Uncommon Ground

Uncommon Ground

Botany

Causes of genetic differentiation in Protea repens

American Journal of Botany Volume 104, Number 5. May 2017.

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 

May 17, 2017 Botany, Population genetics 0 Read more >

The beauty of fynbos

The beauty of our fynbos from CapeNature on Vimeo.

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.

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January 25, 2017 Botany, Outdoors 0 Read more >

A new phylogeny for Protea

Protea compacta

Protea compacta near Kleinmond, Western Cape, South Africa

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

January 23, 2017 Botany 0 Read more >

Summary of tweeting from #Botany2016

Twitter activity for #Botany2016 has declined now that the conference has been over for a couple of days.

Botany-2016-tweets

Spirts remained high throughout the runup to the conference, dipping below zero only once about a week before everyone arrived.

Botany-2016-sentiment

@JChrisPires contributed a larger number of tweets (including tweets of others that he retweeted) than anyone else,

Botany-2016-tweeters-cumulative

but @uribe_convers had a larger impact, regardless of whether you measure impact in number of retweets

Botany-2016-impact

or in terms of number of likes

Botany-2016-likes

If you’d like to play around with the code, it’s available in Github: https://github.com/kholsinger/Twitter-stats.

August 7, 2016 Botany 0 Read more >