Plastid Regions Research Articles

Andean Mountain Building Did not Preclude Dispersal of Lowland Epiphytic Orchids in the Neotropics

The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical lineages. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models, we infer that the most recent common ancestor of Cycnoches originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, these rare biological exchanges occurred well after major mountain building periods. The Andes have limited plant migration, yet it has seldom allowed episodic gene exchange of lowland epiphyte lineages such as orchids with great potential for effortless dispersal because of the very light, anemochorous seeds.

Phylogeny, taxonomy and biogeography of Neotropical Quiinoideae (Ochnaceae s.l.)

AbstractAmazonia arguably harbours the highest plant species diversity of all wet tropical regions on earth. There is increasing evidence that this enormous diversity is the product of a rather long and complex process and not of a single cause. Here, we investigated divergence times and diversification dynamics in the Neotropical Quiinoideae (Malpighiales: Ochnaceae s.l.) to explore different evolutionary hypotheses for the accumulation of high species diversity. Additionally, we reappraised the phylogenetic relationships and species circumscriptions using sequences of six plastid and nuclear DNA regions and the most comprehensive taxon sampling of the subfamily to date. Molecular dating indicated that Quiinoideae originated during the late Cretaceous, whereas crown group taxa started to diverge at the Eocene‐Oligocene boundary. The lack of rate shifts in this subfamily supports the “museum” model of diversification. The rather constant species accumulation also suggests that the Pleistocene glacial cycles did not play an important role for the diversification of Quiinoideae. While ancestral area reconstruction was inconclusive, the post‐Miocene divergence times of the west Amazonian species provided some evidence that these areas might not have been available for colonization until the demise of the Lake Pebas and Acre wetlands. New infrageneric groups were inferred, and some species were found to be non‐monophyletic, requiring taxonomic reassessment and demonstrating the need for including multiple individuals per species in species‐level phylogenies.

Plastid and Seed Morphology Data Support a Revised Infrageneric Classification and an African Origin of the Pantropical Genus Xylopia (Annonaceae)

Abstract The floristic treatment of Engler and Diels, published in 1901, provides the only infrageneric classification of the pantropical genus Xylopia (Annonaceae). Here we test and extend that classification using molecular and seed morphology characters. Phylogenetic relationships were reconstructed using data from four plastid regions obtained from 44 of the approximately 165 species in the genus, recovering four well-supported major clades. Seed characters were examined for these taxa, and six aril morphologies, three previously undocumented, were distinguished; we also document the presence of a sarcotesta on the seeds of many species. Molecular and seed data support recognition of five sections within the genus; one, Xylopia sect. Rugosperma, is proposed here as new. Our phylogenetic results suggest an African origin for the genus and reveal complex biogeographic patterns, likely facilitated by long-distance dispersal.

Evaluation of Genetic Diversity by DNA Barcoding of Local Tomato Populations from North-Western Romania

Tomato is one of the most important crops worldwide. DNA barcoding is a molecular based method that has been successfully used for species identification, but a few studies have used this method for cultivated varieties identification. The aim of this study was to test the utility of DNA barcoding for the identification of five local salt tolerant tomato varieties and two commercial varieties. To assess the genetic diversity of tomato varieties, the non-coding plastid trnH-psbA intergenic spacer and three plastid regions (rbcL, rpoC1, rpoB) were used. Based on the sequence variation of the trnH-psbA barcode, three haplotypes were detected among the seven tomato varieties. A neighbor-joining tree was generated and separated the local tomato varieties from the commercial varieties into two distinct clusters. We found very low levels of variation in the chosen plastial markers, but additional markers could be tested in order to assess the utility of DNA barcodes in tomato varieties identification.

Towards a complete generic‐level plastid phylogeny of the paleotropical woody bamboos (Poaceae: Bambusoideae)

AbstractPaleotropical woody bamboos (PWB) are phylogenetically and taxonomically intractable. Because previous studies included deficient samples or lacked informative characters for tree construction, phylogenetic relationships within the PWB remain incompletely resolved. This study presents the most extensively sampled phylogeny of the PWB with 18 plastid regions and a sample of 144 (35%) ingroup species representing 40 (85%) genera and 8 outgroup species. Results confirmed Melocanninae as the earliest diverging lineage from the rest of the group, and Hickeliinae (including Nastus s.str.) and Racemobambosinae are separately placed within the PWB. Bambusinae is phylogenetically heterogeneous and consists of the Dinochloa-Greslania-Mullerochloa-Neololeba-Sphaeroambos (DGMNS) assemblage, Temburongia simplex, and the core Bambusinae. The core Bambusinae may be redefined to include a basal grade, which contains Kinabaluchloa, Holttumochloa, Bonia, Neomicrocalamus, Temochloa, Soejatmia and an unidentified taxon, and the Bambusa-Dendrocalamus-Gigantochloa (BDG) complex. The BDG complex is extremely diverse in morphology and is subdivided into six subclades. Within the Melocanninae, Davidsea, Neohouzeaua and Ochlandra are closely related to Schizostachyum. Phylogenetic relationships are mostly supported by morphological and geographical evidence. In addition, novel interpretations are provided in the redelimitation of some taxa.

Phylogenetic and biogeographical history of the Afro-Madagascan genera Delonix, Colvillea and Lemuropisum (Fabaceae: Caesalpinioideae)

Our understanding of the taxonomic limits and biogeographical evolution of the Afro-Madagascan genus Delonix and the closely related monospecific Madagascan endemic genera Colvillea and Lemuropisum have been hampered by unresolved intergeneric and interspecific relationships. Here we study the phylogenetics of the group using nucleotide sequences from ribosomal ITS, four low-copy nuclear genes and four plastid regions. We find poorly resolved gene trees typical of closely related species, but most species are resolved as monophyletic, and we report conflicting phylogenetic placements only for D. brachycarpa and C. racemosa. A time-calibrated biogeographical analysis of the concatenated matrix of all nine loci suggests that the ancestral area of the Delonix, Lemuropisum and Colvillea clade was in south-western Madagascar c. 24–18 Ma. An out-of-Madagascar dispersal to Africa took place during the Miocene, most likely by vegetative rafting. Delonix is not monophyletic due to the robustly supported placement of L. edule in Delonix, warranting treatment of Lemuropisum as congeneric with Delonix and establishment of the new name combination Delonix edule, in line with the close morphological similarities between these two genera. In contrast, the phylogenetic position of C. racemosa is unstable occurring in the Delonix–Lemuropisum clade in the nuclear gene trees, but sister to this clade in the plastid gene tree. The status of Colvillea as a distinct genus, therefore, remains questionable, but it is here maintained based on a suite of morphological distinctions, pending further insights into the relationships of this elusive genus.

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

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

The Mediterranean: the cradle of Anthoxanthum (Poaceae) diploid diversity.

Knowledge of diploid phylogeny and ecogeography provide a foundation for understanding plant evolutionary history, diversification patterns and taxonomy. The genus Anthoxanthum (vernal grasses, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and poorly resolved evolutionary relationships. The aims of the study were to reveal: (1) evolutionary lineages of the diploid taxa and their genetic differentiation; (2) the past distribution of the rediscovered 'Mediterranean diploid'; and (3) possible migration routes of diploids in the Mediterranean. A combined approach involving sequencing of two plastid regions ( trnL-trnF and rpl32-trnL ), nrDNA ITS, rDNA FISH analyses, climatic niche characterization and spatio-temporal modelling was used. Among the examined diploid species, only two well-differentiated evolutionary lineages were recognized: Anthoxanthum gracile and A. alpinum . The other taxa - A. aristatum, A. ovatum, A. maderense and the 'Mediterranean diploid' - form a rather intermixed group based on the examined molecular data. In situ rDNA localization enabled identification of the ancestral Anthoxanthum karyotype, shared by A. gracile and two taxa from the crown group. For the studied taxa, ancestral location probabilities for six discrete geographical regions in the Mediterranean were proposed and likely scenarios of gradual expansion from them were suggested. Modelling past and present distributions shows that the 'Mediterranean diploid' has already been occurring in the same localities for 120 000 years. Highly congruent results were obtained and dated the origin and first diversification of Anthoxanthum to the Miocene. The later divergence probably took place in the Pleistocene and started polyploid evolution within the genus. The most recent diversification event is still occurring, and incomplete lineage sorting prevents full diversification of taxa at the molecular level, despite clear separation based on climatic niches. The 'Mediterranean diploid' is hypothesized to be a possible relic of the most recent common ancestor of Anthoxanthum due to their sharing of ancestral features.

Adetogramma (Polypodiaceae), a new monotypic fern genus segregated from Polypodium

Polypodiaceae is one of the most diverse and abundant families of ferns in tropical and subtropical forests. Despite multiple studies investigating its phylogeny and taxonomy, several generic boundaries within the family still need clarification. One of the most problematic circumscriptions is that of Polypodium L., and one species that still contributes to this uncertainty is Polypodium chrysolepis Hook. The main goal of this study was to use molecular and morphological data to clarify the relationships of P. chrysolepis inside the polygrammoid clade. Sequences from three plastid regions (cpDNA – rbcL, rps4 and rps4–trnS IGS) from fifty species belonging to thirty-two genera of Polypodiaceae were analyzed using maximum likelihood and Bayesian inference. Polypodium chrysolepis constitutes an isolated lineage among the neotropical polygrammoid ferns, close to Serpocaulon and the grammitids, and is recognized here in a new genus. It can be distinguished by its entire leaves with free veins and peltate, pedicellate, lanceolate paraphyses. A new combination, Adetogramma chrysolepis, is proposed and a new taxonomic treatment is presented; its conservation status was assessed using IUCN Red List Categories and Criteria.

Geographic barriers and Pleistocene climate change shaped patterns of genetic variation in the Eastern Afromontane biodiversity hotspot

The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations. A strong phylogeographic structure was found, with two reciprocally monophyletic lineages on each side of the Great Rift System, high genetic exclusivity, and restricted gene flow among mountain ranges. We explain this pattern by topographic and ecological changes driven by geological rifting in Eastern Africa. Subsequent genetic structure is attributed to Pleistocene climatic changes, in which sky-islands acted as long-term refuges and cradles of genetic diversity. Our study highlights the importance of climate change and geographic barriers associated with the African Rift System in shaping population genetic patterns, as well as the need to preserve the high levels of exclusive and critically endangered biodiversity harboured by current patches of the Afromontane forest.

Systematics of the Cosmopolitan Aquatic Genus Elatine

Abstract The cosmopolitan genus Elatine (Elatinaceae) includes about 25 aquatic species of mostly diminutive aquatic plants, whose relationships have not been evaluated using a phylogenetic approach. The taxonomic study of this group has been complicated by the small stature of the plants, their minute reproductive structures, and their cosmopolitan distribution. Consequently, much uncertainty exists with respect to species delimitations, their geographical distributions, and interspecific relationships. To clarify the infrageneric classification of Elatine and to provide insights on interspecific relationships within the genus, we conducted a phylogenetic study of nearly all (24) of the currently recognized species using both morphological and molecular data. The tree topology obtained based on morphological data (including vegetative and reproductive characters) was less-resolved than the trees based on molecular data, derived from either nuclear (ITS) or two plastid regions (matK/trnK and rbcL). Howeve...

Reticulate Evolution in Elatine L. (Elatinaceae), a Predominantly Autogamous Genus of Aquatic Plants

Abstract The study of hybridization in aquatic plants is complicated by rarity of flower production, absence of roots, and asexuality. Elatine is a cosmopolitan genus of aquatic flowering plants with about 25 species worldwide. Historically, there has been little concern regarding hybridization in the genus due to the prevalence of autogamy (i.e. self-pollination), which potentially limits xenogamous pollen transfer among the species. Two morphologically complex species (Elatine hexandra and E. americana) are the only known polyploids in the genus. In previous phylogenetic analyses, both species resolved incongruently in gene trees obtained from nuclear (ITS) versus plastid (matK/trnK and rbcL) regions. Suspecting that the phylogenetic incongruence might be a consequence of past hybridization events, we tested that hypothesis by conducting an additional phylogenetic analysis of Elatine, which incorporated sequences from a low copy nuclear gene (phyC). Elatine hexandra and E. americana were the only Elatin...

Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera.

DNA barcoding is expected to be one of the most promising tools in biological taxonomy. However, there have been no agreements on which core barcode should be used in plants, especially in species-rich genera with wide geographical distributions. To evaluate their discriminatory power in large genera, four of the most widely used DNA barcodes, including three plastid regions (matK, rbcL, trnH-psbA) and nuclear internal transcribed spacer (nrITS), were tested in seven species-rich genera (Ficus, Pedicularis, Rhodiola, Rhododendron,Viburnum, Dendrobium and Lysimachia) and a moderate size genus, Codonopsis. All of the sequences from the aforementioned seven large genera were downloaded from NCBI. The related barcodes for Codonopsis were newly generated in this study. Genetics distances, DNA barcoding gaps and phylogenetic trees of the four single barcodes and their combinations were calculated and compared in the seven genera. As for single barcode, nrITS has the most variable sites, the clearest intra- and inter-specific divergences and the highest discrimination rates in the seven genera. Among the combinations of barcodes, ITS+matK performed better than all the single barcodes in most cases and even the three- and four-loci combinations in the seven genera. Therefore, we recommend ITS+matK as the core barcodes for large plant genera.

New insights into the phylogeny and relationships within the worldwide genus Riccardia (Aneuraceae, Marchantiophytina)

With 280 accepted species, the genus Riccardia S.F.Gray (Aneuraceae) is one of the most speciose genera of simple thalloid liverworts. The current classification of this genus is based on morphological and limited-sampling molecular studies. Very few molecular data are available and a comprehensive view of evolutionary relationships within the genus is still lacking. A phylogeny focusing on relationships within the large genus Riccardia has not been conducted. Here we propose the first worldwide molecular phylogeny of the genus Riccardia, based on Bayesian inference and parsimony ratchet analyses of sequences from three plastid regions (psbA-trnH, rps4, trnL-F). The results support the monophyly of Riccardia and a new monospecific genus, Afroriccardia Reeb & Gradst. gen. nov., is described based on molecular and morphological evidence. The results indicate that several currently recognized infrageneric divisions and a few species are not monophyletic, suggesting that further analyses are needed to arrive at a proper understanding of the phylogeny of the genus. Although evidence for an Andean clade was found, most of the species appear scattered in different clades without clear geographical segregation. Broader sampling and further analyses are necessary in order to improve our understanding of the phylogeny of this poorly known liverwort genus.

Phylogeny and biogeography of the amphi-Pacific genus Aphananthe.

Aphananthe is a small genus of five species showing an intriguing amphi-Pacific distribution in eastern, southern and southeastern Asia, Australia, and Mexico, also with one species in Madagascar. The phylogenetic relationships of Aphananthe were reconstructed with two nuclear (ITS & ETS) and two plastid (psbA-trnH & trnL-trnF) regions. Clade divergence times were estimated with a Bayesian approach, and the ancestral areas were inferred using the dispersal-extinction-cladogenesis and Bayesian Binary MCMC analyses. Aphananthe was supported to be monophyletic, with the eastern Asian A. aspera resolved as sister to a clade of the remaining four species. Aphananthe was inferred to have originated in the Late Cretaceous (71.5 mya, with 95% HPD: 66.6–81.3 mya), and the crown age of the genus was dated to be in the early Miocene (19.1 mya, with 95% HPD: 12.4–28.9 mya). The fossil record indicates that Aphananthe was present in the high latitude thermophilic forests in the early Tertiary, and experienced extinctions from the middle Tertiary onwards. Aphananthe originated in Europe based on the inference that included fossil and extant species, but eastern Asia was estimated to be the ancestral area of the clade of the extant species of Aphananthe. Both the West Gondwanan vicariance hypothesis and the boreotropics hypothesis could be excluded as explanation for its amphi-Pacific distribution. Long-distance dispersals out of eastern Asia into North America, southern and southeastern Asia and Australia, and Madagascar during the Miocene account for its wide intercontinental disjunct distribution.

DNA barcoding of some medicinal plants, family Labiatae

DNA barcoding is currently a widely used and effective tool that enables rapid and accurate identification of plant species. In the current study, the performance of plastid and nuclear regions as DNA barcodes in some plants from family Labiatae were tested. The purpose of the present study is to evaluate the utility of DNA barcoding in discriminating some Labiatae species present in Egypt. Two cpDNA regions (ITS and rbcL) were chosen that were proposed by previous studies and were tested either as single locus or as loci barcodes determined by Consortium for the Barcode of Life (CBOL). The rbcL region presented a higher discrimination power among species than ITS region. However, both ITS and rbcL were useful in discrimination among the collected species of the family Labiatae. ITS and rbcL both together could serve as single- region barcodes for Labiatae species contributing plant species identification, conservation and the trade control of valuable plant resources.

Evolutionary history of the endangered shrub snapdragon (Galvezia leucantha) of the Galápagos Islands

AbstractAimThe endangered Galápagos shrub snapdragon (Galvezia leucantha, Antirrhineae, Plantaginaceae) is restricted to small populations on four islands. In this study, we appraised results from taxonomy, genetics, phylogenetics, phylogeography and pollination ecology to reconstruct the evolutionary history of the genus Galvezia.LocationPeru, continental Ecuador and Galápagos.MethodsWe sequenced the nuclear ribosomal ITS and two plastid regions, ndhF and ndhF‐rpL32, to infer the origin of Galvezia and patterns of colonization to and across the Galápagos archipelago, based on Bayesian inference and statistical parsimony analyses. To investigate genetic diversity and differentiation within G. leucantha, we screened the genome of six populations and obtained 194 AFLP fingerprints. Autogamy tests and pollination network analyses were performed to evaluate the colonization potential and to investigate the structure of the pollinators’ assemblage of Galvezia.ResultsRelationships of seven nucleotide‐substitution haplotypes and 11 nucleotide‐substitution ribotypes of Galvezia revealed monophyly for the Galapagos species. Dating estimates indicated divergence of the insular Galvezia lineage in the Middle‐Upper Pleistocene (0.66–0.09 Ma). In addition, distribution of genotypes (seven haplotypes, eight ribotypes) across the three continental species showed geographical differentiation, while low differentiation and distribution of G. leucantha. AFLP genetic diversity is relatively high (HT = 0.109), but a low proportion of the total allelic variance is attributed to variation among subspecies/islands (Hb = 0.035, hierarchical AMOVA: 3.77% of total variance). The endemic bee (Xylocopa darwinii) accounted for 87.30% of the floral visits to G. leucantha.Main conclusionsWe inferred a single origin for an insular lineage that colonized the Galápagos Islands from northern Peru in the Pleistocene. Recent colonization of the archipelago, Pleistocene land bridges between islands and active gene flow promoted by X. darwinii may account for the low‐moderate genetic differentiation of G. leucantha subspecies. An unusual pollination shift from ornithophily (hummingbirds on the continent) to entomophily (Xylocopa in the Galápagos Islands) is supported.

A molecular phylogeny and classification of the Cynodonteae (Poaceae: Chloridoideae) with four new genera: Orthacanthus, Triplasiella, Tripogonella, and Zaqiqah; three new subtribes: Dactylocteniinae, Orininae, and Zaqiqahinae; and a subgeneric classification of Distichlis

AbstractMorphologically, the tribe Cynodonteae is a diverse group of grasses containing about 839 species in 96 genera and 18 subtribes, found primarily in Africa, Asia, Australia, and the Americas. Because the classification of these genera and species has been poorly understood, we conducted a phylogenetic analysis on 213 species (389 samples) in the Cynodonteae using sequence data from seven plastid regions (rps16‐trnK spacer, rps16 intron, rpoC2, rpl32‐trnL spacer, ndhF, ndhA intron, ccsA) and the nuclear ribosomal internal transcribed spacer regions (ITS 1 & 2) to infer evolutionary relationships and refine the current classification. The phylogenetic tree from the combined plastid and nuclear region is well resolved depicting a strongly supported monophyletic Cynodonteae that includes 17 strongly supported clades corresponding to the subtribes Tripogoninae, Pappophorinae, Traginae, Muhlenbergiinae, Hilariinae, Scleropogoninae, Boutelouinae, Monanthochloinae, Dactylocteniinae, Eleusininae, Aeluropodinae, Triodiinae, Orcuttiinae, Zaqiqahinae, Farragininae, Perotidinae, and Gouiniinae, and two moderately supported clades corresponding to the Orininae and Hubbardochloinae. The plastid data places Odyssea paucinervis as sister to Neobouteloua in the Dactylocteniinae whereas the nuclear ITS data places it as sister to Aeluropus in the Aeluropodinae. Odyssea mucronata is strongly supported sister to the Cteniinae, Trichoneurinae, Farragininae, Perotidinae, Hubbardochloinae, and the Gouiniinae, and not closely related to Odyssea paucinervis. The nuclear data placed Acrachne racemosa as sister to Dactyloctenium in the Dactylocteniinae while the plastid data places it near the base of the Eleusininae. Our new classification recognizes three new subtribes (bringing the total to 21 subtribes): Dactylocteniinae that includes Acrachne, Brachychloa, Dactyloctenium, and Neobouteloua; Orininae with Cleistogenes and Orinus; and Zaqiqahinae with a single genus, Zaqiqah gen. nov.; Hubbardochloinae (resurrected here) with seven genera; and describes four new genera: Orthacanthus (Traginae) with a single species, Triplasiella (Gouiniinae) with a single species, Tripogonella (Tripogoninae) with three species, and Zaqiqah with a single species. We additionally provide a subgeneric classification of Distichlis recognizing three sections: D. sect. Monanthochloe, D. sect. Bajaenses, and D. sect. Spicatae, the latter two representing new sections. The following nine new combinations are made: Distichlis sect. Monanthochloe, Orthacanthus pedunculatus, Tridentopsis buckleyana, Tridentopsis mutica var. elongata, Triplasiella eragrotoides, Tripogonella loliiformis, Tripogonella minima, Tripogonella spicata, and Zaqiqah mucronata. We lectotypify the following five names: Festuca loliiformis, F. minima, F. mucronata, Triodia eragrostoides, and Uralepis elongata.

A molecular phylogeny of the Laelia alliance (Orchidaceae) and a reassessment of Laelia and Schomburgkia

AbstractWe provide a molecular phylogenetic analysis of the Laelia alliance based on sampling of 20 of an estimated 24 species, and seven plastid regions plus nrITS 1 & 2 analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. Furthermore, we used coded indels to evaluate their effect on the phylogenetic relationships and/or support values (bootstrap and posterior probabilities). Our results confirm the existence of two clades, the long known Laelia (endemic to México at middle to high elevations) and Schomburgkia (a more widely distributed taxon). Both clades were strongly supported by PP values and moderate BS; thus, we preferred to recognize them as separate genera with a reappraised morphology and taxonomic delimitation. The inclusion of coded indels in the analyses was of great utility; we could identify the probable hybrid origin of L. gouldiana and L. halbingeriana. We propose new combinations to accommodate the taxonomic changes resulting from our study. We transfer L. anceps subsp. anceps, L. anceps subsp. dawsonii, L. aurea, L. mottae, and L. rubescens to Schomburgkia, with the second taxon elevated to species level; the molecular evidence together with previous published work on the morphology, phenology and geography of the group support these decisions. Lastly, the recently described genus Encabarcenia is considered as a synonym of Schomburgkia and, as a result, a new combination is proposed.

Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia.

BackgroundSpecies delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species’ divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure.ResultsWest African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination’ corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance.ConclusionsOur genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0831-9) contains supplementary material, which is available to authorized users.