Interview with the author: Integrating life history traits into predictive phylogeography

In this exciting research, Jack Sullivan and Megan Smith and colleagues use machine learning techniques to create a powerful predictive framework for phylogeographic studies. Learn about their experiences building this novel research approach!

What led to your interest in this topic / what was the motivation for this study? 
We’ve been interested in the question of whether or not we can predict phylogeographic patterns for some time. Initially, we attempted to predict whether or not unstudied species harbored cryptic diversity using climate and taxonomic information (https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2016.1529). We used taxa that were known to either harbor or lack cryptic diversity to train a Random Forest classifier, and then made predictions about unstudied taxa. We found that we could predict the presence or absence of cryptic diversity (with low error rates when based on cross-validation!) We also saw that taxonomy was a powerful predictor of cryptic diversity, and we began to wonder why. In this study, we evaluate whether life history traits can explain this result.

What difficulties did you run into along the way? 
When trying to use life history traits to make predictions across taxonomic levels, the most difficult problem is finding appropriate traits. Many traits, while likely very informative for specific taxa, are difficult to score across taxonomic groups. Our dataset included mammals, plants, arthropods, gastropods, amphibians, and birds. The biggest difficulty was finding life history traits that we could score across all of these groups and that we hypothesized would be meaningful predictors of phylogeographic patterns.

What is the biggest or most surprising finding from this study? 
Life history traits are great predictors of phylogeographic patterns. In one of the systems we studied, these traits can even replace taxonomy as a predictor, suggesting that taxonomy was serving as a proxy for these traits. We find that traits related to reproduction (e.g. reproductive mode, clutch size) and trophic level are particularly informative in our predictive framework.

The reticulate taildropper slug (Prophysaon andersoni), like many other invertebrates from the rainforests of the Pacific Northwest, lacks deep divergence between inland and coastal rainforest populations.

Moving forward, what are the next steps for this research? 
There is a wealth of data on phylogeographic patterns available, but most studies have focused on one or a few species. The framework developed in Espíndola et al. (2016) and expanded upon here provides a mechanism for integrating these studies into a predictive framework. As data continue to become available, our approach will allow policymakers and scientists alike to make predictions about what patterns are expected in unstudied species. Further, this approach can provide insight into which life history traits drive differences in species responses to historic events, and this may allow us to begin to understand why species respond to similar events in idiosyncratic ways.

What would your message be for students about to start their first research projects in this topic? 
Think early and often about how your work can be integrated into the field in a broader way. Particularly as molecular data become easier to collect, more and more single species studies accumulate. By looking at these studies in a new light and integrating across studies, we can learn a lot about communities and overarching patterns.

What have you learned about science over the course of this project? 
Over the course of this project, I’ve learned to look at data in many different ways. Our initial work on this topic suggested that taxonomy was the most important predictor of phylogeographic patterns. While true, this told us little about the biology of the taxa we were studying. By delving deeper and adding life history traits to our study we were able to draw biologically meaningful conclusions about why species responded differently to geologic and climatic events.

We used our predictive framework to understand cryptic diversity in the temperate rainforests of the Pacific Northwest. Pictured is the Siuslaw National Forest, where many of the temperate rainforest endemics in our study can be found.

Describe the significance of this research for the general scientific community in one sentence.
By using machine learning, we can integrate genomic, ecological, and trait data to make predictions about how species have responded to historic events, and to understand which factors lead to idiosyncratic responses.

Describe the significance of this research for your scientific community in one sentence.
Using publicly available data and machine learning techniques, we can make predictions about phylogeographic patterns across broad taxonomic groups, and we can draw conclusions about how life history traits influence these patterns.

Summary from the authors: What do gut microbes do for their hosts?

Despite a flood of recent interest in this question for humans, the answer remains a mystery for the vast majority of animals. Gut microbiota are often assumed to provide nutritional benefits, but many insects acquire the majority of their nutrients during larval feeding, leaving less opportunity for bacterial contributions to adult nutrition. In fact, when food is scarce the adult gut flora might even impose a net reproductive cost.

Photo courtesy of A. Ravenscraft

We tested this prediction in the Mormon fritillary butterfly (Speyeria mormonia), a denizen of mountain meadows in the American Rockies. We experimentally subjected wild caught butterflies to a brief burst of antibiotics to disrupt their gut flora and then maintained them with either ad lib feeding or a 50% starvation diet. Contrary to our
predictions, the number of bacteria in the gut did not correlate with butterfly fitness even if the butterfly was starved, though a few individual bacteria species were associated with increased or decreased lifespan.

Overall, these results suggest that gut bacteria may have little net
effect on some animals. – Alison Ravenscraft, NIH PERT Postdoctoral Fellow, University of Arizona

Ravenscraft A, Kish N, Peay K, Boggs C. No evidence that gut microbiota impose a net cost on their butterfly host. Mol Ecol. 2019;28:2100–2117. https://doi.org/10.1111/mec.15057

Summary from the authors: A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog

Sex chromosomes evolve when recombination ceases between the X and Y chromosomes, and the X and Y chromosome accumulate differences between them. We examined sex chromosomes across three populations of the common frog, Rana temporaria. In one population, we confirm that the sex chromosome and an autosome have undergone a reciprocal translocation, a rearrangement in which two chromosomes swap arms. The resulting chromosome pair is coinherited as sex chromosomes. Furthermore, because frog chromosomes only recombine near the ends, much of the newly added chromosome is incorporated into the sex-determining region. This provides a large amount of new genetic material to the selective environment of the sex chromosomes, in which sequence on the X chromosome are under selection in females twice as often as males, and sequence on the Y are subject sex-specific selection in males. We further confirmed unique sex-chromosome arrangements in the other two populations, demonstrating that Rana temporaria has extensive structural polymorphism in its sex chromosomes. — Melissa Toups

Toups, M., Rodrigues, N, Perrrin, N, and M. Kirkpatrick. (2019). Genomics, environment and balancing selection in behaA reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology28(8), 1877–1889. https://doi.org/10.1111/mec.14990

Interview with the author: A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog

In this Blog post, we hear from Dr. Melissa Toups on how new sex chromosomes can evolve! Mellisa and her colleagues show that reciprocal translocations can incorporate large pieces of chromosome into a sex-determining region, thus making the to be co-inherited as sex chromosomes. Join us in learning more about this exciting research directly from Mellisa.

Picture by Christophe Dufresnes

What led to your interest in this topic / what was the motivation for this study? 
I’m interested in the diversity of genetic sex-determination mechanisms. Ranid frogs are a fantastic study species for this because sex determination moves between chromosomes on a fast evolutionary time scale. In Rana temporaria, the study species for this paper, sex chromosome arrangements differ between populations.  We knew from previous linkage maps using microsatellites that the southernmost population had only one small sex-determining region, one northern population had one a larger sex-determining region on the same chromosome, and finally a second northern population had two sex chromosomes formed by reciprocal translocation, which occurs when two chromosomes swap arms and become coinherited.  This was a great opportunity to use genomic techniques to study three different arrangements of sex chromosomes within a single species.

What difficulties did you run into along the way? 
During breeding season, frogs migrate to nearby ponds.  In the evening, the males swim around and sing to females. The successful males attach to females, and we catch them as a couple.  The two northernmost populations, Kilpisjärvi and Ammarnas, breed at the roughly the same time.  We started in Ammarnas, but catching the frogs we needed took longer than expected.  By the time we arrived in Kilpisjärvi, breeding season was almost over.  Most of the frogs remaining in the ponds were single males. We were only able to catch two breeding pairs, and we were lucky enough to eventually find two solo females, but it took weeks of effort, which was nerve-wracking. \

What is the biggest or most surprising finding from this study? 
We are the first to use genomic techniques to characterize a reciprocal translocation of a sex chromosome. We don’t know how common these rearrangements are because they are only cytologically detectable at pairing during meiosis.  Here, we show that they can incorporate large regions of an additional chromosome into the sex-determining region, which are subject to very different selective forces than the autosomes.  The most surprising finding was detecting evidence for another small nonrecombining region in Kilpisjärvi on a different chromosome. These frogs are full of surprises!

Moving forward, what are the next steps for this research?
We are currently investigating whether different sex chromosome arrangements affect male gene expression.  To answer this question, we are focusing on an alpine population of Rana temporaria in Switzerland that has males with two types of Y chromosomes.  Some Y chromosomes only differ from the X chromosome in a small region around the sex-determining locus, and other Y chromosomes are differentiated from the X chromosome throughout their length. We are also working on using high-density linkage mapping of RAD sequences to confirm the novel sex-chromosome rearrangement in the Kilpisjärvi populations.

What would your message be for students about to start their first research projects in this topic? 
Our standard models for sex-chromosome evolution are mostly based on the mammalian XY system, which are more than 160 million years old.  However, the more organisms we study, the more we realize that ancient, highly diverged sex chromosomes may be the exception rather than the rule. My message would be to keep an open mind about what you might find, and let your organism surprise you!

What have you learned about science over the course of this project? 
One thing I’ve learned working on this project is the importance of assembling a team of researchers with complementary strengths.  Each person brought unique and critical skills to this project. We were able to combine knowledge of our study system, bioinformatics, and coalescent modeling to produce a comprehensive examination at sex chromosomes in Rana temporaria.

Describe the significance of this research for the general scientific community in one sentence.
We provide the first genomic view of an entirely different way that new sex chromosomes can evolve.

Describe the significance of this research for your scientific community in one sentence.
We show that the reciprocal translocations can dramatically increase the portion of the genome that is incorporated into the sex-determining region.

Interview with the author: Phototactic tails- Evolution and molecular basis of a novel sensory trait in sea snakes

In this blog post, we learn about how coming across an an old paper describing a strange behavior in sea snakes led Jenna Crowe-Riddell to a topic of their PhD research. In this integrative study, Crowe-Riddell and colleagues use a combination of behavioral experiments and transcriptomics to identify a set of candidate genes related to the curious behavior of tail withdrawal in response to light observed in some species of sea snakes. Read on for more details behind the study in our interview with Jenna, with a link to the paper at the end.

Photo from Jenna Crowe-Riddell

What led to your interest in this topic / what was the motivation for this study? 
I was about to embark on my first field trip to catch sea snakes in Broome, Western Australia, as part of my honours research project. I was digging around the old literature and came across a brief and curious paper on how olive sea snakes react to light on their tail paddles. Olive sea snakes (Aipysurus laevis) are a common species in Broome so I asked my supervisor whether we could repeat the experiment. We were both surprised to see a baby olive sea snake repeatedly withdrew its paddle-tail away from our flashlight. I had so many questions about this strange behaviour that I was compelled to continue studying it for my PhD!

What difficulties did you run into along the way? 
There were a lot of challenging aspects to this project because we were studying a novel sensory system in a non-model organism with no genome sequence data available, which meant that analysing RNA-sequencing data was especially difficult. However, one of the most difficult (and enjoyable!) aspects of the research was bringing together a diverse team of people-bioinformaticians, physiologists, vision biologists, wildlife workers, statisticians, etc. to investigate the genetic pathways, ecological mechanisms and behaviour of tail phototaxis. Weaving together these different approaches to tell the evolutionary story of tail phototaxis made writing the manuscript a tricky but rewarding part of the project.

What is the biggest or most surprising finding from this study? 
In snakes, tail phototaxis has only been described in Aipysurus laevis, leading us to predict that this trait evolved in all sea snakes as a response to the ecological shift to the sea. However, our behavioural results show that only three out of eight species tested respond to light on their tails, inferring that tail phototaxis probably evolved in the ancestor of a clade of six Aipysurus sea snakes. That’s only 10% of the approximately 60 species of sea snakes!

Moving forward, what are the next steps for this research?
Expanding the sample size both within and among species to confirm the evolutionary origin of tail phototaxis. Employing a range of anatomical techniques (perhaps in situ hybridisation) to locate the photoreceptive structures within the tail skin. Discover the physiological pathways –e.g. how is light transduced or perceived by the snakes? What intensity and part of the spectrum are snakes most sensitive to? I would also like to gather more data on how these species behave in the wild to better understand ecological factors that contribute to the evolution of dermal photoreception. Finally, we can use our discoveries in sea snakes to make predictions on how this trait convergently evolved in other vertebrates like hagfish, lamprey and aquatic salamanders.

What would your message be for students about to start their first research projects in this topic? 
Be patient. Things never work out the way you think they will but that’s okay because being on the edge of the unknown means that 99.99% of your ideas will probably be wrong! That’s how new knowledge is discovered: by testing out ideas and having them be knocked back, one by one. As my colleague used to say to me “you are cracking stone!” Furthermore, always ask for help. The perception of science as the endeavour of a lone genius is a myth, science is only achieved in teams.

What have you learned about science over the course of this project? 
See above!

Describe the significance of this research for the general scientific community in one sentence.
Our research exemplifies the power of an integrative approach to understanding the evolution of complex sensory traits.

Citation
Crowe-Riddell, J. M., Simões, B. F., Partridge, J. C., Hunt, D. M., Delean, S., Schwerdt, J. G., … Sanders, K. L. (2019). Phototactic tails: Evolution and molecular basis of a novel sensory trait in sea snakes. Molecular Ecology, 28(8), 2013–2028. https://onlinelibrary.wiley.com/doi/10.1111/mec.15022

Interview with the author: Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon

Populations of salmon in the eastern and western Atlantic ocean diverged more than 600,000 years ago. They survived in isolated refugia during the glacial maxima, and later expanded their ranges. When colonizing northern areas after the retreat of the glaciers, eastern and western populations came back into contact. Lehnert et al. studied the genome-wide consequences of secondary contact, with a particular focus on regions of the genome near chromosome rearrangements. One chromosomal rearrangement shows evidence of European ancestry in North American individuals, suggesting that secondary contact occurred during the colonization of northern part of the species’ range. However, another chromosomal rearrangement showed a contrasting pattern: evidence of a derived North American chromosome fusion. In both rearrangements, the authors find evidence of natural selection, suggesting that chromosomal rearrangements may serve an adaptive role in salmon. Below, we go behind the scenes with Dr. Sarah Lehnert, currently Postdoctoral Fellow at Fisheries and Oceans Canada, to learn more about the findings of the paper and the work that went into this research. You can find the associated paper here: https://onlinelibrary.wiley.com/doi/10.1111/mec.15065

Atlantic salmon (Salmo salar) Gaspe Peninsulsa, Quebec, Canada. October 2017.
Photo credit: Nick Hawkins

What led to your interest in this topic / what was the motivation for this study? 
Atlantic salmon populations across the North Atlantic have been declining in recent decades. Our lab is interested in better characterizing genetic structure and diversity of salmon populations in North America to improve conservation and management. When we started this project, I was interested in identifying genomic regions associated with large-scale differences among individuals across populations. We were particularly interested in identifying genomic variation associated with historical secondary contact (~10,000 years ago) between European and North American Atlantic salmon. These groups diverged >600,000 years ago and mitochondrial evidence suggest contact has occurred but genomic evidence is limited. For our project, we investigated if and how secondary contact has influenced contemporary population structure and considered the implications for salmon management and conservation.

What led to your interest in this topic / what was the motivation for this study? 
Atlantic salmon populations across the North Atlantic have been declining in recent decades. Our lab is interested in better characterizing genetic structure and diversity of salmon populations in North America to improve conservation and management. When we started this project, I was interested in identifying genomic regions associated with large-scale differences among individuals across populations. We were particularly interested in identifying genomic variation associated with historical secondary contact (~10,000 years ago) between European and North American Atlantic salmon. These groups diverged >600,000 years ago and mitochondrial evidence suggest contact has occurred but genomic evidence is limited. For our project, we investigated if and how secondary contact has influenced contemporary population structure and considered the implications for salmon management and conservation.

What difficulties did you run into along the way? 
We first investigated genomic regions that showed large-scale inter-individual variation across North American populations. One difficulty was that many approaches are designed to investigate population level differences rather than individual differences. By using methods that allow the investigation of individual variation in addition to population level differences, this enabled us to resolve karyotypic differences within populations that may have been missed by other analyses. This led us to identify variation in two chromosomal rearrangements (translocation and fusion). The next difficulty was trying to understand why these rearrangements show different geographic structure and different levels of diversity. Through additional analyses and by incorporating European samples, we determined that variation in each chromosomal rearrangement evolved through different mechanisms.

What is the biggest or most surprising finding from this study? 
Our work suggests that Atlantic salmon within rivers in North America have different numbers of chromosomes. This corroborates earlier karyotyping studies in a few rivers, but our study is the first to show genomic evidence of chromosome variation at the continental scale and our work also identifies which chromosomes are responsible for this variation and how this variation came to be. What was most exciting to me was being able to use SNP data to understand the different evolutionary histories of these chromosomal rearrangements. Our study revealed an interesting story as we found that variation in one chromosomal rearrangement was introduced from European salmon coming to North America whereas variation in the other chromosomal rearrangement evolved within North America independently.

Moving forward, what are the next steps for this research?
We found that chromosome variation exists in North American Atlantic salmon and our next step is to further understand why this variation exists. Our study suggested that these regions were under selection and thus we hypothesize that chromosome variation may relate to life history diversity or local adaptation. In other salmonids, chromosomal rearrangements have been associated with important traits such as migration phenotype. The fusion identified in our study has recently been suggested to be associated with precipitation within a single river system. Therefore, we plan to sample a wider range of populations in North America and examine environmental and life history variation associated with karyotype differences at a continental scale

What would your message be for students about to start their first research projects in this topic? 
My advice would be to read new papers but also old papers on your study system. By reading older papers, I learned that some earlier studies had identified karyotype variation within and between Atlantic salmon populations. This was not often discussed in more recent population genetic studies that focused on microsatellites or SNPs. Reading older karyotyping studies on Atlantic salmon in conjunction with new papers (reviews) on chromosomal variation helped me formulate hypotheses and interpret the patterns we were finding in the genome. It can be easy to focus on recent literature, but older work can often help shed a different light on unresolved questions.

What have you learned about science over the course of this project? 
Through this work, I have learned that variation in chromosome structure is prevalent across taxa. Dobzhansky highlighted this as early as the 1930s but the field of genetics moved away from this earlier focus on chromosome level differences. Only recently have we started to appreciate how important chromosomal structure variation may be to adaptation. Within the last decade, chromosomal inversions have been associated with complex phenotypes such as mating tactics in the ruff and migration strategy in species like cod, warblers, and rainbow trout. Although inversions have recently garnered a lot of attention, our study also highlights the importance of variation in chromosomal fusions and translocations, which have not been identified within many animal populations to date.

Describe the significance of this research for the general scientific community in one sentence.
Our research demonstrates variability in chromosomal translocations and fusions within populations of a vertebrate species that may play a role in adaptation and highlights how historical events (glaciations and secondary contact) can influence contemporary diversity.

Describe the significance of this research for your scientific community in one sentence. 
Our work suggests that differences in chromosome number are prevalent in Atlantic salmon populations and this potentially adaptive variation can provide information about different evolutionary events, highlighting the importance of such genetic variation to salmonid populations management.

Summary from the authors: Genomics, environment and balancing selection in behaviourally bimodal populations: The caribou case

Like people, caribou are individuals. Each animal has a different colouration pattern, size, metabolism and other characteristics. And each behaves differently, including in specific environments. But what drives such differences, or diversity, in caribou? Are such mechanisms similar in other animals, including people? And can understanding what gives rise to such diversity help conserve caribou, a threatened species in Canada, which recently became functionally extinct in the Lower 48 US? This study has identified a natural mechanism in caribou that preserves and ensures long-term genetic and behavioural diversity of the species in various habitats across western North America, from Alaska to the Southern Canadian Rockies. This mechanism, called “balancing selection,” has resulted in caribou populations having not only distinctly different genetic traits but also diverse and likely adaptive behaviours, including whether individual animals migrate or not. Balancing selection could ensure that two or more behaviours or characteristics are selected at the same time, by balancing the benefits of one type of behaviour or appearance with the benefits of other types. This research is the first genomic study of caribou and perhaps the first to confirm the gene-driven balancing selection mechanism in a wild species in nature. – Marco Musiani

Cavedon, M., Gubili, C., Heppenheimer, E., vonHoldt, B., Mariani, S., Hebblewhite, M., … Musiani, M. (2019). Genomics, environment and balancing selection in behaviourally bimodal populations: The caribou case. Molecular Ecology, 28(8), 1946–1963.https://doi.org/10.1111/mec.15039