Abstract: Premise of the study: Microsatellite primers were developed for Carex helodes, a western Mediterranean endemic locally distributed in southern Portugal and southwestern Spain, and rare in northern Morocco. Methods and Results: 109 nuclear microsatellite markers were developed using a shotgun pyrosequencing method, resulting in 91 polymorphic and 18 monomorphic loci when tested using 19 individuals sampled from 5 populations from Portugal, Spain and Morocco. Loci averaged 3.23 alleles per locus (SD = 1.15). In a single population (Cortelha population, Portugal), the 34 most polymorphic loci showed a mean observed heterozygosity of 0.357 (SD = 0.292) and expected heterozygosity mean of 0.384 (SD = 0.255). Conclusions: Next generation sequencing allows us to develop a high number of genetic markers whose levels of polymorphism are adequate to study gene flow among populations. However, when genotyping the individuals within a population, we found low levels of variation. Juan Miguel Arroyo, Marcial Escudero & pedro jordano. 2016. Isolation of 91 polymorphic loci in the western Mediterranean endemic Carex helodes (Cyperaceae). Applications in Plant Sciences, 4, 1500085. LINK.
Abstract: Background. Fahrenholz’s rule states that common ancestors of extant parasites were parasites of the common ancestors of extant hosts. Consequently, parasite phylogeny should mirror host phylogeny. The smut fungi genus Anthracoidea (Anthracoideaceae) is mainly hosted by species of genus Carex (Cyperaceae). Whether or not smut fungi phylogeny mirrors sedge phylogeny is still under debate. Material and methods. The nuclear DNA region LSU (large subunit; 57 accessions) from 31 different Anthracoidea species and ITS, ETS and trnL-F spacer – trnL intron complex from 41 different Carex species were used to infer the phylogenetic history of parasites and their hosts using a maximum likelihood approach. Event-based and distance-based cophylogenetic methods were used to test the hypothesis of whether or not the phylogeny of smut fungi from the genus Anthracoidea matches the phylogeny of the sedge Carex species they host. Results. Cophylogenetic reconstructions taking into account phylogenetic uncertainties based on event-based analyses demonstrated that Anthracoidea phylogeny shows significant topological congruence with the phylogeny of their Carex hosts. A distance-based test was also significant; the phylogenies of Anthracoide and Carex are partially congruent. Conclusions. The phylogenetic congruence of Anthracoidea and Carex is partially based on smut fungi species being preferentially hosted by closely related sedges (host conservatism). In addition, many different events rather than only codivergence are inferred. All of this evidence suggests that host-shift speciation rather than cospeciation seems to explain the cophylogenetic patterns of Anthracoidea and Carex.
Marcial Escudero. 2015. Phylogenetic congruence of parasitic smut fungi (Anthracoidea, Anthracoideaceae) and their host plants (Carex, Cyperaceae): cospeciation or host-shift speciation? American Journal of Botany, 102, 1108-1114. LINK.
Abstract: Premise of the study: The circumboreal Carex section Glareosae comprises 20-25 currently accepted species. High variability in geographic distribution, ecology, cytogenetics and morphology has led to historical problems both in species delimitation and in circumscribing the limits of the section which is one of the major tasks facing caricologist today. Methods: Phylogenetic reconstructions were performed based on ETS, ITS, G3PDH and matK DNA sequences from 204 samples. Concatenation of gene regions in a supermatrix approach to phylogenetic reconstruction was compared to coalescent-based species-tree estimation. Ancestral state reconstructions were performed for eight morphological characters to evaluate for correspondence between phylogeny and traits used in traditional classification within the section. Key results: The results confirm the existence of a core Glareosae comprising 23-25 species. Most species constitute exclusive lineages, and relationships among species are highly resolved with both the supermatrix and coalescent-based species-tree approaches. We use ancestral state reconstruction to investigate sources of homoplasy underlying traditional taxonomy and species circumscription. We find that even species apparently not constituting exclusive lineages are morphologically homogeneous, raising the question of whether paraphyly of species is a phylogenetic artifact in our study or evidence of widespread homoplasy in characters used to define species. Conclusions: This study demonstrates the monophyly of Carex section Glareosae and establishes a phylogenetic framework for the section. Homoplasy makes many of morphological characters difficult to apply for taxon delimitation. This finding of strong concordance between supermatrix and species-tree approaches to phylogenetic reconstructions suggests that even in the face of incongruence among molecular markers, section-level or species-level phylogenies in Carex are tractable.
Enrique Maguilla, Marcial Escudero, Marcia j. Waterway, Andrew L. Hipp, & Modesto Luceño. 2015. Phylogeny, systematics and trait evolution of Carex section Glareosae. American Journal of Botany, 102, 1128-1144. LINK.