A stochastic movement simulator improves estimates of landscape connectivity.

Conservation actions often focus on restoration or creation of natural areas designed to facilitate the movements of organisms among populations. To be efficient, these actions need to be based on reliable estimates or predictions of landscape connectivity. While circuit theory and least-cost paths (LCPs) are increasingly being used to estimate connectivity, these methods also have proven limitations. We compared their performance in predicting genetic connectivity with that of an alternative approach based on a simple, individual-based "stochastic movement simulator" (SMS). SMS predicts dispersal of organisms using the same landscape representation as LCPs and circuit theory-based estimates (i.e., a cost surface), while relaxing key LCP assumptions, namely individual omniscience of the landscape (by incorporating perceptual range) and the optimality of individual movements (by including stochasticity in simulated movements). The performance of the three estimators was assessed by the degree to which they correlated with genetic estimates of connectivity in two species with contrasting movement abilities (Cabanis's Greenbul, an Afrotropical forest bird species, and natterjack toad, an amphibian restricted to European sandy and heathland areas). For both species, the correlation between dispersal model and genetic data was substantially higher when SMS was used. Importantly, the results also demonstrate that the improvement gained by using SMS is robust both to variation in spatial resolution of the landscape and to uncertainty in the perceptual range model parameter. Integration of this individual-based approach with other developing methods in the field of connectivity research, such as graph theory, can yield rapid progress towards more robust connectivity indices and more effective recommendations for land management.

Post-fragmentation population structure in a cooperative breeding Afrotropical cloud forest bird: emergence of a source-sink population network.

The impact of demographic parameters on the genetic population structure and viability of organisms is a long-standing issue in the study of fragmented populations. Demographic and genetic tools are now readily available to estimate census and effective population sizes and migration and gene flow rates with increasing precision. Here we analysed the demography and genetic population structure over a recent 15-year time span in five remnant populations of Cabanis's greenbul (Phyllastrephus cabanisi), a cooperative breeding bird in a severely fragmented cloud forest habitat. Contrary to our expectation, genetic admixture and effective population sizes slightly increased, rather than decreased between our two sampling periods. In spite of small effective population sizes in tiny forest remnants, none of the populations showed evidence of a recent population bottleneck. Approximate Bayesian modelling, however, suggested that differentiation of the populations coincided at least partially with an episode of habitat fragmentation. The ratio of meta-Ne to meta-Nc was relatively low for birds, which is expected for cooperative breeding species, while Ne /Nc ratios strongly varied among local populations. While the overall trend of increasing population sizes and genetic admixture may suggest that Cabanis's greenbuls increasingly cope with fragmentation, the time period over which these trends were documented is rather short relative to the average longevity of tropical species. Furthermore, the critically low Nc in the small forest remnants keep the species prone to demographic and environmental stochasticity, and it remains open if, and to what extent, its cooperative breeding behaviour helps to buffer such effects.

Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.

House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.

Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5' splice-site disruption.

We describe 94 pathogenic NF1 gene alterations in a cohort of 97 Austrian neurofibromatosis type 1 patients meeting the NIH criteria. All mutations were fully characterized at the genomic and mRNA levels. Over half of the patients carried novel mutations, and only a quarter carried recurrent minor-lesion mutations at 16 mutational warm spots. The remaining patients carried NF1 microdeletions (7%) and rare recurring mutations. Thirty-six of the mutations (38%) altered pre-mRNA splicing, and fall into five groups: exon skipping resulting from mutations at authentic splice sites (type I), cryptic exon inclusion caused by deep intronic mutations (type II), creation of de novo splice sites causing loss of exonic sequences (type III), activation of cryptic splice sites upon authentic splice-site disruption (type IV), and exonic sequence alterations causing exon skipping (type V). Extensive in silico analyses of 37 NF1 exons and surrounding intronic sequences suggested that the availability of a cryptic splice site combined with a strong natural upstream 3' splice site (3'ss)is the main determinant of cryptic splice-site activation upon 5' splice-site disruption. Furthermore, the exonic sequences downstream of exonic cryptic 5' splice sites (5'ss) resemble intronic more than exonic sequences with respect to exonic splicing enhancer and silencer density, helping to distinguish between exonic cryptic and pseudo 5'ss. This study provides valuable predictors for the splicing pathway used upon 5'ss mutation, and underscores the importance of using RNA-based techniques, together with methods to identify microdeletions and intragenic copy-number changes, for effective and reliable NF1 mutation detection.

Spectrum of single- and multiexon NF1 copy number changes in a cohort of 1,100 unselected NF1 patients.

Neurofibromatosis type 1 (NF1), the most common tumor-predisposing disorder in humans, is caused by defects in the NF1 tumor-suppressor gene. Comprehensive mutation analysis applying RNA-based techniques complemented with FISH analysis achieves mutation detection rates of approximately 95% in NF1 patients. The majority of mutations are minor lesions, and approximately 5% are total gene deletions. We found 13 single- and/or multiexon deletions/duplications out of 1,050 detected mutations using our RNA-based approach in a cohort of 1,100 NF1 patients and confirmed these changes using multiplex ligation-dependent probe amplification (MLPA). With MLPA, we found another 12 novel multiexon deletion/duplications in 55 NF1 patients for whom analysis with multiple assays had not revealed a NF1 mutation, including 50 previously analyzed comprehensively. The extent of the 22 deletions and 3 duplications varied greatly, and there was no clustering of breakpoints. We also evaluated the sensitivity of MLPA in identifying deletions in a mosaic state. Furthermore, we tested whether the MLPA P122 NF1 area assay could distinguish between type I deletions, with breakpoints in low-copy repeats (NF1-LCRs), and type II deletions, caused by aberrant recombination between the JJAZ gene and its pseudogene. Our study showed that intragenic deletions and/or duplications represent only approximately 2% of all NF1 mutations. Although MLPA did not substantially increase the mutation detection rate in NF1 patients, it was a useful first step in a comprehensive mutation analysis scheme to quickly pinpoint patients with single- or multiexon deletions/duplications as well as patients with a total gene deletion who will not need full sequencing of the complete coding region.

Exhaustive mutation analysis of the NF1 gene allows identification of 95% of mutations and reveals a high frequency of unusual splicing defects.

Neurofibromatosis type 1 (NF1) is one of the most common autosomal dominant disorders and is caused by mutations in the NF1 gene. Mutation detection is complex due to the large size of the NF1 gene, the presence of pseudogenes and the great variety of possible lesions. Although there is no evidence for locus heterogeneity in NF1, mutation detection rates rarely exceed 50%. We studied 67 unrelated NF1 patients fulfilling the NIH diagnostic criteria, 29 familial and 38 sporadic cases, using a cascade of complementary techniques. We performed a protein truncation test starting from puromycin-treated EBV cell lines and, if no mutation was found, continued with heteroduplex, FISH, Southern blot and cytogenetic analysis. We identified the germline mutation in 64 of 67 patients and 32 of the mutations are novel. This is the highest mutation detection rate reported in a study of typical NF1 patients. All mutations were studied at the genomic and RNA level. The mutational spectrum consisted of 25 nonsense, 12 frameshift, 19 splice mutations, six missense and/or small in-frame deletions, one deletion of the entire NF1 gene, and a translocation t(14;17)(q32;q11.2). Our data suggest that exons 10a-10c and 37 are mutation-rich regions and that together with some recurrent mutations they may account for almost 30% of the mutations in classical NF1 patients. We found a high frequency of unusual splice mutations outside of the AG/GT 5 cent and 3 cent splice sites. As some of these mutations form stable transcripts, it remains possible that a truncated neurofibromin is formed.

Exon 10b of the NF1 gene represents a mutational hotspot and harbors a recurrent missense mutation Y489C associated with aberrant splicing.

PURPOSE: To analyze the spectrum and frequency of NF1 mutations in exon 10b. METHODS: Mutation and sequence analysis was performed at the DNA and cDNA level. RESULTS: We identified nine exon 10b mutations in 232 unrelated patients. Some mutations were recurrent (Y489C and L508P), others were unique (1465-1466insC and IVS10b+2delTAAG). Surprisingly, at the RNA level, Y489C causes skipping of the last 62 nucleotides of exon 10b. Another recurrent mutation, L508P, is undetectable by the Protein Truncation Test. CONCLUSION: As exon 10b shows the highest mutation rate yet found in any of the 60 NF1 exons, it should be implemented with priority in mutation analysis.

Human myosin V gene produces different transcripts in a cell type-specific manner.

In mice, tissue-specific alternative splicing of the myosin V gene in the C-terminal tail domain is well documented with exclusion of exon F from brain transcripts, but present in skin, particularly in melanocytes. As alternative splicing of the myosin V C-terminal tail domain in human tissues is undocumented, we studied the presence of myosin V splice forms in different types of human cultured normal skin cells, i.e., dermal fibroblasts, melanocytes, and keratinocytes as well as in human blood leukocytes, using an RT-PCR-based method. In all cell types studied, several different length transcripts were present containing different exon combinations, including exon F. This is the first report showing the presence of exon F as well as alternative splicing in the human myosin V tail domain. As the full-length transcript is most abundant in melanocytes and leukocytes and both cell types are involved in Griscelli syndrome, a tissue-specific role of this particular transcript needs further investigation.

Characterisation of two different nonsense mutations, C6792A and C6792G, causing skipping of exon 37 in the NF1 gene.

Neurofibromatosis type 1 (NF1), characterised by peripheral neurofibromas, café-au-lait spots and iris Lisch nodules, is one of the most common inherited disorders. We have analysed exons 35 to 49 in 21 unrelated NF1 patients using reverse transcription-polymerase chain reaction and protein truncation analysis. In two unrelated patients we found skipping of exon 37 at the cDNA level. Sequence analysis of genomic DNA revealed the presence of a C6792A transversion in one patient and a C6792G transversion in a second patient; both transversions change the codon for tyrosine to a nonsense codon. Sequencing of the exonic sequences as well as the branch sites, and the 3' and 5' splice sites of exons 36, 37 and 38 did not reveal any additional sequence abnormality. This is the first report showing that nonsense mutations in the NF1 gene can induce the skipping of a constitutive exon.

Identification of two different mutations causing protein S deficiency in two unrelated Belgian families using a nonisotopic scanning and sequencing method.

Hereditary protein S deficiency is a risk factor for developing recurrent venous thromboembolic disease and is caused by a defect in the protein S 1 (PROS1) gene. Identification of the mutation in the PROS1 gene can overcome diagnostic uncertainty in family members with borderline protein S levels. We describe a novel nonisotopic method for molecular diagnosis of protein S deficiency, using fluorescein-labeled amplification and sequencing primers. As a first step, all exons of the PROS1 gene are selectively amplified, and heteroduplex analysis is performed. As a second step, all exons are analyzed by direct sequencing. Using this method, we have characterized the molecular defect in two Belgian families with hereditary protein S deficiency type I: a frameshift mutation in exon XIV (1881insTC) and a missense mutation caused by a T-to-C transition, resulting in substitution of Leu405 by Pro (L405P).