RESUMO

Lentinula (Basidiomycota, Agaricales) includes the most widely cultivated mushroom in the world, Lentinula edodes, also known as shiitake (Japanese) or xiang-gu (Chinese). At present, nine species are recognized in the genus, based on morphology, mating criteria, and geographic distribution. However, analyses of internal transcribed spacers (ITS) of ribosomal RNA genes have suggested that there are cryptic lineages. We analyzed a global-scale phylogenetic dataset from 325 Lentinula individuals from 24 countries in Asia-Australasia and the Americas plus Madagascar, with 325 sequences of ITS, 80 LSU sequences, and 111 sequences of translation elongation factor (tef1-α) genes. We recovered 15 independent lineages (Groups 1-15) that may correspond to species. Lineages in Asia-Australasia (Groups 1-5) and the Americas plus Madagascar (Groups 6-15) formed sister clades. Four lineages are represented only by sequences from single individuals and require further molecular sampling, including L. aff. raphanica (Group 7), L. ixodes (Group 8), L. boryana (Group 12), and L. aff. aciculospora (Group 14). Groups 1 and 5 are here referred to L. edodes and L. aff. edodes, respectively. However, these groups most likely represent the same species and are only recognized as (unsupported) monophyletic lineages by maximum likelihood analyses of ITS alone. Other putative species resolved here include L. lateritia (Group 2), L. novae-zelandieae (Group 3), L. aff. lateritia (Group 4), L. raphanica (Group 6), L. aff. detonsa (Group 9), L. detonsa (Group 10), L. guzmanii sp. nov. (Group 11), L. aciculospora (Group 13), and L. madagasikarensis (Group 15). Groups 9-12 represent the "L. boryana complex". Molecular clock and historical biogeographic analyses suggest that the most recent common ancestor (MRCA) of Lentinula can be placed in the middle Oligocene, ca. 30 million years ago (Ma), and had a likely presence in neotropical America. The MRCA of Lentinula in the Americas and Madagascar lived ca. 22 Ma in the Neotropics and the MRCA of Lentinula in Asia-Australasia lived ca. 6 Ma in Oceania. Given the current knowledge about plate tectonics and paleoclimatic models of the last 30 Myr, our phylogenetic hypothesis suggests that the extant distribution of Lentinula is likely to have arisen, in large part, due to long-distance dispersal. Lentinula collections include at least four dubious taxa that need further taxonomic studies: L. reticeps from the USA (Ohio); L. guarapiensis from Paraguay; Lentinus puiggarii from Brazil (São Paulo); and "L. platinedodes" from Vietnam. Approximately ten of the fifteen Groups are reported on Fagaceae, which appears to be the ancestral substrate of Lentinula.

Assuntos

RESUMO

The use of genome-scale data in phylogenetics has enabled recent strides in determining the relationships between taxa that are taxonomically problematic because of extensive morphological variation. Here, we employ a phylogenomic approach to infer evolutionary relationships within Ranitomeya (Anura: Dendrobatidae), an Amazonian lineage of poison frogs consisting of 16 species with remarkable diversity in color pattern, range size, and parental care behavior. We infer phylogenies with all described species of Ranitomeya from ultraconserved nuclear genomic elements (UCEs) and also estimate divergence times. Our results differ from previous analyses regarding interspecific relationships. Notably, we find that R. toraro and R. defleri are not sister species but rather distantly related, contrary to previous analyses based on smaller genetic datasets. We recover R. uakarii as paraphyletic, designate certain populations formerly assigned to R. fantastica from Peru as R. summersi, and transfer the French Guianan and eastern Brazilian R. amazonica populations to R. variabilis. By clarifying both inter- and intraspecific relationships within Ranitomeya, our study paves the way for future tests of hypotheses on color pattern evolution and historical biogeography.

Assuntos

RESUMO

The willistoni species subgroup has been the subject of several studies since the latter half of the past century and is considered a Neotropical model for evolutionary studies, given the many levels of reproductive isolation and different evolutionary stages occurring within them. Here we present for the first time a phylogenetic reconstruction combining morphological characters and molecular data obtained from 8 gene fragments (COI, COII, Cytb, Adh, Ddc, Hb, kl-3 and per). Some relationships were incongruent when comparing morphological and molecular data. Also, morphological data presented some unresolved polytomies, which could reflect the very recent divergence of the subgroup. The total evidence phylogenetic reconstruction presented well-supported relationships and summarized the results of all analyses. The diversification of the willistoni subgroup began about 7.3 Ma with the split of D. insularis while D.paulistorum complex has a much more recent diversification history, which began about 2.1 Ma and apparently has not completed the speciation process, since the average time to sister species separation is one million years, and some entities of the D. paulistorum complex diverge between 0.3 and 1 Ma. Based on the obtained data, we propose the categorization of the former "semispecies" of D. paulistorum as a subspecies and describe the subspecies D. paulistorum amazonian, D. paulistorum andeanbrazilian, D. paulistorum centroamerican, D. paulistorum interior, D. paulistorum orinocan and D. paulistorum transitional.

Assuntos

RESUMO

Galápagos snakes are among the least studied terrestrial vertebrates of the Archipelago. Here, we provide a phylogenetic analysis and a time calibrated tree for the group, based on a sampling of the major populations known to occur in the Archipelago. Our study revealed the presence of two previously unknown species from Santiago and Rábida Islands, and one from Tortuga, Isabela, and Fernandina. We also recognize six additional species of Pseudalsophis in the Galápagos Archipelago (Pseudalsophis biserialis from San Cristobal, Floreana and adjacent islets; Pseudalsophis hoodensis from Española and adjacent islets; Pseudalsophis dorsalis from Santa Cruz, Baltra, Santa Fé, and adjacent islets; Pseudalsophis occidentalis from Fernandina, Isabela, and Tortuga; Pseudalsophis slevini from Pinzon, and Pseudalsophis steindachneri from Baltra, Santa Cruz and adjacent islets). Our time calibrated tree suggests that the genus Pseudalsophis colonized the Galápagos Archipelago through a single event of oceanic dispersion from the coast of South America that occurred at approximately between 6.9?Ma and 4.4?Ma, near the Miocene/Pliocene boundary.

RESUMO

Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.

Assuntos

RESUMO

House flies are one of the best known groups of flies and comprise about 5000 species worldwide. Despite over a century of intensive taxonomic research on these flies, classification of the Muscidae is still poorly resolved. Here we brought together the most diverse molecular dataset ever examined for the Muscidae, with 142 species in 67 genera representing all tribes and all biogeographic regions. Four protein coding genes were analyzed: mitochondrial CO1 and nuclear AATS, CAD (region 4) and EF1-α. Maximum likelihood and Bayesian approaches were used to analyze five different partitioning schemes for the alignment. We also used Bayes factors to test monophyly of the traditionally accepted tribes and subfamilies. Most subfamilial taxa were not recovered in our analyses, and accordingly monophyly was rejected by Bayes factor tests. Our analysis consistently found three main clades of Muscidae and so we propose a new classification with only three subfamilies without tribes. Additionally, we provide the first timeframe for the diversification of all major lineages of house flies and examine contemporary biogeographic hypotheses in light of this timeframe. We conclude that the muscid radiation began in the Paleocene to Eocene and is congruent with the final stages of the breakup of Gondwana, which resulted in the complete separation of Antarctica, Australia, and South America. With this newly proposed classification and better understanding of the timing of evolutionary events, we provide new perspectives for integrating morphological and ecological evolutionary understanding of house flies, their taxonomy, phylogeny, and biogeography.

Assuntos

RESUMO

The ecology and evolution of Caribbean anoles are well described, yet little is known about mainland anole species. Lack of phylogenetic information limits our knowledge about species boundaries, morphological evolution, and the biogeography of anoles in South America. To help fill this gap, we provide an updated molecular phylogeny of the Dactyloa (Dactyloidae), with emphasis on the punctata species group. By sampling understudied Amazonian taxa, we (i) assess the phylogenetic placement of the 'odd anole', D. dissimilis; (ii) infer the relationships of the proboscis-bearing D. phyllorhina, testing the hypothesis of independent nasal appendage evolution within the anole radiation; and (iii) examine genetic and dewlap color variation in D. punctata and D. philopunctata. Combining multiple nuclear loci with a review of the fossil record, we also (iv) estimate divergence times within the pleurodont iguanian clade of lizards, including Amazonian representatives of Dactyloa and Norops (Dactyloidae) and of Polychrus (Polychrotidae). We recover the five Dactyloa clades previously referred to as the aequatorialis, heteroderma, latifrons, punctata and roquet species groups, as well as a sixth clade composed of D. dissimilis and the non-Amazonian D. neblinina and D. calimae. We find D. phyllorhina to be nested within the punctata group, suggesting independent evolution of the anole proboscis. We consistently recover D. philopunctata nested within D. punctata, and report limited genetic divergence between distinct dewlap phenotypes. The most recent common ancestor of Dactyloa, Anolis and Norops dates back to the Eocene. Most Amazonian taxa within both Dactyloa and Norops diverged in the Miocene, but some diversification events were as old as the late Eocene and late Oligocene. Amazonian Polychrus diverged in the Pliocene. Our findings have broad implications for anole biogeography, disputing recent suggestions that modern dactyloid genera were present in the Caribbean region during the Cretaceous.

Assuntos

RESUMO

The molecular clock theory has greatly enlightened our understanding of macroevolutionary events. Maximum likelihood (ML) estimation of divergence times involves the adoption of fixed calibration points, and the confidence intervals associated with the estimates are generally very narrow. The credibility intervals are inferred assuming that the estimates are normally distributed, which may not be the case. Moreover, calculation of standard errors is usually carried out by the curvature method and is complicated by the difficulty in approximating second derivatives of the likelihood function. In this study, a standard primate phylogeny was used to examine the standard errors of ML estimates via the bootstrap method. Confidence intervals were also assessed from the posterior distribution of divergence times inferred via Bayesian Markov Chain Monte Carlo. For the primate topology under evaluation, no significant differences were found between the bootstrap and the curvature methods. Also, Bayesian confidence intervals were always wider than those obtained by ML.

Assuntos