Mentawai’s endemic,relictual fauna: is it evidence for Pleistocene extinctions on Sumatra?

Aim The four Mentawai islands, south‐west of Sumatra, have long been isolated from the remainder of Sundaland, resulting in a high level of endemism. We examined the distribution of 151 species of the Mentawai Islands in Sundaland and assessed various processes that may have resulted in the various biogeographical patterns. Location Southeast Asia, particularly the Mentawai Islands and nearby large landmasses (Sumatra, Java, Borneo and Peninsular Malaysia). Methods We compared the faunal composition of the Mentawai Islands for selected taxa (43 mammals, 92 reptiles and 16 amphibians) with that of the four nearby large landmasses of Sundaland using morphological comparisons and the most recent molecular phylogenetic analyses available in the literature. These comparisons yielded sister taxa, which were used to simulate species absence data for the four Sundaland landmasses under several scenarios to investigate how patterns of species absence could have arisen. Results In contrast to our expectations, several Mentawai species did not have their closest relatives on neighbouring Sumatra, but rather on the more distant Borneo, Java or Peninsular Malaysia. For mammals, the similarity between species from Mentawai and Borneo was greater than that observed between species from Mentawai and Sumatra. We conclude that the relationships represent traces of species historically distributed throughout Sundaland that became extinct in Sumatra during the Pleistocene. For reptiles and amphibians the observed pattern of species absences generally resembled the simulated pattern expected under the scenario of absence rates increasing with landmass isolation, whereas for mammals we observed more species than expected missing from Java and Sumatra, and fewer than expected from Borneo. Main conclusions The potential extinctions on Sumatra probably had two causes: changes of climate and vegetation during the Pleistocene and environmental impacts from the Toba supervolcanic eruption.     

Fast and cost‐effective single nucleotide polymorphism (SNP) detection in the absence of a reference genome using semideep next‐generation Random Amplicon Sequencing (RAMseq)

Biodiversity has suffered a dramatic global decline during the past decades, and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and on a genetic level. However, in wild species, the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article, we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost‐effective detection of single nucleotide polymorphisms (SNPs) in nonmodel species by semideep sequencing of random amplicons. By applying RAMseq to the Eurasian otter (Lutra lutra), we identified 238 putative SNPs after quality filtering of all candidate loci and were able to validate 32 of 77 loci tested. In a second step, we evaluated the genotyping performance of these SNP loci in noninvasive samples, one of the most challenging genotyping applications, by comparing it with genotyping results of the same faecal samples at microsatellite markers. We compared (i) polymerase chain reaction (PCR) success rate, (ii) genotyping errors and (iii) Mendelian inheritance (population parameters). SNPs produced a significantly higher PCR success rate (75.5% vs. 65.1%) and lower mean allelic error rate (8.8% vs. 13.3%) than microsatellites, but showed a higher allelic dropout rate (29.7% vs. 19.8%). Genotyping results showed no deviations from Mendelian inheritance in any of the SNP loci. Hence, RAMseq appears to be a valuable tool for the detection of genetic markers in nonmodel species, which is a common challenge in conservation genetic studies.     

Semen cryopreservation and the conservation of endangered species

Currently, more than 16,000 plant and animal species are imminently threatened by extinction, often as a direct consequence of anthropogenic influences. One of the measures to halt that process is genetic resource banking. This short review focuses on mammal sperm cryopreservation in combination with assisted reproduction techniques. It summarizes general problems, recent developments, and currently applied protocols and gives an overview of hitherto existing successes of assisted reproduction measures in wild animals in the light of conservation efforts.     

Phylogenetic relationships and ancestral areas of the bustards (Gruiformes: Otididae), inferred from mitochondrial DNA and nuclear intron sequences

The taxonomy of the bustards is poorly understood phylogenetically and has not been extensively evaluated using molecular methods. We sequenced part of the mitochondrial cytochrome b gene, the control region (central domain II), and an intron-exon crossing fragment of the nuclear chromo-helicase-DNA binding gene (CHD1) in 27 bustard taxa (including multiple subspecies) representing 11 genera and four gruiform outgroup species. Molecular datings suggest a Miocene origin for the family. Inferred phylogenetic relationships include the following: (i) the basal polytomy consists of 10 branches (mostly consistent with traditional genera), suggesting a rapid early radiation; (ii) sister relationships between several couplets of genera include Ardeotis with Neotis, Afrotis with Eupodotis (excluding E. rueppellii), Otis with Chlamydotis, and Houbaropsis with Sypheotides; (iii) the genus Eupodotis may be polyphyletic; and (iv) the currently delimited genera Ardeotis and Neotis do not form independent monophyletic lineages. Molecular evidence for the Afro-tropical origin of the Otididae is provided.     

Very low density and low density lipoprotein subfractions in type III and type IV hyperlipoproteinemia. Chemical and physical properties.

Subfractions of CLDL (VLDL), Sf 100-400; CLDL2, Sf 60--100; VLDL3, Sf 20--60) and LDL (LDL), Sf 12--20; LDL2, Sf 6--12; LDL3, Sf 3--6) were isolated from the plasma of three normal, three type III and four type IV hyperlipoproteinemic subjects. In the type IV group, all VLDL subspecies were of normal composition but were increased in concentration in the order VLDL1 greater than VLDL2 greater than VLDL3. In the same subjects, although LDL2 was lowered and LDL3 increased, the total plasma LDL concentration was normal. All VLDL subfractions were elevated in the type III group, but in this case VLDL3 predominated. These subfractions were enriched in cholesteryl esters and depleted in triglyceride. In the LDL density range there was a shift of mass towards the least dense fraction, LDL1, which was of normal composition. EPR studies of the VLDL and LDL subfractions in a type IV subject demonstrated a decrease in fluidity with increasing density. The major change occurred between VLDL3 and LDL1 and was attributed to a substantial alteration in the cholesteryl ester : triglyceride ratio in the particle. A similar argument was used to explain thction in normal or type IV subjects. Particle diameters, determined by laser light-scattering spectroscopy were in good agreement with the values obtained by electron microscopy. This study provides a baseline for the examination of the relationship between the physical and metabolic properties of VLDL and LDL subfractions in type III and IV hyperlipoproteinemia.     

A single‐nucleotide polymorphism‐based approach for rapid and cost‐effective genetic wolf monitoring in Europe based on noninvasively collected samples

Noninvasive genetics based on microsatellite markers has become an indispensable tool for wildlife monitoring and conservation research over the past decades. However, microsatellites have several drawbacks, such as the lack of standardisation between laboratories and high error rates. Here, we propose an alternative single‐nucleotide polymorphism (SNP)‐based marker system for noninvasively collected samples, which promises to solve these problems. Using nanofluidic SNP genotyping technology (Fluidigm), we genotyped 158 wolf samples (tissue, scats, hairs, urine) for 192 SNP loci selected from the Affymetrix v2 Canine SNP Array. We carefully selected an optimised final set of 96 SNPs (and discarded the worse half), based on assay performance and reliability. We found rates of missing data in this SNP set of <10% and genotyping error of ~1%, which improves genotyping accuracy by nearly an order of magnitude when compared to published data for other marker types. Our approach provides a tool for rapid and cost‐effective genotyping of noninvasively collected wildlife samples. The ability to standardise genotype scoring combined with low error rates promises to constitute a major technological advancement and could establish SNPs as a standard marker for future wildlife monitoring.     

Crossing the border? Structure of the red deer (Cervus elaphus) population from the Bavarian–Bohemian forest ecosystem

Anthropogenic impact such as overhunting and habitat fragmentation has reduced the total red deer population (Cervus elaphus) across Europe. In Germany remaining subpopulations are even confined to designated areas with limited or no gene flow among them. Red deer populations inhabiting the Bavarian–Bohemian forest ecosystem had been divided by a fortified State border between Germany and former Czechoslovakia. To assess red deer genetic diversity more than two decades after the removal of the fortifications, we analysed a population from the Bavarian Forest National Park, Germany, and one from the National Park ?umava, Czech Republic, using 11 microsatellite loci and a 910 bp long section of the mitochondrial control region (mtDNA). Bayesian analyses of microsatellite allele frequencies favoured the presence of a single population in the Bavarian-Bohemian forest ecosystem over other population genetic structures. This admixture was supported by a lack of population pairwise differentiation between German and Czech red deer microsatellite genotypes in the analysis of molecular variance (AMOVA, F_ST = 0.009, p = 0.383). Contrastingly, AMOVA revealed a highly significant matrilinear differentiation of mtDNA between the two samples (Φ_ST = 0.285, p = 0.002), whereby German red deer belonged predominantly to haplogroup A (western Europe) and Czech red deer predominantly to haplogroup C (eastern Europe). In combination, these findings indicated a high degree of philopatry by does and extensive gene flow across the former border mediated by stags. They also identified the Bavarian–Bohemian forest ecosystem as part of a suture zone between western and eastern European red deer matrilines.     

Investigations on reproductive physiology in the male Eurasian lynx (Lynx lynx)

This study characterized (in vivo) morphological and functional parameters of reproductive organs of adult male lynx (n = 3) prior to, during, and after the breeding season (n = 3). Size and morphology of the reproductive tract were monitored by transcutaneous (testes) and transrectal (accessory sex glands) ultrasonography. Semen was collected by electroejaculation. Ejaculate volume, sperm number, motility, and morphology of spermatozoa as well as testosterone concentrations in blood serum and feces were evaluated. The testes and prostate had seasonal changes in size and echotexture. The mean (+/- S.D.) maximum and minimum testicular volume were 2.8 +/- 0.8 cm3 and 1.5 +/- 0.3 cm3, respectively. Fecal testosterone concentrations were highest in February (1240 +/- 393 ng/g feces), with a second increase in May (971 +/- 202 ng/g feces), but concentrations were lowest in January (481 +/- 52.9 ng/g feces). Ejaculate volume, total sperm number and percentage of motile, and intact spermatozoa were maximal in March (the middle of the breeding season). In one of the eight litters, multiple paternity was proven; however, in the remaining seven litters, all 16 cubs were sired by the same male. This particular male had the most developed and active testes and best semen quality, which may be important for sperm competition.