New insights to the molecular phylogenetics and generic assessment in the Rhacophoridae (Amphibia: Anura) based on five nuclear and three mitochondrial genes, with comments on the evolution of reproduction

The phylogenetic relationships among 12 genera of treefrogs (Family, Rhacophoridae), were investigated based on a large sequence data set, including five nuclear (brain-derived neurotrophic factor, proopiomelanocortin, recombination activating gene 1, tyrosinase, rhodopsin) and three mitochondrial (partial 12S and 16S ribosomal RNA and the complete valine t-RNA) genes. Phylogenetic analysis of the nuclear gene sequences resolved three major clades. The first group included Philautus, Pseudophilautus, Kurixalus, Gracixalus, and Theloderma moloch; Pseudophilautus and Kurixalus were sister taxa. The second group consisted of Nyctixalus and Theloderma. The third group contained Feihyla, Polypedates, Rhacophorus, and Chiromantis vittatus; Polypedates and Feihyla were sister taxa. Analyses of the nuclear and mitochondrial genes supported the following results: (1) Genus Liuixalus formed the sister group of all other rhacophorines. (2) Philautus, Theloderma, and Chiromantis were not resolved as monophyletic genera. Four groups, including Philautus ocellatus and P. hainanus, P. longchuanensis and P. gryllus, P. banaensis, and P. quyeti nested well within the genera Liuixalus, Pseudophilautus, Kurixalus, and Gracixalus, respectively. (3) Theloderma moloch and Chiromantis vittatus did not cluster with other species of Theloderma and Chiromantis, respectively. Foam nesting evolved only once, as did laying eggs in a jelly-like matrix containing some bubbles. Terrestrial direct development evolved twice in the Rhacophoridae.     

Phylogenetic resolution and systematics of the Asian tree frogs,Rhacophorus (Rhacophoridae,Amphibia)

Li, J.T., Li, Y., Murphy, R.W., Rao, D.‐Q. & Zhang, Y.‐P. (2012). Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia). —Zoologica Scripta, 41, 557–570. The treefrog genus Rhacophorus, a large genus with 80 species, has a wide range, occurring eastward from India to China, Japan, South‐east Asia, the Greater Sunda Islands and the Philippines. The phylogenetic relationships and taxonomic recognition of many species are very controversial. To stabilize the taxonomy, the phylogenetic relationships among about 52 species are investigated from 96 samples using mtDNA sequence data. Matrilineal relationships based on maximum likelihood and Bayesian inference methods resolve three well‐supported lineages (A, B and C), although the phylogenetic relationships among three lineages remain ambiguous. Analyses support recognition of two previously assigned subgenera, Leptomantis and Rhacophorus, and these correspond to lineages A and B, respectively. Given that we have three strongly supported lineages, that these lineages are morphologically distinct, and the constrained geographic distributions of these groups, we recognize each lineage as a taxon. Subgenus Leptomantis includes species mainly from Malaysia, Indonesia and the Philippines. Subgenus Rhacophorus contains a mix of species occurring in India, Indochina and southern China. Lineage C accommodates species distributed mostly in East Asia, including Japan and China. Based on genetic and morphological data from type localities, the taxonomic recognition of some species needs to be reconsidered. Rhacophorus pingbianensis and Polypedates spinus are considered as junior synonyms of Rhacophorus duboisi. Specimens of Rhacophorus rhodopus from Vietnam and Hainan, China likely represent an undescribed, cryptic species.     

Re-examination of the phylogeny of Rhacophoridae (Anura) based on mitochondrial and nuclear DNA

The phylogenetic relationships among rhacophorid frogs are under dispute. We use partial sequences of three mitochondrial (12S rRNA, 16S rRNA, and cytochrome b) and three nuclear protein-coding (Rag-1, rhodopsin exon 1, and tyrosinase exon 1) genes from 57 ingroup taxa and eight outgroup taxa to propose a hypothesis for phylogenetic relationships within Rhacophoridae. Our results support recognition of the genus Feihyla, and Chiromantis is the sister taxon to the clade formed by Feihyla, Polypedates and Rhacophorus. We place Aquixalus odontotarsus within Kurixalus, and the remaining species of Aquixalus and Philautus jinxiuensis into the genus Gracixalus. We give Philautus (Kirtixalus) the rank of genus and place Philautus menglaensis within it. The division of species groups among Chinese Rhacophorus needs revision, and a cryptic species is revealed within Rhacophorus nigropunctatus. Rhacophorus pingbianensis is considered a synonym of Rhacophorus omeimontis. The validity of Rhacophorus hui is confirmed by present molecular evidence.     

Patterns of reproductive‐mode evolution in Old World tree frogs (Anura,Rhacophoridae)

The Old World tree frogs (Anura: Rhacophoridae), with 387 species, display a remarkable diversity of reproductive modes – aquatic breeding, terrestrial gel nesting, terrestrial foam nesting and terrestrial direct development. The evolution of these modes has until now remained poorly studied in the context of recent phylogenies for the clade. Here, we use newly obtained DNA sequences from three nuclear and two mitochondrial gene fragments, together with previously published sequence data, to generate a well‐resolved phylogeny from which we determine major patterns of reproductive‐mode evolution. We show that basal rhacophorids have fully aquatic eggs and larvae. Bayesian ancestral‐state reconstructions suggest that terrestrial gel‐encapsulated eggs, with early stages of larval development completed within the egg outside of water, are an intermediate stage in the evolution of terrestrial direct development and foam nesting. The ancestral forms of almost all currently recognized genera (except the fully aquatic basal forms) have a high likelihood of being terrestrial gel nesters. Direct development and foam nesting each appear to have evolved at least twice within Rhacophoridae, suggesting that reproductive modes are labile and may arise multiple times independently. Evolution from a fully aquatic reproductive mode to more terrestrial modes (direct development and foam nesting) occurs through intermediate gel nesting ancestral forms. This suggests that gel nesting is not only a possible transitional state for the evolution of terrestriality, but also that it is a versatile reproductive mode that may give rise to other terrestrial reproductive modes. Evolution of foam nesting may have enabled rhacophorids to lay a larger number of eggs in more open and drier habitats, where protection from desiccation is important. Terrestrial direct development allows frogs to lay eggs independent of bodies of water, in a diversity of humid habitats, and may represent a key innovation that facilitated the evolution of nearly half of all known rhacophorid species.     

Using the Zeta (ζ) diversity approach for understanding the effects of variations in climatic covariates,vegetation patterns,and human influence on species composition of arboreal frogs in India

The biodiversity patterns of an ecosystem provide an opportunity for understanding the drivers of the community structure and, together, interpreting better conservation strategies for the species. Here we map the patterns in compositional turnover of the arboreal frog species (Anura: Rhacophoridae) in India and explore the impacts of climatic covariates, vegetation patterns, and human influence on driving their species composition. Using the previously published data, we compiled the occurrence matrix for the species of nine genera of the family Rhacophoridae from India. The species turnover trends were analyzed using the zeta diversity decline and retention-rate analysis. We further used the multisite generalized dissimilarity modeling (MS-GDM) to test the variations in climatic, vegetational, and anthropogenic drivers that better explain the species turnover. The results suggested a low nestedness among the genera of arboreal frogs barring Polypedates and Raorchestes. The difference in the mean temperature of the warmest quarter in the colder temperature regime is the primary driver of the compositional turnover of arboreal frog species. Also, differences in the precipitation seasonality of the lower and higher precipitation regime emerged as a driver of the compositional turnover for some genera. The differences in diversity patterns and their corresponding drivers are ideally only species-specific or group-specific. We suggest their utility while designing conservation efforts for co-occurring groups in a region.     

Amino acid composition of the protein in preemergence nests of Polistes (Polistes) riparius, and its similarity to the consubgeneric wasp, P. (P.) chinensis (Hymenoptera: Vespidae)

Amino acid composition of the protein in the oral secretion, which is widely used for construction and maintenance of social wasp nests, was analyzed in preemergence nests of Polistes (Polistes) riparius. The kinds and proportion (%) of amino acids of the protein detected from nests of P. riparius were very similar to those of a consubgeneric species, P. (P.) chinensis, but were conspicuously different from those of other social wasp genera. Further, it was estimated that protein contents in oral secretion of P. riparius were nearly the same as those of P. chinensis; namely, foundresses of P. riparius, which build much larger nests than those of P. chinensis, did not reduce relative protein contents to produce more oral secretion at a smaller cost. Amino acid composition may reflect phylogenetic relationships among wasp taxa. Received: March 10, 2000 / Accepted: May 29, 2000     

Frankixalus,a New Rhacophorid Genus of Tree Hole Breeding Frogs with Oophagous Tadpoles

Despite renewed interest in the biogeography and evolutionary history of Old World tree frogs (Rhacophoridae), this family still includes enigmatic frogs with ambiguous phylogenetic placement. During fieldwork in four northeastern states of India, we discovered several populations of tree hole breeding frogs with oophagous tadpoles. We used molecular data, consisting of two nuclear and three mitochondrial gene fragments for all known rhacophorid genera, to investigate the phylogenetic position of these new frogs. Our analyses identify a previously overlooked, yet distinct evolutionary lineage of frogs that warrants recognition as a new genus and is here described as Frankixalus gen. nov. This genus, which contains the enigmatic ‘Polypedates’ jerdonii described by Günther in 1876, forms the sister group of a clade containing Kurixalus, Pseudophilautus, Raorchestes, Mercurana and Beddomixalus. The distinctiveness of this evolutionary lineage is also corroborated by the external morphology of adults and tadpoles, adult osteology, breeding ecology, and life history features.     

Behavior of the Avian Parasite Philornis downsi (Diptera: Muscidae) in and Near Host Nests in the Galapagos Islands

The Avian Vampire Fly, Philornis downsi, has invaded the Galapagos Islands, where it causes high mortality of endemic and native landbird species, including most species of Darwin’s finches. Control methods are under development, but key information is missing about the reproductive biology of P. downsi and the behavior of flies in and near nests of their hosts. We used external and internal nest cameras to record the behavior of P. downsi adults within and outside nests of the Galapagos Flycatcher, Myiarchus magnirostris, throughout all stages of the nesting cycle. These recordings showed that P. downsi visited flycatcher nests throughout the day with higher fly activity during the nestling phase during vespertine hours. The observations also revealed that multiple P. downsi individuals can visit nests concurrently, and that there are some interactions among these flies within the nest. Fly visitation to nests occurred significantly more often while parent birds were away from the nest than in the nest, and this timing appears to be a strategy to avoid predation by parent birds. We report fly mating behavior outside the nest but not in the nest cavity. We discuss the relevance of these findings for the adaptive forces shaping P. downsi life history strategies as well as rearing and control measures.

     

Parallel origins of apomixis in two diverged evolutionary lineages in tribe Potentilleae (Rosaceae)

We synthesized the results from a flow cytometric seed screen and the literature to infer the phylogenetic origin and the geographical and taxonomic distribution of apomixis in tribe Potentilleae (Rosaceae). We distinguished between regular sexuality and apomixis, the zygotic and parthenogenetic origin of the embryo, and the pseudogamous (i.e. sexual) versus autonomous origin of the endosperm. The combined evidence provides information on reproductive modes for 11 genera and 120 species. For the first time records on reproductive mode are provided for the genus Farinopsis, 29 species (from five genera), and seven series of Potentilla. Regular sexuality was observed in Aphanes, Argentina, Comarum, Dasiphora, Drymocallis, Farinopsis, Fragaria, Horkeliella, Potentilla, and Sibbaldia. Reliable evidence for apomixis is restricted to two evolutionary lineages of Potentilleae: the Potentilla core group and Alchemilla/Aphanes. Early evolutionary divergence of these lineages (approximately 50 Mya), characterized by pseudogamous and autonomous apomictic seed formation, respectively, suggests parallel origins of apomixis. Apomixis is shown to be taxonomically widespread in the whole Northern Hemisphere distribution range of Potentilla, a pattern that is explained by hybrid transfer and repeated intercontinental dispersals. Taxonomic and geographical coverage is discussed with reference to species diversity centres of genera. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 214–229.     

Generic allocation of Indian and Sri Lankan Philautus (Anura: Rhacophoridae) inferred from 12S and 16S rRNA genes

The generic allocation of Indian and Sri Lankan Philautus needs further examination. In this study, a comprehensive understanding of the phylogeny of Indian and Sri Lankan Philautus is obtained based on 12S and 16S rRNA genes. All phylogenetic analyses indicate that Indian-Sri Lankan Philautus, Philautus menglaensis, Philautus longchuanensis, and Philautus gryllus form a well supported clade, separate from Philautus of Sunda Islands that form another well supported clade representing true Philautus. This result supports the designation of the genus Pseudophilautus to accommodate the Indian and Sri Lankan species. Pseudophilautus consists of two major lineages, one comprises the majority of Indian species, Chinese species, and Southeast Asian species, and one comprises all Sri Lankan species and a few Indian species. Pseudophilautus may have originated in South Asia and dispersed into Southeast Asia and China. Based on the results, we further suggest that Philautus cf. gryllus (MNHN1997.5460) belongs to the genus Kurixalus.     

PHYLOGENY OF THE HYDRODICTYACEAE (CHLOROPHYCEAE): INFERENCES FROM rDNA DATA1

The hydrodictyacean green algal lineage has been the focus of much research due to the fossil record of at least some members, their ornamented cell walls, and their distinctive reproductive strategies. The phylogeny of the family was, until recently, exclusively morphology based. This investigation examines hydrodictyacean isolates from several culture collections, focusing on sequences from ribosomal data: 18S rDNA, 26S rDNA (partial), and internal transcribed spacer (ITS)‐2 data. Results from phylogenetic analyses of independent and combined data matrices support the Hydrodictyaceae as a monophyletic lineage that includes isolates of Chlorotetraedron, Hydrodictyon, Pediastrum, Sorastrum, and Tetraedron. Phylogenetic analyses of rDNA data indicate that the three‐dimensional coenobium of Hydrodictyon is evolutionarily distinct from the three‐dimensional coenobium of Sorastrum. The more robust aspects of the ITS‐2 data corroborate the 18S+26S rDNA topology and provide a structural autapomorphy for the Hydrodictyaceae and Neochloridaceae, that is, an abridgment of helix IV in the secondary structure. The rDNA data do not support monophyly of Pediastrum but rather suggest the existence of four additional hydrodictyacean genera: Monactinus, Parapediastrum, Pseudopediastrum, and Stauridium.     

Igniting taxonomic curiosity: The amazing story of Amazonocrinis with the description of a new genus Ahomia gen. nov. and novel species of Ahomia,Amazonocrinis, and Dendronalium from the biodiversity-rich northeast region of India

Five cyanobacterial strains exhibiting Nostoc-like morphology were sampled from the biodiversity hotspots of the northeast region of India and characterized using a polyphasic approach. Molecular and phylogenetic analysis using the 16S rRNA gene indicated that the strains belonged to the genera Amazonocrinis and Dendronalium. In the present investigation, the 16S rRNA gene phylogeny clearly demarcated two separate clades of Amazonocrinis. The strain MEG8-PS clustered along with Amazonocrinis nigriterrae CENA67, which is the type strain of the genus. The other three strains ASM11-PS, RAN-4C-PS, and NP-KLS-5A-PS clustered in a different clade that was phylogenetically distinct from the Amazonocrinis sensu stricto clade. Interestingly, while the 16S rRNA gene phylogeny exhibited two separate clusters, the 16S–23S ITS region analysis did not provide strong support for the phylogenetic observation. Subsequent analyses raised questions regarding the resolving power of the 16S–23S ITS region at the genera level and the associated complexities in cyanobacterial taxonomy. Through this study, we describe a novel genus Ahomia to accommodate the members clustering outside the Amazonocrinis sensu stricto clade. In addition, we describe five novel species, Ahomia kamrupensis, Ahomia purpurea, Ahomia soli, Amazonocrinis meghalayensis, and Dendronalium spirale, in accordance with the International Code of Nomenclature for algae, fungi, and plants (ICN). Apart from further enriching the genera Amazonocrinis and Dendronalium, the current study helps to resolve the taxonomic complexities revolving around the genus Amazonocrinis and aims to attract researchers to the continued exploration of the tropical and subtropical cyanobacteria for interesting taxa and lineages.     

A REVISED CLASSIFICATION OF THE DICTYOTEAE (DICTYOTALES,PHAEOPHYCEAE) BASED ON rbcL AND 26S RIBOSOMAL DNA SEQUENCE ANALYSES1

Dictyota is a genus of tropical to warm temperate brown algae characterized by parenchymatous, flattened thalli that grow from a single, transversely oriented apical cell. Dictyota is currently distinguished from allied genera of the tribe Dictyoteae (Dilophus, Glossophora, Glossophorella, and Pachydictyon) by the structure of the cortical and medullary layers, as well as the relative abundance of surface proliferations. Even though the traditional classification of the Dictyoteae has repeatedly been criticized in the past, the absence of sound molecular data has so far discouraged any new taxonomic proposals apart from a merger of Dilophus with Dictyota, which has been accepted by only part of the phycological community. Phylogenetic analysis of rbcL gene, partial 26S rDNA sequence, and combined data sets, including four of five generitypes, demonstrates that the traditional classification does not accurately reflect the evolutionary history of the group. None of the genera are resolved as a monophyletic clade. Hence, a merger of Glossophora, Glossophorella, and Pachydictyon in Dictyota is proposed. Two new genera, Canistrocarpus (incorporating D. cervicornis, D. crispata, and D. magneana) and Rugulopteryx (accommodating D. radicans, Dil. suhrii, and Dil. marginata), are proposed. Both genera are supported by molecular indications and a combination of reproductive and vegetative characters. The position of Dil. fastigiatus as a clade sister to Dictyota s.l. and the absence of Dil. gunnianus, the generitype of Dilophus, from the analyses, prevented us from making a more definite statement on the status of the latter genus.     

Nestbox provisioning in a rural population of Eurasian Kestrels: breeding performance,nest predation and parasitism

The breeding biology of the Eurasian Kestrel Falco tinnunculusin nestboxes in farmland was studied to test for differences between artificial and natural sites. We report on the direct effect of nestbox provisioning on some life-history traits and how nestbox use affects nest predation and parasitism. Five types of nest-sites were available: nestboxes on poles and trees (artificial sites), stick nests on trees, stick nests on pylons and holes in buildings (‘natural’ sites). The Kestrel population increased from 23 pairs in 1993 (prior to nestbox installation) to 55 in 1998 as nestboxes were provided. In general, pairs breeding in trees started to lay later than those nesting in nestboxes on poles or in building holes, but this difference was probably associated with habitat quality rather than nest type. Differences in clutch size were found between nest-sites in some years, and were associated with laying date and, probably, with variation in territory quality. Using only data from successful nests, pairs breeding in nestboxes produce more fledglings than those in building holes or pylons. The frequency of nest predation was higher in natural sites than in nestboxes. The number of fledglings from pairs breeding in nestboxes was higher than from those breeding in old stick nests in trees when all nests were considered. Nestbox provisioning had no effect on the occurrence of the ectoparasite Carnus hemapterus, but chicks from nestboxes showed higher intensity of infection. Our results suggest that nestbox provisioning increases reproductive success and the frequency of nest predation or intensity of parasite infestation in Kestrels.     

A phylogenetic analysis of Pleurodema (Anura: Leptodactylidae: Leiuperinae) based on mitochondrial and nuclear gene sequences,with comments on the evolution of anuran foam nests

Species of the genus Pleurodema are relatively small, plump frogs that mostly occur in strong‐seasonal and dry environments. The genus currently comprises 14 species distributed from Panama to southern Patagonia. Here we present a phylogenetic analysis of Pleurodema, including all described species and several outgroups. Our goals include testing its monophyly and the monophyly of the species groups that were historically proposed, and studying the evolution of some character systems, particularly macroglands and egg‐clutch structure; this last point also provided the chance for a discussion of foam nest evolution in anurans. Our dataset includes portions of the mitochondrial genes cytochromeb, 12S, 16S, and the intervening tRNA^Val; the nuclear gene sequences include portions of rhodopsin exon 1 and seven in absentia homolog I. Our results support a clade composed of Pleurodema and including the monotypic Somuncuria Lynch, 1978 nested within it. The latter genus is therefore considered a junior synonym of Pleurodema and its sole species is added to this genus. Furthermore, our results indicate the non‐monophyly of several species groups proposed previously. We recognize four clades in Pleurodema: the P. bibroni clade (P. bibroni, P. cordobae and P. kriegi), the P. thaul clade (P. bufoninum, P. marmoratum, P. somuncurensis and P. thaul), the P. brachyops clade (P. alium, P. borellii, P. brachyops, P. cinereum, P. diplolister and P. tucumanum) and the P. nebulosum clade (P. guayapae and P. nebulosum). Our results further indicate the need for a taxonomic reassessment of P. borellii and P. cinereum (as did previous studies), P. guayapae and P. nebulosum, and the three species in the P. bibroni clade. Pleurodema shows a striking pattern of variation in presence/absence of lumbar glands. Our results indicate multiple losses or independent gains of this character associated with defensive displays. The reproductive modes of Pleurodema include four different egg‐clutch structures. The optimization of these indicates that there are at least two independent transformations from the plesiomorphic mode of foam nests to egg‐clutch structures involving gelatinous masses of different sorts (ovoid plates, masses, or strings). We hypothesize that these independent transformations could involve changes at the behavioural (the loss of foam beating behaviour by the parent) and/or structural level (transformations involving the pars convoluta dilata, the section of the oviduct where the foam‐making substance is secreted). Finally, our study of foam nest evolution in Pleurodema is extended to the other groups of anurans where foam‐nesting occurs, on the basis of available data and recent phylogenetic hypotheses. In the different hyloid groups where it occurs, foam‐nesting evolved from clutches laid in water. However, in all ranoids in which foam‐nesting occurs, it evolved from terrestrial clutches, with eggs laid hanging in vegetation, or, if the clutches are laid on a restricted volume of water, involving endotrophic development. © The Willi Hennig Society 2012.     

Physical gills in Elmidae (Coleoptera: Byrrhoidea): Structure and evolutionary pattern of plastron in Stenelmis and related genera

Many species within Elmidae (Coleoptera: Byrrhoidea) have plastrons composed of flattened setae. However, some genera display fine plastrons on the epicuticle, called plastron hairs. In Japanese elmids, members of the genera Stenelmis, Ordobrevia, Nomuraelmis and Leptelmis bear ventral plastron hairs. Based on a maximum likelihood tree including most Japanese genera within Elmidae, we found that these genera are monophyletic and that plastron hairs are a derived character in Elmidae. We also found that the genus Graphelmis bears jigsaw puzzle‐like plastron scales with plastron hair‐like projections, and is sister to the group with plastron hairs.