Interview with the author: Landscape genomic signatures indicate reduced gene flow and forest‐associated adaptive divergence in an endangered neotropical turtle

The Dahl’s Toad-headed turtle (Mesoclemmys dahli) is one of the 25 most endangered turtle species on Earth and one of the unlucky few that is constantly being compared to a toad. A previous study has shown that extensive habitat conversion and fragmentation in its native range in Colombia has led to genetic differentiation among populations. However, critical questions remain for the conservation and management of this species: how does habitat type and quality in this rapidly changing region influence gene flow? How can genomic data inform the management of this endangered species?

Dr. Natalia Gallego García (@NataGalle) and colleagues set out to answer these questions. Read below for an interview with Natalia about the challenges of working with such a rare species and how this study provides the foundation for a genetic rescue program for the Dahl’s Toad-headed turtle.

The critically endangered Dahl’s Toad‐headed turtle (Mesoclemmys dahli). Photo by N. Gallego García

What led to your interest in this topic / what was the motivation for this study? 
We conducted a previous population genetics study using microsatellite loci on this highly endangered species, in which we found significant genetic evidence of population fragmentation. In this follow-up study, we wanted to know how the current landscape, now composed of open grasslands for cattle instead of tropical dry forest, might be restricting gene flow and thus causing the observed fragmentation. We also wanted to know how this new anthropogenic environment was potentially driving local adaptation.

What difficulties did you run into along the way? 
The main difficulty was finding this rare species across its range to get the samples. Another difficulty was standardizing the RADseq protocol, as our research was the first genomic-level study on any side-necked (pleurodiran) turtle. Also, there is no reference genome for this species or for any closely related one, making the analysis of our data difficult. We had to assembly a de novo genome, which prevented us from running other analyses that could have allowed us to learn more about adaptive mechanisms to new environments.

What is the biggest or most surprising finding from this study? 
First of all, we were able to show that population fragmentation was related to habitat loss. However, we were expecting movement through grasslands to be costly, given that this is a forest species, but we found that from a scale of 1 (easy) to 1000 (hard) the cost of traversing grassland was only 13. We believe that this low cost is associated with the presence of water ponds built in the pastures for the cattle to drink, which are increasingly being used by this species. These ponds might be serving as a sort of stepping stone array of lower quality but still usable aquatic habitat, enabling movement over an otherwise hostile matrix. Our second surprising finding was observing possible adaptive divergence between populations occupying areas with more forest than populations in areas with almost no forest. This result suggests that the populations might be adapting to this new transformed environment. However, adaptation alone is not rescuing this species from the negative effects of fragmentation, and currently the species is facing a high risk of extinction.

Moving forward, what are the next steps for this research?
The next steps can be divided in terms of management and research. In terms of management, we are currently designing a genetic rescue program to reduce inbreeding and increase population genetic diversity, without disrupting the potential ongoing adaptation that we observed. In terms of research, we are currently assembling the genome of a closely related species, which will allow us to map the putatively adaptive loci found, and better understand how this species is adapting to its new transformed environment. This will also allow us to design a field and/or laboratory experiment to further explore the possibility of adaptation to altered, and degraded habitat.

What would your message be for students about to start their first research projects in this topic? 
Working with non-model, rare, and threatened organisms, although challenging, can lead to valuable information that is vital in their conservation. So, accept the challenge and stand up for those forgotten species. Any new information on a data deficient species will increase its chance of survival, which in itself already makes the research worthwhile.

What have you learned about science over the course of this project? 
Science always comes with exciting surprises that do not always comply with our expectations, and it usually leaves more questions than answers. But it is gratifying to contribute, even in a small way, to the understanding of complex processes that can eventually be applied to solve difficult problems, such as the conservation of an endangered species.

Describe the significance of this research for the general scientific community in one sentence.
Adaptation to habitat change can happen, but perhaps not quickly or completely enough to overcome the negative effects of population reduction and fragmentation.

Describe the significance of this research for your scientific community in one sentence.
Landscape genomics analyses provide evidence of reduced gene flow in a fragmented habitat, leading to harmful effects on a critically endangered neotropical turtle, despite its possible adaptation to the new anthropogenically created environment.

Citation
Natalia Gallego‐García, Germán Forero‐Medina, Mario Vargas‐Ramírez, Susana Caballero, & Howard Bradley Shaffer. (2019). Landscape genomic signatures indicate reduced gene flow and forest‐associated adaptive divergence in an endangered neotropical turtle. Molecular Ecology, 28(11), 2757-2771. https://onlinelibrary.wiley.com/doi/10.1111/mec.15112

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 authors: Parallel introgression and selection on introduced alleles in a native species

Species introductions serve as a natural laboratory to study introgression and selection. In a recent paper in Molecular Ecology, Rachael Bay and colleagues use introduced rainbow trout and native cutthroat trout to study hybridization, introgression, and selection. Bay et al. find evidence that some alleles have repeatedly introgressed from rainbow trout into cutthroat trout in independent populations. Their results suggest that selection has played an important role in this introgression, and highlight the usefulness of species introductions for understanding the predictability of evolution. Below, get a behind the scenes look at this work from author Rachael Bay.

West slope cutthroat trout. Photo by Ernest Keeley.

What led to your interest in this topic / what was the motivation for this study? 
This study combined two of my primary research interests. The first is: How do humans alter the evolutionary trajectories of species? By introducing rainbow trout, we have provided access to an extended gene pool for native cutthroat trout species. Previous studies have shown that hybrids have lower fitness, but with hybridization and recombination continuing over decades we can investigate whether particular rainbow trout alleles might be adaptive in westslope cutthroat trout. This study also speaks to the predictability of evolution. The stocking of rainbow trout has resulted in a highly replicated evolutionary experiment. Do we find the same alleles repeatedly under positive selection in independent watersheds?

What difficulties did you run into along the way? 
One of the main difficulties was trying to understand the null expectation. How much introgression should we expect between the two species and what fraction of that introgression is a result of selection? This depends on not only the strength of selection, but also on other demographic factors like population size, and stocking history. Ultimately, we decided to use simulations in order to understand the level of selection necessary to produce the patterns of introgression we were seeing in hybrid populations.

What is the biggest or most surprising finding from this study? 
We found that across multiple independent locations, the same rainbow trout alleles rose to high frequency in hybrid populations, suggesting they were under positive selection. This is somewhat surprising because previous studies have suggested that hybrids have reduced fitness and have found broad signals of purifying selection against rainbow trout alleles. However, hybridization and backcrossing has been occurring for many generations, allowing plenty of time for recombination and allowing different parts of the rainbow trout genome to segregate more independently. So despite the fact that hybrids have lower fitness, there seem to be a few regions of the rainbow trout genome that may be advantageous to westslope cutthroat trout.

Moving forward, what are the next steps for this research?
While our results suggest that some rainbow trout alleles provide an adaptive advantage we still have yet to identify the selective force. Is there some component of the abiotic environment to which these alleles are better adapted? Do these alleles confer higher reproductive success or fecundity? Rainbow trout have been successfully introduced to many different environments across North America – do alleles at high frequency in hybrid populations also explain the invasion success of rainbow trout?

What would your message be for students about to start their first research projects in this topic? 
I think it’s really important to choose your system carefully. We didn’t start out thinking about this as a project on trout, we started thinking about human-induced evolution and repeatability. It took a long time and a lot of thought to realize that a broadly introduced species was the perfect natural experiment for the questions we had.

What have you learned about science over the course of this project?
One of the cool things about this project is that it is a demonstration of how science evolves as technology evolves. Through a collaboration with Rick Taylor, we were able to learn something new from samples that had been sitting in a freezer for many years. Previous researchers had used these samples to analyze rates of hybridization across British Columbia and Alberta, but the increasing ease of high-throughput sequencing allowed us to take a deeper dive and look at genome-wide signals of introgression. So you never know how experiments you are doing now will contribute to knowledge in the future!

Describe the significance of this research for the general scientific community in one sentence.
Some genes from introduced rainbow trout can confer an adaptive advantage in native cutthroat trout species.

Describe the significance of this research for your scientific community in one sentence.
Rainbow trout alleles show consistently high levels of introgression into the westslope cutthroat trout genome across multiple independent watersheds.

Read the full article:
Bay RA, Taylor EB, Schluter D. Parallel introgression and selection on introduced alleles in a native species. Mol Ecol. 2019;28:2802-2813. https://doi.org/10.1111/mec.15097

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: Antimicrobial resistance in gull populations

Antimicrobial resistance is an increasing concern worldwide, but our knowledge of how multi-drug resistant bacteria get around in wildlife populations is relatively poor. In their recent paper, Ahlstrom et al. triangulate results from multiple approaches to help address this important issue in gulls in Alaska. Christina Ahlstrom from the USGS  Alaska Science Center gives us an insider take on their really interesting work..

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

It has been speculated that birds could potentially transport antimicrobial resistant bacteria via their local movements and long distance migration, however there has been little direct research to investigate this. We previously detected antimicrobial resistant E. coli in gulls at a local Alaska landfill and at the mouth of a nearby river where Alaska residents harvest sockeye salmon during the summer. Therefore, we sought to investigate whether there was evidence for dissemination of antimicrobial resistant bacteria by gulls at these two locations and other nearby sites.

cahlstrom_gull.jpg
Image credit: Andrew Ramey, USGS

What difficulties did you run into along the way? 

In order to assess dispersal of antimicrobial resistant bacteria, we had to first understand movement patterns of birds. However, capturing gulls is no easy feat! To catch birds, we hand tied ~2,000 nooses made of fishing line attached to mats,  camouflaged them with plastic grocery bags, baited them with chips and fish guts, and spent long days in the landfill waiting for wary gulls to land on our “noose carpets”. The elation of finally capturing and successfully tagging a gull overpowered the discomfort of the bites and scratches received while attaching a satellite transmitter.

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

We found multidrug resistant bacteria in many samples collected from gulls in Alaska, a state with relatively little intensive agriculture. I think this finding is surprising, since many people associate antimicrobial resistance with this sector. It was also noteworthy that, although we found extensive evidence for dispersal of antibiotic resistant bacteria between the landfill and the mouth of a nearby river, we found much less evidence for dispersal between these sites and an area further upstream. This finding was congruent with few detected gull movements between this upriver site and the landfill or river mouth and highlights the strength of using multiple research approaches.

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

We are interested in exploring if gulls may disperse antibiotic resistant bacteria via long distance migratory movements. Many of the gulls that we marked in southcentral Alaska migrated to the Pacific Northwest and California. Other birds that we marked as part of ongoing research migrated to East Asia. We hypothesize that there may be differences in antimicrobial resistant bacteria harbored by gulls that have different migratory tendencies. We aim to investigate if there are indeed differences and whether they could be related to different areas that gulls inhabit during the annual cycle.

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

Start small and then build up to investigate larger research questions. The epidemiology of antimicrobial resistance is extremely complex. I found it was helpful to first explore what was happening in a single system and then work up from there. We analyzed antimicrobial resistant bacteria from wild birds at a single site, followed by a similar analyses at multiple nearby sites (this study), and our future research will explore similarities/differences at locations across Alaska. This approach has allowed us to fine-tune our analytical methods and hone in on the most relevant research questions.

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

Science is so diverse, but different disciplines can be surprisingly complementary. When I first became interested in molecular epidemiology, I never imagined I would someday use satellite telemetry to quantify wild bird movements. Collaborating with experts in other fields and combining information from diverse scientific disciplines is a powerful (and fun!) way to approach a research question. 

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

Antimicrobial resistance is not confined to hospitals nor to agricultural areas, but can be found in, and dispersed by, landfill-foraging gulls in Alaska.

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

Wildlife and the environment are important, yet often overlooked, components of the One Health triad – investigating these ecosystems can enhance our understanding of the epidemiology of antimicrobial resistant bacteria.

Find the paper here: Ahlstrom, CA, Bonnedahl, J, Woksepp, H, et al. Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial‐resistant Escherichia coli on the Kenai Peninsula, Alaska. Mol Ecol. 2019; 28: 2531– 2545. https://doi.org/10.1111/mec.15101

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.