Reconstructing the evolutionary history of the radiation of the land snail genus Xerocrassa on Crete based on mitochondrial sequences and AFLP markers

Sauer J, Hausdorf B. Reconstructing the evolutionary history of the radiation of the land snail genus Xerocrassa on Crete based on mitochondrial sequences and AFLP markers. BMC Evolutionary Biology. 2010;10(1): 299.Background: A non-adaptive radiation triggered by sexual selection resulted in ten endemic land snail species of the genus Xerocrassa on Crete. Only five of these species and a more widespread species are monophyletic in a mitochondrial gene tree. The reconstruction of the evolutionary history of such closely related species can be complicated by incomplete lineage sorting, introgression or inadequate taxonomy. To distinguish between the reasons for the nonmonophyly of several species in the mitochondrial gene tree we analysed nuclear AFLP markers. Results: Whereas six of the eleven morphologically delimited Xerocrassa species from Crete are monophyletic in the mitochondrial gene tree, nine of these species are monophyletic in the tree based on AFLP markers. Only two morphologically delimited species could not be distinguished with the multilocus data and might have diverged very recently or might represent extreme forms of a single species. The nonmonophyly of X. rhithymna with respect to X. kydonia is probably the result of incomplete lineage sorting, because there is no evidence for admixture in the AFLP data and the mitochondrial haplotype groups of these species coalesce deeply. The same is true for the main haplotype groups of X. mesostena. The nonmonophyly of X. franciscoi might be the result of mitochondrial introgression, because the coalescences of the haplotypes of this species with some X. mesostena haplotypes are shallow and there is admixture with neighbouring X. mesostena. Conclusion: The most likely causes for the nonmonophyly of species in the mitochondrial gene tree of the Xerocrassa radiation on Crete could be inferred using AFLP data by a combination of several criteria, namely the depth of the coalescences in the gene tree, the geographical distribution of shared genetic markers, and concordance with results of admixture analyses of nuclear multilocus markers. The strongly subdivided population structure increases the effective population size of land snail species and, thus, the likelihood of a long persistence of ancestral polymorphisms. Our study suggests that ancestral polymorphisms are a frequent cause for nonmonophyly of species with a strongly subdivided population structure in gene trees

Biotic Element Analysis in Biogeography

Biotic element analysis is an alternative to the areas-of-endemism approach for recognizing the presence or absence of vicariance events in a given region. If an ancestral biota was fragmented by vicariance events, biotic elements or clusters of distribution areas should emerge. We propose a statistical test for clustering of distribution areas based on a Monte Carlo simulation with a null model that considers the spatial autocorrelation in the data. The hypothesis tested is that the observed degree of clustering of ranges can be explained by the range size distribution, the varying number of taxa per cell, and the spatial autocorrelation of the occurrences of a taxon alone. A method for the delimitation of biotic elements which uses model-based Gaussian clustering is introduced. We demonstrate our methods and show the importance of grid size by means of a case study, an analysis of the distribution patterns of southern African species of the weevil genus Scobius. The example highlights the difficulties in delimiting areas of endemism if dispersal has occurred and illustrates the advantages of the biotic element approac

PUPINIDAE OF JAVA (GASTROPODA: CAENOGASTROPODA)

The systematics and distribution of the family Pupinidae (Gastropoda: Cyclophoroidea) in Java is reviewed. The family is represented in Java by four species of the genus Pupina, P. bipalatalis, P. compacta, P. junghuhni, and P. treubi. The shells of the species are described and figured, and the distribution data of the species are summarized. We have synonymized Pupina verbeeki Möllendorff, 1897 with Pupina treubi Boettger, 1890. All of the species except P. treubi, which is also known from Sumatra, are endemic to Java. Most previous records of Pupina from Java were from the western part of the island. Our new records show that the Pupina species are also more widespread in the drier central and eastern parts of Java. Their conservation status is therefore Least Concern.

DIVERSITY AND ECOLOGY OF LAND SNAILS IN GUNUNG HALIMUN SALAK NATIONAL PARK (GHSNP) IN JAVA, INDONESIA

The land snail fauna of the largest tropical montane forest in Java, the Gunung Halimun Salak National Park (GHSNP), was surveyed during the dry season (June-July) in 2015, concentrating on four park’s resorts, i.e. Cikaniki, Mt. Botol, Cisarua (Halimun area) and Cidahu (Salak area). In total, 399 specimens representing 43 species were collected. Prior to the surveys, 48 land snail species were known from the GHSNP. Fifteen new records for the GHSNP were discovered so 63 species are now known to inhabit the Park. This number represent 25% of the total land snail fauna of Java. 21 of the species found in GHSNP are endemic to Java. The species richness of the plots in GHSNP was correlated with soil pH and the composition of the land snail communities was correlated with elevation, annual mean temperature, and amount of deadwood

The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships

<p>Abstract</p> <p>Background</p> <p>The phylogenetic relationships of the lophophorate lineages, ectoprocts, brachiopods and phoronids, within Lophotrochozoa are still controversial. We sequenced an additional mitochondrial genome of the most species-rich lophophorate lineage, the ectoprocts. Although it is known that there are large differences in the nucleotide composition of mitochondrial sequences of different lineages as well as in the amino acid composition of the encoded proteins, this bias is often not considered in phylogenetic analyses. We applied several approaches for reducing compositional bias and saturation in the phylogenetic analyses of the mitochondrial sequences.</p> <p>Results</p> <p>The complete mitochondrial genome (16,089 bp) of <it>Flustra foliacea </it>(Ectoprocta, Gymnolaemata, Cheilostomata) was sequenced. All protein-encoding, rRNA and tRNA genes are transcribed from the same strand. <it>Flustra </it>shares long intergenic sequences with the cheilostomate ectoproct <it>Bugula</it>, which might be a synapomorphy of these taxa. Further synapomorphies might be the loss of the DHU arm of the tRNA L(UUR), the loss of the DHU arm of the tRNA S(UCN) and the unique anticodon sequence GAG of the tRNA L(CUN). The gene order of the mitochondrial genome of <it>Flustra </it>differs strongly from that of the other known ectoprocts. Phylogenetic analyses of mitochondrial nucleotide and amino acid data sets show that the lophophorate lineages are more closely related to trochozoan phyla than to deuterostomes or ecdysozoans confirming the Lophotrochozoa hypothesis. Furthermore, they support the monophyly of Cheilostomata and Ectoprocta. However, the relationships of the lophophorate lineages within Lophotrochozoa differ strongly depending on the data set and the used method. Different approaches for reducing heterogeneity in nucleotide and amino acid data sets and saturation did not result in a more robust resolution of lophotrochozoan relationships.</p> <p>Conclusion</p> <p>The contradictory and usually weakly supported phylogenetic reconstructions of the relationships among lophotrochozoan phyla based on mitochondrial sequences indicate that these alone do not contain enough information for a robust resolution of the relations of the lophotrochozoan phyla. The mitochondrial gene order is also not useful for inferring their phylogenetic relationships, because it is highly variable in ectoprocts, brachiopods and some other lophotrochozoan phyla. However, our study revealed several rare genomic changes like the evolution of long intergenic sequences and changes in the structure of tRNAs, which may be helpful for reconstructing ectoproct phylogeny.</p

Native and introduced land snail species as ecological indicators in different land use types in Java

We investigated the effects of different land use types and environmental parameters on the number and abundance of native and introduced land snail species in East Java. 2919 specimens were sampled and assigned to 55 species of which 8 are introduced. Whereas species richness was highest in primary forest, the highest number of introduced species was found in agroforest. The snail assemblages in different habitat types differ much clearer in composition than in total species richness. Plantations and agroforest are dominated by introduced pulmonates with regard to number of individuals, while primary forest is dominated by native prosobranchs. The habitat requirements of the introduced pulmonates differ from those of the native species. In the study area, the abundance of native as well as introduced pulmonate species increased with increasing human impact. However, the abundance of introduced pulmonate species decreased with increasing density of the canopy cover, whereas the abundance of native pulmonate species increased with increasing canopy cover. The abundance of native prosobranch land snails also tends to increase with increasing canopy cover and with the availability of deadwood, but decreased with increasing human impact. Improving the canopy cover and retaining deadwood in plantations and agroforests might help to control the populations of introduced species or even prevent their establishment in these habitats. Land snails are good indicators for the long-term stability of natural habitats, because several species are restricted to undisturbed natural habitats and because of their low dispersal abilities. However, complete inventories of land snail species are costly. Therefore we propose two indices that can be scored with much less effort, namely the percentage of prosobranch individuals and the percentage of individuals of introduced species. Both indices are significantly correlated with the number of native species. Dense plantations and agroforests bordering primary forests may protect the latter from introduced species and help to conserve the native fauna by reducing desiccation and buffering the human impact on the primary forests

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.info:eu-repo/semantics/publishedVersio

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics