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

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Title:Evolution of the Native Freshwater Fish Fauna in the Central Pacific: Phylogeography and Population Structure of Amphidromous Gobies (Teleostei: Gobiiformes)
Authors:Vinnikov, Kirill
Contributors:Cole, Kathleen S. (advisor)
Zoology (department)
Keywords:Zoology
Evolution & development
Bioinformatics
amphidromy
exon capture
show 4 moreEXONtools
larval dispersal
speciation
Stenogobius
show less
Date Issued:2019
Publisher:University of Hawai'i at Manoa
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.
Description:Ph.D. Thesis. Ph.D. Thesis. University of Hawaiʻi at Mānoa 2019
Pages/Duration:233 pages
URI:http://hdl.handle.net/10125/63277
Rights:All UHM dissertations and theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission from the copyright owner.
Appears in Collections: Ph.D. - Zoology


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