Evolution of the Native Freshwater Fish Fauna in the Central Pacific: Phylogeography and Population Structure of Amphidromous Gobies (Teleostei: Gobiiformes)

Vinnikov, Kirill

Evolution of the Native Freshwater Fish Fauna in the Central Pacific: Phylogeography and Population Structure of Amphidromous Gobies (Teleostei: Gobiiformes)

Date

2019

Authors

Vinnikov, Kirill

Advisor

Cole, Kathleen S.

Department

Zoology

Abstract

A large number of species of indigenous freshwater fish fauna on tropical and subtropical oceanic islands is represented by amphidromous gobies. Amphidromy means that these fishes live and reproduce in a freshwater environment but also have a marine planktonic larval stage, which may encourage extensive dispersal in the ocean. As a result of larval dispersal, high levels of gene flow between island populations of amphidromous gobies would have a strong influence on rates of species divergence and population sustainability. In contrast, isolated insular populations with limited gene flow and low genetic diversity resulting from occasional founder events can be highly vulnerable to extinction. In my dissertation, I investigate the population structure and larval dispersal patterns of eight species of amphidromous gobies from the genus Stenogobius (Teleostei, Gobiiformes). The population connectivity was inferred for multiple nested geographic scales, including streams, islands, archipelagos and different regions in the Central Pacific. The extent of gene flow and possible lineage divergence among stream subpopulations were estimated based on exon capture sequencing data. In order to retrieve and to analyze this kind of molecular markers on non-model species, I developed the EXONtools bioinformatics pipeline, written in Python. Using this program on the data produced from a single lane sequencing on Illumina HiSeq 4000, I was able to generate the dataset comprising ~50,000 SNPs from the exon regions and ~70,000 SNPs from the intron regions representing jointly ~9,000 annotated genes for 126 individuals of Stenogobius. Additionally, this exon capture dataset included the complete sequences of mitochondrial genomes for every individual. Both mitochondrial and nuclear genomic analyses revealed similar biogeographic and population connectivity patterns for Stenogobius in the Central Pacific. These findings provide strong evidence for a metapopulation structure within each archipelago but relatively low population connectivity among archipelagos. The latter was highly correlated with the geographic distances among archipelagos. I also found genomic signatures of positive selection resulting in within-stream differentiation of the Society and Hawaiian populations of Stenogobius. However, in contrast to the revealed population structure, the phylogenomic analysis hasn’t confirmed significant divergence among any of the eight species of Stenogobius used in the current study suggesting that their taxonomic status as valid species is questionable.

Keywords

Zoology, Evolution & development, Bioinformatics, amphidromy, exon capture, EXONtools, larval dispersal, speciation, Stenogobius

URI

http://hdl.handle.net/10125/63277

Extent

233 pages

Rights

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Collections

Ph.D. - Zoology

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