Mitochondrial evidence uncovers a refugium for the fat dormouse (Glis glis Linnaeus, 1766) in Hyrcanian forests of northern Iran

Fat dormouse is a squirrel-like rodent which is closely tied to deciduous forest ecosystem in southwestern Eurasia. As such it is a valuable indicator of forest survival in refugia during glacial-interglacial periods. Previous phylogeographic analyses uncovered divergent fat dormouse lineages in southern refugia in Italy and the Balkans, but retrieved a surprisingly low overall genetic diversity across the majority of the species’ range. We explored 812 bp long fragment of a cytochrome b (cyt b) gene in ten fat dormice from refugial Hyrcanian forests in northern Iran. We identified 10 new cyt b haplotypes, which generated a total dataset of 28 fat dormouse haplotypes. The phylogenetic reconstruction clustered the new haplotypes into the Iranian lineage which hold a sister position against all other fat dormouse haplotypes from Europe and Asia Minor. The divergence between these lineages suggests a fragmentation event of an ancestral population at 5.76 mya (95% HPD = 3.21–8.92). This early evolutionary divergence was possibly triggered in the Middle East by dramatically divergent environmental conditions at the Messinian Salinity Crisis. The divergence clearly exceeds the intraspecific divergence, and is well within the range between congeneric rodent species. We suggest a long-term persistence of the Iranian lineage in the Hyrcanian refugium which is consitent with a high number of endemics along the southern Caspian coastal areas.     

Phylogeny and biogeography of the Poecilia sphenops species complex (Actinopterygii,Poeciliidae) in Central America

We inferred the phylogenetic relationships among members of the Poecilia sphenops species complex to resolve the colonization process and radiation of this group in Central America. We analyzed 2550 base pairs (bp) of mitochondrial DNA (mtDNA), including ATP synthase 6 and 8, cytochrome oxidase subunit I and NADH dehydrogenase subunit 2 genes, and 906 bp of the nuclear S7 ribosomal protein of 86 ingroup individuals from 61 localities spanning most of its distribution from Mexico to Panama. Our mitochondrial data rendered a well-supported phylogeny for the P. sphenops complex that differed with the nuclear data set topology, which did not recover the monophyly of the P. mexicana mitochondrial lineage. Coalescent-based simulations tests indicated that, although hybridization cannot be completely ruled out, this incongruence is most likely due to incomplete lineage sorting in this group, which also showed the widest geographic distribution. A single colonization event of Central America from South America was estimated to have occurred between the early Paleocene and Oligocene (53–22 million years ago). Subsequently, two largely differentiated evolutionary lineages diverged around the Early Oligocene–Miocene (38–13 million years ago), which are considered two separate species complexes: P. sphenops and P. mexicana, which can also be distinguished by their tricuspid and unicuspid inner jaw teeth, respectively. Ultimately, within lineage diversification occurred mainly during the Miocene (22–5 million years ago). All major cladogenetic events predated the final closure of the Isthmus of Panama. The allopatric distribution of lineages together with the long basal internodes suggest that vicariance and long term isolations could be the main evolutionary forces promoting radiation in this group, although dispersal through water barriers might also have occurred. Lastly, our results suggest the need to review the current species distribution and taxonomy of the P. sphenops complex sensu lato.     

Speciation and phylogeography of giant petrels Macronectes

We examine global phylogeography of the two forms of giant petrel Macronectes spp. Although previously considered to be a single taxon, and despite debate over the status of some populations and the existence of minimal genetic data (one mitochondrial cytochrome b sequence per form), the current consensus based on morphology is that there are two species, Northern Giant Petrel M. halli and Southern Giant Petrel M. giganteus. This study examined genetic variation at cytochrome b as well as six microsatellite loci in giant petrels from 22 islands, representing most island groups at which the two species breed. Both markers support separate species status, although sequence divergence in cytochrome b was only 0.42% (corrected). Divergence was estimated to have occurred approximately 0.2 mya, but with some colonies apparently separated for longer (up to 0.5 my). Three clades were found within giant petrels, which separated approximately 0.7 mya, with the Southern Giant Petrel paraphyletic to a monophyletic Northern Giant Petrel. There was evidence of past fragmentation during the Pleistocene, with subsequent secondary contact within Southern Giant Petrels. The analysis also suggested a period of past population expansion that corresponded roughly to the timing of speciation and the separation of an ancestral giant petrel population from the fulmar Fulmarus clade.     

The complete mitochondrial genome of the endangered Apollo butterfly,Parnassius apollo (Lepidoptera: Papilionidae) and its comparison to other Papilionidae species

The Apollo butterfly, Parnassius apollo is a representative species of the butterfly subfamily Parnassiinae. This charming species is one of the most endangered butterfly species in the world. In this study, we sequenced its complete mitochondrial genome (mitogenome), with the aim of accumulating genetic information for further studies of population genetics and mitogenome evolution in the Papilionidae. The 15,404-bp long mitogenome harbors a typical set of 37 genes and is the largest butterfly mitogenome determined, except for Papilio maraho (16,094 bp). Like many other sequenced lepidopteran species, one tRNA^Trp-like and one tRNA^Leu(UUR)-like sequences were detected in the AT-rich region. A total of 164 bp of non-coding sequences are dispersed in 14 regions throughout the genome. The longest intergenic spacer (68 bp) is located between tRNA^Ser(AGN) and tRNA^Glu, and is the largest spacer at this location among Papilionidae species. This spacer may have resulted from an 8-fold repetition of a TTTCTTCT motif or a 4-fold repetition of a CTTTATTT motif.     

A multilocus coalescent analysis of the speciational history of the Australo-Papuan butcherbirds and their allies

Changes in geology, sea-level and climate are hypothesised to have been major driving processes of evolutionary diversification (speciation and extinction) in the Australo-Papuan region. Here we use complete species-level sampling and multilocus (one mitochondrial gene, five nuclear loci) coalescent analyses to estimate evolutionary relationships and test hypotheses about the role of changes in climate and landscape in the diversification of the Australo-Papuan butcherbirds and allies (Cracticinae: Cracticus, Strepera, Peltops). Multilocus species trees supported the current classification of the morphologically, ecologically and behaviourally divergent Australian Magpie (Cracticus tibicen (previously Gymnorhina tibicen)) as a member of an expanded genus Cracticus, which includes seven other species with ‘butcherbird’ morphology and behaviour. Non-monophyly of currently recognised species within Peltops and the white-throated butcherbird species-group (C. argenteus, C. mentalis, C. torquatus) at both mtDNA and nuclear loci suggest that a comprehensive taxonomic revision is warranted for both of these groups. The time-calibrated multilocus species tree revealed an early divergence between the New Guinean rainforest-restricted Peltops lineage and the largely open-habitat inhabiting Cracticus (butcherbirds and magpies) plus Strepera (currawongs) lineage around 17–28 Ma, as well as a relatively recent radiation of lineages within Cracticus over the past 8 Ma. Overall, patterns and timings of speciation were consistent with the hypothesis that both the expansion of open sclerophyllous woodlands 25–30 Ma and the formation of extensive grassland-dominated woodlands 6–8 Ma allowed the radiation of lineages adapted to open woodland habitats.     

Speciation by monobrachial centric fusions: A test of the model using nuclear DNA sequences from the bat genus Rhogeessa

Members of Rhogeessa are hypothesized to have undergone speciation via chromosomal rearrangements in a model termed speciation by monobrachial centric fusions. Recently, mitochondrial cytochrome-b sequence data tentatively supported this hypothesis but could not explicitly test the model’s expectations regarding interbreeding among karyotypic forms. These data showed potential evidence for hybridization or incomplete lineage sorting between the karyotypically distinct R. tumida and R. aeneus and identified multiple lineages of karyotypically identical R. tumida. Here, we present a more comprehensive test of speciation by monobrachial centric fusions in Rhogeessa. Our analysis is based on sequence data from two nuclear loci: paternally inherited ZFY and autosomal MPI genes. These data provide results consistent either with incomplete lineage sorting or ancient hybridization to explain alleles shared at low frequency between R. aeneus and R. tumida. Recent and ongoing hybridization between any species can be ruled out. These data confirm the presence of multiple lineages of the 2n = 34 karyotypic form (“R. tumida”) that are not each other’s closest relatives. These results are generally consistent with speciation by monobrachial centric fusions, although additional modes of speciation have also occurred in Rhogeessa. Phylogeographic analyses indicate habitat differences may be responsible for isolation and divergence between different lineages currently referred to as R. tumida.     

Phylogeny,biogeography, and electric signal evolution of Neotropical knifefishes of the genus Gymnotus (Osteichthyes: Gymnotidae)

The Neotropical knifefish genus Gymnotus is the most broadly distributed and the most diverse (34 + species) gymnotiform genus. Its wide range includes both Central and South American drainages, including the Amazon, Orinoco, and La Plata Basins. Like all gymnotiforms, Gymnotus species produce weak electric fields for both navigation and communication, and these fields exhibit interspecific variation in electric waveform characteristics. Both biogeography and electric signal evolution can profitably be analyzed in a phylogenetic context. Here, we present a total evidence phylogeny for 19 Gymnotus species based on data from the mitochondrial cytochrome b and 16S genes (1558 bp), the nuclear RAG2 gene (1223 bp), and 113 morphological characters. Our phylogenetic hypothesis resolves five distinct Gymnotus lineages. In a previous morphology-based analysis, the Central American Gymnotus cylindricus lineage was hypothesized as the sister group to all other Gymnotus species. In our analysis, the G. cylindricus lineage is nested within South American species, and molecular age estimates support a relatively recent origin for the clade in Central America. Phylogenetic optimization of electric signal waveforms indicate that the ancestral state in Gymnotus is a multiphasic (4 + phases of alternating polarity) condition, and independent phase loss has occurred in multiple lineages. Gymnotus is a model group for understanding Neotropical diversification and the evolution of communication at a continental scale.     

The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda

The complete mitochondrial (mt) genome sequence of Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda) was determined; a circular molecule of 15,783 bp in length. The gene content and arrangement are consistent with the pancrustacean ground pattern. The mt control region of O. oratoria is characterized by no GA-block near the 3′ end and different position of [TA(A)]n-blocks compared with other reported Stomatopoda species. The sequence of the second hairpin structure is relative conserved which suggests this region may be a synapomorphic character for the Stomatopoda. In addition, a relative large intergenic spacer (101 bp) with higher A + T content than that in control region was identified between the tRNA^Glu and tRNA^Phe genes. Phylogenetic analyses based on the current dataset of complete mt genomes strongly support the Stomatopoda is closely related to Euphausiacea. They in turn cluster with Penaeoidea and Caridea clades while other decapods form a separate group, which rejects the monophyly of Decapoda. This challenges the suitability of Stomatopoda as an outgroup of Decapoda in phylogenetic analyses. The basal position of Stomatopoda within Eumalacostraca according to the morphological characters is also questioned.     

The mitochondrial calcium uniporter is involved in mitochondrial calcium cycle dysfunction: Underlying mechanism of hypertension associated with mitochondrial tRNAIle A4263G mutation

Recent studies have shown that the mitochondrial DNA mutations are involved in the pathogenesis of hypertension. Our previous study identified mitochondrial tRNA^Ile A4263G mutation in a large Chinese Han family with maternally-inherited hypertension. This mutation may contribute to mitochondrial Ca²⁺ cycling dysfuntion, but the mechanism is unclear. Lymphoblastoid cell lines were derived from hypertensive and normotensive individuals, either with or without tRNA^Ile A4263G mutation. The mitochondrial calcium ([Ca²⁺]_m) in cells from hypertensive subjects with the tRNA^Ile A4263G mutation, was lower than in cells from normotension or hypertension without mutation, or normotension with mutation (P < 0.05). Meanwhile, cytosolic calcium ([Ca²⁺]_c) in hypertensive with mutation cells was higher than another three groups. After exposure to caffeine, which could increase the [Ca²⁺]_c by activating ryanodine receptor on endoplasmic reticulum, [Ca²⁺]_c/[Ca²⁺]_m increased higher than in hypertensive with mutation cells from another three groups. Moreover, MCU expression was decreased in hypertensive with mutation cells compared with in another three groups (P < 0.05). [Ca²⁺]_c increased and [Ca²⁺]_m decreased after treatment with Ru360 (an inhibitor of MCU) or an siRNA against MCU. In this study we found decreased MCU expression in hypertensive with mutation cells contributed to dysregulated Ca²⁺ uptake into the mitochondria, and cytoplasmic Ca²⁺ overload. This abnormality might be involved in the underlying mechanisms of maternally inherited hypertension in subjects carrying the mitochondrial tRNA^Ile A4263G mutation.     

Cyclestheria hislopi (Crustacea: Branchiopoda): A group of morphologically cryptic species with origins in the Cretaceous

Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hislopi represents a single circumtropic species. South American (French Guiana), Asian (India, Indonesia, Singapore) and several Australian populations were included in our investigation. Phylogenetic and genetic distance analyses revealed remarkable intercontinental genetic differentiation (uncorrected p-distances COI > 13%, EF1α > 3% and 28S > 4%). Each continent was found to have at least one distinct Cyclestheria species, with Australia boasting four distinct main lineages which may be attributed to two to three species. The divergence of these species (constituting crown group Cyclestherida) was, on the basis of phylogenetic analyses of COI and EF1α combined with molecular clock estimates using several fossil branchiopod calibration points or a COI substitution rate of 1.4% per million years, dated to the Cretaceous. This was when the South American lineage split from the Asian–Australian lineage, with the latter diverging further in the Paleogene. Today’s circumtropic distribution of Cyclestheria may be best explained by a combination of Gondwana vicariance and later dispersal across Asia and Australia when the tectonic plates of the two continents drew closer in the early Miocene. The lack of morphological differentiation that has taken place in this taxon over such a long evolutionary period contrasts with the high level of differentiation and diversification observed in its sister taxon the Cladocera. Further insights into the evolution of Cyclestheria may help us to understand the evolutionary success of the Cladocera.     

Peptidomic analysis of skin secretions supports separate species status for the tailed frogs,Ascaphus truei and Ascaphus montanus

The tailed frog Ascaphus truei Stejneger, 1899 is the most primitive extant anuran and the sister taxon to the clade of all other living frogs. The species occupies two disjunct ranges in the Northwest region of North America: the Cascade Mountains and coastal area from British Columbia to Northern California, and an inland range in the northern Rocky Mountains and the Blue and Wallowa mountains. A previous study led to the isolation of eight peptides with antimicrobial activity (termed the ascaphins) from skin secretions of A. truei from the coastal range. The present study has used peptidomic analysis to identify the products of orthologous ascaphin genes in electrically-stimulated skin secretions from inland range specimens. Structural characterization of the peptides demonstrated that ascaphins from the inland range contained the following amino acid substitutions compared with orthologs from the coastal range frogs: ascaphin-1 (Ala¹² → Glu), ascaphin-3 (Asp⁴ → Glu), ascaphin-4 (Ala¹⁹ → Ser), ascaphin-5 (Lys¹² → Thr), and ascaphin-7 (Gly⁸ → Ser and Ser²⁰ → Asn). Orthologs of ascaphins-2, -6, and -8 were not identified but a paralog of ascaphin-5, identical to ascaphin-5 from coastal range frogs, was found. The data support the claims, derived from analysis of the nucleotide sequences of mitochondrial genes, that the inland populations of the tailed frog should be recognized as a distinct species, the Rocky Mountain tailed frog Ascaphus montanus and that the divergence of the species from A. truei probably occurred in the late Miocene (approximately 10 Mya).     

Discrimination of Iranian honeybee populations (Apis mellifera meda) from commercial subspecies of Apis mellifera L. using morphometric and genetic methods

The morphological characters of honeybees have an important role for discriminating honeybee subspecies. In the present research, Iranian populations of honeybee (Apis mellifera) were collected from 19 areas in Iran. The samples were collected from stationary beekeeping sites. Moreover, pictures of honeybee forewings held in the Bee Data Bank in Oberursel were compared with Iranian honeybee populations. 19 morphological characters were measured for each forewing of worker honeybee to evaluate differentiation of Iranian honeybee populations from the commercial honeybee subspecies A. m. mellifera, A. m. carnica, A. m. caucasica and A. m. ligustica. Additionally, part of the tRNA^leu gene, an intergenic region and part of COII was used to confirm differentiation of the commercial subspecies from Iranian honeybee populations. Results of the cluster analyses showed that 19 morphological characters of forewings differentiated Iranian populations from the commercial subspecies. Moreover, the phylogenetic tree of part of the tRNA^leu gene, an intergenic region and part of COII differentiated the commercial subspecies from Iranian honeybee populations. Results of the discriminant function analyses (DFA) indicated that the references samples of A. m. meda overlapped with Iranian populations.     

Dating the origin of the major lineages of Branchiopoda

Despite the well-established phylogeny and good fossil record of branchiopods, a consistent macro-evolutionary timescale for the group remains elusive. This study focuses on the early branchiopod divergence dates where fossil record is extremely fragmentary or missing. On the basis of a large genomic dataset and carefully evaluated fossil calibration points, we assess the quality of the branchiopod fossil record by calibrating the tree against well-established first occurrences, providing paleontological estimates of divergence times and completeness of their fossil record. The maximum age constraints were set using a quantitative approach of Marshall (2008). We tested the alternative placements of Yicaris and Wujicaris in the referred arthropod tree via the likelihood checkpoints method. Divergence dates were calculated using Bayesian relaxed molecular clock and penalized likelihood methods. Our results show that the stem group of Branchiopoda is rooted in the late Neoproterozoic (563 ± 7 Ma); the crown-Branchiopoda diverged during middle Cambrian to Early Ordovician (478–512 Ma), likely representing the origin of the freshwater biota; the Phyllopoda clade diverged during Ordovician (448–480 Ma) and Diplostraca during Late Ordovician to early Silurian (430–457 Ma). By evaluating the congruence between the observed times of appearance of clade in the fossil record and the results derived from molecular data, we found that the uncorrelated rate model gave more congruent results for shallower divergence events whereas the auto-correlated rate model gives more congruent results for deeper events.     

Holocene environmental changes as recorded by mineral magnetism of sediments from Anguli-nuur Lake,southeastern Inner Mongolia Plateau,China

Two cores, one 1141-cm long (An-S) and the other 885-cm long (An-A), were retrieved from Anguli-nuur Lake (41°18′–24′N, 114°20′–27′E, ～ 1315 masl), one of the largest lakes in the transition zone between a semi-humid and semi-arid climate parallel to the present limit of the southeast monsoon along the southeastern Inner Mongolia Plateau in north China. Mineral-magnetic parameters (χ_lf, ARM, IRM_300mT, SIRM and IRM_? 300mT) were measured on An-S and two additional parameters (χ_ARM and HIRM) and four inter-parametric ratios (χ_ARM/SIRM, IRM_300mT/SIRM, IRM_? 300mT/SIRM and SIRM/χ_lf) were calculated. Potential sources of these lake sediments (catchment soils and dune materials close to the lake and in a distant sand plain) were sampled, and the magnetic properties of the surface-material specimens were measured. A chronological model was developed for An-S by comparing and combining AMS¹⁴C dates of An-S with ¹³⁷Cs, ²¹⁰Pb and AMS¹⁴C dates of An-A. With the help of surface-material magnetism, the magnetic data of An-S in combination with particle size, TOC and C/N and pollen analyses indicate the environmental changes during the last ～ 10,000 years around this lake. Conditions began to ameliorate at 10,900 cal. yr BP (9600 ¹⁴C yr BP) and thus relatively wet and warm environments prevailed during 10,900–8900 cal. yr BP (9600–8000 ¹⁴C yr BP). The Holocene optimum or the wettest and warmest conditions, was during 8900–7400 cal. yr BP (8000–6500 ¹⁴C yr BP). The environment began to deteriorate from 7400 cal. yr BP (6500 ¹⁴C yr BP) and the driest and coolest conditions occurred during 2200–480 cal. yr BP. There may have been a minor amelioration after 480 cal. yr BP. The inferred changes in palaeoenvironmental conditions around Anguli-nuur Lake are broadly in agreement with those around most other sites on the Inner Mongolia Plateau.     

Effect of yak rumen content treatments on seed germination of 11 alpine meadow species on the Qinghai-Tibetan Plateau

The Qinghai-Tibetan Plateau is located in the ‘Third Pole’ of the world, characterized by a harsh environment. Despite this, the alpine meadow ecosystem have developed over a wide area but serious grassland degradation is threatening the ecological environment on the Plateau. Recruitment of new plants to the population, via germination and establishment, is vital to plant community survival. Previous work on the seeds in this area has mainly focused on community-wide germination strategies, seed germination characteristics and their correlations with seed size and seed mass. However, there have been no studies on the effects of soaking in rumen contents on the plant seed germination characteristics of alpine meadow species. The present study had two main objectives: (i) to determine the effect of fresh rumen content from yaks on seed germination characteristics and seedling growth of species common to the eastern Tibetan Plateau alpine meadow, and (ii) to develop an effective method to enhance seed germination. Seeds of 11 common species were collected together with fresh rumen content from three yaks that grazed there. Seed germination tests were conducted after they had been soaked in rumen content for one of six soaking periods (12, 24, 36, 48, 60 or 72 h). The seeds were incubated under natural light conditions of 8 h light at 25 °C and 16 h darkness at 15 °C, for the germination period of 34 days. The results showed that seed germination and seedling growth were affected by soaking time, seed coat completeness and seed type. After soaking in rumen content, the germination percentages of scarified (peeled or with the seed coat cut through) seeds of some species (true seeds Oxytropis ochrocephala and Medicago ruthenia var inschanica, nutlet Carex enervis, achenes Anemone rivularis and Polygonum sibiricum) and complete seeds of C. enervis, and A. rivularis were improved but the duration of soaking was also important. Seed germination of caryopsis Achnatherum inebrians (a toxic grass) was significantly inhibited by any exposure to rumen fluids. Scarified seeds generally had higher germination percentages than complete ones after treatment, but with the increase in soaking time, germination percentages declined and scarified seeds were more sensitive to the treatment than the complete seeds. After soaking in yak rumen content, the germination indices of scarified M. ruthenia at 12 h treatment, O. ochrocephala and achene Rumex acetosa at 12–24 h treatment, nutlet Kobresia humilis at 24 h treatment, P. sibiricum at 24–48 h treatment, C. enervis at 12–48 h treatment and A. rivularis at 12–60 h treatment were significantly higher than the control (P < 0.05), while the germination indices of complete C. enervis seeds at 12 h and 36 h treatment, and A. rivularis at 12–60 h treatment were significantly higher compared with the control. The germination indices of other species gradually decreased with the increase in soaking time. We concluded that yak rumen digestion could enhance, inhibit or not affect seed germination and seedling growth of the alpine meadow species, which might influence seedling recruitment, interspecific competition, and the plant community structure of the eastern Tibetan Plateau alpine meadow. Overall, yak digestion has a positive effect on alpine meadow seed germination and seed dispersal.     

Effects of yak dung patch dropped in cold season on soil and pasture on the Qinghai-Tibetan Plateau

To clarify how dung patches from grazing yaks affect soil and pasture in the alpine meadow of Qinghai-Tibetan Plateau, yak dung was collected, mixed and redistributed in a cold grazing season. The soil physical and chemical properties and forage growth were then monitored under the yak dung patch, and 10 cm and 50 cm from the edge of yak dung patches. The result has shown that yak dung significantly improved soil moisture, total organic matter, and soil available N and P under or close to the dung patches. The forage production at 10 cm from the dung patch (303 g/m²) was significantly higher than that at 50 cm from the dung patch (control) (284 g/m²) in the second year, while the production was similar to the control in the first and the third year. The process of yak dung decomposition was slow and yak dung remains were observed 3 years after the drop. The dung patches also formed a strong ‘shell’, very difficult for plant underneath to penetrate and grow. Therefore, almost all plants under yak dung patches died, leading to decline in forage yield in the first, second, and the third year. In practice in the Qinghai-Tibetan Plateau regions, yak dung is often collected as fuel by the local farmers. Removing yak dung from alpine meadow may on one hand lead to losses in soil nutrients, but on the other hand reduces some of the negative effects, e.g. the reduction of forage yield under yak dung patches.     

Multilocus phylogeny and recent rapid radiation of the viviparous sea snakes (Elapidae: Hydrophiinae)

The viviparous sea snakes (Hydrophiinae: Hydrophiini) comprise a young but morphologically and ecologically diverse clade distributed throughout the Indo-Pacific. Despite presenting a very promising model for marine diversification studies, many relationships among the 62 species and 16 genera in Hydrophiini remain unresolved. Here, we extend previous taxonomic and genomic sampling for Hydrophiini using three mitochondrial fragments and five nuclear loci for multiple individuals of 39 species in 15 genera. Our results highlight many of the impediments to inferring phylogenies in recent rapid radiations, including low variation at all five nuclear markers, and conflicting relationships supported by mitochondrial and nuclear trees. However, concatenated Bayesian and likelihood analyses, and a multilocus coalescent tree, recovered concordant support for primary clades and several previously unresolved inter-specific groupings. The Aipysurus group is monophyletic, with egg-eating specialists forming separate, early-diverging lineages. All three monotypic semi-aquatic genera (Ephalophis, Parahydrophis and Hydrelaps) are robustly placed as early diverging lineages along the branch leading to the Hydrophis group, with Ephalophis recovered as sister to Parahydrophis. The molecular phylogeny implies extensive evolutionary convergence in feeding adaptations within the Hydrophis group, especially the repeated evolution of small-headed (microcephalic) forms. Microcephalophis (Hydrophis) gracilis is robustly recovered as a relatively distant sister lineage to all other sampled Hydrophis group species, here termed the ‘core Hydrophis group’. Within the ‘core Hydrophis group’, Hydrophis is recovered as broadly paraphyletic, with several other genera nested within it (Pelamis, Enhydrina, Astrotia, Thalassophina, Acalyptophis, Kerilia, Lapemis, Disteira). Instead of erecting multiple new genera, we recommend dismantling the latter (mostly monotypic) genera and recognising a single genus, Hydrophis Latreille 1802, for the core Hydrophis group. Estimated divergence times suggest that all Hydrophiini last shared a common ancestor ～6 million years ago, but that the majority of extant lineages diversified over the last ～3.5 million years. The core Hydrophis group is a young and rapidly speciating clade, with 26 sampled species and 9 genera and dated at only ～1.5–3 million years old.     

Dating an impressive Neotropical radiation: Molecular time estimates for the Sigmodontinae (Rodentia) provide insights into its historical biogeography

With about 400 living species and 82 genera, rodents of the subfamily Sigmodontinae comprise one of the most diverse and more broadly distributed Neotropical mammalian clades. There has been much debate on the origin of the lineage or the lineages of sigmodontines that entered South America, the timing of entrance and different aspects of further diversification within South America. The ages of divergence of the main lineages and the crown age of the subfamily were estimated by using sequences of the interphotoreceptor retinoid binding protein and cytochrome b genes for a dense sigmodontine and muroid sampling. Bayesian inference using three fossil calibration points and a relaxed molecular clock estimated a middle Miocene origin for Sigmodontinae (～12 Ma), with most tribes diversifying throughout the Late Miocene (6.9–9.4 Ma). These estimates together results of analyses of ancestral area reconstructions suggest a distribution for the most recent common ancestor of Sigmodontinae in Central-South America and a South American distribution for the most recent common ancestor of Oryzomyalia.     

Multivariate morphometry and rates of morphologic evolution within the Pennsylvanian fusulinid Beedeina (Ardmore Basin,Oklahoma, USA)

Ten species in the genus Beedeina from Desmoinesian (Middle Pennsylvanian) rocks in the Ardmore Basin (southern Oklahoma, USA) were discriminated on the basis of 29 measured variates. Each species was characterized by its mean scores on the first and second axes in canonical variates analysis (CVA) and by its lowest stratigraphic occurrence in order to identify evolutionary lineages. The pumila → plattensis → erugata lineage involved overall size increase without appreciable changes in shape. The insolita → haworthi → aff. whitakeri → acme and insolita → cf. novamexicana → euryteines lineages both exhibited axial lengthening, but the former involved relative elongation and the latter involved relative inflation. CVA function coefficients were used to identify taxonomically important characters for the analysis of rates of morphologic evolution, and it was discovered that three of the five most important characters occur in the embryonic portion of the shell (proloculus diameter, half-length and wall thickness of the first volution). Rates of evolution are variable among ancestor-descendant pairs in the three lineages, but they do not differ significantly from rates documented in other groups of fossil and extant organisms. Apparent variation in rates is an artifact of the unequal time intervals over which morphologic change was measured, with shorter intervals resulting in faster rates. Among the five variates examined in all ancestor-descendant pairs (i.e., across a range of time intervals), proloculus size and half-length of the first and sixth volutions exhibited the fastest mean rates of change, whereas wall thickness in the first volution and radius vector of the fifth volution exhibited slower mean rates of change.