Phylogenomic analysis reveals the evolutionary history of Paleartic needle-leaved junipers.

Needle-leaved junipers (Juniperus sect. Juniperus, Cupressaceae) are coniferous trees and shrubs with red or blue fleshy cones. They are distributed across Asia, Macaronesia and the Mediterranean Basin, with one species (J. communis) having a circumboreal distribution. Here we aim to resolve the phylogeny of this clade to infer its intricate evolutionary history. To do so, we built a comprehensive, time-calibrated phylogeny using genotyping-by-sequencing (GBS) and combine it with species occurrence using phylogeographic tools. Our results provide solid phylogenetic resolution to propose a new taxonomic classification and a biogeographical history of the section. Specifically, we confirm the monophyly of two groups within J. sect. Juniperus: the Asian (blue-cone) species including the circumboreal J. communis, and the Mediterranean-Macaronesian (red-cone) species. In addition, we provide strong phylogenetic evidence for three distinct species (J. badia, J. conferta, J. lutchuensis) previously considered subspecies or varieties, as well as for the differentiation between the eastern and western Mediterranean lineages of J. macrocarpa. Our findings suggest that the Mediterranean basin was the primary center of diversification for Juniperus sect. Juniperus, followed by an East Asian-Tethyan disjunction resulting from uplifts of the Qinghai-Tibetan Plateau and climatic shifts. The colonization history of Macaronesia by red-cone junipers from the western Mediterranean appears to have taken place independently in two different geological periods: the Miocene (Azores) and the Pliocene (Madeira-Canary Islands). Overall, genomic data and phylogenetic analysis are key to consider a new taxonomic proposal and reconstruct the biogeographical history of the iconic needle-leaved junipers across the Paleartic.

Time-calibrated phylogenies reveal mediterranean and pre-mediterranean origin of the thermophilous vegetation of the Canary Islands.

BACKGROUND AND AIMS: The Canary Islands have strong floristic affinities with the Mediterranean Basin. One of the most characteristic and diverse vegetation belts of the archipelago is the thermophilous woodland (between 200 and 900 m.a.s.l.). This thermophilous plant community consists of many non-endemic species shared with the Mediterranean Floristic Region together with Canarian endemic species. Consequently, phytogeographic studies have historically proposed the hypothesis of an origin of the Canarian thermophilous species following the establishment of the summer-dry mediterranean climate in the Mediterranean Basin around 2.8 million years ago. METHODS: Time-calibrated phylogenies for 39 plant groups including Canarian thermophilous species were primarily analysed to infer colonization times. In particular, we used 26 previously published phylogenies together with 13 new time-calibrated phylogenies (including newly generated plastid and nuclear DNA sequence data) to assess whether the time interval between stem and crown ages of Canarian thermophilous lineages postdates 2.8 Ma. For lineages postdating this time threshold, we additionally conducted ancestral area reconstructions to infer the potential source area for colonization. KEY RESULTS: A total of 43 Canarian thermophilous lineages were identified from 39 plant groups. Both mediterranean (16) and pre-mediterranean (9) plant lineages were found. However, we failed to determine the temporal origin for 18 lineages because a stem-crown time interval overlaps with the 2.8-Ma threshold. The spatial origin of thermophilous lineages was also heterogeneous, including ancestral areas from the Mediterranean Basin (nine) and other regions (six). CONCLUSIONS: Our findings reveal an unexpectedly heterogeneous origin of the Canarian thermophilous species in terms of colonization times and mainland source areas. A substantial proportion of the lineages arrived in the Canaries before the summer-dry climate was established in the Mediterranean Basin. The complex temporal and geographic origin of Canarian thermophilous species challenges the view of the Canary Islands (and Madeira) as a subregion within the Mediterranean Floristic Region.

A snapshot of progenitor-derivative speciation in Iberodes (Boraginaceae).

Traditional classification of speciation modes has focused on physical barriers to gene flow. Allopatric speciation with complete reproductive isolation is viewed as the most common mechanism of speciation. Parapatry and sympatry, by contrast, entail speciation in the face of ongoing gene flow, making them more difficult to detect. The genus Iberodes (Boraginaceae, NW Europe) comprises five species with contrasting morphological traits, habitats and species distributions. Based on the predominance of narrow and geographically distant endemic species, we hypothesized that geographical barriers were responsible for most speciation events in Iberodes. We undertook an integrative study including: (i) phylogenomics through restriction-site-associated DNA sequencing (RAD-seq), (ii) genetic structure analyses, (iii) demographic modelling, (iv) morphometrics, and (v) climatic niche modelling and niche overlap analysis. The results revealed a history of recurrent progenitor-derivative speciation manifested by a paraphyletic pattern of nested species differentiation. Budding speciation mediated by ecological differentiation is suggested for the coastal lineage, deriving from the inland widespread Iberodes linifolia during the Late Pliocene. Meanwhile, geographical isolation followed by niche shifts are suggested for the more recent differentiation of the coastland taxa. Our work provides a model for distinguishing speciation via ecological differentiation of peripheral, narrowly endemic I. kuzinskyanae and I. littoralis from a widespread extant ancestor, I. linifolia. Ultimately, our results illustrate a case of Pliocene speciation in the probable absence of geographical barriers and get away from the traditional cladistic perspective of speciation as producing two species from an extinct ancestor, thus reminding us that phylogenetic trees tell only part of the story.

Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data.

Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci. Furthermore, biological phenomena responsible for topological incongruence such as Incomplete Lineage Sorting (ILS) and hybridisation complicate the resolution of phylogenetic relationships among closely related taxa. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. This complex includes seven taxa distributed through Central America and the Colombian Chocó, and is nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from few loci failed to provide support for internal relationships within the complex. Our Neighbour-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches taxa provided a robust phylogeny for this group. The genus Cycnoches includes three main clades that are further supported by morphological traits and geographic distributions. Similarly, a topology reconstructed through maximum likelihood (ML) inference of concatenated GBS loci produced results that are comparable with those reconstructed through coalescence and network-based methods. Our comparative phylogenetic informativeness analyses suggest that the low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species or subspecies might actually represent only three distinct segregates. We further discuss the limited phylogenetic informativeness found in our GBS approach and its utility to disentangle relationships within recent and rapidly evolving species complexes. Our study is the first to demonstrate the utility of GBS data to reconstruct relationships within young (~2 Ma) Neotropical plant clades, opening new avenues for studies of species complexes that populate the species-rich orchid family.

Macroevolutionary dynamics of nectar spurs, a key evolutionary innovation.

Floral nectar spurs are widely considered a key innovation promoting diversification in angiosperms by means of pollinator shifts. We investigated the macroevolutionary dynamics of nectar spurs in the tribe Antirrhineae (Plantaginaceae), which contains 29 genera and 300-400 species (70-80% spurred). The effect of nectar spurs on diversification was tested, with special focus on Linaria, the genus with the highest number of species. We generated the most comprehensive phylogeny of Antirrhineae to date and reconstructed the evolution of nectar spurs. Diversification rate heterogeneity was investigated using trait-dependent and trait-independent methods, and accounting for taxonomic uncertainty. The association between changes in spur length and speciation was examined within Linaria using model testing and ancestral state reconstructions. We inferred four independent acquisitions of nectar spurs. Diversification analyses revealed that nectar spurs are loosely associated with increased diversification rates. Detected rate shifts were delayed by 5-15 Myr with respect to the acquisition of the trait. Active evolution of spur length, fitting a speciational model, was inferred in Linaria, which is consistent with a scenario of pollinator shifts driving diversification. Nectar spurs played a role in diversification of the Antirrhineae, but diversification dynamics can only be fully explained by the complex interaction of multiple biotic and abiotic factors.

Resolving Recent Plant Radiations: Power and Robustness of Genotyping-by-Sequencing.

Disentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, interspecific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genus Linaria that radiated in the Quaternary. After confirming the morphological and genetic distinctness of eight species, we evaluated the relative performances of concatenation and coalescent methods to resolve phylogenetic relationships. Specifically, we focused on assessing the robustness of both approaches to variations in the parameter used to estimate sequence homology (clustering threshold). Concatenation analyses suffered from strong systematic bias, as revealed by the high statistical support for multiple alternative topologies depending on clustering threshold values. By contrast, topologies produced by two coalescent-based methods (NJ$_{\mathrm{st}}$, SVDquartets) were robust to variations in the clustering threshold. Reticulate evolution may partly explain incongruences between NJ$_{\mathrm{st}}$, SVDquartets and concatenated trees. Integration of morphometric and coalescent-based phylogenetic results revealed (i) extensive morphological divergence associated with recent splits between geographically close or sympatric sister species and (ii) morphological convergence in geographically disjunct species. These patterns are particularly true for floral traits related to pollinator specialization, including nectar spur length, tube width and corolla color, suggesting pollinator-driven diversification. Given its relatively simple and inexpensive implementation, GBS is a promising technique for the phylogenetic and systematic study of recent radiations, but care must be taken to evaluate the robustness of results to variation of data assembly parameters.

Phylogenetic and phylogeographic evidence for the colonization success of the diplochorous Astydamia latifolia across the Canary Islands.

Astydamia latifolia is the only species of the genus Astydamia, which forms an early-diverging lineage of Apiaceae, subfamily Apioideae. This species is subendemic to the Canary Islands and one of the most representative species of the coastal environments of this archipelago. Astydamia displays diplochory, that is, diaspores with two long-distance dispersal (LDD) syndromes. In particular, A. latifolia has both anemochorous and thalassochorous fruit traits (corky and winged mericarps). Although we expect this species to have a high dispersal capacity, there is no genetic study addressing it. The divergence time of this species from its sister taxon is also unknown. In this study, we aimed (i) to unveil the phylogenetic relationships and divergence times of A. latifolia; (ii) to reconstruct its phylogeographic structure across the Canary Islands; and (iii) to estimate the number of inter-island colonization events. To these ends, we first sequenced the internal transcribed spacer (ITS) region for A. latifolia, reconstructed the phylogenetic relationships of Astydamia and Apiaceae relatives and estimated divergence times. Then, two plastid DNA regions (psaI-aacD and psbK-trnS) were sequenced for 158 individuals (from 36 Canarian population and one NW African population) to reconstruct a haplotype network. The recently developed method Phylogeographic Analysis of Island Colonization Events (PAICE) was used to estimate the number of inter-island colonization events. Results show that A. latifolia is a phylogenetically isolated lineage that diverged from the most closely related genus (Molopospermum) in the Eocene-Miocene. It displays a low plastid DNA diversity (only four haplotypes detected), which is accompanied by a high degree of haplotype sharing between islands and highly linear rarefaction curves of colonization obtained in PAICE. These findings suggest a high colonization ability for this species, most likely related to the availability of two LDD syndromes.

Unveiling the diversification and dispersal of the Lewinskya firma complex (Orthotrichaceae, Bryophyta) across Africa and India.

Intercontinental disjunctions are one of the most attractive and interesting biogeographical patterns. Bryophytes often exhibit such distributions, which is partly explained by their great ability to disperse over long distances. However, such intercontinental ranges are sometimes a distorted reality caused by the existence of unnoticed species. This study investigates whether the disjunction between East Africa and southern India of the moss Lewinskya firma reflects the genuine distribution of a single species or implies pseudo-cryptic species (whose morphological differentiation is subtle and have therefore been masked). An integrative taxonomic approach combining morphological and molecular methods (genotyping by sequencing, GBS) was used, based on a representation of samples specifically collected from all the major mountainous regions where this moss occurs. Two species, L. firma s. str. and L. afroindica sp. nov. are involved, whose ranges completely overlap in East Africa, although genetic distance and morphological differences in leaf apex shape, vaginula hairs shape and papillosity, spore ornamentation and peristome constitution and ornamentation allow distinguishing both. In addition, the range of L. afroindica extends into both southern Africa and southern India. The phylogenetic reconstruction obtained shows a certain degree of differentiation of the Indian populations, although they are yet morphologically indistinguishable from African populations. The results thus highlight both the existence of overlooked species and the complexity of bryophyte biogeography.

Congruence between distribution modelling and phylogeographical analyses reveals Quaternary survival of a toadflax species (Linaria elegans) in oceanic climate areas of a mountain ring range.

· The role of Quaternary climatic shifts in shaping the distribution of Linaria elegans, an Iberian annual plant, was investigated using species distribution modelling and molecular phylogeographical analyses. Three hypotheses are proposed to explain the Quaternary history of its mountain ring range. · The distribution of L. elegans was modelled using the maximum entropy method and projected to the last interglacial and to the last glacial maximum (LGM) using two different paleoclimatic models: the Community Climate System Model (CCSM) and the Model for Interdisciplinary Research on Climate (MIROC). Two nuclear and three plastid DNA regions were sequenced for 24 populations (119 individuals sampled). Bayesian phylogenetic, phylogeographical, dating and coalescent-based population genetic analyses were conducted. · Molecular analyses indicated the existence of northern and southern glacial refugia and supported two routes of post-glacial recolonization. These results were consistent with the LGM distribution as inferred under the CCSM paleoclimatic model (but not under the MIROC model). Isolation between two major refugia was dated back to the Riss or Mindel glaciations, > 100 kyr before present (bp). · The Atlantic distribution of inferred refugia suggests that the oceanic (buffered)-continental (harsh) gradient may have played a key and previously unrecognized role in determining Quaternary distribution shifts of Mediterranean plants.

The role of birds and insects in pollination shifts of Scrophularia (Scrophulariaceae).

The mixed vertebrate-insect pollination system is rare in Holarctic plants. Phylogenetic relationships of 116 Scrophularia taxa were investigated based on two plastid (ndhF and trnL-trnF) and one nuclear (ITS) DNA regions. A wider time-calibrated analysis of ndhF sequences of the Lamiales revealed that Scrophularia diverged as early as in the Miocene (<22 Ma). Results of maximum-likelihood optimizations supported wasp pollination as the ancestral pollination system from which other systems derived (hoverfly, mixed vertebrate-insect and bird systems). Four origins for a mixed vertebrate-insect (MVI) pollination system were inferred, in which two western Mediterranean species (S. sambucifolia and S. grandiflora) and two island species (the Tirrenian S. trifoliata and the Canarian S. calliantha) were involved. S. calliantha is the only species in which a more complex MVI system, including pollination by the lizard Gallotia stehlini, has evolved. In addition, bird (hummingbird) floral traits found in the New Mexican S. macrantha appear to have been independently acquired. In contrast, we failed to find evidence for an ancient role of hummingbirds in the evolution of European Scrophularia. Indeed, paleontological data revealed that extinction of European hummingbirds (30-32 Ma) occurred earlier than the divergence of European MVI lineages of Scrophularia. In conclusion, our results showed that a role of birds in pollination of Scrophularia may not have been effective in the Miocene-Pliocene, but bird pollination that shows its origin in the Pliocene-Pleistocene is still operating independently in different islands and continents.

Corolla morphology influences diversification rates in bifid toadflaxes (Linaria sect. Versicolores).

BACKGROUND AND AIMS: The role of flower specialization in plant speciation and evolution remains controversial. In this study the evolution of flower traits restricting access to pollinators was analysed in the bifid toadflaxes (Linaria sect. Versicolores), a monophyletic group of ~30 species and subspecies with highly specialized corollas. METHODS: A time-calibrated phylogeny based on both nuclear and plastid DNA sequences was obtained using a coalescent-based method, and flower morphology was characterized by means of morphometric analyses. Directional trends in flower shape evolution and trait-dependent diversification rates were jointly analysed using recently developed methods, and morphological shifts were reconstructed along the phylogeny. Pollinator surveys were conducted for a representative sample of species. KEY RESULTS: A restrictive character state (narrow corolla tube) was reconstructed in the most recent common ancestor of Linaria sect. Versicolores. After its early loss in the most species-rich clade, this character state has been convergently reacquired in multiple lineages of this clade in recent times, yet it seems to have exerted a negative influence on diversification rates. Comparative analyses and pollinator surveys suggest that the narrow- and broad-tubed flowers are evolutionary optima representing divergent strategies of pollen placement on nectar-feeding insects. CONCLUSIONS: The results confirm that different forms of floral specialization can lead to dissimilar evolutionary success in terms of diversification. It is additionally suggested that opposing individual-level and species-level selection pressures may have driven the evolution of pollinator-restrictive traits in bifid toadflaxes.

Evolutionary genomics of oceanic island radiations.

A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.

Climatic niche pre-adaptation facilitated island colonization followed by budding speciation in the Madeiran ivy (Hedera maderensis, Araliaceae).

The path followed by species in the colonization of remote oceanic islands ultimately depends on their phylogenetic constraints and ecological responses. In this study, we aim to evaluate the relative role of geographical and ecological forces in the origin and evolution of the Madeiran ivy (Hedera maderensis), a single-species endemic belonging to the western polyploid clade of Hedera. To determine the phylogenetic placement of H. maderensis within the western polyploid clade, we analyzed 40 populations (92 individuals) using genotyping-by-sequencing and including Hedera helix as outgroup. Climatic niche differences among the study species were evaluated using a database with 867 records representing the entire species ranges. To test species responses to climate, 13 vegetative and reproductive functional traits were examined for 70 populations (335 individuals). Phylogenomic results revealed a nested pattern with H. maderensis embedded within the south-western Iberian H. iberica. Gradual niche differentiation from the coldest and most continental populations of H. iberica to the warm and stable coastal population sister to H. maderensis parallels the geographical pattern observed in the phylogeny. Similarity in functional traits is observed for H. maderensis and H. iberica. The two species show leaves with higher specific leaf area (SLA), lower leaf dry matter content (LDMC) and thickness and fruits with lower pulp fraction than the other western polyploid species H. hibernica. Acquisition of a Macaronesian climatic niche and the associated functional syndrome in mainland European ivies (leaves with high SLA, and low LDMC and thickness, and fruits with less pulp content) was a key step in the colonization of Madeira by the H. iberica/H. maderensis lineage, which points to climatic pre-adaptation as key in the success of island colonization (dispersal and establishment). Once in Madeira, budding speciation was driven by geographical isolation, while ecological processes are regarded as secondary forces with a putative impact in the lack of further in situ diversification.

The genomic basis of the plant island syndrome in Darwin's giant daisies.

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the 'plant island syndrome', include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin's giant daisies.

Evolution in the Model Genus Antirrhinum Based on Phylogenomics of Topotypic Material.

Researchers in phylogenetic systematics typically choose a few individual representatives of every species for sequencing based on convenience (neighboring populations, herbarium specimens, samples provided by experts, garden plants). However, few studies are based on original material, type material or topotypic material (living specimens from the locality where the type material was collected). The use of type or topotypic material in phylogenetic studies is paramount particularly when taxonomy is complex, such as that of Antirrhinum (Plantaginaceae). In this paper, we used topotypic materials of Antirrhinum at the species level (34 species proposed by previous authors), 87 specimens representing the species distributions and >50,000 informative nucleotide characters (from ∼4,000 loci) generated by the genotyping-by-sequencing (GBS) technique: (i) to test two explicit taxonomic hypotheses widely followed by local taxonomic treatments; (ii) to robustly estimate phylogenetic relationships; (iii) to investigate the evolution of key morphological characters and biogeographic centers of differentiation. Two GBS phylogenies based on two datasets (87 localities and 34 topotypic specimens) revealed that: (1) Sutton's (1988) taxonomic account is the most congruent with phylogenetic results, whereas division of Antirrhinum into three major clades disagrees with Rothmaler's (1956) infrageneric classification; (2) monophyly of populations currently included in the same species is primarily supported; (3) the historically recognized Antirrhinum majus group is not monophyletic; (4) sister-group relationships are robust for eight species pairs; (5) the evolutionary radiation of 26 species since the Pliocene is underpinned given a high rate of diversification (0.54 spp. Myr-1); (6) a geographic pattern of speciation is reconstructed, with northern Iberia as the center of early diversification followed by more recent speciation in southeastern Iberia; and (7) multiple acquisitions of key taxonomic characters in the course of Antirrhinum diversification are strongly supported, with no evidence of hybridization between major clades. Our results also suggest incipient speciation in some geographic areas and point to future avenues of research in evolution and systematics of Antirrhinum.

The Radiation of Darwin's Giant Daisies in the Galápagos Islands.

Evolutionary radiations on oceanic islands have fascinated biologists since Darwin's exploration of the Galápagos archipelago [1, 2]. Island radiations can provide key insights for understanding rapid speciation, including evolutionary patterns and the processes behind them. However, lack of resolution of species relationships has historically hindered their investigation, particularly in the plant kingdom [3-5]. Here, we report a time-calibrated phylogenomic analysis based on genotyping-by-sequencing data [6] of the 15 species of Scalesia (Darwin's giant daisies), an iconic and understudied plant radiation endemic to the Galápagos Islands and considered the plant counterpart to Darwin's finches [1, 7-9]. Results support a Pliocene to early Pleistocene divergence between Scalesia and the closest South American relatives, and rapid diversification of extant Scalesia species from a common ancestor dated to the Middle Pleistocene. Major evolutionary patterns in Scalesia include the following: (1) lack of compliance with the "progression rule" hypothesis, in which earlier diverging lineages are expected to occupy older islands; (2) a predominance of within-island speciation over between-island speciation; and (3) repeated convergent evolution of potentially adaptive traits and habitat preferences on different islands during the course of diversification. Massive sequencing provided the essential framework for investigating evolutionary and ecological processes in the complex natural laboratory of the Galápagos, thereby advancing our understanding of island plant radiations.

Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae).

A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually entail remarkable bioinformatic challenges due to the inherent trade-off between the number of SNPs and the magnitude of associated error rates. The genus Helianthemum (Cistaceae) is a species-rich and taxonomically complex Palearctic group of plants that diversified mainly since the Upper Miocene. It is a challenging case study since previous attempts using Sanger sequencing were unable to resolve the intrageneric phylogenetic relationships. Aiming to obtain a robust phylogenetic reconstruction based on genotyping-by-sequencing (GBS), we established a rigorous methodological workflow in which we i) explored how variable settings during dataset assembly have an impact on error rates and on the degree of resolution under concatenation and coalescent approaches, ii) assessed the effect of two extreme parameter configurations (minimizing error rates vs. maximizing phylogenetic resolution) on tree topology and branch lengths, and iii) evaluated the effects of these two configurations on estimates of divergence times and diversification rates. Our analyses produced highly supported topologically congruent phylogenetic trees for both configurations. However, minimizing error rates did produce more reliable branch lengths, critically affecting the accuracy of downstream analyses (i.e. divergence times and diversification rates). In addition to recommending a revision of intrageneric systematics, our results enabled us to identify three highly diversified lineages in Helianthemum in contrasting geographical areas and ecological conditions, which started radiating in the Upper Miocene.

The evo-devo of plant speciation.

Speciation research bridges the realms of macro- and microevolution. Evolutionary developmental biology (evo-devo) has classically dealt with macroevolutionary questions through a comparative approach to distantly related organisms, but the field later broadened in focus to address recent speciation and microevolution. Here we review available evidence of the power of evo-devo approaches to understand speciation in plants at multiple scales. At a macroevolutionary scale, evidence is accumulating for evolutionary developmental mechanisms giving rise to key innovations promoting speciation. At the macro microevolution transition, we review instances of evo-devo change underlying both the origin of reproductive barriers and phenotypic changes distinguishing closely related species. At the microevolutionary scale, the study of developmental variation within species provides insight into the processes that generate the raw material for evolution and speciation. We conclude by advocating a strong interaction between developmental biology and evolutionary biology at multiple scales to gain a deeper understanding of plant speciation.

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.

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.