Effective population size (Ne) is crucial parameter in evolutionary biology that reflects the number of individuals in a theoretically ideal population having the same magnitude of loss of genetic variation as the population in question. There are several types of Ne estimates, and they vary in definition and application. For example, contemporary Ne represents the size of a population in the previous generation/s and is a parameter of relevance in many species. Estimating contemporary Ne is, however, difficult and remains in practice often unknown. This is particularly the case for large populations where the amount of drift in the short term is limited. We used genomic data from 85 collared flycatchers of an island population sampled at two time points, and applied several methods to estimate Ne. These methods either compared genetic variation between the two time points (temporal methods) or analyzed variation patterns from a single time point (LD-based methods). The temporal methods estimated Ne at a level of few thousand, while the approach based on LD provided ambiguous estimates associated with high variance. Our results suggest that whole-genome data can help to estimate large contemporary Ne, but temporal sampling seems to be necessary.
Article: Nadachowska-Brzyska K, Dutoit L, Smeds L, Kardos M, Gustafsson L, Ellegren H. 2021. Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis). Molecular Ecology https://doi.org/10.1111/mec.16025.
In a recent issue of Molecular Ecology, Taylor et al. explore how between population translocations of a small and endangered freshwater fish may break the long-term evolutionary boundaries between populations in this species. In this study, the researchers used a combination of genomic and phenotypic data to show that translocation efforts, which were necessary for meeting species conservation goals, could alter some important genetic and morphological differences between populations. To read the complete story, see the full article now available online as well as the interview with the authors below.
What led to your interest in this topic / what was the motivation for this study? Some excellent work with microsatellites had previously identified three populations of Bluemask Darters across their small range (Robinson et al. 2013, Cons. Gen.). One population, larger and more genetically diverse than the others, was in the Collins River, in the western portion of the range. A second population was in Rocky River, more central. A third population was in Cane Creek and the Caney Fork to the east. There was also a population in the Calfkiller River, which has been extirpated for several decades. In this context, captive-reared Bluemask Darter progeny from the Collins River population were being introduced to the Calfkiller River. But the location of the Calfkiller, near the center of the range, gave an important quirk to the system. If the three populations were not equally distinct, then Calfkiller River might be better suited with individuals from Rocky River, Cane Creek, or Caney Fork, rather than the western Collins River. In other words, the geography of the system meant that we needed to know the phylogenetic or hierarchical structure of population structure to know what boundaries might be lurking between Collins River and an introduced population in the Calfkiller River.
What difficulties did you run into along the way? One challenge in our project was navigating the connection between our scientific discoveries and the underlying goals of conservation. Our analyses were focused on the quantitative aspects of Bluemask Darters phylogenetics. However, at the end of the day, we are talking about an endangered species, incredibly imperiled, with a tiny range and an uncertain future. No quantitative value can give us strict guidance about the normative problems of conservation. So a challenge was to unpack, as best as we could, how our conclusions about the phylogenetics, population structure, and demography of this species could ultimately help us conserve the multiple diverging lineages of Bluemask Darters. The reviewers and editors from Molecular Ecology helped us refine our logic and our language, and the final result is a paper that acknowledges the complexities and competing concerns of translocation in a system like this.
What is the biggest or most surprising innovation highlighted in this study? One of the most significant findings of this study was the discovery of two divergent clades of Bluemask Darters — precisely the boundary being broken by current conservation management decisions that move fish between clades! One clade includes western individuals and the other includes eastern individuals. To top it off, we had the unique opportunity to use historic morphological data from across the range, including the Calfkiller River site where the fish had been extirpated, and which was now being restored with fish originating from the western population. The consistent result was that eastern sites harbor a distinct population from western sites, and that the Calfkiller River was associated with the eastern population. It is now apparent that translocated individuals should be from a source consistent with the clade that previously occupied the Calfkiller River, and from a source that will not artificially perturb existing evolutionary boundaries. In our study, there are additional complicating factors — the ideal eastern translocation sources are low abundance and not as genetically diverse. So our study was also a new opportunity to address how we might balance multiple concerns, with genetic details, while addressing a complicated conservation issue.
Moving forward, what are the next steps in this area of research? In our paper, we discuss how there are juvenile Bluemask Darters that drift into the reservoir at the center of the range and may not be able to migrate upstream to appropriate habitats needed as adults. These young fish are from the Rocky River, and are part of the appropriate clade for restocking the Calfkiller River. However, the success of this strategy would depend on the population dynamics of young fish in the reservoir. Jeff Simmons, co-author on this paper, and colleagues will be pushing forward with the critical next steps. There will be studies of the density and abundance of juvenile fish in the reservoir, including whether juveniles recruit into a breeding population or simply perish before maturity. There is also ongoing monitoring of the translocated fish in the Calfkiller, and across the species range. All of this work is being combined with habitat quality monitoring aimed at unraveling the location, frequency, and cause(s) of water quality issues that are harming darters in this system. All together, we’re continuing to build a picture of how best to conserve the distinct lineages of Bluemask Darters.
What have you learned about methods and resources development over the course of this project? Making this project successful meant combining dozens of different analyses — assembling, aligning, and filtering sequences, phylogenetics, population structure, genetic differentiation statistics, demographic simulations, to name a few — each of which have their own traps and idiosyncrasies. Getting these methods working required, first, well, getting everything to run, and then getting everything to run correctly. As useful as online documentation is, I learned there is no substitute for learning with colleagues who are engaging in similar research. Shout out especially to Dan MacGuigan, Daemin Kim, and Ava Ghezelayagh, all students with Tom Near. My conversations with these and other colleagues were critical for avoiding analytical pitfalls. These conversations also spurred ideas about new analyses and perspectives that will continue moving phylogenetic and population genetic work forward.
What would your message be for students about to start developing or using novel techniques in Molecular Ecology? It’s been said before, but it really was important to have reproducible code for this project. Working with next-generation sequence data meant an enormous number of different files and analysis packages. Being able to switch between versions (like with git), automate programs (like with bash scripts), and manage software environments (like with conda) saved us hundreds of hours. At the end, you can neatly package everything up; all of our data and code, for example, is now stored on a dryad repository that could basically reproduce our paper from scratch in just a few commands. Even after publication, sharing code has also meant starting new conversations with other scientists about best practices, alternate methods, and new ideas for genetic analyses.
Describe the significance of this research for the general scientific community in one sentence. Our study uses genetic and morphological data to unravel how translocation strategies for an endangered freshwater fish might balance the competing conservation concerns of phylogenetic divergence, genetic diversity, and population demography.
Describe the significance of this research for your scientific community in one sentence. Our study identifies two distinct clades of endangered Bluemask Darters across their small range, where current management decisions are translocating individuals across those diverging lineages.