The first of hopefully many papers from the Genealogy of Flagellate Plants project is out, in Applications in Plant Sciences (link here)! In this paper, we present the GoFlag 451 and GoFlag 408 probe sets, both of which target hundreds of low-copy nuclear loci and can be used across land plants (our focus is non-flowering plants), providing a powerful resource for generating large nuclear data sets to resolve phylogenetic relationships at varying evolutionary scales. These probe sets are extremely effective at capturing hundreds of loci even in samples with very low DNA yields, which helps allow researchers to leverage old specimens for phylogenomic-scale analyses. The paper is open access, and the probes and a pipeline for processing the data are available!
The GoFlag project was the central part of my postdoc at the University of Florida, so I am particularly glad to see this paper out. Keep an eye out for other papers from this project coming out in the near future, and reach out if you have any questions about using this probe set for your own research!
Time to pack the bags! Alejandra Vasco (Botanical Research Institute of Texas), Michael Sundue (University of Vermont), and myself have recently been awarded a $1.1 million grant from NSF to study fern diversity in Colombia, with a focus on improving understanding of diversity in this species-rich but understudied country. The project, titled "PurSUiT: Collaborative Research: Accelerating Lineage Discovery to Document Neotropical Fern Diversity", will seek to advance our knowledge of fern diversity in the American tropics by tying together field work, collections-based research, phylogenomics, and biodiversity informatics. To make the study of fern diversity in this hotspot more efficient, we will be developing a data portal that will integrate the resources developed as part of this work.
This project involves extensive collaborations with colleagues in Colombia, and a large part of this research will be carried out there, both doing fieldwork and working in collections. Along with improving our understanding of fern diversity, this research initiative will help develop research connections between US and Colombian partners and hopefully support conservation efforts in Colombia. We also have secured significant funding to support student training and research, which will also be an important part of what we'll be doing! Looking forward to having more to say about this soon!
Our paper on the flora of New Guinea has just come out in Nature! This effort, headed by Rodrigo Cámara-Leret, included nearly 100 contributors, including myself. The goal of the paper was to generate the first-ever taxonomically verified species checklist for the island, which required a large group of taxonomic experts to achieve. I did the treatment for Lycopodiaceae and contributed to some fern families - a small task compared to that facing those who worked on families like Rubiaceae (784 species) or Orchidaceae (2856 species!!!).
It was a lot of fun to work on this project and I am so glad to see this sort of floristic work be published in such a prominent journal. There is still a lot (!) to do to understand New Guinean plant diversity, but this is a big step forward.
You can read the paper here. Here is a very nice commentary on the paper that accompanied our paper in Nature - so far, more than 270 online news articles and commentaries have been published for our paper!
A little over a month ago, I chatted with Matt Candeias on his podcast 'In Defense of Plants" about a bunch of themes related to fern and lycophyte evolution. I had a lot of fun, and we covered a diverse array of topics, from hybridization and polyploidy to the connection between mountain uplift and plant speciation.
You can follow our discussion here (Episode 236); http://www.indefenseofplants.com/podcast!
This week, I am putting the final touches on a paper dealing with the systematics and taxonomy of several groups of ferns from Australasia (and elsewhere) and have been going through the process of making species distribution maps based on georeferenced herbarium specimens. There are a lot of different ways to make these maps - some are much more streamlined than others - but I haven't settled on an approach that I really am pleased with. Although my GIS skills are not very advanced, I find that I can make pretty nice maps using a GIS-based approach, but the abundance of different base maps can be a bit bewildering.
I used this opportunity to try out an R package that was published by Marcelo Reginato in 2016 (see reference at bottom of the post), around the same time he was publishing his treatments of Leandra (Melastomataceae). I had played around with the package a little bit previously, but never got very far with it before today. The package is really appealing because it allows for taxonomists to automatically generate species descriptions, indices to collectors, distribution maps, etc. from carefully formatted specimen databases. It even can generate phenology plots and species richness heat maps!
After a half hour or so of tinkering around with the code, I was able to make some nice distribution maps for the species in my study group. I did have to use Illustrator to deal with a few issues that I was not able to deal with directly in monographaR, but I think if I spend some more time at it, I should be able to get the final product I want in R alone. Once I get that figured out, I'll post some code (it's very easy to use!)
If you are working on a taxonomic treatment or some other research project dealing with species distributions or descriptions, I recommend taking a look at monographaR. Marcelo has a really nice overview of the package available online (here). Thanks, Marcelo!
Reginato, M. (2016). monographaR: an R package to facilitate the production of plant taxonomic monographs. Brittonia, 68(2), 212-216.
Today, I just heard that Testo et al. (2019) ""The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae)" has been paginated in the most recent issue of New Phytologist (here it is) along with a commentary by Louisiana State University's Laura Lagomarsino (available here)! I think Laura's PhD work on Andean bellflowers (Campanulaceae) is some of the best work out there with respect to resolving the drivers of diversification in an Andean plant clade, and her work strongly influenced my own dissertation research, so I am really humbled to have her write such a nice commentary on my work! There are so many Andean plant lineages whose evolutionary histories still have not been examined in a rigorous hypothesis-driven manner; I hope this work will encourage other workers to include comparative macroevolutionary models in their own studies. Thanks again to Laura and New Phytologist for putting clubmosses in the spotlight!