A Bird Survey of Gunung Lumut Protection Forest, East Kalimantan and a Recommendation for its Designation as an Important Bird Area - Part 1

We report on a bird survey in and near Gunung Lumut Protection Forest in East Kalimantan, and evaluate our results against the BirdLife International criteria for recognition as an Important Bird Area. Five globally threatened species (Storm 's Stork Ciconia stormi, Bomean Peacock-pheasant Polyplectron schleiermacheri, Large Green Pigeon Treron capellei, Short-toed Coucal Centropus rectunguis and Blue-headed Pitta Pitta baudii) were encountered, as well as 91 species endemic to the Sundaic Lowland Forest biome, and up to 1% of the biogeographic population of the congregatory Storm's Stork. Based on these observations, we recommend Gunung Lumut Protection Forest to be included in Birdlife International 's Important Bird Area network

Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts

The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted

Medida cautelar de secuestro en el proceso de extinción de dominio

Artículo de investigaciónEste trabajo se realiza para tener un entendimiento más claro respecto de la aplicación de la medida cautelar de secuestro en el proceso de extinción del derecho de dominio. Además, saber si se ha logrado una independencia de la acción civil y penal frente a la acción extintiva del dominio de acuerdo al artículo 34 de la Constitución de 1991, reconociendo los mecanismos efectivos para perseguir los bienes adquiridos ilegalmente derivados de actividades como el enriquecimiento ilícito y otros delitos, en perjuicio del tesoro público o con grave deterioro de la moral social, o utilizados para la comisión de conductas ilícitas y posteriormente declararlos en titularidad a favor del Estado sin contraprestación ni compensación alguna del que los tenía. De igual manera, se hará énfasis del secuestre encargado de dar una efectiva administración a los bienes puestos a su disposición.55 p.INTRODUCCIÓN 1. REFERENCIAS DEL SECUESTRO COMO MEDIDA CAUTELAR 2. MEDIDAS CAUTELARES CONCLUSIONES BIBLIOGRAFÍA ANEXOSPregradoAbogad

An extended mtDNA phylogeography for the alpine newt illuminates the provenance of introduced populations

Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt is still incompletely understood and certain regions are severely undersampled. We collect mtDNA sequence data of over seven hundred individuals, from both the native and the introduced range. The main new insights from our extended mtDNA phylogeography are that 1) haplotypes from Spain do not form a reciprocally monophyletic clade, but are nested inside the mtDNA clade that covers western and eastern Europe; and 2) haplotypes from the northwest Balkans form a monophyletic clade together with those from the Southern Carpathians and Apuseni Mountains. We also home in on the regions where the distinct mtDNA clades meet in nature. We show that four out of the seven distinct mtDNA clades that comprise the alpine newt are implicated in the introductions in the Netherlands, United Kingdom and Ireland. In several introduced localities, two distinct mtDNA clades co-occur. As these mtDNA clades presumably represent cryptic species, we urge that the extent of genetic admixture between them is assessed from genome-wide nuclear DNA markers. We mobilized a large number of citizen scientists in this project to support the collection of DNA samples by skin swabbing and underscore the effectiveness of this sampling technique for mtDNA barcoding

Data from: The Carpathians hosted extra-Mediterranean refugia-within-refugia during the Pleistocene Ice Age: genomic evidence from two newt genera

Part of Europe’s temperate species survived the Pleistocene glacial cycles in refugia north of the Mediterranean peninsulas. For one such extra-Mediterranean refugia, the Carpathians, an intricate ‘refugia-within-refugia’ scenario has been suggested, involving species surviving in multiple discrete glacial refugia. We test the Carpathian refugia-within-refugia hypothesis, employing genome-wide multilocus data sets for two newt species (Triturus cristatus and Lissotriton montandoni). We first use Bayesian clustering to delineate intraspecific evolutionary lineages. The number of intraspecific lineages identified, and the allocation of localities to these lineages, were used to construct testable hypotheses on the spatial arrangement of glacial refugia in both newt species. Next we employ approximate Bayesian computation to date whether these lineages are of Holocene ( 12 Ka) origin. We identify three intraspecific evolutionary lineages for T. cristatus and two for L. montandoni. For both newt species, intraspecific divergence is rooted in the Pleistocene, in line with species survival in distinct range fragments during the last glacial period. Hence, our findings firmly support the Carpathian refugia-within-refugia hypothesis. Furthermore, we show that mitochondrial DNA overestimates the age of intraspecific evolutionary lineages and we urge caution in basing refugia-within-refugia scenarios on mitochondrial DNA alone

Structure analyses

Files associated with the Structure analyses

An update on the avifauna of Gunung Lumut Protection Forest (East Kalimantan) and reflections on the potential conservation value of hutan adat

We present results of a second survey of the hutan adat (forest traditionally exploited on a small scale by local people) situated in the Gunung Lumut Protection Forest, East Kalimantan, conducted in 2007 and closely following the first survey in 2005 (Wielstra & Pieterse 2009. Kukila 14: 1-15). An additional 29 species were observed. These comprise two globally threatened (Vulnerable) species, 16 “Sundaic Lowland Forest” biome-restricted species, one “Sundaic montane forest” biome-restricted species and a congregatory waterbird species of which 1% of its biogeographic population is present. The findings substantiate our previous suggestion to recognize Gunung Lumut Protection Forest as an Important Bird Area. We also provide some remarks on the potential conservation value of hutan adat and raise issues to be addressed in further studies

Ion torrent data

Raw Ion Torrent reads in FASTQ format; scripts associated with the bioinformatics pipeline; BWA alignments in SAM format; raw SNP reports in VCF and BCF format; the filtered SNP report used to construct consensus sequences; an overview of the number of reads in total and per marker and/or individual; nuclear DNA data in genotypic format; nuclear DNA sequence alignments

Data from: Is the Danube crested newt Triturus dobrogicus polytypic? A review and new nuclear DNA data

The Danube crested newt Triturus dobrogicus has been proposed to comprise two subspecies: T. d. dobrogicus and T. d. macrosoma. Uncertainty exists in the literature over their distribution and diagnosability. We conduct a multilocus phylogeographical survey and review published data to determine whether a two taxon treatment is warranted. Newly produced and published nuclear DNA data suggest intraspecific variation in the Pannonian Plain part of the range, but with extensive genetic admixture, whereas mitochondrial DNA data shows a lack of geographical structuring in T. dobrogicus altogether. None of the studied morphological characters suggest the presence of two geographical groups in T. dobrogicus unequivocally. Although Danube Delta newts do have relatively short bodies compared to the remainder of the range (the Pannonian and Lower Danube Plains and the Dnepr Delta), we argue that this finding can be explained by phenotypic plasticity – particularly in light of the incongruent evolutionary scenario suggested by genetic data. We conclude that the total body of evidence does not support the two subspecies hypothesis and recommend that T. dobrogicus is treated as a monotypic species