Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats.

Poales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test six hypotheses regarding the evolution and assembly of Poales in open and closed habitats throughout the world, and examine whether diversification patterns demonstrate parallel evolution. We sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalisation analyses, historical biogeography and ancestral state estimations. Diversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time and space, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae. Smaller families display unique and often divergent evolutionary trajectories. The Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats.

The holocentric chromosome microevolution: From phylogeographic patterns to genomic associations with environmental gradients.

Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.

Using ChromEvol to Determine the Mode of Chromosomal Evolution.

The ChromEvol software was the first to implement a likelihood-based approach, using probabilistic models that depict the pattern of chromosome number change along a specified phylogeny. The initial models have been completed and expanded during the last years. New parameters that model polyploid chromosome evolution have been implemented in ChromEvol v.2. In recent years, new and more complex models have been developed. The BiChrom model is able to implement two distinct chromosome models for the two possible trait states of a binary character of interest. ChromoSSE jointly implements chromosome evolution, speciation, and extinction. In the near future, we will be able to study chromosome evolution with increasingly complex models.

Carexquixotiana (Cyperaceae), a new Iberian endemic from Don Quixote's land (La Mancha, S Spain).

Despite centuries of work, the basic taxonomic knowledge of the flora of the Iberian Peninsula is still incomplete, especially for highly diverse and/or difficult genera such as Carex. In this study, we conducted an integrative systematic study based on molecular, morphological and cytogenetic data to elucidate the taxonomic status of several problematic Carex populations from La Mancha region (S Spain) belonging to Carexsect.Phacocystis. These populations have been traditionally considered of uncertain taxonomic adscription, but close to C.reuteriana due to their morphological appearance and ecological preferences. A detailed morphological and cytogenetic study was performed on 16 La Mancha's problematic populations (Sierra Madrona and Montes de Toledo) to compare them with the other Iberian sect. Phacocystis species. In addition, a phylogenetic analysis was conducted using two nuclear (ITS, ETS) and two plastid (rpl32-trnLUAG, ycf6-psbM) DNA regions, including representatives from all species of sect. Phacocystis. We found a significant degree of molecular and morphological differentiation that supports the recognition of La Mancha's problematic populations as a new Iberian endemic species, described here as Carexquixotiana Ben.Benítez, Martín-Bravo, Luceño & Jim.Mejías. Our results reveal that C.quixotiana, unexpectedly, is more closely related to C.nigra than to C.reuteriana on the basis of phylogenetic relationships and chromosome number. These contrasting patterns reflect the taxonomic complexity in sect. Phacocystis and highlight the need for integrative systematic approaches to disentangle such complicated evolutionary scenarios.

New relevant chorological and conservation data on Carex (Cyperaceae) and Hypericum (Hypericaceae) from Ecuador.

Background: Knowledge of Carex L. (true sedges) and Hypericum L. (St. John's wort) in the Neotropics is fragmentary. New information: As a result of a fieldwork campaign in Ecuador and revision of herbarium collections (K, QCA and QCNE), we present here relevant records of twelve Carex (Cyperaceae) and four Hypericum (Hypericaceae) species. Regarding Carex, we present the novel report for South America of C.aztecica, as well as the first Ecuadorian records for C.brehmeri, C.collumanthus, C.fecunda, C.melanocystis and C.punicola. The three later records have additional biogeographical significance, as they represent the new northern limit of these species. We also include observations for another five species included in the Ecuadorian Red List of Endemic Plants. As a result, the list of native Carex reported for Ecuador would now include 52 taxa. With regard to Hypericum, we include the new report of H.sprucei for the province of Bolívar, and the confirmation of the presence of three rare species (H.acostanum, H.matangense, H.prietoi) in their type localities, although with extremely low population sizes. We discuss their conservation status and implications.

Chromosome size matters: genome evolution in the cyperid clade.

BACKGROUND AND AIMS: While variation in genome size and chromosome numbers and their consequences are often investigated in plants, the biological relevance of variation in chromosome size remains poorly known. Here, we examine genome and mean chromosome size in the cyperid clade (families Cyperaceae, Juncaceae and Thurniaceae), which is the largest vascular plant lineage with predominantly holocentric chromosomes. METHODS: We measured genome size in 436 species of cyperids using flow cytometry, and augment these data with previously published datasets. We then separately compared genome and mean chromosome sizes (2C/2n) amongst the major lineages of cyperids and analysed how these two genomic traits are associated with various environmental factors using phylogenetically informed methods. KEY RESULTS: We show that cyperids have the smallest mean chromosome sizes recorded in seed plants, with a large divergence between the smallest and largest values. We found that cyperid species with smaller chromosomes have larger geographical distributions and that there is a strong inverse association between mean chromosome size and number across this lineage. CONCLUSIONS: The distinct patterns in genome size and mean chromosome size across the cyperids might be explained by holokinetic drive. The numerous small chromosomes might function to increase genetic diversity in this lineage where crossovers are limited during meiosis.

Dramatic impact of future climate change on the genetic diversity and distribution of ecologically relevant Western Mediterranean Carex (Cyperaceae).

Anticipating the evolutionary responses of species to ongoing climate change is essential to propose effective management and conservation measures. The Western Mediterranean Basin constitutes one of the hotspots of biodiversity where the effects of climate change are expected to be more dramatic. Plant species with ecological relevance constitute ideal models to evaluate and predict the impact of climate change on ecosystems. Here we investigate these impacts through the spatio-temporal comparison of genetic diversity/structure (AFLPs), potential distribution under different future scenarios of climate change, and ecological space in two Western Mediterranean sister species of genus Carex. Both species are ecologically key in their riparian habitats, but display contrasting distribution patterns, with one widespread in the Iberian Peninsula and North Africa (C. reuteriana), while the other (C. panormitana) is a restricted, probably endangered, Central Mediterranean endemic. At present, we found a strong genetic structure driven by geography in both species, and lower values of genetic diversity and a narrower ecological space in C. panormitana than in C. reuteriana, while the allelic rarity was higher in the former than in C. reuteriana subspecies. Future projections predict an overall dramatic reduction of suitable areas for both species under all climate change scenarios, which could be almost total for C. panormitana. In addition, gene diversity was inferred to decrease in all taxa, with genetic structure reinforcing in C. reuteriana by the loss of admixture among populations. Our findings stress the need for a reassessment of C. panormitana conservation status under IUCN Red List criteria and the implementation of conservation measures.

Are Cenozoic relict species also climatic relicts? Insights from the macroecological evolution of the giant sedges of Carex sect. Rhynchocystis (Cyperaceae).

PREMISE: Most of the Paleotropical flora widely distributed in the Western Palearctic became extinct during the Mio-Pliocene as a result of global geoclimatic changes. A few elements from this Cenozoic flora are believed to remain as relicts in Macaronesia, forming part of the laurel forests. Although the origins of the present species assembly are known to be heterogeneous, it is unclear whether some species should be considered climatic relicts with conserved niches. An ideal group for studying such relict characteristics is a Miocene lineage of Carex sect. Rhynchocystis (Cyperaceae), which comprises four species distributed in mainland Palearctic and Macaronesia. METHODS: We reconstructed the current and past environmental spaces for extant mainland and Macaronesian species, as well as for Pliocene fossils. We also studied the bioclimatic niche evolution. Species distribution modeling and ensemble small modeling were performed to assess the potential distribution over time. RESULTS: Climatic niche analyses and distribution modeling revealed that the ecological requirements of Macaronesian species did not overlap with those of either mainland species or with the Pliocene fossils. Conversely, the niches of mainland species displayed significant similarity and equivalence. CONCLUSIONS: Macaronesian species are not climatic relicts from the Paleotropical flora, but instead seem to have changed the ecological niche of their ancestors. By contrast, despite their ancient divergence (Late Miocene), mainland C. pendula and C. agastachys show conserved niches, with competitive exclusion likely shaping their mostly allopatric ranges.

An Evolutionary Study of Carex Subg. Psyllophorae (Cyperaceae) Sheds Light on a Strikingly Disjunct Distribution in the Southern Hemisphere, With Emphasis on Its Patagonian Diversification.

Carex subgenus Psyllophorae is an engaging study group due to its early diversification compared to most Carex lineages, and its remarkable disjunct distribution in four continents corresponding to three independent sections: sect. Psyllophorae in Western Palearctic, sect. Schoenoxiphium in Afrotropical region, and sect. Junciformes in South America (SA) and SW Pacific. The latter section is mainly distributed in Patagonia and the Andes, where it is one of the few Carex groups with a significant in situ diversification. We assess the role of historical geo-climatic events in the evolutionary history of the group, particularly intercontinental colonization events and diversification processes, with an emphasis on SA. We performed an integrative study using phylogenetic (four DNA regions), divergence times, diversification rates, biogeographic reconstruction, and bioclimatic niche evolution analyses. The crown age of subg. Psyllophorae (early Miocene) supports this lineage as one of the oldest within Carex. The diversification rate probably decreased over time in the whole subgenus. Geography seems to have played a primary role in the diversification of subg. Psyllophorae. Inferred divergence times imply a diversification scenario away from primary Gondwanan vicariance hypotheses and suggest long-distance dispersal-mediated allopatric diversification. Section Junciformes remained in Northern Patagonia since its divergence until Plio-Pleistocene glaciations. Andean orogeny appears to have acted as a northward corridor, which contrasts with the general pattern of North-to-South migration for temperate-adapted organisms. A striking niche conservatism characterizes the evolution of this section. Colonization of the SW Pacific took place on a single long-distance dispersal event from SA. The little ecological changes involved in the trans-Pacific disjunction imply the preadaptation of the group prior to the colonization of the SW Pacific. The high species number of the section results from simple accumulation of morphological changes (disparification), rather than shifts in ecological niche related to increased diversification rates (radiation).

An integrative monograph of Carex section Schoenoxiphium (Cyperaceae).

Carex section Schoenoxiphium (Cariceae, Cyperaceae) is endemic to the Afrotropical biogeographic region and is mainly distributed in southern and eastern Africa, with its center of diversity in eastern South Africa. The taxon was formerly recognized as a distinct genus and has a long history of taxonomic controversy. It has also an important morphological and molecular background in particular dealing with the complexity of its inflorescence and the phylogenetic relationships of its species. We here present a fully updated and integrative monograph of Carex section Schoenoxiphium based on morphological, molecular and cytogenetic data. A total of 1,017 herbarium specimens were examined and the majority of the species were studied in the field. Previous molecular phylogenies based on Sanger-sequencing of four nuclear and plastid DNA regions and RAD-seq were expanded. For the first time, chromosome numbers were obtained, with cytogenetic counts on 44 populations from 15 species and one hybrid. Our taxonomic treatment recognizes 21 species, one of them herein newly described (C. gordon-grayae). Our results agree with previous molecular works that have found five main lineages in Schoenoxiphium. We provide detailed morphological descriptions, distribution maps and analytical drawings of all accepted species in section Schoenoxiphium, an identification key, and a thorough nomenclatural survey including 19 new typifications and one nomen novum.

Inferring hypothesis-based transitions in clade-specific models of chromosome number evolution in sedges (Cyperaceae).

Large-scale changes in chromosome number have been associated with diversification rate shifts in many lineages of plants. For instance, several ancient rounds of polyploidization events have been inferred to promote genomic differentiation and/or isolation and, consequently, angiosperm diversification. Dysploidy, although less studied, has been suggested to also play an important role in angiosperm diversification. In this article, we aim to elucidate the role of chromosomal rearrangements on lineage diversification by analyzing a new comprehensive sedge (Cyperaceae) phylogenetic tree. Our null hypothesis is that the mode and tempo of chromosome evolution are to be homogeneous across the complete phylogeny. In order to discern patterns of diversification shifts and chromosome number changes within the family tree, we tested clade-specific chromosome evolution models for several subtrees according to previously reported increments of diversification rates. Results show that a complex, heterogeneous model composed of different clade-specific chromosome evolution transitions are significantly supported against the null hypothesis of a model with no chromosome number model transition events along the phylogeny. This could suggest a link between diversification and changes in chromosome number evolution although other possibilities are not discarded. Our methodological approach may allow identifying different patterns of chromosome evolution, as found for Cyperaceae, for other lineages at different evolutionary levels.

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.

Long-distance dispersal explains the bipolar disjunction in Carex macloviana.

PREMISE OF THE STUDY: The sedge Carex macloviana d'Urv presents a bipolar distribution. To clarify the origin of its distribution, we consider the four main hypotheses: long-distance dispersal (either by mountain hopping or by direct dispersal), vicariance, parallel evolution, and human introduction. METHODS: Phylogenetic, phylogeographic, and divergence time estimation analyses were carried out based on two nuclear ribosomal (ETS and ITS) regions, one nuclear single copy gene (CATP), and three plastid DNA regions (rps16 and 5'trnK introns, and psbA-trnH spacer), using Bayesian inference, maximum likelihood, and statistical parsimony. Bioclimatic data were used to characterize the climatic niche of C. macloviana. KEY RESULTS: Carex macloviana constitutes a paraphyletic species, dating back to the Pleistocene (0.62 Mya, 95% highest posterior density: 0.29-1.00 Mya). This species displays strong genetic structure between hemispheres, with two different lineages in the Southern Hemisphere and limited genetic differentiation in Northern Hemisphere populations. Also, populations from the Southern Hemisphere show a narrower climatic niche with regards to the Northern Hemisphere populations. CONCLUSIONS: Carex macloviana reached its bipolar distribution by long-distance dispersal, although it was not possible to determine whether it was caused by mountain hopping or by direct dispersal. While there is some support that Carex macloviana might have colonized the Northern Hemisphere by south-to-north transhemisphere dispersal during the Pleistocene, unlike the southwards dispersal pattern inferred for other bipolar Carex L. species, we cannot entirely rule out north-to-south dispersion.

Molecular evidence supports ancient long-distance dispersal for the amphi-Atlantic disjunction in the giant yellow shrimp plant (Barleria oenotheroides).

PREMISE OF THE STUDY: Barleria is a large, pantropical genus of ca. 265 species mainly distributed in the Old World with only one species, B. oenotheroides, extending to the neotropics. This amphi-Atlantic disjunction, frequently displayed by pantropical taxa, has been traditionally explained with vicariance or geodispersal hypotheses and increasingly with long-distance dispersal. The native status of this species in the New World is controversial. METHODS: A molecular phylogeographic study based on the nuclear ribosomal ITS region and plastid trnL-F, rps16, and trnS-G sequences was done to clarify the origin of this tropical intercontinental disjunction. Divergence times were estimated with various analytical approaches, including different markers and primary calibration points. KEY RESULTS: Divergence ages estimated for Barleria lineages disagree with vicariance or geodispersal hypotheses. Genetic differentiation of American vs. African populations of B. oenotheroides does not support a recent anthropogenic introduction to the New World. Our data suggest ancient long-distance dispersal from the Old to the New World probably during the Pliocene or Upper Miocene. The number of dispersal events remains unclear. CONCLUSIONS: Our study demonstrates the native status of Barleria in the New World, resolving one of only three presumed natural Old World-New World disjunctions at the species level among Acanthaceae. This case constitutes a further documented example of the "out-of-Africa" pattern in the family, despite their lack of documented assisted-dispersal syndromes, and highlights the importance of long-distance dispersal to explain pantropical distributions in many families.

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.

Monophyly, phylogenetic position and the role of hybridization in Schoenoxiphium Nees (Cariceae, Cyperaceae).

Incongruence between gene trees, even within genomes, is often the result of hybridization and/or other processes such as incomplete lineage sorting, and can cause problems for phylogenetic analyses. We show here that the radiation of the Cyperaceae genus Schoenoxiphium involved at least one hybridization event with a closely related species of Carex, as indicated by a recombinant nuclear ITS region shared by all species in the S. rufum clade and C. camptoglochin. Recombinant sequences were confirmed with cloning experiments and recombination analyses. The monophyly of Schoenoxiphium has, in previous analyses, been suspected but not sufficiently supported, possibly due in part to this problem. Our phylogenetic analyses include an appropriate representation of Schoenoxiphium and other related Cariceae species and an extended sampling of the nuclear ITS and plastid marker regions, trnLF and rps16. We demonstrate that Schoenoxiphium is monophyletic, nested within Carex, and that several supported clades exist in Schoenoxiphium.

Is Oligomeris (Resedaceae) indigenous to North America? Molecular evidence for a natural colonization from the Old World.

Oligomeris linifolia constitutes one of the few examples of intercontinental disjunctions at the species level between the arid regions of the Old World and SW North America. The status of the American populations has been obscure, with some authors considering the populations to be introduced, whereas others believe them to be native. To clarify these conflicting opinions, we performed phylogeographic analyses using nuclear ribosomal ITS and plastid trnL-F and rps16 sequences to infer the origin of the disjunct American populations. Two independent molecular clock approaches based on ITS and cpDNA sequences (rbcL, matK, trnL-F) were used to estimate a divergence time of O. linifolia. Low levels of sequence divergence and estimates of relatively recent splits of Oligomeris lineages disagree with the vicariance hypotheses traditionally suggested to account for New-Old World disjunctions. In addition, significant genetic differentiation of American populations does not indicate a recent anthropogenic introduction. Morphological uniformity and the sharing of haplotypes between disjunct populations, together with the molecular clock results, suggest that a long-distance dispersal event from the Old Word to SW North America may have taken place during the Quaternary, in spite of limited dispersal mechanisms in Oligomeris.

Molecular systematics and biogeography of Resedaceae based on ITS and trnL-F sequences.

The Resedaceae, containing 6 genera and ca. 85 species, are widely distributed in the Old World, with a major center of species diversity in the Mediterranean basin. Phylogenetic analyses of ITS and plastid trnL-trnF sequences of 66 species from all genera of the Resedaceae reveal (1) monophyly of the family, in congruence with preliminary phylogenetic studies; (2) molecular support for the traditional morphological subdivision of the Resedaceae into three tribes according to ovary and placentation types, and carpel number; (3) two monophyletic genera (Caylusea, Sesamoides), and one natural group (core Reseda), which includes the remaining four genera of the family (Ochradenus, Oligomeris, Randonia, Reseda); (4) a monophyletic origin for four of the six taxonomic sections recognized within Reseda (Leucoreseda, Luteola, Glaucoreseda, Phyteuma). Our results lead us to interpret an increment of the basic chromosome number in the family from x=5 to x=6 in at least two independent instances, and a broad representation of polyploids in multiple lineages across phylogenies, including association between octoploids and alien invasion in many parts of the world. Species diversity, endemism number, phylogenetic relationships and sequence divergence in Resedaceae suggest two major centers of differentiation, one in the western Mediterranean, and the other in the eastern Mediterranean and SW Asia. Two independent colonization events to the Canary Islands from Africa are indicated for the two Canarian Reseda endemics.