Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in non-model organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region.
In this paper, we define the Mallomonas alata group and describe M. alpestrina sp. nov. from an oligotrophic high mountain glacial lake on the slopes of Haba Xue Shan (Haba Snow Mountain), China. The Mallomonas alata group is excluded from the M. pumilio group primarily based on the approximately triangular shape of the collar scales, the small hook-like protruded dome, and one considerably broader anterior flange of the body scale. We extend previous research on small species from the section Torquatae with reticulated scale-shield pattern.
The coexistence of agamospermy and sexuality characterizes most of the ~60 sections of the genus Taraxacum. Section Dioszegia, comprising T. serotinum and its allies, are an exception because only sexuals are reported for all the members of this group. On the basis of the analysis of microsatellite (SSRs) variation, distribution and morphology, we addressed problems related to their mode of reproduction, among-population relationships, taxonomy and within-population variation, using samples from populations in an area extending from southern France to the European part of southern Russia and Iran.
Structure is very popular software for revealing population structure. Here I describe easy workflow how to run independent runs of Structure in parallel to speed up whole process using statistical software R and how to facilitate use of CLUMPP and distruct with easy BASH scripts. Of course, we work on Linux (although another UNIX systems like Mac OS X will be very similar).
Arlequin is very popular tool for population genetics and in recent version (3.5) it has version running on Linux (arlecore, only computational core without GUI) as well as possibility to parse output using R statistical language. Those two features are described only briefly in official manual. I faced some issues when running Arlequin on Linux and parsing output using R.