The historical evolutionary development of Hemerocallis middendorfii (Hemerocallidaceae) revealed by non-coding regions in chloroplast DNA

A procedure in which combined molecular phylogeographical analyses among populations of Hemerocallis middendorfii (Hemerocallidaceae, Asparagales) were applied allowed comparisons to be made with the geological history. Information on geographical areas in which synapomorphic mutations occurred was used in molecular phylogeographical analyses for the first time in this study, in addition to molecular maximum-parsimonious analyses and TCS analyses. Nucleotide sequences of the intergenic region between the rbcL and atpB genes and the trnL (UAA) intron in chloroplast DNA were analyzed for 28 Japanese and three Chinese populations of H. middendorfii, 10 populations of closely related species and four outgroup species. The data of the three analyses in general agreed with one another and indicated that the separation of this species had proceeded in conjunction with the geological vicariance or orogeny. Where the synapomorphic mutations occurred, three patterns were recognized. They correlated with the geological history, namely, the age when the Japanese Archipelago and the Continent had joined, when the Sea of Japan was formed, and when there was separation from the Continent and the formation of each of the islands in the Japanese Archipelago. It was suggested that ancestors of H. middendorfii originated at latest 25 million years ago when the Japanese Archipelago and the Continent had joined; that is, before the formation of the Sea of Japan.We are greatly obliged to three anonymous reviewers for their constructive comments.     

The fate of balanced,phenotypic polymorphisms in fragmented metapopulations

In large populations, genetically distinct phenotypic morphs can be maintained in equilibrium (at a 1 : 1 ratio in the simplest case) by frequency‐dependent selection, as shown by Sewall Wright. The consequences of population fragmentation on this equilibrium are not widely appreciated. Here, I use a simple computational model to emphasize that severe fragmentation biases the morph ratio towards the homozygous recessive genotype through drift in very small populations favouring the more common recessive allele. This model generalizes those developed elsewhere for heterostylous plants and major histocompatibility complex alleles, emphasizes one particular outcome and avoids the restricting assumptions of more analytical models. There are important implications for both fundamental evolutionary biology and conservation genetics. I illustrate this with a range of examples but refer particularly to shell polymorphism in snails. These examples show how habitat fragmentation could have a direct and often unappreciated effect on species at the level of their population genetics.     

Interaction of Apolipoprotein E ε 4 With Other Genetic and Non-Genetic Risk Factors in Late Onset Alzheimer Disease: Problems Facing the Investigator

The Apolipoprotein E4 allele (Apo-4) is the major susceptibility gene for late onset Alzheimer Disease (AD) but epidemiological data suggest that the effect of this allele is modified in different individuals by genetic or environmental factors. Age and head injury are major non-genetic factors modifying the Apo-4 risk. There is conflicting data as to whether alleles of other chaperon proteins (such as alpha-1-antichymotrypsin (ACT)) or Apo-4 receptors (such as the VDRL receptor) modify the Apo-4 risk for AD. We analyze problems posed by genetic association studies including those of multiple comparisons and selection of controls, the latter problem exacerbated by the wide variations in Apolipoprotein E allele frequencies observed in different groups and localities.     

Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity

Evidence‐based conservation planning is crucial for informing management decisions for species of extreme rarity, but collection of robust data on genetic status or other parameters can be extremely challenging for such species. The Hainan gibbon, possibly the world's rarest mammal, consists of a single population of ~25 individuals restricted to one protected area on Hainan Island, China, and has persisted for over 30 years at exceptionally low population size. Analysis of genotypes at 11 microsatellite loci from faecal samples for 36% of the current global population and tissue samples from 62% of existing historical museum specimens demonstrates limited current genetic diversity (Na = 2.27, Ar = 2.24, H_e = 0.43); diversity has declined since the 19th century and even further within the last 30 years, representing declines of ~30% from historical levels (Na = 3.36, Ar = 3.29, H_e = 0.63). Significant differentiation is seen between current and historical samples (F_ST = 0.156, P = 0.0315), and the current population exhibits extremely small N_e (current N_e = 2.16). There is evidence for both a recent population bottleneck and an earlier bottleneck, with population size already reasonably low by the late 19th century (historical N_e = 1162.96). Individuals in the current population are related at the level of half‐ to full‐siblings between social groups, and full‐siblings or parent–offspring within a social group, suggesting that inbreeding is likely to increase in the future. The species' current reduced genetic diversity must be considered during conservation planning, particularly for expectations of likely population recovery, indicating that intensive, carefully planned management is essential.     

Kin Discrimination in Protists: From Many Cells to Single Cells and Backwards

During four decades (1960–1990s), the conceptualization and experimental design of studies in kin recognition relied on work with multicellular eukaryotes, particularly Unikonta (including invertebrates and vertebrates) and some Bikonta (including plants). This pioneering research had an animal behavior approach. During the 2000s, work on taxa‐, clone‐ and kin‐discrimination and recognition in protists produced genetic and molecular evidence that unicellular organisms (e.g. Saccharomyces, Dictyostelium, Polysphondylium, Tetrahymena, Entamoeba and Plasmodium) could distinguish between same (self or clone) and different (diverse clones), as well as among conspecifics of close or distant genetic relatedness. Here, we discuss some of the research on the genetics of kin discrimination/recognition and highlight the scientific progress made by switching emphasis from investigating multicellular to unicellular systems (and backwards). We document how studies with protists are helping us to understand the microscopic, cellular origins and evolution of the mechanisms of kin discrimination/recognition and their significance for the advent of multicellularity. We emphasize that because protists are among the most ancient organisms on Earth, belong to multiple taxonomic groups and occupy all environments, they can be central to reexamining traditional hypotheses in the field of kin recognition, reformulating concepts, and generating new knowledge.     

hp‐rare 1.0: a computer program for performing rarefaction on measures of allelic richness

The number of alleles in a sample (allelic richness) is a fundamental measure of genetic diversity. However, this diversity measure has been difficult to use because large samples are expected to contain more alleles than small samples. The statistical technique of rarefaction compensates for this sampling disparity. Here I introduce a computer program that performs rarefaction on private alleles and hierarchical sampling designs.     

Bulgarian Bone Marrow Donors Registry—past and future directions

Recently Bulgarian Bone Marrow Donors Registry (BBMDR) has been established and since August 2005 it has been a member of Bone Marrow Donors Worldwide. Currently the number of healthy donors included in the BBMDR is relatively low. All donors included in the BBMDR are typed for HLA-A, -B, -DRB loci. Phylogenetic analysis based on HLA allele frequencies shows that Bulgarians were characterized with closest genetic similarity to Macedonians, Greeks, Romanians, Cretans and Sardinians in comparison to the other European and Mediterranean populations. On the contrary the second largest ethnic minority–the Roma were the closest to the other Roma populations and North Indians. These differences were due to the predominance of alleles and haplotypes that are specific for the Asian and the other Roma populations. These specific genetic profiles in the Bulgarian ethnic minorities justify the need of an adequate representation of minorities in BBMDR. Future directions for BBMDR development are discussed, including an increase of the total number of donors and these for ethnic minorities, as well the enhancement of the level of resolution of the HLA typing for the donors in the registry.