Botany picture #59: Ruellia longipedunculata

Ruellia longipedunculata (Acanthaceae), Bolivia, 2007. Ruellia is one of the largest genera of the Acanths. The American species that I am familiar with are mostly butterfly- or, as in this case, hummingbird-pollinated. The species shown here is a shrub and grows in eastern Bolivia.

"Monophylogenetic" species

This continues a series on species. The previous episodes introduced the topic, provided an intuitive classification of species concepts, and dealt with biological, genotypic cluster and "typological" species.

 The term "phylogenetic" became so popular after phylogenetic systematics gained ascendency in the systematic and taxonomic community that several quite unrelated species concepts were published under that label. In the previous post you may have noticed that I call something the autoapomorphic species concept following this list compiled by a philosopher of science although it was really published as “The phylogenetic species concept (sensu Wheeler and Platnick)”. Not only does that clarification in the brackets nicely demonstrate the problem of homonymy here, but I am also unsure what exactly is so phylogenetic about a concept considering species to be groups of samples with a unique character combination.

I will therefore limit this post to discussing the so-called phylogenetic species concepts that demand species be monophyletic (i.e. the Phylogenetic Taxon Species in the list mentioned above), although that necessarily means that I will in part reiterate what I already wrote before.

Botany picture #58: Scutellaria ventenatii

Scutellaria ventenatii (Lamiaceae), Botanic Garden of Bogota, Colombia, 2007. The skullcap genus Scutellaria is perhaps the easiest to recognize of all Lamiaceae because of its very distinct calyx. It is two-lipped, both lips are smooth (i.e. the five calyx teeth are not really distinct any more), and there is generally a scale-like protrusion on the upper lip. The calyx closes around the fertilized ovule; when the seeds are ripe, it dries out and the upper calyx lip falls off, like a lid. This species is, like many other of its striking South American congeners, clearly hummingbird-pollinated, but the northern hemisphere species are generally bee-pollinated.

Comparison of species tree methods

Update 10 June 2013: This post originally from 24 April 2013 has been updated extensively because I have since tried out a set of new species tree methods, got STEM to run and a bit more experience with some others. I have also promoted the post to one of the "recommended phylogenetic systematics" posts on this site despite not being about theory of classification.

Update 27 March 2016: Added ASTRAL and iGTP, restructured the post to be more software-focused.

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I spent part of the last few days trying out different species tree methods, partly to help a colleague produce an example tree that he can use in a workshop he is planning and partly because I want to infer a species tree for one of my own projects in the next few weeks. This post was written for two reasons: as a note to myself for future reference and as a pointer for somebody who might want to infer a species tree and does not know which of the many programs to choose. A person like myself a few days ago, one could say, only if they find this post via search engine it might save them some of the frustrations I experienced.

Note that this is not a post for a methods wonk or for somebody who wants to learn about the theoretical or methodological background. It is strictly from the end user perspective, directed at those who want to know what is available, how user friendly the tools are and where to get them.

If you don't know what this is about you might want to refer to my earlier post on the topic. To summarize: these days we mostly use molecular data, in particular the DNA sequences of genes or intergenic spacers, to infer the evolutionary relationships of species. However, any individual gene phylogeny may or may not be congruent with the species phylogeny or with other gene phylogenies because each species inherits a random subset of the pre-existing allele diversity in of its ancestral species. Alternatively, discrepancies between a gene tree and the species tree or between different gene trees may also arise from introgression, rare gene flow between distinct species.

Botany picture #57: Arthropodium milleflorum

Arthropodium milleflorum (Anthericaceae), the "vanilla lily", Australia, 2012. I took this picture on a weekend trip this summer up in the mountains. The flowers are intricately beautiful but rather small as you can see from the size of my fingers.

Watson Woodlands Open Day

Today we spent the morning at the Watson Woodlands Open Day at Justice Robert Hope Park. This is a patch of bush next to the much better known Mt Majura Nature Reserve. It was protected after some controversy in the 1990ies but unfortunately still has development creeping up onto its borders.

At the entrance the event looked deceptively small but it had much more going on than you would think from the picture above. The stall on the right had information booklets, an exhibit of local fossils, cookies and drinks. The stall on the left were Reptiles Inc., a group offering reptile exhibitions. In this case, visitors could pet a constricting snake from Queensland and admire several blue tongue and shingleback lizards and turtles. Finally, there was some very enjoyable didgeridoo music.

This is one of the fossils that were exhibited. Unfortunately, I do not know from what geological epoch it comes but considering that there is a trilobite it must be pretty damn old.

Our greatest interest, however, was in the guided tour offered by botanist John Briggs. He related the local efforts to improve habitat quality, keep weeds at bay and reestablish rarer native plants, and he named native and weedy species and explained how to recognize them. The above picture shows a specimen of Eucalyptus blakelyi that he estimated at ca 400 years old.

Finally, this is a detail of the local dominant 'yellow box gum' Eucalyptus melliodora in flower. I am still not very good at naming eucalypts, so it is good to have a picture of a local species with a name on it. I may use it in a lecture later this year...

Botany picture #56 1/2: Hottonia palustris

Hottonia palustris (Primulaceae), Germany, 2008. Called Wasserfeder in German and Featherfoil in English due to its feather-shaped leaves, this beautiful member of the primrose family is a water plant. While the roots and leaves are submerged, the large inflorescences are held stiffly erect above the water surface.