From Gondwana to Europe: inferring the origins of Mediterranean Macrothele spiders (Araneae : Hexathelidae) and the limits of the family Hexathelidae

Ancient origins of the Mediterranean trap-door spiders of the family Ctenizidae (Araneae, Mygalomorphae)

Our goal was to infer the phylogenetic relationships and historical biogeography of the genus Dryopteris with a focus on taxa in sub-Saharan Africa and neighboring islands. In general, little is known about the relationships between African fern species and their congeners in other geographic regions, and our aim was to determine whether the sub-Saharan African species of Dryopteris are monophyletic and evolved within Africa or arrived there via repeated dispersals into Africa from other regions. We obtained sequence data for five chloroplast markers from 214 species of Dryopteris and 18 outgroups. We performed phylogenetic and molecular dating analyses using a Bayesian relaxed clock method in BEAST with fossil and secondary calibration points and estimated ancestral ranges for the genus globally by comparing multiple models in BioGeoBEARS. We found that 22 of 27 accessions of sub-Saharan African Dryopteris belong to a large clade of 31 accessions that also includes taxa from Indian and Atlantic Ocean islands. Additional accessions of taxa from our regions of interest have Asian, Hawaiian, European, or North American species as their closest relatives. The majority of sub-Saharan African Dryopteris species are descended from a shared common ancestor that dispersed to Africa from Asia approximately 10 Ma. There have been subsequent dispersal events from the African mainland to islands in the Atlantic and Indian Oceans, including Madagascar. Several additional species are estimated to have descended from ancestors that reached Africa via separate events over the last roughly 20 million years.

Phylogenetic Analysis of HIV-1 CRF65_CPX Reveals Yunnan Province Is Still a Source Contributing to the Spread of HIV-1 in China

Even though marsupials are taxonomically less diverse than placentals, they exhibit comparable morphological and ecological diversity. However, much of their fossil record is thought to be missing, particularly for the Australasian groups. The more than 330 living species of marsupials are grouped into three American (Didelphimorphia, Microbiotheria, and Paucituberculata) and four Australasian (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelemorphia) orders. Interordinal relationships have been investigated using a wide range of methods that have often yielded contradictory results. Much of the controversy has focused on the placement of Dromiciops gliroides (Microbiotheria). Studies either support a sister-taxon relationship to a monophyletic Australasian clade or a nested position within the Australasian radiation. Familial relationships within the Diprotodontia have also proved difficult to resolve. Here, we examine higher-level marsupial relationships using a nuclear multigene molecular data set representing all living orders. Protein-coding portions of ApoB, BRCA1, IRBP, Rag1, and vWF were analyzed using maximum parsimony, maximum likelihood, and Bayesian methods. Two different Bayesian relaxed molecular clock methods were employed to construct a timescale for marsupial evolution and estimate the unrepresented basal branch length (UBBL). Maximum likelihood and Bayesian results suggest that the root of the marsupial tree is between Didelphimorphia and all other marsupials. All methods provide strong support for the monophyly of Australidelphia. Within Australidelphia, Dromiciops is the sister-taxon to a monophyletic Australasian clade. Within the Australasian clade, Diprotodontia is the sister taxon to a Notoryctemorphia + Dasyuromorphia + Peramelemorphia clade. Within the Diprotodontia, Vombatiformes (wombat + koala) is the sister taxon to a paraphyletic possum group (Phalangeriformes) with kangaroos nested inside. Molecular dating analyses suggest Late Cretaceous/Paleocene dates for all interordinal divergences. All intraordinal divergences were placed in the mid to late Cenozoic except for the deepest splits within the Diprotodontia. Our UBBL estimates of the marsupial fossil record indicate that the South American record is approximately as complete as the Australasian record.

The uplift and final connection of the Central American land bridge is considered the major event that allowed biotic exchange between vertebrate lineages of northern and southern origin in the New World. However, given the complex tectonics that shaped Middle America, there is still substantial controversy over details of this geographical reconnection, and its role in determining biogeographic patterns in the region. Here, we examine the phylogeography of Bothrops asper, a widely distributed pitviper in Middle America and northwestern South America, in an attempt to evaluate how the final Isthmian uplift and other biogeographical boundaries in the region influenced genealogical lineage divergence in this species. We examined sequence data from two mitochondrial genes (MT-CYB and MT-ND4) from 111 specimens of B. asper, representing 70 localities throughout the species’ distribution. We reconstructed phylogeographic patterns using maximum likelihood and Bayesian methods and estimated divergence time using the Bayesian relaxed clock method. Within the nominal species, an early split led to two divergent lineages of B. asper: one includes five phylogroups distributed in Caribbean Middle America and southwestern Ecuador, and the other comprises five other groups scattered in the Pacific slope of Isthmian Central America and northwestern South America. Our results provide evidence of a complex transition that involves at least two dispersal events into Middle America during the final closure of the Isthmus.

1. The aquatic Coleoptera of some major wetlands in the Mediterranean coast of Spain were surveyed, with the aim of assessing their conservation value and the status of some coastal species in the Iberian Peninsula. 2. Classification of 59 species from 13 sites between the deltas of the rivers Ebro and Llobregat using TWINSPAN suggested that water origin and amount and structure of vegetation were major factors influencing the composition of the coastal water beetle communities. 3. The Ebro delta is considered to be a key biogeographical area, being the limit of the distribution of a number of north African and European species. Coastal sites in the Iberian peninsula sustain the only known populations in continental Europe of at least three Ethiopian species, although two of them may have become extinct. Some European species known to have reached the north of Catalonia were also considered to be possibly extinct in the Iberian peninsula owing to the destruction of their habitats. Three circum-Mediterranean coastal species were recorded for the first time in the Iberian peninsula, one of them in a genus new to its fauna. 4. Despite the scarcity of true endemics—the result of the recent geological origin and the temporal dynamics of coastal systems—some species were exclusive to temporary habitats, and had very restricted distributions. 5. Although most of the areas studied have some form of protection, this is mainly focused in large, permanent lagoons and on the vertebrate fauna. The need to include marginal areas and invertebrates in the protection plans for the area is stressed.

The aquatic Coleoptera of some major wetlands in the Mediterranean coast of Spain were surveyed, with the aim of assessing their conservation value and the status of some coastal species in the Iberian Peninsula. 2. Classification of 59 species from 13 sites between the deltas of the rivers Ebro and Llobregat using TWINSPAN suggested that water origin and amount and structure of vegetation were major factors influencing the composition of the coastal water beetle communities. 3. The Ebro delta is considered to be a key biogeographical area, being the limit of the distribution of a number of north African and European species. Coastal sites in the Iberian peninsula sustain the only known populations in continental Europe of at least three Ethiopian species, although two of them may have become extinct. Some European species known to have reached the north of Catalonia were also considered to be possibly extinct in the Iberian peninsula owing to the destruction of their habitats. Three circum-Mediterranean coastal species were recorded for the first time in the Iberian peninsula, one of them in a genus new to its fauna. 4. Despite the scarcity of true endemics-the result of the recent geological origin and the temporal dynamics of coastal systems-some species were exclusive to temporary habitats, and had very restricted distributions. 5. Although most of the areas studied have some form of protection, this is mainly focused in large, permanent lagoons and on the vertebrate fauna. The need to include marginal areas and invertebrates in the protection plans for the area is stressed.

Molecular clocks: Closing the gap between rocks and clocks

AimHow disjunct distributions arise and why organisms differ in diversification patterns remain some of the most compelling fundamental questions in biogeography. We carry out phylogeographical analyses of the pantropical liverwort genus Ceratolejeunea to identify its geographical origin and the dispersal routes by which it gained its Neotropical‐African disjunction. Furthermore, we investigate whether there is geographical structure in Ceratolejeunea on islands and whether island diversity is a result of radiations or recurrent migration.LocationAmerica, Africa and Australasia.MethodsSequences of two chloroplast regions (trnL–F, rbcL) and the nuclear ribosomal ITS region were obtained for 55 accessions of 20 species to explore the phylogeny, divergence times and ancestral areas of Ceratolejeunea. The phylogeny was reconstructed using maximum likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method and fossil and secondary calibrations. Ancestral areas were estimated using BioGeoBEARS.ResultsCeratolejeunea likely originated in the Neotropics during the Palaeogene (42.2 Ma, 95% HPD: 22.2–64.8) and the initial diversification of its crown group took place between the Eocene and Miocene (25.5 Ma, 95% HPD: 16.6–35.8). Although boreotropical migration and subsequent extinction in northern regions cannot be rejected, the observed disjunctions are best explained by four transoceanic dispersal events from the Neotropics to Africa during the late Oligocene to Pleistocene. Geographical structure is prevalent on islands, particularly in the C. cornuta complex. Three species and the subgenus Ceratolejeunea are recovered as paraphyletic.Main conclusionsWidespread paraphyly and sister group relationships between disjunct taxa indicate an important role of cryptic speciation and transoceanic dispersal with subsequent genetic differentiation in the evolution of Ceratolejeunea. On islands, recurrent migration, rather than radiation, has shaped bryophyte diversity.

BackgroundThe island of Madagascar and surrounding volcanic and coralline islands are considered to form a biodiversity hotspot with large numbers of unique taxa. The origin of this endemic fauna can be explained by two different factors: vicariance or over-water-dispersal. Deciphering which factor explains the current distributional pattern of a given taxonomic group requires robust phylogenies as well as estimates of divergence times. The lineage of Indian Ocean scops-owls (Otus: Strigidae) includes six or seven species that are endemic to Madagascar and portions of the Comoros and Seychelles archipelagos; little is known about the species limits, biogeographic affinities and relationships to each other. In the present study, using DNA sequence data gathered from six loci, we examine the biogeographic history of the Indian Ocean scops-owls. We also compare the pattern and timing of colonization of the Indian Ocean islands by scops-owls with divergence times already proposed for other bird taxa.ResultsOur analyses revealed that Indian Ocean islands scops-owls do not form a monophyletic assemblage: the Seychelles Otus insularis is genetically closer to the South-East Asian endemic O. sunia than to species from the Comoros and Madagascar. The Pemba Scops-owls O. pembaensis, often considered closely related to, if not conspecific with O. rutilus of Madagascar, is instead closely related to the African mainland O. senegalensis. Relationships among the Indian Ocean taxa from the Comoros and Madagascar are unresolved, despite the analysis of over 4000 bp, suggesting a diversification burst after the initial colonization event. We also highlight one case of putative back-colonization to the Asian mainland from an island ancestor (O. sunia). Our divergence date estimates, using a Bayesian relaxed clock method, suggest that all these events occurred during the last 3.6 myr; albeit colonization of the Indian Ocean islands were not synchronous, O. pembaensis diverged from O. senegalensis about 1.7 mya while species from Madagascar and the Comoro diverged from their continental sister-group about 3.6 mya. We highlight that our estimates coincide with estimates of diversification from other bird lineages.ConclusionOur analyses revealed the occurrence of multiple synchronous colonization events of the Indian Ocean islands by scops-owls, at a time when faunistic exchanges involving Madagascar was common as a result of lowered sea-level that would have allowed the formation of stepping-stone islands. Patterns of diversification that emerged from the scops-owls data are: 1) a star-like pattern concerning the order of colonization of the Indian Ocean islands and 2) the high genetic distinctiveness among all Indian Ocean taxa, reinforcing their recognition as distinct species.

Horse flies, family T abanidae, are the most diverse family‐level clade of bloodsucking insects, but their phylogeny has never been thoroughly explored using molecular data. Most adult female T abanidae feed on nectar and on the blood of various mammals. Traditional horse fly classification tends towards large heterogeneous taxa, which impede much‐needed taxonomic work. To guide renewed efforts in the systematics of horse flies and their relatives, we assembled a dataset of 110 exemplar species using nucleotide data from four genes—mitochondrial CO1 , and nuclear 28S , CAD and AATS . All commonly recognized tribes in T abanidae are represented, along with outgroups in T abanomorpha. The phylogeny is reconstructed using Bayesian inference, and divergence times are estimated using B ayesian relaxed clock methods with time constraints from tabanid fossils. Our results show A thericidae strongly supported as the lineage most closely related to T abanidae, and P angoniinae and T abaninae as monophyletic lineages. However, C hrysopsinae is nonmonophyletic, with strong support for both a nonmonophyletic B ouvieromyiini and for R hinomyzini as sister to T abaninae. Only the tribes P hilolichini, C hrysopsini, R hinomyzini and H aematopotini are recovered as monophyletic, although S cionini is monophyletic with exclusion of the peculiar genus Goniops A ldrich. Mycteromyia P hilippi and Adersia A usten, two enigmatic genera sometimes placed in separate family‐level groups, are recovered inside P angoniini and C hrysopsini, respectively. Several species‐rich genera are not recovered as monophyletic, including Esenbeckia R ondani , Silvius M eigen, Dasybasis M acquart and Tabanus L. Tabanidae likely originated in the C retaceous, and all major extant groups were present by the early P alaeogene. This newly revised phylogenetic framework for T abanidae forms the basis for a new assessment of tabanid diversification and provides context for understanding the evolution of trophic specialization in horse flies.

Nesticidae is a small family of spiders with a worldwide distribution that includes 15 genera and 272 described species. Seven genera and 56 species are known from Europe, distributed from the Iberian Peninsula to the Caucasus and the Ural Mountains. Most of these European species are cave dwellers and many of them are troglobites. In this study we present the first molecular phylogeny of the family Nesticidae in Europe with a wide geographical sampling across the continent. In our analysis the European nesticid fauna is well represented, including six genera and 40 of the 56 currently accepted species including the type species of all sampled genera. We have included in the analysis representatives of the North American and Asian fauna to test the monophyly of the European species and the phylogenetic relationships of European lineages. Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference. As part of our Bayesian analyses, we also dated the phylogeny using two approaches, one based only on fossil calibrations and one that included an additional biogeographical constraint.Our results show paraphyly of the European nesticids with respect to the Asian and North American taxa. We recover four main lineages within Europe. These four European lineages and all European genera have 100% bootstrap support and high posterior probability support in the BEAST2 analysis. The Typhlonesticus lineage is the earliest branching clade present in Europe and includes seven species, the five currently accepted species plus T. parvus from Bosnia and Herzegovina and T. silvestrii from western North America. The Eastern lineage includes the genus Aituaria and is the sister group of the Asian genera Nesticella and Wraios. The Domitius lineage is likely the sister group of the Central European lineage and spreads over the Iberian and Italian peninsulas. Finally, the Central European lineage includes three genera: Kryptonesticus, distributed from the karstic massifs of the Balkan Peninsula to Turkey, Nesticus with a single synanthropic species N. cellulanus and Carpathonesticus, exclusive to the Carpathian Mountains. With the exception of the genus Typhlonesticus, all European genera show an allopatric distribution (except for the two European synanthropic species). The results obtained in this study together with the revision of the original descriptions, redescriptions, and illustrations, lead us to propose 11 nomenclatural changes (new combinations) concerning the genera Typhlonesticus, Nesticus and Carpathonesticus.

A timescale and phylogeny for “Bandicoots” (Peramelemorphia: Marsupialia) based on sequences for five nuclear genes

Udea Guenée, 1845, comprising more than 200 species, predominantly occurs in temperate Eurasia and the New World, with few representatives on the southern continents of the Old World. We present a fi rst phylogenetic analysis for the genus, mainly based on European species. We applied Bayesian and Maximum Parsimony approaches to a combined dataset of coxI (1,415 bp) and wingless (363 bp) sequences as well as morphological characters. The analysis of the concatenated dataset partitions with Bayesian inference yielded a hypothetical tree with 26 well supported (posterior probability ≥ 0.95) monophyla. A clade including the genera Deana, Mnesictena and Udeoides from the southern continents of the Old World is found as sister group to Udea. European Udea species do not form a monophyletic group in itself. There are four monophyla found within European Udea, the ferrugalis, itysalis, alpinalis, and numeralis species groups. These are well supported by molecular and morphological data. According to morphology, all four species groups have representatives also in other parts of the Holarctic region. Our data support the hypothesis that all Udea species endemic to oceanic islands in the Atlantic and Pacifi c belong to the ferrugalis group and all those endemic to the European Alps to the alpinalis group. Our data imply that the ancestors of two island species (Udea azorensis, U. delineatalis) have colonised the respective islands via ocean surface currents. Altogether, we are able to place 54 of the 213 described Udea species into species groups.

AimIndian biodiversity is concentrated in the wet zone, which is disjunctly distributed in the north‐east and in the peninsular Western and Eastern Ghats. The Eastern Ghats region is smaller and less well explored biologically and the affinities and origins of its biota poorly understood. Our aim was to assess whether divergence between east and west lineages might have been caused by fragmentation of the wet zone during Pleistocene climatic fluctuations, by Late Miocene wet‐zone contraction or by more ancient events. We present the first dated phylogenetic test of these alternatives by inferring relationships and dating divergences within a wet‐zone‐restricted lineage endemic to the Eastern and Western Ghats.LocationThe Eastern and Western Ghats regions of peninsular India.MethodsMolecular genetic data (one nuclear and four mitochondrial genes) were newly generated for the only known Eastern Ghats teresomatan caecilian amphibian (Gegeneophis orientalis) and the only Western Ghats congener (G. pareshi) for which molecular data were not previously available. Phylogenetic relationships were inferred for Indian indotyphlids using maximum likelihood and Bayesian inference methods. Divergence times within the inferred phylogeny were estimated using a Bayesian relaxed clock method, with the Seychelles versus Indian indotyphlid divergence calibrated based on the geological separation of their respective continental land masses.ResultsThe single Eastern Ghats species ofGegeneophisis sister to all other (Western Ghats)Gegeneophis. The basalmost (and east–west) split withinGegeneophislikely occurred > 35 Ma.Main conclusionsDivergence between Eastern and Western GhatsGegeneophisis too ancient to have been caused by wet‐zone contraction in the Miocene or by Pleistocene climatic fluctuations. Our results are consistent with a relatively ancient origin of wet‐zone lineages in the Eastern Ghats and a lack of gene flow between Eastern and Western GhatsGegeneophisfor tens of millions of years.