This year’s Molecular Ecology Prize is awarded to Dr. Uma Ramakrishnan, a Professor of Ecology and Evolution at the National Centre for Biological Sciences, Bangalore, India.
Dr. Ramakrishnan is best known for her studies on the tiger and other large mammals, which are the “poster children” for India’s natural resources. Her studies have included census estimates from combined camera trap and genetic surveys, historical inferences from genetic data and museum specimens, and demonstrations of gene flow impacting genomic variation and inbreeding depression. Dr. Ramakrishnan’s research has led to valuable conservation applications, for example by providing evidence used in a Supreme Court ruling that wildlife corridors must be included in certain highway expansions. Dr. Ramakrishnan’s work on science communication and community service is exemplary, and she is an important role model to scientists around the world.
Dr. Ramakrishnan joins the previous winners of the Molecular Ecology Prize: Godfrey Hewitt, John Avise, Pierre Taberlet, Harry Smith, Terry Burke, Josephine Pemberton, Deborah Charlesworth, Craig Moritz, Laurent Excoffier, Johanna Schmitt, Fred Allendorf, Louis Bernatchez, Nancy Moran, Robin Waples, Scott Edwards, Victoria Sork, Fuwen Wei, and Kerstin Johannesson.
The editorial board is seeking nominations for the Harry Smith Prize, which recognizes the best paper published in Molecular Ecology or Molecular Ecology Resources in the previous year by graduate students or early career scholars with no more than five years of postdoctoral or fellowship experience. The prize comes with a cash award of US$1000 and an announcement in the journal and in the Molecular Ecologist. The winner will also be asked to join a junior editorial board for the journal to offer advice on changing research needs and potentially serve as a guest editor. The winner of this annual prize is selected by the junior editorial board.
The prize is named after Professor Harry Smith FRS, who founded Molecular Ecology and served as both Chief and Managing Editor during the journal’s critical early years. He continued as the journal’s Managing Editor until 2008, and he went out of his way to encourage early career scholars. In addition to his editorial work, Harry was one of the world’s foremost researchers in photomorphogenesis, where he determined how plants respond to shading, leading to concepts such as “neighbour detection” and “shade avoidance,” which are fundamental to understanding plant responses to crowding and competition. More broadly his research provided an early example of how molecular data could inform ecology, and in 2008 he was awarded the Molecular Ecology Prize that recognized both his scientific and editorial contributions to the field.
Please send a PDF of the paper you are nominating, with a short supporting statement (no more than 250 words; longer submissions will not be accepted) directly to Dr. Kaichi Huang (kaichi.huang@botany.ubc.ca) and Dr. Arne Jacobs (arne.jacobs@glasgow.ac.uk) by Friday 31 March 2023. Self-nominations are encouraged.
We are soliciting nominations for the annual Molecular Ecology Prize.
The field of molecular ecology is young and inherently interdisciplinary. As a consequence, research in molecular ecology is not currently represented by a single scientific society, so there is no body that actively promotes the discipline or recognizes its pioneers. The editorial board of the journal Molecular Ecology therefore created the Molecular Ecology Prize in order to fill this void, and recognize significant contributions to this area of research. The prize selection committee is independent of the journal and its editorial board.
The prize will go to an outstanding scientist who has made significant contributions to molecular ecology. These contributions would mostly be scientific, but the door is open for other kinds of contributions that were crucial to the development of the field. The previous winners are: Godfrey Hewitt, John Avise, Pierre Taberlet, Harry Smith, Terry Burke, Josephine Pemberton, Deborah Charlesworth, Craig Moritz, Laurent Excoffier, Johanna Schmitt, Fred Allendorf, Louis Bernatchez, Nancy Moran, Robin Waples, Scott Edwards, Victoria Sork, Fuwen Wei, and Kerstin Johannesson.
Please send your nomination with a short supporting statement (no more than 250 words; longer submissions will not be accepted) and the candidate’s CV directly to Joanna Freeland (joannafreeland@trentu.ca) by Friday, March 31, 2023. Organized campaigns to submit multiple nominations for the same person are not necessary and can be counterproductive. Also, note that nominations from previous years do not roll over.
With thanks on behalf of the Molecular Ecology Prize Selection Committee.
In a recent paper in Molecular Ecology, Szukala et al. quantified the degree of gene expression and functional parallelism across polytopic divergence of montane and alpine ecotypes of in Heliosperma pusillum (Caryophyllaceae) and gained insights into the architecture of adaptive traits. They performed RNA-seq analyses of plants grown in a common garden and detected a large proportion of differentially expressed genes in each replicate ecotype pair. Functional enrichment of these genes, however, revealed that the traits affected by significant expression divergence are largely consistent across ecotype pairs, suggesting a polygenic architecture for the diverged adaptive traits and multiple routes for adaptation. A new genome assembly for H. pusillum was also presented in this study.
We sent a number of questions to lead authors of this work, Aglaia Szukala and Ovidiu Paun, to get more detail on this study.
Upper panels: Graphical representations of the alpine (A) and montane (M) ecotypes of Heliosperma pusillum and their ecological niches. Lower panel: Map showing the study sites of ecotype pairs that evolved in parallel.
What led to your interest in this topic / what was the motivation for this study?
We are fascinated by the concept of parallel evolution and the molecular mechanisms behind this process. Given that drift is a major driver of evolution and due to the traditional focus on mono- or oligogenic traits, parallel evolution has been considered to be a rare process until recently. However, together with the increasing understanding of polygenic adaptation (Barghi et al., 2020), it has become clear that parallel evolution is relatively frequent, with implications across evolutionary biology and ecology. Specifically, for our study, previous works (Trucchi et al., 2017; Bertel et al., 2018) reported some evidence that altitudinal ecotypes in H. pusillum diverged in parallel. We wanted to rigorously test this hypothesis using demographic modeling and understand the level of molecular parallelism, with regard to divergent gene expression and outlier SNPs.
What difficulties did you run into along the way?
For several reasons related to the planning of field work and the development of the wider project over years, we had to deal with uneven sampling sizes across populations, which needed to be taken into account, especially for the demographic modeling analyses. Fun fact: in reciprocal translocation experiments of a complementary study (Szukala et al., 2022) on the same species, whose data is also included in the present paper, we chose to use alpine microsites to plant our accessions that were fairly flat (in an otherwise steep area) and free of other plants. At the end of the vegetation season, those sites proved to be resting places for chamois which squeezed and munched most of our plants, while overfertilizing them. In previous years, when reciprocal transplantations were performed as preparation for this study, we faced droughts, poor germination and survival rates at some sites, leading to uneven sampling sizes across sites. Take-home message: experiments in the wild are always a challenge.
What is the biggest or most surprising innovation highlighted in this study?
It is unclear how much overlap of divergence outliers is to be expected across natural evolutionary replicates. Our study showed a surprisingly low amount of shared molecular differentiation, which we did not expect given that the geographic range considered is relatively small and our study system is in a phase of incipient speciation with no reproductive isolation detectable (Bertel et al., 2016). The extremely low sharing of differentially expressed genes and outlier SNPs, but high similarity of GO terms involved across independent divergence events, indicates that the polygenic architecture of traits is relevant for adaptation of these populations to distinct altitudinal zones in the Alps.
Moving forward, what are the next steps in this area of research?
We further investigated the role of phenotypic plasticity for the development of parallel evolution in our system (Szukala et al., 2022) towards a better understanding of the relative role of genetic and environmentally-induced phenotypic variation in such replicated divergence events. We are also interested if other molecular mechanisms, which are sensitive to environmental input, such as epigenetic signals, could play an important role in parallel evolution. Further, we wish to understand how polygenic adaptation affects signatures of parallel evolution. Very interesting is to question if adaptation can use different genes to produce similar outcomes even in very closely related lineages, and how frequent this process takes place compared to the re-use of standing variation.
Alpine (blue) and montane (light orange) ecotypes of Heliosperma pusillum and their environments. In the alpine environment glabrous plants grow on more humid screes and meadows, also in proximity of streams. In the montane environment below the tree line, pubescent plants typically grow under rocks overhangs or on the rock as chasmophytes. Photo credit: Szukala A and Paun O.
What would your message be for students about to start developing or using novel techniques in Molecular Ecology?
Being curious and exploiting the most advanced and newest methods is good, but don´t forget to be robust, careful, and bias-aware when it comes to the interpretation of results.
What have you learned about methods and resource development over the course of this project?
It is often difficult to quantify and describe results relative to expectations in an objective way, because it is hard to formulate objective expectations in natural systems.
Describe the significance of this research for the general scientific community in one sentence.
Repeated evolution of similar phenotypes can involve different sets of genes.
Describe the significance of this research for your scientific community in one sentence.
Polygenic traits offer different genetic substrates for parallel evolution of similar phenotypes.
References
Barghi N, Hermisson J, Schlötterer C. 2020. Polygenic adaptation: a unifying framework to understand positive selection. Nature Reviews Genetics 21: 769–781.
Bertel C, Hülber K, Frajman B, Schönswetter P. 2016. No evidence of intrinsic reproductive isolation between two reciprocally non-monophyletic, ecologically differentiated mountain plants at an early stage of speciation. Evolutionary Ecology 30: 1031–1042.
Bertel C, Rešetnik I, Frajman B, Erschbamer B, Hülber K, Schönswetter P. 2018. Natural selection drives parallel divergence in the mountain plant Heliosperma pusillum s.l. Oikos 127: 1355–1367.
Trucchi E, Frajman B, Haverkamp THA, Schönswetter P, Paun O. 2017. Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae). New Phytologist 216: 267–278.
Szukala A, Bertel C, Frajman B, Schönswetter P, Paun O. 2022. Parallel adaptation to lower altitudes is associated with enhanced plasticity in Heliosperma pusillum (Caryophyllaceae). bioRxiv 2022.05.28.493825; doi: 10.1101/2022.05.28.493825.
Featured study
Szukala A, Lovegrove-Walsh J, Luqman H, Fior S, Wolfe TM, Frajman B, Schönswetter P, Paun O. 2022. Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae). Molecular Ecology. https://doi.org/10.1111/mec.16356.
In a recent paper in Molecular Ecology, Singh et al. used genome sequencing, bioinformatics and population genetic analyses to gain insight into the genetics and evolution of a fascinating mating system. The species in question, Lamprologous callipterus, exhibits a mating system with two males morphs. Large “bourgeois” males carry empty snail shells that are inhabited and used as nests by the females. An alternate male morph, much smaller than the “bourgeois” males, also exists and inhabits shells along with the females. Previous genetic work had established that this mating system was Y-linked and that the male body size was a Mendelian trait, but the sex-determining locus had not been identified until this study.
We sent some questions to Pooja Singh, the author who led this work, to get more detail on this study.
Photo credit: Drawing by Pooja Singh, based on Barbara Taborsky’s original image.
What is the biggest or most surprising innovation highlighted in this study?
The most novel aspect of this study is that we found an example of a young sex chromosome that may have evolved due to sexual antagonism over body size. While the sexual antagonism theory is considered the classical model of sex chromosome evolution, few empirical examples exist to support it. The other exciting finding was that the candidate body size/dwarfism gene that we propose for L. callipterus, GHRHR, is a well-known dwarfism gene in mammals. Fish and mammals shared a common ancestor over 440 million years ago, so the body size development pathway is genetically constrained through deep evolutionary time.
What difficulties did you run into along the way?
The major challenge for me was that I knew little about sex chromosome evolution when I started this project, so I really had to do a lot of groundwork reading relevant literature and researching methods to be able to get things going. I had to start thinking beyond the classical XY and WZ old sex systems and familiarize myself with the workings of early stages of sex chromosome evolution.
When I read your paper, I had never heard of the fascinating mating system of these cichlids. They reminded me of the ruff, and the multiple inversions that seem to be involved in the different reproductive strategies in that system. You mention in the paper that you were not able to identify inversions based on the bioinformatic approaches you used. Is there a sense for how much chromosome evolution during the radiation? Could the use of the divergent reference genome have anything to do with the lack of a signal of inversions?
To my knowledge the broad scale chromosomal structure of African cichlid species is similar. However, small scale structural variations (inversions, indels, translocations etc.) have not been investigated systematically. So yes, it is totally possible that our short read data and the divergent (and fragmented) reference genome assembly may have hindered our ability to detect inversions. The system really needs a long-read de novo genome assembly to resolve the inversion question.
In the Discussion, you talk about the possibility of different male Y-haplotypes. Is your data sufficiently high resolution that you could examine insertion/deletion polymorphisms in your dataset?
Yes, we could technically identify small insertions/deletions in our data. Might certainly be something to investigate in the future, in combination with long-read Y assembly.
A recently proposed model of sex-chromosome evolution indicates that gene expression differences may predominate at the early stages of sex chromosome evolution (Lenormand and Roze 2022 Science – https://doi.org/10.1126/science.abj1813). This is intriguing given that you didn’t find any smoking gun loci with signals of sexual antagonism. Do you have plans to look at patterns of gene expression across the different morphs?
While Lenormand and Roze’s theory is certainly exciting for the field of sex chromosome evolution, I think it is less plausible for the L. callipterus mating system because antagonistic body sizes in females and males are crucial shell-brooding success and fitness. And because we found the candidate sex-determining gene and body-size gene to be physically linked. I am certainly not a proponent of the ‘one classical theory explains all’ narrative and I really look forward to seeing what RNA-seq data reveal about sex chromosome evolution in this species. It would be especially interesting to see the landscape of cis/trans eQTLs of genes in our proposed L. callipterus sex chromosome and how much it reflects the expectations from Lenormand and Roze’s model. Beyond just this species, cichlid fishes are an excellent system to test the sexual antagonism vs gene regulation models of sex chromosome evolution.
Regarding the coverage analysis you used to identify the putative sex-linked locus. Given the hypothesis that the divergence of the sex chromosomes is recent, reads sampled from Y-linked regions may still map well to the orthologous region on the putative X-chromosome. Did you tweak mapping quality filters at all?
I did run a less stringent mapping analysis, which overall had slightly higher mapping statistics, but the reduced coverage pattern on the L. callipterus sex chromosome was still significant.
Snail shell nest of L. callipterus with the nest owner in the left centre. Photo credit: Koblmueller et al. 2007
Could you describe the significance of this research for the general scientific community in one sentence?
Sexual antagonism over body-size may have driven sex chromosome evolution in a shell-brooding cichlid fish where giant and dwarf male reproductive types have evolved.
Moving forward, what are the next steps in this area of research (unless otherwise covered)?
Our main priority right now is to keep the L. callipterus dwarf males alive and breeding. Our fish were recently moved from the University of Bern in Switzerland to the University of Graz in Austria, and it has proved difficult to get the dwarf males happy and breeding in the new facility. This is (probably) the only collection in the world of L. callipterus dwarf males outside Lake Tanganyika so they are very precious. Our next step is to write a convincing grant to get funding to build a long-read improved genome assembly, conduct RNA-seq, and sample and sequence more individuals from natural populations. I would like to use the RNA-seq data to map expression QTLs and investigate the regulatory interactions of candidate genes related to sex, morphology, physiology, and behaviour that we found in or around the L. callipterus sex region. It would also be interesting to study sex chromosomes in related lamprologine species, as our pre-liminary analysis in this manuscript suggests that the sex region may be shared across the lamprologine tribe
In a recent paper in Molecular Ecology, Portinha et al. used population genomic data to analyse the speciation history of two closely related species of wood ants, Formica polyctena and F. aquilonia. Using a demographic modelling approach, the authors reconstruct the history of divergence for multiple heterospecific pairs of populations. In all cases, the authors found that there was evidence for divergence with gene flow. However, for a sympatric population pair sampled in Finland there was evidence for substantially elevated gene flow between the species. Their findings imply that population genomic analysis of speciation history may be geographically variable for particular species.
We sent some questions to Beatriz Portinha and Pierre Nouhaud, the corresponding authors of this work, to get more detail on this study.
Ant mound surface covered in ants. Photo credit: Jack Beresford
What led to your interest in this topic / what was the motivation for this study?
Knowledge on the demographic and speciation histories is essential for understanding contemporary genomic patterns in natural populations, which is why we wanted to reconstruct it for the emerging Formica model system. Our study species, Formica polyctena and F. aquilonia, are known to hybridize naturally in Southern Finland, where their hybrids have been studied for over 10 years (Kulmuni et al., 2010; Martin-Roy et al. 2021). We wanted to test whether a similar divergence history was consistently inferred across the European ranges of both species, or whether the Finnish populations would stand apart, possibly because of gene flow mediated by hybrid populations in the area.
What difficulties did you run into along the way?
Formica polyctena and F. aquilonia had a limited genomic toolbox when we started the project, and we initially relied on a distant and non-contiguous reference assembly. Meanwhile, our group assembled a high quality reference genome (Nouhaud et al., 2022), which improved the quality of our inferences.
The demographic modelling software we used, fastsimcoal2, can simulate a large panel of evolutionary scenarios. When planning this study, we wanted to design models that considered alternative scenarios for the divergence of the species which would be as biologically meaningful as possible, while keeping the number of models low enough that the project 1) would not be a huge computational burden and 2) would be executable in the available time frame (Beatriz’s MSc. project, funded by Erasmus+ and Societas pro Fauna et Flora Fennica). This was an especially important aspect as we used four distinct population pairs to reconstruct the history of the two species, so each model had to be run, at least, four different times.
What is the biggest or most surprising innovation highlighted in this study?
We found that there was already bidirectional gene flow occurring in Finland before the hybridization events that led to the present-day hybrid populations. This was not suspected before, as there is no evidence in the literature, and it suggests that F. polyctena in Finland may be admixed, which is supported by the fact that we have not found non-admixed F. polyctena individuals in Finland.
Moving forward, what are the next steps in this area of research?
The divergence history we inferred between F. polyctena and F. aquilonia can be used to run simulations about the evolution of the hybrid populations, which is what we did in a subsequent work (Nouhaud et al. 2022). In the longer run, it would also be important to extend this work by reconstructing the divergence history of the whole F. rufa species group, which encompasses 5 species (including F. aquilonia and F. polyctena) and where gene flow is prevalent (Seifert, 2021).
Describe the significance of this research for the general scientific community in one sentence.
Genomes from individuals sampled thousands of kilometers apart tell the same ancient history, while their most recent history may be different.
Describe the significance of this research for your scientific community in one sentence.
The divergence history between two species can be reliably and consistently inferred from a small number of individuals sampled across the species’ ranges.
Portinha, B., Avril, A., Bernasconi, C., Helanterä, H., Monaghan, J., Seifert, B., Sousa, V. C., Kulmuni, J., & Nouhaud, P. (2022). Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges. Molecular Ecology, 31, 3416– 3431.
Kulmuni, J., Seifert, B. & Pamilo, P. (2010). Segregation distortion causes large-scale differences between male and female genomes in hybrid ants. Proceedings on the National Academy of Sciences, 107(16), 7371-7376.
Martin-Roy, R., Nygård, E., Nouhaud, P. & Kulmuni, J. (2021). Differences in thermal tolerance between parental species could fuel thermal adaptation in hybrid wood ants. American Naturalist, 198(2), 278-294.
Nouhaud, P., Beresford, J. & Kulmuni, J. (2022). Assembly of a hybrid Formica aquilonia× F. polyctena ant genome from a haploid male. Journal of Heredity, esac019, 1-7.
Nouhaud, P., Martin, S. H., Portinha, B., Sousa, V. C. & Kulmuni, J. (2022). Rapid and repeatable genome evolution across three hybrid ant populations. bioRxiv.
Seifert, B. (2021). A taxonomic revision of the Palaearctic members of the Formica rufa group (Hymenoptera: Formicidae) – the famous mound-building red wood ants. Myrmecological News, 31, 133-179.
The Molecular Ecology Prize Committee is pleased to announce that the 2022 Molecular Ecology prize has been awarded to Dr. Kerstin Johannesson, Professor of Marine Ecology, University of Gothenburg, Sweden. Trained as a marine ecologist, her research over the past 40 years has focussed on understanding how marine organisms become adapted to their environment. Towards this goal, she performed pioneering molecular ecology work that fully integrated ecological and molecular approaches to study the sea snail, Littorina saxatilis, which she developed into a model species. Her work has inspired numerous researchers across Europe to also use Littorina as an ideal model to study the ‘tug of war’ between evolutionary forces that have driven ecotypic divergence across different habitats of littoral zones. She has authored 150 peer-reviewed articles, which have been cited nearly 9,000 times with an h-index of 56. She has trained 35 Ph.D. students and postdocs from Europe and abroad. Her impressive accomplishments have earned her 10 major awards, the most prestigious being The Swedish Börssällskapet Research Award and election to the Royal Swedish Academy of Sciences. She also has received awards (e.g., the Swedish “Kunskapspriset”) in recognition of her outreach activities and the impact of her science on society. In brief, Dr. Johannesson has been a pioneer and is still an influential leader in the field of marine molecular ecology in Europe and beyond.
Dr. Johannesson joins the previous winners of the Molecular Ecology Prize: Godfrey Hewitt, John Avise, Pierre Taberlet, Harry Smith, Terry Burke, Josephine Pemberton, Deborah Charlesworth, Craig Moritz, Laurent Excoffier, Johanna Schmitt, Fred Allendorf, Louis Bernatchez, Nancy Moran, Robin Waples, Scott Edwards, Victoria Sork, and Fuwen Wei.
In a recent paper in Molecular Ecology, Enright et al. examined how soil microbiomes are affected by extreme fires. The Soberanes mega-fire provided the authors with an opportunity to study how such extreme events, which are increasingly common with climate-change, can have lasting effects on ecology. By sampling the soil microbiome before and after the Soberanes mega-fire, Enright at al. demonstrated dramatically altered soil communities and a reduction in species richness associated with the mega-fire. There was a clear phylogenetic pattern to the particular microbes that increased or decreased abundance after the fire. Drawing from their results, Enright et al. propose a framework to predict the traits that post-fire microbial communities might exhibit.
We sent some questions to Sydney Glassman, one of the corresponding authors of this work, to get more detail on this new study.
Aerial view of the Soberanes mega-fire. Photo credit: Calfire
What led to your interest in this topic / what was the motivation for this study?
I had originally been interested in sampling the redwood tanoak forests of Big Sur because I was interested in what the cascading effects of sudden oak death (SOD) induced mortality would be on soil fungal communities during my PhD at UC Berkeley. Prof Dave Rizzo at UC Davis had a large plot network investigating the effects of SOD on plant mortality. I teamed up with him in 2011 to select a subset of plots to collect soils to investigate the impacts on the soil microbial community via amplicon sequencing. Then, in 2016, I learned that half my plots burned in the catastrophic Soberanes Megafire. It’s extremely rare to have pre- and post-fire samples from the same sampling locations before and after a mega-fire. I was really curious about what the impact of a mega-fire would be on soil microbial communities especially since they had never been studied in redwood tanoak forests before. These forests are endemic and charismatic megflora of Califronia that are facing multiple global change factors and it is really unclear how the soil microbial communities will respond to wildfires and how that will influence the recovery of the vegetation. I had already moved to southern California at this time to start a post-doc at UC Irvine, so I asked Kerri Frangioso, who lived in Big Sur, if she would be able to re-sample any of the plots that burned. Using GPS, she was able to collect soils from the exact same sampling locations that I had sampled in 2011 from 3 of the plots (2 burned and 1 unburned) within 30 days of the fire being declared over. She mailed these soils to me, I extracted the DNA, and froze everything until I was able to start my own lab at UC Riverside in 2018.
What difficulties did you run into along the way?
The terrain in Big Sur is notoriously challenging to traverse. It is extremely steep, lots of windy dirt roads, and there is a lot of poison oak. There is no cell reception in any of our plots and most are at least an hour from the nearest town. Collecting the soil even before the fire was challenging enough. However, after fires, it is really challenging to access sites because roads are closed, landslides are common, and dead or dying trees are extremely hazardous especially in the case of wind. We were very lucky to be able to re-sample even 3 of our plots so fast after the fire.
What is the biggest or most surprising innovation highlighted in this study?
I was really surprised that many of the same pyrophilous “fire loving” microbes that have been found to increase in frequency after pine forest fires also increased in frequency after redwood tanoak fires. That indicates that soil microbes are selected for by slightly different pressures than plants because the plants that regenerate post-fire in pine forests vs redwood tanoak forests are very different. It seems more likely that microbes instead survive via temperature thresholds and if fire is high severity enough, similar groups of microbes will respond. We collaborated with Kazuo Isobe to implement the CONSENTRAIT analysis and identified that microbial response to fire was indeed phylogenetically conserved, and it seemed that related groups of bacteria and fungi did indeed positively or negatively respond to fires. This will greatly enhance our ability to predict which microbes will respond to fire in any ecosystem since certain lineages seem evolutionarily adapted to survive fires. We also found that a basidiomycete yeast Basidioascus, dominated the fungal sequences at 30 days post-fire, and that had never been found before, probably because most post-fire sampling historically has been based on fruiting bodies.
Morphological diversity of soil microbes. Photo credit: Jenna Maddox
Moving forward, what are the next steps in this area of research?
I was able to leverage some of these results and results from my work sampling wildfires in Southern California chaparral to help me acquire a USDA grant from their Agricultural Microbiomes program (described here). The purpose of this grant is to characterize the traits of pyrophilous microbes and begin to get our knowledge of fire adaptation in microbes to that of plants. We understand a lot of the traits that enable plants to survive wildfires (like thick bark, vegetative resprouting, serotinous cones, etc) but we don’t have similar understanding of those traits in microbes. In order to understand these traits, Dylan Enright has begun performing biophysical trait assays on these microbes to determine their traits based on a large culture collection of pyrophilous microbes that I have been developing since I started my lab in July 2018. Over the last four years, 2 lab managers, one PhD student (Dylan Enright), 13 UCR undergraduates, and one part time laboratory technician have been involved in developing this culture collection of over 400 isolates of bacteria and fungi from burned soils from wildfires. Our goal is to characterize their traits with biophysical assays and eventually with genomics.
Have you gone back (or have you any plans to go back) to sample soils in the post-fire period? How long lasting do you think the effects of fire on microbial communities would be?
Unfortunately, I have not been able to get this particular project funded (despite several attempts) and everything I did for this paper was completely unfunded. So I have not been able to return to these plots to sample again. I would be interested in returning to them eventually. I would predict the effects of the fire on the microbial communities could last decades if not longer, depending on if the plants themselves have been able to recover. Most of the literature on pyrophilous microbes suggests that high severity fire can have long term impacts on soil microbes that can last at least a decade or more. Given that the richness of both bacteria and fungi was reduced by up to 70% in one of our plots, I would predict it will take a long time to recover.
Describe the significance of this research for the general scientific community in one sentence.
Megafires have long lasting impacts on both plants and soil microbes alike, and it is important to understand the impacts on soil microbes since they drive plant and soil regeneration.
Describe the significance of this research for your scientific community in one sentence.
The pyrophilous microbes that respond to a mega-fire in redwood tanoak forests are similar to those that respond to high severity wildfires in better studied pine forest systems, and the fact that they are phylogenetically conserved indicates that we will be able to predict what microbes will respond to wildfires in any system. Further, we are beginning to identify conserved trait responses that enable wildfire response that are analogous to plants and will help us bin and better understand fire adaptation traits in microbes.
Enright, D. J., Frangioso, K. M., Isobe, K., Rizzo, D. M., & Glassman, S. I. (2022). Mega-fire in redwood tanoak forest reduces bacterial and fungal richness and selects for pyrophilous taxa that are phylogenetically conserved. Molecular Ecology, 31, 2475– 2493.
We are soliciting nominations for the annual Molecular Ecology Prize.
The field of molecular ecology is young and inherently interdisciplinary. As a consequence, research in molecular ecology is not currently represented by a single scientific society, so there is no body that actively promotes the discipline or recognizes its pioneers. The editorial board of the journal Molecular Ecology therefore created the Molecular Ecology Prize in order to fill this void, and recognize significant contributions to this area of research. The prize selection committee is independent of the journal and its editorial board.
The prize will go to an outstanding scientist who has made significant contributions to molecular ecology. These contributions would mostly be scientific, but the door is open for other kinds of contributions that were crucial to the development of the field. The previous winners are: Godfrey Hewitt, John Avise, Pierre Taberlet, Harry Smith, Terry Burke, Josephine Pemberton, Deborah Charlesworth, Craig Moritz, Laurent Excoffier, Johanna Schmitt, Fred Allendorf, Louis Bernatchez, Nancy Moran, Robin Waples, Scott Edwards, Victoria Sork, and Fuwen Wei.
Please send your nomination with a short supporting statement (no more than 250 words; longer submissions will not be accepted) and the candidate’s CV directly to Anne Yoder (anne.yoder@duke.edu) by Monday, June 6, 2022. Organized campaigns to submit multiple nominations for the same person are not necessary and can be counterproductive. Also, note that nominations from previous years do not roll over.
With thanks on behalf of the Molecular Ecology Prize Selection Committee
In a recent paper in Molecular Ecology, Espindola and Vázquez-Domínguez et al. combined comprehensive fieldwork, genetic analyses and a novel niche modeling approach to investigate population genetic patterns, distribution patterns of native and non-native red-eared slider turtle (Trachemys scripta elegans), one of the worst invasive species across the world, and its congeners. They found very little naturally occurring distribution overlap and genetic admixture between red-eared slider and other Trachemys species studied. In addition, they demonstrated that the native Trachemys species in Mexico have distinct climatic niche suitability, which probably prevents the invasion of red-eared slider in the area. However, major niche overlap was found between non-native red-eared slider and native species from different parts of the world, indicating that sites closer to ecological optima of invasive species have higher establishment risk than those closer to the niche-centre of the native species.
We sent a number of questions to lead authors of this work, Sayra Espindola and Ella Vázquez-Domínguez, to get more detail on this study.
What led to your interest in this topic / what was the motivation for this study?
We have interest in population genetics of invasive species. In addition, Trachemys scripta elegans, one of the World’s 100 worst invasive species, is native to NE North America, and several native congeneric species are naturally distributed along the eastern coast of Mexico, which is an extraordinary scenario to test the effect of congeners on potential invasion patterns and evaluate their climatic and niche differences.
Trachemys spp (T. scripta, T. venusta, T. cataspila, T. taylori) and their distributions along the west coast of USA and Mexico. Trachemys scripta (red dots) in Mexico is non-native. A turtle trapping net is shown. Figure credit: Sayra Espindola/Ella Vázquez-Domínguez
What difficulties did you run into along the way?
Maybe the most significant was that, at the time we did the molecular laboratory work, extracting DNA from samples that had been stored in formaldehyde (museum samples) was rather difficult, thus we could not obtain genomic data (SNPs) for those samples (extraction kits are much more efficient now). Nonetheless, we did sequence nuclear microsatellites loci, which provided adequate genetic information that enabled us to show the significant contemporary genetic differentiation present between native and non-native Trachemys scripta elegans individuals.
What is the biggest or most surprising innovation highlighted in this study?
There are two interesting findings. One is that non-native Trachemys scripta elegans individuals have very little naturally occurring distribution overlap and admixture with its congeners – they exhibited reduced gene flow and clear genetic separation despite having zones of contact. Also, we demonstrate that the native Trachemys species studied (T. cataspila, T. venusta) have distinct climatic niche suitability, which prevents the establishment of and displacement by the non-native Trachemys scripta elegans. Yet, as T. s. elegans has invaded and displaced native turtle species worldwide, we show that sites closer to T. s. elegans’ niche-center have higher establishment risk than those closer to the niche-center of the native species.
Moving forward, what are the next steps in this area of research?
We are working with our genomic data to identify loci under selection to evaluate the potential connection between specific genes and adaptive traits in these turtles. Considering the distinct climatic niches and distribution we found for the turtles, we are very kin to elucidate if there are adaptive differences among them. In addition, our results set the basis for future work – whole genome or gene-targeted sequencing, as well as a higher number of field-sampled individuals, would allow assessment of hybridization and specific gene introgression.
What would your message be for students about to start developing or using novel techniques in Molecular Ecology?
We would first tell them that molecular ecology research, combining ecological fieldwork and laboratory tasks, is absolutely amazing! We recommend choosing to work with the species/taxa that you more deeply like – this makes the journey very enjoyable; and also selecting a laboratory and research group with ample experience in molecular work and analyses, while at the same time not afraid of proposing novel questions and ways of analyzing them.
What have you learned about methods and resource development over the course of this project?
In this project, we proposed and developed a novel modeling approach, in which by contrasting the niche suitability of the species, we were able to include, indirectly, the interactions that can occur when a species is introduced to habitats occupied by other species. The model is based on analyses of climatic niche suitability and the environmental centrality hypothesis, where fitness is expected to be highest in sites with environments closest to the center of the niche of the species. The development of this model and algorithms required an immense number of trials and errors, and once we had the final version, we had to again improve it after revision. The lesson then is that developing analytical models can take a lot, lot of time, but it is always worth the while!
Little climatic niche overlap between Trachemys scripta and two of its congeners, T. venusta and T. cataspila. Figure credit: Sayra Espindola/Ella Vázquez-Domínguez
Describe the significance of this research for the general scientific community in one sentence.
The distribution, range limits and potential risk of the invasion of invasive species can be evaluated with genetic information and ecological niche modeling.
Describe the significance of this research for your scientific community in one sentence.
Evaluating interspecific interactions between native and non-native closely related species with genetic information and niche modeling approach was key to determine the distribution patterns, range limits and invasion risks of Trachemys scripta elegans.
Wetlands system in the valley of Cuatrocienegas, Coahuila, Mexico, where the endemic Trachemys taylori lives. Photo credit: Ella Vázquez-Domínguez
Espindola S, Vázquez-Domínguez E, Nakamura M, Osorio-Olvera L, Martínez-Meyer E, Myers EA, Overcast I, Reid BN, Burbrink FT. 2022. Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red-eared slider turtle. Molecular Ecology. https://doi.org/10.1111/mec.16356.
Molecular Ecology Spotlight 