Phylogeny and age of cockroaches: a reanalysis of mitogenomes with selective fossil calibrations

In spite of big data and new techniques, the phylogeny and timing of cockroaches remain in dispute. Apart from sequencing more species, an alternative way to improve the phylogenetic inference and time estimation is to improve the quality of data, calibrations and analytical procedure. This study emphasizes the completeness of data, the reliability of genes (judged via alignment ambiguity and substitution saturation), and the justification for fossil calibrations. Based on published mitochondrial genomes, the Bayesian phylogeny of cockroaches and termites is recovered as: Corydiinae + (((Cryptocercidae + Isoptera) + ((Anaplectidae + Lamproblattidae) + (Tryonicidae + Blattidae))) + (Pseudophyllodromiinae + (Ectobiinae + (Blattellinae + Blaberidae)))). With two fossil calibrations, namely, Valditermes brenanae and Piniblattella yixianensis, this study dates the crown Dictyoptera to early Jurassic, and crown Blattodea to middle Jurassic. Using the ambiguous ‘roachoid’ fossils to calibrate Dictyoptera+sister pushes these times back to Permian and Triassic. This study also shows that appropriate fossil calibrations are rarer than considered in previous studies.

Insights on Lulworthiales Inhabiting the Mediterranean Sea and Description of Three Novel Species of the Genus Paralulworthia

The order Lulworthiales, with its sole family Lulworthiaceae, consists of strictly marine genera found on a wide range of substrates such as seagrasses, seaweeds, and seafoam. Twenty-one unidentified Lulworthiales were isolated in previous surveys aimed at broadening our understanding of the biodiversity hosted in the Mediterranean Sea. Here, these organisms, mostly found in association with Posidonia oceanica and with submerged woods, were examined using thorough multi-locus phylogenetic analyses and morphological observations. Maximum-likelihood and Bayesian phylogeny based on nrITS, nrSSU, nrLSU, and four protein-coding genes led to the introduction of three novel species of the genus Paralulworthia: P. candida, P. elbensis, and P. mediterranea. Once again, the marine environment is a confirmed huge reservoir of novel fungal lineages with an under-investigated biotechnological potential waiting to be explored.

Corollospora mediterranea: A Novel Species Complex in the Mediterranean Sea

The genus Corollospora, typified by the arenicolous fungus Corollospora maritima, consists of twenty-five cosmopolitan species that live and reproduce exclusively in marine environments. Species of this genus are known to produce bioactive compounds and can be potentially exploited as bioremediators of oil spill contaminated beaches; hence their biotechnological importance. In this paper, nine fungal strains isolated in the Mediterranean Sea, from the seagrass Posidonia oceanica (L.) Delile, from driftwood and seawater contaminated by an oil spill, were investigated. The strains, previously identified as Corollospora sp., were examined by deep multi-loci phylogenetic and morphological analyses. Maximum-likelihood and Bayesian phylogeny based on seven genetic markers led to the introduction of a new species complex within the genus Corollospora: Corollospora mediterranea species complex (CMSC). The Mediterranean Sea, once again, proves an extraordinary reservoir of novel fungal species with a still undiscovered biotechnological potential.

Evolution and genomic insight into methicillin-resistant Staphylococcus aureus ST9 in China

Objectives To reconstruct the evolutionary history and genomic epidemiology of Staphylococcus aureus ST9 in China. Methods Using WGS analysis, we described the phylogeny of 131 S. aureus ST9 isolates collected between 2002 and 2016 from 11 provinces in China, including six clinical samples from Taiwan. We also investigated the complex structure and distribution of the lsa(E)-carrying multiresistance gene cluster, and genotyped prophages in the genomes of the ST9 isolates. Results ST9 was subdivided into one major (n = 122) and one minor (n = 9) clade. Bayesian phylogeny predicted the divergence of ST9 isolates in pig farming in China as early as 1987, which then evolved rapidly in the following three decades. ST9 isolates shared similar multiresistance properties, which were likely acquired before the ST9 emergence in China. The accessory genome is highly conserved, and ST9 harboured similar sets of phages, but lacked certain virulence genes. Conclusions Host exchange and regional transmission of ST9 have occurred between pigs and humans. Pig rearing and trading might have favoured gene exchanges between ST9 isolates. Resistance genes, obtained from the environment and other isolates, were stably integrated into the chromosomal DNA. The abundance of resistance genes among ST9 is likely attributed to the extensive use of antimicrobial agents in livestock. Phages are present in the genomes of ST9 and may play a role in the rapid evolution of this ST. Although human ST9 infections are rare, ST9 isolates may constitute a potential risk to public health as a repository of antimicrobial resistance genes.

Distinct late Pleistocene subtropical-tropical divergence revealed by fifteen low-copy nuclear genes in a dominant species in South-East China

In East Asia, genetic divergence is usually considered to be correlated to different floristic regions, however, subtropical-tropical divergence is largely ignored, compared to widely explored temperate-subtropical divergence. Lindera aggregata (Lauraceae), a dominant species in South-East China was selected to address this issue. Fifteen low-copy nuclear genes (LCGs) and four chloroplast DNA (cpDNA) fragments were used to detect its evolutionary history. In LCGs, STRUCTURE and dated Bayesian phylogeny analyses detect distinct subtropical-tropical divergence since late Pleistocene. Approximate Bayesian calculation (ABC) further supports the distinct subtropical-tropical divergence, and close related Taiwan and South China populations are diverged at the last interglacial. Isolation by distance, isolation by environment and isolation by resistance analyses suggest the current climatic difference rather than geographical distance contributes to the genetic differentiation. Principle component analysis shows populations of tropical cluster occur in warmer area with higher precipitation. Ancestral area reconstruction based on Bayesian phylogeny indicates that ancestral L. aggregata populations are distributed in tropical region. In cpDNA, although unique haplotypes are found in tropical region, distinct subtropical-tropical divergence is absent. In conclusion, distinct late Pleistocene subtropical-tropical divergence of L. aggregata is triggered by climate. It is likely that L. aggregata is originated in Southwest-South China and experienced hierarchical dispersal from south to north. The South China Sea land bridge has dual role in connecting or isolating Taiwan and mainland populations since the last glaciation.

Métodos de reconstrucción filogenética II: inferencia bayesiana

Phylogenetic reconstruction through Bayesian inference is currently widely used. The main advantage of this method is the direct output of posterior probabilities for each clade on the final phylogeny. Thus, it does not require bootstrapping as a measure of uncertainty. Moreover, Bayesian inference is perfectly fit for dating phylogenies through molecular clocks. In this paper, the basics of Bayesian inference applied to phylogenetic reconstruction are described, starting with an explanation of Bayes’ theorem. Then, the use of the Metropolis-Hastings algorithm to sample topologies from the posterior distribution is characterized and illustrated through a simple example. At the end, there is a mention of the software used for Bayesian phylogeny reconstruction.

Discovery of A New Mammal Species (Soricidae: Eulipotyphla) From Narcondam Volcanic Island, India

The present study discovered the existence of a new Crocidura species of shrew (Soricidae: Eulipotyphla) from Narcondam Island, India by using both morphological and molecular approaches. The new species, Crocidura narcondamica sp. nov. is medium-sized and has a distinct external morphology (darker-grey dense fur with a thick and darker tail) and craniodental (braincase is rounded and elevated with weak lambdoidal ridges) characters in comparison with other close congeners. This description illuminates the first discovery of soricid fauna (shrew) from this volcanic island and a total of 12 Crocidura species catalogued in the Indian checklist of mammals. The newly discovered species maintained sufficient genetic distances (12% to 16.6%) with other Crocidura species known from the Indian mainland, Andaman and Nicobar Archipelago, and Myanmar. Both Maximum-Likelihood and Bayesian phylogeny showed distinct clustering of all soricid species and exhibited congruence with the previous evolutionary hypothesis. The present phylogenetic analyses also furnished the oldest evolutionary lineages of this newly discovered species in comparison with other congeners, which assumed to be possible colonization of this species due to immature radiation in Narcondam Island.

Baetis (Rhodobaetis) molecularis sp. nov., a new mayfly species (Ephemeroptera: Baetidae) from the Russian Far East

A new species Baetis (Rhodobaetis) molecularis sp. nov. is described and illustrated based on larvae and reared adults from the Far East of Russia. The differential diagnosis of this species is provided with regard to other representatives of the subgenus Rhodobaetis Jacob, 2003 from East Palaearctic and Nearctic Regions. A dataset including novel and publicly available COI mtDNA sequences of 16 species of Rhodobaetis has been assembled to provide a reference dataset for DNA barcoding. The comparison between Baetis (Rhodobaetis) molecularis sp. nov. and other species produced K2P genetic distances of 0.201 in average, values well above those associated with intraspecific variation. The closest species was Baetis foemina McDonough with a K2P distance value 0.114. A Bayesian phylogeny of available Rhodobaetis is also provided.

Crocus adamioides (Iridaceae) in Bulgarian flora

Crocus adamioides Kernd. et Pasche, as recently known, was originally treated as C. biflorus Mill. subsp. adamii B. Mathew in the flora of Bulgaria by Mathew (1982) and verified by Rukšāns (2017). The taxon was afterwards described as a separate species (Kerndorff et al. 2012), with the holotype collected in Kırklareli Province, European Turkey. The species was for the first time mapped in two floristic regions of Bulgaria. The diagnostic characters based on the general morphology and leaf anatomy were defined from the natural populations of the species and compared to the type specimen and relevant data from the literature. The phylogenetic position of the species was clarified by sequencing of the internal transcribed spacer region (ITS: ITS1 + 5.SsrDNA + ITS2) and comparison of the obtained sequence with those annotated in NCBI. A phylogenetic tree was built using Bayesian phylogeny. Results have shown highest phylogenetic similarity with C. adamioides from Turkey. The closest relative C. ranjeloviciorum Kernd., Pasche, Harpke et Raca remains in proximity. Our morphological, anatomical and molecular analyses have revealed that the Bulgarian population shows a peculiar combination of characters specific to C. adamioides.

Genetic evidence for allopatric speciation of the Siberian ibex Capra sibirica in India

Montane systems, formed by a series of climatic oscillations and temporal topographic metamorphoses, have broken up the contiguous distribution of widespread species and accelerated allopatric speciation. We used a partial fragment of the mitochondrial cytochrome b (cytb) gene to address speciation across the entire range of the Siberian ibex Capra sibirica. We demonstrated that the Siberian ibex is a polytypic species, plausibly formed by a combination of at least 2 species and/or 3 to 4 sub-species. Bayesian phylogeny showed that the Indian-Tajikistan (I-T) clade is adequately diverged from the other clades based on the mean intra-specific distance criterion, and warrants recognition as a distinct species. We provide pragmatic evidence for the endorsement of the I-T clade as a distinct species of Siberian ibex and urge prioritization of the conservation of this species at global and regional scales.