Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

Markov models of codon substitution are powerful inferential tools for studying biological processes such as natural selection and preferences in amino acid substitution. The equilibrium character distributions of these models are almost always estimated using nucleotide frequencies observed in a sequence alignment, primarily as a matter of historical convention. In this note, we demonstrate that a popular class of such estimators are biased, and that this bias has an adverse effect on goodness of fit and estimates of substitution rates. We propose a “corrected” empirical estimator that begins with observed nucleotide counts, but accounts for the nucleotide composition of stop codons. We show via simulation that the corrected estimates outperform the de facto standard estimates not just by providing better estimates of the frequencies themselves, but also by leading to improved estimation of other parameters in the evolutionary models. On a curated collection of sequence alignments, our estimators show a significant improvement in goodness of fit compared to the approach. Maximum likelihood estimation of the frequency parameters appears to be warranted in many cases, albeit at a greater computational cost. Our results demonstrate that there is little justification, either statistical or computational, for continued use of the -style estimators.     

Core histone genes of <Emphasis Type="Italic">Giardia intestinalis</Emphasis>: genomic organization,promoter structure,and expression

Background  

Giardia intestinalis is a protist found in freshwaters worldwide, and is the most common cause of parasitic diarrhea in humans. The phylogenetic position of this parasite is still much debated. Histones are small, highly conserved proteins that associate tightly with DNA to form chromatin within the nucleus. There are two classes of core histone genes in higher eukaryotes: DNA replication-independent histones and DNA replication-dependent ones.     

Population growth confounds phylogeographic inference in Namaqua sandgrouse

The Namaqua sandgrouse, Pterocles namaqua, is a highly nomadic granivore of semiarid to arid habitats. As a result of nomadic movements in response to rainfall, the size of the breeding population in any one area fluctuates dramatically between breeding seasons. This high mobility in response to spatial and temporal abundance of food resources is expected to result in little population genetic structuring. Namaqua sandgrouse also shows a seasonally predictable partial migration between the southeast and northwest regions of South Africa, and a further possible north-south migration between southwestern South Africa and central Namibia. It is unclear whether birds migrating between these regions breed in only one or both regions. If populations breed in only one region of their migratory range, then population genetic structuring is predicted to occur. This study addresses Namaqua sandgrouse movements with the analysis of mitochondrial DNA control region sequences. In general, little population genetic structure was evident, yet strong signals of population growth were detected. Several populations have private alleles, which is in direct contradiction to the spatial genetic pattern expected under high levels of gene flow. We suggest that the inference of high levels of female gene flow could be an artifact of population growth and that additional loci will allow a greater understanding of Namaqua sandgrouse movements.     

Restoration potential of invaded abandoned agricultural fields: what does the seed bank tell us?

Soil seed banks can play an important role in the restoration of degraded ecosystems, especially where indigenous species are well represented in, and invasive species are largely absent from, the seed bank. Here, we studied the potential contribution of the soil seed bank to the restoration of invaded, abandoned agricultural fields in the Eastern Cape, South Africa. We recorded the aboveground cover and belowground abundance of all vascular plant species from 120 quadrats that differ in cover of the extralimital woody invader, Pteronia incana. Our results show that higher cover of P. incana is associated with lower species richness, aboveground cover, and belowground seed abundance. Furthermore, community similarity between the above‐ and belowground component was low, with the seed bank and standing vegetation having only 15 species in common and 49 species being recorded only from the seed bank. We suggest that this large number of seed bank‐only species is a relic of previous vegetation, prior to large‐scale invasion by P. incana. The most important finding from our study is the absence of P. incana from the soil seed bank. This finding, combined with the large number of mostly native species from the seed bank, holds promise from a restoration perspective. However, given the susceptibility of the invaded systems to erosion, coupled with the low grazing value of the seed bank species, we suggest that P. incana removal should be accompanied by both erosion control measures and reseeding with palatable grass species, to secure the livelihoods of local communities.     

Convergence Between Dung Beetle Assemblages of a Post-Mining Vegetational Chronosequence and Unmined Dune Forest

Abstract In Maputaland, South Africa vegetative and microclimatic changes on mined dunes drive the composition of the dung beetle fauna toward convergence with that in natural dune forest on unmined dunes. We assessed the pattern of these changes using a 23‐year vegetational chronosequence on mined dunes, which passes from grassland (approximately 1 year) to open Acacia shrubland thicket to Acacia karroo‐dominated woodland (approximately 9 years). Across this sequence, which represents successional stages in the restoration of dune forest, there was a sequential trend toward convergence in dung beetle species composition in both the entire species complement and, particularly, in shade specialist species. However, species abundance patterns showed a trend toward convergence only in early chronosequence Acacia woodland, followed by a decline in similarity between dung beetle assemblages of older Acacia woodland and unmined natural forest. This trend toward divergence was common both to the entire species complement, which includes widespread taxa, and to species endemic to Maputaland or the east coast. These trends in similarity and dissimilarity between dung beetle assemblages closely parallel the greater physiognomic and microclimatic similarity between early Acacia woodland and natural forest and the relative dissimilarity of older Acacia woodland. In conclusion, although percentage similarities between dung beetle assemblages of approximately 12‐year woodland and natural forests were comparable with those between each natural forest stand, decline in similarity in older woodland stands suggests that lasting convergence in dung beetle species abundance will only be attained once the Acacia woodland is replaced by secondary natural forest.     

Investigating the origin and spread of hepatitis C virus genotype 5a

Epidemiological and phylogenetic studies of hepatitis C virus (HCV) have identified six major HCV genotypes and have attempted to characterize their origin and spread worldwide. Putative regions of endemic infection have been identified for all HCV genotypes except HCV genotype 5a. Although HCV genotype 5a was previously thought to be largely restricted to the northern part of South Africa, this study reports an unexpected cluster of the genotype in West Flanders Province in Belgium. To investigate the molecular epidemiology of this cluster and of HCV genotype 5a in general, a rigorous phylogenetic analysis of Belgian and South African HCV genotype 5a samples was performed. Remarkably, the Belgian and South African strains form two distinct clusters of similar diversity. We used a Bayesian coalescent method to estimate the rate of virus spread through time for HCV genotype 5a in both regions. Our results indicate that HCV genotype 5a strains have been spreading independently in Belgium and South Africa for more than 100 years, with a rate of spread characteristic of an epidemic genotype. These findings have major implications for tracing the origin of HCV genotype 5a. Here, we speculate about the possible origins of these clusters.     

A population genetics pedigree perspective on the transmission of Helicobacter pylori

The inference of transmission pathways for medicinally important bacteria is important to our understanding of pathogens. Here we report analyses of transmission in Helicobacter pylori, a major carcinogen. Our study is novel in that the focal community comprises detailed family pedigrees and has a high prevalence of H. pylori. To infer transmission, we performed high-resolution analyses of nucleotide sequences for three genes and accounted for the occurrence of mutation and recombination through the use of simulation modeling. Our results demonstrate that transmission has a strong nonfamilial component potentially the result of a large proportion of infections derived from the community. These results are interesting from both a medical and an evolutionary standpoint. First, efficient control measures and beliefs about the sources of H. pylori infection should be reevaluated. Evolutionarily, our results contradict the hypothesis of strict vertical transmission, presented as an explanation for the strong correlation between human population history and H. pylori diversity. Thus the paradox of persistent phylogenetic structure, despite a permissive mode of transmission and high recombination rates, must be solved elsewhere. Here we consider the potential for recombination events to maintain genetic structure in light of horizontal transmission.     

Imaging Carrier Transport Properties in Halide Perovskites using Time‐Resolved Optical Microscopy

Halide perovskites have remarkable properties for relatively crudely processed semiconductors, including large optical absorption coefficients and long charge carrier lifetimes. Thanks to such properties, these materials are now competing with established technologies for use in cost‐effective and efficient light‐harvesting and light‐emitting devices. Nevertheless, the fundamental understanding of the behavior of charge carriers in these materials—particularly on the nano‐ to microscale—has, on the whole, lagged behind empirical device performance. Such understanding is essential to control charge carriers, exploit new device structures, and push devices to their performance limits. Among other tools, optical microscopy and spectroscopic techniques have revealed rich information about charge carrier recombination and transport on important length scales. In this progress report, the contribution of time‐resolved optical microscopy techniques to the collective understanding of the photophysics of these materials is detailed. The ongoing technical developments in the field that are overcoming traditional experimental limitations in order to visualize transport properties over multiple time and length scales are discussed. Finally, strategies are proposed to combine optical microscopy with complementary techniques in order to obtain a holistic picture of local carrier photophysics in state‐of‐the‐art perovskite devices.     

Models of coding sequence evolution

Probabilistic models of sequence evolution are in widespreaduse in phylogenetics and molecular sequence evolution. Thesemodels have become increasingly sophisticated and combined withstatistical model comparison techniques have helped to shedlight on how genes and proteins evolve. Models of codon evolutionhave been particularly useful, because, in addition to providinga significant improvement in model realism for protein-codingsequences, codon models can also be designed to test hypothesesabout the selective pressures that shape the evolution of thesequences. Such models typically assume a phylogeny and canbe used to identify sites or lineages that have evolved adaptively.Recently some of the key assumptions that underlie phylogenetictests of selection have been questioned, such as the assumptionthat the rate of synonymous changes is constant across sitesor that a single phylogenetic tree can be assumed at all sitesfor recombining sequences. While some of these issues have beenaddressed through the development of novel methods, others remainas caveats that need to be considered on a case-by-case basis.Here, we outline the theory of codon models and their applicationto the detection of positive selection. We review some of themore recent developments that have improved their power andutility, laying a foundation for further advances in the modelingof coding sequence evolution.      

Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape

Admixed populations present unique opportunities to discover the genetic factors underlying many multifactorial diseases. The geographical position and complex history of South Africa has led to the establishment of the unique admixed population known as the South African Coloured. Not much is known about the genetic make-up of this population, and the historical record is patchy. We genotyped 959 individuals from the Western Cape area, self-identified as belonging to this population, using the Affymetrix 500k genotyping platform. This resulted in nearly 75,000 autosomal SNPs that could be compared with populations represented in the International HapMap Project and the Human Genome Diversity Project. Analysis by means of both the admixture and linkage models in STRUCTURE revealed that the major ancestral components of this population are predominantly Khoesan (32–43%), Bantu-speaking Africans (20–36%), European (21–28%) and a smaller Asian contribution (9–11%), depending on the model used. This is consistent with historical data. While of great historical and genealogical interest, this information is also essential for future admixture mapping of disease genes in this population.