Towards a global perspective for Salvia L: Phylogeny, diversification, and floral evolution

Premise of this study: Salvia is the most species-rich genus in Lamiaceae, encompassing approximately 1000 species distributed all over the world. We sought a new evolutionary perspective for Salvia by employing macroevolutionary analyses to address the tempo and mode of diversification. To study the association of floral traits with speciation and extinction, we modeled and explored the evolution of corolla length and the lever-mechanism pollination system across our Salvia phylogeny. Methods: We reconstructed a multigene phylogeny for 366 species of Salvia in the broad sense including all major recognized lineages and numerous species from Iran, a region previously overlooked in studies of the genus. Our phylogenetic data in combination with divergence time estimates were used to examine the evolution of corolla length, woody vs. herbaceous habit, and presence vs. absence of a lever mechanism. We investigated the timing and dependence of Salvia diversification related to corolla length evolution through a disparity test and BAMM analysis. A HiSSE model was used to evaluate the dependency of diversification on the lever-mechanism pollination system in Salvia. Key Results: Based on recent investigations and classifications, Salvia is monophyletic and comprises ~1000 species. Our inclusion, for the first time, of a comprehensive sampling for Iranian species of Salvia provides higher phylogenetic resolution for southwestern Asian species than obtained in previous studies. A medium corolla length (15-18mm) was reconstructed as the ancestral state for Salvia with multiple shifts to shorter and longer corollas. Macroevolutionary model analyses indicate that corolla length disparity is high throughout Salvia evolution, significantly different from expectations under a Brownian motion model during the last 28 million years of evolution. Our analyses show evidence of a higher diversification rate of corolla length for some Andean species of Salvia compared to other members of the genus. Based on our tests of diversification models, we reject the hypothesis of a direct effect of the lever mechanism on Salvia diversification. Conclusions: Using a broader species sampling than previous studies, we obtained a well-resolved phylogeny for southwest Asian species of Salvia. Corolla length is an adaptive trait throughout the Salvia phylogeny with a higher rate of diversification in the South American clade. Our results suggest caution in considering the lever-mechanism pollination system as one of the main drivers of speciation in Salvia.

Hidden diversity within a polytypic species: The enigmatic Sceloporus torquatus Wiegmann, 1828 (Reptilia, Squamata, Phrynosomatidae)

The spiny lizard genus Sceloporus was described by Wiegmann in 1828, with S. torquatus posteriorly designated as the type species. The taxonomic history of S. torquatus is complicated, as it has been confused with other taxa by numerous authors. Many modern systematics works have been published on Sceloporus, but none have included all five recognized S. torquatus subspecies: S. t. torquatus, S. t. melanogaster, S. t. binocularis, S. t. mikeprestoni, and S. t. madrensis. Additionally, there is previous evidence for at least one unnamed taxon. The present study is the first taxonomic revision of the enigmatic S. torquatus based on molecular phylogenies using combined molecular data from 12S, ND4 and RAG1 genes, and Maximum Likelihood and Bayesian inference phylogenetic methods. This work includes the most extensive sampling across the entire distribution, as well as divergence time estimates and environmental niche modelling, which combined offer a spatio-temporal framework for understanding the evolution of the species. Additionally, a series of morphological characters are analyzed to identify significant differences between lineages consistently recovered in the molecular phylogenies. Using this integrative approach, evidence is presented for eight lineages within the S. torquatus complex, five of which correspond to previously recognized subspecies and three represent unnamed taxa masked by morphological conservatism. Finally, to maintain taxonomic stability a lectotype and paralectoype are designated for S. torquatus, and certain taxonomic changes are suggested in order to reflect the phylogenetic relationships within the S. torquatus complex.

Impacts of Taxon-Sampling Schemes on Bayesian Molecular Dating under the Unresolved Fossilized Birth-Death Process

Evolutionary timescales can be estimated using a combination of genetic data and fossil evidence based on the molecular clock. Bayesian phylogenetic methods such as tip dating and total-evidence dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of these diversified sampling schemes on Bayesian molecular dating under the unresolved fossilized birth-death (FBD) process, in which fossil taxa are topologically constrained but their exact placements are not inferred. We used synthetic data generated by simulation of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses show that increasing sampling density does not substantially improve divergence-time estimates under benign conditions. However, when the tree topologies were fixed to those used for simulation or when evolutionary rates varied among lineages, the performance of Bayesian tip dating improves with sampling density. By exploring three situations of model mismatches, we find that including all relevant fossils without pruning off those inappropriate for the FBD process can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have useful implications for Bayesian molecular dating in the era of phylogenomics.

Phylogeography and morphometric variation in the Cinnamon Hummingbird complex: Amazilia rutila (Aves: Trochilidae)

Background The Mesoamerican dominion is a biogeographic area of great interest due to its complex topography and distinctive climatic history. This area has a large diversity of habitats, including tropical deciduous forests, which house a large number of endemic species. Here, we assess phylogeographic pattern, genetic and morphometric variation in the Cinnamon Hummingbird complex Amazilia rutila, which prefers habitats in this region. This resident species is distributed along the Pacific coast from Sinaloa—including the Tres Marías Islands in Mexico to Costa Rica, and from the coastal plain of the Yucatán Peninsula of Mexico south to Belize. Methods We obtained genetic data from 85 samples of A. rutila, using 4 different molecular markers (mtDNA: ND2, COI; nDNA: ODC, MUSK) on which we performed analyses of population structure (median-joining network, STRUCTURE, FST, AMOVA), Bayesian and Maximum Likelihood phylogenetic analyses, and divergence time estimates. In order to evaluate the historic suitability of environmental conditions, we constructed projection models using past scenarios (Pleistocene periods), and conducted Bayesian Skyline Plots (BSP) to visualize changes in population sizes over time. To analyze morphometric variation, we took measurements of 5 morphological traits from 210 study skins. We tested for differences between sexes, differences among geographic groups (defined based on genetic results), and used PCA to examine the variation in multivariate space. Results Using mtDNA, we recovered four main geographic groups: the Pacific coast, the Tres Marías Islands, the Chiapas region, and the Yucatán Peninsula together with Central America. These same groups were recovered by the phylogenetic results based on the multilocus dataset. Demography based on BSP results showed constant population size over time throughout the A. rutila complex and within each geographic group. Ecological niche model projections onto past scenarios revealed no drastic changes in suitable conditions, but revealed some possible refuges. Morphometric results showed minor sexual dimorphism in this species and statistically significant differences between geographic groups. The Tres Marías Islands population was the most differentiated, having larger body size than the remaining groups. Conclusions The best supported evolutionary hypothesis of diversification within this group corresponds to geographic isolation (limited gene flow), differences in current environmental conditions, and historical habitat fragmentation promoted by past events (Pleistocene refugia). Four well-defined clades comprise the A. rutila complex, and we assess the importance of a taxonomic reevaluation. Our data suggest that both of A. r. graysoni (Tres Marías Islands) and A. r. rutila (Pacific coast) should be considered full species. The other two strongly supported clades are: (a) the Chiapas group (southern Mexico), and (b) the populations from Yucatán Peninsula and Central America. These clades belong to the corallirostris taxon, which needs to be split and properly named.

Taxonomy, Phylogeny, Molecular Dating and Ancestral State Reconstruction of Xylariomycetidae (Sordariomycetes)

Xylariomycetidae ( Ascomycota ) is a highly diversified group with variable stromatic characters. Our research focused on inconspicuous stromatic xylarialean taxa from China, Italy, Russia, Thailand and the United Kingdom. Detailed morphological descriptions, illustrations and combined ITS-LSU- rpb 2- tub 2- tef 1 phylogenies revealed 38 taxa from our collections belonging to Amphisphaeriales and Xylariales . A new family ( Appendicosporaceae ), five new genera ( Magnostiolata , Melanostictus , Neoamphisphaeria , Nigropunctata and Paravamsapriya ), 27 new species ( Acrocordiella photiniicola , Allocryptovalsa sichuanensis , Amphisphaeria parvispora , Anthostomella lamiacearum , Apiospora guiyangensis , Ap. sichuanensis , Biscogniauxia magna , Eutypa camelliae , Helicogermslita clypeata , Hypocopra zeae , Magnostiolata mucida , Melanostictus longiostiolatus , Me. thailandicus , Nemania longipedicellata , Ne. delonicis , Ne. paraphysata , Ne. thailandensis , Neoamphisphaeria hyalinospora , Neoanthostomella bambusicola , Nigropunctata bambusicola , Ni. nigrocircularis , Ni. thailandica , Occultitheca rosae , Paravamsapriya ostiolata , Peroneutypa leucaenae , Seiridium italicum and Vamsapriya mucosa ) and seven new host/geographical records are introduced and reported. Divergence time estimates indicate that Delonicicolales diverged from Amphisphaeriales + Xylariales at 161 (123–197) MYA. Amphisphaeriales and Xylariales diverged 154 (117–190) MYA with a crown age of 127 (92–165) MYA and 147 (111–184) MYA, respectively. Appendicosporaceae ( Amphisphaeriales ) has a stem age of 89 (65–117) MYA. Ancestral character state reconstruction indicates that astromatic, clypeate ascomata with aseptate, hyaline ascospores that lack germ slits may probably be ancestral Xylariomycetidae having plant-fungal endophytic associations. The Amphisphaeriales remained mostly astromatic with common septate, hyaline ascospores. Stromatic variations may have developed mostly during the Cretaceous period. Brown ascospores are common in Xylariales , but they first appeared in Amphisphaeriaceae , Melogrammataceae and Sporocadaceae during the early Cretaceous. The ascospore germ slits appeared only in Xylariales during the Cretaceous after the divergence of Lopadostomataceae . Hyaline, filiform and apiospores may have appeared as separate lineages providing the basis to Xylariaceae , which may have diverged independently. The future classification of polyphyletic xylarialean taxa will not be based on stromatic variations, but the type of ring, the colour of the ascospores, and the presence or absence of the type of germ slit.

Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

Stingless bees in Miocene amber of southeastern China (Hymenoptera: Apidae)

Among the many inclusions from the exceptionally rich fossiliferous amber of Zhangpu, China (Middle Miocene: Langhian), stingless bees (Apinae: Meliponini) are particularly common, analogous to the merely slightly older amber sites of Mexico and the Dominican Republic. While there is a large number of workers in Zhangpu amber, only two species are represented. The systematics and morphology of the tribe Meliponini is outlined, including a revision to terms of orientation and direction when discussing surfaces and features of appendages, all in order to better discuss the traits of the fossils as well as place them into a broader context in the global systematics of stingless bees. The two amber species are representative of two Old World genera of Meliponini: Tetragonula Moure and Austroplebeia Moure. While the former is widespread across southern Asia, Malesia, Papuasia, and Australia, the latter is today known only from New Guinea and Australia. Neither genus occurs in the environs of Zhangpu today. Tetragonula (Tetragonula) florilega Engel, new species, is a generally typical species of the subgenus although it intermingles traits otherwise found in two large species groups of non-Australian Tetragonula s.str. The species of Austroplebeia from Zhangpu is sufficiently distinct to place in a new subgenus, Anteplebeina Engel. Austroplebeia (Anteplebeina) fujianica Engel, new species, shares a long list of character states with Austroplebeia s.str., including the presence of yellow maculation on the face, mesoscutum, mesoscutellum, and metepisternum, found only in this clade among Asiatic Meliponini. Nonetheless, the species differs in the length of the malar space and various features of wing venation. Keys are provided to the genera in Zhangpu amber and the subgenera of both genera. The diversity of stingless bees in amber is discussed, as well as the presence of these two fossils in the Middle Miocene of mainland Asia in relation to prior divergence time estimates, phylogenetic relationships, as well as the paleogeography of the region and potential biogeographic hypotheses. The biological association of stingless bees with resins, particularly the collection of dipterocarp resins, is discussed as Zhangpu amber is a Class II resin likely produced by an extinct species of Dipterocarpaceae (Malvales). Also discussed are the ecological preferences of modern Tetragonula and Austroplebeia relative to the reconstructed paleoenvironment of the Zhangpu amber rainforest. Emendations to the classification of Meliponini are appended, with the following new taxa proposed: Atrichotrigona Engel, new subgenus of Axestotrigona Moure; Lispotrigona V.H. Gonzalez & Engel, new subgenus of Nannotrigona Cockerell; Asperplebeia Engel, new genus; Nanoplebeia Engel, new subgenus of Plebeia Schwarz; Aphaneuropsis Engel, Koilotrigona Engel, Necrotrigona Engel, Dichrotrigona Engel, Nostotrigona Engel, Ktinotrofia Engel, all new subgenera of Trigona Jurine; Chapadapis Engel, new subgenus of Schwarziana Moure. The following higher groups are also established: Hypotrigonina Engel, new sutribe; Heterotrigonitae Engel, new infratribe; Trigoniscitae Engel, new infratribe.

Systematics of the Giant Sedges of Carex Sect. Rhynchocystis (Cyperaceae) in Macaronesia with Description of Two New Species

Abstract— Populations of Carex sect. Rhynchocystis (Cyperaceae) from the Macaronesian archipelagos (Azores and Madeira) have traditionally been treated either as a variety of the widely distributed Western Palearctic C. pendula, or directly synonymized under it. However, recent phylogenetic studies have shown that Azorean populations of C. pendula display a certain degree of differentiation from mainland plants, while the phylogenetic relationships of Madeiran populations remain unclear. Here we perform an integrated systematic study focused on the Macaronesian populations of Carex sect. Rhynchocystis to elucidate their phylogenetic relationships and taxonomic status. We reconstructed a molecular phylogeny based on five DNA regions and conducted a multivariate morphological analysis. Divergence time estimates show that the Macaronesian populations can be traced back to a Plio-Pleistocene origin. Our results suggest that these island populations of C. pendula are better treated as two distinct species within Carex sect. Rhynchocystis (i.e. C. leviosa from the Azores and C. sequeirae from Madeira). We provide morphological characters to differentiate the new species from C. pendula s. s., detailed descriptions of the three taxa, a revised key for the entire section, as well as detailed analytical drawings of the two newly described species. We also perform a critical evaluation of the taxonomic diversity of Carex in the Azores and Madeira. Finally, we informally assessed the conservation status of the new species at a global scale under IUCN categories and criteria, resulting in the proposal of the categories Least Concern for C. leviosa and Critically Endangered for C. sequeirae.

Mesozoic origin and ‘out-of-India’ radiation of ricefishes (Adrianichthyidae)

The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, ‘into-India’ or ‘out-of-India’. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai , the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast–East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward ‘out-of-India’ after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast–East Asia. A review of geographic distributions of ‘out-of-India’ taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.

Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been instrumental to resolving the suprafamilial backbone of the charadriiform tree, several higher-level relationships, including the monophyly of plovers (Charadriidae) and the phylogenetic positions of several monotypic families, have remained unclear. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 336 ingroup taxa (89\% of all extant species), 24 loci (15 mitochondrial and 9 nuclear), and 69 morphological characters. Using this phylogeny, we clarify the charadriiform evolutionary timeline by conducting a node-dating analysis based on a subset of 8 loci tested to be clock-like and 16 carefully selected, updated, and vetted fossil calibrations. Our concatenated, species-tree, and total-evidence analyses consistently support plover monophyly and are generally congruent with the topologies of previous studies, suggesting that the higher-level relationships among shorebirds are largely settled. However, several localized conflicts highlight areas of persistent uncertainty within the gulls (Laridae), true auks (Alcinae), and sandpipers (Scolopacidae). At shallower levels, our phylogenies reveal instances of genus-level nonmonophyly that suggest changes to currently accepted taxonomies. Our node-dating analyses consistently support a mid-Paleocene origin for the Charadriiformes and an early diversification for most major subclades. However, age estimates for more recent divergences vary between different relaxed clock models, and we demonstrate that this variation can affect phylogeny-based macroevolutionary studies. Our findings demonstrate the impact of fossil calibration choice on the resulting divergence time estimates, and the sensitivity of diversification rate analyses to the modeling assumptions made in time tree inference.