ECR Feature: Isabel Haro-Bilbao & Josh Thia on the use of genomics to identify fisheries stocks

Isabel Haro-Bilbao and Josh Thia met while completing their PhD’s at the University of Queensland, Australia. Both had interests in the ecology of marine organisms, which led them to collaborate on a project investigating genetic differentiation in the wahoo, a large, highly dispersive pelagic fish. Isabel and Josh share how they used population genomic approaches to characterise previously unidentified stocks in this important species of recreational, subsistent and commercial fisheries.

(left) Isabel in Santa Barbera while attending a tuna conference and catching up with coauthor, John Baldwin, to get wahoo samples. (right) Josh out surveying experimental plots in rural Australia for agricultural pests (sporting his signature field work bucket hat).

Personal links. [Josh]: Twitter | Webpage | Google Scholar | ResearchGate

Institute. [Isabel]: The University of Queensland. [Josh]: The University of Melbourne.

Career life stage. [Isabel]: Masters of Economics. [Josh]: Postdoc.

Major research themes.

[Isabel]: I am currently completing a master’s degree in economics, and my interest focuses on multidisciplinary small-scale fisheries management that combines ecology and economics. I aim to find tailored solutions for sustainable fisheries that balance the environmental, social, and economic impacts.

[Josh]: My current main research focus is on arthropod pests of Australian agriculture, specifically with respect to the molecular mechanisms and evolution of pesticide resistance. However, I am interested in all sorts of organisms and systems, including the wonders of the wet and watery ocean!

Recent paper in JBI. Haro‐Bilbao, Isabel, Riginos, Cynthia, Baldwin, John D., Zischke, Mitchell, Tibbetts, Ian R., Thia, Joshua A. (2021). Global connections with some genomic differentiation occur between Indo‐Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish. Journal of Biogeography 


Wiley Content Link:

Motivation behind this paper. This paper was birthed as a collaboration during our respective PhDs at the University of Queensland. We wanted to test the long-standing assumption that wahoo, Acanthocybium solandri, exist as a single, globally homogeneous population. Wahoo are an important fish in subsistent and recreational fisheries, are increasing in their commercial value, and there is a need to understand their stock structure for fisheries management. Like many large, pelagic fish, wahoo have extraordinary dispersal capacity and large population sizes. These factors have likely limited the ability of prior works to identify putative stocks, which have inferred genetic differentiation from a small number of genetic markers. We wanted to exploit population genomic techniques to increase our power to detect subtle genetic differentiation in a globally distributed sample of wahoo populations.

(left) A fisherman processing wahoo at a local market, Santa Cruz Island, Galapagos… he isn’t the only one with an interest in wahoo! (Photo credit: Jonathan Erazo) (right) Isabel taking notes at the fish market. (Photo credit: Jonathan Erazo)

Key methods. Our sampled wahoo populations spanned the Indo-Pacific and Atlantic Oceans. We tested for genetic differentiation between the Indo-Pacific and Atlantic, a well-known biogeographic break, and tested whether patterns of genetic differentiation were due to ongoing gene flow, low drift due to large population sizes, or a combination of both. We characterised genetic variation using single nucleotide polymorphisms (SNPs) obtained through a pooled reduced-representation (ezRAD) method. These SNPs were used to estimate genetic differentiation of populations across oceanic regions. We also used demographic analyses to test three population genetic scenarios: isolation with no gene flow, symmetric gene flow, and asymmetric gene flow. These scenarios were tested both within and between ocean basins to understand the spatial scales of gene flow.

Challenges overcame. One of the obvious financial and logistic challenges of a global study is obtaining samples representing as many sites as possible across the species distribution. Whilst Isabel had the opportunity to collect samples, we also pulled in samples from collaborations with Jonh Baldwin and Mitchell Zischke. Both had researched wahoo and had well-preserved, documented samples from across the globe, which were essential in our tests of inter-oceanic differentiation.

Fishing boats in Santa Cruz Island, Galapagos, adorned with pelicans. (Photo credit: Jonathan Erazo)

Major results. Our paper is the first to use genome-wide SNPs to examine genetic differentiation across the global distribution of wahoo. With the power of thousands of genomic markers, we debunked the previous hypothesis that wahoo is a single homogeneous population. We found that two discrete genetic stocks exist, one in the Indo-Pacific and one in the Atlantic. This regional structuring shows similarity to the yellowfin tuna, suggesting that similar forces may influence large, pelagic fish species. The genetic differentiation between ocean regions was subtle, and our demographic analyses indicated that this differentiation occurs against a background of high gene flow throughout the evolution history of wahoo. We did not find any clear support for asymmetric gene flow, as might be expected from other marine taxa that exhibit greater movement from the Indo-Pacific into the Atlantic. However, high dispersal and subtleties in genetic differentiation probably reduced our ability to identify asymmetries in gene flow.

Next steps. There are two major extensions of this work. Firstly, although we had great representation of the Atlantic and Indo-Pacific, we did not have any populations from the Mediterranean. The Mediterranean Sea has a unique environment, and it would be intriguing to know whether the classic Atlantic–Mediterranean break also exists in wahoo. Secondly, our study utilised a pooled sequencing approach to maximise the number of individuals and populations we could sample. But pooled sequencing precluded individual-based analyses that could provide insights into processes of dispersal and selection that might shape patterns of genetic differentiation among populations. Future works using individual genotypes would provide more power to unravel the demographic and evoltuionary processes opertating in this species.

If you could study any organism on Earth, what would it be?

[Isabel]: My main interest is in fisheries, and I can think of many fascinating marine animals. However, the most intriguing organisms are still humans. Specifically, I would like to study the mechanisms behind our decision-making process around natural resources exploitation and consumption. Our behaviour has such a significant impact on shaping life on Earth that unveiling those patterns could substantially affect how we address environmental challenges.

[Josh]: There are so many species that spring to mind! But I would love to study pikas, genus Ochotona. I fell in love with these cute little lagomorphs when I saw them featured on a David Attenborough documentary. They live in beautiful alpine talus and meadow habitats and are incredibly industrious; they make hay to survive through the winter!… adorable.

Published by jbiogeography

Contributing to the growth and societal relevance of the discipline of biogeography through dissemination of biogeographical research.

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