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Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases. [ABSTRACT FROM AUTHOR]

Motivation Phylogenetic and phylogenomic analyses require multi-gene input files in different formats, but there are few user-friendly programs facilitating the workflow of combining, concatenating or separating, aligning and exploring multi-gene datasets. Results We present Concatenator, a user-friendly GUI-driven program that accepts single-marker and multi-marker DNA sequences in different input formats, including Fasta, Phylip and Nexus, and that outputs concatenated sequences as single-marker or multi-marker Fasta, interleaved nexus or Phylip files, including command files for downstream model selection in IQ-TREE. It includes the option to (re)align markers with MAFFT and produces exploratory trees with FastTree. Although tailored for medium-sized phylogenetic projects, Concatenator is able to process phylogenomic datasets of up to 30 000 markers. Availability and implementation Concatenator is written in Python, with C extensions for MAFFT and FastTree. Compiled stand-alone executables of Concatenator for MS Windows and Mac OS along with a detailed manual can be downloaded from www.itaxotools.org ; the source code is openly available on GitHub (https://github.com/iTaxoTools/ConcatenatorGui). [ABSTRACT FROM AUTHOR]

Based on recent discoveries and an integrative study including external morphology, osteology and molecular genetics, we continue to revise the Madagascar-endemic chameleons of the Calumma boettgeri complex (within the Calumma nasutum species group). We describe three new species of these small-sized, occipital-lobed chameleons. Calumma uetzi sp. nov. is a species from the Sorata and Marojejy massifs (northern Madagascar), with a spectacular display coloration in males, clearly notched occipital lobes, and females with a dorsal crest. Calumma lefona sp. nov. is described based on a male specimen from Tsaratanana (northern Madagascar), with widely notched occipital lobes, a long and pointed rostral appendage, a dorsal crest, and a frontoparietal fenestra in the skull roof. This last character also occurs in six other Calumma species, and its presence and width are correlated with the elevational distribution of the species. Calumma juliae sp. nov. is known only from a small, isolated forest fragment near Moramanga in eastern Madagascar, and only females have been found so far. It is a relatively large member of the C. nasutum group, with a distinct dorsal crest and numerous infralabial scales. Two of the new species are known exclusively from their type localities, and we recommend protection of the habitats of all three as soon as possible. [ABSTRACT FROM AUTHOR]

Assortative mating is a common pattern in sexually reproducing species, but the mechanisms leading to assortment remain poorly understood. By using the European common frog (Rana temporaria) as a model, we aim to understand the mechanisms leading to sizeassortative mating in amphibians. With data from natural populations collected over several years, we first show a consistent pattern of size-assortative mating across our 2 study populations. We subsequently ask if assortative mating may be explained by mate availability due to temporal segregation of migrating individuals with specific sizes. With additional experiments, we finally assess whether size-assortative mating is adaptive, i.e. influenced by mating competition among males, or by reduced fertilization in size-mismatched pairs. We find that size-assortative mating is in accordance with differences in mate availability during migration, where larger individuals of both sexes reach breeding ponds earlier than smaller individuals. We observe an indiscriminate mate choice behavior of small males and an advantage of larger males pairing with females during scramble competition. The tactic of small males, to be faster and less discriminative than large males, may increase their chances to get access to females. Experimental tests indicate that the fertilization success is not affected by size assortment. However, since female fecundity is highly correlated with body size, males preferring larger females should maximize their number of offspring. Therefore, we conclude that in this frog species mate choice is more complex than formerly believed. [ABSTRACT FROM AUTHOR]

Marine iguanas are among the most highly emblematic taxa of the Galápagos archipelago but have paradoxically received little attention from taxonomists. Amblyrhynchus is currently considered as a monotypic genus with a total of seven subspecies, A. cristatus cristatus, A. c. nanus, A. c. venustissimus, A. c. albemarlensis, A. c. hassi, A. c. mertensi and A. c. sielmanni. Although consensually followed for more than half a century, this classification does not properly reflect the main natural subdivisions inferred by more recent molecular evolutionary studies. We integrate population genetics, phylogenomics and comparative morphology to propose an updated taxonomy reflecting the evolutionary history of this group. We recognize a single species with 11 divergent population clusters at the level of subspecies: A. c. albermarlensis is recognized as a junior synonym of A. c. cristatus, and five new subspecies are described: A. c. godzilla subsp. nov. (San Cristóbal-Punta Pitt), A. c. jeffreysi subsp. nov. (Wolf and Darwin), A. c. hayampi subsp. nov. (Marchena), A. c. trillmichi subsp. nov. (Santa Fé) and A. c. wikelskii subsp. nov. (Santiago). Recognizing the genetically divergent population clusters as subspecies also highlights several of them as management units in need of conservation efforts, such as the two subspecies endemic to San Cristóbal. [ABSTRACT FROM AUTHOR]

Males of all reed frog species ( Anura: Hyperoliidae) have a prominent, often colourful, gular patch on their vocal sac, which is particularly conspicuous once the vocal sac is inflated. Although the presence, shape, and form of the gular patch are well-known diagnostic characters for these frogs, its function remains unknown. By integrating biochemical and histological methods, we found strong evidence that the gular patch is a gland producing volatile compounds, which might be emitted while calling. Volatile compounds were confirmed by gas chromatography-mass spectrometry in the gular glands in 11 species of the hyperoliid genera Afrixalus, Heterixalus, Hyperolius, and Phlyctimantis. Comparing the gular gland contents of 17 specimens of four sympatric Hyperolius species yielded a large variety of 65 compounds in species-specific combinations. We suggest that reed frogs might use a complex combination of at least acoustic and chemical signals in species recognition and mate choice. © 2013 The Authors. Biological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 828-838. [ABSTRACT FROM AUTHOR]

Amphibians often show complex histories of intraspecific and interspecific genetic introgression, which might differ in mitochondrial and nuclear genes. In our study of the genetic differentiation of the European common frog, Rana temporaria (159 specimens from 23 populations were analyzed for 24 presumptive allozyme loci; 82 specimens were sequenced for a 540-bp fragment of the mitochondrial 16S rRNA gene), multilocus correspondence analysis (CA) and Bayesian assignment tests of the nuclear data were concordant in identifying 2 population groups corresponding to 1) the Pyrenees in the east and 2) the Galicia and Asturias regions in the west, the latter corresponding to the subspecies R. temporaria parvipalmata. Geographically intermediate populations were genetically intermediate in the allozyme CA and, less clearly in the Bayesian assignment, with mitochondrial haplotypes exclusively belonging to the parvipalmata group. This indicates different degrees of introgression in the mitochondrial and nuclear genomes. Although Pyrenean high-altitude populations are morphologically distinct from low-altitude populations, these 2 groups were not separate clusters in any analysis. This suggests that the morphological differences may be due to fast adaptation to elevational gradients, likely under maintenance of gene flow, and that the underlying genetic changes are not detectable by the analyzed markers. We argue that a parsimonious explanation for the observed pattern along the east–west axis in northern Spain may be competition between invading and resident populations, with no need to invoke selection. However, in order to conclusively rule out selective processes, additional and finer scale data are required to test for asymmetric mating preference/behaviour, sex-biased gene flow, or sex-biased survival of potential hybrids. [ABSTRACT FROM PUBLISHER]

We report results of a morphological and ecological study on the funnel-mouthed tadpoles of litter frogs in the subgenus Chonomantis, genus Mantidactylus, from Madagascar. The larvae of these riparian frogs are characterized by umbelliform oral discs and absence of well developed keratodonts. Based on specimens identified by DNA barcoding we provide general morphological descriptions for the larvae of all eight nominal species plus two candidate species of Chonomantis, and describe the buccal anatomy of seven species. We detected only minor morphometric differences amongst species in mainly the relative size of the oral disc. In addition we found one candidate species (here named Mantidactylus sp. 59) to be characterized by rudimentary keratodont rows, Mantidactylus brevipalmatus by enlarged lungs, and Mantidactylus aerumnalis by a distinct colour pattern. Ecological data gathered in 30 streams in the Ranomafana area indicated important abundance differences amongst species. Mantidactylus melanopleura and Mantidactylus opiparis, which are the two most widespread species over Madagascar, were also locally most abundant in Ranomafana but interestingly showed no diagnostic morphological differences and fully overlapped in morphometric variables. Microhabitat choice of Chonomantis in Ranomafana was characterized by a clear preference for slow-moving stretches of streams with a substrate of submerged dead leaves. In general Chonomantis tadpoles were thus remarkably similar in their morphology and ecology. Considering the high degree of sympatric occurrence, with up to five species of the subgenus co-occurring along the same stream, this indicates a rather low influence of larval competition in creating selective pressures for specialization in these frogs. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, , 149-183. [ABSTRACT FROM AUTHOR]

Madagascar's flora and fauna are remarkable both for their diversity and supraspecific endemism. Moreover, many taxa contain large numbers of species with limited distributions. Several hypotheses have been proposed to explain this high level of microendemism, including 1) riverine barrier, 2) mountain refuge, and 3) watershed contraction hypotheses, the latter 2 of which center on fragmentation due to climatic shifts associated with Pliocene/Pleistocene glaciations. The Malagasy leaf chameleon genus Brookesia is a speciose group with a high proportion of microendemic taxa, thus making it an excellent candidate to test these vicariance scenarios. We used mitochondrial and nuclear sequence data to construct a Brookesia phylogeny, and temporal concordance with Pliocene/Pleistocene speciation scenarios was tested by estimating divergence dates using a relaxed-clock Bayesian method. We strongly reject a role for Pliocene/Pleistocene climatic fluctuations in species-level diversification of Brookesia. We also used simulations to test the spatial predictions of the watershed contraction model in a phylogenetic context, independent of its temporal component, and found no statistical support for this model. The riverine barrier model is likewise a qualitatively poor fit to our data, but some relationships support a more ancient mountain refuge effect. We assessed support for the 3 hypotheses in a nonphylogenetic context by examining altitude and species richness and found a significant positive correlation between these variables. This is consistent with a mountain refuge effect but does not support the watershed contraction or riverine barrier models. Finally, we find repeated higher level east-west divergence patterns 1) between the 2 sister clades comprising the Brookesia minima group and 2) within the clade of larger leaf chameleons, which shows a basal divergence between western and eastern/northern sister clades. Our results highlight the central role of phylogeny in any meaningful tests of species-level diversification theories. [ABSTRACT FROM PUBLISHER]

Three species of boid snakes are recognized in Madagascar, namely the genus Sanzinia (one species and two subspecies) and the genus Acrantophis (two species). In the present study, we studied the patterns of genetic variation of these species across Madagascar using a fragment of the mitochondrial 16S rRNA gene in 77 specimens. To support the phylogenetic relationships of the lineages identified, three further gene fragments (cytochrome b, 12S rRNA and c-mos) were analyzed in a reduced but representative set of samples. The results obtained corroborate that the genus Sanzinia includes two highly divergent mitochondrial lineages that evolved independently from each other on the east versus the west side of Madagascar. Each of these lineages presents a further subdivision that separates northern from southern groups. The nuclear marker showed no variation among the Malagasy boas, indicating either very low substitution rates in this gene or relatively recent speciation events coupled with high mitochondrial substitution rates. Because the broad geographic sampling detected no admixture among haplotypic lineages within Sanzinia, it is hypothesized that these may represent distinct species. Deviant haplotypes of snakes morphologically similar to Acrantophis dumerili indicate that this taxon may be a complex of two species as well. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 640–652. [ABSTRACT FROM AUTHOR]

Cophyline narrow-mouthed frogs (Anura: Microhylidae) are a diverse endemic radiation of Madagascar. Cophylines contain a high proportion of range restricted species and constitute a good model system to understand patterns of evolutionary diversification in tropical ecosystems. We combine spatial and phylogenetic analyses for a near-complete taxon sample to test competing explanations for patterns of species richness (SR) and endemism. Our reconstruction of the phylogeny of cophylines indicates the presence of 22 new species and several instances of nonmonophyly. We found a strong historical signal in current cophyline ranges indicating a high degree of spatial niche conservatism in clade diversification, with clades occurring in the North of Madagascar constituting the most derived in the phylogeny. We identified six positively correlated centers of SR and endemism that can neither be explained by stochastic models such as elevational or latitudinal mid-domain effect, nor by low-elevation river catchments. Instead, the locations of these centers in areas spanning a high altitudinal range in combination with specific climatic parameters support a key role of mountainous areas for speciation of these anurans, although we cannot exclude an influence of habitat loss due to human impact. High conservation priority is ascribed to these areas. [ABSTRACT FROM AUTHOR]

Several genera of frogs from Madagascar, classified in the family Mantellidae, subfamily Mantellinae, possess structures commonly called ‘femoral glands’ on the ventral side of their shanks. The question arises as to the origin and phylogenetic significance of these glands. A molecular phylogeny based on 3601 nucleotide DNA sequences of three mitochondrial and two nuclear genes of 30 mantellid species provided strong support for monophyly of the included mantellines, all characterized by enlarged femoral gland clusters, as well as for those with gland clusters of coordinated central arrangement of secretion ducts. However, the phylogeny also strongly supported the hypothesis of convergent evolution of structurally similar glands in unrelated frogs ( Indirana, Petropedetes), and several trends of convergent evolution of gland structure within mantellines. We studied the light microscopic structure of the femoral glands in a representative array of 18 mantellid species. Males of all species of the subfamily Mantellinae were characterized by clusters of distinct single glands. Each was structurally similar to an enlarged granular gland and secreted independently, probably through a single duct. By contrast, the largely semi-aquatic frogs in the genus Mantidactylus had a specialized cluster of glands, in which the secretion ducts led into a macroscopically recognizable central depression. In Boophis opisthodon, a mantellid species of the subfamily Boophinae without externally recognizable femoral glands, we observed a large number of enlarged granular glands of various sizes in the ventral skin of the shank. This observation is consistent with the hypothesis that the large and more uniform organs of mantellines are derived granular glands. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92, 529–539. [ABSTRACT FROM AUTHOR]

The larval morphology of Madagascan frogs of the family Microhylidae, subfamilies Dyscophinae and Scaphiophryninae, is described based on material from the genera Dyscophus ( D. insularis), Paradoxophyla ( P. palmata) and five species of the enigmatic genus Scaphiophryne: S. brevis, S. calcarata, S. madagascariensis, S. menabensis and S. spinosa. The latter are known to have larvae that are intermediate between the filter-feeding larval type typical for most microhylids and the generalized tadpole of most ranoid and hyloid frogs. However, the two detailed descriptions available to date, referring to Scaphiophryne calcarata and S. gottlebei, pointed to important differences in size and oral morphology within Scaphiophryne. Our data confirm that all studied Scaphiophryne have horny beaks but lack keratodonts and are to be referred to the psammonektonic ecomorphological guild. Scaphiophryne brevis and S. calcarata have rather small tadpoles (up to 22 mm total length) whereas S. madagascariensis, S. menabensis and S. spinosa, as well as S. gottlebei, have larger tadpoles (up to 48 mm total length) with a striking distance between the skin and the internal organs, giving the head and body a balloon-like appearance. These two morphological tadpole groups agree with previously published molecular phylogenetic data and support the classification of these species in the two subgenera Pseudohemisus and Scaphiophryne. The larva of the genus Paradoxophyla, the sister group of Scaphiophryne, has a typical microhylid filter-feeding morphology and shares many synapomorphies with other microhylids. Since a convergent evolution of these features is unlikely, the ancestors of Scaphiophryne appear to have re-acquired their beak and other characters that at first view are plesiomorphic. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 151, 555–576. [ABSTRACT FROM AUTHOR]

The Seychelles harbour an endemic frog family, the Sooglossidae, currently containing two genera: Sooglossus, with three species, and Nesomantis, with one species. These unique frogs are generally considered to be basal neobatrachians, although their relationships to other neobatrachian taxa, except the Nasikabatrachidae, remain unresolved. Our molecular phylogeny based on a dataset consisting of fragments of the nuclear rag-1 and rag-2 genes, as well as mitochondrial 16S rRNA in representatives of the major neobatrachian lineages, confirmed the previously postulated Sooglossidae + Nasikabatrachidae clade and the placement of the South American Caudiverbera with the Australian Myobatrachidae, but did not further resolve the position of sooglossids. Our results do, however, unambiguously show sooglossids to be monophyletic but the genus Sooglossus to be paraphyletic, with the type species Sooglossus sechellensis being more closely related to Nesomantis thomasseti than to Sooglossus gardineri and Sooglossus pipilodryas, in agreement with morphological, karyological, and bioacoustic data. As a taxonomic consequence, we propose to consider the genus name Nesomantis as junior synonym of Sooglossus, and to transfer the species thomasseti to Sooglossus. For the clade composed of the species gardineri and pipilodryas, here, we propose the new generic name Leptosooglossus. A significant genetic differentiation of 3% was found between specimens of Sooglossus thomasseti from the Mahé and Silhouette Islands, highlighting the need for further studies on their possible taxonomic distinctness. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 91, 347–359. [ABSTRACT FROM AUTHOR]

Madagascar harbors four large adaptive radiations of endemic terrestrial mammals: lemurs, tenrecs, carnivorans, and rodents. These rank among the most spectacular examples of evolutionary diversification, but their monophyly and origins are debated. The lack of Tertiary fossils from Madagascar leaves molecular studies as most promising to solve these controversies.We provide a simultaneous reconstruction of phylogeny and age of the four radiations based on a 3.5-kb dataset from three nuclear genes (ADRA2B, vWF, and AR). The analysis supports each as amonophyletic clade, sister to Africantaxa, and thereby identifies four events of colonization out of Africa. To infer the time windows for colonization, we take into account both the divergence from the closest noninsular sister group and the initial intrainsular radiation, which is a novel but conservative approach in studies of the colonization history of Madagascar. We estimate that lemurs colonized Madagascar between 60 million years ago (Mya) (split from lorises) and 50 Mya (lemur radiation) (70-41 Mya taking 95% credibility intervals into account), tenrecs between 42 and 25 Mya (50-20 Mya), carnivorans between 26 and 19 Mya (33-14 Mya),and rodents between 24 and 20 Mya (30-15 Mya). These datings suggest at least two asynchronous colonization events: by lemurs in the Late Cretaceous-Middle Eocene, and by carnivorans and rodents in the Early Oligocene-Early Miocene. The colonization by tenrecs may have taken place simultaneously with either of these two events, or in a third event in the Late Eocene-Oligocene. Colonization by at least lemurs, rodents, and carnivorans appears to have occurred by overseas rafting rather than via a land bridge hypothesized to have existed between 45 and 26 Mya, but the second scenario cannot be ruled out if credibility intervals are taken into account. [ABSTRACT FROM AUTHOR]

Amphibians are characterized both by a strongly increasing number of newly discovered species and by a high degree of decline. The observed increase in species numbers, over 25 percent in 11 years, is largely due to the intensified exploration of tropical areas and the application of more efficient techniques such as bioacoustics and molecular genetics, rather than to the elevation of subspecies to species rank or the distinction of species that were formerly considered synonymous. In the mantellid frogs of Madagascar, the many species newly described between 1992 and 2004 were as genetically divergent as those described in previous research periods, and most had not been collected previously, corroborating the lack of "taxonomic inflation" in this vertebrate class. Taxonomic exploration is still desperately needed to avoid misinterpretations in global conservation policy. [ABSTRACT FROM AUTHOR]

Several house gecko species of the genus Hemidactylus are almost cosmopolitan lizards, with distributions that have probably been shaped by natural transoceanic dispersal as well as by more recent human introductions. Here we revise the Hemidactylus populations of Madagascar and compare them genetically with populations from other sites in the Indian Ocean region. Morphological data strongly confirm the occurrence of three Hemidactylus species on Madagascar: Hemidactylus frenatus, distributed along the western coast of Madagascar; H. platycephalus, restricted to the north-west and the widespread H. mercatorius that occurs throughout the island, including coastal areas at sea level as well as big cities (Antananarivo, Fianarantsoa) at altitudes of 1200–1300 m above sea level. Analyses of partial sequences of the 16S rRNA gene in 46 Hemidactylus specimens from Madagascar, East Africa, South Asia, and the Comoro and Mascarene archipelagos demonstrated the presence of a fourth species, H. brooki, on the Mascarenes (Réunion, Rodrigues, and Mauritius) and Comoros (Moheli). The Malagasy populations of H. platycephalus were genetically uniform and differentiated from the African and Comoroan specimens studied. H. frenatus had a relatively low genetic differentiation over the whole region with no recognizable phylogeographical structure, indicating more recent colonizations or introductions. In contrast, H. mercatorius showed a strong phylogeographical structure of haplotypes, with two distinctly different lineages in Madagascar. Moreover, all Malagasy specimens differed strongly from the single African specimen included. This indicates that populations of H. mercatorius in Madagascar have a long history that predates human settlement. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 83, 115–130. [ABSTRACT FROM AUTHOR]

We describe the larval stages of three species of the Asian-African tiger frogs Hoplobatrachus chinensis, H. occipitalis and H. tigerinus. The tadpoles of all three species are very similar, with peculiar oral features: (1) double rows of needle-like labial teeth, (2) strong emarginations on the large jaw sheaths and (3) keratinized spurs on the buccal floor. Characters 1 and 2 (and perhaps 3) are probably related to the carnivorous habits of these tadpoles. A molecular phylogeny based on 2430 base pairs of two nuclear and four mitochondrial genes corroborated monophyly of Asian and African Hoplobatrachus, and identified Euphlyctis as their sister group. Tadpoles of the latter genus lack buccal spurs and double labial tooth rows but share large jaw sheaths, the upper with a medial projection. Therefore, the common ancestor of Euphlyctis and Hoplobatrachus probably was also characterized by this state, and may have been facultatively carnivorous. Further carnivorous specializations in Hoplobatrachus could explain why tiger frogs have been so successful in populating arid environments where ponds are at high risk of desiccation. Larval morphology may prove to be the key innovation which enabled them to disperse, in the Late Cenozoic, into their current very wide distribution area in Asia and Africa. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 171–181. [ABSTRACT FROM AUTHOR]