Niche shifts after long-distance dispersal events in bipolar sedges (Carex, Cyperaceae)

PREMISE OF THE STUDY: Bipolar species represent the greatest biogeographical disjunction on Earth, raising many questions about the colonization and adaptive processes behind such striking distribution. We investigated climatic niche differences of five Carex bipolar species in North and South America to assess niche shifts between these two regions. Moreover, we assessed potential distribution changes with future climate change. METHODS: We used 1202 presence data points from herbarium specimens and 19 bioclimatic variables to assess climatic niche differences and potential distributions among the five species using ordination methods and Maxent. KEY RESULTS: The niche overlap analyses showed low levels of niche filling and high climatic niche expansion between North and South America. Carex macloviana and C. maritima showed the greatest niche expansion (60% and 96%, respectively), followed by C. magellanica (45%) and C. microglochin (39%). Only C. canescens did not colonize new environments (niche expansion = 0.2%). In contrast, all species but C. magellanica had niche filling that was <40%; hence, they are absent in the south from many environments they inhabit in North America. Climate change will push all species toward higher latitudes and elevation, reducing the availability of suitable environments. CONCLUSIONS: The colonization of South America seems to have involved frequent climatic niche shifts. Most species have colonized new environments from those occupied in the North. Observed niche shifts appear congruent with time since colonization and with current genetic structure within species. In these cold-dwelling species, climate change will most likely decrease their suitable environments in the future.Ministerio de Economía y Competitividad CGL2012-3874, CGL2016-77401-

Geometric Morphometrics sheds light on the systematics affinities of two enigmatic dwarf Neotropical sedges (Carex, Cyperaceae)

Geometric morphometrics (GM) is a powerful analytical tool that enables complete quantification of shapes. Its use in Botany has a great potential for complementing plant evolutionary and ecological studies. Taxonomic delimitation in Carex has been complicated due to reduction of characters and frequent homoplasy. This problem is more marked in cases where the species exhibit dwarfism. South America is the continent with the least understood Carex flora. The systematic relationships of some bizarre-looking groups were not unraveled until molecular phylogenetic studies resolved their relationships. In particular, there are two species only known from their type material whose affinities remain uncertain: Carex herteri and C. hypsipedos. These two taxa are acaulescent plants that respectively grow in the Uruguayan pampa and Peruvian high-altitude meadows. Recently, both species were ascribed to the Carex phalaroides group (subgen. Psyllophorae, sect. Junciformes) due to superficial morphological similarities, such as the androgynous peduncled spikes. However, their character combination is also coincident for its circumscription to sect. Abditispicae species. Nevertheless, in the absence of confirmation from molecular analyses, their placement must be considered preliminary until additional data can be provided. In this work we employ for the first time geometric morphometrics (GM) tools to assess the systematic affinities of two taxonomically problematic sedge species based on fruit shape. We compared utricle morphology of C. herteri and C. hypsipedos with that of C. phalaroides group and species in sect. Abditispicae. To this end we used GM and traditional morphometric approaches. Utricle shape variation along with other morphological features support the exclusion of these two species from the C. phalaroides gr. and, at the same time, show clear affinities of C. herteri to sect. Abditispicae. Carex hypsipedos remains as an incertae sedis species. Our work shows the potential utility of GM for the exploration of systematic affinities in sedges and in other graminoids

Tackling Rapid Radiations With Targeted Sequencing

In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiationsEspaña Ministry of Economy and Competitiveness (project CGL2016- 77401-P

Rare and widespread: integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma

Premise Genera that are widespread, with geographically discontinuous distributions and represented by few species, are intriguing. Is their achieved disjunct distribution recent or ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale pattern in which closely related species appear codistributed in isolated regions over the continental margins of Africa. Genus Camptoloma (Scrophulariaceae) is the most notable example, comprising three species isolated from each other on the northwest, eastern, and southwest Africa. Methods We employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of Camptoloma within Scrophulariaceae by using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian Markov chain Monte Carlo (MCMC) approaches. The population history was estimated with phylogeographic coalescent methods. Results Camptoloma rotundifolium, restricted to Southern Africa, was shown to be a sister species to the disjunct clade formed by C. canariense, endemic to the Canary Islands, and C. lyperiiflorum, distributed in the Horn of Africa–Southern Arabia. Camptoloma was inferred to be sister to the mostly South African tribes Teedieae and Buddlejeae. Stem divergence was dated in the Late Miocene, while the origin of the extant disjunction was inferred as Early Pliocene. Conclusions The current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction and/or population bottlenecking events associated with historical aridification cycles during the Neogene; the pattern of species divergence, from south to north, is consistent with the “climatic refugia” Rand Flora hypothesis

An NGS-based phylogeny of Orthotricheae (Orthotrichaceae, Bryophyta) with the proposal of the new genus Rehubryum from Zealandia

Phylogenomic data increase the possibilities of resolving the evolutionary and systematic relationships among taxa. This is especially valuable in groups with few and homoplasious morphological characters, in which systematic and taxonomical delimitations have been traditionally difficult. Such is the case of several lineages within Bryophyta, like Orthotrichaceae, the second most diverse family of mosses. Members of tribe Orthotricheae are common in temperate and cold regions, as well as in high tropical mountains. In extratropical areas, they represent one of the main components of epiphytic communities, both in dry and oceanic or hyperoceanic conditions. The epiphytic environment is considered a hostile one for plant development, mainly due to its low capacity of moisture retention. Thus, the diversification of the Orthotrichaceae in this environment could be seen as striking. Over the last two decades, great taxonomic and systematic progresses have led to a rearrangement at the generic level in this tribe, providing a new framework to link environment to patterns of diversification. Here, we use nuclear loci targeted with the GoFlag 408 enrichment probe set to generate a well-sampled phylogeny with well-supported suprageneric taxa and increasing the phylogenetic resolution within the two recognized subtribes. Specifically, we show that several genera with Ulota-like morphology jointly constitute an independent lineage. Within this lineage, the recently described Atlantichella from Macaronesia and Western Europe appears as the sister group of Ulota bellii from Zealandia. This latter species is here segregated in the new genus Rehubryum. Assessment of the ecological and biogeographical affinities of the species within the phylogenetic framework suggests that niche adaptation (including climate and substrate) may be a key evolutionary driver that shaped the high diversification of Orthotrichea

Tackling rapid radiations with targeted sequencing

In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations

PHYLOPYR: The genetic information of Pyrenean plants accessible to society

Póster presentado en el IV Simposio Anual de la Sociedad Española de Botánica, Universidad de León, 17-18 de noviembre de 202