Tropical rainforests are teeming with life, and species inventories are far from complete. We know even less about the intricate ecological interactions that form the basis of tropical communities. One fascinating but poorly studied example is the host-symbiont network between army ants and their rich assemblages of arthropod guests. In issue 20 of Molecular Ecology, we studied the biodiversity and host specificity of such a network in a Costa Rican rainforest. Combining DNA barcoding with morphological identification, we discovered 62 species parasitizing the six available Eciton army ant host species, including beetles, flies, a millipede, and a silverfish. At least 14 of these species were new to science. Host specificity varied markedly, ranging from specialists parasitizing a single host, to host generalists occurring with all available host species. This highlights the immense diversity of army ant guests, both in terms of their species numbers and their ecological interactions with the ants. Like many of their cohabitants in tropical ecosystems, army ants are sensitive to habitat degradation, and extinction of the ants will go hand in hand with an extinction cascade of their numerous guests. We must therefore enhance our efforts to protect tropical rainforests to preserve such marvelous host-symbiont systems.
Article: Christoph von Beeren, Nico Blüthgen, Philipp O. Hoenle, Sebastian Pohl, Adrian Brückner, Alexey K. Tishechkin, Munetoshi Maruyama, Brian V. Brown, John M. Hash, W. E. Hall, Daniel J. C. Kronauer (2021). A remarkable legion of guests: Diversity and host specificity of army ant symbionts. Molecular Ecology, 30(20), 5229-5246. https://doi.org/10.1111/mec.16101
In a recent paper in Molecular Ecology, Argyropoulos and Ruybal-Pesántez et al. (2021) investigated the effects of indoor spraying on Plasmodium falciparum, the human malaria-causing protist. They find that 3 consecutive years of indoor spraying reduced transmission and prevalence of malaria by 90% and 35%, respectively, in the high malaria transmission site they surveyed. Despite these large reductions, a change in genetic diversity in P. falciparum that would indicate a large reduction in population size was not detected, illustrating the incredible resiliency of this parasite. Based on these data, the authors suggest that limiting malaria transmission in high transmission areas will require continued indoor spraying or other interventions such as mass drug administration. See the full article and interview with first authors Argyropoulos and Ruybal-Pesántez below for more details of this exciting work.
What led to your interest in this topic / what was the motivation for this study? Global efforts over the past 20 years have significantly reduced malaria mortality and morbidity around the world, but malaria transmission remains high in many countries in sub-Saharan Africa. A major challenge is the fact that most Plasmodium falciparum infections are asymptomatic creating a persistent parasite reservoir that continually fuels transmission to mosquitos. Our group has a long-standing collaboration with colleagues at the Navrongo Health Research Centre and Noguchi Memorial Institute of Medical Research in Ghana, and the University of Chicago in the US, to conduct longitudinal field-based epidemiological studies of the P. falciparumreservoir in Bongo District, Ghana (Tiedje et al., 2017). Our motivation for this study was to understand P. falciparum transmission dynamics in the context of the roll-out of a malaria control intervention by combining population genetics with more traditional epidemiological and entomological parameters. Our previous research in Bongo District established there was high levels of P. falciparum genetic diversity with no population structure (Ruybal‐Pesántez et al., 2017). We were therefore interested in exploring whether the addition of a short-term indoor residual spraying (IRS) programme against a background of widespread long-lasting insecticidal nets (LLINs) would bottleneck this P. falciparum population in Bongo and lead to reductions in diversity and changes in population structure.
What difficulties did you run into along the way? One of the major technical limitations in P. falciparum genotyping is phasing multi-genome infections to assign multilocus haplotypes. Eighty per cent of the population of all ages where we work in Ghana have multiple diverse parasite genomes. This is also a problem for whole genome sequencing of isolates. To get around this problem, we focus on genotyping monoclonal infections using panels of multi-allelic microsatellite markers or biallelic SNPs. In high-transmission settings like our study site in Ghana microsatellite genotyping of P. falciparum provides increased power of inference and higher resolution than biallelic SNPs (Anderson et al., 2000; Ellegren, 2004; Selkoe and Toonen, 2006).
What is the biggest or most surprising innovation highlighted in this study? In our paper, we find that despite the addition of three-rounds of IRS against a background of LLINs between 2013 – 2015, it did not lead to a population bottleneck or dramatic change in parasite genetic diversity. This was striking because IRS did achieve a >90% reduction in local malaria transmission intensity and 37.5% fewer malaria infections in the community. The potential for rebound of P. falciparum transmission is therefore highly likely if these control programmes are not implemented long-term.
Moving forward, what are the next steps in this area of research? Population genomic approaches are increasingly being applied to enhance our understanding of epidemiology, transmission dynamics, and public health strategies for a variety of pathogens. In the malaria field, the potential of genomic data to guide control and elimination strategies has been recognized but is still in early stages with respect to its translation into general practice. In our paper, we highlight that genomic surveillance is pivotal to assess progress towards achieving the World Health Organisation Global Technical Strategy for Malaria 2016-2030 targets. Along with our collaborators in Ghana, we have conducted follow-up surveys in our study site to track the long-term implications of this IRS intervention, as well as other interventions that have been rolled out across Bongo District since 2015. We are also applying phylodynamic approaches to characterize variant antigen genes to further explore the impact of interventions on P. falciparum adaptation and fitness, as alternate but complementary surveillance metrics in this high-transmission setting.
Dionne Argyropoulos, co-first author on this paper, is investigating the neutral and adaptive genetic diversity of P. falciparum in these follow-up surveys and in the context of other control interventions as part of her PhD research. Shazia Ruybal-Pesántez, co-first author on this paper, is now currently applying a suite of genomic epidemiology approaches to better understand residual and resurgent malaria transmission dynamics in the Asia-Pacific and Americas regions as part of her post-doctoral research.
What have you learned about methods and resources development over the course of this project? Firstly, it is important that you understand the basic principles of the concepts that you are using. It may seem rudimentary, but these principles will ensure that you are answering the scientific question that you are interested in and are maintaining scientific integrity throughout the research process. Asking for help or support from others in your field is also useful to bounce ideas and enhance your understanding of your research findings. The most exciting part of Molecular Ecology is how we utilise the insights molecular techniques to answer big picture questions. Our study integrated population genetics and genomic surveillance to address key research questions about malaria transmission and control interventions. To do this, we used existing molecular techniques (i.e., microsatellites) in new ways (i.e., to evaluate IRS over time). We also believe that it is important to not be afraid to apply novel techniques to new research questions, such as using bioinformatic tools and various packages in R.
What would your message be for students about to start developing or using novel techniques in Molecular Ecology? This project was unique as it involved field sample collection and processing, parasite genotyping, data generation and for the analysis required combining traditional epidemiological methods with population genetics and genomics approaches. When working with large sample sets and datasets, it is critical to pay attention to detail during data generation, curation and downstream analyses. Developing and strengthening coding skills was instrumental in enabling us to execute the necessary analyses of these data. We found R to be an incredibly useful resource to document our analyses and facilitate discussion and interpretation of the data with colleagues, while ensuring reproducibility of our work. We used several well-established R packages for data management and the population genetics analyses. Overall, this multidisciplinary project would not have been possible without being part of a multi-disciplinary team with a wealth of knowledge and the strong collaborations with experienced researchers in Ghana.
Describe the significance of this research for the general scientific community in one sentence. We show how parasite genetics can be harnessed to better understand the efficacy of malaria control interventions, particularly by identifying key factors leading to parasite resilience that may not be reflected in other commonly used evaluation metrics.
Describe the significance of this research for your scientific community in one sentence. Short-term indoor residual spraying with insecticides did not cause a dramatic change on the genetic diversity of P. falciparum in Bongo District, Ghana, therefore long-term strategies are necessary to genetically bottleneck the parasite population.
Argyropoulos DC*, Ruybal-Pesántez S*, Deed SL, Oduro AR, Dadzie SK, Apparu MA, Asoala V, Pascual M, Koram KA, Day KP, Tredje KE. THe impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa. Molecular Ecology. https://doi.org/10.1111/mec.16029. (*joint lead authors)
Effective population size (Ne) is crucial parameter in evolutionary biology that reflects the number of individuals in a theoretically ideal population having the same magnitude of loss of genetic variation as the population in question. There are several types of Ne estimates, and they vary in definition and application. For example, contemporary Ne represents the size of a population in the previous generation/s and is a parameter of relevance in many species. Estimating contemporary Ne is, however, difficult and remains in practice often unknown. This is particularly the case for large populations where the amount of drift in the short term is limited. We used genomic data from 85 collared flycatchers of an island population sampled at two time points, and applied several methods to estimate Ne. These methods either compared genetic variation between the two time points (temporal methods) or analyzed variation patterns from a single time point (LD-based methods). The temporal methods estimated Ne at a level of few thousand, while the approach based on LD provided ambiguous estimates associated with high variance. Our results suggest that whole-genome data can help to estimate large contemporary Ne, but temporal sampling seems to be necessary.
Article: Nadachowska-Brzyska K, Dutoit L, Smeds L, Kardos M, Gustafsson L, Ellegren H. 2021. Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis). Molecular Ecology https://doi.org/10.1111/mec.16025.
In a recent issue of Molecular Ecology, Taylor et al. explore how between population translocations of a small and endangered freshwater fish may break the long-term evolutionary boundaries between populations in this species. In this study, the researchers used a combination of genomic and phenotypic data to show that translocation efforts, which were necessary for meeting species conservation goals, could alter some important genetic and morphological differences between populations. To read the complete story, see the full article now available online as well as the interview with the authors below.
What led to your interest in this topic / what was the motivation for this study? Some excellent work with microsatellites had previously identified three populations of Bluemask Darters across their small range (Robinson et al. 2013, Cons. Gen.). One population, larger and more genetically diverse than the others, was in the Collins River, in the western portion of the range. A second population was in Rocky River, more central. A third population was in Cane Creek and the Caney Fork to the east. There was also a population in the Calfkiller River, which has been extirpated for several decades. In this context, captive-reared Bluemask Darter progeny from the Collins River population were being introduced to the Calfkiller River. But the location of the Calfkiller, near the center of the range, gave an important quirk to the system. If the three populations were not equally distinct, then Calfkiller River might be better suited with individuals from Rocky River, Cane Creek, or Caney Fork, rather than the western Collins River. In other words, the geography of the system meant that we needed to know the phylogenetic or hierarchical structure of population structure to know what boundaries might be lurking between Collins River and an introduced population in the Calfkiller River.
What difficulties did you run into along the way? One challenge in our project was navigating the connection between our scientific discoveries and the underlying goals of conservation. Our analyses were focused on the quantitative aspects of Bluemask Darters phylogenetics. However, at the end of the day, we are talking about an endangered species, incredibly imperiled, with a tiny range and an uncertain future. No quantitative value can give us strict guidance about the normative problems of conservation. So a challenge was to unpack, as best as we could, how our conclusions about the phylogenetics, population structure, and demography of this species could ultimately help us conserve the multiple diverging lineages of Bluemask Darters. The reviewers and editors from Molecular Ecology helped us refine our logic and our language, and the final result is a paper that acknowledges the complexities and competing concerns of translocation in a system like this.
What is the biggest or most surprising innovation highlighted in this study? One of the most significant findings of this study was the discovery of two divergent clades of Bluemask Darters — precisely the boundary being broken by current conservation management decisions that move fish between clades! One clade includes western individuals and the other includes eastern individuals. To top it off, we had the unique opportunity to use historic morphological data from across the range, including the Calfkiller River site where the fish had been extirpated, and which was now being restored with fish originating from the western population. The consistent result was that eastern sites harbor a distinct population from western sites, and that the Calfkiller River was associated with the eastern population. It is now apparent that translocated individuals should be from a source consistent with the clade that previously occupied the Calfkiller River, and from a source that will not artificially perturb existing evolutionary boundaries. In our study, there are additional complicating factors — the ideal eastern translocation sources are low abundance and not as genetically diverse. So our study was also a new opportunity to address how we might balance multiple concerns, with genetic details, while addressing a complicated conservation issue.
Moving forward, what are the next steps in this area of research? In our paper, we discuss how there are juvenile Bluemask Darters that drift into the reservoir at the center of the range and may not be able to migrate upstream to appropriate habitats needed as adults. These young fish are from the Rocky River, and are part of the appropriate clade for restocking the Calfkiller River. However, the success of this strategy would depend on the population dynamics of young fish in the reservoir. Jeff Simmons, co-author on this paper, and colleagues will be pushing forward with the critical next steps. There will be studies of the density and abundance of juvenile fish in the reservoir, including whether juveniles recruit into a breeding population or simply perish before maturity. There is also ongoing monitoring of the translocated fish in the Calfkiller, and across the species range. All of this work is being combined with habitat quality monitoring aimed at unraveling the location, frequency, and cause(s) of water quality issues that are harming darters in this system. All together, we’re continuing to build a picture of how best to conserve the distinct lineages of Bluemask Darters.
What have you learned about methods and resources development over the course of this project? Making this project successful meant combining dozens of different analyses — assembling, aligning, and filtering sequences, phylogenetics, population structure, genetic differentiation statistics, demographic simulations, to name a few — each of which have their own traps and idiosyncrasies. Getting these methods working required, first, well, getting everything to run, and then getting everything to run correctly. As useful as online documentation is, I learned there is no substitute for learning with colleagues who are engaging in similar research. Shout out especially to Dan MacGuigan, Daemin Kim, and Ava Ghezelayagh, all students with Tom Near. My conversations with these and other colleagues were critical for avoiding analytical pitfalls. These conversations also spurred ideas about new analyses and perspectives that will continue moving phylogenetic and population genetic work forward.
What would your message be for students about to start developing or using novel techniques in Molecular Ecology? It’s been said before, but it really was important to have reproducible code for this project. Working with next-generation sequence data meant an enormous number of different files and analysis packages. Being able to switch between versions (like with git), automate programs (like with bash scripts), and manage software environments (like with conda) saved us hundreds of hours. At the end, you can neatly package everything up; all of our data and code, for example, is now stored on a dryad repository that could basically reproduce our paper from scratch in just a few commands. Even after publication, sharing code has also meant starting new conversations with other scientists about best practices, alternate methods, and new ideas for genetic analyses.
Describe the significance of this research for the general scientific community in one sentence. Our study uses genetic and morphological data to unravel how translocation strategies for an endangered freshwater fish might balance the competing conservation concerns of phylogenetic divergence, genetic diversity, and population demography.
Describe the significance of this research for your scientific community in one sentence. Our study identifies two distinct clades of endangered Bluemask Darters across their small range, where current management decisions are translocating individuals across those diverging lineages.
Landscape features, such as land use, vegetation cover, roads, and topography, strongly influence genetic connectivity yet these relationships can vary across spatial scales which therefore requires multi-scale approaches for evaluating landscape genetics relationships. We used the federally threatened eastern indigo snake (Drymarchon couperi), a terrestrial habitat generalist endemic to the southeastern United States, as a case study with which to evaluate the consequences of different approaches for accounting for spatial scale when optimizing genetics resistance surfaces using the software ResistanceGA. Resistance surfaces with scale selected using a true optimization approach simultaneously comparing all possible combinations of scale across each set of covariates performed better than resistance surfaces where scale was selected individually for each covariate. Truly optimized resistance surfaces also outperformed resistance surfaces based on habitat selection models and categorical land cover maps. Optimal scales were usually larger than average indigo snake home range sizes suggesting that gene flow was mediated mostly by extra-home range dispersal. Large tracts of undeveloped upland habitat with intermediate habitat heterogeneity most promoted indigo snake gene flow while roads did not appear to restrict gene flow. Our results show the importance of testing a wide range of spatial scales in landscape genetics studies.
Article: Bauder JM, Peterman WE, Spear SF, Jenkins CL, Whiteley AR, McGarigal K. 2021. Multiscale assessment of functional connectivity: Landscape genetics of eastern indigo snakes in an anthropogenically fragmented landscape in central Florida. Molecular Ecology https://doi.org/10.1111/mec.15979.
The Molecular Ecology Prize Committee is pleased to announce that the 2021 Molecular Ecology prize has been awarded to Dr. Fuwen Wei, Professor of Animal Ecology and Conservation Biology in the Institute of Zoology, Chinese Academy of Sciences. Dr. Wei is a pioneer in conservation genomics and metagenomics of endangered animals, focusing mainly on giant and red pandas. He has applied genetic and genomic techniques to assess the past, present and future of giant panda populations, infer their evolutionary and demographic processes, and reveal their adaptive mechanisms for feeding on their specialized bamboo diet. He also has proposed and elaborated targeted strategies for the long‐term survival of pandas, which were featured in Science as “Hope for Wild Pandas”. With 5 books and over 270 peer-reviewed journal articles, he is a global leader in molecular ecology and conservation genomics. He has also trained numerous students and postdocs, and fostered international cooperation among zoologists and conservation biologists. His impressive accomplishments have earned him numerous awards and recognition, for instance, the Lifetime Achievement Award for Giant Panda Research and Conservation and the Outstanding Science and Technology Achievement Prize of Chinese Academy of Sciences.
Dr. Wei 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, and Victoria Sork.
Telomeres function like the plastic caps at the end of shoelaces. They cap the end of chromosomes and protect the coding DNA by shortening during every cell division. When they reach a critically short length, the cell stops dividing and dies. Telomeres are often used as a marker of ageing and different environmental conditions in ecology and evolution. Blood is commonly used to measure telomeres but is not always representative of all tissues and can be difficult to obtain from smaller animals, such as bats. We measured telomere length across different tissues in the Egyptian fruit bat to see if wing tissue biopsies, a quick and relatively non-invasive method of collecting tissue for bat DNA studies, could be used for measuring telomere length in bats. We found that wing telomeres correlated with most tissues. Wing telomere length measured from multiple samples taken from the same individual were highly repeatable. Even with training, taking blood from bats can be extremely difficult, while wing tissue biopsies with the required training are a faster and more straightforward method. Our findings provide robust support for the use of wing tissue in bat telomere studies as an alternate to otherwise harder to obtain tissues.
This summary was written by lead author Megan Power. Read the paper here.
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, and Victoria Sork.
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 Scott Edwards (firstname.lastname@example.org) by Friday, April 16, 2021. 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.
The editorial board recently established a new prize that recognizes the best paper published in Molecular Ecology or Molecular Ecology Resources by early career scholars in the last year by graduate students or early career scholars with no more than five years of postdoctoral or fellowship experience. 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, leading to concepts such as “neighbour detection” and “shade avoidance,” which are essential to understanding plant responses to crowding and competition. 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. As with the Molecular Ecology Prize, the winner of this annual prize is selected by an independent award committee, but the Harry Smith Prize comes with a 1,000 USD cash award, an announcement in the journal and on social media, as well as an invitation to join the Molecular Ecology Junior Editorial Board. Please send a short supporting statement (no more than 250 words; longer submissions will not be accepted) and PDF of the paper you are nominating to Dr. Alison Nazareno (email@example.com) or Dr. Katrina West (firstname.lastname@example.org) by Friday 31 May 2021. Self-nominations are accepted.
Molecular barcoding of bird malaria and related parasites has unravelled a remarkable diversity of potentially cryptic species that may count in tens of thousands compared to the few hundred morphologically described species. The database MalAvi (Bensch et al., 2009) was initiated to structure the growing numbers of findings of these bird blood parasites. The polymerase chain reaction (PCR) is irrefutably a powerful method to detect and identify pathogens, however the high sensitivity of the method comes with a cost; any of the millions of artificial DNA copies generated by PCR can serve as a template in a following experiment. If such PCR-contaminations go undetected, it will result in erroneous findings of parasites and thus misrepresent their distribution. We address this problem by re-analysing samples of surprising records in the MalAvi database, these being unusual host species or geographic locations for the parasites. Our analyses suggest that many of these are PCR contaminations, presumably originating from previous or parallel projects in the laboratory. The highlighted examples are from bird parasites, but the problem of contaminations, and the suggested actions to reduce such errors, should apply generally to all kinds of studies using PCR for identification.
References Bensch, S., Hellgren, O. & Pérez-Tris, J. MalAvi: 2009. A public database of malaria parasites and related haemosporidians in avian hosts based on mitochondrial cytochrome b lineages. Molecular Ecology Resources, 9: 1353-1358.