Travers, S. L. | bioRxiv Science

bioRxiv2019

FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Despite the increasing use of high-throughput sequencing in phylogenetics, many phylogenetic relationships remain difficult to resolve because of conflict between gene trees and species trees. Selection of different types of markers (i.e. protein-coding exons, non-coding introns, ultra-conserved elements) is becoming important to alleviate these phylogenomic challenges. For evolutionary studies in frogs, we introduce the new publicly available FrogCap suite of genomic resources, which is a large and flexible collection of probes corresponding to [~]15,000 markers that unifies previous frog sequencing work. FrogCap is designed to be modular, such that subsets of markers can be selected based on the phylogenetic scale of the intended study. FrogCap uses a variety of molecular marker types that include newly obtained exons and introns, previously sequenced UCEs, and Sanger-sequencing markers, which span a range of alignment lengths (100-12,000 base pairs). We tested three probe sets from FrogCap using 105 samples across five phylogenetic scales, comparing probes designed using a consensus- or genome-based approach. We also tested the effects of using different bait kit sizes on depth of coverage and missing data. We found that larger bait kits did not result in lowered depth of coverage or increased missing data. We also found that sensitivity, specificity, and missing data are not related to genetic distance in the consensus-based probe design, suggesting that this approach has greater success and overcomes a major hurdle in probe design. We observed sequence capture success (in terms of missing data, quantity of sequence data, recovered marker length, and number of informative sites) and compared them at all phylogenetic scales. The incorporation of different molecular marker types allowed recovery of the variation required for resolving difficult phylogenetic relationships and for performing population genetic studies. Altogether, FrogCap is a valuable and adaptable resource for performing high-throughput sequencing projects across variable timescales.

genomics↗

bioRxiv2019

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread \"generalist\" clades. This is especially true in the Australasia, where the monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately \"derived\" parachute geckos of the genus Ptychozoon. Here we employ sequence capture targeting 5060 ultraconserved elements to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyzed multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods. Our sampling scheme was designed to address four persistent systematic questions in this group: (1) Are Luperosaurus and Ptychozoon monophyletic and are any of these named species truly nested within Gekko? (2) Are prior phylogenetic estimates of Sulawesis L. iskandari as sister to Melanesian G. vittatus supported by our genome-scale dataset? (3) Is the high elevation L. gulat of Palawan Island correctly placed within Gekko? (4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny? We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not related to Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our final, well-supported topologies, we recognize seven newly defined subgenera to accommodate [~]60 species within the more broadly defined and maximally-inclusive Australasian genus Gekko. The newly defined subgenera will aide taxonomists and systematists in species descriptions by allowing them to only diagnose putatively new species from the most relevant members of the same subgenus, not necessarily the phenotypically variable genus Gekko as a whole, and we argue that it appropriately recognizes geographically circumscribed units (e.g., a new subgenus for a novel clade, entirely endemic to the Philippines) while simultaneously recognizing several of the most systematically controversial, phenotypically distinct, and phylogenetically unique lineages. An added benefit of recognizing the most inclusive definition of Gekko, containing multiple phylogenetically-defined subgenera, is that this practice has the potential to alleviate taxonomic vandalism, if widely adopted, by creating formally available, supraspecific taxa, accompanied by character-based diagnoses and properly assigned type species, such that future, more atomized classifications would necessarily be required to adopt todays subgenera as tomorrows genera under the guidelines of The Code of Zoological Nomenclature. Not only does this simple practice effectively eliminate the nefarious motivation behind taxonomic vandalism, but it also ensures that supraspecific names are created only when accompanied by data, that they are coined with reference to a phylogenetic estimate, and that they explicitly involve appropriate specifiers in the form of type species and, ultimately, type specimens.

zoology↗