A comprehensive phylogeny of night adders (Causus)

Why are we blind to cryptic species? Lessons from the eyeless

Pontoscolex corethrurus is the most widespread earthworm species in tropical and sub-tropical zones and one of the most studied in soil science. Although, ecological interactions of P. corethrurus with its environment are well documented, the taxonomic status of the species remains unclear. In this study, we investigated phylogenetic relationships within the genus Pontoscolex, in particular focusing on morphologically indistinguishable (i.e., cryptic) lineages. A total of 792 specimens collected from 25 different countries and islands all over the world were analyzed using two mitochondrial (COI and 16S rDNA) and two nuclear (internal transcribed spacers 2 and 28S rDNA) markers, and a total of 11 morphological characters both internal and external were investigated in all genetically characterized lineages. A large-scale multilocus sequence data matrix was also obtained for Pontoscolex spp. specimens using the Anchored Hybrid Enrichment (AHE) method. Multilocus phylogenetic and phylogenomic analyses, combined with species delimitation methods; including single locus (mPTP, ABGD) and multilocus (BPP) approaches, revealed congruent results. Four cryptic species were supported within the P. corethrurus species complex, and four potentially new species within the genus Pontoscolex. One widespread lineage (L1), within P. corethrurus complex was observed in the current population of Fritz Müller’s garden where P. corethrurus was first described in 1856. Cryptic lineages were observed in sympatry at several localities. This, in combination with observed heteroplasmy in COI gene in one population raises an important question of reproductive isolation between these species.

Venomous snakes are important parts of the ecosystem, and their behavior and evolution have been shaped by their surrounding environments over the eons. This is reflected in their venoms, which are typically highly adapted for their biological niche, including their diet and defense mechanisms for deterring predators. Sub-Saharan Africa is rich in venomous snake species, of which many are dangerous to humans due to the high toxicity of their venoms and their ability to effectively deliver large amounts of venom into their victims via their bite. In this study, the venoms of 26 of sub-Saharan Africa's medically most relevant elapid and viper species were subjected to parallelized toxicovenomics analysis. The analysis included venom proteomics and in vitro functional characterization of whole venom toxicities, enabling a robust comparison of venom profiles between species. The data presented here corroborate previous studies and provide biochemical details for the clinical manifestations observed in envenomings by the 26 snake species. Moreover, two new venom proteomes (Naja anchietae and Echis leucogaster) are presented here for the first time. Combined, the presented data can help shine light on snake venom evolutionary trends and possibly be used to further improve or develop novel antivenoms.

A cryptic lineage is a genetically diverged but morphologically unrecognized variant of a known species. Clarifying cryptic lineage evolution is essential for quantifying species diversity. In sympatric cryptic lineage divergence compared with allopatric divergence, the forces of divergent selection and mating patterns override geographical isolation. Introgression, by supplying preadapted or neutral standing genetic variations, can promote sympatric cryptic lineage divergence via selection. However, most studies concentrated on extant species introgression, ignoring the genetic legacy of introgression from extinct or unsampled lineages ("ghost introgression"). Cycads are an ideal plant for studying the influence of ghost introgression because of their common interspecific gene flow and past high extinction rate. Here, we utilized reference-based ddRADseq to clarify the role of ghost introgression in the evolution of a previously identified sympatric cryptic lineage in Cycas revoluta. After re-evaluating the evolutionary independency of cryptic lineages, the group-wise diverged single-nucleotide polymorphisms among sympatric and allopatric lineages were compared and functionally annotated. Next, we employed an approximate Bayesian computation method for hypothesis testing to clarify the cryptic lineage evolution and ghost introgression effect. SNPs with the genomic signatures of ghost introgression were further annotated. Our results reconfirmed the evolutionary independency of cryptic lineage among C. revoluta and demonstrated that ghost introgression to the noncryptic lineage facilitated their divergence. Gene function related to heat stress and disease resistance implied ecological adaptation of the main extant populations of C. revoluta.

King or royal family? Testing for species boundaries in the King Cobra, Ophiophagus hannah (Cantor, 1836), using morphology and multilocus DNA analyses

Aim Phylogeographic analyses have confirmed high dispersal in many marine taxa but have also revealed many cryptic lineages and species, raising the question of how population and regional genetic diversity arise and persist in dynamic oceanographic settings. Here we explore the geographic evolution of Emerita analoga, an inter-tidal sandy beach crab with an exceptionally long pelagic larval phase and wide latitudinal, amphitropical, distribution. We test the hypothesis that eastern Pacific E. analoga constitute a single panmictic population and examine the location(s), timing and cause(s) of phylogeographic differentiation. Location Principally the eastern Pacific Ocean. Methods We sequenced cytochrome c oxidase subunit I (COI) from 742 E. analoga specimens collected between 1997 and 2000 and downloaded homologous sequences of congeners from GenBank. We reconstructed a phylogeny for Emerita species using maximum likelihood and Bayesian methods and estimated times to most recent common ancestors (TMRCAs), using a COI divergence rate of 1% Myr−1 and timing of closure of the Central American Seaway. We constructed the COI haplotype network of E. analoga using statistical parsimony, calculated population genetic and spatial structure statistics in Arlequin, and estimated the demographic history of E. analoga using Bayesian skyline analysis. Results Population subdivision and allele frequency differences were insignificant among north-eastern Pacific locations over 2000 km apart (ΦST = 0.00, P = 0.70), yet two distinct phylogroups were recovered from the north-eastern and south-eastern Pacific (ΦCT = 0.87, P < 0.001). Amphitropical differentiation of these temperate clades occurred after TMRCA 1.9 ± 0.02 (mean ± SE) Ma and E. analoga has expanded into its present-day north-eastern Pacific range since c. 250 ka. Main conclusions Emerita analoga is not panmictic but is very widely dispersed and approaching genetic homogeneity, i.e. ‘eurymixis’, in the north-eastern Pacific. North-eastern and south-eastern Pacific populations of E. analoga probably became isolated c. 1.5 Ma as the tropical eastern Pacific Ocean warmed and expanded, intensifying barriers to gene flow. The fragmentation of a widespread ancestral species previously connected by long-distance gene flow (‘soft vicariance’) coincident with changing oceanographic conditions may be a common theme in the evolution of Emerita species and in other highly dispersive taxa. Highly dispersive species may differentiate because of, not despite, the dynamic oceanographic setting.

Aim We reconstructed the phylogeny of the lichen genus Nephroma (Peltigerales) to assess the relationships of species endemic to Macaronesia. We estimated dates of divergences to test the hypothesis that the species arose in Macaronesia (neo-endemism) versus the oceanic archipelagos serving as refugia for formerly widespread taxa (palaeo-endemism). Location Cosmopolitan with a special focus on the archipelagos of the Azores, Madeira and the Canary Islands. Methods DNA sequences were obtained from 18 species for three loci and analysed using maximum parsimony, maximum likelihood and Bayesian inferences. Divergence dates were estimated for the internal transcribed spacer (ITS)-based phylogeny using a relaxed molecular clock. Reconstruction of the ancestral geographical range was conducted using the Bayesian 50% majority rule consensus tree under a parsimony method. Results The backbone phylogenetic tree was fully supported, with Nephroma plumbeum as sister to all other species. Four strongly supported clades were detected: the Nephroma helveticum, the N. bellum, the N. laevigatum and the N. parile clades. The latter two share a common ancestor and each includes a widespread Holarctic species (N. laevigatum and N. parile, respectively) and all species endemic to Macaronesia. The data suggest a neo-endemic origin of Macaronesian taxa, a recent range expansion from Macaronesia of both widespread species, a range expansion limited to the Mediteranean Basin and south-western Europe for another taxon, and a long dispersal event that resulted in a speciation event in the western parts of North America. Main conclusions The Macaronesian endemic species belong to two sister clades and originated from a most recent common ancestor (MRCA) shared with one widely distributed taxon, either N. parile or N. laevigatum. Estimates of the mean divergence dates suggest that the endemics originated in the archipelagos after the rise of the volcanic islands, along with the ancestor to the now widespread species, which probably expanded their range beyond Macaronesia via long-distance dispersal. This study provides the first phylogenetic evidence of Macaronesian neo-endemism in lichenized fungi and provides support for the hypothesis that oceanic islands may serve as a source for the colonization of continents. However, further data are needed to properly assess the alternative hypothesis, namely colonization from western North America.

Molecular detection of blood protozoa and identification of black flies of the Simulium varicorne species group (Diptera: Simuliidae) in Thailand

Phylogeny and biogeography of the African burrowing snake subfamily Aparallactinae (Squamata: Lamprophiidae)

Inferring habitat-suitability areas with ecological modelling techniques and GIS: A contribution to assess the conservation status of Vipera latastei

The Cape Floristic Region (CFR) of South Africa is renowned for its botanical diversity, but the evolutionary origins of this diversity remain controversial. Both neutral and adaptive processes have been implicated in driving diversification, but population-level studies of plants in the CFR are rare. Here, we investigate the limits to gene flow and potential environmental drivers of selection in Protea repens L. (Proteaceae L.), a widespread CFR species. We sampled 19 populations across the range of P. repens and used genotyping by sequencing to identify 2066 polymorphic loci in 663 individuals. We used a Bayesian FST outlier analysis to identify single-nucleotide polymorphisms (SNPs) marking genomic regions that may be under selection; we used those SNPs to identify potential drivers of selection and excluded them from analyses of gene flow and genetic structure. A pattern of isolation by distance suggested limited gene flow between nearby populations. The populations of P. repens fell naturally into two or three groupings, which corresponded to an east-west split. Differences in rainfall seasonality contributed to diversification in highly divergent loci, as do barriers to gene flow that have been identified in other species. The strong pattern of isolation by distance is in contrast to the findings in the only other widespread species in the CFR that has been similarly studied, while the effects of rainfall seasonality are consistent with well-known patterns. Assessing the generality of these results will require investigations of other CFR species.

Genetic molecular markers to accelerate genetic gains in crops.

Labeo umbratus (Smith, 1841) is a widespread species with populations distributed across isolated southern African river systems. Given that cryptic lineages have been detected in freshwater fishes with a similar distribution, a phylogeographic study of L. umbratus was conducted, considering populations sampled from nine currently isolated river systems between 2008 and 2013. Analyses of mitochondrial DNA (cyt b) and nuclear DNA (S7) sequence data demonstrated that two unique lineages occur in the west-flowing Orange River and south-flowing drainages, respectively. The southern lineage was further divided into three sublineages: one restricted to the Gouritz River, the second largely confined to the Gamtoos River and the last distributed across catchments to the east (the Sundays, Bushmans, Great Fish, Keiskamma, Buffalo and Nahoon rivers). The Great Escarpment and deep incisions along the south coast were identified as potentially influencing the geographic genetic structure of this species. For conservation purposes and pending future taxonomic assessment, the two major lineages were identified as Evolutionarily Significant Units, and Management Units were identified within the southern lineage.

The diversity of Philippine amphibians and reptiles has increased over the last few decades, in part due to re-evaluation of species formerly believed to be widespread. Many of these investigations of widespread species have uncovered multiple closely related cryptic lineages comprising species complexes, each restricted to individual Pleistocene Aggregate Island Complexes (PAICs). One group in particular for which widespread cryptic diversity has been common is the clade of Philippine skinks of the genus Brachymeles. Recent phylogenetic studies of the formerly recognized widespread species Brachymeles bonitae have indicated that this species is actually a complex distributed across several major PAICs and smaller island groups in the central and northern Philippines, with numerous species that exhibit an array of digit loss and limb reduction patterns. Despite the recent revisions to the B. bonitae species complex, studies suggest that unique cryptic lineages still exist within this group. In this paper, we resurrect the species Brachymeles burksi Taylor 1917, for a lineage of non-pentadactyl, semi-fossorial skink from Mindoro and Marinduque islands. First described in 1917, B. burksi was synonymized with B. bonitae in 1956, and has rarely been reconsidered since. Evaluation of genetic and morphological data (qualitative traits, meristic counts, and mensural measurements), and comparison of recently-obtained specimens to Taylor’s original description support this species’ recognition, as does its insular distribution on isolated islands in the central portions of the archipelago. Morphologically, B. burksi is differentiated from other members of the genus based on a suite of unique phenotypic characteristics, including a small body size, digitless limbs, a high number of presacral vertebrae, the absence of auricular openings, and discrete (non-overlapping) meristic scale counts. The recognition of this central Philippine species further increases the diversity of non-pentadactyl members of the B. bonitae complex, and reinforces the biogeographic uniqueness of the Mindoro faunal region. KEYWORDS: biodiversity, endemism, faunal region, fossoriality, limb reduction

Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa