Southern Clade Research Articles

Phylogenetic divergence and population genetics of the hydrothermal vent annelid genus Hesiolyra along the East Pacific Rise: Reappraisal using multi‐locus data

AbstractAimMaintaining genetic connectivity is crucial for species that inhabit the disjunct and unstable deep‐sea hydrothermal vents. We aimed to re‐assess the connectivity of the annelid genus Hesiolyra distributed at hydrothermal vents along the East Pacific Rise (EPR). A previous study detected a major clade among five Hesiolyra populations spanning from 13°N to 21°S and a minor sympatric southern clade with ~1% divergence from the major clade. However, this study was based on a short locus of 366‐bp COI gene, which might not contain sufficient informative sites.LocationEast Pacific Rise.MethodsWe sequenced 188 specimens of Hesiolyra from five hydrothermal vent fields along the East Pacific Rise for six mitochondrial and two nuclear loci to infer their genetic divergence, population diversity and gene flow.ResultsWe found a minor southern clade (Hesiolyra aff. bergi) which was genetically distinct from Hesiolyra bergi sensu stricto for all gene markers explored except 16S. We also found shared genotypes between H. bergi and H. aff. bergi likely resulted from incomplete lineage sorting. For H. bergi s.s., we found a low but fixed divergence between the north and south EPR populations. We estimated the northern and southern metapopulations of H. bergi s.s. split ~0.45 Mya (HPD: 0.27–0.74 Mya). The northern metapopulation had a higher haplotype diversity than the southern metapopulation, indicating historical gene flow and loss of genetic diversity in the southern clade.Main conclusionsWe confirmed that the equatorial dispersal filter observed previously on several other vent species also applies to H. bergi. Our results highlight the power of the multi‐locus approach in revealing the divergence and population genetic history of marine species with strong dispersal capabilities, indicating that the NEPR and the SEPR should be considered as separate biogeographic regions in environmental management and biological conservation.

A new species of land planarian split off from Luteostriata ernesti (Leal-Zanchet & Froehlich, 2006) based on an integrative approach

ABSTRACT The genus Luteostriata Carbayo, 2010, currently comprises 10 species distributed in southeastern and southern Brazil. Species of this genus represent a taxonomic challenge because many have very similar external and internal features. Some species were described based on specimens from many localities using anatomical and histological features without phylogenetical analyses, such as Luteostriata ernesti, known from various localities in southeastern and southern Brazil. We conducted an integrative taxonomic approach of southeastern and southern specimens of L. ernesti, performing morphological analyses and using two molecular markers. Our results reveal that there are at least two clades (southeastern and southern) under the designation L. ernesti, and phylogenetic analyses show that they are not sister groups. Thus, we took the taxonomic decision to describe a new species, Luteostriata dissimilis Iturralde & Leal-Zanchet, sp. nov., which is split off from L. ernesti based on specimens of the southern clade. The phylogenetic analyses suggest a close relationship between Luteostriata dissimilis and Luteostriata muelleri and indicate that Luteostriata ernesti is more closely related to Luteostriata caissara. Our results also indicate that species delineation may be the first approach to understanding the diversity and distribution of species in this genus and that a complete taxonomic revision of Luteostriata species is necessary. http://www.zoobank.org/urn:lsid:zoobank.org:act:F83EE656-A491-493D-9F25-97413097D007

Taxonomic reappraisal of Hynobius tokyoensis, with description of a new species from northeastern Honshu, Japan (Amphibia: Caudata).

Previous phylogenetic studies based on mitochondrial DNA data have consistently suggested that Hynobius tokyoensis consists of two major clades, clade A (northern clade) and clade B (southern clade). In this study, we newly estimated their population genetic structure and phylogenetic relationships by nuclear SNPs, and the results suggested heterospecific relationships of the two mitochondrial clades, without present hybridization in between. They were also recognized as morphologically different. The type locality of H. tokyoensis is in Tokyo Prefecture, and therefore clade B corresponds to H. tokyoensis sensu stricto, leaving clade A without available scientific name. We, thus, describe the clade A from northeastern Kanto to southern Tohoku as a new species Hynobius sengokui. The new species is distinguished from H. tokyoensis by its relatively longer axilla-groin distance, shorter trunk, and deeper vomerine teeth series, and is estimated to have diverged from it during the late Pliocene.

A new species of Delma Gray 1831 (Squamata: Pygopodidae) from the Hunter Valley and Liverpool Plains of New South Wales.

The Striped Legless Lizard Delma impar Fischer 1882 occurs in grasslands of south-eastern Australia where it is sometimes sympatric with several congeners. Previous molecular analyses have revealed mitochondrial divergence between the northern and southern lineages of D. impar, but the status of a recently detected population assigned to the species in the Hunter Valley of New South Wales (NSW), 250 km north of other populations, remains unknown. Via morphological and molecular analyses across the known distribution of D. impar, we distinguish the population from the Hunter Valley, Liverpool Plains region as a unique taxon and describe this species as D. vescolineata sp. nov. The new species is divergent from D. impar in both nuclear and mitochondrial analysis, and differing facial scalation and colour patterning from the limited number of specimens available. The degree of mitochondrial and nuclear divergence between the previously identified northern and southern clades of D. impar is consistent with a single species. This is the first description of a Delma from south-eastern Australia since 1974, but the second new vertebrate taxon identified from the Hunter Valley region within a decade. Our research highlights our incomplete understanding of the biodiversity of the Hunter Valley region, despite its relative proximity to populous areas. The range of D. vescolineata sp. nov. is restricted and heavily overlaps with major habitat modification including mining and grazing, with no parks or reserves in this distribution protecting the species grassland habitat. Gathering more data to understand conservation status of this species should be a priority.

A cryptic species of Ensis (Bivalvia: Pharidae) from the southeastern Pacific coast revealed by geometric morphometric methods

A new cryptic species of Ensis from the Pacific coast of South America based on geometric morphometrics is revealed. Ensis macha (Molina, 1782) is one of the most important shellfish resources in South America. It was historically reported from San Matías Gulf, Argentina in the Atlantic Ocean to the Peruvian coast in the Pacific. A recent study analysed the intraspecific variation of this species along its distribution range and the genetic results indicated the presence of cryptic diversity. Two evolutionary clades were found: a southern clade (from cold-temperate waters) and a northern clade (from warm-temperate waters). New results based on geometric morphometrics supported the description of Ensis loboi n. sp. for the northern clade. The southern clade retains the name due to type locality of E. macha in Chiloé, Chile. The description of Ensis loboi n. sp. for the southeastern Pacific Ocean has important implications for future studies focused on fisheries management and biogeographical radiation of the group.

Testing Phylogeographic Hypotheses in Mepraia (Hemiptera: Reduviidae) Suggests a Complex Spatio-Temporal Colonization in the Coastal Atacama Desert

Simple SummaryMepraia is a blood-sucking bug endemic to Chile and a vector of the parasite that causes Chagas disease. Different colonization routes have been suggested for this bug; therefore, we tested different colonization routes using DNA sequences and bioinformatics approaches to select the most probable route. Our results suggest that, after the split of Triatoma, Mepraia divided into two main groups ~2.1 Mya. The northern group would have speciated between 1.7–1.4 Mya, giving rise to M. parapatrica, M. gajardoi and to a new, still undescribed lineage (Mepraia sp.). The southern group formed M. spinolai ~1.68 Mya. We suggest that Mepraia originated from the north-central Andes due to the last Andes uplift and hyperaridity. The hyperarid cycle would have separated the southern and northern groups. Then, within the northern group, colonization would have occurred from the centre to the north and south through corridors influenced by Pleistocene climatic changes. The habitat colonized by the southern clade led to only one species (M. spinolai). Fluctuations in climatic changes probably influenced speciation strongly in this kissing bug in the Atacama Desert.Mepraia is a genus (Triatominae) endemic to Chile and a vector of Trypanosoma cruzi. Alternative phylogeographic hypotheses have been suggested for Mepraia. We tested different colonization routes hypothesized using mitochondrial sequences and phylogeographic approaches to select the best-supported hypothesis. Our results suggest that, after the split from the sister genus Triatoma at ~4.3 Mya, Mepraia formed two main clades at ~2.1 Mya. The northern clade diverged from Mepraia sp. ~1.7 Mya, giving rise to M. parapatrica and M. gajardoi about ~1.4 Mya. The southern clade originated M. spinolai ~1.68 Mya. We suggest that Mepraia had an origin in the north-central Andes along with orogenic processes, reinforced by hyperaridity during the Pliocene. The hyperarid cycle would have separated the southern and northern clades. Then, in the northern clade, dispersal occurred north and south from the centre through corridors during the Pleistocene Climatic Oscillations. Climate changes may have induced a major speciation process in the Atacama Desert, while the more homogeneous habitat colonized by the southern clade led to only one, but structured, species.

Phylogeography of the Chocó Endemic Rainbow Characin (Teleostei: Rhoadsia)

South America's Chocó, part of the North Andean Pacific Slopes–Rio Atrato ecoregion, is a biodiversity hotspot with many disjunct rivers, yet phylogeographic and population genetic studies of the Chocó's aquatic species are scarce. Rhoadsia is a Chocó endemic freshwater fish genus with two recognized species: R. minor from the upper Esmeraldas River drainage and R. altipinna from the lower Guayas River drainage, Ecuador. Little is known about the evolutionary history of Rhoadsia, and due to morphological similarities, the validity of the two nominal species has been questioned. We conducted a phylogeographic study using two mitochondrial genes and 12 microsatellite markers to examine the evolutionary history of Rhoadsia and the validity of its two species. Samples collected in drainages throughout western Ecuador from sea level to 1260 m.a.s.l. were included, as were samples of species in the closely related genera Parastremma and Carlana from Colombia and Central America. Phylogenetic analysis of the mtDNA markers confirmed the reciprocal monophyly of a northern and southern clade, and the presence of mitochondrial haplotypes of both clades in the northern Guayas basin. Structure analysis with the microsatellite markers pointed to introgression at the border between the species ranges as the likely cause of the mixing of mitochondrial haplotypes in the northern Guayas. Bayesian analysis of the microsatellite data revealed the existence of ten populations throughout western Ecuador, divided into three main geographically segregated groups. Group I coincided with the northern distribution of R. minor, while groups II and III seemed to represent geographic subgroups of R. altipinna in the Guayas and southern coastal drainages. Patterns of genetic divergence and diversity support the recognition of multiple evolutionarily significant units within both species and allowed reevaluation of previously reported freshwater biogeographic zones in the Ecuadorian Chocó. This study provides a baseline for future studies examining freshwater biogeographical patterns throughout the Ecuadorian Chocó, as well as a phylogeographic framework to examine the genetic basis of adaptation of morphologically divergent populations of Rhoadsia inhabiting Andean mountain streams in the region.

Geographic Variation in the Green Rat Snake Senticolis triaspis (Squamata: Colubridae): Evidence from Mitochondrial DNA, Morphology, and Niche Modeling

Senticolis triaspis is a widespread polytypic colubrid snake that ranges from the southwestern United States southward along the Pacific Coast and part of the Atlantic Coast of Mexico to Costa Rica. Three subspecies have been described based on differences in color pattern and scutellation: S. t. intermedia, S. t. mutabilis, and S. t. triaspis. The last taxonomic revision was completed in 1960. Here, we present an integrative taxonomic analysis of geographic variation using multiple sources of evidence: mitochondrial DNA (817 bp ND4 from 62 samples), traditional morphology (meristic and mensural characters), geometric morphometrics of head shape, and bioclimatic estimates of environmental niche similarity. Molecular data revealed two deeply divergent mitochondrial lineages corresponding to northern and southern clades and eight well-supported clades within these two main groups. Head shape and niche models also showed north–south differences, while traditional morphological analyses did not discriminate among mtDNA lineages. Thus, our study suggests there are at least two candidate species within Senticolis triaspis based on the mtDNA divergence, differences in head shape, and non-overlapping ecological niches. However, we refrain from making taxonomic recommendations pending the addition of nuclear DNA sequence data, finer sampling at contact zones, and additional morphological data; these data are warranted to provide a more robust, stable species delimitation.

Filling the gaps: phylogeography of the self-fertilizing Kryptolebias species (Cyprinodontiformes: Rivulidae) along South American mangroves.

Mangrove killifishes of the genus Kryptolebias have been historically classified as rare because of their small size and cryptic nature. Major gaps in distribution knowledge across mangrove areas, particularly in South America, challenge the understanding of the taxonomic status, biogeographical patterns and genetic structuring of the lineages composing the self-fertilizing "Kryptolebias marmoratus species complex." In this study, the authors combined a literature survey, fieldwork and molecular data to fill major gaps of information about the distribution of mangrove killifishes across western Atlantic mangroves. They found that selfing mangrove killifishes are ubiquitously distributed across the Caribbean, Central and South American mangroves and report 14 new locations in South America, extending the range of both the "Central clade" and "Southern clade" lineages which overlap in the Amazon. Although substantial genetic differences were found between clades, the authors also found further genetic structuring within clades, with populations in Central America, north and northeast Brazil generally showing higher levels of genetic diversity compared to the clonal ones in southeast Brazil. The authors discuss the taxonomic status and update the geographical distribution of the Central and Southern clades, as well as potential dispersal routes and biogeographical barriers influencing the distribution of the selfing mangrove killifishes in the western Atlantic mangroves.

The biogeography of Dromiciops in southern South America: Middle Miocene transgressions, speciation and associations with Nothofagus

The current distribution of the flora and fauna of southern South America is the result of drastic geological events that occurred during the last 20 million years, including marine transgressions, glaciations and active vulcanism. All these have been associated with fragmentation, isolation and subsequent expansion of the biota, south of 35°S, such as the temperate rainforest. This forest is mostly dominated by Nothofagus trees and is the habitat of the relict marsupial monito del monte, genus Dromiciops, sole survivor of the order Microbiotheria. Preliminary analyses using mtDNA proposed the existence of three main Dromiciops lineages, distributed latitudinally, whose divergence was initially attributed to recent Pleistocene glaciations. Using fossil-calibrated dating on nuclear and mitochondrial genes, here we reevaluate this hypothesis and report an older (Miocene) biogeographic history for the genus. We performed phylogenetic reconstructions using sequences from two mitochondrial DNA and four nuclear DNA genes in 159 specimens from 31 sites across Chile and Argentina. Our phylogenetic analysis resolved three main clades with discrete geographic distributions. The oldest and most differentiated clade corresponds to that of the northern distribution (35.2°S to 39.3°S), which should be considered a distinct species (D. bozinovici, sensu D’Elía et al. 2016). According to our estimations, this species shared a common ancestor with D. gliroides (southern clades) about ~13 million years ago. Divergence time estimates for the southern clades (39.6°S to 42.0°S) ranged from 9.57 to 6.5 Mya. A strong genetic structure was also detected within and between clades. Demographic analyses suggest population size stability for the northern clade (D. bozinovici), and recent demographic expansions for the central and southern clades. All together, our results suggest that the diversification of Dromiciops were initiated by the Middle Miocene transgression (MMT), the massive marine flooding that covered several lowlands of the western face of Los Andes between 37 and 48°S. The MMT resulted from an increase in global sea levels at the Miocene climatic optimum, which shaped the biogeographic origin of several species, including Nothofagus forests, the habitat of Dromiciops.

Phylogeographic analysis of Saxifraga fortunei complex (Saxifragaceae) reveals multiple origins of morphological and ecological variations in the Japanese Archipelago

Phenotypic polymorphism within a species is a notable phenomenon in evolutionary biology to understand the process of adaptive speciation and other historical events. The Saxifraga fortunei complex is a widespread herb found in East Asia. It includes several ecotypic taxa corresponding to their habitat environments. The distribution of the various ecotypes in a limited area of the Japanese Archipelago makes the species a suitable model to investigate the impact of population demographic history and natural selection on lineage diversification. Here, Sanger-based sequencing was used to estimate the divergence timeframe between populations of the Eurasian continent and Japan. Genome-wide SNPs obtained by ddRAD sequencing were used to investigate the phylogeographic origins of ecotypic taxa. The phylogenetic analyses revealed the divergence of the Japanese population from the continental population in the late Miocene. Two distinct regional clades of North and South Japan were identified; phenotypic diversification was evident only in the southern clade. The South Japan clades displayed a historical distribution expansion from north to south. The phenotypic variations appeared to have generated during the expansion. The ecotypic boundaries were incongruent with the genetic grouping. We propose that morphological and ecological specialization in Japanese populations was repeatedly generated by local natural selection.

Diversification of the Balloon bushcrickets (Orthoptera, Hexacentrinae, Aerotegmina) in the East African mountains

East African mountains constitute a network of isolated habitat islands among dry savannah and are thus ideal for studying species diversification processes. This study elucidated the phylogenetic and phylogeographic relationships of all bushcricket species comprising the genus Aerotegmina. Our analysis indicated that large-scale climatic and topographic processes in Africa are likely to have driven speciation in this group, and revealed the cytogenetic traits of the species. Molecular phylogeny supported the monophyly of Aerotegmina and showed that the genus probably originated in the old Eastern Arc Mountains of Tanzania and Kenya. Two lineages were distinguished: small- and large-sized species with geographically distinct habitats. The underlying processes are thought to be eight dispersals, ten vicariance events, and one extinction event linked to repeated fragmentation of the African rainforest. Those processes, in conjunction with habitat change, probably also led to the spatial separation of the species into a northern clade with a diploid number of chromosomes 2n = 32 + X0 or 2n = 30 + neo-XY and a southern clade with a reduced number of chromosomes (2n = 28 + X0 or 24 + neo-X1X2Y). Karyotype analysis suggests that Aerotegmina is currently in the process of speciation.

North-south and climate-landscape-associated pattern of population structure for the Atlantic Forest White Morpho butterflies

Atlantic Forest White Morpho butterflies, currently classified as Morpho epistrophus and M. iphitus, are endemic to the Atlantic Forest, where they are widely distributed throughout heterogeneous environmental conditions. Studies with endemic butterflies allow to elucidate questions on both patterns of diversity distribution and current and past processes acting on insect groups in this biodiversity hotspot. In the present study, we characterized one mtDNA marker (COI sequences) and developed 11 polymorphic loci of microsatellite for 22 sampling locations distributed throughout the entire Atlantic Forest domain. We investigated both the taxonomic limits of taxa classified as White Morpho and the structure and distribution of the genetic diversity throughout their populations. Genetic markers and distribution data failed to identify species diversification, population structure, or isolation among subpopulations attributed to different taxa proposed for the White Morpho, suggesting that the current distinction between two species is unreasonable. The Bayesian coalescent tree based on COI sequences also failed to recover monophyletic clades for the putative species, and pointed instead to a north–south oriented pattern of genetic structure, with the northern clade coalescing later than the southern clade. Northern samples also showed more intragroup structure than southern samples based on mtDNA data. Clustering tests based on microsatellites indicated the existence of three genetic clusters, with turnover between the states of Paraná and São Paulo. The north–south pattern found for the White Morpho populations is showed for the first time to a endemic AF insect and coincides with the two different bioclimatic domains previously described for vertebrates and plants. Population structure observed for these butterflies is related to climate- and landscape-associated variables, mainly precipitation and elevation.

Review of Chilean Cyrtinae (Diptera: Acroceridae) with the Description of Three New Species and the First Record of Villalus inanis from Argentina.

Acrocerid flies are endoparasitoids of spiders that are distributed in all ecosystems except deserts and the poles. This group was historically classified into three subfamilies. However, molecular analyses have indicated two new subfamilies. One of these is Cyrtinae Newman, which is made up of two clades: the north, with Palearctic species, and the south, with Chilean species (except for the fossil genus Villalites Hennig). In the southern clade, endemic genera Holops Philippi and Villalus Cole have been poorly described over time by different authors. The aim of this study is to re-describe the known species of Holops and Villalus and describe three new Holops species based on collected material: Holops grezi sp. nov., Holops anarayae sp. nov., and Holops pullomen sp. nov. In addition, an identification species key with updated distributions for all species and the first record of Villalus inanis from Argentina is also provided. New species are mainly characterized by the length of flagellum; colors of the postocellar lobe and thoracic segments, pilosity and legs; wing cells and veins, and shape of the abdomen. Holops and Villalus do not share morphological traits with any other known extant genus of Acroceridae in the southern hemisphere. The real biodiversity of this group must be evaluated with a molecular phylogeny in the future. In addition, the new species in the Pehuén and Valdivian forest provinces, areas considered to have been sheltered during the last glacial period, promoting speciation in several taxa. New and cryptic Holops species open the doors to disentangling the real biodiversity of spider flies in Chile.

Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere.

The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.].

Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States

A major driver generating amphibian diversity in the Appalachian Mountains is the complex paleogeography of the zone. Although the Appalachian Mountains have been widely studied, much of its amphibian phylogeography remains poorly known. The Mountain Chorus Frog (Pseudacris brachyphona) is one example of an understudied organism due to its elusiveness, patchy distribution, and short breeding seasons. Phylogenetic studies have suggested the existence of divergent lineages within P. brachyphona; however, insufficient sampling and the lack of diagnostic morphological traits have prevented further assessment of their taxonomic status. Using a genome-wide nuclear data set obtained via anchored hybrid enrichment, acoustic data, and ecological modeling, we tested for the existence of cryptic species within P. brachyphona. Our species tree estimation supports previous mitochondrial-based phylogenetic hypotheses that separate P. brachyphona into the Northern and Southern clades. Population genetic clustering also shows a sharp genetic break, which is concordant with these clades. Admixture was observed between the Northern clade and another chorus frog species (P. feriarum). Analysis of advertisement calls shows a divergent, faster pulse rate, and higher dominant frequency call for the Southern clade in comparison to the Northern clade and other trilling chorus frogs. Furthermore, species distribution models showed that habitat suitability for the Southern clade included pine-dominated and drier areas compared to the Northern clade. In light of the genetic, acoustic, and ecological divergence between the clades, we propose to elevate the taxonomic status of the Southern clade and name this new species the Collinses' Mountain Chorus Frog (P. collinsorum, new species). The new species ranges across northern Alabama, and extends into Georgia, eastern Mississippi, and southern Tennessee. Pseudacris collinsorum, new species, is geographically separated from its sister species, P. brachyphona, by the Tennessee River and surrounding Blue Ridge Escarpment. This study highlights the need for genus-wide, population-level genetic assessments and integrative data sets to uncover diversity within anurans.

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

BackgroundClimatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.ResultsWe investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group.ConclusionClimatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-A.

Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers

South American racers of the tribe Philodryadini are a widespread and diverse group of Neotropical snakes with a complex taxonomic and systematic history. Recent studies failed to present a robust phylogenetic hypothesis for the tribe, mainly due to incomplete taxon sampling. Here we provide the most extensive molecular phylogenetic analysis of Philodryadini available so far, including 20 species (83% of the known diversity) from which six were not sampled previously. Our results reveal that Philodryadini is not monophyletic, but instead includes a central Andean clade formed by Philodryas simonsii, P. tachymenoides, and P. amaru, and a southern and cis-Andean clade including all remaining philodryadines. This discovery requires resurrection of two genera as well as erection of a new tribe of Xenodontinae for the central Andean clade. Within the southern and cis-Andean radiation, our analyses resolve a basal dichotomy separating two main lineages: Clade A, containing the Common Green Racers P. laticeps and P. viridissima and the South American Vine snakes P. georgeboulengeri and P. argentea; and Clade B, including the remaining species of Philodryas sensu stricto. We resurrect the genera Chlorosoma and Xenoxybelis to better represent the monophyly of lineages within the southern and cis-Andean clade.

Ixodes spp. from Dogs and Cats in the United States: Diversity, Seasonality, and Prevalence of Borrelia burgdorferi and Anaplasma phagocytophilum.

Ixodes spp. are commonly found on dogs and cats throughout the world. In the eastern United States, 16S rDNA sequence of Ixodes scapularis, the predominant species, reveals two clades-American and Southern. To confirm the species and clades of Ixodes spp. ticks submitted from pets, we examined ticks morphologically and evaluated 16S rDNA sequence from 500 ticks submitted from 253 dogs, 99 cats, 1 rabbit, and 1 ferret from 41 states. To estimate pathogen prevalence, flaB of Borrelia burgdorferi (Bb) sensu stricto and 16S rDNA of Anaplasma phagocytophilum (Ap) were amplified and sequenced. Most Ixodes spp. from the Northeast (n = 115/115; 100%) and the Midwest (n = 77/80; 96.3%) were I. scapularis, American clade. Borrelia spp. were identified in 34 of 192 (17.8%) and Ap in 5 of 192 (2.6%) I. scapularis. Two Ixodes cookei and one Ixodes texanus were identified from Ohio, Illinois, and Michigan. In contrast, 156 of 261 (59.8%) Ixodes spp. from the Southeast were I. scapularis, American clade; 86 of 261 (33.0%) were I. scapularis, Southern clade; 9 of 261 (3.4%) were Ixodes affinis; and 10 of 261 (3.8%) were I. cookei. Southern clade was significantly more common in Florida and less common in the upper South (p < 0.0001). One I. scapularis (1/242; 0.4%) from the Southeast (Kentucky) tested positive for Bb and 6 of 242 (2.5%) were positive for Ap. In the West, most (34/44; 77.3%) Ixodes spp. were Ixodes pacificus, with Ixodes angustus (n = 6) submitted from dogs in Alaska, Washington, and Oregon and Ixodes haerlei (n = 4) preliminarily identified from a dog in Montana. Pathogens were not detected in any ticks from the West. Although I. scapularis, American clade, predominated in the Northeast and Midwest, additional Ixodes spp. were found on dogs and cats in other regions and pathogens were less commonly detected. The role of less common Ixodes spp. as disease vectors, if any, warrants continued investigation.

A new species of Cnemaspis Strauch (Squamata: Gekkonidae) of the C. siamensis group from Tenasserim Mountains, Thailand.

An integrative taxonomic analysis recovered the new species Cnemaspis selenolagus sp. nov. of the C. siamensis group as the sister species to C. punctatonuchalis. The new species was discovered in mountain evergreen tropical forests of in Suan Phueng District of Ratchaburi Province, western Thailand. Additionally, the analysis recovered a deep genetic divergence between northern and southern clades within the C. siamensis group that occur on opposite sides of the Isthmus of Kra-a well-known biogeographic region of cladogenic turnover. The description of C. selenolagus sp. nov. brings the total number of species of Cnemaspis in Thailand to 16, 11 of which compose the C. siamensis group-a lineage endemic to the Thai-Malay Peninsula. This underscores the physiographic complexity of this narrow peninsula in that it can support a large number of closely related species in only the northern two-thirds of its length.