The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera.

BACKGROUND AND AIMS: Biogeographical relationships between the Canary Islands and north-west Africa are often explained by oceanic dispersal and geographical proximity. Sister-group relationships between Canarian and eastern African/Arabian taxa, the 'Rand Flora' pattern, are rare among plants and have been attributed to the extinction of north-western African populations. Euphorbia balsamifera is the only representative species of this pattern that is distributed in the Canary Islands and north-west Africa; it is also one of few species present in all seven islands. Previous studies placed African populations of E. balsamifera as sister to the Canarian populations, but this relationship was based on herbarium samples with highly degraded DNA. Here, we test the extinction hypothesis by sampling new continental populations; we also expand the Canarian sampling to examine the dynamics of island colonization and diversification. METHODS: Using target enrichment with genome skimming, we reconstructed phylogenetic relationships within E. balsamifera and between this species and its disjunct relatives. A single nucleotide polymorphism dataset obtained from the target sequences was used to infer population genetic diversity patterns. We used convolutional neural networks to discriminate among alternative Canary Islands colonization scenarios. KEY RESULTS: The results confirmed the Rand Flora sister-group relationship between western E. balsamifera and Euphorbia adenensis in the Eritreo-Arabian region and recovered an eastern-western geographical structure among E. balsamifera Canarian populations. Convolutional neural networks supported a scenario of east-to-west island colonization, followed by population extinctions in Lanzarote and Fuerteventura and recolonization from Tenerife and Gran Canaria; a signal of admixture between the eastern island and north-west African populations was recovered. CONCLUSIONS: Our findings support the Surfing Syngameon Hypothesis for the colonization of the Canary Islands by E. balsamifera, but also a recent back-colonization to the continent. Populations of E. balsamifera from northwest Africa are not the remnants of an ancestral continental stock, but originated from migration events from Lanzarote and Fuerteventura. This is further evidence that oceanic archipelagos are not a sink for biodiversity, but may be a source of new genetic variability.

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: Carexherteri 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 Carexphalaroides 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. Carexhypsipedos 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.

Phylogenomics sheds new light on the drivers behind a long-lasting systematic riddle: the figwort family Scrophulariaceae.

The figwort family, Scrophulariaceae, comprises c. 2000 species whose evolutionary relationships at the tribal level have proven difficult to resolve, hindering our ability to understand their origin and diversification. We designed a specific probe kit for Scrophulariaceae, targeting 849 nuclear loci and obtaining plastid regions as by-products. We sampled c. 87% of the genera described in the family and use the nuclear dataset to estimate evolutionary relationships, timing of diversification, and biogeographic patterns. Ten tribes, including two new tribes, Androyeae and Camptolomeae, are supported, and the phylogenetic positions of Androya, Camptoloma, and Phygelius are unveiled. Our study reveals a major diversification at c. 60 million yr ago in some Gondwanan landmasses, where two different lineages diversified, one of which gave rise to nearly 81% of extant species. A Southern African origin is estimated for most modern-day tribes, with two exceptions, the American Leucophylleae, and the mainly Australian Myoporeae. The rapid mid-Eocene diversification is aligned with geographic expansion within southern Africa in most tribes, followed by range expansion to tropical Africa and multiple dispersals out of Africa. Our robust phylogeny provides a framework for future studies aimed at understanding the role of macroevolutionary patterns and processes that generated Scrophulariaceae diversity.

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 Orthotricheae.

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 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.

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.

Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above.

Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study. Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multispecies-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times. Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern. We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths.

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.

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.

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.