Session 50: Herpetology Systematics & Biogeography IRoom: Room 206D2022-07-31 13:30 - 14:45 |
| Moderator: Todd Jackman |
|
1. 13:30 Cost-effective Long Amplicon Sequencing of Hundreds of Full Mitochondrial Genomes Reveals an Incredible Radiation of Sulawesi Skinks (Sphenomorphus and Tytthoscincus). Benjamin Karin*, Museum of Vertebrate Zoology and Department of Integrative Biology, University of California; Jimmy McGuire, Museum of Vertebrate Zoology and Department of Integrative Biology, University of California benkarin@berkeley.edu
Mitochondrial DNA has long been used to study biodiversity as it evolves rapidly and contains abundant phylogenetic signal, though most researchers only sequence one gene at a time due to the constraints of Sanger and Illumina sequencing. We developed a protocol to sequence hundreds of whole mitochondrial genomes in parallel at low-cost using long-read sequencing technology. We applied this protocol to over 500 specimens representing two genera of skinks across the island of Sulawesi in Indonesia. We implemented several cost-saving measures to reach a per-sample cost of less than $5 each, which is less than the typical cost of a single Sanger sequence. We tested and compared this protocol on both PacBio Sequel II and Oxford Nanopore Technologies MinION flowcells. Both sequencing runs were relatively successful, and we compare the resulting sequence data and discuss possible ways to improve upon our methodology. We show that whole mitochondrial genomes produce more strongly supported phylogenetic trees and allow for assessment of structural variation and gene rearrangements. Our results provide a first look at the biogeography and evolution of an incredible radiation of skinks on Sulawesi, with up to 70 species-level lineages in a group with less than 10 described species. Several lineages independently invaded high-elevation environments on Sulawesi, and we use this system to test hypotheses of the taxon-cycle in a unique island system. |
|
2. 13:45 Duplications, Deletions, and Phylogenetic Consistency of the PKDREJ Gene in Squamates. Todd Jackman*, Villanova University todd.jackman@villanova.edu
PKDREJ is a sperm receptor present in a single copy as a large intronless gene (~7,600 bases) in most vertebrates except squamates. Using testes transcriptomes, whole genome data, targeted exon capture, and unassembled whole genome reads I found 300 copies of PKDREJ in 107 species of squamates, aligned them and analyzed DNA, amino acid, and protein structural features to both understand the evolution of the protein and how consistently phylogenies based on the gene perform. Ancestrally, squamates have three tandemly duplicated copies of PKDREJ with convergent losses of the middle copy in geckos and anguimorphs. Losses of the entire REJ module in one of the three paralogs occurred convergently in three clades of Anolis lizards. All three paralogs are expressed only in the testes (and presumably in sperm) and in equal amounts in nearly all cases where transcriptome data was available. All three copies appear to have retained their function as sperm receptors. The combination of long length and high amounts of variation at all 3 codon positions allows PKDREJ to produce reliable gene trees on many time scales. Phylogenies of squamates overall as well as phylogenies of some groups of closely related species produce remarkably consistent results both between paralogs and compared to phylogenetic hypotheses based on other markers. This consistency is reflected in both DNA and amino acid analyses. |
|
3. 14:00 A Study in Brown and White: A Revision of the New Caledonian Diplodactylid Geckos of the Genus Bavayia. Aaron Bauer*, Villanova University; Todd Jackman, Villanova University; Ross Sadlier, Australian Museum Research Institute aaron.bauer@villanova.edu
Bavayiais the most speciose of the gecko genera endemic to New Caledonia, with 12 recognized species. The presence of many undescribed taxa has been signaled by previous studies using mito-nuclear data sets and by a comprehensive DNA barcoding study. However, the conservative morphology of the group has hindered formal description of additional species. We examined more than 2000 specimens of Bavayiafrom throughout New Caledonia and its satellite islands and included ~600 specimens in a phylogenetic analysis of the mitochondrial ND2 gene. Our tree topology was consistent with previous, though less comprehensive, results from other molecular data sets and supported our recognition of 29 new species in the genus, bringing the total diversity.to 41 species distributed in 12 well-supported clades. Although variation in size, precloacal pores and arrangement of apical scansors of the first digit are useful characters to diagnose the species of Bavayia, many taxa are supported by subtle differences in coloration pattern, which is typically characterized by alternating brownish and whitish markings. In situ radiation and microendemism in New Caledonia is common in both geckos and skinks, but Bavayiais exceptional, accounting for 30% of the known terrestrial herpetofauna. Although as many as five Bavayia species may occur in sympatry, these are almost always representatives of different clades within the genus. We consider the radiation of Bavayia, which has been dated to the Early Miocene, to represent a "non-adaptive radiation" with many of the species distributed allopatrically and lacking genetic continuity but living similar lifestyles and retaining plesiomorphic features. |
|
4. 14:15 Implications of Introgression on Phylogeny and Diversification in Rattlesnakes. Edward Myers*, Clemson University; Rhett Rautsaw, Clemson University; Christopher Parkinson, Clemson University eddie.a.myers@gmail.com
The evolutionary history of rattlesnakes has been notoriously difficult to estimate, with different datasets and methods of phylogeny reconstruction resulting in different topologies. Recent population genomic and small scale phylogenetic studies have suggested that divergence with gene flow is common within this group. Whether gene flow and introgression among species has influenced past interpretations of phylogenetic relationships is not known. Here, we generate transcriptomic data for nearly all named species of rattlesnake (genera Crotalus and Sistrurus), generate a fossil calibrated phylogeny, and conduct genomic tests for introgression across this radiation. We discuss these results in the context of the consequences of hybridization and introgression in rattlesnakes and across the tree of life. |