Summary from the authors – Wing: A suitable nonlethal tissue type for repeatable and rapid telomere length estimates in bats

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.

2021 Molecular Ecology Prize

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 (sedwards@fas.harvard.edu) 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.

Nominations are now open for the Harry Smith Prize 2021

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 (nazareno@umich.edu) or Dr. Katrina West (katrina.m.west@postgrad.curtin.edu.au) by Friday 31 May 2021. Self-nominations are accepted. 

Summary from the authors: Contaminations contaminate common databases

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.

Read the full text here.

Fig 1. The database MalAvi (http://130.235.244.92/Malavi/) presently contains >4,400 unique mitochondrial lineages of avian malaria parasites obtained from >2,000 species of birds.

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.

Associate Editor vacancies

Molecular Ecology and Molecular Ecology Resources are looking for new Editorial Board members to join the journals as Associate Editors in the key subject areas below:

  • Eco-immunology/emerging diseases/disease resistance
  • Proteomics/protein evolution
  • Computer programs/statistical approaches
  • Environmental DNA/metabarcoding

Experience with genome assemblies would also be advantageous.  

Nominations and applications are welcome and whilst scientific qualifications are paramount, we would particularly appreciate nominations and applications from suitably qualified researchers from underrepresented groups (including women, ethnic minority scientists, scientists with disabilities and other underrepresented groups). Please email nominations/applications by October 15th, 2020 to manager.molecol@wiley.com with the following items:

  • Cover letter stating the reasons for your nomination, of if applying for yourself, your interest in the role and familiarity with the journals,
  • Abbreviated CV (Education, Publications, Outreach) if you have it.

Interview with the authors: the genomic basis of adaptation in an invasive sea squirt

In this interview, Professor Bo Dong tells us about his team’s recent study exploring the genomic basis of environmental adaptation in the leathery sea squirt (Styela clava), a highly invasive species of tunicate that has adapted to a broad range of environments. In this study, the authors assembled a chromosomal-level genome and transcriptome of the leathery sea squirt and undertook in situ hybridization and drug inhibition experiments in order to elucidate molecular mechanisms of adaptation. Continue reading to find out what the team found and why it matters, and click here to read the article.

Styela clava, the leathery sea squirt. Photograph by Xiang Li, an author of the study

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

Our lab works on organ morphogenesis and developmental genomics using an ascidian model. When we collected animals at the sea in Qingdao, China, we found many leathery sea squirts. Previous research has found that the leathery sea squirt is invasive across the globe, and impacts on both marine biodiversity and aquaculture industries. Therefore, we were interested in revealing the genomic basis of its adaptation. In addition, the Wellcome Sanger Institute, in celebration of its 25th anniversary, created a poll of species where the winners would have their genomes decoded. The leathery sea squirt was included in the ‘Dangerous Zone’ category of the poll, and although it did not win this strengthened our determination to decode its genome.

The leathery sea squirt was an option in the vote for the Wellcome Sanger Institute’s ’25 Genomes for 25 Years’.

What difficulties did you run into along the way? 

In order to obtain a better genome assembly, we used the PacBio sequencing and combined this with Hi-C approach. Because of the small size of leathery sea squirt adults, we tried many times to get enough high-quality DNA from one individual for library construction. In addition, the approaches for functional analysis is fairly limited in this ascidian species. We tried different ways to do dechorionation or microinject the DNA into the eggs, but it was not working well. We are continuing our work on this now.

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

Compared with the classical ascidian model species Ciona robusta, we found that Styela clava has a genome double the size but with comparable gene number. Another intriguing finding is that cold-shock protein genes were transferred horizontally into the S. clava genome from bacteria. Transfer of these genes provides one of the possible molecular mechanisms for S. clava to adapt the environmental stress, particularly low-temperature stress.

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

We obtained the genetic information and molecular network of environmental adaptation and metamorphosis of leathery sea squirts through high quality genome assembly. Next, we are focusing on two further aspects of this project: 1) we are further digging into the signaling molecules that control the larval metamorphosis experimentally and 2) we plan to reveal the mechanisms for gene transfer from bacteria to ascidians.

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

First, you should know clearly what kinds of scientific questions you want to ask by genome assembly approaches. Second, try to discuss your research projects with scientists with different backgrounds to adjust your research strategies and analyze your results. Third, compare your genome data with the data from other species to see if your conclusion is a universal one. 

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

Animals are so smart. They use different and unexpected strategies to adapt to environmental stress. Genomic approaches are a powerful way to elucidate the biological mechanisms of adaptation. Experimental results are often different from your expectations.

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

The present study provides a chromosomal-level genome for understanding environmental adaptation in invasive tunicates.

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

Our study provides the chromosomal-level genome resources of leathery sea squirt (S. clava) and a comprehensive genomic basis for understanding environmental adaptation and larval metamorphosis.

Citation:

Wei, Jiankai, et al. “Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava).” Molecular Ecology Resources (2020). doi.org/10.1111/1755-0998.13209

Interview with the authors: Habitat light sets the boundaries for the rapid evolution of cichlid fish vision, while sexual selection can tune it within those limits

Non-model organisms provide an interesting avenue to explore evolution in real time in natural populations. Here, we speak to Ralf F. Schneider and Sina J. Rometsch of University of Konstanz, Germany about their co-authored Molecular Ecology article, where they investigate sex‐specific opsin expression of several cichlids from Africa and the Neotropics which they coupled with data sets on sex‐specific body coloration, species‐specific visual sensitivities, lens transmission and habitat light properties. They illustrate how integrative approaches can address specific questions on the factors and mechanisms driving diversification, and the evolution of cichlid vision in particular.  Read on to get a behind-the-scenes view of this study.

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

Cichlid fishes are an amazing system to work with. They are one of the most species rich vertebrate families and adapted to a wide range of ecological niches. This is reflected in outstanding phenotypic diversity in numerous traits. Their striking variation in body coloration, which can sometimes differ considerably between the sexes, has even been acknowledged in their German name “Buntbarsche”, which translates to colorful perches. Moreover, their visual system is intriguingly complex, because cichlids possess a total of seven opsin genes that allow for color vision (humans only have three). While sexual selection has been recognized as a major driver in the evolution of cichlid body coloration (coloration being the “sender”), less is known about what shapes visual sensitivities (the receiving end of the system) in cichlids. Therefore, we were interested in whether the phenotypic diversity found across cichlid visual sensitivities is primarily driven by sexual selection (e.g., vision co-evolves with body colors), or whether environmental factors, such as light availability and water turbidity, turn out to have a stronger effect on the evolution of cichlid vision.

2. What difficulties did you run into along the way? 

The main challenge in addressing the question on whether the light environment (“ecological selection”) or conspecifics’ body colorations (“sexual selection”) are driving the diversification in cichlid vision was that both potential drivers are very complex and can be challenging to quantify. The visual environment across cichlids’ habitats varies tremendously, and is dependent on factors, such as water depth and turbidity. Coloration patterns often change across the fish’s body and only photospectrometric measurements across the whole range of visible light wavelengths can objectively quantify a color. Moreover, the fish’s visual system is highly complex. Visual sensitivity can be modified physiologically or by phenotypic plasticity by a number of factors including expressing different subsets of the seven opsin genes, changing their expression level, lens filtering etc. Combining all this information, either obtained from our own experiments or from published studies, in a common framework allowing for meaningful statistical analyses was challenging.

3. What is the biggest or most surprising innovation highlighted in this study? 

Most surprising, in terms of results, was to us that we did not find sexual dimorphism in opsin expression in any cichlid – not even those with very strong dimorphism in body coloration (such as in Pseudotropheus lombardoi (attached photo), where females are blue and males are yellow). While we did expect that evaluating mating partners based on their body color would favor associated sexual dimorphism in the visual system, this seemingly has not (yet?) happened in these fish. In terms of methodology, our study integrates a complex data-set on ecological and physiological parameters that can affect the visual sensitivity. This allowed us to evaluate the potential interactions of these parameters in a very comprehensive way.

4. Moving forward, what are the next steps in this area of research?

In our study, we show that a wide range of data can be integrated in a single model, which allowed us to investigate interactions among variables that are rarely used in a common framework. Thus, we encourage future studies to also consider comprehensive approaches when addressing questions concerning the visual ecology of these (or other) fish, if this information is available or obtainable. Additionally, while we have a relatively good understanding of how visual information is perceived by cichlids, there is only very little information on how visual information is processed in the neuronal circuitry of the eye and later in the brain. Understanding signal processing in cichlid eyes will provide a new information layer for evolutionary ecologists to work with.

5. What would your message be for students about to start developing or using novel techniques in Molecular Ecology? 

In the last decades, due to ever-increasing computational power, storage capacities and high-throughput techniques, such as next-gen sequencing, large amounts of data can be more reasonably collected and are accessible by more researchers. New methods can benefit from incorporating these data into analysis pipelines to consolidate them or broaden their scope. Being aware of available data can thus be very useful. However, it is also important to us to stress that approaching a scientific question from several angles and across biological disciplines that don’t frequently communicate is often the soundest approach. Classical lab methods, such as in situ hybridization or histology, as well as cutting edge techniques, such as Crispr/Cas9, can provide valuable validation/falsification of formulated hypotheses.

6. What have you learned about methods and resources development over the course of this project? 

It was great to see how this study evolved: one question and technique lead to another until we finally aimed at developing an analysis frame-work for the complex data-sets that are obtained in visual ecology of (cichlid) fishes. This comprised changing and further developing our pipeline while analyzing the data. Several preliminary pipelines had to be discarded as they did not properly address our core hypotheses. Thus, an important lesson for us was that it can take a while until a newly developed analysis pipeline does actually what one envisioned roughly at the beginning of the project. Overall, collaborating in a team with members of quite different backgrounds such as ecology, molecular biology and data science and working in a large and well-established lab made it possible to learn and apply new techniques.

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

Evaluating the relative strengths of natural vs. sexual selection is a very interesting question and these two forces are often very hard to disentangle, but using a set of multidisciplinary approaches combined with a comprehensive statistical analysis allowed us to show that in narrow light environments visual sensitivity is tuned to exploit all available light, while broader light environments allow for more specialized visual sensitivities.

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

We show that ambient light is a prime driver for the evolution of visual sensitivities through natural selection in cichlid fishes, whereas sexual selection seems to finetune the observed diversity within the limits set by natural selection.

9. How has COVID-19 affected work in your group?

For the last two months we’ve all been confined to working from home which – on the plus side – allowed us to dedicate more time to data analyses and finishing manuscripts, but on the down side required lab experiments to be currently on hold – unfortunately.

Full paper: Schneider, R. F., Rometsch, S. J., Torres-Dowdall, J., & Meyer, A. (2020). Habitat light sets the boundaries for the rapid evolution of cichlid fish vision, while sexual selection can tune it within those limits. Molecular Ecology. https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15416

Interview with the authors: Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna

Non-model organisms provide an interesting avenue to explore evolution in real time in natural populations.Here, we speak to Edgar Wong of Department of Plant Sciences, University of Oxford, UK about his Molecular Ecology article, which investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations.  Wong and his co-authors found an extremely strong selection (up to 0.78) against hybrids in the system. This estimate is one of the highest reported in literature, and much higher than the one reported in the same system in the past. Read on to get a behind-the-scenes view of this study.

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

Speciation and hybridisation have always been interesting topics to me. In the case of Senecio on Mount Etna, they have an especially fascinating story: first, Mount Etna is a relatively young mountain (less than half a million years old), and previous research hypothesized that the formation of the mountain led to the divergence of the two species, Senecio aethnensis and S. chrysanthemifolius. These species are thought to be a rare example of clear-cut, recent speciation subject to divergent selection – the formation of new species driven by adaptation to distinct conditions – high- and low-elevations in our study. Second, botanists around 300 years ago brought some live Senecio specimens of the plants from Mount Etna back to the UK, and led to hybrid speciation of S. squalidus that has since spread all over the UK (although crossing experiments using plants from Mount Etna suggested hybrid breakdown). A lot is still unknown about the plants both on Mount Etna and in the UK. Hence, I was intrigued to find out unknown aspects in the system and focused on the species on Mount Etna.

2. What difficulties did you run into along the way?

One big difficulty was that Asteraceae (which Senecio belongs to) is notorious for being hard to extract clean DNA. It was a struggle to extract good-quality DNA for this study, which was resolved in the end. Also, we only had a draft genome for the hybrid species, S. squalidus, which limited the scope of analyses we could carry out. Luckily, we managed to find some interesting, highly differentiated genes that might be underlying speciation and adaptation.

3. What is the biggest or most surprising innovation highlighted in this study?

The most surprising finding in our study is that we estimated an extremely strong selection (up to 0.78) against hybrids in the system. This estimate is one of the highest reported in literature, and much higher than the one reported in the same system in the past. Such strong selection was surprising to us because hybrids between the two species are (apparently) happily growing at intermediate elevations between the typical habitats of ‘pure’ S. aethnensis and S. chrysanthemifolius. We think this strong cumulative selection on multiple loci works together with intrinsic incompatibility to maintain the phenotypic and genotypic divergence between the two target species.

4. Moving forward, what are the next steps in this area of research?

In the future, we hope to identify the environmental and ecological selective forces that had shaped this system. We also hope to characterise the genetic aspect of the species by improving the genome assembly and study more in detail the intrinsic incompatibility between the two target species (such as hybrid breakdown). With more data on both extrinsic and intrinsic processes, we can integrate these findings to get a more comprehensive picture of reproduction isolation in this system.

5. What would your message be for students about to start developing or using novel techniques in Molecular Ecology?

I would say to spend enough time understanding the experimental techniques and different types of data analyses (and the theories behind them). Most importantly, make sure that the type of data you generate are suitable for answering your research questions. As a graduate student myself, I would also suggest not to rush your work and not get transfixed on certain issues/ problems along the way – taking a step back and asking for advice and opinions from other researchers are always helpful in getting another perspective, which often helps to find a solution.

6. What have you learned about methods and resources development over the course of this project?

The type of data I used and subsequent data analyses were all new to me when I started the project, so there is no doubt I learnt a great deal about handling new types of data and how to analyse it. Another thing I have learnt is that there are always newer or ‘better’ technologies and methods that give you more data and/ or data with higher accuracy. It is inevitable that sometimes you would be worried whether what you have is not good enough. However, I have come to realise that more isn’t always better and there will always be more advanced methods; the most important thing is to use what you have and try to answer your research questions.

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

Non-model organisms inform us a lot about evolutionary processes such as hybridisation, adaptation and speciation.

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

Strong multifarious selection could be crucial in maintaining species divergence despite on-going gene flow.