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opencc-zeroSep 2021View details →

UCE alignments and phylogenetic trees

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a timeframe for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provide highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in BPP and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of northeastern Mexico, and erected a new genus to better reflect evolutionary history. In sum, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbor substantial unrecognized diversity.

publicJul 2021View details →

UCE phylogenomics, detection of a putative hybrid population, and one older mitogenomic node age of Batrachuperus salamanders

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publicApr 2016View details →

Data from: Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

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publicSep 2021View details →

UCE alignments and phylogenetic trees

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opencc-zeroAug 2020View details →

Genomic characterization and curation of UCEs improves species tree reconstruction: Supplementary Material S1

Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated 4 different sets of UCE markers by genomic category from 5 different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees) and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by 2 or more UCEs, corresponding to non-overlapping segments of a single gene. We considered these UCEs to be non-independent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging co-genic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all datasets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses.

opencc-zeroDec 2015View details →

Data from: Analysis of a rapid evolutionary radiation using ultraconserved elements (UCEs): Evidence for a bias in some multi-species coalescent methods

Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10–15 Ma. Relationships among gallopheasant genera have been difficult to establish. We used this rapid radiation to assess the performance of species tree methods, using ∼600 kilobases of DNA sequence data from ∼1500 UCEs. We also integrated information from traditional markers (nuclear intron data from 15 loci and three mitochondrial gene regions). Species tree methods exhibited troubling behavior. Two methods [Maximum Pseudolikelihood for Estimating Species Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to perform optimally when the set of input gene trees was limited to the most variable UCEs, though ASTRAL appeared to be more robust than MP-EST to input trees generated using less variable UCEs. In contrast, the rooted triplet consensus method implemented in Triplec performed better when the largest set of input gene trees was used. We also found that all three species tree methods exhibited a surprising degree of dependence on the program used to estimate input gene trees, suggesting that the details of likelihood calculations (e.g., numerical optimization) are important for loci with limited phylogenetic information. As an alternative to summary species tree methods we explored the performance of SuperMatrix Rooted Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences due to the multispecies coalescent. We found that SMRT-ML performed well for UCE data. Our results suggest that UCE data have excellent prospects for the resolution of difficult evolutionary radiations, though specific attention may need to be given to the details of the methods used to estimate species trees.

opencc-zeroDec 2012View details →

Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)

Ray-finned fishes constitute the dominant radiation of vertebrates with over 32,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within fishes, leaving much of the enormous potential of massively parallel sequencing technologies for resolving major radiations in ray-finned fishes unrealized. Here, we provide a genomic perspective on longstanding questions regarding the diversification of major groups of ray-finned fishes through targeted enrichment of ultraconserved nuclear DNA elements (UCEs) and their flanking sequence. Our workflow efficiently and economically generates data sets that are orders of magnitude larger than those produced by traditional approaches and is well-suited to working with museum specimens. Analysis of the UCE data set recovers a well-supported phylogeny at both shallow and deep time-scales that supports a monophyletic relationship between Amia and Lepisosteus (Holostei) and reveals elopomorphs and then osteoglossomorphs to be the earliest diverging teleost lineages. Our approach additionally reveals that sequence capture of UCE regions and their flanking sequence offers enormous potential for resolving phylogenetic relationships within ray-finned fishes.

Fig. 11 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 11. Holotype of Cryptopone gilvatumida (unique specimen identifier CASENT0631951).

Fig. 10 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 10. Holotype of Cryptopone gilvagrande (unique specimen identifier CASENT0614525).

opencc-zeroOct 2021View details →

UCE and Sanger sequenced data for phylogenetic analysis of jumping spiders (Baviini and Nungia, Salticidae)

The systematics and taxonomy of the tropical Asian jumping spiders of the tribe Baviini is reviewed, with a molecular phylogenetic study (UCE sequence capture, traditional Sanger sequencing) guiding a reclassification of the group's genera. The well-studied members of the group are placed into six genera: Bavia Simon, 1877, Indopadilla Caleb & Sankaran, 2019, Padillothorax Simon, 1901, Piranthus Thorell, 1895, Stagetillus Simon, 1885, and one new genus, Maripanthus Maddison. The identity of Padillothorax is clarified, and Bavirecta Kanesharatnam & Benjamin, 2018 synonymized with it. Hyctiota Strand, 1911 is synonymized with Stagetillus. The molecular phylogeny divides the baviines into three clades, the Piranthus clade with a long embolus (Piranthus, Maripanthus), the genus Padillothorax with a flat body and short embolus, and the Bavia clade with a higher body and (usually) short embolus (remaining genera). In general, morphological synapomorphies support or extend the molecularly-delimited groups. Eighteen new species are described (all with taxonomic authority W. Maddison): Bavia nessagyna, Indopadilla bamilin, I. kodagura, I. nesinor, I. redunca, I. redynis, I. sabivia, I. vimedaba, Maripanthus draconis (type species of Maripanthus), M. jubatus, M. reinholdae, Padillothorax badut, P. mulu, Piranthus api, P. bakau, P. kohi, P. mandai, and Stagetillus irri. The distinctions between baviines and the astioid Nungia Żabka, 1985 are reviewed, leading to four species being moved into Nungia from Bavia and other genera. Fifteen new combinations are established, and one combination is restored. Five of these new or restored combinations correct previous errors of placing species in genera that have superficially similar palps but extremely different body forms, in fact belonging in distantly related tribes — emphasizing that the general shape of male palps should be used with caution in determining relationships. A little-studied genus, Padillothorus Prószyński, 2018, is tentatively assigned to the Baviini. Ligdus Thorell, 1895 is assigned to the Ballini.

opencc-zeroDec 2019View details →

Integrating UCE phylogenomics with traditional taxonomy reveals a trove of New World Syscia species (Formicidae, Dorylinae)

The ant genus Syscia is part of the cryptic ant fauna inhabiting leaf litter and rotten wood in the Asian and American tropics. It is a distinct clade within the Dorylinae, the subfamily from which army ants arose. Prior to this work the genus comprised seven species, each known from a single or very few collections. Extensive collecting in Middle America revealed an unexpected and challenging diversity of morphological forms. Locally distinct forms could be identified at many sites but assignment of specimens to species spanning multiple sites was problematic. To improve species delimitation, Ultra-Conserved Element (UCE) phylogenomic data were sequenced for all forms, both within and among sites, and a phylogeny was inferred. Informed by phylogeny, species delimitation was based on monophyly, absence of within-clade sympatry, and a subjective degree of morphological uniformity. UCE phylogenomic results for 130 specimens were complemented by analysis of mitochondrial COI (DNA barcode) data for an expanded taxon set. The resulting taxonomy augments the number of known species in the New World from 3 to 57. We describe and name 31 new species, and 23 species are assigned morphospecies codes pending improved specimen coverage. Queens may be fully alate or brachypterous, and there is a wide variety of intercaste female forms. Identification based on morphology alone is very difficult due to continuous character variation and high similarity of phylogenetically distant species. An identification aid is provided in the form of a set of distribution maps and standard views, with species ordered by size.

Fig. 11 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 11. Holotype of Cryptopone gilvatumida (unique specimen identifier CASENT0631951).

Fig. 10 in UCE Phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) Elucidates Genus Boundaries, Species Boundaries, and the Vicariant History of a

Fig. 10. Holotype of Cryptopone gilvagrande (unique specimen identifier CASENT0614525).

opencc-zeroJul 2019View details →

Data from: Ultraconserved element (UCE) probe set design: base genome and initial design parameters critical for optimization

Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using Phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open‐source UCE probe set for beetles of the suborder Adephaga.

opennotspecifiedMar 2021View details →

Fig. 5 in Integrating UCE Phylogenomics With Traditional Taxonomy Reveals a Trove of New World Syscia Species (Formicidae: Dorylinae)

Fig. 5. Mesosomal structure of fully alate (A) vs. brachypterous (B) queen.

opencc-by-4.0May 2023View details →

Madrepora_UCE_alignment

UCEs alignment for Madrepora

publicJul 2019View details →

Data from: Ultraconserved element (UCE) probe set design: base genome and initial design parameters critical for optimization

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