Phylogenomics reconciles molecular data with the rich fossil record on the origin of living turtles.

Although a consensus exists that all living turtles fall within either Pleurodira or Cryptodira clades, estimating when these lineages split is still under debate. Most molecular studies date the split in the Triassic Period, whereas a Jurassic age is unanimous among morphological studies. Each hypothesis implies different paleobiogeographical scenarios to explain early turtle evolution. Here we explored the rich turtle fossil record with the Fossilized Birth-Death (FBD) and the traditional node dating (ND) methods using complete mitochondrial genomes (147 taxa) and a set of nuclear orthologs with over 10 million bp (25 taxa) to date the major splits in Testudines. Our results support an Early Jurassic split (191-182 Ma) for the crown Testudines with great consistency across different dating methods and datasets, with a narrow confidence interval. This result is independently supported by the oldest fossils of Testudines that postdate the Middle Jurassic (174 Ma), which were not used for calibration in this study. This age coincides with the Pangaea fragmentation and the formation of saltwater barriers such as the Atlantic Ocean and the Turgai Strait, supporting that diversification in Testudines was triggered by vicariance. Our ages of the splits in Pleurodira coincide with the geologic events of the Late Jurassic and Early Cretaceous. Conversely, the early Cryptodira radiation remained in Laurasia, and its diversification ensued as all its major lineages expanded their distribution into every continent during the Cenozoic. We provide the first detailed hypothesis of the evolution of Cryptodira in the Southern Hemisphere, in which our time estimates are correlated with each contact between landmasses derived from Gondwana and Laurasia. Although most South American Cryptodira arrived through the Great American Biotic Interchange, our results indicate that the Chelonoidis ancestor probably arrived from Africa through the chain islands of the South Atlantic during the Paleogene. Together, the presence of ancient turtle diversity and the vital role that turtles occupy in marine and terrestrial ecosystems underline South America as a chief area for conservation.

Bootstrap and Rogue Identification Tests for Phylogenetic Analyses.

Most phylogenetic tree-generating programs produce a fully dichotomous phylogenetic tree. However, as different markers may produce distinct topologies for the same set of organisms, topological tests are used to estimate the statistical reliability of the clades. In this protocol, we provide step-by-step instructions on how to perform the widely used bootstrap test using MEGA. However, a single unstable lineage, also known as a rogue lineage, may decrease the bootstrap proportions in many branches of the tree. This occurs because rogue taxa tend to bounce between clades from one pseudo-replicate to the next, lowering bootstrap proportions for many correct clades. Thus, it is important to identify and exclude rogue taxa before initiating a final phylogenetic analysis; here, we provide this protocol using the RogueNaRok platform.

An African Origin of the Eurylaimides (Passeriformes) and the Successful Diversification of the Ground-Foraging Pittas (Pittidae).

The Eurylaimides is one of the few passerine groups with a pantropical distribution. In this study, we generated a multi-calibrated tree with 83% of eurylaimid species diversity based on 30 molecular loci. Particular attention was given to the monotypic Sapayoidae to reconstruct the biogeography of this radiation. We conducted several topological tests including nonoverlapping subsampling of the concatenated alignment and coalescent species tree reconstruction. These tests firmly placed the South American Sapayoidae as the sister group to all other Eurylaimides families (split at ∼28 Ma), with increasing branch support as highly variable sites were removed. This topology is consistent with the breakup of the insular connection between Africa and South America (Atlantogea) that took place between the middle Eocene and the early Oligocene. We recovered Africa as the cradle of the core Eurylaimides, and this result is supported by all African lineages corresponding to the oldest splits within each family in this group. Our timescale suggests that desertification and the uplift of the Tibetan Plateau caused a parallel divergence between African and Asian lineages in all major clades in the core Eurylaimides at 22-9 Ma. We also propose that the ground-foraging behavior in the Pittidae ancestor allowed the pitta lineage to thrive and coexist with the older arboreal lineages of the core Eurylaimides. In contrast, the diversification of pittas in Australia was likely hindered by direct competition with the endemic ground-foraging oscines that had been well established in that continent since the Eocene.

Mitochondrial genome of the Christmas tree worm Spirobranchus giganteus (Annelida: Serpulidae) reveals a high substitution rate among annelids.

Here we describe, for the first time, the mitochondrial genome of Spirobranchus giganteus (Annelida: Serpulidae) and compare it with all available annelid mitogenomes. The entire mitogenome has 22,058bp in length and bears 12 protein-coding genes (the ATP8 gene is missing), two rRNA, and 24 tRNA genes. The nucleotide composition and GC-skew are surprisingly different from those reported for other annelids. In addition, the pairwise genetic distances between the mitogenomes of S. giganteus and other annelids are higher than the distances for all annelid taxa analyzed. This result is consistent with a faster rate of mitochondrial sequence evolution in S. giganteus, which may explain the difficulty in obtaining PCR products with the available primers. The mitochondrial gene order of S. giganteus was remarkably different not only from that of the Sedentaria lineage, which includes S. giganteus, but also from the mitochondrial gene order of other major annelid lineages. The mitogenome of S. giganteus has no repetitive motifs despite its long control region (4769bp), but genes are shorter and have a lower AT content than other members of Annelida. Finally, we show that mitochondrial gene order rearrangements can directly correlate to variations in gene length.

The Gondwana Breakup and the History of the Atlantic and Indian Oceans Unveils Two New Clades for Early Neobatrachian Diversification.

The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand extant species. Here, we propose a new hypothesis for the historical aspects of the neobatrachian evolution with a formal biogeographical analysis. We selected 12 genes for 144 neobatrachian genera and four archaeobatrachian outgroups and performed a phylogenetic analysis using a maximum likelihood algorithm with the rapid bootstrap test. We also estimated divergence times for major lineages using a relaxed uncorrelated clock method. According to our time scale, the diversification of crown Neobatrachia began around the end of the Early Cretaceous. Our phylogenetic tree suggests that the first split of Neobatrachia is related to the geological events in the Atlantic and Indian Oceans. Hence, we propose names for these clades that indicate this connection, i.e., Atlanticanura and Indianura. The Atlanticanura is composed of three major neobatrachian lineages: Heleophrynidae, Australobatrachia and Nobleobatrachia. On the other hand, the Indianura consists of two major lineages: Sooglossoidea and Ranoides. The biogeographical analysis indicates that many neobatrachian splits occurred as a result of geological events such as the separation between South America and Africa, between India and the Seychelles, and between Australia and South America.

A Paleogene origin for crown passerines and the diversification of the Oscines in the New World.

In this study, we present a detailed family-level phylogenetic hypothesis for the largest avian order (Aves: Passeriformes) and an unmatched multi-calibrated, relaxed clock inference for the diversification of crown passerines. Extended taxon sampling allowed the recovery of many challenging clades and elucidated their position in the tree. Acanthisittia appear to have diverged from all other passerines at the early Paleogene, which is considerably later than previously suggested. Thus, Passeriformes may be younger and represent an even more intense adaptive radiation compared to the remaining avian orders. Based on our divergence time estimates, a novel hypothesis for the diversification of modern Suboscines is proposed. According to this hypothesis, the first split between New and Old World lineages would be related to the severing of the Africa-South America biotic connection during the mid-late Eocene, implying an African origin for modern Eurylaimides. The monophyletic status of groups not recovered by any subsequent study since their circumscription, viz. Sylvioidea including Paridae, Remizidae, Hyliotidae, and Stenostiridae; and Muscicapoidea including the waxwing assemblage (Bombycilloidea) were notable topological findings. We also propose possible ecological interactions that may have shaped the distinct Oscine distribution patterns in the New World. The insectivorous endemic Oscines of the Americas, Vireonidae (Corvoidea), Mimidae, and Troglodytidae (Muscicapoidea), probably interfered with autochthonous Suboscines through direct competition. Thus, the Early Miocene arrival of these lineages before any other Oscines may have occupied the few available niches left by Tyrannides, constraining the diversification of insectivorous Oscines that arrived in the Americas later. The predominantly frugivorous-nectarivorous members of Passeroidea, which account for most of the diversity of New World-endemic Oscines, may not have been subjected to competition with Tyrannides. In fact, the vast availability of frugivory niches combined with weak competition with the autochthonous passerine fauna may have been crucial for passeroids to thrive in the New World.

A molecular phylogeny for the order Clathrinida rekindles and refines Haeckel's taxonomic proposal for calcareous sponges.

Most biological groups are still longing for a phylogenetically sound taxonomic organization. In this article, we aimed to verify the consistency of morphological characters in calcarean sponges of the well-known non-monophyletic order Clathrinida using a molecular phylogeny. For this we included 50 species, including six type species, currently assigned to eight different genera. A maximum likelihood topology was generated for the nuclear ITS marker using the General Time Reversible model and the bootstrap reliability test. Our topology indicated 10 clathrinid clades that included species with consistent morphological characters. In the present study, we defined nine of these clades as clathrinid genera, including four newly described and two newly diagnosed genera. Recent studies have indicated that not much phylogenetic information may be found in morphology, but our findings contradict this general assertion. Our study confirms the suitability of skeleton and body anastomosis as valid characters in a phylogenetically sound taxonomy for the order. Interestingly, we have also found that, apart from the Calcinea/Calcaronea split and a few minor details, Haeckel's original proposal is remarkably similar to our own, which was based on a molecular phylogeny 140 years later.

O caramujo exótico invasor Achatina fulica (Stylommatophora, Mollusca) no Estado do Rio de Janeiro (Brasil): situação atual / The exotic invasive snail Achatina fulica (Stylommatophora, Mollusca) in the State of Rio de Janeiro (Brazil): current status

O caramujo africano invasor Achatina fulica foi introduzido no Brasil a partir de Estados do Sul e Sudeste em pelo menos três ocasiões. Atualmente sua distribuição já abrange 24 dos 26 estados e o Distrito Federal. Populações densas dessa espécie vêm causando incômodos à populações humanas, danos à jardins e pequenas plantações, além de atuarem como transmissoras de duas zoonoses (angiostrongilíase abdominal e meningoencefalite eosinofílica) e outras parasitoses de interesse veterinário. No presente estudo, apresentamos novas ocorrências de A. fulica no Estado do Rio de Janeiro (Brasil) assim como dados sobre as larvas de nematódeos de interesse médico e veterinário encontradas em exemplares dessa espécie coletados neste estado. A. fulica está presente em 26 municípios adicionais em relação aos dados obtidos em 2006, ano do último levantamento, representando um aumento de 50 por cento no número de municípios infestados. Apenas nove dos 92 municípios do estado ainda não registram a presença dessa espécie. Larvas dos nematódeos Aelurostrongylus abstrusus, Rhabditis sp. e Strongyluris-like, todas com importância veterinária, foram encontradas em exemplares de A. fulica de onze municípios. A rápida dispersão de A. fulica evidencia a necessidade de planos de manejo contínuos e eficientes em todo o país visando o controle efetivo dessa invasão. A erradicação de A. fulica é pouco provável devido ao nível atual de infestação.

The invasive African snail Achatina fulica was introduced in Brazil through South and Southeast States in at least three separate occasions. A. fulica is currently present in 24 out of 26 Brazilian States and in the Federal District. Dense populations of A. fulica are nuisance to human populations and pest to gardens and small crops. Such populations also act in the transmission of two zoonosis (abdominal angiostrongyliasis and eosinophilic meningitis) as well as other parasitosis of veterinary importance. Here, we report new records of A. fulica and of nematode larvae of medical and veterinary importance found in this snail in the state of Rio de Janeiro (Brazil). A. fulica is present in 26 additional municipalities of the state when compared to the information obtained in 2006, year of the last census. This result represents an increase of 50 percent in the number of municipalities infested. Only nine out of the 92 municipalities of the state have not yet registered the presence of this invasive species. Nematode larvae of Aelurostrongylus abstrusus, Rhabditis sp. e Strongyluris-like, all of veterinary importance, have been registered in A. fulica individuals from eleven municipalities of the state. The rapid range expansion of A. fulica calls attention for the need of a general and continuous management plan throughout the country in order to effectively control the invasion. The current level of infestation makes a full eradication unlikely.