Sergi Massó

Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae)

Target enrichment is a cost-effective sequencing technique that holds promise for elucidating evolutionary relationships in fast-evolving lineages. However, potential biases and impact of bioinformatic sequence treatments in phylogenetic inference have not been thoroughly explored yet. Here, we investigate this issue with an ultimate goal to shed light into a highly diversified group of Compositae (Asteraceae) constituted by four main genera: Arctium, Cousinia, Saussurea, and Jurinea. Specifically, we compared sequence data extraction methods implemented in two easy-to-use workflows, PHYLUCE and HybPiper, and assessed the impact of two filtering practices intended to reduce phylogenetic noise. In addition, we compared two phylogenetic inference methods: (1) the concatenation approach, in which all loci were concatenated in a supermatrix; and (2) the coalescence approach, in which gene trees were produced independently and then used to construct a species tree under coalescence assumptions. Here we confirm the usefulness of the set of 1061 COS targets (a nuclear conserved orthology loci set developed for the Compositae) across a variety of taxonomic levels. Intergeneric relationships were completely resolved: there are two sister groups, Arctium-Cousinia and Saussurea-Jurinea, which are in agreement with a morphological hypothesis. Intrageneric relationships among species of Arctium, Cousinia, and Saussurea are also well defined. Conversely, conflicting species relationships remain for Jurinea. Methodological choices significantly affected phylogenies in terms of topology, branch length, and support. Across all analyses, the phylogeny obtained using HybPiper and the strictest scheme of removing fast-evolving sites was estimated as the optimal. Regarding methodological choices, we conclude that: (1) trees obtained under the coalescence approach are topologically more congruent between them than those inferred using the concatenation approach; (2) refining treatments only improved support values under the concatenation approach; and (3) branch support values are maximized when fast-evolving sites are removed in the concatenation approach, and when a higher number of loci is analyzed in the coalescence approach.

One species, one genotype: no genotypic variability in the extremely narrow endemic tetraploid Agrostis barceloi (Gramineae)

We used allozyme electrophoresis to survey genetic diversity of Agrostis barceloi L.Sáez & Rosselló, an extremely narrow endemic species from the island of Majorca (Balearic Islands, Western Mediterranean Basin). This species is a tetraploid with a single natural population of less than 100 individuals. All analyzed individuals of A. barceloi showed the same genotype. Four out of 18 interpretable loci showed fixed heterozygosity (thus supporting an allopolyploid origin). The genotypic uniformity of this species may be attributed to a founder effect associated with a dispersal event of its ancestor from the continent, a very small current effective population size (Ne), and a series of natural or anthropogenic threats affecting the population. We propose several conservation measures such as seed storing and plant production for further reinforcements (which do not need any previous work for selecting individuals because of the genetic uniformity). In addition, we suggest the preservation of the mountain summit where the species is found (Puig Major), which would also positively influence the conservation of other co-occurring ENEs and other rare and threatened species.

Conservation Genetics of Dichoropetalum schottii (Apiaceae): Is the Legal Protection of Edge Populations Consistent with the Genetic Data?

Dichoropetalum schottii is a species that lives at low to medium altitudes in the southern European mountain ranges, from the Balkans (N Greece) to the Pyrenees. Its legal protection status is not homogeneous along its distribution range, as only some of its edge populations, in the Pyrenees, are protected. Here, by means of allozyme electrophoresis, we examine the genetic variability of populations representing four different regions within its distribution area (Pyrenees, Maritime Alps, Karst Plateau in the SW Slovenia—NE Italy border region, and Pindus Mountains in Greece). The species as a whole exhibits relatively high levels of genetic diversity, partly due to the occurrence of several duplications among the loci surveyed. Genetic differentiation among populations and regions was low, which could be interpreted as the result of recent allopatric fragmentation. We conclude that the species as a whole is not threatened, and that the currently protected populations are, paradoxically, the least valuable from the genetic point of view.