Comparative phylogeography of the western Indian Ocean reef fauna

Assessing patterns of connectivity at the community and population levels is relevant to marine resource management and conservation. The present study reviews this issue with a focus on the western Indian Ocean (WIO) biogeographic province. This part of the Indian Ocean holds more species than expected from current models of global reef fish species richness. In this study, checklists of reef fish species were examined to determine levels of endemism in each of 10 biogeographic provinces of the Indian Ocean. Results showed that the number of endemic species was higher in the WIO than in any other region of the Indian Ocean. Endemic species from the WIO on the average had a larger body size than elsewhere in the tropical Indian Ocean. This suggests an effect of peripheral speciation, as previously documented in the Hawaiian reef fish fauna, relative to other sites in the tropical western Pacific. To explore evolutionary dynamics of species across biogeographic provinces and infer mechanisms of speciation, we present and compare the results of phylogeographic surveys based on compilations of published and unpublished mitochondrial DNA sequences for 19 Indo-Pacific reef-associated fishes (rainbow grouper Cephalopholis argus, scrawled butterflyfish Chaetodon meyeri, bluespot mullet Crenimugil sp. A, humbug damselfish Dascyllus abudafur/Dascyllus aruanus, areolate grouper Epinephelus areolatus, blacktip grouper Epinephelus fasciatus, honeycomb grouper Epinephelus merra, bluespotted cornetfish Fistularia commersonii, cleaner wrasse Labroides sp. 1, longface emperor Lethrinus sp. A, bluestripe snapper Lutjanus kasmira, unicornfishes Naso brevirosris, Naso unicornis and Naso vlamingii, blue-spotted maskray Neotrygon kuhlii, largescale mullet Planiliza macrolepis, common parrotfish Scarus psicattus, crescent grunter Terapon jarbua, whitetip reef shark Triaenodon obesus) and three coastal Indo-West Pacific invertebrates (blue seastar Linckia laevigata, spiny lobster Panulirus homarus, small giant clam Tridacna maxima). Heterogeneous and often unbalanced sampling design, paucity of data in a number of cases, and among-species discrepancy in phylogeographic structure precluded any generalization regarding phylogeographic patterns. Nevertheless, the WIO might have been a source of haplotypes in some cases and it also harboured an endemic clade in at least one case. The present survey also highlighted likely cryptic species. This may eventually affect the accuracy of the current checklists of species, which form the basis of some of the recent advances in Indo-West Pacific marine ecology and biogeography.

Zmienność genetyczna, specyficzność żywicielska i zdolność do przenoszenia wirusa mozaiki smugowatej pszenicy (WSMV) w obrębie kompleksu gatunków Aceria tosichella

Wydział Biologii: Instytut Biologii Środowiska

Absence of consistent genetic differentiation among several morphs of Actinia (Actiniaria: Actiniidae) occurring in the portuguese coast

Actinia equina, the beadlet sea anemone, is a very labile species, displaying variable colour patterns, broad habitat choice and diverse modes of reproduction. Historically, studies using genetic markers such as allozymes and differences in habitat choice lead several authors to propose that different colour morphs could represent different species. One of the species defined was A. fragacea. In this paper, the relationships between brown, red and green colour morphs of A. equina and A. fragacea were studied, using two DNA fragments (one mitochondrial and one nuclear). Individuals were sampled from three different areas in Portugal separated by a maximum distance of 500 km. This is the first study applying direct sequencing of selected gene fragments to approach the validity of Actinia morphs as different genetic entities. The results show that, at least in the Portuguese coast, these colour morphs do not correspond to the two valid species recognized in the literature. The existence of cryptic species is discussed.

The taxonomy, zoogeography and ecology of amphibians and reptiles of Hin Nam No National Protected Area (Laos) in comparison with data from Phong Nha – Ke Bang National Park (Vietnam).

In this thesis the mostly unknown herpetofauna in Hin Nam No National Protected Area Laos in the northern Truong Son Range was for the first time intensively investigated, and its diversity was compared to the bordering, and well-investigated Phong Nha - Ke Bang National Park in Vietnam. Twelve new vertebrate species were described comprising 11 geckonids (Cyrtodactylus bansocensis, C. calamei, C. hinnamnoensis, C. jaegeri, C. rufford, C. sommerladi, C. soudthichaki, Gekko boehmei, G. bonkowskii, G. sengchanthavongi, G. thakhekensis, Lycodon banksi and one colubrid snake (Lycodon banksi). Seven species were discovered for the first time in Laos including three frogs (Gracixalus quyeti, G. supercornutus, Rhacophorus maximus), two geckos (Cyrtodactylus cryptus, C. pseudoquadrivirgatus) and two snakes (Lycodon futsingensis, L. ruhstrati abditus). The main hypothesis that the Truong Son Range acted as a biogeographic barrier for the distribution of amphibians and reptiles could be confirmed at least for karst adapted gekkonids. Compared to other herpetofaunal groups the number of gekkonids in karst formations was particularly high (seven bent-toed geckos, four true geckos). By comparing the relative amounts of shared species in Hin Nam No and Phong Nha - Ke Bang, it is interesting to note that fewer reptile species (38%) than amphibian species (66%) were shared between both regions. This might indicate that the Truong Son Range acts as a stronger biogeographical barrier for reptiles than for amphibians. Two pairs of karst-adapted cryptic gecko species (i.e. species with distinct genetic differences, but a similar phenotype) occurred on both sides of the Truong Son Range. Only in one case these were sibling species (Crytodactylus sommerladi in Laos versus C. roesleri in Vietnam), but not in the other (C. hinnamnoensis in Laos versus C. phongnhakebangensis in Vietnam). On the Laotian side, nine gecko species (Cyrtodactylus bansocensis, C. calamei, C. darevskii, C. hinnamnoensis, C. khammouanensis, C. multiporus, C. sommerladi, G. boehmei, G. sengchanthavongi) currently have to be regarded as endemic to the Hin Nam No region. On the Vietnamese side, seven species including two bent-toed geckos (Cyrtodactylus phongnhakebangensis and C. roesleri), three skinks (Lygosoma boehmei, Sphenomorphus tetradactylus and Tropidophorus noggei), and two snakes (Hebius andreae and Boiga bourreti) are currently only known from Phong Nha - Ke Bang and adjacent regions. These high numbers of potential endemic species together with the cryptic species complex in Cyrtodactylus provide strong evidence that the karst formations in the northern Truong Son Range represent a hot spot of reptile diversity and of speciation in Crytodactylus in particular. Correct species identification is a fundamental requirement for conservation measures. The discovery of cryptic species complexes poses a challenge for alpha taxonomy and species conservation, because the true distribution ranges of the species are in fact much smaller than previously assumed. Species conservation in this area of Laos is facing a number of further problems. New and potentially endemic species were discovered in highly populated and disturbed areas. Conversion of the Ho Chi Minh Trail into a highway provided easy access for farmers and still continues to accelerate the destruction of remote forest areas. Southern Hin Nam No with its high diversity of endemic species was identified as the first priority area for conservation. Also Ban Soc, an area isolated from Hin Nam No, should be among the conservation priorities because this region houses a so far overlooked population of the critically endangered Siamese crocodile. Efforts to establish a legal conservation status for this habitat are in progress.

Towards better management of Australia’s shark fishery: genetic analyses reveal unexpected ratios of cryptic blacktip species Carcharhinus tilstoni and C. limbatus

The common blacktip shark (Carcharhinus limbatus) and the Australian blacktip shark (C. tilstoni) are morphologically similar species that co-occur in subtropical and tropical Australia. In striking contrast to what has been previously reported, we demonstrate that the common blacktip shark is not rare in northern Australia but occurs in approximately equal frequencies with the Australian blacktip shark. Management of shark resources in northern Australia needs to take account of this new information. Species identification was performed using nucleotide sequences of the control, NADH dehydrogenase subunit 4 (ND4) and cytochrome oxidase I (COI) regions in the mitochondrial genome. The proportion of overall genetic variation (FST) between the two species was small (0.042, P < 0.01) based on allele frequencies at five microsatellite loci. We confirm that a third blacktip species (C. amblyrhynchoides, graceful shark) is closely related to C. tilstoni and C. limbatus and can be distinguished from them on the basis of mtDNA sequences from two gene regions. The Australian blacktip shark (C. tilstoni) was not encountered among 20 samples from central Indonesia that were later confirmed to be common blacktip and graceful sharks. Fisheries regulators urgently need new information on life history, population structure and morphological characters for species identification of blacktip shark species in Australia.

Morphologically cryptic biological species within the liverwort Frullania asagrayana.

UNLABELLED: PREMISE OF THE STUDY: The Frullania tamarisci complex includes eight Holarctic liverwort species. One of these, F. asagrayana, is distributed broadly throughout eastern North America from Canada to the Gulf Coast. Preliminary genetic data suggested that the species includes two groups of populations. This study was designed to test whether the two groups are reproductively isolated biological species. • METHODS: Eighty-eight samples from across the range of F. asagrayana, plus 73 samples from one population, were genotyped for 13 microsatellite loci. Sequences for two plastid loci and nrITS were obtained from 13 accessions. Genetic data were analyzed using coalescent models and Bayesian inference. • KEY RESULTS: Frullania asagrayana is sequence-invariant at the two plastid loci and ITS2, but two clear groups were resolved by microsatellites. The two groups are largely reproductively isolated, but there is a low level of gene flow from the southern to the northern group. No gene flow was detected in the other direction. A local population was heterogeneous but displayed strong genetic structure. • CONCLUSIONS: The genetic structure of F. asagrayana in eastern North America reflects morphologically cryptic differentiation between reproductively isolated groups of populations, near-panmixis within groups, and clonal propagation at local scales. Reproductive isolation between groups that are invariant at the level of nucleotide sequences shows that caution must be exercised in making taxonomic and evolutionary inferences from reciprocal monophyly (or lack thereof) between putative species.

The status of the cryptic bat species, Myotis mystacinus and Myotis brandtii in Ireland

The recent identification of Myotis brandtii in Ireland raised the possibility that many roosts previously identified as M. mystacinus had the potential of being misidentified M. brandtii. Thus, the distribution and population estimates for M. mystacinus may have been over-estimated, while M. brandtii may have been under-estimated. Results from an all Ireland genetic survey of known M. mystacinus maternity roosts confirm that no long term misidentification has taken place. All specimens caught and sampled were M. mystacinus. Additonally, no further records of M. brandtii were found during six nights of woodland trapping using the acoustic lure. While the status of M. mystacinus in Ireland is now listed as ‘least concern’ in the Irish Red List, M. brandtii is listed as ‘data deficient’ and cannot currently be considered a resident species

Further evidence for cryptic north-western refugia in Europe? Mitochondrial phylogeography of the sibling species Pipistrellus pipistrellus and Pipistrellus pygmaeus

The geographic ranges of European plants and animals underwent periods of contraction and re-colonisation during the climatic oscillations of the Pleistocene. The southern Mediterranean peninsulas (Iberian, Italian and Balkan) have been considered the most likely refugia for temperate/warm adapted species. Recent studies however have revealed the existence of extra-Mediterranean refugia, including the existence of cryptic north-west European refugia during the Last Glacial Maxima (24-14.6 kyr BP). In this study we elucidated the phylogeographic history of two sibling bat species, Pipistrellus pipistrellus and P. pygmaeus in their western European range. We sequenced the highly variable mtDNA D-loop for 167 samples of P. pipistrellus (n = 99) and P. pygmaeus (n = 68) and combined our data with published sequences from 331 individuals. Using phylogenetic methodologies we assessed their biogeographic history. Our data support a single eastern European origin for populations of P. pygmaeus s.str., yet multiple splits and origins for populations of P. pipistrellus s.str., including evidence for refugia within refugia and potential cryptic refugia in north western Europe and in the Caucasus. This complex pattern in the distribution of mtDNA haplotypes supports a long history for P. pipistrellus s.str. in Europe, and the hypothesis that species with a broad ecological niche may have adapted and survived outside southern peninsula throughout the LGM.

Identification of cryptic Anopheles mosquito species by molecular protein profiling.

Vector control is the mainstay of malaria control programmes. Successful vector control profoundly relies on accurate information on the target mosquito populations in order to choose the most appropriate intervention for a given mosquito species and to monitor its impact. An impediment to identify mosquito species is the existence of morphologically identical sibling species that play different roles in the transmission of pathogens and parasites. Currently PCR diagnostics are used to distinguish between sibling species. PCR based methods are, however, expensive, time-consuming and their development requires a priori DNA sequence information. Here, we evaluated an inexpensive molecular proteomics approach for Anopheles species: matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS is a well developed protein profiling tool for the identification of microorganisms but so far has received little attention as a diagnostic tool in entomology. We measured MS spectra from specimens of 32 laboratory colonies and 2 field populations representing 12 Anopheles species including the A. gambiae species complex. An important step in the study was the advancement and implementation of a bioinformatics approach improving the resolution over previously applied cluster analysis. Borrowing tools for linear discriminant analysis from genomics, MALDI-TOF MS accurately identified taxonomically closely related mosquito species, including the separation between the M and S molecular forms of A. gambiae sensu stricto. The approach also classifies specimens from different laboratory colonies; hence proving also very promising for its use in colony authentication as part of quality assurance in laboratory studies. While being exceptionally accurate and robust, MALDI-TOF MS has several advantages over other typing methods, including simple sample preparation and short processing time. As the method does not require DNA sequence information, data can also be reviewed at any later stage for diagnostic or functional patterns without the need for re-designing and re-processing biological material.

Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida), supplementary material

Introduction Many marine planktonic crustaceans such as copepods have been considered as widespread organisms. However, the growing evidence for cryptic and pseudo-cryptic speciation has emphasized the need of re-evaluating the status of copepod species complexes in molecular and morphological studies to get a clearer picture about pelagic marine species as evolutionary units and their distributions. This study analyses the molecular diversity of the ecologically important Paracalanus parvus species complex. Its seven currently recognized species are abundant and also often dominant in marine coastal regions worldwide from temperate to tropical oceans. Results COI and Cytochrome b sequences of 160 specimens of the Paracalanus parvus complex from all oceans were obtained. Furthermore, 42 COI sequences from GenBank were added for the genetic analyses. Thirteen distinct molecular operational taxonomic units (MOTU) and two single sequences were revealed with cladistic analyses (Maximum Likelihood, Bayesian Inference), of which seven were identical with results from species delimitation methods (barcode gaps, ABDG, GMYC, Rosenberg's P(AB)). In total, 10 to 12 putative species were detected and could be placed in three categories: (1) temperate geographically isolated, (2) warm-temperate to tropical wider spread and (3) circumglobal warm-water species. Conclusions The present study provides evidence of cryptic or pseudocryptic speciation in the Paracalanus parvus complex. One major insight is that the species Paracalanus parvus s.s. is not panmictic, but may be restricted in its distribution to the northeastern Atlantic.