ECR feature: Emily Booth on the evolution of Australian freshwater fishes

Emily Booth is a PhD student at the Flinders University in Australia. She is a molecular ecologist interested in understanding the effects of climate changes on the evolution of species. Here, Emily shares her recent work on the ‘genomic vulnerability’ of Australian freshwater fishes to climate change.

Emily Booth during fieldwork in Australia.

Personal links. Twitter

Institute. Flinders University, Australia

Academic life stage. PhD candidate

Major research themes. I am interested in understanding the effects of climate change (both historical and contemporary) on the evolution of species, particularly freshwater fishes.

Current study system. I am currently working with four species of Australian freshwater fish: golden perch (Macquaria ambigua), Murray cod (Maccullochella peelii), Murray River rainbowfish (Melanotaenia fluviatilis), and southern pygmy perch (Nannoperca australis). These species exhibit a variety of different life history and ecological traits; I am incredibly fascinated by the amount of biodiversity hidden away in our river systems! My PhD aims to assess the ‘genomic vulnerability’ of these species to anthropogenic climate change — that is, to predict how much adaptive genetic change is needed for populations to keep up with climate change. My recent JBI paper focussed on golden perch, which is a large-bodied, socioeconomically important species. Golden perch have evolved to tolerate a broad range of hydroclimatic conditions, including the Australian arid zone where river flow is highly variable. Golden perch undergo seasonal migration and have an amazing dispersal capacity, making them ideal for studying the effects of environmental change on highly vagile freshwater species.

The Murray River, Australia, is home to a variety of freshwater fishes (Photo credit: Kade Storey-Byrnes).

Recent JBI paper. Booth, E. J., Sandoval-Castillo, J., Attard, C. R., Gilligan, D. M., Unmack, P. J. & Beheregaray, L. B. (2022). Aridification-driven evolution of a migratory fish revealed by niche modelling and coalescence simulations. Journal of Biogeography, 49, 1726– 1738.

Motivation behind this paper. This paper is derived from my Honours thesis (equivalent to a MSc thesis in several other countries). My co-authors and I wanted to understand the processes that have led to the divergence of three golden perch lineages from three different river basins. Previous research had found these lineages to be so genetically distinct that they could be considered as separate species, but further investigation was needed. Since golden perch are extensively stocked from hatcheries into rivers to support the recreational fishing industry, it is important that we clarify how many species we are dealing with! We tested the hypothesis that historical aridification of Australia during the Pleistocene caused reduced habitat connectivity between river basins and facilitated the divergence of the three lineages.

Key methodologies. A cool thing about this study is that we used two independent data sets (genomic and environmental) to investigate the biogeographic and demographic history of golden perch. We began by using genome-wide SNP data to reconstruct the phylogenetic relationship between the three major golden perch lineages. Next, we built species distribution models (SDMs) based on environmental data to estimate the contemporary and historical ranges of those lineages. The SDMs allowed us to develop hypotheses (for example, about the historical size and connectivity of populations), which we then tested using genomic-based coalescent modelling.

Unexpected challenges. The most challenging part of this research was definitely the coalescent modelling. As somebody who was brand-new to coding, it certainly took some time to get my head around how to use the program fastsimcoal. But once I got the hang of it, it was difficult to know when to stop! In the end, I tested somewhere around >30 different models. It was a good thing I had hypotheses from the SDMs to keep me on track about which scenarios to test…otherwise I would have been there forever.

Major results. Our research found phylogenetic support for the delimitation of three golden perch cryptic species, each endemic to one of three major drainage basins. We discovered that aridification of Australia during the late Pleistocene likely played a role in facilitating the divergence of these lineages. Our SDMs found that during the Last Glacial Maximum (~21 thousand years ago) the amount of suitable habitat for golden perch was extremely reduced and there was far less connectivity between drainage basins. This theory was also supported by our coalescent models, which found that population sizes were much smaller during the Last Glacial Maximum compared to the current day. It was remarkable to find such a similar signal from two independent data sets. This work strongly highlights the benefit of integrating multiple types of data and analyses to develop and test biogeographic hypotheses.

Golden perch, Macquaria ambigua (Photo credit: Peter Unmack).

Next steps for this research. The evolution of arid zone species, especially obligate freshwater organisms, is a poorly studied topic in the literature. Many Australian freshwater species exhibit cryptic diversity between drainage basins, yet little research has been done to understand how this has arisen. I would be interested to use a similar analytical framework for other taxa to determine some broader scale patterns regarding the influence of historical aridification on the evolution of Australian freshwater diversity.

If you could study any organism on Earth, what would it be? I think it isn’t so much a question of what I want to study, but where. During undergrad I fell in love with island biogeography after reading David Quammen’s book The song of the dodo. Islands provide amazing natural experiments for testing evolutionary theories, and I am fascinated by processes like adaptive radiation and body size change that frequently occur on them. It might sound cliché for a biogeographer, but I would love to study species from the Galapagos Islands. Maybe marine iguanas (Amblyrhynchus cristatus) to start with, they’re pretty cool!

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