Genus-level phylogeny of snakes reveals the origins of species richness in Sri Lanka

Snake diversity in the island of Sri Lanka is extremely high, hosting at least 89 inland (i.e., non-marine) snake species, of which at least 49 are endemic. This includes the endemic genera Aspidura, Balanophis, Cercaspis, Haplocercus, and Pseudotyphlops, which are of uncertain phylogenetic affinity. We present phylogenetic evidence from nuclear and mitochondrial loci showing the relationships of 40 snake species from Sri Lanka (22 endemics) to the remaining global snake fauna. To determine the phylogenetic placement of these species, we create a molecular dataset containing 10 genes for all global snake genera, while also sampling all available species for genera with endemic species occurring in Sri Lanka. Our sampling comprises five mitochondrial genes (12S, 16S, cyt-b, ND2, and ND4) and five nuclear genes (BDNF, c-mos, NT3 RAG-1, and RAG-2), for a total of up to 9582 bp per taxon. We find that the five endemic genera represent portions of four independent colonizations of Sri Lanka, with Cercaspis nested within Colubrinae, Balanophis in Natricinae, Pseudotyphlops in Uropeltidae, and that Aspidura + Haplocercus represents a distinct, ancient lineage within Natricinae. We synonymize two endemic genera that render other genera paraphyletic (Haplocercus with Aspidura, and Cercaspis with Lycodon), and discover that further endemic radiations may be present on the island, including a new taxon from the blindsnake family Typhlopidae, suggesting a large endemic radiation. Despite its small size relative to other islands such as New Guinea, Borneo, and Madagascar, Sri Lanka has one of the most phylogenetically diverse island snake faunas in the world, and more research is needed to characterize the island’s biodiversity, with numerous undescribed species in multiple lineages.     

Systematics and biogeography of the Neotropical genus Mabuya,with special emphasis on the Amazonian skink Mabuya nigropunctata (Reptilia,Scincidae)

Phylogenetic analyses using up to 1532 base pairs (bp) of mitochondrial DNA from 106 specimens of Neotropical Mabuya, including 18 of the 19 recognized South American and Mesoamerican species, indicate that most species of the genus are monophyletic, including M. nigropunctata that had previously been reported to be paraphyletic. The present results shows that this species includes three highly divergent and largely allopatric lineages restricted to occidental, meridional, and oriental Amazonia. Our dataset demonstrates that previous claims regarding the paraphyletic status of M. nigropunctata and the phylogenetic relationships within this species complex based on the analysis of three mitochondrial and four nuclear genes (approx. 5000 bp) were erroneous and resulted from two contaminated cytochrome b sequences.The phylogenetic results indicate that diversification in the Neotropical genus Mabuya started approximately in the Middle Miocene (15.5–13.4 Ma). The divergence dates estimated for the Mabuya nigropunctata species complex suggest that the major cladogenetic events that produced the three main groups (occidental (oriental + meridional)) occurred during the Late Miocene. These estimations show that diversification within the M. nigropunctata species complex was not triggered by the climatic changes that occurred during the Pleistocene, as has been suggested by several authors. Rather, our data support the hypothesis that the late tertiary (essentially Miocene epoch) was a period that played a very important role in the generation of biological diversity in the Amazonian forests.Speciation between Mabuya carvalhoi, endemic to the coastal mountain range of Venezuela, and M. croizati, restricted to the Guiana Shield, occurred during the Middle Miocene and may have been as the result of a vicariant event produced by the formation of the present day Orinoco river drainage basin and the consequent appearance of the Llanos del Orinoco, which acted as a barrier to dispersal between these two species. The split between M. bistriata and M. altamazonica and between the occidental and (meridional + oriental) clades of M. nigropunctata fits very well with the biogeographic split between the eastern and western Amazon basins reported for several other taxa.     

Molecular systematics and evolutionary origins of the genus Petaurus (Marsupialia: Petauridae) in Australia and New Guinea

The glider genus Petaurus comprises a group of arboreal and nocturnal marsupial species from New Guinea and Australia. Molecular data were generated in order to examine phylogenetic relationships among species within the genus and explore the time-scale of diversification and biogeographic history of the genus in Australia and New Guinea. All known species and subspecies of Petaurus (with the exception of P. biacensis) were sequenced for two mitochondrial genes (ND2 and ND4) and one nuclear marker (omega-globin gene). Phylogenetic analyses confirmed the monophyly of the genus relative to other petaurids and showed a sister relationship of P. australis to the rest of Petaurus. The analyses revealed that currently recognised species of Petaurus formed distinct mitochondrial DNA (mtDNA) clades. Considerable mtDNA diversity and seven distinct clades were identified within the species P. breviceps, with the distribution of each clade showing no correspondence with the distributional limits of known subspecies. Molecular dating analyses using BEAST suggested an early to mid-Miocene origin (18–24 mya) for the genus. Ancestral area reconstructions, using BayesTraits, did not resolve the location for the centre of origin of Petaurus, but provided evidence for at least one dispersal event from New Guinea to Australia that led to the evolution of extant Australian populations of P. breviceps, P. norfolcensis and P. gracilis. The timing of this dispersal event appears to pre-date the Pleistocene, adding to the growing number of studies that suggest faunal connections occurred between Australia and New Guinea in the Late Miocene to Pliocene period.     

Phylogenetic structure of the Thomomys bottae–umbrinus complex in North America

The phylogeography of the Thomomys bottae–umbrinus complex in the United States and Mexico was assessed with sequences of the mitochondrial cytochrome b gene. These sequences were obtained from 225 individuals representing 108 locations over the range, including 56 sequences from GenBank. 110 (500 bp) sequences were used for Bayesian inference and neighbor-joining analyses, and 34 (1140 bp) specimens from the main clades obtained from the Bayesian inference were used in maximum-parsimony and maximum-likelihood analyses. The different analyses indicate significant variation within the species complex that averages 13% among major groups of genetic differences among Thomomys bottae–umbrinus. The overall pattern of geographic variation is not concordant with the current taxonomy. To the contrary, eight monophyletic groups are supported by all analyses and can be considered phylogenetic species. Overall divergence among these groups appears influenced by historical biogeographic events active during the Pliocene and Pleistocene.     

Molecular phylogeny of black fungus gnats (Diptera: Sciaroidea: Sciaridae) and the evolution of larval habitats

The phylogeny of the family Sciaridae is reconstructed, based on maximum likelihood, maximum parsimony, and Bayesian analyses of 4809 bp from two mitochondrial (COI and 16S) and two nuclear (18S and 28S) genes for 100 taxa including the outgroup taxa. According to the present phylogenetic analyses, Sciaridae comprise three subfamilies and two genus groups: Sciarinae, Chaetosciara group, Cratyninae, and Pseudolycoriella group + Megalosphyinae. Our molecular results are largely congruent with one of the former hypotheses based on morphological data with respect to the monophyly of genera and subfamilies (Sciarinae, Megalosphyinae, and part of postulated “new subfamily”); however, the subfamily Cratyninae is shown to be polyphyletic, and the genera Bradysia, Corynoptera, Leptosciarella, Lycoriella, and Phytosciara are also recognized as non-monophyletic groups. While the ancestral larval habitat state of the family Sciaridae, based on Bayesian inference, is dead plant material (plant litter + rotten wood), the common ancestors of Phytosciara and Bradysia are inferred to living plants habitat. Therefore, shifts in larval habitats from dead plant material to living plants may have occurred within the Sciaridae at least once. Based on the results, we discuss phylogenetic relationships within the family, and present an evolutionary scenario of development of larval habitats.     

Highly glycosylated flavonols at the genistoid boundary and the systematic position of Dermatophyllum

Among papilionoid legumes known to express the phenotype of quinolizidine alkaloid production, only Dermatophyllum occurs outside of the genistoid clade in phylogenetic analyses of DNA sequence data. Analysis of the foliar flavonoid glycosides of Dermatophyllum and possibly related clades, by liquid chromatography-UV spectrophotometry-mass spectrometry, revealed that taxa sampled from Dermatophyllum, Amphimas and the Cladrastis, lecointeoid and vataireoid clades contained mostly flavonol O-glycosides whereas taxa sampled from early-branching genistoid clades, the Andira clade and Aldina contained mostly flavone C-glycosides. Furthermore, leaves of Dermatophyllum secundiflorum and Dermatophyllum arizonicum contained, as their main flavonoids, two highly glycosylated flavonols: kaempferol 3-O-α-rhamnopyranosyl(1 → 2)[α-rhamnopyranosyl(1 → 6)]-β-galactopyranoside-7-O-α-rhamnopyranoside and its quercetin analogue. These compounds also occurred in Cladrastis kentukea, Styphnolobium japonicum and Pickeringia montana in the Cladrastis clade, Uribea tamarindoides and some samples of Zollernia in the lecointeoid clade, and in Amphimas pterocarpoides (another genus of uncertain relationships). The alkaloid and flavonoid phenotypes of Dermatophyllum each suggest affinities to different groups — a conflict which is accommodated by the current phylogenetic hypothesis, based on molecular data, that the genus is a possible sister to the genistoid clade but not a member of it.     

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.     

Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura: Bufonidae)

We investigated the phylogenetic relationships and estimated the history of species diversification and biogeography in the bufonid genus Ansonia from Southeast Asia, a unique organism with tadpoles adapted to life in strong currents chiefly in montane regions and also in lowland rainforests. We estimated phylogenetic relationships among 32 named and unnamed taxa using 2461 bp sequences of the mitochondrial 12S rRNA, tRNA^val, and 16S rRNA genes with equally-weighted parsimony, maximum likelihood, and Bayesian methods of inference. Monophyletic clades of Southeast Asian members of the genus Ansonia are well-supported, allowing for the interpretation of general biogeographic conclusions. The genus is divided into two major clades. One of these contains two reciprocally monophyletic subclades, one from the Malay Peninsula and Thailand and the other from Borneo. The other major clade primarily consists of Bornean taxa but also includes a monophyletic group of two Philippine species and a single peninsular Malaysian species. We estimated absolute divergence times using Bayesian methods with external calibration points to reconstruct the relative timing of faunal exchange between the major landmasses of Southeast Asia.     

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data,and a revised phylogeny for Sceloporus

Phrynosomatid lizards are among the most common and diverse groups of reptiles in western North America, Mexico, and Central America. Phrynosomatidae includes 136 species in 10 genera. Phrynosomatids are used as model systems in many research programs in evolution and ecology, and much of this research has been undertaken in a comparative phylogenetic framework. However, relationships among many phrynosomatid genera are poorly supported and in conflict between recent studies. Further, previous studies based on mitochondrial DNA sequences suggested that the most species-rich genus (Sceloporus) is possibly paraphyletic with respect to as many as four other genera (Petrosaurus, Sator, Urosaurus, and Uta). Here, we collect new sequence data from five nuclear genes and combine them with published data from one additional nuclear gene and five mitochondrial gene regions. We compare trees from nuclear and mitochondrial data from 37 phrynosomatid taxa, including a “species tree” (from BEST) for the nuclear data. We also present a phylogeny for 122 phrynosomatid species based on maximum likelihood analysis of the combined data, which provides a strongly-supported hypothesis for relationships among most phrynosomatid genera and includes most phrynosomatid species. Our results strongly support the monophyly of Sceloporus (including Sator) and many of the relationships within it. We present a new classification for phrynosomatid lizards and the genus Sceloporus, and offer a new tree with branch lengths for use in comparative studies.     

Timing of clade divergence and discordant estimates of genetic and morphological diversity in the Slender Madtom,Noturus exilis (Ictaluridae)

Phylogeographic relationships, the timing of clade diversification, and the potential for cryptic diversity in the Slender Madtom, Noturus exilis, was investigated using mitochondrial Cyt b, nuclear RAG2, shape analysis, and meristic and pigmentation data. Three well-supported and deeply divergent clades were recovered from analyses of genetic data: Little Red River (White River drainage) clade, Arkansas + Red River (Mississippi River) clade, and a large clade of populations from the rest of the range of the species. Recovered clades showed little to no diagnostic morphological differences, supporting previous hypotheses of morphological conservatism in catfishes, and indicating morphology may commonly underestimate diversity in this group of fishes. The Little Red River clade is the most distinct lineage of N. exilis with 11 POM pores (vs. 10 in other populations) and unique Cyt b haplotypes and RAG 2 alleles. However, treating it as a species separate from N. exilis would imply that the other major clades of N. exilis are more closely related to one another than they are to the Little Red River clade, which was not supported.The UCLN age estimate for Noturus was 23.9 mya (95% HPD: 13.49, 35.43), indicating a late Oligocene to early Miocene origin. The age of N. exilis was estimated as late Miocene at 9.7 mya (95% HPD: 5.32, 14.93). Diversification within the species spanned the late Miocene to mid-Pleistocene. The largest clade of N. exilis, which dates to the late Miocene, includes populations from the unglaciated Eastern and Interior Highlands as well as the previously glaciated Central Lowlands. Diversification of this clade coincides with a drastic drop in sea-level and diversification of other groups of Central Highlands fishes (Centrarchidae and Cyprinidae). Sub-clades dating to the Pleistocene show that northern populations occurring in previously glaciated regions resulted from dispersal from populations in the Ozarks up the Mississippi River following retreat of the Pleistocene glaciers. Pre-Pleistocene vicariance, such as drainage pattern changes of the Mississippi River, also played a prominent role in the history of the species. The incorporation of a temporal estimate of clade diversification revealed that in some instances, phylogeographic breaks shared with other aquatic species were best explained by different or persistent vicariant events through time, rather than a single shared event.     

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.     

Understanding the formation of ancient intertropical disjunct distributions using Asian and Neotropical hinged-teeth snakes (Sibynophis and Scaphiodontophis: Serpentes: Colubridae)

Numerous taxa show ancient intertropical disjunct distributions. Many can be explained by well-known processes of historical vicariance, such as the breakup of Gondwanaland. Others, such as Asian–Neotropical divergences are not as well understood. To clarify the phylogenetic position and understand biogeographic and temporal origins of the geographically disjunct and morphologically unique genera of hinged-teeth snakes, Scaphiodontophis (n = 1) and Sibynophis (n = 9; Colubridae), we inferred a time-calibrated phylogeny with additional 107 taxa representing the superfamily Colubroidea using four genes (c-mos, cyt-b, ND2, RAG-1; 3085 bp). We used this tree to estimate ancestral areas for the group. The results show that Scaphiodontophis is sister to Sibynophis, both originated in the late Eocene/Oligocene in Asia and likely dispersed through Beringia to the New World, but unlike other snake groups left no extant species in temperate North America. Current recognition of Scaphiodontophiinae renders Colubrinae paraphyletic, and we resurrect the previously named subfamily Sibynophiinae to encompass both genera and use the tribes Sibynophiini (Sibynophis) and Scaphiodontophiini (Scaphiodontophis) to highlight the geographically distinct areas occupied by these taxa. These results suggest that intercontinental dispersal with extinction in intermediate areas can explain puzzling patterns of ancient intertropical disjunct distributions.     

Phylogeny and character evolution in the bee-assassins (Insecta: Heteroptera: Reduviidae)

Apiomerus, the charismatic bee-assassins (>108 spp.), belong to the New World resin bugs in the harpactorine tribe Apiomerini (12 extant genera) that is characterized by a novel predation strategy, resin trap predation. Apiomerini also exhibit striking genitalic diversity that has shaped subgeneric classifications within the genus Apiomerus and females of some species of Apiomerus are known to engage in unique maternal care behaviors. The lack of a phylogenetic framework currently hinders evolutionary interpretations of genitalic morphology and maternal care. We here present a molecular phylogeny based on 4, 477 bp of six ribosomal and protein coding genes and 95 terminal taxa using parsimony and maximum likelihood approaches as a way of addressing these shortcomings. Apiomerini are monophyletic, with Heniartes being the sistergroup to all remaining taxa that form the monophyletic Manicocoris (Calliclopius, Manicocoris, Micrauchenus, and Ponerobia) and Apiomerus (Agriocoris, Apiomerus, and Sphodrolestes) clades. Previously proposed subgeneric groups are polyphyletic, but several proposed species groups are recovered as monophyletic. Ancestral state reconstruction of the metatibial comb indicates that this structure evolved in the ancestor of all Apiomerini where it was present in males and in females; it became strongly sexually dimorphic (better developed in females than in males) in the Apiomerus clade (Apiomerus + Agriocoris + Sphodrolestes). Genitalic features reveal a pattern of homoplasy, but frequently are nonetheless useful to diagnose supraspecific groups within Apiomerus. The complex genitalia found within Apiomerus are derived for that clade. We conclude that, using the metatibial comb as a proxy, maternal care is relatively common in the tribe Apiomerini and propose that it likely evolved at the base of the Apiomerus clade if not at the base of Apiomerini.     

Fixed,free, and fixed: The fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian–Triassic origin

Although the status of Crinoidea (sea lilies and featherstars) as sister group to all other living echinoderms is well-established, relationships among crinoids, particularly extant forms, are debated. All living species are currently placed in Articulata, which is generally accepted as the only crinoid group to survive the Permian–Triassic extinction event. Recent classifications have recognized five major extant taxa: Isocrinida, Hyocrinida, Bourgueticrinina, Comatulidina and Cyrtocrinida, plus several smaller groups with uncertain taxonomic status, e.g., Guillecrinus, Proisocrinus and Caledonicrinus. Here we infer the phylogeny of extant Crinoidea using three mitochondrial genes and two nuclear genes from 59 crinoid terminals that span the majority of extant crinoid diversity. Although there is poor support for some of the more basal nodes, and some tree topologies varied with the data used and mode of analysis, we obtain several robust results. Cyrtocrinida, Hyocrinida, Isocrinida are all recovered as clades, but two stalked crinoid groups, Bourgueticrinina and Guillecrinina, nest among the featherstars, lending support to an argument that they are paedomorphic forms. Hence, they are reduced to families within Comatulida. Proisocrinus is clearly shown to be part of Isocrinida, and Caledonicrinus may not be a bourgueticrinid. Among comatulids, tree topologies show little congruence with current taxonomy, indicating that much systematic revision is required. Relaxed molecular clock analyses with eight fossil calibration points recover Articulata with a median date to the most recent common ancestor at 231–252 mya in the Middle to Upper Triassic. These analyses tend to support the hypothesis that the group is a radiation from a small clade that passed through the Permian–Triassic extinction event rather than several lineages that survived. Our tree topologies show various scenarios for the evolution of stalks and cirri in Articulata, so it is clear that further data and taxon sampling are needed to recover a more robust phylogeny of the group.     

Capsid protein evolution and comparative phylogeny of novel porcine parvoviruses

In addition to the well known “classical” porcine parvovirus (PPV1; responsible for reproductive failure of susceptible sows) several new porcine parvoviruses have been recognized (PPV2, PPV3 and PPV4) in recent years. The genetic variation, characteristics and evolutionary factors shaping these novel PPVs were studied by comparing the complete capsid (cap) genes of PPVs from domestic pigs and wild boars. Using Bayesian coalescent methods we estimated the rate of nucleotide substitution for PPV2, PPV3 and PPV4 to be of the order of 3.86 × 10^?4–8.23 × 10^?4 subs site^?1 year^?1, similar to those commonly measured for RNA viruses, although this rate in case of PPV2 is probably influenced by frequent recombination events. Given such rapid evolutionary dynamics, it is likely that novel PPVs will continue to improve their capacity to spread among Suidae hosts worldwide. The mean time to the most recent common ancestor for the sampled genetic diversity of the newly discovered porcine parvoviruses was estimated. The results indicated that novel PPVs originated within approximately the last 70 years. Incongruent phylogenetic relationships of several strains suggested recombination events supported by several recombination-detecting methods and by split-decomposition phylogenetic networks. Analyses of the selective constraints acting on each codon suggest that some regions of PPV cap genes were under positive selection. This study showed that inter- and intraspecies recombination and diversifying selection pressures are prevalent across the cap genes of novel PPVs, and beside host switching and gene flow are important driving forces of their evolution and may be significant factors in the emergence of new viral variants.     

Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses

Despite many efforts to resolve evolutionary relationships among major clades of Cyprinidae, some nodes have been especially problematic and remain unresolved. In this study, we employ four nuclear gene fragments (3.3 kb) to infer interrelationships of the Cyprinidae.A reconstruction of the phylogenetic relationships within the family using maximum parsimony, maximum likelihood, and Bayesian analyses is presented. Among the taxa within the monophyletic Cyprinidae, Rasborinae is the basal-most lineage; Cyprinine is sister to Leuciscine. The monophyly for the subfamilies Gobioninae, Leuciscinae and Acheilognathinae were resolved with high nodal support. Although our results do not completely resolve relationships within Cyprinidae, this study presents novel and significant findings having major implications for a highly diverse and enigmatic clade of East-Asian cyprinids. Within this monophyletic group five closely-related subgroups are identified. Tinca tinca, one of the most phylogenetically enigmatic genera in the family, is strongly supported as having evolutionary affinities with this East-Asian clade; an established yet remarkable association because of the natural variation in phenotypes and generalized ecological niches occupied by these taxa.Our results clearly argue that the choice of partitioning strategies has significant impacts on the phylogenetic reconstructions, especially when multiple genes are being considered. The most highly partitioned model (partitioned by codon positions within genes) extracts the strongest phylogenetic signals and performs better than any other partitioning schemes supported by the strongest 2Δln Bayes factor. Future studies should include higher levels of taxon sampling and partitioned, model-based analyses.     

Phylogeography of Phrynocephalus erythrurus from the Qiangtang Plateau of the Tibetan Plateau

Phrynocephalus erythrurus of the Qiangtang Plateau occupies the highest regions of any reptile on earth. Here, we report mitochondrial DNA haplotypes sampled throughout the distribution of P. erythrurus and analyze patterns of genetic divergence among populations. The species diverged into two major lineages/subspecies at 3.67 mya corresponding to the Northern and Southern Qiangtang Plateau. The Northern Qiangtang lineage diverged into two subpopulations at 2.76 mya separated by the Beilu River Region and Wulanwula Mountains. Haplotypes from the southern Qiangtang lineage diverged 0.98 mya as a star-shaped pattern. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruptions to gene flow. There was no evidence of sudden recent range expansions within any of the clades/lineages. NCPA infers allopatric fragmentation and restricted gene flow as the most likely mechanisms of population differentiation. Our results also indicate the presence of at least three refugia since the Hongya glaciation. Mountain movement and glaciations since mid-Pliocene are considered to have shaped phylogenetic patterns of P. erythrurus. P. erythrurus parva is suggested as a valid subspecies of P. erythrurus. Using four calibration points, we estimate an evolutionary rate of 0.762% divergence per lineage per million years for a mitochondrial genomic segment comprising the genes encoding ND2, tRNA^Trp and tRNA^Ala.     

Biogeographic origin and radiation of Cuban Eleutherodactylus frogs of the auriculatus species group,inferred from mitochondrial and nuclear gene sequences

We studied phylogenetic relationships of the Eleutherodactylus auriculatus species group to infer colonization and diversification patterns in this endemic radiation of terrestrial frogs of the genus Eleutherodactylus in the largest of the Greater Antilles, Cuba. An initial screening of genetic diversity based on partial sequences of the 16S rRNA gene in almost 100 individuals of all species of the group and covering the complete known geographic range of their occurrence found most species endemic to small ranges in the eastern Cuban mountains while a single species was widespread over most of Cuba. Our molecular phylogeny, based on 3731 bp of four mitochondrial and one nuclear gene, suggests that most cladogenetic events within the group occurred among clades restricted to the eastern mountains, which acted as refugia and facilitated the diversification in this group. Our results reveal two separate colonization events of Central and Western Cuba and allow inferring the timing of the subsequent diversification events that occurred between 11 and 2 Mya. Because populations previously assigned to E. auriculatus represent four genetically strongly divergent lineages that also differ in their advertisement calls, we propose that E. auriculatus as currently recognized comprises four species. The difficulties in assigning the name auriculatus to any of these four species, and the fact that E. principalis is nested within one of them, stress the need for a thorough taxonomic revision of this group.     

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.     

Genetic studies in the recently divergent Eligmodontia puerulus and E. moreni (Rodentia,Cricetidae, Sigmodontinae) from Puna and Monte deserts of South America

Eligmodontia is a genus of phyllotine rodents adapted to arid environments with seven recognized species. The sister species E. puerulus and E. moreni are distributed in the adjacent highland Puna and lowland Monte deserts respectively, and show remarkable morphological and chromosomal differences. However, analyses of the cytochrome b gene showed important variability, without reciprocal monophyly between them. In order to study the evolutionary processes involved in the diversification of both taxa, we analyzed 1161 bp of the mitochondrial control region and flanking sequences (N = 60), as well as 759 bp of the first exon of the nuclear gene IRBP (N = 14). Individuals of both species from Jujuy, Catamarca and Mendoza Provinces of Argentina were previously karyotyped. Results showed that the mitochondrial sequences present high haplotype and nucleotide diversity within all population, and no haplotype was shared between both species. F_ST indicated that populations of both species were moderately structured. The network was constituted by two major haplogroups, one composed by E. puerulus samples from Jujuy, and the other composed of sequences of all studied populations. The Bayesian analysis showed three clusters, matching the network. Phylogenetic analysis recovered two clades with high support, in coincidence with the network groups. There was only one close join between sequences of both species, corresponding to samples from Catamarca. Thus, mitochondrial data suggested hybridization between both species in Catamarca, with asymmetric introgression. The IRBP showed low variability and, in the phylogenetic analysis, the sequences of E. puerulus form a monophyletic group with intermediate support, whereas those of E. moreni collapse into a basal polytomy. Our data indicated a recent divergence and absence of introgression in the nuclear genomes. The results at the population level with mitochondrial sequences, together with integrative taxonomy at the species level in a biogeographic context, suggest that climatic and geologic changes could have had an important role in the determination of genetic variability patterns observed in these rodents.