Pedro Jiménez-Mejías

Karyotypic Changes through Dysploidy Persist Longer over Evolutionary Time than Polyploid Changes

Chromosome evolution has been demonstrated to have profound effects on diversification rates and speciation in angiosperms. While polyploidy has predated some major radiations in plants, it has also been related to decreased diversification rates. There has been comparatively little attention to the evolutionary role of gains and losses of single chromosomes, which may or not entail changes in the DNA content (then called aneuploidy or dysploidy, respectively). In this study we investigate the role of chromosome number transitions and of possible associated genome size changes in angiosperm evolution. We model the tempo and mode of chromosome number evolution and its possible correlation with patterns of cladogenesis in 15 angiosperm clades. Inferred polyploid transitions are distributed more frequently towards recent times than single chromosome gains and losses. This is likely because the latter events do not entail changes in DNA content and are probably due to fission or fusion events (dysploidy), as revealed by an analysis of the relationship between genome size and chromosome number. Our results support the general pattern that recently originated polyploids fail to persist, and suggest that dysploidy may have comparatively longer-term persistence than polyploidy. Changes in chromosome number associated with dysploidy were typically observed across the phylogenies based on a chi-square analysis, consistent with these changes being neutral with respect to diversification.

Systematics and Taxonomy of Carex sect. Ceratocystis (Cyperaceae) in Europe: A Molecular and Cytogenetic Approach

Abstract Carex sect. Ceratocystis is distributed in Eurasia and North America, with a few disjunct taxa in the Southern Hemisphere. Despite being one of the most intensively studied groups within Carex, its taxonomy remains a complex issue due to hybridization and faint morphological boundaries. Two main contrasting approaches to its taxonomy may be distinguished, synthetic and analytical, widely differing in the number of considered taxa. The status of several morphotypes from Europe and the Mediterranean Basin are particularly problematic. We used phylogenetic analyses of nuclear ITS and plastid rps16 and 5′trnK sequences along with cytogenetic data to evaluate the main taxonomic approaches and to infer evolutionary patterns in Europe and North Africa, with a special focus on the problematic morphotypes. Three major clades were found which mostly match morphological features of the utricle. Carex durieui should be excluded from section Ceratocystis. Although a linear agmatoploid series has been generally proposed to account for the cytogenetic evolution of section Ceratocystis, our results suggest chromosome number increase but not in a linear fashion. Different extensive hybridization areas in South Europe are suggested for some of the problematic morphotypes (Pyrenean-Cantabrian Mountains, Atlantic-Iberian Strip and Corsica).

Taxonomic delimitation and drivers of speciation in the Ibero-North African Carex sect. Phacocystis river-shore group (Cyperaceae).

PREMISE OF THE STUDY The Ibero-North African Carex sect. Phacocystis river-shore group is a set of perennial helophytic species with poorly defined taxonomic boundaries. In the present study, we delimited the different taxonomic units, addressed the phylogeographic history, and evaluated the drivers of differentiation that have promoted diversification of these plants. METHODS We analyzed molecular data using statistical parsimony for plastid sequences (26 samples from 26 populations) and principal coordinate analysis, neighbor joining, and Bayesian analysis of population structure for AFLPs (186 samples from 26 populations). Chromosome numbers from 14 samples (9 populations) are newly reported. KEY RESULTS Three species can be distinguished (C. acuta, C. elata, and C. reuteriana). Unexpectedly for rhizome-growing helophytes, the vegetative reproduction detected was incidental. The widespread C. elata was found to be a genetically poorly differentiated taxon, whereas the local C. reuteriana displayed geographical structuring. Geographical factors seem to be the main driver of differentiation for both taxa. CONCLUSIONS Despite apparent morphological and ecological similarities, C. elata and C. reuteriana have disparate genetic structures and evolutionary histories, which may have originated from small ecological differences. Carex elata is broadly distributed throughout Europe, and its northern populations were recently founded, probably after the last glacial maximum. In contrast, C. reuteriana is an Ibero-North African endemic, with long-standing populations affected by isolation and limited gene flow. It is likely that high-density blocking effects and different gene-flow barriers act together to delimit its distribution and promote its relatively high population differentiation.

Megaphylogenetic Specimen-Level Approaches to the Carex (Cyperaceae) Phylogeny Using ITS, ETS, and matK Sequences: Implications for Classification

Abstract We present the first large-scale phylogenetic hypothesis for the genus Carex based on 996 of the 1983 accepted species (50.23%). We used a supermatrix approach using three DNA regions: ETS, ITS and matK. Every concatenated sequence was derived from a single specimen. The topology of our phylogenetic reconstruction largely agreed with previous studies. We also gained new insights into the early divergence structure of the two largest clades, core Carex and Vignea clades, challenging some previous evolutionary hypotheses about inflorescence structure. Most sections were recovered as non-monophyletic. Homoplasy of characters traditionally selected as relevant for classification, historical misunderstanding of how morphology varies across Carex, and regional rather than global views of Carex diversity seem to be the main reasons for the high levels of polyphyly and paraphyly in the current infrageneric classification.

Toward an accurate taxonomic interpretation of Carex fossil fruits (Cyperaceae): A case study in section Phacocystis in the Western Palearctic

PREMISE OF THE STUDY Despite growing interest in the systematics and evolution of the hyperdiverse genus Carex, few studies have focused on its evolution using an absolute time framework. This is partly due to the limited knowledge of the fossil record. However, Carex fruits are not rare in certain sediments. We analyzed carpological features of modern materials from Carex sect. Phacocystis to characterize the fossil record taxonomically. METHODS We studied 374 achenes from modern materials (18 extant species), as well as representatives from related groups, to establish the main traits within and among species. We also studied 99 achenes from sediments of living populations to assess their modification process after decay. Additionally, we characterized 145 fossil achenes from 10 different locations (from 4-0.02 mya), whose taxonomic assignment we discuss. KEY RESULTS Five main characters were identified for establishing morphological groups of species (epidermis morphology, achene-utricle attachment, achene base, style robustness, and pericarp section). Eleven additional characters allowed the discrimination at species level of most of the taxa. Fossil samples were assigned to two extant species and one unknown, possibly extinct species. CONCLUSIONS The analysis of fruit characters allows the distinction of groups, even up to species level. Carpology is revealed as an accurate tool in Carex paleotaxonomy, which could allow the characterization of Carex fossil fruits and assign them to subgeneric or sectional categories, or to certain species. Our conclusions could be crucial for including a temporal framework in the study of the evolution of Carex.

Clarification of the Use of the Terms Perigynium and Utricle in Carex L. (Cyperaceae)

Abstract Despite previous efforts to unify the terminology for Cyperaceae, two different terms, perigynium and utricle, are in common use for the prophyllar bract enclosing the female flower of Carex. Use of these terms is divided largely on geographic lines (mainly North American versus European and other authors, respectively). The recent merging of Kobresia with Carex requires a single term to refer to both the open prophyll of Kobresia and the laterally closed one of Carex. However, even when authors use utricle for Carex species, these same authors do not refer to the open prophyll of Kobresia as a utricle. We show that perigynium was apparently coined earlier than utricle, at the end of the 18th century, but the term utricle became more widespread than perigynium by the 20th century. Neither of the two terms is unambiguous, as both have also been used for other structures in other plant groups. Given this background, we propose revised definitions of both terms based on two facts: 1) the greater semantic accuracy of perigynium to refer to both the prophylls of Carex and the former genus Kobresia; and 2) the greater spread, and thus social utility, of the term utricle. We also discuss the terminology used for the fertile prophylls of lower branching orders found in some Carex groups and recommend use of the terms cladoprophyll, tubular cladoprophyll, and utriculiform cladoprophyll.

Cut from the same cloth: The convergent evolution of dwarf morphotypes of the Carex flava group (Cyperaceae) in Circum-Mediterranean mountains

Plants growing in high-mountain environments may share common morphological features through convergent evolution resulting from an adaptative response to similar ecological conditions. The Carex flava species complex (sect. Ceratocystis, Cyperaceae) includes four dwarf morphotypes from Circum-Mediterranean mountains whose taxonomic status has remained obscure due to their apparent morphological resemblance. In this study we investigate whether these dwarf mountain morphotypes result from convergent evolution or common ancestry, and whether there are ecological differences promoting differentiation between the dwarf morphotypes and their taxonomically related large, well-developed counterparts. We used phylogenetic analyses of nrDNA (ITS) and ptDNA (rps16 and 5’trnK) sequences, ancestral state reconstruction, multivariate analyses of macro- and micromorphological data, and species distribution modeling. Dwarf morphotype populations were found to belong to three different genetic lineages, and several morphotype shifts from well-developed to dwarf were suggested by ancestral state reconstructions. Distribution modeling supported differences in climatic niche at regional scale between the large forms, mainly from lowland, and the dwarf mountain morphotypes. Our results suggest that dwarf mountain morphotypes within this sedge group are small forms of different lineages that have recurrently adapted to mountain habitats through convergent evolution.

Bipolar distributions in vascular plants: A review

Bipolar disjunct distributions are a fascinating biogeographic pattern exhibited by about 30 vascular plants, whose populations reach very high latitudes in the northern and southern hemispheres. In this review, we first propose a new framework for the definition of bipolar disjunctions and then reformulate a list of guiding principles to consider how to study bipolar species. Vicariance and convergent evolution hypotheses have been argued to explain the origin of this fragmented distribution pattern, but we show here that they can be rejected for all bipolar species, except for Carex microglochin. Instead, human introduction and dispersal (either direct or by mountain-hopping)-facilitated by standard and nonstandard vectors-are the most likely explanations for the origin of bipolar plant disjunctions. Successful establishment after dispersal is key for colonization of the disjunct areas and appear to be related to both intrinsic (e.g., self-compatibility) and extrinsic (mutualistic and antagonistic interactions) characteristics. Most studies on plant bipolar disjunctions have been conducted in Carex (Cyperaceae), the genus of vascular plants with the largest number of bipolar species. We found a predominant north-to-south direction of dispersal, with an estimated time of diversification in agreement with major cooling events during the Pliocene and Pleistocene. Bipolar Carex species do not seem to depend on specialized traits for long-distance dispersal and could have dispersed through one or multiple stochastic events, with birds as the most likely dispersal vector.

Specimens at the Center: An Informatics Workflow and Toolkit for Specimen-Level Analysis of Public DNA Database Data

Abstract Major public DNA databases — NCBI GenBank, the DNA DataBank of Japan (DDBJ), and the European Molecular Biology Laboratory (EMBL) — are invaluable biodiversity libraries. Systematists and other biodiversity scientists commonly mine these databases for sequence data to use in phylogenetic studies, but such studies generally use only the taxonomic identity of the sequenced tissue, not the specimen identity. Thus studies that use DNA supermatrices to construct phylogenetic trees with species at the tips typically do not take advantage of the fact that for many individuals in the public DNA databases, several DNA regions have been sampled; and for many species, two or more individuals have been sampled. Thus these studies typically do not make full use of the multigene datasets in public DNA databases to test species coherence and select optimal sequences to represent a species. In this study, we introduce a set of tools developed in the R programming language to construct individual-based trees from NCBI GenBank data and present a set of trees for the genus Carex (Cyperaceae) constructed using these methods. For the more than 770 species for which we found sequence data, our approach recovered an average of 1.85 gene regions per specimen, up to seven for some specimens, and more than 450 species represented by two or more specimens. Depending on the subset of genes analyzed, we found up to 42% of species monophyletic. We introduce a simple tree statistic—the Taxonomic Disparity Index (TDI)—to assist in curating specimen-level datasets and provide code for selecting maximally informative (or, conversely, minimally misleading) sequences as species exemplars. While tailored to the Carex dataset, the approach and code presented in this paper can readily be generalized to constructing individual-level trees from large amounts of data for any species group.

Linum flos-carmini (Linaceae), a New Species from Northern Morocco

Linum bicolor is a problematic North African taxon associated with L. setaceum. A consensus on the taxonomic status of a putative form (L. setaceum var. bicolor f. robusta) has not been achieved yet. We conducted a morphological study based on herbarium and field collections, combined with nuclear (ITS) and plastid (ndhF5–8 and trnL-F) phylogenies to clarify its status. The phylogenetic analysis did not reveal molecular divergence, but a comparative morphological study revealed substantial differences in traits previously used to distinguish the two taxa (stems, leaves, corolla and calyx size). In addition, we found that the indumentum of sepals, petal colour, and the arrangement of anthers and stigmas differed so clearly between the form robusta and L. setaceum s. stricto, that recognizing the former taxon as an independent species was justified. We provide an identification key to the yellow- and white-flowered Linum species in NW Africa. We also revised the unplaced name L. bicolor Schoubs. ex DC. and lectotypified it to avoid nomenclatural problems.