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Fig. 4 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 4. Measures of population structure and diversity of the Neotropical "ruber group." (A) ASTRAL_I tree constructed from 2,615 UCE gene trees—dots indicate posterior probability (red> 0.9, blue = 1). (B) Principal component analysis of SNP loci from the UCE sequences—inset in B illustrates the amount of variance explained by PCs 1 to 11. (C) Map of sample collection locations. (D) Neighbor-joining tree constructed from SNPs. Colors in B–D are the same for each individual and are based on the first 3 components of the principal component analysis.

Fig. 3 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 3. Measures of population structure and diversity of Neotropical "albescens group." (A) ASTRAL_I tree constructed from 2,615 UCE gene trees—dots indicate posterior probability (red> 0.9, blue = 1). (B) Principal component analysis of SNP loci from the UCE sequences—inset in B illustrates the amount of variance explained by PCs 1 to 11. (C) Map of sample collection locations. (D) Neighbor-joining tree constructed from SNPs. Colors in B–D are the same for each individual and are based on the first 3 components of the principal component analysis. Individuals indicated with colored symbols in A and D are individuals with discordant positions on the trees and are discussed further in the text.

Fig. 1 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 1. (A) Myotis ASTRAL_S species tree inferred from 2,615 UCE gene trees. Pie charts show the percentage of trees supporting each of 3 possible quartet topologies. All branches received posterior probabilities> 0.90. All others indicated with dots. Colored bars on the right of the tree show

Fig. 2 in Unraveling the Myotis morass: ultraconserved-element analysis reveals introgression, cryptic diversity, and taxonomic trouble

Fig. 2. Comparison of tree conflict by marker for 3 broad phylogeographic Myotis groups: (A) Nearctic group; (B) Neotropical "albescens group"; (C) Neotropical "ruber group." This is a subset of individuals shown in Fig. 1A. For each group, the left tree displays the ASTRAL_I UCE phylogeny while the right displays the maximum likelihood Cyt b phylogeny. The same individuals are shown in each tree pair. Lines between trees denote notable topological differences between markers. Colors for highlighting by species are an approximated average color for that species as determined by the first 3 components of the PCAs shown in Figs. 3–5.

opencc-zeroOct 2021View details →

Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: When data agree to disagree

Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different datasets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel dataset of ultraconserved elements (UCEs) and a recently published exon dataset of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of diversification and colonization of Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent datasets disagreed in areas with low phylogenetic signal that were overwhelmed by noise and non-phylogenetic signals. For UCEs, high levels of incomplete lineage sorting (ILS) seem to be a major cause of noise, whereas, for exons, non-phylogenetic signal may be caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.

opencc-zeroOct 2021View details →

A phylogenomic perspective on the evolutionary history of the stonefly genus Suwallia (Plecoptera: Chloroperlidae) revealed by ultraconserved genomic elements

Evolutionary biologists have long sought to disentangle phylogenetic relationships among taxa spanning the tree of life, an increasingly important task as anthropogenic influences have caused, and are expected to continue to cause, population declines and species extinctions, particularly in insects. Advances in DNA sequencing techniques have increasingly facilitated the ability of researchers to apply genomic methods to phylogenetic analyses, even for non-model organisms which have historically lacked the genomic resources to do so. Phylogenetic relationships within the stonefly genus Suwallia (Insecta: Plecoptera: Chloroperlidae) are poorly understood, and have never been assessed using molecular data. We used DNA sequence data from genome-wide ultraconserved element loci to generate the first molecular phylogeny for the group and assess its monophyly. Our results reveal that the monospecific chloroperlid Neaviperla forcipata renders Suwallia paraphyletic, and we recommend a taxonomic revision for its inclusion in Suwallia. We also found that Palearctic and Nearctic Suwallia do not form reciprocally monophyletic clades, and that a biogeographic history including dispersal, vicariance, and founder event speciation via jump dispersal best explains the geographic distribution of this group. Moreover, some Suwallia species (e.g., S. amoenacolens, S. kerzhneri, S. marginata, S. pallidula, and S. starki) exhibit pronounced cryptic diversity that is worthy of further investigation. These findings provide a first glimpse into the evolutionary history of Suwallia, improve our understanding of stonefly diversity, and highlight areas where additional research is needed.

opencc-zeroNov 2021View details →

A phylogeny of white-eyes based on ultraconserved elements

White-eyes are an iconic radiation of passerine birds that have been the subject of studies in evolutionary biology, biogeography, and speciation theory. Zosterops white-eyes in particular are thought to have radiated rapidly across continental and insular regions of the Afro- and Indo-Pacific tropics, yet, their phylogenetic history remains equivocal. Here, we sampled 77% of the genera and 47% of known white-eye species and sequenced thousands of ultraconserved elements to infer the phylogeny of the avian family Zosteropidae. We used concatenated maximum likelihood and species tree methods and found strong support for seven clades of white-eyes and three clades within the species-rich Zosterops radiation.

opencc-zeroMar 2022View details →

Evolutionary relationships of anglerfishes (Lophiiformes) reconstructed using ultraconserved elements

The macroevolutionary consequences of evolving in the deep-sea remain poorly understood and are compounded by the fact that convergent adaptations for living in this environment makes elucidating phylogenetic relationships difficult. Lophiiform anglerfishes exhibit extreme habitat and predatory specializations, including the use of a fin-spine system as a luring device and unique reproductive strategies where parasitic males attach and fuse to females. Despite their notoriety for these odd characteristics, evolutionary relationships among these fishes remain unclear. We sought to clarify the evolutionary history of Lophiiformes using data from 1,000 ultraconserved elements and phylogenomic inference methods with particular interest paid to the Ceratioidei (deep-sea anglerfishes) and Antennarioidei (frogfishes and handfishes). At the suborder level, we recovered similar topologies in separate phylogenomic analyses: The Lophioidei (monkfishes) are the sister group to the rest of the Lophiiformes, Ogcocephaloidei (batfishes) and Antennarioidei (frogfishes) form a sister group, and Chaunacioidei (coffinfishes) and Ceratioidei (deep-sea anglerfishes) form a clade. The relationships we recover within the ceratioids disagree with most previous phylogenetic investigations, which used legacy phylogenetic markers or morphology. We recovered non-monophyletic relationships in the Antennarioidei and proposed three new families based on molecular and morphological evidence: Histiophrynidae, Rhycheridae, and Tathicarpidae. Antennariidae was re-evaluated to include what was known as Antennariinae, but not Histiophryninae. Non-bifurcating signal in splits network analysis indicated reticulations among and within suborders, supporting the complicated history of the Lophiiformes previously found with morphological data. Although we resolve relationships within Antennarioidei, Ceratioidei relationships remain somewhat unclear without better taxonomic sampling.

opencc-zeroJun 2022View details →

Data from: Using ultraconserved elements to reconstruct the termite tree of life

The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting 50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of Cryptocercus, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted in silico between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: <a href="https://github.com/oist/TER-UCE-DB/">https://github.com/oist/TER-UCE-DB/</a>.

opennotspecifiedSep 2019View details →

Fig. 3 in Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

Fig. 3. Breakdown of the phylogenetic programs used by arthropod UCE-based publications (as of July 2019).

opennotspecifiedSep 2019View details →

Fig. 1 in Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

Fig. 1. Breakdown of the number of arthropod UCEs-based publications per year (as of July 2019) by taxonomic group and taxonomic hierarchy.

opencc-zeroJun 2018View details →

Supplementary material 1 from: Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M (2018) A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys 760: 1-36. https://doi.org/10.3897/zookeys.760.24937

Data Table. Taxon sample and UCE sequencing results : Explanation note: Samples highlighted in red were sequenced for Starrett et al. (2017).

opencc-zeroDec 2015View details →

Data from: High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements

Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27–43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 106 bp (Arachnothera, modern samples) to 1.98 × 106 bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering.

Fig. 5 in To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe

Fig. 5. Phylogenetic trees of Scarabaeidae generated using UCEs; node values indicate bootstrap support. A)The tree produced with the Scarab 3kv1 probe set. B) The topology produced with the Adephaga 2.9kv1 probe set.

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

Fig. 1. Phylogenetic relationships based on McKenna et al. (2019) among select Coleoptera taxa relevant to or included in UCE probe design. Color (online),

Fig. 3 in To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe

Fig. 3. UCE loci recovery during in silico testing plotted against different metrics: A) average genetic distance estimated based on common gene fragments used in phylogenetics; B) average genetic distance estimated using BUSCO genes; C) N50 assembly metrics; and D) BUSCO S values.

Fig. 2 in To design, or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe

Fig. 2. Schematical overview of the workflow for the present study.Workflow proceeds from left to right and top to bottom.The tablets correspond to the three broader segments of the study: genomic resource generation, probe design, and in silico testing; within tablet boundaries can be found associated taxon sets, data, experimentation, and results. Arrows indicate the flow of data, associated results, and the location results can ultimately be found. Color corresponds to membership within a taxon set or probe set.The red boxes around Hydro 2.7kv1 and Scarab 3kv1 denote final optimized, tailored probe set design tailored for Hydrophiloidea and Scarabaeidae based on the results of this study. Length of 75CM box corresponds to alignment length. Abbreviations used: NCBI, National Center for Biotechnology Information; 75CM, 75% complete matrix; AMAS, alignment manipulation and summary statistics (Borowiec 2016); R-F, Robinson– Foulds distance (Robinson and Foulds 1981).

publicDec 2023View details →

Ultraconserved element data from Integrating morphology with phylogenomics to describe four Siculo-Maltese endemic Temnothorax species (Hymenoptera, Formicidae)

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publicOct 2021View details →

Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: When data agree to disagree

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