE) data for phylogenetic reconstruction, the relatively limited taxon sampling likely precluded resolution within the problematic groups. Our study, also targeting AHE loci, greatly expand taxon odonate genera, which resulted in 729 newly generated samples in a addition to 142 samples from Bybee et al. (2021) for a total of 831. With around 500 AHE loci, we aim to resolve historically difficult relationships and construct a robust ordinal phylogeny of Odonata, which will be used as the evolutionary framework to clarify taxonomic classifications and test evolutionary hypotheses regarding shifts in flight behaviours, colours, and diversification rates. 

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2. A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae

   https://doi.org/10.1002/aps3.11554  

   Ball, Laymon D ; Bedoya, Ana M ; Taylor, Charlotte M ; Lagomarsino, Laura P ( November 2023 , Applications in Plant Sciences)

   Rubiaceae is among the most species‐rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large‐scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single‐copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae‐specific probe set that allows for comparable phylogenetic inference across clades is lacking.

   Here, we use publicly accessible genomic resources to identify putatively single‐copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent‐aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae.

   We recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance.

   Our probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.

    

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3. Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

   https://doi.org/10.1093/molbev/msz263  

   Karin, Benjamin R ; Gamble, Tony ; Jackman, Todd R ; Vidal, Nicolas ( November 2019 , Molecular Biology and Evolution)

   Abstract Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups. 

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4. A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility: From order to species

   https://doi.org/10.1111/1755-0998.13555  

   Bangs, Max R. ; Steppan, Scott J. ( December 2021 , Molecular Ecology Resources)

   Rodents are the largest order of mammals and contain several model organisms important to scientific research in a variety of fields, yet no large set of genomic markers have been designed for this group to date, hindering evolutionary studies into relationships of the group as a whole. Here we present a genomic probe set designed and optimized for rodents with a protocol that is easy to replicate with little laboratory investment. This design utilizes an anchored hybrid enrichment approach specifically targeting rodents to generate longer loci with a higher substitution rate than existing vertebrate probes to provide utility at various taxonomic levels. Using a test set of rodents from all five suborders, we successfully obtained alignments for 416 of the 418 target loci with an average of 1379 bp per locus and a total alignment of more than half a million base pairs. This genomic data set performed well in all phylogenetic analyses, especially in recent phylogenetic splits, with ample parsimony‐informative sites within genera and even within species, showing more than four times as many single nucleotide polymorphisms per locus than a recent vertebrate ultraconserved elements study. Additional support is provided in resolving deeper clades in Rodentia. By providing this probe design, we hope that more laboratories can easily generate data for answering questions in rodents from species delimitation to understanding relationships among families in rapid radiations.

    

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5. An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

   https://doi.org/10.1002/aps3.11295  

   Jones, Katy E. ; Fér, Tomáš ; Schmickl, Roswitha E. ; Dikow, Rebecca B. ; Funk, Vicki A. ; Herrando‐Moraira, Sonia ; Johnston, Paul R. ; Kilian, Norbert ; Siniscalchi, Carolina M. ; Susanna, Alfonso ; et al ( October 2019 , Applications in Plant Sciences)

   Hybrid capture with high‐throughput sequencing (Hyb‐Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family‐specific Hyb‐Seq probe set and the outcomes of different phylogenetic analyses are investigated here.

   Hyb‐Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non‐paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae.

   Alignments of the Asteraceae family‐wide Hyb‐Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches.

   The approach used to build a Hyb‐Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb‐Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage‐specific.

    

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