Reviews and Syntheses in Molecular Ecology

The Junior Editorial Board at Molecular Ecology have released a survey to gauge which topics current researchers in the field would like to be reviewed or synthesised. This survey is designed to help us understand which review and synthesis topics will be relevant, helpful and inspiring for our readership, and will guide our review and synthesis invitations over the coming months.

Before completing this survey, it may be beneficial to read the journal’s expectations for the scope of such manuscripts.

Review papers should aim to move the field forward by summarising past research on a given topic, highlighting questions that remain unanswered and proposing new directions for the field. Click here for an example of one of our most popular recent review papers.

Syntheses should bring together data from many studies in order to address an important hypothesis in ecology or evolution. Click here for an example of one of our most popular recent synthesis papers.

Both Reviews and Syntheses should aim to make a major contribution to the field of molecular ecology by presenting fresh perspectives on important topics

The survey asks for broad Review and Synthesis themes that you would be interested in reading. In addition, you are given the opportunity to pitch Review and Synthesis ideas. While we ask for suggested authors, please bear in mind that there is no guarantee that suggested authors will be invited to submit a review. If you have a specific review or synthesis idea that you would like to write, please visit this webpage. Here you will find details on presubmission enquiries, manuscript formatting and final submission.

A remarkable legion of guests: Diversity and host specificity of army ant symbionts (Author Summary)

A myrmecoid, or ant mimicking, staphylinid beetle, Ecitophya simulans, grooms an Eciton burchellii army ant worker. This beetle occurs with a single army ant host species, Eciton burchellii. Photo credit: Daniel Kronauer

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 Ecology30(20), 5229-5246.

Summary written by Christoph von Beeren

A symbiotic staphylinid beetle, Proxenobius borgmeieri, runs among army ant workers in an emigration column of its single host species, Eciton hamatum. Photo credit: Daniel Kronauer
A symbiotic featherwing beetle, Cephaloplectus mus, sits on the head of an army ant queen (Eciton burchellii). This host generalist parasitizes all six Eciton army ant species in Costa Rica. Photo credit: Daniel Kronauer

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.

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 ( 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: 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.


Wei, Jiankai, et al. “Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava).” Molecular Ecology Resources (2020).

Interview with the authors: Applying genomic data in wildlife monitoring

Massive parallel sequencing has led to an explosion of sequence data in recent years. However, the methods used to obtain such data are usually high-cost and time-intensive, and often require high-quality samples. This creates limits as to whether and how well such data can be used by researchers working in applied conservation science. Here, we speak to Alina von Thaden about her recent study in Molecular Ecology Resources. Using European wildcats as a case study, Alina and co-authors present a relatively low-cost and time-efficient workflow for the development and optimisation of microfluidic SNP panels, which can be used to obtain SNP data from minimally invasive samples. Beyond outlining the workflow and its applications, they go so far as to estimate the costs of their pipeline, providing valuable practical information for conservation scientists. Read on for an in-depth view of this study.

Monitoring elusive European wildcats (Felis silvestris) is heavily reliant on noninvasively collected DNA samples. Photo credit: Annsophie Schmidt.

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

We are mainly working on genetic monitoring of large carnivores and most of our research is based on noninvasively collected wildlife samples such as hairs, faeces and saliva traces. The field demands for very fast and reliable genetic analyses of samples with degraded DNA. And since funding is generally sparse in applied conservation, our methods need to be cost-effective and suitable for high-throughput approaches.

Genomic tools, on the other hand, usually involve large amounts of data, complex bioinformatic pipelines and typically rely on samples with high-quality DNA. We have been looking into ways to combine the advantages of genomics with the challenges of conservation monitoring. For some years now, we have been working with microfluidic arrays combined with reduced SNP panels and wanted to share our experiences with other labs interested in applying them.

What difficulties did you run into along the way? 

Setting-up and optimizing methodological resources comes along with several challenges – but there is a lot to learn! Most important to me was to remain skeptical about the results and to constantly validate them through analyzing the data from several perspectives and with different software. The validation of the technology also took a lot of extra lab hours, but we are confident that the workflow and guidelines that we present now will save others a lot of hands-on time and costs when optimizing SNP panels for degraded samples.

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

First of all, after years of developing the framework, we applied it to a new SNP panel designed for dog-wolf hybridization assessment (to be published) and found that the lab work for generating a new ready-to-use marker panel took us only a few weeks. To see the approach being proved effective was great and encouraged us to share it with the community.

Secondly, a large proportion of noninvasively collected samples could be run without or with only very few genotyping errors as compared to more traditional microsatellite-based genotyping (see also von Thaden et al. 2017). This has direct implications for genotyping costs and thus promotes the broader establishment of a genomic technology in applied conservation.

Alina von Thaden collecting reference samples of European wildcat (Felis silvestris) for testing a newly developed SNP panel. Photo credit: Annsophie Schmidt.

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

One of our next steps is to apply the technology to historical samples from museum collections. Additionally, we are going to implement the SNP panel from our current paper in routine genetic monitoring of European wildcats in Germany.

We currently develop other reduced SNP panels for a variety of endangered species in our lab, such as dormice and European bison. Besides neutral variation, we also aim to integrate functional markers, such as SNPs associated with disease susceptibility.

Further, we will test alternative platforms that will allow generating larger SNP sets for degraded samples. Ultimately, our long-term goal is the effective implementation of an “applied genomic wildlife monitoring” approach.

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

Get in contact with other groups working in this area! Sharing ideas and experience really helps to shape your project and refine the aims of your research. Most people are very cooperative and happy to contribute or answer questions.

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

Perseverance and tenacity. When exploring new directions the research journey may well become bumpy and lead you somewhere else than you initially expected. But it’s worth it – keep your goal in mind and be ready to rethink your strategy.

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

Bridging the gap between genomics and applied conservation is a key prerequisite for effective wildlife management, especially in the light of rapid biodiversity declines.

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

We demonstrate how reduced SNP panels can be efficiently developed and optimized for genotyping based on degraded wildlife samples.


von Thaden, A., Cocchiararo, B., Jarausch, A., Jüngling, H., Karamanlidis, A. A., Tiesmeyer, A. … Muñoz-Fuentes, V. (2017). Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays. Scientific Reports, 7, 83.

Full paper

von Thaden, A., Nowak, C., Tiesmeyer, A., Reiners, T. E., Alves, P. C., Lyons, L. A., … & Hegyeli, Z. (2020). Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism (SNP) panels. Molecular Ecology Resources.


Summary from the authors: A metagenomic assessment of microbial eukaryotic diversity in the global ocean

Marine microbial eukaryotes are key components of planktonic ecosystems in all ocean biomes. They are, along with cyanobacteria, responsible for nearly half of the global primary production, and play important roles in food-web dynamics as grazers and parasites, carbon export to the deep ocean, and nutrient remineralization. Currently, one of the most common approaches to survey their diversity is sequencing marker genes amplified from genomic DNA extracted from microbial assemblages. However, this approach requires a PCR step, which is known to introduce biases in microbial diversity estimates. One alternative to overcome this issue involves exploiting the taxonomic information contained in metagenomes, which use massive shotgun sequencing of the same DNA extracts with the goal of assessing the putative functions of environmental microbes.

In this study we investigated the potential of metagenomics to provide taxonomic reports of marine microbial eukaryotes. The overall diversity reported by this approach was similar to that obtained by amplicon sequencing, although the latter performed poorly for some taxonomic groups. We then studied the diversity of picoeukaryotes and nanoeukaryotes using 91 metagenomes from surface down to bathypelagic layers in different oceans, unveiling a clear separation of taxonomic groups between size fractions and depth layers.

Overall, this study shows metagenomics as an excellent resource for taxonomic exploration of marine microbial eukaryotes.

Summary of the relevance of main eukaryotic taxonomic groups within two size fractions of marine plankton (picoeukaryotes [0.2-3 µm] and nanoeukaryotes [3-20µm]) and in two different layers of the global ocean (photic [0-200 m] and aphotic [200-4000m]) as seen by metagenomics. The median of the relative abundance was calculated for each taxonomic group with samples from the 4 categories (pico-photic, pico-aphotic, nano-photic, nano-aphotic) and dots represent these median values transformed to a 0-100 scale. Dots are then colored based on the category where the taxonomic group is most relevant.

This summary was written by the study’s first author, Aleix Obiol.

Full article:
Obiol, A., Giner, C. R., Sánchez, P., Duarte, C. M., Acinas, S. G., & Massana, R. (2020). A metagenomic assessment of microbial eukaryotic diversity in the global ocean. Molecular Ecology Resources.

Interview with the authors: Which software is best to use for de novo assembly?

Reduced representation sequencing (e.g. RAD and GBS) is becoming ever more popular, but for species which lack a reference genome, little work has been done to assess which software may be best suited to building de novo assemblies from this data. Here, we speak to Melanie LaCava of the University of Wyoming about her recent Molecular Ecology Resources article, which explores the accuracy of de novo assemblies built by various software programs using DNA generated from double-digest libraries. Melanie and her co-authors found highly variable degrees of accuracy of assemblies built by six different software programs, and discuss which programs are best suited to this application. They also highlight the importance of optimising parameter settings within any given software. Read on to get a behind-the-scenes view of this study.

The completeness of assemblies in simulations of unmutated genomes (a, d), in simulations of an equal number of SNPs and indels (b, e), and simulations of 1–5 base pair indels (c, f). Values are reported for five assemblers: CDHIT (green), STACkS (blue), STACkS2 (purple), VelVeT (pink) and VSeARCH (orange). The hue of each color corresponds to the percent match parameter setting used in the assembly. For more information on this figure go to Figure 1’s caption here.

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

This study began as a research project in a graduate-level course on computational biology at the University of Wyoming led by the senior author on the paper, Alex Buerkle. Dr. Buerkle initiated the project and worked with the rest of the coauthors to pursue this de novo assembly software comparison. As reduced representation genotyping-by-sequencing has become more popular, new and repurposed software programs have been applied to each step in the bioinformatics pipeline. When a reference genome is unavailable for a study species, de novo assembly is essential, yet we recognized a gap in the evaluation of software used for this important step.

What difficulties did you run into along the way? 

Technology and software associated with genotyping-by-sequencing and de novo genome assembly are rapidly changing. During the course of our project, some of the software programs we tested were significantly updated, so we chose to rerun our analyses using the new software versions to ensure we were providing up-to-date information in our manuscript.

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

We were surprised to find such a substantial difference in performance among these assembly programs. We were especially surprised at the variation in performance among software for our first simulation where no mutations were introduced. In this scenario, we made many identical copies of genome fragments and then performed de novo assembly using each software program. Without any mutations introduced, the job is basically to generate a list of unique sequences – it should be very straightforward. In some cases, however, these genome fragments were broken into shorter sequences and rearranged beyond recognition, leading to incorrect reconstruction of the simple, unmutated data.

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

For our study, we selected a sample of assemblers from peer-reviewed literature that use different assembly algorithms, are freely available, and have updated user resources available online. However, this was not a comprehensive evaluation of all software capable of de novo assembly. Therefore, the evaluation of other programs would be valuable. Additionally, as new software programs are introduced or existing programs are updated, continued efforts to evaluate de novo assembly performance is warranted.

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

Reduced representation genotyping-by-sequencing is becoming less expensive and more accessible, making it a viable option for more research projects. While it is exciting to apply these emerging technologies and methods, it is important to recognize that approaches to filter and analyze these large datasets are still in development. Doing your background research to ensure you are applying the best available tools and using the most appropriate methods for your study is essential to doing good research in this field and in any field of research.

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

Doing this study has reaffirmed the importance of simulations to test how software works. Testing analyses on simulated data and altering parameters of the simulation or analysis can provide immense insight into how the software works and how variation in real data may affect software performance. Larger simulation projects like our study can provide information that many people can use, but I also find it incredibly helpful to run a simulated dataset through an analysis before analyzing my own data to ensure I understand what the software is doing. Taking advantage of simulated datasets available in vignettes for software is a great tool to get acquainted with the analyses you plan to do.

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

Our study demonstrates the importance of ensuring that software you use is really doing what you think it is supposed to do; and simulations can help evaluate software performance.

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

Researchers who need to perform de novo assembly of reduced representation genotyping-by-sequencing data can use our study as a guide for which software to use and the importance of different parameter settings for assembly.

LaCava, M. E., Aikens, E. O., Megna, L. C., Randolph, G., Hubbard, C., & Buerkle, C. A. (2019). Accuracy of de novo assembly of DNA sequences from double‐digest libraries varies substantially among software. Molecular ecology resources.

Interview with the authors: utilising GT‐seq for minimally invasive DNA samples

Minimally-invasive sampling is commonly used to obtain samples from rare, elusive or dangerous animals. However, this sampling technique often results in samples that are too low in quality or quantity for successful use with most high-throughput sequencing methods. Using cloacal swabs from the threatened Western Rattlesnake (Crotalus oreganus), Danielle Schmidt and colleagues show that Genotyping-in-Thousands by sequencing (GT-seq) can successfully be used to generate high-throughput sequence data from low-quality, low-quantity samples. We interviewed Danielle Schmidt (first author) and Professor Michael Russello (last author) to find out more about what went on behind-the-scenes of this study.

The Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. Photo credit: Marcus Atkins

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

Conservation genomics has become an increasingly common term in the literature, yet many study systems that involve elusive or at-risk species must rely on minimally- or non-invasive sampling to meet research and management objectives. Although a valuable source of biological material, DNA extracted from minimally- or non-invasive samples is typically of low quantity, poor quality, and contaminated with exogenous DNA, all of which may be incompatible with modern sequencing technologies. Implementing leading-edge genetic and genomic tools to study conservation-related questions has been a long-standing interest in the Russello Lab.

What difficulties did you run into along the way?

Based on earlier work that came out of our lab (Russello et al. 2015 PeerJ), we suspected that employing a non-targeted sequencing approach like RADseq would not be efficient for collecting genotypic data from minimally-invasive samples. Therefore, we decided to test the efficacy of GT-seq (Campbell et al., 2015), as it is a targeted method that could help circumvent the typical issues involved with sequencing and genotyping lower quality DNA. Our biggest challenge was designing a GT-seq SNP panel that minimized ascertainment bias to ensure our downstream estimates of within- and among-population variation would be accurate. Also, given the number of samples and loci we planned to analyze simultaneously, optimizing the workflow for data collection took some time.

Library designs for A) RADseq and B) GT-seq. Included samples selected to facilitate within- and among-method genotype comparisons

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

One of the most surprising findings was the exceptionally high genotype consistency between paired blood and cloacal swab samples genotyped with GT-seq, and those blood samples genotyped with both RADseq and GT-seq. We even found that samples with initial concentrations as low as ~0.5 ng/uL successfully amplified, which is promising for future applications of GT-seq with minimally- and non-invasive DNA samples.

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

We are now exploring the application of GT-seq on a host of species to provide rapid, cost-effective genetic information to support research in molecular ecology and to assist wildlife and fisheries management. We are also testing the performance of this workflow with other non-invasive sample types, including feces and hair. Moving forward, we will be exploring ways of deploying these tools in the field to inform management decisions in real-time.

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

An important message we would like to convey is to think carefully about potential biases when designing a panel of markers to target, as the composition of your panel must be tailored to your research questions. For example, some applications of GT-seq may seek to intentionally maximize the among-population component of genetic variation in order to identify individuals of unknown origin to a particular fish stock with high confidence. In other cases, as with our study, we wanted a panel that could be used to most accurately reconstruct population structure and connectivity, which we were able to subsequently validate relative to a larger RADseq dataset.

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

This project highlighted the benefits of taking a new approach to address a long-standing challenge. In molecular ecology and conservation genetic studies, minimally-invasive sampling is commonly employed as either a required or a preferential approach for obtaining sufficient sample sizes. Yet, it has been recognized since the advent of non-invasive genetic sampling in the 1990’s that issues associated with DNA quality and quantity require careful consideration and extra quality control steps. Today, these considerations also apply to the use of modern DNA sequencing technologies from suboptimal starting material; however, GT-seq provides a versatile approach for overcoming DNA quality issues and providing the population-level data needed to address research and management objectives.

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

Multiplexed, amplicon DNA sequencing, such as that employed in GT-seq, is compatible with the minimally-invasive sampling often required for obtaining population-level data to inform biodiversity conservation.

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

GT‐seq offers an effective approach for genotyping minimally-invasive samples, providing accurate and precise estimates of within‐ and among‐population diversity metrics relative to genome-wide approaches such as RAD-seq.

Read the full study here:
Schmidt, Danielle A., et al. “Genotyping‐in‐Thousands by sequencing (GT‐seq) panel development and application to minimally invasive DNA samples to support studies in molecular ecology.” Molecular ecology resources (2020).

Summary from the authors: Individualized mating system estimation using genomic data

Mimulus guttatus

Hermaphroditic species of plants and animal can produce a mixture of outcrossed and self-fertilized offspring. Estimating the relative frequency of these two outcomes, i.e. the outcrossing rate, has been a major focus in the evolutionary study of reproductive strategies. Outcrossing rate is also a key parameter for plant breeding and for conservation efforts. This paper generalizes a Bayesian method to estimate outcrossing rate (BORICE) using genomic data. Application of the program to an experimental study of Mimulus guttatus illustrates estimation (10% of progeny were selfed), and also how inference of mating system parameters can set up “downstream” evolutionary studies. In the Mimulus study, these downstream analyses included pollination biology (the genetic composition of pollen changed over the season) and local adaptation (inversion polymorphisms exhibit unique patterns of micro spatial structure within the population).

-Professor John K Kelly, University of Kansas

Full article: Colicchio, J., Monnahan, P. J., Wessinger, C. A., Brown, K., Kern, J. R., & Kelly, J. K. (2020). Individualized mating system estimation using genomic data. Molecular ecology resources.