Evolution 2023: Highlights of evolution and ecological genetics at Albuquerque

Fendler’s globemallow (Sphaeralcea fendlerii) along the riverfront bike trail. (jby)

Evolution is back, folks. That is, the 2023 joint annual meeting of the American Society of NaturalistsSociety of Systematic Biologists, and Society for the Study of Evolution, held last week in Albuquerque, New Mexico, felt just about like its pre-pandemic self. The meeting was cancelled in 2020, then ran a fully virtual program in 2021, and went hybrid in 2022, running two days of virtual talks and a comparatively in-person event in Cleveland, Ohio. But Evolution 2023 felt like an expansion of its old form, filling five days of contributed talks and plenaries at the Albuquerque convention center, as well as a two-day virtual conference that included the SSE and SSB student award symposia and online versions of many of the meeting’s networking events.

Someday it would be nice to write a conference recap without also writing an introductory paragraph about COVID-19, but we’re not there yet. Masking was pretty sparse in the convention center, and organizers alerted us to some positive tests among attendees towards the end of the in-person meeting … and two days after I got home (by way of an unmasked layover in Phoenix) I woke up congested and achey and pegged the meter on an antibody test. I’m on the mend thanks to Paxlovid, which works as advertised — but my experience is as good a caution as any, as you depart for summer conferences and travel.

It also delayed my write up of the conference, but this has been my first post-recovery priority, because I saw a lot of good molecular ecology work, and some exciting methods and utilities, on display at Albuquerque. Without further ado, some highlights from my notes:

One connecting theme among talks I saw was parallel adaptation — as a phenomenon of interest in itself, but more often as a source of patterns that turn out to be useful for identifying molecular targets of selection.

Rachel Moran described work on the molecular evolution underlying adaptation to caves in Mexican tetra fish, a great system for capturing parallel adaptation. Moran’s comparison of selective targets in different cave populations is finding lots of parallel selection on de novo mutation — fish in different cave systems adapted via changes to the same genes, but changes which arose independently after they colonized the caves. A neat consequence of this is that genes with longer coding regions, which provide more mutational targets, are more likely to underlie parallel adaptive changes.

Brian Myers presented population genomic work to trace the origins of adaptation to human-modified landscapes in Oceanic swallows — the relatives of North America’s barn swallows in East Asia and Oceania. Like barn swallows, multiple species in the clade have adapted to use human structures for nesting, and Myers’ work suggests these are independent, parallel changes.

Julia Kreiner described exciting work studying adaptation to agricultural landscapes — and herbicides applied to them — by Amaranthus tuberculatus, a native North American plant that has become a major agricultural weed. Genomic data from pairs of populations in natural and agricultural settings, and from historic herbarium samples, validates an old hypothesis about the species’ pre-adaptation for agricultural weediness and identifies really strong and specific replicated divergence at loci targeted by a major class of herbicides.

There were also a bunch of great talks on species interactions — as usual for the Evolution meetings, more than I could actually attend. The ones I caught, though, had lots of exciting examples of molecular data applied to understand complex, potentially coevolutionary, interactions.

Dylan Gallinson had some impressive data on Tasmanian devils’ coevolution with transmissible facial cancer. He’s used genomic data from devils and tumors in a joint association scan, which identifies a number of known “cancer genes” as candidates for determining the tumors’ infectivity.

Brian Gall presented a rundown of his work on an under-studied angle on the classic coevolutionary “story” of toxic rough-skinned newts: in addition to predation by garter snakes, the newts must cope with egg-eating caddisflies — and the caddisflies, like the garter snakes, have evolved resistance to the newts’ protective and highly potent tetrodotoxin. The caddisfly sodium channel targeted by tetrodotoxin is also a target of widely used insecticides, which offers the intriguing possibility that insecticide use helped the caddisflies evolve to prey on newt eggs? Wild stuff.

There were also multiple exciting talks from a couple of emerging systems for host-symbiont coevolution: Corlett Wood’s lab, which has been digging into the interaction of root-knot nematodes with the legume-rhizobium mutualism, and a bunch of folks at the Strassman-Queller and Haselkorn Labs investigating microbes that have established symbiosis with Dictyostelium social amoebas.

I didn’t explicitly seek out “methods” talks, but two I ran across in sessions on topics of interest showed me utilities that my lab may very well come to use on a daily basis:

E. Sally Chang described updates to NCBI’s system for recording inferring, inferring, and querying annotated gene functions, including lots of useful-looking new tools and revisions to standard tools, including taxonomically clustered visualization of BLAST results, a soon-to-be containerized version of the eukaryotic genome annotation pipeline, and a new comparative genome viewer that presents pre-computed comparisons of alignments for species of interest (with the option to request new pairs).

Anne Chambers presented the plans of the California Conservation Genomics Project, which is collecting “individual-based landscape genomics” data for species of concern in the state — that is, sequencing genomes of individuals dispersed across the landscape, a study design near and dear to my heart. Most excitingly, Chambers described a new R package that wraps together many of the standard analyses for this kind of dataset with some nice spatial interpolation methods: A Landscape Genomic Analysis Toolkit in R, or algatr. The package is under review right now, but it looks like it could become a real go-to for the field.

And finally, there were a bunch of great presentations on topics beyond my usual wheelhouse of genomics and coevolution — an advantage of attending a big meeting like this.

ASN President Maria Servedio gave a real master class theory talk as her presidential plenary, walking through a series of “truthy” understandings about the genetics of speciation that become complicated when they’re explicitly addressed in population genetic models.

Melody Sain presented some really interesting work to identify the basis of sex determination in two species of meadow rue (Thalictrum) that have independently evolved dioecy after transitioning to wind pollination. Sequencing individuals pooled from full-sib crosses let her quantify sex-associated kmers across the genome, and excesses of male-associated kmers suggest that the emerging sex-determination system is XY, with males heterogametic.

Species with haplodiploid sex determination, like wasps, provide a unique view of mutation accumulation, since recessive deleterious mutations are fully expressed in the haploid sex. Sara Miller discussed work with Polistes wasps that demonstrated a lot of the predicted effects: diploid females carry more nucleotide diversity than males, and hundreds of genes that carry nonsense mutations in females carry no such mutations in males.

It wasn’t quite molecular ecology, but one of the best talks I saw was by Xuening “Shirley” Zhang, who showed that across New York, pairs of species in the genus Bidens co-occur in a way consistent with facilitation: species with discoid flowering heads, which lack showy ray florets, are facilitated by growing among members of species with radiate flowering heads, whose showy sunflower-style ray florets help attract pollinators to both species.

Last but certainly not least, the IDEA plenary, by award co-recipient Melanie Duc Bo Massey, was an inspirational account of her work to build the Diversity of Nature outreach program with co-recipient Suchinta Arif. Diversity of Nature offers ecological field experiences to BIPOC students in Nova Scotia, free of charge, with the explicit goal of creating the kinds of formative encounters with nature that bring so many natural scientists into scientific careers. The talk made the case, not only for the value of Diversity of Nature as an important means to improve representation in the life sciences, but as a valuable element of its founders’ professional development — countering the general idea that “diversity work” has to trade off with advancement of a scientific career.

About Jeremy Yoder

Jeremy B. Yoder is an Associate Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.
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