Skipwith, Philip

RESEARCH OVERVIEW:

Research in my lab focuses on understanding the patterns and processes underlying speciation dynamics and morphological diversification within and between lineages, particularly in relation to ecological opportunity. Vacant ecological space is typically thought to facilitate species diversification as diverging lineages adapt to novel niches with subsequent expansion of ecomorphospace. However, there is little consensus on how these expectations apply to empirical systems with a growing body of evidence suggesting some level of idiosyncrasy amongst taxa. Our lab uses species assemblages of squamate reptiles (lizards and snakes) to determine how empirical, non-model systems diversify and if these patterns fall in line with accepted macroevolutionary theory. Using geckos and other squamate groups, we implement phylogenomics and comparative phylogenetics to reconstruct evolutionary histories. We will further combine these data with whole-genome sequencing and reduced representation sequencing to better understanding the genomic regions underlying speciation, genotype-phenotype associations, and the genomics of convergent evolution. Specifically, we aim to: (1) reconstruct the tempo of lineage accumulation within and between lineages, (2) determine how speciation dynamics and trait diversification relate to one another, (3) identify regions of the genome underlying ecomorphologically relevant traits, and (4) investigate the hierarchical nature of convergent evolution (i.e.- morphological vs. molecular).

PROJECT 1 – DE-NOVO ASSEMBLY OF SQUAMATE GENOMES:

Genomic resources for most squamates are largely lacking for non-avian reptiles, complicating initiatives to understand genotype-phenotype correlations. We are currently sampling species from across Squamata, particularly gekkotans and lacertoids to ascertain common and divergent molecular changes responsible phenotypic diversification. Sequencing will be done on a PacBio Sequel IIe SMRT Cell 8M platform.

PERSONNEL:
Phillip Skipwith
Yuanxing Liao
Rommy Parra

COMPUTATIONAL METHODS:
De-novo genome assembly, read processing, transcriptome assembly, read mapping, annotation, and differential expression analysis

SOFTWARE:
Velvet, Abyss, fastx_toolkit, ea-utils, Jellyfish, Trinity, GMAP, GSNAP, PASA, RSEM, NCBI BLAST, BLAST2GO), DESeq, edgeR, baySeq, BLAST+, TOGA, RERconverge, PhastCons, ReForge, BRAKER, Augustus

PROJECT 2 – SQUAMATE PHYLOGENOMICS

The abovementioned whole genomes will be combined with reduced representation sequencing of ultraconserved elements (UCEs) and anchored tags (AHEs). These will be used for phylogenomic reconstruction of gekkotans and lacertoids and downstream comparative phylogenetic analyses.

PERSONNEL:
Phillip Skipwith
Yuanxing Liao
Rommy Parra

COMPUTATIONAL METHODS:
Phylogenomic estimation using concatenated and multispecies coalescent methods.

SOFTWARE:
RAxML, ExaBayes, IQtree, PAUP, RevBayes, MrBayes, PAML (and all extensions), R programming language

PROJECT 3 – INTERROGATION OF TORTOISE GENOMES

In addition to the work on squamate listed above, my doctoral student Rommy Parra will also interrogate the genomes of tortoises to better understand the underpinnings of body-size evolution.

PERSONNEL:
Rommy Parra

COMPUTATIONAL METHODS:
Genome annotation

SOFTWARE:
TOGA, RERconverge, PhastCons, ReForge, BRAKER, Numpy, Gdata, Editdist, Genome Analysis Toolkit (GATK) Unified Genotyper

PUBLICATIONS

· Skipwith, P. L., Oliver, P. M. (2023) Ecologically diverse island-associated lizard radiation shows idiosyncratic trait diversification shifts and homogenous speciation dynamics. Evolution.

· Chang, L., Skipwith, P. L. (2020) Relatedness and the composition of communities over time: evaluating phylogenetic community structure in the late Cenozoic record of bivalves. Paleobiology.

· Oliver, P. M., Jolly, J. C., Skipwith, P. L., Tedeschi, L. G., Gillespie, G. R. (2020) A new velvet gecko (Oedura: Diplodactylidae) from Groote Eylandt, Northern Territory; highlighting another overlooked hotspot of vertebrate endemism in Northern Australia. Zootaxa.

· Skipwith, P. L., Oliver, P. M., Bi, K. (2019) Relicts and radiations: Phylogenomics of an Australasian lizard clade with east Gondwanan origins (Gekkota: Diplodactyloidea). Molecular Phylogenetics and Evolution.

· Segall, M., Palci, A., Skipwith, P.L., Herrel, A. (2023). Evolution of the Form and Function of the Head of Snakes. In: Penning, D. (Ed.), Snakes: Morphology, Function, and Ecology.