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.

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.

A new combination for a neglected member of Linaria subsect. Versicolores (Plantaginaceae, Antirrhineae) endemic to the Algarve, Portugal

Linariabimaculata comb. et stat. nov., from the overlooked Central Algarve plant endemism centre, is here lectotypified and redescribed as a full species based on Linariaviscosavar.bimaculata, which was historically misidentified under allopatric L.spartea and L.viscosa. Traditional herbarium taxonomy and citizen science observations were combined to document the geographical range of the four species of Linariasubsect.Versicolores in the Algarve and amend an identification key for the Iberian clade of this subsection. Geographical patterns and morphological similarity suggest a sister relationship between L.bimaculata and L.algarviana, unveiling a new possible example of parallel speciation linked to a purple to yellow shift in corolla colour. Besides the yellow flowers, L.bimaculata differs from L.algarviana in the more elongate fertile stems and the invariably erect-patent corolla tube. It is assessed as Vulnerable (VU) according to the IUCN Categories and Criteria.

Spur development and evolution: An update

Floral spurs, widely recognized as a classic example of key morphological and functional innovation and thought to have promoted the origin and adaptive evolution of many flowering plant lineages, have attracted the attention of researchers for centuries. Despite this, the mechanisms underlying the development and evolution of these structures remain poorly understood. Recent studies have discovered the phytohormones and transcription factor genes that play key roles in regulating patterns of cell division and cell expansion during spur morphogenesis. Spur morphogenesis was also found to be tightly linked with the programs specifying floral zygomorphy, floral organ identity determination, and nectary development. Independent origins and losses of spurs in different flowering plant lineages, therefore, may be attributed to changes in the spur program and/or its upstream ones.

Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data

Gerbillus is one of the most speciose genera among rodents, with ca. 51 recognized species. Previous attempts to reconstruct the evolutionary history of Gerbillus mainly relied on the mitochondrial cyt-b marker as a source of phylogenetic information. In this study, we utilize RAD-seq genomic data from 37 specimens representing 11 species to reconstruct the phylogenetic tree for Gerbillus, applying concatenation and coalescence methods. We identified four highly supported clades corresponding to the traditionally recognized subgenera: Dipodillus, Gerbillus, Hendecapleura and Monodia. Only two uncertain branches were detected in the resulting trees, with one leading to diversification of the main lineages in the genus, recognized by quartet sampling analysis as uncertain due to possible introgression. We also examined species boundaries for four pairs of sister taxa, including potentially new species from Morocco, using SNAPP. The results strongly supported a speciation model in which all taxa are treated as separate species. The dating analyses confirmed the Plio-Pleistocene diversification of the genus, with the uncertain branch coinciding with the beginning of aridification of the Sahara at the the Plio-Pleistocene boundary. This study aligns well with the earlier analyses based on the cyt-b marker, reaffirming its suitability as an adequate marker for estimating genetic diversity in Gerbillus.

Parallel evolution, atavism, and extensive introgression explain the radiation of Epimedium sect. Diphyllon (Berberidaceae) in southern East Asia

East Asia is the richest region of plant biodiversity in the northern temperate zone, and its radiation provides key insights for understanding rapid speciation, including evolutionary patterns and processes. However, it is challenging to investigate the recent evolutionary radiation among plants because of the lack of genetic divergence, phenotypic convergence, and interspecific gene flow. Epimedium sect. Diphyllon is a rarely studied plant lineage endemic to East Asia, especially highly diversified in its southern part. In this study, we report a robust phylogenomic analysis based on genotyping-by-sequencing data of this lineage. The results revealed a clear biogeographic pattern for Epimedium sect. Diphyllon with recognition into two major clades corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms of East Asian Flora and rapid diversification of the extant species dated to the Pleistocene. Evolutionary radiation of Epimedium sect. Diphyllon is characterized by recent and predominant parallel evolution and atavism between the two subkingdom regions, with extensive reticulating hybridization within each region during the course of diversification in southern East Asia. A parallel-atavism-introgression hypothesis is referred to in explaining the radiation of plant diversity in southern East Asia, which represents a potential model for the rapid diversification of plants under global climate cooling in the late Tertiary. Our study advances our understanding of the evolutionary processes of plant radiation in East Asia as well as in other biodiversity hotspot regions.

Genomic data provide a robust phylogeny backbone for Rhodiola L. (Crassulaceae) and reveal extensive reticulate evolution during its rapid radiation

The Tibetan Plateau and adjacent mountain regions (TP; including the Tibetan Plateau, Himalaya, Hengduan Mountains and Mountains of Central Asia) harbor great biodiversity, some lineages on which may have undergone rapid radiations. However, only a few studies have investigated the evolutionary pattern of such diversification in depth using genomic data. In this study, we reconstructed a robust phylogeny backbone of Rhodiola, a lineage that may have undergone rapid radiation in the TP, using Genotyping-by-sequencing data, and conducted a series of gene flow and diversification analyses. The concatenation and coalescent-based methods yield similar tree topologies, and five well-supported clades were revealed. Potential gene flow and introgression events were detected, both between species from different major clades and closely related species, suggesting pervasive hybridization and introgression. An initial rapid and later slowdown of the diversification rate was revealed, indicating niche filling. Molecular dating and correlation analyses showed that the uplift of TP and global cooling in the mid-Miocene might have played an important role in promoting the rapid radiation of Rhodiola. Our work demonstrates that gene flow and introgression might be an important contributor to rapid radiation possibly by quickly reassembling old genetic variation into new combinations.

The role of geography, ecology, and hybridization in the evolutionary history of Canary Island Descurainia

PREMISE

Oceanic islands offer the opportunity to understand evolutionary processes underlying rapid diversification. Along with geographic isolation and ecological shifts, a growing body of genomic evidence has suggested that hybridization can play an important role in island evolution. Here we use genotyping-by-sequencing (GBS) to understand the roles of hybridization, ecology, and geographic isolation in the radiation of Canary Island Descurainia (Brassicaceae).

METHODS

We carried out GBS for multiple individuals of all Canary Island species and two outgroups. Phylogenetic analyses of the GBS data were performed using both supermatrix and gene tree approaches and hybridization events were examined using D-statistics and Approximate Bayesian Computation. Climatic data were analyzed to examine the relationship between ecology and diversification.

RESULTS

Analysis of the supermatrix data set resulted in a fully resolved phylogeny. Species networks suggest a hybridization event has occurred for D. gilva, with these results being supported by Approximate Bayesian Computation analysis. Strong phylogenetic signals for temperature and precipitation indicate one major ecological shift within Canary Island Descurainia.

CONCLUSIONS

Inter-island dispersal played a significant role in the diversification of Descurainia, with evidence of only one major shift in climate preferences. Despite weak reproductive barriers and the occurrence of hybrids, hybridization appears to have played only a limited role in the diversification of the group with a single instance detected. The results highlight the need to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups prone to hybridization; patterns that might otherwise be obscured in species trees.

Phylogenomics and the flowering plant tree of life

The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.

A turn in species conservation for hairpin banksias: demonstration of oversplitting leads to better management of diversity

PREMISE

Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high-throughput sequencing tools are fortunately quickening the resolution of morphological complexes and   thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives.

METHODS

To assist conservation while testing the current taxonomy of this group, we used high-throughput sequencing to infer a population-scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500-km distribution.

RESULTS

Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species.

CONCLUSIONS

The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.

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.

Reticulate evolution in the Pteris fauriei group (Pteridaceae)

The Pteris fauriei group (Pteridaceae) has a wide distribution in Eastern Asia and includes 18 species with similar but varied morphology. We collected more than 300 specimens of the P. fauriei group and determined ploidy by flow cytometry and inferred phylogenies by molecular analyses of chloroplast and nuclear DNA markers. Our results reveal a complicated reticulate evolution, consisting of seven parental taxa and 58 hybrids. The large number of hybrid taxa have added significant morphological complexity to the group leading to difficult taxonomic issues. The hybrids generally had broader ranges and more populations than their parental taxa. Genetic combination of different pairs of parental species created divergent phenotypes of hybrids, exhibited by both morphological characteristics and ecological fidelities. Niche novelty could facilitate hybrid speciation. Apogamy is common in this group and potentially contributes to the sustainability of the whole group. We propose that frequent hybridizations among members of the P. fauriei group generate and maintain genetic diversity, via novel genetic combinations, niche differentiation, and apogamy.

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 geographic barriers were responsible for most speciation events in Iberodes. We undertook an integrative study including: (i) phylogenomics through restriction-site associated DNA sequencing, (ii) genetic structure analyses, (iii) demographic modeling, (iv) morphometrics, and (v) climatic niche modeling and niche overlap analysis. 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 I. linifolia during Late Pliocene. Meanwhile, geographic 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 geographic 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.

A phylogeny of Antirrhinum reveals parallel evolution of alpine morphology

Parallel evolution of similar morphologies in closely related lineages provides insight into the repeatability and predictability of evolution. In the genus Antirrhinum (snapdragons), as in other plants, a suite of morphological characters are associated with adaptation to alpine environments. We tested for parallel trait evolution in Antirrhinum by investigating phylogenetic relationships using restriction-site associated DNA (RAD) sequencing. We then associated phenotypic information to our phylogeny to reconstruct the patterns of morphological evolution and related this to evidence for hybridisation between emergent lineages. Phylogenetic analyses showed that the alpine character syndrome is present in multiple groups, suggesting that Antirrhinum has repeatedly colonised alpine habitats. Dispersal to novel environments happened in the presence of intraspecific and interspecific gene flow. We found support for a model of parallel evolution in Antirrhinum. Hybridisation in natural populations, and a complex genetic architecture underlying the alpine morphology syndrome, support an important role of natural selection in maintaining species divergence in the face of gene flow.

Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava

The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only c. 6 million years ago have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved. Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa. We find that two recently described species from northeast Brazil's Atlantic Forest were the earliest to diverge, strongly suggesting a South American common ancestor of Manihot. Ancestral state reconstruction indicates early Manihot diversification in dry forests, with numerous independent episodes of new habitat colonization, including into savannas and rainforests within South America. We identify the closest wild relatives to Manihot esculenta, including the crop cassava, and we quantify extensive wild introgression into the cassava gene pool from at least five wild species, including Manihot glaziovii, a species used widely in breeding programs. Finally, we show that this wild-to-crop introgression substantially shapes the mutation load in cassava. Our findings provide a detailed case study for neotropical evolutionary history in a diverse and widespread group, and a robust phylogenomic framework for future Manihot and cassava research.

Phylogeography of Artemisia frigida (Anthemideae, Asteraceae) based on genotyping-by-sequencing and plastid DNA data: Migration through Beringia

Artemisia frigida is a temperate grassland species that has the largest natural range among its genus, with occurrences across the temperate grassland biomes of Eurasia and North America. Despite its wide geographic range, we know little about the species' distribution history. Hence, we conducted a phylogeographical study to test the hypothesis that the species' distribution pattern is related to a potential historical migration over the 'Bering land bridge'. We applied two molecular approaches: genotyping-by-sequencing (GBS) and Sanger sequencing of the plastid intergenic spacer region (rpl32 - trnL) to investigate genetic differentiation and relatedness among 21 populations from North America, Middle Asia, Central Asia and the Russian Far East. Furthermore, we identified the ploidy level of individuals based on GBS data. Our results indicate that A. frigida originated in Asia, spread northwards to the Far East and then to North America across the Bering Strait. We found a pronounced genetic structuring between Middle and Central Asian populations with mixed ploidy levels, tetraploids in the Far East, and nearly exclusively diploids in North America except for one individual. According to phylogenetic analysis, two populations of Kazakhstan (KZ2 and KZ3) represent the most likely ancestral diploids that constitute the basally branching lineages, and subsequent polyploidization has occurred on several occasions independently. Mantel tests revealed weak correlations between genetic distance and geographical distance and climatic conditions, which indicates that paleoclimatic fluctuations may have more profoundly influenced A. frigida's spatial genetic structure and distribution than the current environment.

Pleistocene dynamics of the Eurasian steppe as a driving force of evolution: Phylogenetic history of the genus Capsella (Brassicaceae)

Capsella is a model plant genus of the Brassicaceae closely related to Arabidopsis. To disentangle its biogeographical history and intrageneric phylogenetic relationships, 282 individuals of all five currently recognized Capsella species were genotyped using a restriction digest-based next-generation sequencing method. Our analysis retrieved two main lineages within Capsella that split c. one million years ago, with western C. grandiflora and C. rubella forming a sister lineage to the eastern lineage consisting of C. orientalis. The split was attributed to continuous latitudinal displacements of the Eurasian steppe belt to the south during Early Pleistocene glacial cycles. During the interglacial cycles of the Late Pleistocene, hybridization of the two lineages took place in the southwestern East European Plain, leading to the allotetraploid C. bursa-pastoris. Extant genetic variation within C. orientalis postdated any extensive glacial events. Ecological niche modeling showed that suitable habitat for C. orientalis existed during the Last Glacial Maximum around the north coast of the Black Sea and in southern Kazakhstan. Such a scenario is also supported by population genomic data that uncovered the highest genetic diversity in the south Kazakhstan cluster, suggesting that C. orientalis originated in continental Asia and migrated north- and possibly eastwards after the last ice age. Post-glacial hybridization events between C. bursa-pastoris and C. grandiflora/rubella in the southwestern East European Plain and the Mediterranean gave rise to C. thracica. Introgression of C. grandiflora/rubella into C. bursa-pastoris resulted in a new Mediterranean cluster within the already existing Eurasian C. bursa-pastoris cluster. This study shows that the continuous displacement and disruption of the Eurasian steppe belt during the Pleistocene was the driving force in the evolution of Capsella.

Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

Foundational hypotheses addressing plant-insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude 1H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other's state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.

Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

PREMISE

Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships with standard phylogenetic markers. Target sequence capture of many independent nuclear loci has the potential to improve phylogenetic resolution for rapid radiations.

METHODS

Here we applied target sequence capture with 353 protein-coding genes (Angiosperms353 bait kit) to Veronica sect. Hebe (common name hebe) to determine its utility for improving the phylogenetic resolution of rapid radiations. Veronica section Hebe originated 5-10 million years ago in New Zealand, forming a monophyletic radiation of ca 130 extant species.

RESULTS

We obtained approximately 150 kbp of 353 protein-coding exons and an additional 200 kbp of flanking noncoding sequences for each of 77 hebe and two outgroup species. When comparing coding, noncoding, and combined data sets, we found that the latter provided the best overall phylogenetic resolution. While some deep nodes in the radiation remained unresolved, our phylogeny provided broad and often improved support for subclades identified by both morphology and standard markers in previous studies. Gene-tree discordance was nonetheless widespread, indicating that additional methods are needed to disentangle fully the history of the radiation.

CONCLUSIONS

Phylogenomic target capture data sets both increase phylogenetic signal and deliver new insights into the complex evolutionary history of rapid radiations as compared with traditional markers. Improving methods to resolve remaining discordance among loci from target sequence capture is now important to facilitate the further study of rapid radiations.

Hundreds of nuclear and plastid loci yield novel insights into orchid relationships

PREMISE

The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed.

METHODS

We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses.

RESULTS

Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes.

CONCLUSIONS

Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.

A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.

Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data

BACKGROUND AND AIMS

Several biogeographical models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model best explains the current distribution of the 15 species endemic to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae).

METHODS

We performed robust phylogenetic reconstructions based on genotyping-by-sequencing data and analysed the timing, biogeographical history and ecological niche conservatism of this endemic Canarian clade.

KEY RESULTS

Our phylogenetic analyses provided strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (~1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor.

CONCLUSIONS

The rapid and abundant diversification (0.75-1.85 species per million years) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, making an important contribution to the overall diversification history of this clade.

Resolved phylogenetic relationships in the Ocotea complex (Supraocotea) facilitate phylogenetic classification and studies of character evolution

PREMISE

The Ocotea complex contains the greatest diversity of Lauraceae in the Neotropics. However, the traditional taxonomy of the group has relied on only three main floral characters, and previous molecular analyses have used only a few markers and provided limited support for relationships among the major clades. This lack of useful data has hindered the development of a comprehensive classification, as well as studies of character evolution.

METHODS

We used RAD-seq data to infer the phylogenetic relationships of 149 species in the Ocotea complex, generating a reference-based assembly using the Persea americana genome. The results provide the basis for a phylogenetic classification that reflects our current molecular knowledge and for analyses of the evolution of breeding system, stamen number, and number of anther locules.

RESULTS

We recovered a well-supported tree that demonstrates the paraphyly of Licaria, Aniba, and Ocotea and clarifies the relationships of Umbellularia, Phyllostemonodaphne, and the Old World species. To begin the development of a new classification and to facilitate precise communication, we also provide phylogenetic definitions for seven major clades. Our ancestral reconstructions show multiple origins for the three floral characters that have routinely been used in Lauraceae systematics, suggesting that these be used with caution in the future.

CONCLUSIONS

This study advances our understanding of phylogenetic relationships and character evolution in a taxonomically difficult group using RAD-seq data. Our new phylogenetic names will facilitate unambiguous communication as studies of the Ocotea complex progress.

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.

Integrative Study of Genotypic and Phenotypic Diversity in the Eurasian Orchid Genus Neotinea

Knowledge of population variation across species' ranges is a prerequisite for correctly assessing the overall variability of any group of organisms and provides an invaluable basis for unraveling evolutionary history, optimizing taxonomy and devising effective conservation strategies. Here, we examine the genus Neotinea, which represents a relatively recently delimited monophyletic genus of orchids, for which a detailed study of its overall variability was lacking. We applied a suite of biosystematic methods, consisting of flow cytometry, multivariate and geometric morphometrics, and analysis of genomic SNP data, to identify phylogenetic lineages within the genus, to delineate phenotypic variation relevant to these lineages, and to identify potential cryptic taxa within lineages. We found clear differentiation into four major lineages corresponding to the groups usually recognized within the genus: Neotinea maculata as a distinct and separate taxon, the Neotinea lactea group comprising two Mediterranean taxa N. lactea and Neotinea conica, the Neotinea ustulata group comprising two phenologically distinct varieties, and the rather complex Neotinea tridentata group comprising two major lineages and various minor lineages of unclear taxonomic value. N. conica constitutes both a monophyletic group within N. lactea and a distinct phenotype within the genus and merits its proposed subspecies-level recognition. By contrast, the spring and summer flowering forms of N. ustulata (var. ustulata and var. aestivalis) were confirmed to be distinct only morphologically, not phylogenetically. The most complex pattern emerged in the N. tridentata group, which splits into two main clades, one containing lineages from the Balkans and eastern Mediterranean and the other consisting of plants from Central Europe and the central Mediterranean. These individual lineages differ in genome size and show moderate degrees of morphological divergence. The tetraploid Neotinea commutata is closely related to the N. tridentata group, but our evidence points to an auto- rather than an allopolyploid origin. Our broad methodological approach proved effective in recognizing cryptic lineages among the orchids, and we propose the joint analysis of flow cytometric data on genome size and endopolyploidy as a useful and beneficial marker for delineating orchid species with partial endoreplication.

Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos

Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology and molecular) or genetic markers (e.g., nuclear and organelle) often yield inconsistent results. The tribe Arundinarieae, that is, the temperate bamboos, is a clade of tetraploid originated 22 Ma and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and parallel sampling of chloroplast genomes from genome skimming for 147 taxa. We first assess the feasibility of using ddRAD-seq data for phylogenetic estimates of paleopolyploid and rapidly radiated lineages, optimize clustering thresholds, and analysis workflow for orthology identification. Reference-based ddRAD data assembly approaches perform well and yield strongly supported relationships that are generally concordant with morphology-based taxonomy. We recover five major lineages, two of which are notable (the pachymorph and leptomorph lineages), in that they correspond with distinct rhizome morphologies. By contrast, the phylogeny from chloroplast genomes differed significantly. Based on multiple lines of evidence, the ddRAD tree is favored as the best species tree estimation for temperate bamboos. Using a time-calibrated ddRAD tree, we find that Arundinarieae diversified rapidly around the mid-Miocene corresponding with intensification of the East Asian monsoon and the evolution of key innovations including the leptomorph rhizomes. Our results provide a highly resolved phylogeny of Arundinarieae, shed new light on the radiation and reticulate evolutionary history of this tribe, and provide an empirical example for the study of recalcitrant plant radiations. [Arundinarieae; ddRAD; paleopolyploid; genome skimming; rapid diversification; incongruence.]

The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae

The reconstruction of relationships within recently radiated groups is challenging even when massive amounts of sequencing data are available. The use of restriction site-associated DNA sequencing (RAD-Seq) to this end is promising. Here, we assessed the performance of RAD-Seq to infer the species-level phylogeny of the rapidly radiating genus Cereus (Cactaceae). To examine how the amount of genomic data affects resolution in this group, we used datasets and implemented different analyses. We sampled 52 individuals of Cereus, representing 18 of the 25 species currently recognized, plus members of the closely allied genera Cipocereus and Praecereus, and other 11 Cactaceae genera as outgroups. Three scenarios of permissiveness to missing data were carried out in iPyRAD, assembling datasets with 30% (333 loci), 45% (1440 loci), and 70% (6141 loci) of missing data. For each dataset, Maximum Likelihood (ML) trees were generated using two supermatrices, i.e., only SNPs and SNPs plus invariant sites. Accuracy and resolution were improved when the dataset with the highest number of loci was used (6141 loci), despite the high percentage of missing data included (70%). Coalescent trees estimated using SVDQuartets and ASTRAL are similar to those obtained by the ML reconstructions. Overall, we reconstruct a well-supported phylogeny of Cereus, which is resolved as monophyletic and composed of four main clades with high support in their internal relationships. Our findings also provide insights into the impact of missing data for phylogeny reconstruction using RAD loci.

Miocene Diversification in the Savannahs Precedes Tetraploid Rainforest Radiation in the African Tree Genus Afzelia (Detarioideae, Fabaceae)

The dating of diversification events, including transitions between biomes, is key to elucidate the processes that underlie the assembly and evolution of tropical biodiversity. Afzelia is a widespread genus of tropical trees, threatened by exploitation for its valuable timber, that presents an interesting system to investigate diversification events in Africa. Africa hosts diploid Afzelia species in the savannahs north and south of the Guineo-Congolian rainforest and autotetraploid species confined to the rainforest. Species delimitation and phylogenetic relationships among the diploid and tetraploid species remained unresolved in previous studies using small amounts of DNA sequence data. We used genotyping-by-sequencing in the five widespread Afzelia species in Africa, the savannah species A. africana and A. quanzensis and the rainforest species A. bipindensis, A. pachyloba, and A. bella. Maximum likelihood and coalescent approaches resolved all species as monophyletic and placed the savannah and rainforest taxa into two separate clades corresponding to contrasted ploidy levels. Our data are thus compatible with a single biome shift in Afzelia in Africa, although we were unable to conclude on its direction. SNAPP calibrated species trees show that the savannah diploids started to diversify early, at 12 (9.09-14.89) Ma, which contrasts with a recent and rapid diversification of the rainforest tetraploid clade, starting at 4.22 (3.12 - 5.36) Ma. This finding of older diversification in a tropical savannah clade vs. its sister rainforest clade is exceptional; it stands in opposition to the predominant observation of young ages for savannahs lineages in tropical regions during the relatively recent expansion of the savannah biome.

Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico

We utilize the efficient GBS technique to obtain thousands of nuclear loci and SNPs to reconstruct the evolutionary history of Mexican leaf-toed geckos (Phyllodactylus). Through the incorporation of unprecedented sampling for this group of geckos, in combination with genomic data analysis, we generate mostly consistent phylogenetic hypotheses using two approaches: supermatrix and coalescent-based inference. All topologies depict three, mutually exclusive major clades. Clade I comprises P. bordai and all species closer to P. bordai than to any other Phyllodactylus. Clade II comprises P. nocticolus and all species closer to P. nocticolus than to any other Phyllodactylus. Clade III comprises P. tuberculosus and all species closer to P. tuberculosus than to any other Phyllodactylus. Analyses estimate the age for the most recent common ancestor of Phyllodactylus in the Eocene (~43 mya), and the ancestors of each major clade date to the Eocene-Oligocene transition (32-36 mya). This group includes one late-Eocene lineage (P. bordai), Oligocene lineages (P. paucituberculatus, P. delcampi), but also topological patterns that indicate a recent radiation occurred during the Pleistocene on islands in the Gulf of California. The wide spatial and temporal scale indicates a complex and unique biogeographic history for each major clade. The 33 species delimited by BPP and stepping-stone BFD*coalescent based genomic approaches reflect this history. This diversity delimited for Mexican leaf-toed geckos demonstrates a vast underestimation in the number of species based on morphological data alone.

Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov

We present a multilocus phylogeny of the class Dacrymycetes, based on data from the 18S, ITS, 28S, RPB1, RPB2, TEF-1α, 12S, and ATP6 DNA regions, with c. 90 species including the types of most currently accepted genera. A variety of methodological approaches was used to infer phylogenetic relationships among the Dacrymycetes, from a supermatrix strategy using maximum likelihood and Bayesian inference on a concatenated dataset, to coalescence-based calculations, such as quartet-based summary methods of independent single-locus trees, and Bayesian integration of single-locus trees into a species tree under the multispecies coalescent. We evaluate for the first time the taxonomic usefulness of some cytological phenotypic characters, i.e., vacuolar contents (vacuolar bodies and lipid bodies), number of nuclei of recently discharged basidiospores, and pigments, with especial emphasis on carotenoids. These characters, along with several others traditionally used for the taxonomy of this group (basidium shape, presence and morphology of clamp connections, morphology of the terminal cells of cortical/marginal hyphae, presence and degree of ramification of the hyphidia), are mapped on the resulting phylogenies and their evolution through the class Dacrymycetes discussed. Our analyses reveal five lineages that putatively represent five different families, four of which are accepted and named. Three out of these four lineages correspond to previously circumscribed and published families (Cerinomycetaceae, Dacrymycetaceae, and Unilacrymaceae), and one is proposed as the new family Dacryonaemataceae. Provisionally, only a single order, Dacrymycetales, is accepted within the class. Furthermore, the systematics of the two smallest families, Dacryonaemataceae and Unilacrymaceae, are investigated to the species level, using coalescence-based species delimitation on multilocus DNA data, and a detailed morphological study including morphometric analyses of the basidiospores. Three species are accepted in Dacryonaema, the type, Da. rufum, the newly combined Da. macnabbii (basionym Dacrymyces macnabbii), and a new species named Da. macrosporum. Two species are accepted in Unilacryma, the new U. bispora, and the type, U. unispora, the latter treated in a broad sense pending improved sampling across the Holarctic.

Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)

Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.

Taming the Red Bastards: Hybridisation and species delimitation in the Rhodanthemum arundanum-group (Compositae, Anthemideae)

Delineating species boundaries in a group of recently diverged lineages is challenging due to minor morphological differences, low genetic differentiation and the occurrence of gene flow among taxa. Here, we employ traditional Sanger sequencing and restriction-site associated DNA (RAD) sequencing, to investigate species delimitation in the close-knit Moroccan daisy group around Rhodanthemum arundanum B.H.Wilcox & al. that diverged recently during the Quaternary. After evaluation of genotyping errors and parameter optimisation in the course of de-novo assembly of RADseq reads in Ipyrad, we assess hybridisation patterns in the study group based on different data assemblies and methods (Neighbor-Net networks, FastStructure and ABBA-BABA tests). RADseq data and Sanger sequences are subsequently used for delimitation of species, using both, multi-species coalescent methods (Stacey and Snapp) and a novel approach based on consensus k-means clustering. In addition to the unveiling of two novel subspecies in the R. arundanum-group, our study provides insights into the performance of different species delimitation methods in the presence of hybridisation and varying quantities of data.

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.

Phylogeny of Hawaiian Melicope (Rutaceae): RAD-seq Resolves Species Relationships and Reveals Ancient Introgression

Hawaiian Melicope are one of the major adaptive radiations of the Hawaiian Islands comprising 54 endemic species. The lineage is monophyletic with an estimated crown age predating the rise of the current high islands. Phylogenetic inference based on Sanger sequencing has not been sufficient to resolve species or deeper level relationships. Here, we apply restriction site-associated DNA sequencing (RAD-seq) to the lineage to infer phylogenetic relationships. We employ Quartet Sampling to assess information content and statistical support, and to quantify discordance as well as partitioned ABBA-BABA tests to uncover evidence of introgression. Our new results drastically improved resolution of relationships within Hawaiian Melicope. The lineage is divided into five fully supported main clades, two of which correspond to morphologically circumscribed infrageneric groups. We provide evidence for both ancestral and current hybridization events. We confirm the necessity for a taxonomic revision of the Melicope section Pelea, as well as a re-evaluation of several species complexes by combining genomic and morphological data.

Evolutionary networks from RADseq loci point to hybrid origins of Medicago carstiensis and Medicago cretacea

PREMISE

Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. Restriction-site-associated DNA sequencing (RADseq) has been a popular sequencing technique for the reconstruction of hybridization in the next-generation sequencing era. However, the utility of RADseq for the reconstruction of complex evolutionary networks has not been thoroughly investigated. Conflicting phylogenetic relationships in the genus Medicago have been mainly attributed to hybridization, but the specific hybrid origins of taxa have not been yet clarified.

METHODS

We obtained new molecular data from diploid species of Medicago section Medicago using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with data sets that include several species and complex hybridization patterns.

RESULTS

Our analyses revealed that assembly filters to exclusively select a small set of loci with high phylogenetic information led to the most-divergent network topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus had a lower impact on networks. A strong hybridization signal was detected for M. carstiensis and M. cretacea, while signals were less clear for M. rugosa, M. rhodopea, M. suffruticosa, M. marina, M. scutellata, and M. sativa.

CONCLUSIONS

Complex network reconstructions from RADseq gene trees were not robust under variations of the assembly parameters and filters. But when the most-divergent networks were discarded, all remaining analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea.

Using nuclear loci and allelic variation to disentangle the phylogeny of Phyllostachys (Poaceae, Bambusoideae)

With the development of sequencing technologies, the use of multiple nuclear genes has become conventional for resolving difficult phylogenies. However, this technique also presents challenges due to gene-tree discordance, as a result of incomplete lineage sorting (ILS) and reticulate evolution. Although alleles can show sequence variation within individuals, which contain information regarding the evolution of organisms, they continue to be ignored in almost all phylogenetic analyses using randomly phased genome sequences. Here, we tried to incorporate alleles from multiple nuclear loci to study the phylogeny of the economically important bamboo genus Phyllostachys (Poaceae, Bambusoideae). Obtaining a total of 3926 sequences, we documented extensive allelic variation for 61 genes from 39 sampled species. Using datasets consisting of selected alleles, we demonstrated substantial discordance among phylogenetic relationships inferred from different alleles, as well as between concatenation and coalescent methods. Furthermore, ILS and hybridization were suggested to be underlying causes of the discordant phylogenetic signals. Taking these possible causes for conflicting phylogenetic results into consideration, we recovered the monophyly of Phyllostachys and its two morphology-defined sections. Our study also suggests that alleles deserve more attention in phylogenetic studies, since ignoring them can yield highly supported but spurious phylogenies. Meanwhile, alleles are helpful for unraveling complex evolutionary processes, particularly hybridization.

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.

Evolution of nectar spur length in a clade of Linaria reflects changes in cell division rather than in cell expansion

BACKGROUND AND AIMS

Nectar spurs (tubular outgrowths of a floral organ which contain, or give the appearance of containing, nectar) are hypothesized to be a 'key innovation' which can lead to rapid speciation within a lineage, because they are involved in pollinator specificity. Despite the ecological importance of nectar spurs, relatively little is known about their development. We used a comparative approach to investigate variation in nectar spur length in a clade of eight Iberian toadflaxes.

METHODS

Spur growth was measured at the macroscopic level over time in all eight species, and growth rate and growth duration compared. Evolution of growth rate was reconstructed across the phylogeny. Within the clade we then focused on Linaria becerrae and Linaria clementei, a pair of sister species which have extremely long and short spurs, respectively. Characterization at a micromorphological level was performed across a range of key developmental stages to determine whether the difference in spur length is due to differential cell expansion or cell division.

KEY RESULTS

We detected a significant difference in the evolved growth rates, while developmental timing of both the initiation and the end of spur growth remained similar. Cell number is three times higher in the long spurred L. becerrae compared with L. clementei, whereas cell length is only 1.3 times greater. In addition, overall anisotropy of mature cells is not significantly different between the two species.

CONCLUSIONS

We found that changes in cell number and therefore in cell division largely explain evolution of spur length. This contrasts with previous studies in Aquilegia which have found that variation in nectar spur length is due to directed cell expansion (anisotropy) over variable time frames. Our study adds to knowledge about nectar spur development in a comparative context and indicates that different systems may have evolved nectar spurs using disparate mechanisms.

Phylogenomics resolves evolutionary relationships and provides insights into floral evolution in the tribe Shoreeae (Dipterocarpaceae)

A supra-annual, community-level synchronous flowering prevails in several parts of the tropical forests of Southeast Asia and its evolution has been hypothesized to be linked to pollinator shifts. The aseasonal Southeast Asian lowland rainforests are dominated by Dipterocarpaceae, which exhibit great floral diversity, a range of pollination syndromes and include species with annual and supra-annual gregarious flowering. Phylogenetic relationships within this family are still unclear, especially in the tribe Shoreeae. Here, we develop a pipeline to maximize recovery of genome-wide SNPs from restriction-site associated DNA sequencing (RADseq) in non-model organisms across wide phylogenetic scales. We then infer phylogenomic relationships in the tribe Shoreeae using both traditional and coalescent analyses. The phylogenetic trees obtained with these methods are congruent to each other and highly resolved. They allow reconstructing the evolutionary patterns of floral traits (number of stamens, anther structure and anther/appendage size) in the group. Our inferences indicate that species with many stamens, but smaller, globose anthers and longer appendages and have evolved multiple times from species with fewer stamens, but larger, oblong anthers and shorter appendages. This could have happened in parallel to iterative shifts in pollinators across the uncovered phylogeny from larger, longer generation to smaller, shorter-generation insects that can quickly build up the necessary population sizes during mass flowering episodes.

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

PREMISE OF THE STUDY

The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales.

METHODS

We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses.

KEY RESULTS

Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling.

CONCLUSIONS

Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets.