Fuwen Wei awarded the 2021 Molecular Ecology Prize

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.

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.

Interview with the authors: Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Written by Beatriz Mello and Sudhir Kumar

The work presents the most extensive evaluation to date of relaxed-clock methods’ performance to infer molecular times for datasets that contain a mixture of population and species divergences. Such datasets are commonly used in phylogeography, phylodynamics, and species delimitation studies. A wide range of biological scenarios was explored, which allowed us to compare and contrast the accuracies and precisions of divergence times for a Bayesian (BEAST) and a non-Bayesian (RelTime in MEGA)  method. Results showed that both RelTime and BEAST generally perform well and that RelTime presents a reliable and computationally efficient alternative to speed up molecular dating.

Read the full text here.

Lead author Beatriz Mello.

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

Our interest in this topic was driven by a major dilemma faced by researchers when analyzing data containing molecular sequences from closely related individuals and individuals from distinct species. This is because the Bayesian framework requires a tree prior to model the inference of divergence times. There is a myriad of tree priors available, but most importantly, they either model divergence between species or intra-species divergences. Thus, the adopted tree prior will be suboptimal to describe the evolutionary process for datasets with mixed sampling. So, our question was, although misspecified, would the use of the same tree prior produce good time estimates? Also, no one has previously examined how well non-Bayesian methods perform for such datasets, as they do not require specification of priors.

What difficulties did you run into along the way? 

One of the major difficulties we faced was the computational burden of Bayesian analysis. We all know that molecular dating using Bayesian methods can be time-consuming. However, they can become onerous in computer simulation studies because many datasets need to be analyzed. Each Bayesian analysis took several hours to complete, and we had to conduct thousands of Bayesian analyses. This was not an issue with the RelTime method, which finished computing in minutes. 

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

Our biggest finding is that, although the tree prior will frequently be an erroneous description of biological evolution, the accuracy of time estimates is not greatly impacted for most choices of the tree prior. This is good news to researchers working with phylogenies containing a mix of population and species. On top of that, RelTime is much faster than the Bayesian approach and produces similar results. This finding is important since the amount of sequence data is increasingly growing. A fast and accurate method allows hypotheses testing to be done using different assumptions and data subsets, improving the scientific rigor and reproducibility by others.

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

For Bayesian methods, it will be useful to develop faster approaches. However, the excellent performance of the RelTime approach that does not require prior specification is very encouraging. Evolutionary simulations employing even more diverse biological conditions and tree topologies, especially involving many sequences, will be a very useful next step, which may only be feasible with RelTime and other fast methods.

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

Our main message for students is to realize that no method is almighty. For those aspiring to develop new methods, it is our first step to apply different methods to a diversity of datasets and examine how the results differ, why they differ, and whether we can solve the problem discovered. It is again important for those applying new methods to use different methods and scrutinize differences in results. It is not a good idea to assume that a popular protocol is better than others by default; we need to keep an open mind and make decisions with evidence.

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

All of us learned quite a lot about the multispecies coalescent approach by analyzing simulated data because we know the correct result. The lesson was that some methods require many assumptions and that sometimes even small changes can have a big impact, resulting in distinct evolutionary inferences. So, we need to be very careful and explore a wide range of biological assumptions. Also, there is a strong need for more realistic simulation studies.

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

Researchers will now be able to decide which methods and approaches to apply in their particular dataset using results from this study.

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

The accuracy and precision of divergence time estimation for datasets that contain both intra- and interspecies molecular sequences is tested for slow (Bayesian) and fast (RelTime) molecular dating approaches.

References

Mello B, Tao Q, Barba-Montoya J, Kumar S. Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches. Mol Ecol Resour. 2021;21:122–136. https://doi.org/10.1111/1755-0998.13249

Summary from the authors: Detecting selected haplotype blocks in evolve and resequence experiments

How organisms adapt to changes in the environment is not only a central question of evolutionary biology but also relevant to the threat of recent global warming. Evolution experiments in controlled laboratory settings (Experimental Evolution) are a great tool for evaluating evolutionary processes. When combined with genome sequencing (Evolve and Resequence), genomic changes related to adaptation can be identified. Although these genomic changes can occur in large parts of a chromosome (selected haplotype block), most approaches focus only on single genomic sites, and in consequence might overestimate the signal of evolution. Here, we present a novel method for detecting such selected haplotype blocks in evolve and resequence experiments. Our approach requires only few input parameters and is based on the grouping of neighboring genomic sites and on a comparison of different chromosomes. Analyzing computer simulations and experimental data, we describe distinct haplotype block patterns related to the number of genomic sites under selection and to the speed of adaptation. Our results indicate that the analysis of selected haplotype blocks has indeed the potential to deepen our understanding of adaptation.

Read the full text here.

Figure 1: Left: Flies are a powerful model organism to study temperature adaptation from standing genetic variation in evolve and resequence experiments (modified from Mallard et al., 2018). Right: Selected haplotype blocks (blue) spanning large parts of a chromosome are present in the majority of individuals after 60 generations of experimental evolution.

References

Otte KA, Schlötterer C. Detecting selected haplotype blocks in evolve and resequence experiments. Mol Ecol Resour. 2021;21:93–109. https://doi.org/10.1111/1755-0998.13244

Mallard, François, et al. A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila. Genome biology 2018:19.1: 1-15. https://doi.org/10.1186/s13059-018-1503-4.

Interview with the authors: Museum epigenomics: Characterizing cytosine methylation in historic museum specimens

Recent work has shown that it may be possible to characterize epigenetic markers from museum specimens, suggesting yet another potential contribution of collections-based research. In their recent Molecular Ecology Resources paper, Rubi et al. used ddRAD and bisulphite treatment to characterize cytosine methylation in deer mice (Peromyscus spp.). They characterized methylation in specimens from 1940, 2003, and 2013-2016. While they were able to characterize patterns in all specimens, older specimens had reduced methylation estimates, less data, and more interindividual variation in data yield than did new specimens. Rubi et al. demonstrate the promise of museum epigenetics while highlighting technical challenges that researchers should consider. Read the interview with lead author Dr. Tricia Rubi below to get a behind-the-scenes look at the research behind the paper.

Read the full paper here.

Peromyscus maniculatus skull collected in 2002 and housed in the University of Michigan Museum of Zoology collection. Photo Credit: Dr. Tricia Rubi

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

When I wrote the original proposal for this work, the earliest papers had just been published in the field of ancient epigenomics (epigenetic studies using paleontological or archaeological specimens). My proposal centered around museum specimens, and I realized that no work had been done looking at epigenetic effects in more recent historic specimens (decades to centuries old), which comprise the bulk of museum collections. The recent field of museum genomics has already opened up a range of new directions for research using collections; I believe that museum epigenomics could be a similar frontier in collections-based research. In particular, epigenomic studies using museum collections could allow us to characterize change over time, which may help clarify the role of epigenetic effects in ecological and evolutionary processes.

What difficulties did you run into along the way? 

As is the case when developing any novel protocol, we encountered a variety of challenges and dead ends. However, we found that the main challenge for DNA methylation work using museum specimens was actually the same as the main challenge for regular genetic work using museum specimens: recovering usable amounts of DNA in the initial DNA extraction. DNA quantity and quality seemed to be a better predictor of success than specimen age; our oldest specimens (~76 years old) with higher DNA concentrations yielded a similar amount of methylation data relative to much “younger” specimens. The upside is that this challenge is already a familiar one to researchers conducting museum genomics work. Our data suggests that historic DNA samples that have been successfully used for genomic analyses are probably also well suited for methylation analyses.

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

I think the main takeaway from this study is that DNA methylation analyses using historic collections is feasible, even for lower quality specimens such as traditional bone preparations that are several decades old. Our oldest specimens in this study were dried skulls collected in 1940; while those specimens showed considerable variation in the amount of recoverable DNA, the specimens that yielded higher DNA concentrations performed well in our analyses.

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

There is plenty of work to be done! In this paper we highlight future directions for both developing methodology and applying museum epigenomics to ecological and evolutionary questions. Increasing the number of sequenced methylation markers or refining protocols for targeted sequencing are some obvious first steps in improving methods. Museum epigenomics approaches could be used to tackle a variety of questions in ecological and evolutionary epigenomics. In particular, epigenomic studies using museum specimens could be used to infer gene expression in past populations, or to directly measure how epigenetic markers change over time. 

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

Developing or refining novel techniques is an important and potentially rewarding process, but it requires enormous patience, as well as correctly managed expectations about the outcomes of the work. Researchers should be prepared for slower progress and a higher failure rate. Even when protocols do work, it may be more difficult to test broader ecological hypotheses due to unforeseen problems or non-optimal results. However, the upside is that projects using novel approaches can provide an important contribution to the field regardless of the specific outcomes of the work. My advice would be to design projects with several contingency plans to ensure that publishable data can be produced, and to factor in extra time for troubleshooting each step of the novel protocols.

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

Natural history specimens retain patterns of in vivo DNA methylation, the best studied epigenetic marker; museum epigenomics may be the next frontier in collections-based research.

References

Rubi TL, Knowles LL, Dantzer B. Museum epigenomics: Characterizing cytosine methylation in historic museum specimens. Mol Ecol Resour. 2020;20:1161–1170.

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.

The story behind the Special Feature: Genomics of natural history collections

We are really excited to get a sneak peak into the story behind a new Special Feature in Molecular Ecology Resources focusing on the use of genomic techniques to better understand natural history collections. In this Special Feature, the authors led by Assistant Professor Lua Lopez, compiled a broad range of studies using a variety of methods to illustrate the enormous potential of museum samples to answer question fundamental to molecular ecology. See below for a video interview with Lua and the article. Check out the great set of articles in the special feature here.

  1. What led you to put together a special issue on this topic?
Lua Lopez. Assistant Professor at California State University

My first contact with ancient genomics was during my postdoc at PSU at the Lasky Lab. As soon as I started looking for literature to help me get the project started I realized that, except in the field of human ancient genomics, information was scattered and it was not easy to find methodological papers for wet-lab or bioinformatics of this type of data. We were lacking a strong foundation of studies using a combination of ancient, historical and modern samples stored in museums. Because of all this I wanted to put together an issue compiling a critical mass of studies using Natural History Collections (NCH) to advance the field of evolutionary biology. Although I had been thinking for a while about this, I only adventured to put this together when two new postdocs also working with NHC samples joined the lab, Dr. Kathryn Turner and Dr. Emilly Bellis. The three of us, together with our postdocsupervisor Jesse Lasky, decided it was time to get this running and I am very excited with the result.

2. Of the papers in the special feature, can you identify any broad trends?

All papers provide a significant advance in important methodological steps (from DNA extraction to data analysis) facilitating the use of NHC sample in evolutionary studies. The data used to test the methods in these papers provide a glimpse of the new research avenues that NHC samples can open.

3. What did you find the most surprising about the papers in this feature?

It was incredible to see how many fields can benefit from using NHC samples. This issue does not only cover methodological aspects but it shows how NHC samples can help answer long-standing questions in the fields of metagenomics, epigenetics, conservation genomics, evolutionary ecology and phylogenetics.

4. What do you recommend to researchers trying to collect genomic data from natural history collections?

Contact as many NHCs as you can. There are still many collections that are not digitized and being aware of what is available that can have a large impact in your experimental design. If this is your first time working with NHC samples, team up, genetic studies with NCH samples can be a big challenge (high risk, high reward). Having someone with experience to guide you is going to be one of the best things you can do to ensure the success of your research.

5. What do you think are crucial next research steps to effectively utilizing natural history collections?

I strongly believe that the next steps include digitizing NHC collections and archiving DNA data. Many  NHC samples are not yet digitized and researchers looking a particular species can only obtain a partial picture of what’s available for their studies. The accuracy we have to answer particular questions is, in most cases, determined by the samples we have access to (i.e. number of samples, geographical and temporal distribution).  In addition, any genetic data obtained from NHC samples should be publicly available. By having access to larger data sets we can not only increase the accuracy of our results but we can also better predict future scenarios.

6. What (if any) method advances are needed?

In the past 10-20 years, we have improved enormously in our wet lab protocols and bioinfomatics but the intrinsic nature of DNA from NHC samples means that we still have a long way to go. Ideally, we want standardize protocols for large taxonomic groups and identify what kind of factors have a larger impact in DNA damage. This also applies for pipelines for data analysis, in general the more standardized protocols are the best, it will hep us comparing results among studies and trying to identify broad evolutionary patters.

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

Understand what kind of samples you have in your hands. It’s not only about how old they are, it’s also about how where they preserve after sampling and during storage, where are they coming from, how much material you have, etc. Many factors are going to influence the success of obtaining DNA of enough quality for downstream analysis. And the same goes for the data analysis, make sure you are considering the particular nature of the genetic data that you are analyzing. NHC samples are precious and destructive sampling cannot be done lightly. So, always do a test run and ask all the questions that you have.