More Like this

1. To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

   https://doi.org/10.1093/isd/ixad014  

   Gustafson, Grey T; Glynn, Rachel D; Short, Andrew E; Tarasov, Sergei; Gunter, Nicole L (July 2023, Insect Systematics and Diversity)

   Marvaldi, Adriana (Ed.)

   Abstract Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference or whether tailored probe design will be desirable. Here we investigate the utility of 8 different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (i) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (ii) breadth of phylogenetic inference probe set was designed for, and (iii) method of probe design. As part of this study, 2 new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We confirm that probe set utility decreases with increasing phylogenetic distance from target taxa. In addition, narrowing the phylogenetic breadth of probe design decreases the phylogenetic capture range. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design. 

   more » « less
2. Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective

   https://doi.org/10.1093/sysbio/syaa054  

   Singhal, Sonal; Colston, Timothy J; Grundler, Maggie R; Smith, Stephen A; Costa, Gabriel C; Colli, Guarino R; Moritz, Craig; Pyron, R Alexander; Rabosky, Daniel L (August 2020, Systematic Biology)

   Ruane, Sara (Ed.)

   Abstract Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).] 

   more » « less
3. Comparison between p‐distance and single‐locus species delimitation models for delineating reproductively tested strains of pennate diatoms (Bacillariophyceae) using cox 1, rbcL and ITS

   https://doi.org/10.1111/jeu.12986  

   Franco, Andréa de; Ashworth, Matt P.; Odebrecht, Clarisse (September 2023, Journal of Eukaryotic Microbiology)

   Abstract Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single‐locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partialcox1,rbcL,5.8S + ITS2,ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species ofEunotia,Seminavis, Nitzschia, SellaphoraandPseudo‐nitzschiacorresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences. 

   more » « less
4. 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. 

   more » « less
5. A comparison of phylogenomic inference pipelines for low‐coverage whole‐genome sequencing in Formica ants

   https://doi.org/10.1111/syen.12670  

   Zhang, Junxia; Lin, Long; Mu, Yannan; Brelsford, Alan; Purcell, Jessica (January 2025, Systematic Entomology)

   Blaimer, Bonnie (Ed.)

   Abstract A rapid proliferation in the availability of whole genome sequences (WGS), often with relatively low read depth, offers an unprecedented opportunity for phylogenomic advances using publicly available data, but there are several key challenges in applying these data. Using low‐coverage WGS data for the ant species ofFormica, we conducted detailed comparisons on two different analytical pipelines (reference‐based vs. de novo genome assembly), four types of datasets (5‐kbp‐window, ultra‐conserved element [UCE], single‐copy ortholog [BUSCO] and mitogenome), and a series of analytical procedures (e.g. concatenation vs. coalescent analyses) to identify which are robust to typical WGS data. The results show that at a shallow scale of phylogenetic relationships of closely related species 5‐kbp‐windows from the reference‐based pipeline and UCEs from the de novo assemblies are more successful than the BUSCOs in recovering informative markers for phylogenetic inference. Compared with concatenation analyses, coalescent analyses often resulted in disparate deeper relationships in the phylogeny. This study also uncovers evident mito‐nuclear discordance and demonstrates genome‐wide gene conflicts in phylogenetic signals, both pointing to possible incomplete lineage sorting and/or hybridization during the early, rapid radiation ofFormicaants. Divergence dating analyses show that different types of data and analytical methods could result in inconsistent time estimates, highlighting the potential need for multiple approaches to better understand species divergence. The strengths and weaknesses of different analytical pipelines and strategies are discussed. Findings from this study provide valuable insights for large‐scale phylogenomic projects using WGS data. 

   more » « less