Interview with the Author: Conservation of old individual trees and small populations is integral to maintain species’ genetic diversity of a historically fragmented woody perennial

What is the unit of conservation? Is it similar for different types of plants? How does the reproductive biology of the organism can inform the best practices in conserving threatened species? In her Doctoral research, Nicole Bezemer is studying Eucaliptus species from South Western Australia to better understand population dynamics in long-lived organisms and how this can lead to better management of their populations. Surprisingly, many of the small and fragmented populations of the two subspecies of E. caesia she studied are genetically differentiated at a fine spatial scale, and high levels of heterozygosity persists even in populations with a dozen of individuals. Nicole and colleagues suggest the clonal and perennial nature of E. caesia might contribute to these unusual patterns of genetic diversity and divergence, and suggest that traditional conservation genetic approaches might be detrimental for naturally fragmented species with these life-history characteristics. Read here about her experience in developing this research.

A multi-stemmed genet of Eucalyptus caesia at Mocardy Hill, Western Australia. Photo by NB.

What led to your interest in this topic / what was the motivation for this study? 
Eucalyptus caesia is an intriguing study species, given the combination of a distribution on scattered granite outcrops, a long history of geographic and genetic insularity, a capacity for individual longevity via lignotuber re-sprouting, a lack of recent recruitment in most known stands, and adaptation for pollination by nectarivorous birds. After completing my Honours research at the Boyagin stand of E. caesia, I was hooked. The present study came into fruition upon discovering that one of my PhD experiments, involving 6 months of controlled cross-pollinations, was killed by a series of frosts. I had already genotyped two large stands of E. caesia and I was curious about what patterns of genetic structure might exist in other stands, and across the species’ landscape distribution. 

What difficulties did you run into along the way? 
Some stands of E. caesia are located on immense granite outcrops, often hidden in hard-to-access gullies or behind thick barricades of vegetation. The first challenging aspect of the project was to find the sub-populations of E. caesia at each new location. For many populations, I did so by embarking on a Google Earth tour led by my supervisor, Steve Hopper, who has worked on the granite outcrop flora of south-west Australia and on E. caesia for nearly four decades. Nonetheless, I spent many hours traversing granite outcrops, sometimes in circles, which occasionally led to finding additional plants or, in the case of the E. caesia at Old Muntadgin, a previously undocumented population of several hundred plants.

What is the biggest or most surprising innovation highlighted in this study? 
I was surprised by the apparent lack of genetic interconnection between some stands over relatively small spatial scales. Given the long history of population fragmentation and reproductive biology of E. caesia (multiple modes of reproduction and gravity-dispersed seed), I anticipated that high levels of genetic differentiation would feature. Regardless, it was surprising to find that, in some instances, the level of genetic differentiation within stands exceeded that among stands. Another interesting result revealed by comprehensive genotyping were some very small census population sizes. Seven stands were comprised of fewer than ten unique multi-locus genotypes, and three locations had only one or two genotypes. Localised clonal reproduction is clearly of paramount importance to the persistence of these stands.

Moving forward, what are the next steps in this area of research?
The next step is to further test the genetic integrity of the two subspecies, E. caesia subsp. caesia and E. caesia subsp. magna, by genotyping plants from additional stands. Walyamoning and Yanneymooning are geographical outliers to other stands of subsp. caesia and occur within relatively close proximity to the group of subsp. magna populations located in the north-east of the species distribution. We propose to genotype a sample of individuals from the two outlier populations of subsp. caesia stands, and at three additional locations of subsp. magna, to test whether the two subspecies are genetically distinct even when populations are sympatric, and to determine if hybridisation has occurred.

What would your message be for students about to start developing or using novel techniques in Molecular Ecology? 
My message to other young or early-career researchers is to have a clear research outcome in mind before exploring the application of novel techniques. Avoid putting yourself in the position of having to come up with a hypothesis after the fact.

What have you learned about methods and resources development over the course of this project? 
Comprehensive genotyping at multiple spatial scales may provide a more complete picture of spatial genetic structure compared to studies where sampling efforts are focused on few individuals from many populations, or on many individuals from few populations. There is still much to be gained from population genetic studies, especially in understudied, biodiverse, endemism hotspots such as granite outcrops, and in understudied systems such as small, historically fragmented populations of long-lived trees.

Describe the significance of this research for the general scientific community in one sentence.
Anciently fragmented plant populations may be adept at persisting as small populations with low genetic diversity and limited genetic interconnection, and therefore attempts to connect such populations may be ineffective or even harmful.

Describe the significance of this research for your scientific community in one sentence.
Small populations of long-lived woody perennial plants, even those comprising a handful of individuals, may contain unique genotypes that contribute to overall species genetic diversity, and are worthy of conservation.

Enjoying the afternoon light from my field base camp underneath Eucalyptus caesia at Boyagin Rock. Photo by NB.

Summary from the authors: The rise and fall of differentiated sex chromosomes in geckos

Link to the paper: https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15126

The Madagascar ground gecko (Paroedura picta) is a member of one of the few vertebrate lineages suspicious of the loss of highly differentiated sex chromosomes. Photo credit: Petr Jan Juračka.

Differentiated sex chromosomes such as XX/XY chromosomes of viviparous mammals and ZZ/ZW sex chromosomes of birds with highly degenerated Y and W, respectively, evolved in animals multiple times. Their noteworthy convergent characteristic is the evolutionary stability, documented among amniotes for dozens of millions of years in mammals, birds, and some lineages of lizards, snakes and turtles. The differentiation of sex chromosomes stemming from the cessation of recombination between them is assumed to be largely a one-way process. We found that the differentiated ZZ/ZW sex chromosomes with highly degenerated W of the Madagascan geckos of the genus Paroedura were likely present in the common ancestor of the genus. However, the subclade of the genus seems to reverse the for a considerable evolutionary time highly differentiated ZZ/ZW sex chromosomes back to poorly differentiated state and thus represents a rare case of the loss of once highly differentiated sex chromosomes. Notably, the differentiated ZZ/ZW sex chromosomes of these geckos share genes with the XX/XY sex chromosomes of viviparous mammals and the ZZ/ZW sex chromosomes of lacertid lizards, as well as with the XX/XY sex chromosomes of iguanas and ZZ/ZW sex chromosomes of softshell turtles. Along with other analogous cases which we summarize in our contribution, this finding reinforces the observation that particular chromosomes are repeatedly co -opted for the function of sex chromosomes in amniotes.

The reconstruction of the evolutionary history of sex chromosomes in the gecko genus Paroedura as revealed by the distribution of the sexual differences in copy numbers of genes linked to differentiated ancestral Z chromosome of the genus. Note that these genes were originally likely autosomal, i.e. they had the same number of copies in males and females (yellow). In the common ancestor of the genus, these genes had twice as many copies in males (ZZ) than in females (ZW) as a consequence of their loss from the degenerated W (violet). Still later in a subclade of the genus, the same genes turned back to the same copy numbers in both sexes (light blue) suggesting a reversal of the ancestral differentiated sex chromosomes back to poorly differentiated state.

Interview with the author: A guide to the application of Hill numbers to DNA based diversity analyses

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Diversity assessment procedures in traditional and DNA sequencing‐based approaches. Recorded entities need to be classified into types, before each type is weighed according to its relative abundance and the order of diversity (q). Note the example refers to an abundance‐based, rather than incidence‐based, approach

What are Hill Numbers? What do they have to do with estimating biodiversity? How can you use them as a Molecular Ecologist? Read the recent review in Molecular Ecology Resources by Antton Alberti and Thomas Gilbert on this topic, and read the interview with Antton below to learn how they think about Hill numbers and their applications to metabarcoding. Also, check hilldiv, “an R package to assist analysis of diversity for diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses based on Hill numbers, using OTU tables and associated phylogenetic trees as inputs. The package includes functions for (phylo)diversity measurement, (phylo)diversity profile plotting, (phylo)diversity comparison between samples and groups, (phylo)diversity partitioning and (dis)similarity measurement. All of these grounded in abundance-based and incidence-based Hill numbers.”

What led to your interest in this topic / what was the motivation for this study? 
Measuring, estimating and contrasting biological diversity are central operations in most ecological studies. In the last decades, dozens of diversity indices and metrics have been proposed, each with their individual strengths and weaknesses, and specific mathematical assumptions. The measures that many of them yield are difficult to interpret, because the values might refer to abstract units, which lack an straightforward interpretation for non-specialists. We believe that the statistical framework developed around the Hill numbers overcomes many of these problems, and provides a statistical toolset that is extremely useful for ecologists. Besides, Hill numbers enable incorporating complementary information, such as phylogenetic dissimilarities across organisms, which are really handy for molecular ecologists who can easily build phylogenetic trees from metabarcoding data.

What difficulties did you run into along the way? 
We are a molecular ecologist and an evolutionary biologist that use many different mathematical tools, but are not expert mathematicians. Hence, of the main challenges was to make sure that all the statements and mathematical interpretations were correct!

What is the biggest or most surprising innovation highlighted in this study?
The aim of our review was to demonstrate to ecologists, who like us might have a limited mathematical background, that implementing the framework developed around the Hill numbers is not difficult, and has big potential gains. In our review we gathered information and tools generated by others, mainly Lou Jost, Anne Chao and Chun-Huo Chiu, and displayed them in a comprehensive way for molecular ecologists. We have tried to explain complex mathematical formulations in layman terms, exactly as we would like others to explain us other contents we are not familiar with. We have provided examples and pieces of code, that we hope will encourage other researches to use these tools.

Moving forward, what are the next steps in this area of research?
Our article mainly focuses on diversity measurement from data generated using DNA metabarcoding. While bioinformatic methods to generate metabarcoding data have received much attention in the last decade, the impact of the statistical approaches used to analyse diversity has been less studied. Assessing their impact and providing guidelines for selecting the tool best suited to address specific questions with specific types of data, will be an important next step in the area of metabarcoding-based diversity analyses.

What would your message be for students about to start developing or using novel techniques in Molecular Ecology? 
Despite the fact that they might at first seem complex and abstract, bioinformatic and statistical tools are necessary to address ecological questions. Hence, we would encourage students to try to understand the basic bioinformatic and statistical procedures, so as to be able to select the best tools to address their research questions.

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Differences between abundance‐based and incidence‐based Hill numbers. The Hill numbers yielded for the entire system are different depending on the approach employed. In abundance‐based approaches, the DNA sequence is the unit that the diversity is computed on, while in incidence‐based approaches, it is the sample the unit upon which the diversity is measured. (*) The asterisk indicates that the equations are undefined for q = 1, thus in practice either the 1D formula shown in Table 1 or a limit of the unity must be used, for example, q = 0.9999. However, q = 1 is used for the sake of simplicity

What have you learned about methods and resources development over the course of this project?
That its not the most broadly-employed tools that are always the best way to address scientific questions!

Describe the significance of this research for your scientific community in one sentence.
Hill numbers provide powerful, solid and versatile tools with which to carry out most of the analyses that are needed to assess biological diversity within a common statistical framework.

Interview with the author: Killer whale genomes reveal a complex history of recurrent admixture and vicariance

By Robert Pittman – NOAA (http://www.afsc.noaa.gov/Quarterly/amj2005/divrptsNMML3.htm%5D), Public Domain, https://commons.wikimedia.org/w/index.php?curid=1433661. Two killer whales jump above the sea surface, showing their black, white and grey colouration. The closer whale is upright and viewed from the side, while the other whale is arching backward to display its underside.

In this study, Foote et al. study the complex demographic history of killer whales and show how episodic gene flow is ubiquitous in their natural populations. This observation adds to the incresing recognition that the traditional geographical characterization of populations (i.e., allopatry, parapatry, and sympatry) is dynamic over time. Although in general it is difficult to perform deep sampling across the range of a species, cut through artificial taxonomic boundaries, and access enough genomic resources for a taxon, their journey is a great example as to how to do this, and how powerful population genetic methods can reveal the history of vagile and amply distributed species on earth.

What led to your interest in this topic / what was the motivation for this study? 
I’ve been working together with Phil Morin at Southwest Fisheries Science Centre for the last ten years, using genetic data to try and unravel the complex demographic and evolutionary history of killer whales. Some of the key questions have been, whether killer whale ecotypes arose from independent founder events and secondary contact, or through gradual divergence in sympatry. This study started out trying to model those processes (in collaboration with Laurent Excoffier) using genomes we had previously sequenced for a subset of the well-described killer whale ecotypes. We struggled to find a good model to fit the data, and it eventually became clear that we just had too few pieces of the jigsaw to be able to see the complete picture. We decided to cast a wider net and looked back at our previous global study published in Molecular Ecology in 2015, to select a dataset of samples that was representative of the global genetic variation in killer whales for genome sequencing. Having worked in the Centre for GeoGenetics, Copenhagen and the CMPG, Bern – both largely focused on human genetic variation, and being keen follower of that literature, it was a great opportunity to apply methods developed in that field on the killer whales.

What difficulties did you run into along the way? 
Arguably, the biggest hurdle to overcome was bringing clarity to the very complex relationships between these killer whale populations. This was exacerbated by trying to include too many analyses in earlier drafts. We had a draft manuscript ready almost a year ago, which consisted of two parts: the demographic and evolutionary history of these populations; and the genomic consequences of these different demographic histories. However, this manuscript had become a behemoth! Thankfully, Jochen Wolf, one of the first coauthors to tackle a full read-through of this weighty tome, suggested this might be better digested in separate sittings. So the paper became focused on the evolutionary history and hopefully is an easier read…thanks to Jochen.

What is the biggest or most surprising finding from this study? 
The ghost ancestry in the Antarctic types, which was something I had suspected we might find, was only really possible to test for due to methods being released as we were writing up the paper. Clearly, we weren’t the only ones thinking along these lines, as several other studies on species including seabass and bonobos released similar findings of ghost ancestry around the same time – this is really nicely highlighted in the perspective by Jacobs and Therkildsen, in the same issue of Molecular Ecology.

Moving forward, what are the next steps for this research?
A key interest is how variation in the genomic architecture, principally local recombination rate, influences the frequency of different ancestry components within a population and how that relates to past demographic history. As eluded to above, we have results on the impacts of these complex demographic histories in a study we are just finishing up. As a follow up, we will explore further the history of the ghost ancestry, to find out if it conveys any benefits (adaptive variants) or costs (mutation load), such as we see in Neanderthal ancestry in modern humans.  And ultimately we hope to better understand the underlying processes determining the genetic differentiation between sympatric killer whale ecotypes.

What would your message be for students about to start their first research projects in this topic?
I’d recommend having a good understanding of the concepts, methods and models commonly used in population genetics. I’ve been reading Matt Hahn’s Molecular Population Genetics book and Graham Coop’s Population Genetic Notes, which is freely available to download from Graham’s brilliant blog – gcbias.org. Often methods will give seemingly contradictory results, and so it is important to be able to understand how those analyses work to be able to puzzle out the different signals from different methods. The two resources above will also help you design your sampling scheme and plan your study out ahead of time, so that it is best suited to the question you are trying to address.  

What have you learned about science over the course of this project?
I feel I’ve learned a lot. It has been a labour of love, the sequencing even being partly funded by my Swiss pension scheme which I cashed in when I left Bern. So, I didn’t feel like I had to please anyone but myself, and to be honest, I thought it was such a complex story and quite species-focused that it wouldn’t be of broad interest. But in fact, it is the paper that I’ve had the most direct and positive feedback on from colleagues. So that has been both surprising and satisfying. The lesson I take from that is to always try and work on something that you are passionate about.

I also feel that as I was learning to better understand the methods and the analyses, I was trying to really hard to pass that on to the reader, assuming they may be as naïve as I was before I delved into this study. And based on the feedback, that is something that folk appreciate, and which makes the paper more intuitive and transparent. I have tried to expand upon this in a youtube video.

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(a) Sampling locations of the individuals for which 26, 5× coverage genomes were generated (global data set). Marker colours are as per the PCA legend. An additional 20 low coverage genomes (ecotype data set) were used in some analyses, see Foote et al. (2016) for sampling locations. (b) PCA plots of the combined global and ecotype data sets, and (c) the global data set (one sample per population). (d) Individual admixture proportions, conditional on the number of genetic clusters (K = 2 and K = 3), for the combined global and ecotype data sets, and for (K = 2) (e) when only one 5× coverage genome per population from the global data set is included

Describe the significance of this research for the general scientific community in one sentence.
Genomes sequences are a record of the many genealogies that comprise our ancestry. Our study highlights how a relatively small number of genomes can reveal the complex relationship among populations, past and present, across the globe.

Describe the significance of this research for your scientific community in one sentence.
Our study highlights that marine scientists need to consider connectivity through time, to past populations, as well as space to better understand the genetic composition of present-day populations.

Interview with the author: Ecological gradients drive insect wing loss and speciation: The role of the alpine treeline

Many insects have lost their wings at high altitude, and this might have contributed to their diversification. In their recent paper, Graham A. McCulloch and colleagues study loss of wings in stone flies from New Zealand and found that the alpine tree line, rather than altitude alone better explains the ecotypic distribution of these morphs across geography. Their system paves the way for powerful studies of convergence and adaptation and how, like in other systems, loss of a trait, might be intrinsically related to many cases of deterministic evolution in nature. Below, we learn about their journey in discovering some of the causes of diversification of alpine insects and their assemblages.

Sampling wing-reduced stoneflies in the alpine stream habitats of southern New Zealand. Photo by Graham McCulloch

What led to your interest in this topic / what was the motivation for this study? 
An astonishingly large proportion (20%) of New Zealand’s stonefly species (freshwater insects) have reduced wings as adults, with most of these low-dispersal lineages found in alpine environments. Our research group is interested in the ecological drivers and genomic basis of this fascinating pattern: how and why do insect wings become reduced/lost, and what are the consequences of this? The Zelandoperla fenestrata complex in particular is an outstanding system for studying these questions, as this widespread polymorphic stonefly has full-winged populations at low altitudes, but vestigial-winged populations up in the mountains. When we started looking within individual streams, we were amazed to find strikingly clear altitudinal clines within this ‘species’, where wings become dramatically smaller as we move a few hundred metres up a mountainside. This was an exciting finding, so understanding the ecological and genomic basis of these clines became the focus of our research.

What difficulties did you run into along the way?
Our study involved working in rugged mountain landscapes, which can be both exciting and spectacular – but also carries challenges. You need to be fit, and to persist in sometimes uncomfortable conditions. It also can be notoriously difficult to find adults of these stoneflies in the wild, even in the right season, so it was a big logistical breakthrough to be able to successfully rear large nymphs to adulthood in the lab. This breakthrough really allowed us to get a good handle on the system morphologically.

What is the biggest or most surprising finding from this study?
There were several unexpected and exciting discoveries from this project: (i) We were particularly excited to find a tight association between wing-reduction and the alpine treeline, both at a fine scale (within our transects), and at a broader scale (using distributional analyses). These results suggest that harsh conditions above the alpine treeline (most likely high winds) are a major driver of insect wing loss. (ii) The genome-wide divergence between the full-winged and vestigial-winged ecotypes within each stream was particularly surprising, as these ecotypes have overlapping distributions (and interbreed in the wild). Likewise, the genome-wide divergence between the two independent vestigial-winged alpine populations, from streams less than 3km apart, was astonishing given the small distance involved.

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The alpine treeline governs the distribution of full‐winged versus vestigial‐winged stoneflies. (a) Jitter plot illustrating the bimodal wing‐length data associated with distinct Zelandoperla fenestrata ecotypes collected from two parallel streams (Lug Creek, Six Mile Creek) on the Rock and Pillar Range, South Island, New Zealand. Inset: dorsal view of full‐winged (above) and vestigial‐winged (below) Z. fenestrata ecotypes (body length 15 mm). (b) The alpine treeline in Lug Creek, where riparian tree cover rapidly gives way to tussock grassland. (c) Altitudinal clines in relative proportions of wing ecotypes in Lug Creek (dashed line) and Six Mile Creek (solid line). Vertical green lines indicate the altitude of the alpine treeline for each stream (Lug Creek = dashed line, Six Mile Creek = solid line)

Moving forward, what are the next steps for this research?
We plan to examine additional ecotypic clines in this species across the lower South Island. This next step will allow us to assess whether the genome-wide differentiation we observe between ecotypes in the Rock and Pillar range is found in other regions. By genetically characterising geographically (and phylogenetically) independent clines we can then test for independent wing loss events (associated with the alpine treeline) more broadly. We are also in the process of using genomic (GWAS) and transcriptomic approaches to identify the key genes underpinning wing-reduction in Z. fenestrata (and potentially other alpine stonefly species). We are really keen to find out whether the wing reduction events in different streams and mountains involve the same genes dispersed by winged populations (e.g. transporter hypothesis), or whether they are completely independent.

What would your message be for students about to start their first research project in this topic?
Discovering this fascinating research system took time – including quite a bit of ground-work exploring out in the field, background research to understand the species complex, including discussions with entomologists, taxonomists, looking at museum collections, and then putting a team together with the skills to get the work done. So it didn’t happen overnight, and it took time to set the stage and to know for sure that we’d found a good system. But it really started from curiosity about evolution, as well as our ongoing interest in New Zealand’s landscapes and natural history. So our most important advice is to follow your curiosity, and keep exploring the natural world.

What have you learned about science over the course of this project?
We have learned that there are still plenty of exciting discoveries yet to be made about nature, evolution and ecology – and that the more we discover, the more new questions emerge. It might take five or ten years to really understand a system to the extent that you can begin to answer the most exciting questions. We certainly expect to keep working on this project for many years to come.

Describe the significance of this research for the general scientific community in one sentence.
We have discovered what we believe to be a ‘textbook example’ of speciation in action – one that makes evolutionary biology easier to teach and understand.

Describe the significance of this research for your scientific community in one sentence.
This story brings together ecological and genomic tools to reveal clear-cut cases of parallel ecological speciation over surprisingly small spatial scales.

Interview with the author: Arms races with mitochondrial genome soft sweeps in a gynodioecious plant, Plantago lanceolata

Professor Deborah Charlesworth discusses her research on the origin of mitochondrial male sterility mutations. Some hermaphroditic plant species have a fraction of individuals with flowers that are male sterile and only express the female function. This reproductive system is known as gynodioecy, and it can create conflicts between genes favouring male or female function. In a paper recently published in Molecular Ecology, Bergero et al. explore the persistence of gynodioeccy in the Plantago system and test two fundamental hypothesis for the maintenance of gynodioeccy in nature. Deborah Charlesworth chatted with us and gave us some wonderful insights as to how this research started and where it is going now. Don’t miss it!

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Plantago lanceolata populations studied. The locations are indicated by small black dots for the NES populations, connected by arrows with pie charts showing the frequencies of the two major haplotypes described in the text (the key shows the colours denoting the two haplotypes, which are visible in the online version), and by large pink dots for the non‐NES populations, all of which have only haplotype 1. The sample sizes can be ascertained from Figure S1) [Colour figure can be viewed at wileyonlinelibrary.com]

What led to your interest in this topic / what was the motivation for this study? 
The phenomenon of male-sterility in plants has been a puzzle for a long time, and the discovery that mitochondrial mutations are involved only deepened the mysteries further, because it became clear that the mutations were not the usual kinds, such as point mutations in or deletions of coding sequences. I hoped that getting sequences of the mitochondrial genome might be helpful

What difficulties did you run into along the way? 
There were no major difficulties in getting the sequence data, though because plant mitochondrial genomes are very larger, we could sequence only coding regions of genes. Of course, some genes proved not to include any sequence variants, so the number of genes with useful data was reduced, compared with our initial hoped.

What is the biggest or most surprising finding from this study? 
A surprising finding was that some populations that contain females, and therefore certainly have male-sterility mutations present, did not have variants in the mitochondrial genes we sequenced. Because male-sterility is generally cytoplasmically inherited, it seems unlikely that in this species it is due to nuclear male-sterility mutations (especially as earlier excellent genetic studies in our study species strongly support cytoplasmic inheritance in populations in the Netherlands). It was also unexpected to find that, in most European populations sampled, the only variants were pretty rare, so that the entire mitochondrial genome behaved almost as a single genetic “allele” or “haplotype”, whereas populations from one region in northern UK had two different haplotypes, with variants seen in several genes.  

Moving forward, what are the next steps for this research? 
The next steps will have to be taken by others, as I am too old to continue (I now work on sex chromosome evolution in a fish, and one project is enough at my age). But I hope that others will add mitochondrial sequence data to see whether other plants with cytoplasmic male-sterility have mitochondrial haplotypes that are associated with the femaleness factors. It will also be good to test whether, as in our study species, multiple sequence variants are associated into haplotypes, or not. It is known that mitochondrial genomes can undergo a process of genetic recombination, and studying sequence variants can tell us whether this occurs often in natural populations, or not. If it occurs often, then it should be possible to identify sequence variants that are associated with male-sterility. If, however, exchanges between haplotypes occur very rarely, it could prove to be very difficult to find the actual mutations involved. Another intriguing possibility is that male-sterility is caused by parts of the genome other than the protein-coding genes, and that, even if those genes do not undergo recombination, other parts of the genome might do so, perhaps producing the variants that lead to male-sterility. It has long been known that mitochondrial genome rearrangements seem to be involved in male-sterility, rather than point mutations, and I have sometimes wondered whether perhaps this phenotype occurs when parts of the genome are duplicated, which might lead to down-regulation of genes that suddenly have an extra copy, or partial copy, as occurs in transgenic plants.

What would your message be for students about to start their first research projects in this topic? 
Find something easier unless you are really clever. On the other hand, my experience has been that one often gets puzzling results, and they often prompt one to think about the question in a different way. In fact, I would say that one almost never starts by asking the right questions, but that these tend to emerge as one sees the data and thinks about them.

What have you learned about science over the course of this project? 
You never know what you will turn up, and whatever it is, it often raises more puzzles than it solves.

Describe the significance of this research for the general scientific community in one sentence.
This was the first multi-gene sequence data collected to study mitochondrial male sterility in a plant, and it showed that, in our study species, this genome recombines rarely, at least in the parts we could study, and, by extension, across the entire mitochondrial genome.

Describe the significance of this research for your scientific community in one sentence.
This study is just a small step in attempts to understand the puzzle of how mitochondrial male sterility mutations may arise.

Interview with the author: Dynamics of genomic change during evolutionary rescue in the seed beetle Callosobruchus maculatus

We interviewed graduate student Alexandre Rêgo and Professor Zach Gompert from Utah State University about their work on evolutionary rescue in seed beetles where they explore how demographic history affects parallel evolution at the genetic level. Their results have important implications for or understanding of repeatability and predictability of evolution. Read the full text below:

Alexandre Rêgo, Frank J. Messina, and Zachariah Gompert. (2019) Dynamics of genomic change during evolutionary rescue in the seed beetle Callosobruchus maculatus. https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15085?af=R

Drawing of C. maculatus (by Amy Springer)
Drawing of Callosobruchus maculatus (by Amy Springer)


What led to your interest in this topic / what was the motivation for this study?

(AR and ZG) We were interested in evolutionary rescue, that is in cases where population decline and extinction in a marginal or stressful environment is halted and reversed by adaptive evolution. We were especially interested in what patterns of change and natural selection look like across the genome during rescue. How many genes are involved? How much do gene/allele frequencies change? And how fast? We turned to an evolve-and-resequence experiment with Callosobruchus maculatus seed beetles for this. Past work has shown that these beetles can barely survive on lentils (survival rates are ~1%), but that they sometimes can rapidly adapt and persist on this novel host (survival rates can climb to 80 or 90% in fewer than 20 generations).

What difficulties did you run into along the way?

(AR and ZG) Extinction. We were drawn to this system because of the potential for adaptation or extinction, and because of the related extraordinary pace and degree of adaptation when it occurs. We wanted to measure selection and genome-wide evolutionary change during evolutionary rescue, but (for better and worse) only one of 10 replicate lines was rescued. This limited our ability to assess parallelism during rescue, but also highlighted how real the possibility of extinction (in the absence of rapid adaptation) is in this system.

What is the biggest or most surprising finding from this study?

(AR and ZG) We were most shocked by just how rapid evolutionary changes were at the molecular level. We saw numerous cases where allele frequencies at multiple (albeit not always independent) genetic loci shifted by 20-40% or more in a single generation. This is really much more extreme than rates of change often considered.

Moving forward, what are the next steps for this research?

(AR and ZG) We are taking our work on C. maculatus in two directions. First, we have finished creating and sequencing crosses between the lentil adapted and source populations to identify genetic variants associated with specific fitness components (e.g., development time and adult size) on lentil. This will make a nice comparison with the selection scans. Second, we are now working with additional populations, some of which do a bit better on lentil, to examine consistency in genomic change across lines in lentil adaptation and to figure out whether hybridization facilitates adaptation to this marginal host.

Adult C. maculatus on their ancestral host, mung bean.

What would your message be for students about to start their first research projects in this topic?

(AR) Attention to detail is critical. Be as careful as possible in how you plan and organize your data on analyses. Population genomic analyses, especially with approximate Bayesian computation, generate an inordinate amount of output. And you will almost certainly want to re-run things with slightly different parameters, etc., so carefully documenting everything is critical.

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

(AR) There are many things that must be done in order to complete a study, each requiring a different set of skills. As a graduate student, it can be daunting to acquire and become proficient at so many things. However, at the end of this study, I can look back and see that I have made progress as a scientists on many fronts. What I’ve learned from this project has provided me a solid foundation for my current studies on which I can further improve.

Describe the significance of this research for the general scientific community in one sentence.

(AR and ZG) Very rapid adaptation is possible when species or populations find themselves in harsh environments, sometimes this is enough to prevent extinction, and sometimes it isn’t.

Describe the significance of this research for your scientific community in one sentence.

(AR and ZG) Population genomic patterns associated with evolutionary rescue differ in subtle and not so subtle ways from patterns observed in other situations involving less extreme or softer selection, and thus warrant more study and consideration.