Phylogenomics at the tips: inferring lineages and their demographic history in a tropical lizard,Carlia amax

High‐throughput sequencing approaches offer opportunities to better understand the evolutionary processes driving diversification, particularly in nonmodel organisms. In particular, the 100–1000's of loci that can now be sequenced are providing unprecedented power in population, speciation and phylogenetic studies. Here, we apply an exon capture approach to generate >99% complete sequence and SNP data across >2000 loci from a tropical skink, Carlia amax, and exploit these data to identify divergent lineages and infer their relationships and demographic histories. This is especially relevant to low‐dispersal tropical taxa that often have cryptic diversity and spatially dynamic histories. For C. amax, clustering of nuclear SNPs and coalescent‐based species delimitation analyses identify four divergent lineages, one fewer than predicted based on geographically coherent mtDNA clades (>9.4% sequence divergence). Three of these lineages are widespread and parapatric on the mainland, whereas the most divergent is restricted to islands off the northeast Northern Territory. Tests for population expansion reject an equilibrium isolation‐by‐distance model for two of the three widespread lineages and infer refugial expansion sources in the relatively mesic northeast Top End and northwest Kimberley. The latter is already recognized as a hotspot of endemism, but our results also suggest that a stronger focus on the northeast Top End, and adjacent islands is warranted. More generally, our results show how genome‐reduction methods such as exon capture can yield insights into the pattern and dynamics of biodiversity across complex landscapes with as yet poorly understood biogeographic history and how exon data can link between population and phylogenetic questions.     

Conditions for the invasion of male‐haploidy in diploid populations

Male‐haploidy has independently evolved several times in different phylogenetic groups and has led to various extant lineages in the insects, Arachnida and Rotifera. Although the stability of male‐haploidy as an evolutionary strategy is not well understood, various theories address the invasion of male‐haploidy in diploid populations. Here two of these theories: (i) the maternal transmission hypothesis (MTH) and (ii) the deleterious mutation hypothesis (DMH), are re‐investigated with an agent‐based model to understand the role of genetic drift as a mechanism facilitating the spread of male‐haploidy. These two hypotheses are analysed separately and comparatively, and the results suggest dominance of the MTH. In addition, comparison of the stochastic results to deterministic results using the same model structure shows how genetic drift can enhance the parameter space where male‐haploidy can be expected to invade.     

A novel UV-damaged DNA binding protein emerges during the chromatin-eliminating cleavage period in Ascaris suum.

During the early cleavage period of Ascaris suum , chromatin diminution takes place in the somatic founder cells. In the process of chromatin diminution numerous heterochromatic blocks, consisting predominantly of highly repeated DNA, are discarded during mitotic anaphase and are later on digested in the cytoplasm. Very little is known about proteins that are involved in chromatin diminution. We have detected a nuclear protein and purified it to near homogeneity by its preferential binding to UV-damaged DNA. We termed this protein chromatin diminution associated factor 1 (CDAF1), because maximum binding activity per nucleus was observed to develop in 4-8-cell stages, when chromatin diminution occurs for the first time. CDAF1 recognizes cyclobutane pyrimidine dimers in UV-damaged double-stranded DNA. Its binding properties identify CDAF1 as a novel kind of damaged-DNA binding protein. CDAF1 activity is almost not detectable in 1-celled embryos. It increases dramatically during formation of somatic founder cells and persists up to the first larval stage. However, CDAF1 is absent in tissues of adults. These findings led us to suggest that CDAF1 plays a dual role: during the early segregative cleavage period it might be involved in chromatin diminution as a transfactor and act in nucleotide excision repair as an accessory factor throughout embryogenesis.     

Sociality and the Rate of rDNA Sequence Evolution in Wasps (Vespidae) and Honeybees (Apis)

Sequence data of mitochondrial 16S ribosomal DNA (mt-rDNA) and nuclear 28S ribosomal DNA (nuc-rDNA) were compared in two honeybee species (Apis mellifera and Apis dorsata) and a selection of 22 wasp species (Vespidae) with different levels of sociality. The averge substitution rates in mt-rDNA and nuc-rDNA were almost-equal in solitary species. In species with larger nests, however, the difference between the nuclear and the mitochondrial substitution rate significantly increased. The average substitution ratio, ψ (nucleotide substitutions in mt-rDNA/nucleotide substitutions in nuc-rDNA) was 1.48 ± 0.12 (SE) among the solitary Eumeninae, 3.70 ± 0.15 among five primitive social Stenogastrinae species, 3.24 ± 0.20 among five Polistinae species, 5.76 ± 0.33 among nine highly eusocial Vespinae, and 12.7 in the two Apis species. The high egg-laying rate and the effective population size skew between the sexes may contribute to the rise of the substitution ratio in the highly eusocial species. Drift and bottleneck effects in the mitochondrial DNA pool during speciation events as well as polyandry may further enhance this phenomenon. Received: 12 January 1998 / Accepted: 28 April 1998     

I-cell disease-like phenotype in mice deficient in mannose 6-phosphate receptors

Mannose 6-phosphate receptor deficient mice were generated by crossing mice carrying null alleles for Igf2 and the 300 kDa and 46 kDa mannose 6-phosphate receptors, Mpr300 and Mpr46. Pre- and perinatal lethality of mice nullizygous for Igf2, Mpr300 and Mpr46 was increased. Triple deficient mice surviving the first postnatal day had normal viability and developed a phenotype resembling human I-cell disease. The triple deficient mice were characterized by dwarfism, facial dysplasia, waddling gait, dysostosis multiplex, elevated lysosomal enzymes in serum and histological signs of lysosomal storage predominantly in fibroblasts, but also in parenchymal cells of brain and liver. A paternally inherited Mpr300 wild type allele that is normally inactive in mice due to imprinting was reactivated in some tissues of mice lacking IGF II and MPR 46 and carrying a maternal Mpr300 null allele. Inspite of the partial reactivation the phenotype of these mice was similar to that of triple deficient mice.     

Gibbs-Ensemble Molecular Dynamics: A New Method for Simulations Involving Particle Exchange

We discuss a novel simulation method suitable for simulating phenomena involving particle exchange. The method is a molecular dynamics version of the Gibbs-Ensemble Monte Carlo technique, which has been developed some years ago for the direct simulation of phase equilibria in fluid systems. The idea is to have two separate simulation boxes, which can exchange particles or molecules in a thermodynamically consistent fashion. We discuss the general idea of the Gibbs-Ensemble Molecular Dynamics technique and present examples for different simple atomic and molecular fluids. Specifically we will discuss Gibbs-Ensemble Molecular Dynamics simulations of gas-liquid and liquid-solid equilibria in Lennard-Jones systems and in hexane as well as an application of the method to adsorption.     

Simultaneous saccharification and extractive fermentation of cellulosic substrates

Alcohol fermentation has traditionally been carried out in aqueous environments because of the ready solubility of reactant (sugar) and product (ethanol). However, extraction of the product ethanol into a nonmiscible phase can result in kinetic benefits due to reduced inhibition of the fermentation reactions. In this study, we report the development of a novel simultaneous saccharification and extractive fermentation (SSEF) process. Ethanol productivity was increased by up to 65% over conventional (nonextractive) fed-batch simultaneous saccharification systems when calculated on the basis of aqueous phase volume. The amount of water required for SSEF reactions was dramatically reduced from that required for conventional SSF. In batch SSEF reactors with 2.5% aqueous phase, 50% conversion of 25% (aqueous phase concentration) Solka Floc could be achieved in 48 h using 2 FPU/g cellulase. (c) 1996 John Wiley & Sons, Inc.     

The origin and evolution of parthenogenesis in theHeteronotia binoei complex: Synthesis

TheHeteronotia binoei complex includes several cryptic species of sexually reproducing lizards and parthenogenetic lineages derived from them. This paper synthesizes analyses of distribution and variation of allozymes, chromosomes, mitochondrial DNA and ribosomal DNA genes in order to make inferences about the origins of the parthenogenetic lineages, the extent and source of their genetic diversity, their current and historical biogeography and their ecological properties. The parthenogens appear to have arisen recently (relative to geographic differentiation within the sexual taxa) via episodes of repetitive hybridization between two of the sexual taxa. These events probably occurred within one or two small geographic areas of western Australia, after which some of the parthenogenetic lineages rapidly expanded their ranges to central Australia. The parthenogenetic form has extraordinarily high genetic diversity, mostly derived from the repetitive origins, but with some contribution from mutation and biased gene conversion/recombination being apparent. The rapid and extensive range expansion of the parthenogenetic lineages from western to central Australia attests to the short-term success of this reproductive strategy, in this case perhaps reinforced by the parthenogenetic females having higher fecundity than their smaller sexual relatives. However, the parthenogens are orders of magnitude more susceptible to infection by ectoparasitic mites, suggesting that they could be at a long-term disadvantage. The detailed characterization of this system provides a basis for critical evaluation of hypotheses about the evolutionary advantage of sexual reproduction derived from broad comparative studies.     

Glucose tolerance of postnatally stress-sensitized albino rats following chronic emotional stress in adulthood]

Male albino rats were used to study the effect of electrical stimulation in the postnatal phase (day 1--15) leading to short-time convulsions and cyanosis lasting about 10 min in 5-month-old animals upon the development of glycemic dysregulation induced by emotional stress. The studies involving i.p. glucose administration show that a 3-week stress influence on postnatally stimulated animals caused heavier changes of glycemic regulation than with non-pretreated animals. These results suggest a stress sensitization occurring in the postnatal phase and are discussed in connection with the "stress-sensitive risk personality" by R. BAUMANN. Further studies have shown that the postnatal stress sensitiveness is reversible and cannot only be compensated by a rest period of several weeks but may even cause stress resistance on renewed stressing for three weeks.