An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina

Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the “upstream” colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.

Trichoderma juruarense sp. nov. (Hypocreaceae) a new fungal species from sediments of the Amazonian Juruá River with agricultural potential

The species of Trichoderma are the most common fungi to be used as biocontrol agents, and their metabolic arsenal has a wide variety of applications that places this genus among those with the potential to provide biotechnological products. The ubiquitous nature of Trichoderma has favored a rapid increase in the number of described species, and significant efforts have been made towards the taxonomy of Trichoderma in order to improve the accuracy of identification. During a study of cultivable microbiota from the Juruá River, Amazon, Brazil. Isolates with morphological characteristics of the genus Trichoderma were screened for their capacity to control phytopathogens. A total of five Trichoderma isolates were identified using morphological data combined with phylogenetic analysis of the ITS region, and partial sequences of TEF and RPB2. Trichoderma juruarense sp. nov. form a monophyletic clade that is closely related to T. cyanodichotomus, a species that occupies an unresolved position in the Trichoderma taxonomy. T. cyanodichotomus and T. juruarense sp. nov. present an intracellular blue-green pigment in potato dextrose agar (PDA) and differ in conidia and chlamydospores sizes. These data support the proposition of a new species, named here as Trichoderma juruarense. The holotype of T. juruarense INPA0108 presents in vitro inhibition against phytopathogens, such as Colletotrichum siamense (50%), Corynespora cassiicola (43%), Fusarium decemcellulare (61%) and Sclerotium rolfsii (51%), which demonstrates desirable traits that warrant further studies on plant protection. In addition, T. cyanodichotomus and T. juruarense formed a new clade based on the sequence data of the RPB2 gene.

Rediscovery of the rare Phrynomedusa appendiculata (Lutz, 1925) (Anura: Phyllomedusidae) from the Atlantic Forest of southeastern Brazil

The genus Phrynomedusa Miranda-Ribeiro, 1923 comprises rare and little known phyllomedusid species from southern Atlantic Forest, Brazil. Phrynomedusa appendiculata (Lutz, 1925) is known from three localities since its description and considered a “lost species” because it was last sighted 51 years ago. This pervasive lack of knowledge raised a significant concern about its threat status. Here, we present the rediscovery of P. appendiculata from a breeding population in the Atlantic Plateau forests of the state of São Paulo. This new record allowed the gathering of novel ecological, acoustic and morphological data for this species. Most of the novel data agreed with the variation historically reported for the species, but we found subtle divergences that we interpret as intraspecific variation. Moreover, this record also allowed a reassessment of geographic distribution of the species, and the first inference of its phylogenetic relationships based on molecular data (mitochondrial and nuclear DNA). The resulting phylogeny corroborated the generic placement and evolutionary distinctiveness of P. appendiculata, evidencing the species as sister to the clade P. marginata + P. dryade. Based on novel and historical data, we discuss some putative factors influencing the rarity of P. appendiculata and its congeners, and provide conservation perspectives. We expect that the novel data can support further assessments of threat status for this rare species, as well as initiatives aiming its conservation.

Origin of Symphyotrichum anticostense (Asteraceae: Astereae), an endemic, high polyploid species of the Gulf of St. Lawrence region, based on morphological and nrDNA evidence

Symphyotrichum anticostense (Fernald) G.L.Nesom (Asteraceae: Astereae), a rare endemic of the Gulf of St. Lawrence region is a high allopolyploid (2n=10x=80). It has been hypothesized to be derived from the hybrid between tetraploid (2n=4x=32) individuals of S. boreale (Torr. & A.Gray) Löve & Löve and the hexaploid (2n=6x=48) S. novi-belgii (L.) G.L.Nesom. We investigated this hypothesis using morphological and molecular ITS-sequence data, and we tried to determine the potentially geographic origins of the taxon. Univariate morphological analyses show that 67.5% of the S. anticostense characters are parent-like, 43.5% from S. novi-belgii and 13% from S. boreale, the remainder not differing statistically from either parent; 23.5% are intermediate; and 9% transgressive. Multivariate analyses show that S. anticostense is intermediate between its putative parents. The molecular results support the morphological data, but due to the insufficient resolution among ribotypes on the tree, a more rapidly evolving marker will be needed to ascertain more reliably the origin of S. anticostense. Besides the hypothesis of genetic drift and allele fixation following long-distance dispersals, at least three independent geographic origins may be suggested for S. anticostense; Anticosti Island, Lake St. John, and Gaspé Peninsula-New Brunswick-Maine.

Atypical dependence of excited exciton energy levels and electron-hole correlation on emission energy in pyramidal InP-based quantum dots

We calculate the spectrum of excited exciton states in application-relevant self-assembled pyramidal quantum dots grown in InAs/InP and InAs/AlGaInAs material systems. These types of dots have been recently shown to combine the emission in the third optical fiber window with low surface density and a reasonable level of in-plane symmetry of emitters, which predestines them for studies on single- and entangled-photon emission and for corresponding applications. The spectrum of optically active excited states is crucial for successful resonant and quasi-resonant excitation of emitters, allowing for conservation of angular momentum and addressing individual selected quantum states. Here, we show that in both types of studied dots, due to their specific morphology of truncated pyramid, the density of excited-state ladder, especially the s–p shell splitting may follow an unconventional dependence on emission energy, opposite to the one typically met in regular quantum dots. We obtain this result via modeling based on available morphological data and calculation within the multi-band $${{\varvec{k}} {\cdot } {\varvec{p}}}$$ k · p envelope-function theory combined with the configuration-interaction method used to calculate exciton states. Then, we explain this observation in purely geometric terms, as a result of an increasing effective quantum confinement width in a pyramid that is progressively cut from the top. Additionally, we show that the inverted trend is also manifested in the amount of electron-hole correlation in the exciton ground state, which also shows an anomalous dependence on emission energy and quantum dot volume.

Hydrodroma angelieri (Acari, Hydrachnidia: Hydrodromidae) a new water mite species from Corsica based on morphological and DNA barcode evidence

In the present study we used morphological data and DNA barcodes to describe a new species, Hydrodroma angelieri sp. nov. from Corsica, France. A high genetic distance of 17.3±0.017% K2P from its molecularly most closely related European congener, H. despiciens (Müller, 1776), supports H. angelieri sp. nov. as a distinct species. Morphologically the new species can be identified on the basis of relatively small leg claws, the presence of only one swimming seta on II-L-5 and 4-6 swimming setae on the anterior surface of IV-L-5. An updated key for the European species of Hydrodroma is provided.

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies

Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent "parts", but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies---structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here we assess whether the proximity of ontology-annotated characters within an ontology predicts evolutionary patterns. To do so, we measure phylogenetic information across characters and evaluate if it is hierarchically structured by ontological knowledge---in much the same way as phylogeny structures across-species diversity. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to datasets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially structured by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to addressing particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that ontology does indeed structure phylogenetic information, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological datasets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may structure it: phylogeny, development, or convergence.

Morphological variation of Aceh Pinus (Pinus merkusii)

The genus Pinus is classified as one of the most widely distributed genera of conifer trees, that are majorly distributed in the Northern and Southern hemispheres. Pinus merkusii is the only member of the genus Pinus that is adapted in the tropics and grows naturally in south Equator. Its natural distribution found through-out Southeast Asia, e.g. in Indonesia; particularly on Sumatran Island. Three native strains are known on Sumatra: Aceh, Kerinci, and Tapanuli; with the first one is known as the largest population among the three and grows naturally on the high altitudes. The wood has been utilized in building construction, while the resin collected is classified as one of the most valuable Non Timber Forest Products (NTFP) worth up to US $ 50 million/year and applied in many industries. Planting of citron grass (Cymbopogon sp.) has been ’booming’ over the past seven years in the middle regions of Aceh due to its attractive selling price. As consequences, many Pinus trees have been logged and demanded as fire woods in the distillation process of citron grass. Thus, the citron grass’ plantation has been directly threatening the existence of Pinus forests. Therefore, in-situ conservation effort should be started from now on. Here, we would like to report the morphological variation (N= 15 traits) of natural Pinus (e.g., plant height, diameter of main stem, number of crowns per branch, etc.). The morphological data collected were then analysed with the Principal Component Analyses (PCA), in order to cluster the major agronomical parameters among them. This morphological data would be complemented and benefitted the efforts in the genetic study of Aceh Pinus.

Phylogenetic position of Tropidophorus assamensis Annandale, 1912 with updated morphological data and distributional records

The poorly known northeastern water skink Tropidophorus assamensis is only known from the type locality (Harigaj Range, Sylhet District) in Bangladesh, and few localities in Assam and Mizoram States, north-eastern India. Little is known about the biology including the systematics of the species. In this study, we present for the first time, genetic data (16s rRNA) and inferred its phylogenetic position. In addition to this, we provide updated morphological data along with new distributional records of the species from Mizoram State of north-east India.