Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae.

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species.

Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from the department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct libraries. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotides (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that C. spruceanum is a sister species to Emmenopterys henryi and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond.

Comparative Mitogenomic Analysis Reveals Gene and Intron Dynamics in Rubiaceae and Intra-Specific Diversification in Damnacanthus indicus.

The dynamic evolution of mitochondrial gene and intron content has been reported across the angiosperms. However, a reference mitochondrial genome (mitogenome) is not available in Rubiaceae. The phylogenetic utility of mitogenome data at a species level is rarely assessed. Here, we assembled mitogenomes of six Damnacanthus indicus (Rubiaceae, Rubioideae) representing two varieties (var. indicus and var. microphyllus). The gene and intron content of D. indicus was compared with mitogenomes from representative angiosperm species and mitochondrial contigs from the other Rubiaceae species. Mitogenome structural rearrangement and sequence divergence in D. indicus were analyzed in six individuals. The size of the mitogenome in D. indicus varied from 417,661 to 419,435 bp. Comparing the number of intact mitochondrial protein-coding genes in other Gentianales taxa (38), D. indicus included 32 genes representing several losses. The intron analysis revealed a shift from cis to trans splicing of a nad1 intron (nad1i728) in D. indicus and it is a shared character with the other four Rubioideae taxa. Two distinct mitogenome structures (type A and B) were identified. Two-step direct repeat-mediated recombination was proposed to explain structural changes between type A and B mitogenomes. The five individuals from two varieties in D. indicus diverged well in the whole mitogenome-level comparison with one exception. Collectively, our study elucidated the mitogenome evolution in Rubiaceae along with D. indicus and showed the reliable phylogenetic utility of the whole mitogenome data at a species-level evolution.

Root exudate composition of grass and forb species in natural grasslands.

Plants exude a diverse cocktail of metabolites into the soil as response to exogenous and endogenous factors. So far, root exudates have mainly been studied under artificial conditions due to methodological difficulties. In this study, each five perennial grass and forb species were investigated for polar and semi-polar metabolites in exudates under field conditions. Metabolite collection and untargeted profiling approaches combined with a novel classification method allowed the designation of 182 metabolites. The composition of exuded polar metabolites depended mainly on the local environment, especially soil conditions, whereas the pattern of semi-polar metabolites was primarily affected by the species identity. The profiles of both polar and semi-polar metabolites differed between growth forms, with grass species being generally more similar to each other and more responsive to the abiotic environment than forb species. This study demonstrated the feasibility of investigating exudates under field conditions and to identify the driving factors of exudate composition.

Genus Ophiorrhiza: A Review of Its Distribution, Traditional Uses, Phytochemistry, Biological Activities and Propagation.

Almost 50 species of Ophiorrhiza plants were reviewed in this work and the main objective is to critically analyse their distribution, phytochemical content, biological activity, and propagation. Moreover, the information would be useful in promoting the relevant uses of the plant, especially in the medicinal fields based on in vitro and in vivo studies. To this end, scientific sources, including theses, PubMed, Google Scholar, International Islamic University Malaysia IIUM EBSCO, PubChem, and Elsevier, were accessed for publications regarding the Ophiorrhiza genus in this review. Scientific literature regarding the Ophiorrhiza plants revealed their wide distribution across Asia and the neighbouring countries, whereby they were utilised as traditional medicine to treat various diseases. In particular, various active compounds, such as alkaloids, flavonoids, and terpenoids, were reported in the plant. Furthermore, the Ophiorrhiza species showed highly diverse biological activities, such as anti-cancer, antiviral, antimicrobial, and more. The genus propagation reported could produce a high quality and quantity of potent anticancer compound, namely camptothecin (CPT). Hence, it is believed that the relevant uses of natural compounds present in the plants can replace the existing crop of synthetic anticancer drugs associated with a multitude of unbearable side effects. Additionally, more future studies on the Ophiorrhiza species should be undertaken to establish the links between its traditional uses, active compounds, and pharmacological activities reported.

Phylogenetic affinity of an enigmatic Rubiaceae from the Seychelles revealing a recent biogeographic link with Central Africa: gen. nov. Seychellea and trib. nov. Seychelleeae.

The granitic islands of the Seychelles harbor about 268 native angiosperm species, with 28% being endemics there. The Seychelles biota contains a mix of ancient taxa with Gondwanan origins and young taxa that arrived there via dispersals. We investigate the phylogenetic position of an enigmatic, critically endangered, Seychellean endemic of the coffee family (Rubiaceae), Psathura/Psychotria sechellarum, and assess whether its presence on the granitic islands of the Seychelles is the result of vicariance or long-distance dispersal. Phylogenetic relationships of the family were reconstructed based on the Bayesian and maximum-likelihood phylogenetic analyses of sequence data from five plastid markers of 107 terminals. Divergence times were estimated using a Bayesian-based method. Psathura/Psychotria sechellarum is distantly related to Psychotria s.l. (including Psathura), and is strongly supported as sister to the Central African genus Colletoecema. Their striking morphological differences, coupled with their geographic separation and genetic distinctness, support the recognition of the new genus Seychellea and new tribe Seychelleeae to accommodate the Seychellean species. The Colletoecema-Seychellea clade constitutes an early-divergent lineage in the subfamily Rubioideae, with an old stem and a young crown ages estimated to be in the Late Cretaceous and late Oligocene-early Pliocene, respectively. Colletoecema diverged from Seychellea in the late Oligocene-early Pliocene and their respective crown ages are inferred to be late Miocene-middle Pleistocene and Pleistocene, respectively. The ancestor of the two genera was likely present in Africa, and reached the Seychelles via avian dispersal. Unlike Colletoecema with three species, Seychellea is monospecific, with very few individuals left in the wild. The species should be a top candidate for conservation priority, as its extinction would cause loss of genetic diversity of this entire lineage.

Phytochemical and morpho-anatomical study of the vegetative organs of Psychotria fractistipula L. B.Sm., R.M. Klein & Delprete (Rubiaceae)

Psychotria fractistipula L.B.Sm, R.M. Klein & Delprete (Rubiaceae) is found in the existing Atlantic Forest in the South of Brazil, in the Paraná and Santa Catarina States. The members of Rubiaceae are characterized chemically by the presence of alkaloids, some pharmacological properties of which include antifungal, antibacterial, analgesic, antioxidant, antimutagenic, and antiviral activities. In this study, we report the results of anatomical, morphological, and histochemical analyses of the leaves and stems of the Rubiaceae family member, P. fractistipula. The anatomical analysis involved of light microscopy and scanning electron microscopy. Morpho-anatomical and histochemical characterization were made using standard methodology. The isolated compounds were identified by Nuclear Magnetic Resonance spectroscopic analysis. The following structures are highlighted as the distinctive features of the species: presence of petiolate leaves and a petiole base, leaf blade with smooth cuticle on both surfaces, paracytic stomata, and, dorsiventral mesophyll and presence of trichomes on the leaves and stems. Phytosteroids, identified as β-sitosterol and campesterol, were observed in the hexane fraction of the stem. Future studies should focus on the isolation of other fractions of interest and their characterization through specific biological and cytotoxicity assays.

Comparative analgesic evaluation of Himalrandia tetrasperma and Wendlandia exserta of family Rubiaceae after induction of pain in mice.

Himalrandia tetrasperma and Wendlandia exserta medicinal plants belong to family Rubiaceae commonly known as coffee family were investigated by quantitative analysis of major bioactive compounds and analgesic effect. The analgesic potential was accessed using different parts of H. tetrasperma and W. exserta by induced acetic acid writhing and hot plate test method. Methanolic extracts of these two plants satisfactorily possesses analgesic activity. All the extracts showed good results as compared to standard drug, i.e. aspirin. Seeds of H. tetrasperma possess maximum, i.e. 86.73% inhibition at first phase where as aspirin possesses 52.73%. In second phase, leaves possess 99.8 % inhibition respectively. Hot plate analgesic activity of bark extract displayed maximum activity at 4.5h stage, i.e. 8.6±0.40. W. exserta methanolic extract of bark possesses 97.3% inhibition respectively in first phase and 99.8% in second phase. Bark extract displayed maximum activity at 4.5h stage, i.e., 9.7±0.5. Quantitative analysis of bark of H. tetrasperma possesses highest value of saponins, i.e. 30.21±0.8 where as flavonoids 17.50±1.2, phenolic compounds 23.25±0.5 and tannins 12.32±0.4. The leaf extracts of H. tetrasperma contains maximum value of phenols, i.e. 15.10±0.7 where as W. exserta bark possesses significant value of alkaloids, i.e. 16.41±0.4 and leaf extracts possesses flavonoids, i.e. 14.51±0.3, saponins 12.22±0.1 and phenolic compounds 11.31±0.4. The seeds of both plants possess significant value of tannins, i.e. 07.60±0.3.

Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers.

Gentiana section Cruciata is widely distributed across Eurasia at high altitudes, and some species in this section are used as traditional Chinese medicine. Accurate identification of these species is important for their utilization and conservation. Due to similar morphological and chemical characteristics, correct discrimination of these species still remains problematic. Here, we sequenced three complete chloroplast (cp) genomes (G. dahurica, G. siphonantha and G. officinalis). We further compared them with the previously published plastomes from sect. Cruciata and developed highly polymorphic molecular markers for species authentication. The eight cp genomes shared the highly conserved structure and contained 112 unique genes arranged in the same order, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. We found that four genes (accD, clpP, matK and ycf1) were subject to positive selection, and sixteen InDel-variable loci with high discriminatory powers were selected as candidate barcodes. Our phylogenetic analyses based on plastomes further confirmed the monophyly of sect. Cruciata and primarily elucidated the phylogeny of Gentianales. This study indicated that cp genomes can provide more integrated information for better elucidating the phylogenetic pattern and improving discriminatory power during species authentication.

Kupeantha (Coffeeae, Rubiaceae), a new genus from Cameroon and Equatorial Guinea.

Two new coffee relatives (tribe Coffeeae, Rubiaceae), discovered during botanical expeditions to Cameroon, are examined for generic placement, and the placement of three previously known species (Argocoffeopsis fosimondi, A. spathulata and Calycosiphonia pentamera) is reinvestigated using plastid sequence (accD-psa1, rpl16, trnL-F) and morphological data. Seed biochemistry of the new species and pollen micromorphology (only one of the two species) are also studied. Based on the plastid sequence data, the new taxa are nested in a well-supported monophyletic group that includes Argocoffeopsis and Calycosiphonia. Within this clade, three well-supported subclades are recovered that are morphologically easy to diagnose: (1) Calycosiphonia (excluding C. pentamera), (2) Argocoffeopsis (excluding A. fosimondi and A. spathulata), and (3) a clade including the above excluded species, in addition to the new species. Based on the results, Kupeantha, a new genus of five species, is described, including two new Critically Endangered taxa from the Highlands of Cameroon: Kupeantha ebo and K. kupensis. Phytochemical analysis of Kupeantha seeds reveals compounds assigned as hydroxycinnamic acid derivatives, amino acids and ent-kaurane diterpenoids; caffeine was not detected. Kupeantha is the first new genus described in tribe Coffeeae in 40 years.

The monotypic Brazilian genus Diacrodon is a synonym of Borreria (Spermacoceae, Rubiaceae): morphological and molecular evidences.

Diacrodon is a monotypic genus of the tribe Spermacoceae (Rubiaceae), endemic to northeastern Brazil. Diacrodon compressus is frequently misidentified with a two lobed calyx species of Borreria, B. verticillata. Traditionally, in Spermacoceae the fruit type was considered a diagnostic character among the genera. In this sense, D. compressus presents a strongly compressed, one seeded and indehiscent fruit (vs. globose, two seeded and dehiscent fruit in B. verticillata). In this work, we address two objectives: evaluate the systematic position and determine the identity of Diacrodon in respect to other taxa. Molecular analyses using ITS and ETS indicate that D. compressus is strongly related to other species of Borreria. The morphological results revealed that D. compressus, despite of its type of fruit, is identical to Borreria in floral and palynological features. As conclusion, the new combination Borreria diacrodonta is made and a lectotype is designated. An updated description of the species and a key to the Borreria species with a two lobed calyx are provided. The distribution of B. diacrodonta is extended to Brazilian states Goiás and Minas Gerais, and Paraguay. By this taxonomical change it has become clear that the dehiscence of the fruits lack taxonomic value in the delimitation of Borreria.

Evolution of sexual systems and growth habit in Mussaenda (Rubiaceae): Insights into the evolutionary pathways of dioecy.

Dioecy is a rare sexual system that is thought to represent an "evolutionary dead end". While many studies have addressed the evolution of dioecy and/or its relationship with the evolution of the woody habit, few have explored the relationship between dioecy and climbing habit, and their effects on diversification rates. Here, we study the evolution of sexual systems and growth habit in Mussaenda (Rubiaceae) using a robust phylogeny of the genus based on eight plastid regions and a broad sampling of taxa (92 of the 132 species were sampled). A time-calibrated tree was constructed to estimate diversification rates in different clades and its correlates with focal characters. More specifically, we assess evolutionary correlations between dioecy and climbing habit and their respective influences on diversification rates. Ancestral character state reconstructions revealed that distyly is the most likely ancestral state in Mussaenda. Distyly has subsequently given rise to dioecy, short-styled floral monomorphism, and long-styled floral monomorphism. Dioecy has evolved independently at least four times from distyly, and has reversed to homostylous hermaphroditism at least twice, which does not support the "evolutionary dead end" hypothesis. A significant correlation between the evolution of dioecy and climbing growth form was found in Mussaenda. It is possible that a strong association between high net diversification rates and dioecy may exist in Mussaenda, but no association was found with climbing habit.

When Homoplasy Is Not Homoplasy: Dissecting Trait Evolution by Contrasting Composite and Reductive Coding.

The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs. reductive). Up to now, there is no common agreement to either code characters as complex or simple. Phylogeneticists have discussed which coding method is best but have not incorporated the heuristic process of reciprocal illumination to evaluate the coding. Composite coding allows to test whether 1) several characters were linked resulting in a structure described as a complex character or trait or 2) independently evolving characters resulted in the configuration incorrectly interpreted as a complex character. We propose that complex characters or character states should be decomposed iteratively into simpler characters when the original homology hypothesis is not corroborated by a phylogenetic analysis, and the character or character state is retrieved as homoplastic. We tested this approach using the case of fruit types within subfamily Cinchonoideae (Rubiaceae). The iterative reductive coding of characters associated with drupes allowed us to unthread fruit evolution within Cinchonoideae. Our results show that drupes and berries are not homologous. As a consequence, a more precise ontology for the Cinchonoideae drupes is required.

Role of the Qinghai-Tibetan Plateau uplift in the Northern Hemisphere disjunction: evidence from two herbaceous genera of Rubiaceae.

To assess the role of the Qinghai-Tibetan Plateau uplift in shaping the intercontinental disjunction in Northern Hemisphere, we analyzed the origin and diversification within a geological timeframe for two relict herbaceous genera, Theligonum and Kelloggia (Rubiaceae). Phylogenetic relationships within and between Theligonum and Kelloggia as well as their relatives were inferred using five chloroplast markers with parsimony, Bayesian and maximum-likelihood approaches. Migration routes and evolution of these taxa were reconstructed using Bayesian relaxed molecular clock and ancestral area reconstruction. Our results suggest the monophyly of each Theligonum and Kelloggia. Eastern Asian and North American species of Kelloggia diverged at ca.18.52 Mya and the Mediterranean species of Theligonum diverged from eastern Asian taxa at ca.13.73 Mya. Both Kelloggia and Theligonum are Tethyan flora relicts, and their ancestors might have been occurred in warm tropical to subtropical environments along the Tethys coast. The Qinghai-Tibetan Plateau separated the eastern and western Tethyan area may contribute significantly to the disjunct distributions of Theligonum, and the North Atlantic migration appears to be the most likely pathway of expansion of Kelloggia to North America. Our results highlight the importance role of the QTP uplift together with corresponding geological and climatic events in shaping biodiversity and biogeographic distribution in the Northern Hemisphere.

Ixora (Rubiaceae) on the Philippines - crossroad or cradle?

BACKGROUND: The Philippine archipelago is globally one of the most important model island systems for studying evolutionary processes. However, most plant species on this archipelago have not yet been studied in sufficient detail. The main aim of this study is to unravel the evolutionary history and biogeographic relationships of the Philippine members of the pantropical genus Ixora. RESULTS: The complex plastid and nuclear divergence patterns in Philippine Ixora, documented using tree and network approaches, reveal a highly dynamic evolution in Ixora, involving several phases of radiation and recolonization. Philippine Ixora comprises at least five lineages, of which one is most closely related to species from Wallacea, and the remaining four to species from Asia. CONCLUSIONS: Our study highlights the importance of Philippine species for understanding phytogeographic patterns in the Indomalayan-Australasian eco-region. The overall genetic differentiation, as well as the incongruence between genealogies based on the biparentally inherited nucleome and the maternally inherited plastome in Ixora, reflect the complex tectonic history of the Philippine archipelago. The Ixora lineage related to Wallacean species supports the delimitation of different ecozones along Huxley's line, because it is absent from Palawan. The remaining four lineages are all allied with Asian taxa, reflecting several waves of colonization. Close relationships between some widespread Philippine species and locally adapted narrow endemics suggest that the widespread, genetically diverse species act as pools for the formation of new species in a process of ongoing speciation. Our results suggest that the species concepts of some of the more widespread taxa need to be revised.

Evolution of woody life form on tropical mountains in the tribe Spermacoceae (Rubiaceae).

PREMISE OF THE STUDY: Spermacoceae are mainly an herbaceous group in the Rubiaceae. However, a few lineages are woody and are found in a diverse range of habitat types. Three of the largest woody lineages (Arcytophyllum, Hedyotis, and Kadua) are characterized by their distribution in the moist tropical mountains and have disjunct distribution patterns with respect to their closest relatives. In this study, we explore the cases of derived woodiness in these three lineages and their diversification dynamics in the tropical mountains of Asia, the Pacific, and the Americas. METHODS: By combining phylogenetic results with wood anatomical studies, we estimated timing of origin of the three woody groups, inferred their ancestral traits and ancestral distribution ranges, analyzed their associations with the tropical upland habitat, and elucidated their diversification across tropical mountains. KEY RESULTS: The three woody clades originated and diversified from herbaceous ancestors in close association with the tropical upland habitat during the Miocene. The ancestral range for Asian-Pacific Hedyotis is Africa/Madagascar and continental Asia for Pacific Kadua. The complex geological history of tropical Asia allowed Hedyotis to diversify faster and create narrow endemics near oceans in the highlands of the Western Ghats in India, Sri Lanka, Southeast Asia including southeastern China, and New Guinea. CONCLUSIONS: The three major woody clades in Spermacoceae have gained their woodiness independently from one another, subsequent to colonization by their ancestors from a different geographic environment. The evolution and diversification along the tropical mountain orogeny is strongly linked with the formation of woody habit and many narrow endemic species.

ANTIBACTERIAL PROPERTY TESTING OF TWO SPECIES OF TROPICAL PLANT LASIANTHUS (RUBIACEAE).

Two tropical plant species, Lasianthus pilosus and Lasianthus stipularis are used in traditional medicine but there have been no published studies of the extracts of these plants against bacteria. In this study, we aimed to determine the antimicrobial activities of the above two plants against two gram-positive and seven gram-negative bacterial strains to determine the potential of these two plant species for possible antimicrobial drug development. The antibacterial activities of the lipophilic extracts of these plants were evaluated by disk diffusion and broth microdilution methods. The zone diameters and minimum inhibitory concentrations (MIC) for these plant extracts exhibited their highest antibacterial activity against Pseudomonas aeruginosa, followed by Staphylococcus aureus and Acinetobacter baumannii, respectively. The MIC of these extracts against P. aeruginosa (ATCC 37166 and ATCC 27853) varied from 50 to 200 µg/ml. Thin layer chromatography and detection using different specific reagents revealed the presence of terpenoids, phenolic compounds and iridoid. Cell lysis due to the effect of the lipophilic extracts of these tested plants was demonstrated using scanning electron microscopy. In conclusion, the bioactive compounds of these plants should be studied further to develop potential antimicrobial agents.

DNA Barcodes Confirm the Taxonomic and Conservation Status of a Species of Tree on the Brink of Extinction in the Pacific.

The taxonomic status of a single island, narrow range endemic plant species from Palau, Micronesia (Timonius salsedoi) was assessed using DNA barcode markers, additional plastid loci, and morphology in order to verify its conservation status. DNA barcode loci distinguished T. salsedoi from all other Timonius species sampled from Palau, and were supported by sequence data from the atpB-rbcL intergenic spacer region. Timonius salsedoi was only known from two mature individual trees in 2012. Due to its extremely narrow range and population size, it had previously been recommended to be listed as Critically Endangered Status under three separate IUCN Criteria. In 2014 a second survey of the population following a typhoon revealed that the only two known trees had died suggesting that this species may now be extinct. Comprehensive follow up surveys of suitable habitat for this species are urgently required.

Rubiaceae in Brazilian Atlantic Forest remnants: floristic similarity and implications for conservation / Rubiaceae en remanentes de Bosque Atlántico de Brasil: similitud florística e implicaciones para la conservación

AbstractBrazil holds most of the Atlantic Forest Domain and is also one of the Rubiaceae diversity centers in the Neotropics. Despite the urban expansion in the state of Rio de Janeiro, large areas of continuous vegetation with high connectivity degree can still be found. Recently, new Rubiaceae species have been described in the Rio de Janeiro flora, which present small populations and very particular distribution. The current paper analyzed the similarity in the floristic composition of the Rubiaceae in eight Atlantic Forest remnants of Rio de Janeiro state protected by Conservation Units. We also surveyed and set guidelines for conservation of microendemic species. The similarity analysis were based on previously published studies in Área de Proteção Ambiental de Grumari, Área de Proteção Ambiental Palmares, Parque Estadual da Serra da Tiririca, Parque Nacional do Itatiaia, Parque Nacional de Jurubatiba, Reserva Biológica de Poço das Antas, Reserva Biológica do Tinguá and Reserva Ecológica de Macaé de Cima - using the PAST software (“Paleontological Statistics”) with Sørensen coefficient. The floristic similarity analysis revealed two groups with distinct physiographic characteristics and different vegetation types. Group A consisted in two Restinga areas, Área de Proteção Ambiental de Grumari and Parque Nacional de Jurubatiba, which showed strong bootstrap support (98 %). Group B included forest remnants with distinct phytophisiognomies or altitudes, but with moderate bootstrap support. Low similarity levels among the eight areas were found due to the habitats’ heterogeneity. The current study pointed out 19 microendemic species from the Atlantic Forest, they present a single-site distribution or a distribution restricted to Mountain and Metropolitan regions of Rio de Janeiro state. Concerning the conservation status of microendemic species, discrepancies between the Catalogue of Flora of Rio de Janeiro and the Red Book of Brazilian Flora (two of the main reference catalogs of Brazilian flora) have been identified. We have also highlighted the need for recollecting microendemic species from the Atlantic Forest, and for properly assessing the degree of threat faced by these taxons early. Rev. Biol. Trop. 64 (2): 655-665. Epub 2016 June 01.

ResumenBrasil tiene la mayor parte de bosque del Atlántico y también es uno de los centros de diversidad de Rubiaceas del Neotrópico. A pesar de la expansión urbana en el estado de Río de Janeiro, todavía se pueden encontrar grandes áreas de vegetación con alto grado de conectividad. Recientemente, nuevas especies de Rubiaceae se han descrito en la flora de Río de Janeiro, las cuales presentan poblaciones pequeñas y distribuciones particulares. El presente documento analiza la similitud en la composición florística de Rubiaceae en ocho remanentes del bosque Atlántico del estado de Río de Janeiro, protegidos por las Unidades de Conservación. También se inspeccionaron y establecieron directrices para la conservación de especies microendémicas. El análisis de similitud se basó en estudios publicados anteriormente en el área de Protección Ambiental de Grumari, área de Protección Ambiental Palmares, Parque Estatal de Serra da Tiririca, Parque Nacional de Itatiaia, Parque Nacional de Jurubatiba, Reserva Biológica de Poço das Antas, Reserva Biológica de Tinguá y Reserva Ecológica de Macaé de Cima, utilizando el software PAST (“Paleontological Statistics”) con coeficiente de Sørensen. El análisis de similitud florística reveló dos grupos con características fisiográficas distintas y diferentes tipos de vegetación. El Grupo A consistió en dos áreas, Área de Protección Ambiental de Grumari y el Parque Nacional de Jurubatiba, que mostraron un fuerte bootstrap support (98 %). El Grupo B incluye remanentes de bosque con fitofisionomía o altitudes distintas, pero con moderado bootstrap support. Los bajos niveles de similitud entre las ocho áreas fueron encontrados debido a la heterogeneidad de los hábitats. El estudio señaló que 19 especies microendémicas del Atlántico presentan una distribución de un solo sitio o una distribución restringida a las regiones de montaña y regiones metropolitanas del estado de Río de Janeiro. En cuanto al estado de conservación de especies microendémicas, se han identificado discrepancias entre el Catálogo de la Flora de Río de Janeiro y el Libro Rojo de la Flora de Brasil (dos de los principales catálogos de referencias de la flora brasileña). También se puso de relieve la necesidad de recolectar especies microendémicas del bosque Atlántico para evaluar temprano y adecuadamente el grado de amenaza que enfrentan estos taxones.

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae).

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels - phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important - climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.