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Tropical ecosystems are challenging for pinnipeds due to fluctuating food availability. According to previous research, the Galapagos sea lion (GSL, Zalophus wollebaeki) adopts trophic flexibility to face such conditions. However, this hypothesis comes from studies using traditional methods (hard‐parts analysis of scat and isotopic analysis from tissue). We studied the diet of five rookeries in the southeastern Galapagos bioregion (which harbors the highest GSL density), via DNA‐metabarcoding of scat samples. The DNA‐metabarcoding approach may identify consumed prey with a higher taxonomic resolution than isotopic analysis, while not depending on hard‐parts remaining through digestion. Our study included five different rookeries to look for evidence of trophic flexibility at the bioregional level. We detected 98 prey OTUs (124 scats), mostly assigned to bony‐fish taxa; we identified novel prey items, including a shark, rays, and several deep‐sea fish. Our data supported the trophic flexibility of GSL throughout the studied bioregion since different individuals from the same rookery consumed prey coming from different habitats and trophic levels. Significant diet differentiations were found among rookeries, particularly between Punta Pitt and Santa Fe. Punta Pitt rookery, with a more pronounced bathymetry and lower productivity, was distinguished by a high trophic level and consumption of a high proportion of deep‐sea prey; meanwhile, Santa Fe, located in more productive, shallow waters over the shelf, consumed a high proportion of epipelagic planktivorous fish. Geographic location and heterogeneous bathymetry of El Malecon, Española, and Floreana rookeries would allow the animals therein to access both, epipelagic prey over the shelf, and deep‐sea prey out of the shelf; this would lead to a higher prey richness and diet variability there. These findings provide evidence of GSL adopting a trophic flexibility to tune their diets to different ecological contexts. This strategy would be crucial for this endangered species to overcome the challenges faced in a habitat with fluctuating foraging conditions. [ABSTRACT FROM AUTHOR]

An accurate species‐level taxonomy is paramount for biogeographical research, and conversely, biogeographical data are of importance for species delimitation. We here review recent developments and future perspectives of taxonomy of direct relevance for biogeographers. The understanding that species are independently evolving segments of population‐level lineages, the rise of integrative approaches to delimit such lineages, and the advent of high‐throughput sequencing have considerably renewed the discipline of taxonomy. Using genome‐scale molecular datasets, the extent of admixture across hybrid zones can now be effectively assessed and the evolutionary independence of lineages inferred, leading to more reliable and comparable species delimitation criteria. Substantially divergent but admixing phylogeographical lineages can conveniently be named as subspecies, thus avoiding taxonomic oversplitting and taxonomic inflation. At the same time, comprehensive DNA barcoding and DNA metabarcoding efforts are uncovering an enormous proportion of undiscovered biotic diversity, and we encourage the development of bioinformatic pipelines that combine high‐throughput species discovery and delimitation with diagnosis and scientific naming, to approach a biotic inventory of the globe without abandoning the established Linnaean system. [ABSTRACT FROM AUTHOR]

Increasing complexity and specialisation of modern sciences has led to increasingly collaborative publications, as well as the involvement of commercial services. Modern integrative taxonomy likewise depends on many lines of evidence and is increasingly complex, but the trend of collaboration lags and various attempts at 'turbo taxonomy' have been unsatisfactory. We are developing a taxonomic service in the Senckenberg Ocean Species Alliance to provide fundamental data for new species descriptions. This will also function as a hub to connect a global network of taxonomists, assembling an alliance of scientists working on potential new species to tackle both the extinction and inclusion crises we face today. The current rate of new species descriptions is simply too slow; the discipline is often dismissed as old fashioned, and there is a crisis level need for taxonomic descriptions to come to grips with the scale of Anthropocene biodiversity loss. Here, we envision how the process of describing and naming species would benefit from a service supporting the acquisition of descriptive data. Also see the video abstract here: https://youtu.be/E8q3KJor_F8 [ABSTRACT FROM AUTHOR]

How environmental factors shape patterns of biotic diversity in tropical ecosystems is an active field of research, but studies examining the possibility of ecological speciation in terrestrial tropical ecosystems are scarce. We use the isolated rainforest herpetofauna on the Montagne d'Ambre (Amber Mountain) massif in northern Madagascar as a model to explore elevational divergence at the level of populations and communities. Based on intensive sampling and DNA barcoding of amphibians and reptiles along a transect ranging from ca. 470–1470 m above sea level (a.s.l.), we assessed a main peak in species richness at an elevation of ca. 1000 m a.s.l. with 41 species. The proportion of local endemics was highest (about 1/3) at elevations >1100 m a.s.l. Two species of chameleons (Brookesia tuberculata, Calumma linotum) and two species of frogs (Mantidactylus bellyi, M. ambony) studied in depth by newly developed microsatellite markers showed genetic divergence up the slope of the mountain, some quite strong, others very weak, but in each case with genetic breaks between 1100 and 1270 m a.s.l. Genetic clusters were found in transect sections significantly differing in bioclimate and herpetological community composition. A decrease in body size was detected in several species with increasing elevation. The studied rainforest amphibians and reptiles show concordant population genetic differentiation across elevation along with morphological and niche differentiation. Whether this parapatric or microallopatric differentiation will suffice for the completion of speciation is, however, unclear, and available phylogeographic evidence rather suggests that a complex interplay between ecological and allopatric divergence processes is involved in generating the extraordinary species diversity of Madagascar's biota. Our study reveals concordant patterns of diversification among main elevational bands, but suggests that these adaptational processes are only part of the complex of processes leading to species formation, among which geographical isolation is probably also important. [ABSTRACT FROM AUTHOR]

Species are the fundamental units of life and evolution. Their recognition is essential for science and society. Molecular methods have been increasingly used for the identification of animal species, despite several challenges.Here, we explore with genomic data from nine animal lineages a set of nuclear markers, namely metazoan‐level universal single‐copy orthologs (metazoan USCOs), for their use in species delimitation. Our data sets include arthropods and vertebrates. We use various data assembly strategies and use coalescent‐based species inference as well as population admixture analyses and phenetic methods.We demonstrate that metazoan USCOs distinguish well closely related morphospecies and consistently outperform classical mitochondrial DNA barcoding in discriminating closely related species in different animal taxa, as judged by comparison with morphospecies delimitations. USCOs overcome the general shortcomings of mitochondrial DNA barcodes, and due to standardization across Metazoa, also those of other approaches. They accurately assign samples not only to lower but also to higher taxonomic levels.Metazoan USCOs provide a powerful and unifying framework for DNA‐based species delimitation and taxonomy in animals and their employment could result in a more efficient use of research data and resources. [ABSTRACT FROM AUTHOR]

Understanding the genomic basis of adaptation to different abiotic environments is important in the context of climate change and resulting short‐term environmental fluctuations.Using functional and comparative genomics approaches, we here investigated whether signatures of genomic adaptation to a set of environmental parameters are concentrated in specific subsets of genes and functions in lacertid lizards and other vertebrates.We first identify 200 genes with signatures of positive diversifying selection from transcriptomes of 24 species of lacertid lizards and demonstrate their involvement in physiological and morphological adaptations to climate. To understand how functionally similar these genes are to previously predicted candidate functions for climate adaptation and to compare them with other vertebrate species, we then performed a meta‐analysis of 1,100 genes under selection obtained from ‐omics studies in vertebrate species adapted to different abiotic factors.We found that the vertebrate gene set formed a tightly connected interactome, which was to 23% enriched in previously predicted functions of adaptation to climate, and to a large part (18%) involved in organismal stress response. We found a much higher degree of identical genes being repeatedly selected among different animal groups (43.6%), and of functional similarity and post‐translational modifications than expected by chance, and no clear functional division between genes used for ectotherm and endotherm physiological strategies. In total, 171 out of 200 genes of Lacertidae were part of this network.These results highlight an important role of a comparatively small set of genes and their functions in environmental adaptation and narrow the set of candidate pathways and markers to be used in future research on adaptation and stress response related to climate change. [ABSTRACT FROM AUTHOR]

Madagascar's biota is characterized by an extraordinary species richness, with a high degree of endemism. The island's freshwater habitats harbor numerous micro‐endemic species, restricted to particular regions and thus particularly at risk of extinction, due to deforestation, overfishing, and introduction of exotic species. The present study investigates for which threatened Malagasy freshwater fish species ex situ populations have already been established, as a baseline to prioritize actions to develop an effective ex situ conservation breeding network. Populations in zoos and aquaria were primarily determined using the Zoological Information System. Of 173 fish species recorded from Malagasy freshwater habitats, 123 exclusively inhabit freshwater; 79 of these are endemic to Madagascar, and 50 are classified as threatened. Our survey found 21 Malagasy freshwater fish species kept in zoos worldwide, of which 19 are endemic and threatened (22 if counting species kept by private breeders). Nine of the 19 Malagasy freshwater fish species kept in zoos have successfully reproduced within the 12 months preceding our survey. The ex situ conservation activities for threatened Malagasy freshwater fishes thus have not improved significantly since the strong start in the early 2000s. More than half of the 50 threatened endemic Malagasy freshwater fish species (viz. 31 species) are not kept ex situ, including 11 species ranked as Critically Endangered. Based on these findings we call for a better distribution of offspring among institutions, including private breeders in the framework of citizen conservation initiatives; a closer connection of ichthyological field research in Madagascar with conservation breeding efforts to set up ex situ populations—both in Madagascar and abroad—of species not yet kept in captivity; and the development of effective, integrated in situ and ex situ conservation strategies. RESEARCH HIGHLIGHTS: Of the 79 endemic Malagasy freshwater fish species 50 are ranked as threatened and only 19 kept in zoos worldwide.We propose an ex situ conservation breeding network for threatened Malagasy freshwater fish species linked with in situ strategies. [ABSTRACT FROM AUTHOR]

A wide range of data types can be used to delimit species and various computer‐based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha‐taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the "inferred species". The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them. [ABSTRACT FROM AUTHOR]

Subdivided Pleistocene glacial refugia, best known as "refugia within refugia", provided opportunities for diverging populations to evolve into incipient species and/or to hybridize and merge following range shifts tracking the climatic fluctuations, potentially promoting extensive cytonuclear discordances and "ghost" mtDNA lineages. Here, we tested which of these opposing evolutionary outcomes prevails in northern Iberian areas hosting multiple historical refugia of common frogs (Rana cf. temporaria), based on a genomic phylogeography approach (mtDNA barcoding and RAD‐sequencing). We found evidence for both incipient speciation events and massive cytonuclear discordances. On the one hand, populations from northwestern Spain (Galicia and Asturias, assigned to the regional endemic R. parvipalmata), are deeply‐diverged at mitochondrial and nuclear genomes (~4 My of independent evolution), and barely admix with northeastern populations (assigned to R. temporaria sensu stricto) across a narrow hybrid zone (~25 km) located in the Cantabrian Mountains, suggesting that they represent distinct species. On the other hand, the most divergent mtDNA clade, widespread in Cantabria and the Basque country, shares its nuclear genome with other R. temporaria s. s. lineages. Patterns of population expansions and isolation‐by‐distance among these populations are consistent with past mitochondrial capture and/or drift in generating and maintaining this ghost mitochondrial lineage. This remarkable case study emphasizes the complex evolutionary history that shaped the present genetic diversity of refugial populations, and stresses the need to revisit their phylogeography by genomic approaches, in order to make informed taxonomic inferences. [ABSTRACT FROM AUTHOR]

Using the land‐bound vertebrates on the marine islands as model organisms, two metrics are presented that permit quantitative and succinct synopses of the 'evolutionary maturity' of the hosted faunal assemblages. In turn, these reflect the geo‐physical settings and geological developments of the substrates. The assemblage lineage‐taxonomy spectrum (ALTS) is based on the constituent lineages' taxonomic distinctiveness and diversity. Individual lineages within assemblages can in most cases be assigned to one of six categories, LT1‒LT6: LT1 is a non‐endemic taxon, whereas LT6 comprises multiple endemic genera from a family that arose elsewhere. If required, the scheme can be expanded: LT9 is an endemic order. The data can then be combined to provide an assemblage spectrum, for example, 00:08:38:30:08:15[13]. Here, the first six values denote the number of lineages assigned to each category expressed as percentages of the overall total, with the sum of the processed lineages listed as the seventh (in brackets and bold). The ALTS metric highlights efficiently the key features of a marine island's biological assemblage. Notably, the contrast between spectra for suites on geologically and geo‐physically varied island types can be striking, for instance the squamate suite on the young, proximate orogenic margin island of Taiwan is coded 78:16:05:00:00:00[37] whereas the one on the distantly located, Late Eocene composite terrane island of New Caledonia is 00:11:00:11:33:44[9]. To overcome the subjectivity that is inherent in assigning supraspecific ranks, an alternative assemblage lineage‐age spectrum (ALAS) is also introduced that makes use of the binary logarithm values of the colonization times of the island lineages (0–2, 2–4, ... , 32–64, >64 Ma). It is represented using a seven‐plus‐two‐number code, for instance Madagascar's squamates are 00:06:00:00:19:62:12[19(16)]; most colonizations took place in the Palaeogene (66–23 Ma); there are 19 lineages, but only 16 are presently age‐dated. In addition to marine‐island biogeography studies, the ALTS–ALAS spectrum approach is potentially useful for encapsulating biotas in other sorts of insular setting (e.g. lakes, mountain tops), and for evaluating palaeogeographical models. Furthermore, it may help emphasize the conservation value of an island's faunal assemblage. [ABSTRACT FROM AUTHOR]

In the absence of evidence suggesting former ice or land bridges, the colonization of remote landmasses by non‐aquatic, non‐flying vertebrates is thought to result from long‐distance over‐water rafting (LDOR). However, Mazza et al. (2019) challenge the notion that mammals can make such journeys citing their perceived physiological inadequacies. They claim that lengthy transits combined with lack of food and water plus the stresses imposed by temperature, humidity and salinity render such passages impossible. We, though, contend that this reasoning is wrong. The few cases where LDOR has been invoked for mammal colonization have all involved small‐bodied animals, several of which are able to drastically reduce their metabolic rates through torpor/hibernation when food and water are scarce. Furthermore, there may be sustenance. Crucially, LDOR obviates the need for miraculous short‐lived causeways and the attendant issue of unrecognized large‐scale bidirectional invasions being made by other organisms that had access to the conduits. [ABSTRACT FROM AUTHOR]

Experimental work in the early 20th century showed that background albedo experienced by larvae of the fire salamander (Salamandra salamandra) induce a durable morphological modification of the postmetamorphic color pattern, which needed confirmation due to the controversies regarding Paul Kammerer's experiments. Such a carry‐over effect would be relevant as the black and yellow pattern of the alkaloid‐containing adult fire salamanders has been suggested to serve as an aposematic signal. Hence, we hypothesized that (a) adult coloration is conspicuous to potential predators under light conditions at night, given the nocturnal activity of this species, and (b) a condition affecting the salamander's coloration pattern would also affect its toxicity to maintain a quantitatively honest aposematic signal. To test the first hypothesis, we used spectrometry to model the vision of potential avian and snake predators and confirmed that fire salamander's black‐and‐yellow pattern is contrasting enough against the forest leaf litter to be considered conspicuous at night. To test the second hypothesis, we first confirmed the background carry‐over effect on black and yellow proportions in the dorsal skin of experimentally reared fire salamanders, using a rigorous experimental design. Then, we calculated the conspicuousness and determined the alkaloid profiles of these individuals. We did not find a correlation between conspicuousness and toxicity at the intrapopulation level. Moreover, there was no background carry‐over effect on the alkaloid profile. We discuss our results in a physiological, ecological, evolutionary, and historical context. Fire salamanders are conspicuous to potential predators at night. Confirming historical experiments, the background albedo experienced by a larva has a carry‐over effect on its postmetamorphic black‐and‐yellow coloration but not on its toxicity. [ABSTRACT FROM AUTHOR]

Some amphibians use chemical signals in addition to optical and acoustical signals to transmit information. Males of mantellid frogs from Madagascar and hyperoliid frogs from Africa emit complex, species‐ and sex‐specific bouquets of volatiles from their femoral or gular glands. We report here on the identification, synthesis, and determination of the absolute configuration of a macrocyclic lactone occurring in several species of both families, (S)‐3,7,11‐dodec‐6,10‐dien‐12‐olide (S‐14, frogolide). Macrolides are a preferred compound class of frog volatiles. Nevertheless, frogolide is the first macrocyclic lactone obviously derived from the terpene pathway, in contrast to known frog macrolides that are usually formed via the fatty acid biosynthetic pathway. [ABSTRACT FROM AUTHOR]

Abstract: The postembryonic development of amphibians has been characterized as divided into three predominant periods, hereafter named primary developmental stages: premetamorphosis (PreM), prometamorphosis (ProM), metamorphic climax (Meta), and completion of metamorphosis (PostM), largely based on examination of anuran development. Here, we categorized the postembryonic development of larvae of a poisonous fire salamander (Salamandra salamandra) by integrating morphology and gene expression (transcriptomic) data. Morphological analysis revealed three distinct clusters suggestive of PreM, ProM, and Meta, which were confirmed in parallel by microarray‐derived gene expression analysis. In total, 3,510 probes targeted transcripts differentially expressed between the clusters we identified. Genes upregulated in PreM related to organogenesis, and those upregulated in Meta underlie structural proteins and related to development of anatomical structures and pigmentation. Biosynthesis pathways of pigments (pteridines and melanin) were upregulated during late ProM and Meta. Gas chromatographic analysis of alkaloids indicated the onset of steroidal alkaloid biosynthesis at ProM. When comparing gene expression in the fire salamander to that in other amphibians—three anurans, Xenopus laevis, X. tropicalis, and Michrohyla fissipes, and one caudate, Ambystoma mexicanum— we identified genes with conserved expression patterns involved in basic metamorphic processes such as skin restructuring and tail fin resorption. Our results support that primary stages of postembryonic development in caudates are homologous to those of anurans, and offer a baseline for the study of the evolution of developmental modes. [ABSTRACT FROM AUTHOR]

One of the greatest challenges of effective conservation measures is the correct identification of sites where rare and elusive organisms reside. The recently rediscovered Hula painted frog ( Latonia nigriventer) has not been seen for many decades and was therefore categorized extinct. Since its rediscovery in 2011, individuals from the critically endangered species have been found, with great effort, only in four restricted sites. We applied the environmental DNA ( eDNA) approach to search for new populations of the Hula painted frog in suitable aquatic habitats. We further used the eDNA data to classify the landscape factors associated with the species distribution and to predict its suitable habitats. We sampled 52 aquatic sites in the Hula Valley during the spring of 2015 and 2016 and amplified the samples with a species-specific qPCR assay. DNA of the Hula painted frog was detected in 22 of the sites, all of which clustered within three main areas. A boosting classification model showed that soil type, vegetation cover and the current and former habitats are all key predictors of the frog's current distribution. Intriguingly, the habitat suitability models reveal a high affinity of the species to its long-lost habitat of the historical wetlands. Our findings encourage a series of informed searches for new populations of this threatened frog and provide guidance for future conservation management programmes. In the era of global conservation crisis of amphibians, developing the eDNA approach, a reliable detection method for many critically endangered and elusive amphibians, is of particular importance. [ABSTRACT FROM AUTHOR]

Animal-associated bacterial communities play essential roles for their host's ecology, physiology and health. Temporal dynamics of these communities are poorly understood, but might be of high relevance for amphibians with a well-expressed biphasic biology of adults where the structure of their skin changes drastically between the aquatic and terrestrial phases. Here, we investigated the temporal dynamics of cutaneous bacterial communities of Lissotriton boscai and Triturus marmoratus by monthly sampling populations from a pond and surrounding terrestrial habitats near A Coruña, Spain. These communities were characterized by 16S rRNA gene amplicons from DNA isolated from skin swabs. Newt bacterial communities displayed variation at three levels: between larvae and aquatic adults, between adult life phases (terrestrial versus aquatic), and temporally within life phases. The skin bacterial communities tended to differ to a lesser extent temporally and between larvae and adults, and more strongly between life phases. Larvae had a higher proportion of reads associated with antifungal taxa compared with adults, while no differences were found among adult life phases. Terrestrial specimens exhibited the highest community diversity. The regular transitions of adult newts between aquatic and terrestrial environments might contribute to the diversity of their skin microbiota and could increase disease resistance. [ABSTRACT FROM AUTHOR]

Aim We studied the gecko genus Ebenavia to reconstruct its colonization history, test for anthropogenic versus natural dispersal out of Madagascar, and correlate divergence date estimates of our phylogeny with geological age estimates of islands in the region. Location Madagascar and surrounding islands of the Western Indian Ocean (Comoros, Mayotte, Mauritius, Pemba). Methods We reconstructed the phylogeny of Ebenavia covering its entire geographical range using a molecular data set of three mitochondrial and two nuclear markers. We estimated divergence times based on calibrations using (1) previously calculated mutation rates of mitochondrial markers, (2) a combination of these rates with old or (3) young geological age estimates for some of the islands inhabited by the genus, and (4) an independent data set with fossil outgroup calibration points. Results Ebenavia inunguis, one of two recognized species of the genus, comprises multiple ancient evolutionary lineages. The earliest divergence within this complex (Miocene, 13-20 Ma; 95% credibility interval [ CI]: 4-29 Ma) separates the population of the Comoros Islands, excluding Mayotte, from all other lineages. The age estimates for island lineages coincide with the geological age estimates of the islands except for Grand Comoro, where the age of the local clade (3-5 Ma; 95% CI: 2-7 Ma) significantly predates the estimated island age (0·5 Ma). A clade from north Madagascar + Mayotte + Pemba is estimated to have diverged from an eastern Malagasy clade in the Miocene. Main Conclusions Our results suggest that Grand Comoro Island is geologically older than previously estimated. The islands of the Comoros and Pemba were probably colonized via natural dispersal out of Madagascar (> 1000 km in the case of Pemba). Mauritius was most likely colonized only recently from eastern Madagascar via human translocation. [ABSTRACT FROM AUTHOR]

In this study, we provide an extended multilocus phylogenetic analysis combining mitochondrial and nuclear DNA of a group of fossorial and miniaturized legless lizards (genus Paracontias) from Madagascar , including the description of two species new to science, P. ampijoroensis sp. nov. and P. mahamavo sp. nov. Our analyses revealed the existence of two distinct, parapatric and diagnosable clades within the genus: (i) the 'kankana clade' (including P. kankana and the two newly described species), located in the north (but absent from the extreme northern tip) of the island and characterized by a pattern of cephalic scales very unusual for Malagasy Scincinae, with large loreal scales extending to and meeting each other at dorsal midline, and (ii) the 'brocchii clade' (including all other studied species), endemic to the north of Madagascar and characterized by small loreal scales separated from each other by the rostral and the frontonasal scale. By combining phylogenetic results with morphological traits observed among species, we develop novel hypotheses on the simplification of the cephalic scalation pattern within this genus, a trend frequently encountered among various lineages of legless squamates that convergently adapted to a burrowing lifestyle. Additionally, a user-friendly graphical identification key for species of Paracontias is provided and made available as supplementary information. [ABSTRACT FROM AUTHOR]

Macrolide lactones, the so called cucujolides derived from unsaturated fatty acids, are aggregation pheromones of cucujid grain beetles. Thirty years ago, Oehlschlarger et al. showed that (3 Z,6 Z)-dodeca-3,6-dien-11-olide ( 4) and the respective 12-olide ( 7) attract the sawtoothed grain beetle Oryzaephilus surinamensis, whereas (5 Z,8 Z,13 R)-tetradeca-5,8-dien-13-olide ( 5) increases the response synergistically. The frass of this beetle is attractive for its parasitoid Cephalonomia tarsalis, which potentially can be used for pest control. A GC/MS analysis of attractive frass showed the presence of 5, together with an unknown isomer. Cucujolide V was tentatively identified also in the femoral glands, pheromone-releasing structures, of the Madagascan mantelline frog Spinomantis aglavei. Therefore, a new route to synthesize doubly unsaturated macrolides allowing the flexible attachment of the side chain was developed. A straightforward method to obtain Z configured macrolides involves ring-closing alkyne metathesis (RCAM) followed by Lindlar-catalyzed hydrogenation. This methodology was extended to homoconjugated diene macrolides by using RCAM after introduction of one Z configured double bond in the precursor by Wittig reaction. A tungsten benzylidyne complex was used as the catalyst in the RCAM reaction, which afforded the products in high yield at room temperature. With the synthetic material at hand, the unknown isomer was identified as the new natural product (5 Z,8 Z,12 R)-tetradeca-5,8-dien-12-olide, cucujolide X ( 8). Furthermore, the route also allowed the synthesis of cucujolide V in good yield. The natural products were identified by the synthesis of enantiomerically pure or enriched material and gas chromatography on chiral phases. The new macrolide ( R)- 8 proved to be biologically active, attracting female O. surinamensis, but no males. The synthetic material allowed the identification of ( R)- 5 in both the beetle and the frog. [ABSTRACT FROM AUTHOR]

Madagascar is a biodiversity hotspot with a unique fauna and flora largely endemic at the species level and highly threatened by habitat destruction. The processes underlying population-level differentiation in Madagascar's biota are poorly understood and have been proposed to be related to Pleistocene climatic cycles, yet the levels of genetic divergence observed are often suggestive of ancient events. We combined molecular markers of different variability to assess the phylogeography of Madagascar's emblematic tomato frogs ( Dyscophus guineti and D. antongilii) and interpret the observed pattern as resulting from ancient and recent processes. Our results suggest that the initial divergence between these taxa is probably old as reflected by protein-coding nuclear genes and by a strong mitochondrial differentiation of the southernmost population. Dramatic changes in their demography appear to have been triggered by the end of the last glacial period and possibly by the short return of glacial conditions known as the 8K event. This dramatic change resulted in an approximately 50-fold reduction of the effective population size in various populations of both species. We hypothesize these species' current mitochondrial DNA diversity distribution reflects a swamping of the mitochondrial genetic diversity of D. guineti by that of D. antongilii previous to the populations' bottlenecks during the Holocene, and probably as a consequence of D. antongilii demographic expansion approximately 1 million years ago. Our data support the continued recognition of D. antongilii and D. guineti as separate species and flag D. guineti as the more vulnerable species to past and probably also future environmental changes. [ABSTRACT FROM AUTHOR]

DNA barcoding facilitates the identification of species and the estimation of biodiversity by using nucleotide sequences, usually from the mitochondrial genome. Most studies accomplish this task by using the gene encoding cytochrome oxidase subunit I ( COI; Entrez COX1). Within this barcoding framework, many taxonomic initiatives exist, such as those specializing in fishes, birds, mammals, and fungi. Other efforts center on regions, such as the Arctic, or on other topics, such as health. DNA barcoding initiatives exist for all groups of vertebrates except for amphibians and nonavian reptiles. We announce the formation of Cold Code, the international initiative to DNA barcode all species of these 'cold-blooded' vertebrates. The project has a Steering Committee, Coordinators, and a home page. To facilitate Cold Code, the Kunming Institute of Zoology, Chinese Academy of Sciences will sequence COI for the first 10 specimens of a species at no cost to the steward of the tissues. [ABSTRACT FROM AUTHOR]

Western Palearctic water frogs in the genus Pelophylax are a set of morphologically similar anuran species that form hybridogenetic complexes. Fully reliable identification of species and especially of hybrid ploidy depends on karyological and molecular methods. In central Europe, native water frog populations consist of the Pelophylax esculentus complex, that is, P. lessonae (LL) , P. ridibundus (RR) and the hybrid form P. esculentus that can have different karyotypes (RL, LLR and RRL). We developed existing molecular methods further and propose a simple PCR method based on size-differences in the length of the serum albumin intron-1 and the RanaCR1, a non-LTR retrotransposon of the chicken repeat (CR) family. This PCR yields taxon-specific banding patterns that can easily be screened by standard agarose gel electrophoresis and correctly identify species in all of the 160 samples that had been identified to karyotype with other methods. To distinguish ploidy levels in LR, LLR and RRL specimens, we used the ratio of the peak heights of the larger ( ridibundus specific) to the smaller ( lessonae specific) bands of fluorescently labelled PCR products resolved on a capillary DNA sequencer and obtained a correct assignment of the karyotype in 93% of cases. Our new method will cut down time and expenses drastically for a reliable identification of water frogs of the P. esculentus complex and potentially for identification of other hybridogenetic complexes and/or taxa, and it even serves as a good indicator of the ploidy status of hybrid individuals. [ABSTRACT FROM AUTHOR]

To analyse the phylogeographic structure of the strawberry poison frog, Oophaga pumilio (Dendrobatidae), across a large part of its range using a combination of mitochondrial and nuclear markers. Costa Rica and Panama. Sequence analyses of a mitochondrial (cytochrome b) and a nuclear ( RAG-1) gene fragment as well as analyses of seven microsatellite loci were carried out on 269 individuals of O. pumilio sampled from 24 localities and on two individuals of O. vicentei. Two main mitochondrial haplotype lineages, corresponding to a northern (north Costa Rica) and a southern (south Costa Rica and eastern Panama) lineage, were identified. They differed by up to 7% uncorrected distance. We observed co-occurrence of both lineages in seven populations in Costa Rica and Panama, indicating a pattern of extensive admixture. The two main mitochondrial lineages of O. pumilio roughly corresponded to a previously described phylogeographic pattern. Microsatellites indicate admixture spanning over a wide geographic area, but significant variation between the northern and southern groups was also found with microsatellite data. While microsatellite data reconstructed a separation south of an assumed Caribbean valley barrier, mitochondrial haplotypes of the 'southern lineage' shifted this barrier towards the north. Despite admixture, all three markers showed significant variation between the northern and southern groups. Phylogeographical breaks known from other anuran species in the study region could not be verified for O. pumilio. The unexpected clustering of the population from Escudo de Veraguas and the individuals of O. vincentei with the northern O. pumilio lineage indicates the need for a fundamental and careful taxonomic revision, including an interspecific phylogeography of the entire genus. [ABSTRACT FROM AUTHOR]

Fritz, U., Branch, W. R., Hofmeyr, M. D., Maran, J., Prokop, H., Schleicher, A., Široký, P., Stuckas, H., Vargas-Ramírez, M., Vences, M. & Hundsdörfer, A. K. (2010). Molecular phylogeny of African hinged and helmeted terrapins (Testudines: Pelomedusidae: Pelusios and Pelomedusa). - Zoologica Scripta, 40, 115-125. With 18 currently recognised species, Pelusios is one of the most speciose chelonian genera worldwide, even though the taxonomy of some species is contentious. Recent investigations suggested that the closely related, but morphologically distinct genus Pelomedusa is paraphyletic with respect to Pelusios, and that Pelomedusa consists of nine deeply divergent lineages. Using three mitochondrial and three nuclear DNA fragments (2054 bp mtDNA, 2025 bp nDNA), we examined for the first time the phylogeny of Pelusios by molecular means. Our analyses included all Pelusios species, except the probably extinct P. seychellensis, as well as the nine Pelomedusa lineages. The results showed that Pelusios and Pelomedusa are reciprocally monophyletic. Limited sampling of Pelusios species and homoplasy introduced by remote outgroups most likely explain the paraphyly of Pelomedusa in previous studies. The distinctiveness of most Pelusios species was confirmed, but none of the currently recognised species groups within Pelusios was monophyletic. In Pelusios rhodesianus and P. sinuatus distinct genetic lineages were discovered, suggestive of cryptic taxa. In contrast, the recognition of the weakly differentiated P. castaneus and P. chapini as full species is doubtful, as is the validity of the Malagasy and Seychellois subspecies of P. castanoides. GenBank sequences of P. williamsi were nested within P. castaneus, but the morphological distinctiveness of the two species makes it likely that the GenBank sequences (derived from a turtle from the pet trade) are misidentified. Divergence among the distinct genetic lineages of Pelomedusa equals or exceeds the differences among Pelusios species, supporting the view that Pelomedusa is a species complex. [ABSTRACT FROM AUTHOR]

Nagy, Z. T., Glaw, F. & Vences, M. (2010) Systematics of the snake genera Stenophis and Lycodryas from Madagascar and the Comoros. — Zoologica Scripta, 39, 426–435. Arboreal snakes belonging to the pseudoxyrhophiine genus Stenophis inhabit Madagascar but despite their spectacular appearance, surprisingly little is known about their natural history and systematics. Nonetheless, a close phylogenetic affinity of the genera Stenophis and Lycodryas (the latter genus currently includes a single species from the Comoros) has been hypothesized. Based on recent molecular genetic data, however, the monophyly of Stenophis was challenged. This study aimed at a systematic analysis and taxonomic revision of the genera Stenophis and Lycodryas. On the basis of new molecular genetic and morphological data and analyses, we propose to accommodate these snakes in three monophyletic genera: Lycodryas, Phisalixella and Parastenophis, and to consider Stenophis as a junior synonym of Lycodryas. In the new generic arrangement, the genera can also be well distinguished by morphological characters. On the specific level, Phisalixella tulearensis is resurrected and indications of further, undescribed taxa are revealed. [ABSTRACT FROM AUTHOR]

The pseudoxyrhophiine snake genus Liopholidophis Mocquard, 1904 is endemic to Madagascar and consists of two distinct species groups. We performed molecular phylogenetic analyses using nucleotide sequences of c. 2200 bp from two mitochondrial genes (16S rRNA, cyt b) and one nuclear gene (c-mos) to test the monophyly of the genus Liopholidophis and to investigate the relationships of the known species and an unidentified Liopholidophis population. Our phylogeny strongly supports the polyphyly of the genus Liopholidophis, confirms the monophyly of both species groups, and reveals that the unidentified population belongs to a new species. We therefore transfer the species of the former L. stumpffi group ( L. epistibes, L. infrasignatus, L. lateralis, L. martae, and L. stumpffi) to a new genus Bibilava gen. n. and describe Liopholidophis dimorphus sp. n. from the rainforests of Montagne d’Ambre National Park in northern Madagascar. Finally, we compare our phylogeny with previous hypotheses and discuss the evolution of the extreme sexual dimorphism in tail length of Liopholidophis s. str. [ABSTRACT FROM AUTHOR]

Aim Amphibians are a model group for studies of the biogeographical origins of salt-intolerant taxa on oceanic islands. We used the Gulf of Guinea islands to explore the biogeographical origins of island endemism of one species of frog, and used this to gain insights into potential colonization mechanisms. Location São Tomé and Príncipe, two of the four major islands in the Gulf of Guinea, West Africa, are truly oceanic and have an exceptionally high biodiversity. Methods Mitochondrial DNA is used to test the endemic status of a frog from São Tomé and compare it with congeneric taxa from tropical Africa. Existing data on surface currents, surface salinity, atmospheric circulation and bird migration in the Gulf of Guinea are summarized to address hypotheses concerning colonization mechanisms. Results The endemic status of Ptychadena newtoni (Bocage) is supported here by mitochondrial DNA sequences, and analysis of this and other molecular data indicates that an East African species close to Ptychadena mascareniensis (Duméril and Bibron) is its nearest relative. We refute the possibility that this population was anthropogenically introduced, in favour of a natural dispersal mechanism. Main conclusions With six endemic frogs and one caecilian, the Gulf of Guinea islands harbour a diverse amphibian fauna. Five of these species appear to have their closest relatives in East Africa. Insufficient evidence exists for transportation by storms, birds or rafts alone. However, we propose a synergy of rafting, favourable surface currents and a reduction in salinity of surface waters. Catastrophic events, or wet periods in climatic history, could allow freshwater paths to open far enough to enable continental flora and fauna to reach these and other isolated oceanic islands. [ABSTRACT FROM AUTHOR]

Mantella bernhardi is an endemic species of Malagasy poison frog threatened by loss and fragmentation of its natural habitat and collection for the pet trade. It is classified as threatened according to the International Union for Conservation of Nature and Natural Resources (IUCN) categories and included in Appendix II of the Convention on the International Trade of Endangered Species (CITES). A recent survey has increased the known distributional range of the species from one to eight populations across southeastern Madagascar, but little is known about its biology and genetic diversity. Here we estimate inter- and intrapopulation mitochondrial genetic variation of four populations. Populations from the northern and southern parts of the distributional range showed a high degree of divergence (maximum of 11.35% in cytochrome b) and were recovered as reciprocally monophyletic groups. Nine haplotypes were detected in the northern and 12 in the southern populations. The population from Ranomafana National Park showed the lowest number of haplotypes and nucleotide diversity, and shared its most common haplotype with the second northern population from Tolongoina. All the other detected haplotypes were unique to each of the four populations. This suggests the existence of important barriers to gene flow, pre-dating human colonization of Madagascar at about 2000 years ago, in distinct contrast to other Mantella species that show a high degree of haplotype sharing throughout their range. The continued habitat fragmentation within the distribution range of M. bernhardi prevents any connection between its populations. Our data indicate the existence of at least two different management units for conservation in this species, corresponding to the North and South of its distribution range, and highlight the existence of strong regional endemism in southeastern Madagascar. [ABSTRACT FROM AUTHOR]

Aim Cryptoblepharus is a genus of small arboreal or rock-dwelling scincid lizards, widespread through the Indo-Pacific and Australian regions, with a disjunct outlier in the Malagasy region. The taxonomy within this genus is controversial, with different authors ranking the different forms (now some 36) at various levels, from different species to subspecies of a single species, Cryptoblepharus boutonii. We investigated the biogeography and genetic differentiation of the Cryptoblepharus from the Western Indian Ocean region, in order to understand their origin and history. Location Western Indian Ocean region . Methods We analysed sequences of mitochondrial DNA (partial 12s and 16s rRNA genes, 766 bp) from 48 specimens collected in Madagascar, Mauritius, the four Comoros islands and East Africa, and also in New Caledonia, representing the Australo-Pacific unit of the distribution. Results Pairwise sequence divergences of c. 3.1% were found between the New Caledonian forms and the ones from the Western Indian Ocean. Two clades were identified in Madagascar, probably corresponding to the recognized forms cognatus and voeltzkowi, and two clades were identified in the Comoro islands, where each island population formed a distinct haplotype clade. The East African samples form a monophyletic unit, with some variation existing between Pemba, Zanzibar and continental Tanzania populations. Individuals from Mauritius form a divergent group, more related to populations from Moheli and Grand Comore (Comoros islands) than to the others. Main conclusions The level of divergence between the populations from the Western Indian Ocean and Australian regions and the geographic coherence of the variation within the Western Indian Ocean group are concordant with the hypothesis of a colonization of this region by a natural transoceanic dispersal (from Australia or Indonesia). The group then may have diversified in Madagascar, from where it separately colonized the East African coast, the Comoros islands (twice), and Mauritius. The genetic divergence found is congruent with the known morphological variation, but its degree is much lower than typically seen between distinct species of reptiles. [ABSTRACT FROM AUTHOR]

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The Mascarene ridged frog, Ptychadena mascareniensis, is the only African amphibian species thought to occur on Madagascar and on the Seychelles and also Mascarene islands. We explored its phylogenetic relationships and intraspecific genetic differentiation to contribute to the understanding of transoceanic dispersal in amphibians. Fragments of the mitochondrial 16S rRNA gene were sequenced from specimens collected over most of the distribution area of P. mascareniensis, including populations from Madagascar, Mascarenes and Seychelles. We identified five deeply divergent clades having pairwise divergences >5%, which probably all represent cryptic species in a P. mascareniensis complex. One of these seems to be restricted to Madagascar, the Mascarenes and the Seychelles. Sequences obtained from topotypic material (Réunion) were identical to the most widespread haplotype from Madagascar. The single Mauritian/Seychellean haplotype differed by only one mutation from a Malagasy haplotype. It is likely that the Mascarene and Seychellean populations were introduced from Madagascar by humans. In contrast, the absence of the Malagasy haplotypes from Africa and the distinct divergences among Malagasy populations (16 mutations in one divergent hapolotype from northern Madagascar) suggest that Madagascar was populated by Ptychadena before the arrival of humans c. 2000 years ago. Because Madagascar has been separated from Africa since the Jurassic, this colonization must have taken place by overseas rafting, which may be a more widespread dispersal mode in amphibians than commonly thought. [ABSTRACT FROM AUTHOR]