Systematics of the Southeast Asian mongooses (Herpestidae,Carnivora): solving the mystery of the elusive collared mongoose and Palawan mongoose

Although recent molecular studies have clarified the phylogeny of mongooses, the systematics of the Southeast Asian species was incomplete as the collared mongoose Urva semitorquata and some debatable taxa (Hose's mongoose, Palawan mongoose) were missing in the analyses. We sequenced three mitochondrial (cytochrome b, ND2, control region) and one nuclear (beta‐fibrinogen intron 7) fragments of the Southeast Asian mongooses to clarify the systematic position of the different species and populations occurring in this region. Our results showed that the collared mongoose is closely related to the crab‐eating mongoose Urva urva, these two species forming a sister‐group to the short‐tailed mongoose Urva brachyura. Despite Sumatran collared mongooses having a peculiar orange phenotype, we showed that they exhibited very little genetic divergence to individuals from Borneo. In contrast, the populations of the short‐tailed mongoose from Borneo were strongly divergent to those from Peninsular Malaysia and Sumatra, and these might represent separate species. Within the crab‐eating mongoose, we observed little geographical genetic structure. Our study suggests that Hose's mongoose is not a valid species. The Palawan mongooses did not cluster with the other populations of the short‐tailed mongoose; they were closer to the collared mongoose and should be included in this species. © 2014 The Linnean Society of London     

Systematics of a widespread Southeast Asian frog,Rana chalconota (Amphibia: Anura: Ranidae)

The abundant Sundaland forest frog, Rana chalconota, has long been considered a single widespread species, although some authors have recommended its division into regional subspecies. The discovery of co‐occurring pairs of morphologically distinct populations in three widely separated parts of the range led to a morphological and molecular analysis of populations from all parts of the known range. The results suggest that R. chalconota consists of at least seven species from Thailand through Borneo and Java. Existing names are applied to three of these species, R. chalconota (Schlegel), R. raniceps (Peters) and R. labialis Boulenger. We describe four others as new species and suggest the existence of one or two additional, unnamed species. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 123–147.     

Molecular Phylogeny of Nepenthaceae Based on Cladistic Analysis of Plastid trnK Intron Sequence Data

Abstract: Nepenthaceae are an exceptional family with regard to carnivory and the uniformity of characters. This makes it difficult to resolve phylogenetic relationships due to convergent evolution of morphological features. Using comparative sequencing of the chloroplast trnK intron, the monophyly of this complex family and hypotheses of infrageneric relationships were tested. Sequences from 71 Nepenthes taxa, representing all groups and two taxa of the closely related Ancistrocladaceae and Dioncophyllaceae as outgroup, were determined and analysed using maximum parsimony methods. Results of this analysis show that the isolated taxa N. distillatoria (Sri Lanka) and N. pervillei (Seychelles) are the most basal, clearly separated from the Madagascan taxa N. madagascariensis and N. masoalensis which are placed in a distinct subclade. This corresponds with some plesiomorphic characters shared by these taxa. N. khasiana (North India) has an intermediate position between these relic Western species and the remaining taxa. The species of the Malay Archipelago can be referred to three distinct lineages which indicate a correlation to biogeography. Thus the recent disjunct distribution of Nepenthes is interpreted as a result of an incisive extinction of progenitors, a process of migration and a subsequent diversification on the islands of Borneo, Sumatra, Sulawesi and New Guinea. Based on our molecular data, two interpretations concerning the origin of Nepenthes are possible: i) evolution in the Northern Tethys which is supported by fossil pollen records from the European Focene, or, ii) a Gondwanaland origin at a time when the Indian plate was separated from Madagascar. Molecular data indicate that colonization of SE Asia started from an ancient Indian stock. Subsequently, in the Malay Archipelago a new secondary centre of diversity developed. Madagascar, the Seychelles and New Caledonia were probably reached by migration via land bridges, starting from widespead common ancestors with subsequent extinction leaving the current taxa. There is no evidence for long‐distance dispersal. Current infragenic classification of Nepenthes is only partly in accordance with the phylogeny inferred from trnK intron data.     

Aspects of Pitcher Morphology and Spectral Characteristics of Six BorneanNepenthesPitcher Plant Species: Implications for Prey Capture

Pitcher plants of the genusNepenthesattract and trap invertebrateprey using nectar-secreting pitchers. Pitcher morphology andspectral reflectance characteristics were investigated for sixNepenthesspeciesfrom northwest Borneo (N. albomarginata, N. ampullaria, N. bicalcarata,N. gracilis, N. mirabilisvar.echinostomaandN. rafflesiana).Morphological measurements focused on the size of the pitcherrim (or peristome, the site of the major nectaries) in relationto pitcher length. The results show considerable interspecificvariation in morphology. Spectral reflectance measurements quantifiedthe degree of colour contrast between the peristome and pitcherbody, from ultraviolet (UV) to red wavelengths. The contrastmaxima for each species were compared with insect visual sensitivitymaxima. The six species showed a wide range of reflectance patterns,with pitchers ofN. rafflesianapossessing the greatest degreeof ‘fit’ between contrast maxima and insect sensitivitymaxima, in the UV, blue and green regions of the spectrum. Basedon the morphological and reflectance analyses, we hypothesizedthat pitchers ofN. rafflesianawould be more attractive to anthophilous(flower-visiting) invertebrates than the sympatricN. gracilis.Analysis of prey contents generally supported the hypothesis,suggesting possible interspecific resource partitioning. Morphologicaland spectral characteristics of the other species are discussedin relation to published studies on prey capture by those species.Copyright1999 Annals of Botany Company Borneo, carnivory, colour,Nepenthesspp., pitcher plants, prey attraction.     

The metazoan food webs from six Bornean Nepenthes species

Abstract.

• 1 Two contrasting hypotheses concerning patterns in food web structure within pitchers of Nepenthes are tested using new information from six species of Nepenthes from Borneo.
• 2 In general, predictions that webs will be more complex, and the food chains they contain will be longer, the closer they are to the centre of Nepenthes species diversity, are supported.
• 3 For Nepenthes albomarginata, a widespread species with a distinctive north Bornean form, a contrasting pattern is evident explicable in terms of the morphology of the pitchers and local habitat preferences.
• 4 General explanations for food web patterns will always be susceptible to exception, reflecting nuances of natural history.

     

A molecular test of Huxley's line: Cyrtandra (Gesneriaceae) in Borneo and the Philippines

A biogeographic and phylogenetic study of Cyrtandra (Gesneriaceae) in the Sundaland region (Borneo and Peninsular Malaysia) and the Philippines using nuclear ribosomal (ITS) DNA sequence data reveals a major division between the Cyrtandra floras of Sundaland and the Philippines. Palawan, the most westerly of the Philippine islands, emerges as an area of mixing between these two. The Bornean element in the Cyrtandra flora of Palawan (two species in our sample) appears to result from recent (i.e. Pleistocene) dispersal from Borneo. The remaining seven species sampled from Palawan are most closely related to those from elsewhere in the Philippines. However, the Palawan clade is sister to the other Philippine taxa, suggesting an ancient (possibly Pliocene) vicariance event. Huxley's line–a zoogeographic boundary placing Palawan and Borneo together–receives some support from this study as there is evidence of recent dispersal of Bornean flora into Palawan. However, in terms of more ancient biogeographic patterning of the region, Palawan has stronger links with the other Philippine islands.     

The cave population of Chaerilus Simon, 1877 from Palawan,Philippines, and description of a new species (Scorpiones: Chaerilidae)

The study of an important collection of scorpions, belonging to the genus Chaerilus, recently collected from a cave in the Palawan Island, Philippines, allows the clarification of the identity of this population, often misidentified with Chaerilus chapmani Vachon & Lourenço, 1985 known from caves in the Gunong Mulu National Park in Sarawak (Borneo). Chaerilus agnellivanniorum sp. n. is described from the Puerto Princesa Underground River Cave in Palawan Island based on 14 specimens, males, females, and juveniles. The new species is totally distinct morphologically from Chaerilus chapmani, a true troglobitic species. Chaerilus agnellivanniorum sp. n. may also be a true troglobitic element, but with a less marked degree of regression for several characters. Some comments on the ecology of the new species and on regional biogeography of Borneo and Palawan islands are also proposed.     

How long can insect species exist? Evidence from extant and fossil Micromalthus beetles (Insecta: Coleoptera)

Six new fossils of Micromalthus (Coleoptera: Archostemata) from Dominican amber are compared with extant and previously described fossil micromalthid beetles. The amber inclusions are well preserved and all important morphological features are visible. Taking into account the morphological variability of the extant species Micromalthus debilis LeConte, 1878 , it is not possible to find any morphological features that distinguish the fossils from the extant species. This also applies to the Dominican amber inclusion described as Micromalthus anasi Perkovsky, 2008, which therefore is considered a junior synonym of M. debilis. The lack of morphological change in M. debilis over time might possibly be explained by unusually stable environmental conditions, as this species occupies a very specialized ecological niche in decaying timber. A general survey of fossil insects indistinguishable from extant species is presented. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 300–311.     

A cladistic analysis of the Stygnicranainae Roewer, 1913 (Arachnida,Opiliones, Cranaidae) – where do longipalp cranaids belong?

A character survey compiling the morphological information of the subfamily Stygnicranainae was carried out. Two new species of Stygnicranaus Roewer, 1913 are described from Colombia and the new genus Agathocranaus is described from Ecuador. All known species of the subfamily are included in a matrix of 46 morphological characters. Parsimony analysis under implied weights recovered a monophyletic Stygnicranainae including Tryferos Roewer, 1931 plus Stygnicranaus and Agathocranaus. However, the usage of the four subfamilies of Cranaidae as currently defined is abandoned because the two largest subfamilies of Cranaidae – Cranainae and Prostygninae – represent paraphyletic groups (grades), whereas Heterocranainae is a superfluous subfamily, including only the genus Heterocranaus Roewer, 1913. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 470–494.     

Molecules,morphology, missing data and the phylogenetic position of a recently extinct madtom catfish (Actinopterygii: Ictaluridae)

Taxa missing large amounts of data pose challenges that may hinder the recovery of a well‐resolved, accurate phylogeny and leave questions surrounding their phylogenetic position. Systematists commonly have to contend with one or two species in a group for which there is little or no material available suitable for recovering molecular data. It is unclear whether these taxa can be better placed using analyses based on morphological data only, or should be included in broader analyses based on both morphological and molecular data. The extinct madtom catfish Noturus trautmani is known from few specimens for which molecular data are unavailable. We included this taxon in parsimony and Bayesian analyses of relationships of madtom catfishes based on a combination of morphological and molecular data. Results indicate that using a combination of morphological and molecular data does a better job at providing a phylogenetic placement for N. trautmani than morphology alone, even though it is missing all of its molecular characters. We provide a novel hypothesis of relationships among Noturus species and recommendations for classification within the group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 60–75.     

The distribution of the Malay civet Viverra tangalunga (Carnivora: Viverridae) across Southeast Asia: natural or human‐mediated dispersal?

The Malay civet Viverra tangalunga Gray, 1832 is a fairly large viverrid that has a wide distribution in both the Sundaic and Wallacea regions of Southeast Asia. We investigated the genetic diversity of V. tangalunga by analysing the mitochondrial DNA of 81 individuals throughout its range in order to elucidate the evolutionary history of this species and to test the hypotheses of natural dispersal and/or potential human introductions to some islands and regions. Our phylogenetic analyses revealed that V. tangalunga has a low matrilinear genetic diversity and is poorly structured geographically. Borneo is likely to have served as the ancestral population source from which animals dispersed during the Pleistocene. Viverra tangalunga could have naturally dispersed to Peninsular Malaysia, Sumatra, and Belitung, and also to several other Sunda Islands (Bangka, Lingga, and Bintang in the Rhio Archipelago), and to Palawan, although there is possible evidence that humans introduced V. tangalunga to the latter islands. Our results strongly suggested that V. tangalunga was transported by humans across Wallace's Line to Sulawesi and the Moluccas, but also to the Philippines and the Natuna Islands. Our study has shown that human‐mediated dispersal can be an important factor in understanding the distribution of some species in this region. © 2014 The Linnean Society of London     

An Ancient Origin for the Enigmatic Flat-Headed Frogs (Bombinatoridae: Barbourula) from the Islands of Southeast Asia

Background

The complex history of Southeast Asian islands has long been of interest to biogeographers. Dispersal and vicariance events in the Pleistocene have received the most attention, though recent studies suggest a potentially more ancient history to components of the terrestrial fauna. Among this fauna is the enigmatic archaeobatrachian frog genus Barbourula, which only occurs on the islands of Borneo and Palawan. We utilize this lineage to gain unique insight into the temporal history of lineage diversification in Southeast Asian islands.

Methodology/Principal Findings

Using mitochondrial and nuclear genetic data, multiple fossil calibration points, and likelihood and Bayesian methods, we estimate phylogenetic relationships and divergence times for Barbourula. We determine the sensitivity of focal divergence times to specific calibration points by jackknife approach in which each calibration point is excluded from analysis. We find that relevant divergence time estimates are robust to the exclusion of specific calibration points. Barbourula is recovered as a monophyletic lineage nested within a monophyletic Costata. Barbourula diverged from its sister taxon Bombina in the Paleogene and the two species of Barbourula diverged in the Late Miocene.

Conclusions/Significance

The divergences within Barbourula and between it and Bombina are surprisingly old and represent the oldest estimates for a cladogenetic event resulting in living taxa endemic to Southeast Asian islands. Moreover, these divergence time estimates are consistent with a new biogeographic scenario: the Palawan Ark Hypothesis. We suggest that components of Palawan''s terrestrial fauna might have “rafted” on emergent portions of the North Palawan Block during its migration from the Asian mainland to its present-day position near Borneo. Further, dispersal from Palawan to Borneo (rather than Borneo to Palawan) may explain the current day disjunct distribution of this ancient lineage.     

The allopolyploid origin of Narcissus obsoletus (Alliaceae): identification of parental genomes by karyotype characterization and genomic in situ hybridization

Karyological and genomic in situ hybridization (GISH) approaches provided evidence of the parentage and origin of the hybrid species Narcissus obsoletus. Here, we demonstrate that the putative parental species, N. serotinus L. and N. elegans (Haw.) Spach, recently proposed because of their intermediate morphological traits, have participated in the hybridization process forming this taxon. Karyotype characterization of parental genomes in populations from S Spain and N Morocco has revealed differences in chromosome length and karyotype asymmetry, highlighting their diploid nature. Multicolour GISH on metaphase plates of N. obsoletus, with N. serotinus and N. elegans DNA used as probes, showed differential fluorescent staining of 10 and 20 chromosomes from parental genomes, respectively. Both parental genomes were detected in the allopolyploid, albeit in a duplicated manner. Secondary hybridization between N. obsoletus and N. serotinus was also detected karyologically. Little karyological differentiation between different geographic regions was found in either N. serotinus or N. obsoletus. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 477–498.     

Three new species of deep‐sea Gromia (Protista,Rhizaria) from the bathyal and abyssal Weddell Sea,Antarctica

We describe three new species of the genus Gromia from bathyal and abyssal depths in the Weddell Sea. The new species are characterized by a combination of morphological and molecular criteria. All three species possess a distinct oral capsule and a layer of ‘honeycomb membranes’, which form the inner part of the organic test wall. Both these features are typical of gromiids. Their identification as gromiids is confirmed by analyses of partial small subunit ribosomal DNA (SSU rDNA) gene sequences. Gromia marmorea sp. nov. is a rounded species with a prominent oral capsule and a characteristically mottled appearance. In Gromia melinus sp. nov. , the test surface exhibits a polygonal pattern of ridges, with a layer of clay particles coating the surface between the ridges. Gromia winnetoui sp. nov. represents an elongate morphotype in which the organic test is enclosed within an agglutinated case, a feature previously unknown in gromiids. Phylogenetic analysis using the maximum‐likelihood method revealed that all three species form distinct clades, reflecting the morphological differences among Weddell Sea species, as well as between deep‐water Southern Ocean Gromia and previously described gromiids. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 451–469.     

Different pitcher shapes and trapping syndromes explain resource partitioning in Nepenthes species

Nepenthes pitcher plants display interspecific diversity in pitcher form and diets. This species‐rich genus might be a conspicuous candidate for an adaptive radiation. However, the pitcher traits of different species have never been quantified in a comparative study, nor have their possible adaptations to the resources they exploit been tested. In this study, we compare the pitcher features and prey composition of the seven Nepenthes taxa that grow in the heath forest of Brunei (Borneo) and investigate whether these species display different trapping syndromes that target different prey. The Nepenthes species are shown to display species‐specific combinations of pitcher shapes, volumes, rewards, attraction and capture traits, and different degrees of ontogenetic pitcher dimorphism. The prey spectra also differ among plant species and between ontogenetic morphotypes in their combinations of ants, flying insects, termites, and noninsect guilds. According to a discriminant analysis, the Nepenthes species collected at the same site differ significantly in prey abundance and composition at the level of order, showing niche segregation but with varying degrees of niche overlap according to pairwise species comparisons. Weakly carnivorous species are first characterized by an absence of attractive traits. Generalist carnivorous species have a sweet odor, a wide pitcher aperture, and an acidic pitcher fluid. Guild specializations are explained by different combinations of morpho‐functional traits. Ant captures increase with extrafloral nectar, fluid acidity, and slippery waxy walls. Termite captures increase with narrowness of pitchers, presence of a rim of edible trichomes, and symbiotic association with ants. The abundance of flying insects is primarily correlated with pitcher conicity, pitcher aperture diameter, and odor presence. Such species‐specific syndromes favoring resource partitioning may result from local character displacement by competition and/or previous adaptations to geographically distinct environments.     

Morphological and molecular description of new species of squat lobster (Crustacea: Decapoda: Galatheidae) from the Solomon and Fiji Islands (South‐West Pacific)

The family Galatheidae is among the most diverse families of anomuran decapod crustaceans, and the South‐West Pacific is a biodiversity hot spot for these squat lobsters. Attempts to clarify the taxonomic and evolutionary relationships of the Galatheidae on the basis of morphological and molecular data have revealed the existence of several cryptic species, differentiated only by subtle morphological characters. Despite these efforts, however, relationships among genera are poorly understood, and the family is in need of a detailed systematic review. In this study, we assess material collected in different surveys conducted in the Solomon Islands, as well as comparative material from the Fiji Islands, by examining both the morphology of the specimens and two mitochondrial markers (cytochrome oxidase subunit I, COI, and 16S rRNA). These two sources of data revealed the existence of eight new species of squat lobster, four of which were ascribed to the genus Munida, two to the genus Paramunida, one to the genus Plesionida, and the last species was ascribed to the genus Agononida. These eight species are described along with phylogenetic relationships at the genus level. Our findings support the taxonomic status of the new species, yet the phylogenetic relationships are not yet fully resolved. Further molecular analysis of a larger data set of species, and more conserved genes, will help clarify the systematics of this group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 465–493.     

Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves,Coracii)

We report a nearly complete skeleton of a new species of stem roller (Aves, Coracii) from the early Eocene Green River Formation of North America. The new species is most closely related to two species‐depauperate lineages, Coraciidae (rollers) and Brachypteraciidae (ground rollers), that form a monophyletic crown clade (Coracioidea) with an exclusively Old World extant distribution. Phylogenetic analysis utilizing a matrix of 133 morphological characters and sequence data from three genes (RAG‐1, c‐myc, and ND2) identifies the new species as a stem member of the Coracii more closely related to the crown clade than the only previously identified New World taxon, Primobucco mcgrewi. The phylogenetic placement of the new species and Primobucco mcgrewiindicates a widespread northern hemisphere distribution in the Eocene with subsequent restriction to Africa, Madagascar, Australia, and temperate to tropical parts of Europe and Asia. It provides evidence of further ecological diversity in early stem Coracii and convergence on crown morphologies. The new species contributes to mounting evidence that extant distributions for major avian subclades may be of comparatively recent origin. Further late Palaeogene sampling is needed to elucidate potential drivers for shifting avian distributions and disappearance of Coracii from North America. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 586–611.     

Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae)

Hypotheses on the taxonomic status of two Bolivian Pristimantis with taxonomic problems are assessed by an integrative taxonomic approach that integrates three independent lines of evidence: external morphology, prezygotic reproductive barriers (advertisement calls) and reciprocal monophyly (phylogenetic analyses of partial 16S mtDNA sequences). Central Andean Bolivian populations previously assigned to either P. peruvianus or P. dundeei, and lowland Amazonian populations from southern Peru and northern Bolivia previously considered P. peruvianus do not correspond to these species. Indeed, multivariate analyses of qualitative and quantitative morphological and bioacoustic characters, and phylogenetic analyses support the hypothesis that they represent different, previously unknown, cryptic lineages. They are herein described as new species. The former is a sibling species of P. fenestratus that inhabits the Amazonian and semideciduous forests of the Andean foothills in central Bolivia. The latter is sibling to the Andean species P. danae and is parapatric to it in the Amazonian lowland forests and adjacent foothills of northern Bolivia, southern Peru and adjacent Brazil. Most species of Neotropical frogs, and especially Pristimantis, have been described by using external qualitative morphological characters only. An extended integrative taxonomic approach, as exemplified herein, may lead to the discovery of many other cryptic and sibling lineages that would increase the species numbers of tropical areas. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 97–122.