Eric Menges has been studying rare plants and fire ecology at Archbold Biological Station for more than 30 years. I just learned that he’s the subject (and narrator) of a short, 16-minute video on Vimeo that I’ve embedded above. Please take the time to watch it. You’ll learn a lot.
If you’re reading this post, you know that my colleagues and I have been studying Protea for more than a decade. A lot of our work has focused on documenting and understanding trait-environment associations. We’ve studied those associations both among populations within species (Protea repens: https://doi.org/10.1093/aob/mcv146), among populations within a small, closely related clade (Protea sect. Exsertae: https://doi.org/ and https://doi.org/), and across the entire genus (https://doi.org/10.1086/680051). But all of those studies look at the relationship between the climate as it is now (as reflected in the South African Atlas of Agrohydrology and Climatology). They haven’t examined how traits have evolved in response to changes in climate.
Our latest paper, begins to address that shortcoming. We use the highly resolved phylogeny of Protea that Nora Mitchell constructed as part of her dissertation (http://darwin.eeb.uconn.edu/uncommon-ground/blog/2017/01/23/a-new-phylogeny-for-protea/ and https://doi.org/10.3732/ajb.1600227), and we reconstruct estimates of how traits changed over evolutionary time in concert (or not) with climates. Our reconstructions depend on particular models of evolutionary change, and we explore several alternatives. Here’s the abstract:
Evolutionary radiations are responsible for much of Earth’s diversity, yet the causes of these radiations are often elusive. Determining the relative roles of adaptation and geographic isolation in diversification is vital to understanding the causes of any radiation, and whether a radiation may be labeled as “adaptive” or not. Across many groups of plants, trait–climate relationships suggest that traits are an important indicator of how plants adapt to different climates. In particular, analyses of plant functional traits in global databases suggest that there is an “economics spectrum” along which combinations of functional traits covary along a fast–slow continuum. We examine evolutionary associations among traits and between trait and climate variables on a strongly supported phylogeny in the iconic plant genus Protea to identify correlated evolution of functional traits and the climatic-niches that species occupy. Results indicate that trait diversification in Protea has climate associations along two axes of variation: correlated evolution of plant size with temperature and leaf investment with rainfall. Evidence suggests that traits and climatic-niches evolve in similar ways, although some of these associations are inconsistent with global patterns on a broader phylogenetic scale. When combined with previous experimental work suggesting that trait–climate associations are adaptive in Protea, the results presented here suggest that trait diversification in this radiation is adaptive.
Mitchell, N., J.E. Carlson, and K.E. Holsinger. 2018. Correlated evolution between climate and suites of traits along a fast–slow continuum in the radiation of Protea. Ecology and Evolution 8:1853–1866. doi: 10.1002/ece3.3773.
One of the great pleasures of serving as an associate advisor on PhD committee is that sometimes you contribute enough to the analysis and interpretation of the data that you end up being a co-author on a paper. That’s why I have papers on New Zealand cicadas, deer mice, and tapeworms, among other things. Now I’ve added another group to my list – moss. Lily Lewis finished her PhD at UConn in the spring of 2015 working with Bernard Goffinet. I was a member of her committee, and now a chapter of her dissertation on which I was able to help has appeared in the American Journal of Botany.1 Here’s the title and abstract. You’ll find the DOI and a link to the paper below.
Resolving the northern hemisphere source region for the long-distance dispersal event that gave rise to the South American endemic dung moss Tetraplodon fuegianus.
PREMISE OF THE STUDY: American bipolar plant distributions characterize taxa at various taxonomic ranks but are most common in the bryophytes at infraspecific and infrageneric levels. A previous study on the bipolar disjunction in the dung moss genus Tetraplodon found that direct long-distance dispersal from North to South in the Miocene–Pleistocene accounted for the origin of the Southern American endemic Tetraplodon fuegianus, congruent with other molecular studies on bipolar bryophytes. The previous study, however, remained inconclusive regarding a specific northern hemisphere source region for the transequatorial dispersal event that gave rise to T. fuegianus.
METHODS: To estimate spatial genetic structure and phylogeographic relationships within the bipolar lineage of Tetraplodon, which includes T. fuegianus, we analyzed thousands of restriction-site-associated DNA (RADseq) loci and single nucleotide polymorphisms using Bayesian individual assignment and maximum likelihood and coalescent model based phylogenetic approaches.
KEY RESULTS: Northwestern North America is the most likely source of the recent ancestor to T. fuegianus.
CONCLUSIONS: Tetraplodon fuegianus, which marks the southernmost populations in the bipolar lineage of Tetraplodon, arose following a single long-distance dispersal event involving a T. mnioides lineage that is now rare in the northern hemisphere and potentially restricted to the Pacific Northwest of North America. Furthermore, gene flow between sympatric lineages of Tetraplodon mnioides in the northern hemisphere is limited, possibly due to high rates of selfing or reproductive isolation.
For more than a decade my colleagues Margaret Rubega and Bob Wyss have co-taught a course to graduate students in science and engineering and undergraduates in Journalism.1 The purpose of the course is to help science students improve their skills in working with journalists and to help journalist increase their skills in interviewing scientists and developing stories from those interviews. One of the projects in this fall’s edition of the course was for the journalism students to interview one of the science graduate students and produce a short video describing the student’s research. Daniela Doncel interviewed Tanisha Williams, a PhD student in EEB whom I co-advise with Carl Schlichting. In addition to interviewing Tanisha, Daniela also interviewed Cindi Jones and me. She assembled a video that explains Tanisha’s work very well. I think Daniela did a very nice job of weaving the disparate interviews into a compelling story, and I think the video looks very good (even though it has me in it). I hope that you agree.
Some of you know that Carl Schlichting and I co-advise Tanisha Williams. If you know that, you almost certainly know that Tanisha spent the 2015-2016 academic year as a Fulbright Fellow in South Africa. She was based at the Cape Peninsula University of Technology, and she used her time not only to collect seeds of Pelargonium and establish experimental gardens at Kirstenbosch Botanical Garden and Rhodes University but also to work with two non-profit environmental organizations. She posted an article about her experience on the blog of the Fulbright Student Program. Here’s an excerpt to whet your appetite:
Among the many experiences I had, I must say the residents from the Khayelitsha township have taken a special place in my heart. This is where I taught girls and young women math, science, computer tutoring, life skills, and female empowerment through a community center program. It was such an impactful experience, as these girls are growing up in a community with high rates of unemployment, violence, and other socioeconomic issues. It was empowering for me to see the curiosity and determination these girls had for learning and changing their community. They thought I was there to teach them from my own experiences being raised in a comparable situation and now working on my doctorate as a scientist, but I know I was the one that gained the most from our time together. I learned what it truly means to have hope and persevere. These lessons, along with the ecological and evolutionary insights from my academic research, will be ones that I always remember.
Protea repens is the most widespread member of the genus. It was one of the focal species in our recently completed Dimensions of Biodiversity project. Part of the project involved genotyping-by-sequencing analyses of 663 individuals from 19 populations spanning most of the geographical range of the species. We summarize results of those analyses in a paper that just appeared in advance of the May issue (cover photo featured above) of the American Journal of Botany. Here’s the abstract. You’ll find the citation and a link at the bottom.
PREMISE OF THE STUDY: The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species.
METHODS: We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure.
RESULTS: A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species.
CONCLUSIONS: The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.
Prunier, R., M. Akman, C.T. Kremer, N. Aitken, A. Chuah, J. Borevitz, and K. E. Holsinger. Isolation by distance and isolation by environment contribute to population differentiation in Protea repens (Proteaceae L.), a widespread South African species. American Journal of Botany doi: 10.3732/ajb.1600232
In case you’ve ever wondered why I have spent so much time working in, thinking about, and writing about Protea this video from CapeNature will give you a bit of a clue. The fynbos is a very interesting place. It has an enormous diversity of plants, many of which are found nowhere else in the world, and much of that diversity is concentrated in a relatively small number of big evolutionary radiations, one of which is Protea.1 One of my students,
Kristen Nolting (@KristenNolting on Twitter) pointed me to this video. Thanks, Kristen.
The genus Protea is one of the iconic evolutionary radiations in the Greater Cape Floristic Region of southwestern South Africa. Its range extends north through Mozambique into parts of central Africa, but the vast majority of species are found in South Africa. From 2011-2014 we collected samples from most of the South African species (59 in total), and for most of the species we collected samples from several individuals from different populations. Over the last couple of years, we extracted DNA, built libraries for next generation sequencing using targeted phylogenomics, and constructed a highly-resolved estimate of phylogenetic relationships in the genus. The paper describing our results is now out in “early view” in American Journal of Botany. Most species from which we have multiple samples are supported as monophyletic units, and most relationships we identify are strongly supported (> 90% support in ASTRAL-II and SVDquartets analyses). We use the species tree from our data as a backbone to provide reliable estimates of relationship for additional species included in a paper by Schnitzler and colleagues for which we did not have samples.
Mitchell, N., P.O. Lewis, E.M. Lemmon, A.R. Lemmon, and K.E. Holsinger. 2017. Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L. American Journal of Botany doi: 10.3732/ajb.1600227
The California Botanical Society celebrated its 100th anniversary a little over three years ago. Why do I mention this now? Because I was poking around looking for something this morning and ran across this YouTube video of my Keynote Address at the banquet. If you have 40 minutes to kill, you might find it interesting.
Twitter activity for #Botany2016 has declined now that the conference has been over for a couple of days.
Spirts remained high throughout the runup to the conference, dipping below zero only once about a week before everyone arrived.
@JChrisPires contributed a larger number of tweets (including tweets of others that he retweeted) than anyone else,
but @uribe_convers had a larger impact, regardless of whether you measure impact in number of retweets
or in terms of number of likes
If you’d like to play around with the code, it’s available in Github: https://github.com/kholsinger/Twitter-stats.