Functional relevance of synonymous alleles reflected in allele rareness in the population

We provide theoretical evidence supporting the non-neutrality of synonymous alleles by investigating the rareness of synonymous alleles in the population. We find a significantly greater number of synonymous rare alleles than conventional neutral alleles derived from noncoding regions. A permutation experiment shows that the rareness of synonymous alleles is not a byproduct of random statistical noise. We then compare the frequencies of synonymous rare alleles and common alleles in various functional contexts in which synonymous alleles are known to be involved. Subsequently, we perform logistic regression analysis to elucidate the effect size of each independent factor contributing to the rareness of synonymous alleles. Additionally, we show that changes in optimality caused by synonymous mutations resulting in rare SNPs in the population tend to be biased toward optimality loss. We think that our study will contribute to the development of novel strategies for identifying functional synonymous mutations.     

Universal Protein Families and the Functional Content of the Last Universal Common Ancestor

The phylogenetic distribution of Methanococcus jannaschii proteins can provide, for the first time, an estimate of the genome content of the last common ancestor of the three domains of life. Relying on annotation and comparison with reference to the species distribution of sequence similarities results in 324 proteins forming the universal family set. This set is very well characterized and relatively small and nonredundant, containing 301 biochemical functions, of which 246 are unique. This universal function set contains mostly genes coding for energy metabolism or information processing. It appears that the Last Universal Common Ancestor was an organism with metabolic networks and genetic machinery similar to those of extant unicellular organisms.     

Recognising bias in Common Era temperature reconstructions

A steep decline in the quality and quantity of available climate proxy records before medieval times challenges any comparison of reconstructed temperature and hydroclimate trends and extremes between the first and second half of the Common Era. Understanding of the physical causes, ecological responses and societal consequences of past climatic changes, however, demands highly-resolved, spatially-explicit, seasonally-defined and absolutely-dated archives over the entire period in question. Continuous efforts to improve existing proxy records and reconstruction methods and to develop new ones, as well as clear communication of all uncertainties (within and beyond academia) must be central tasks for the paleoclimate community.     

Reproductive biology of the European Cuckoo Cuculus canorus: early insights, persistent errors and the acquisition of knowledge

The brood parasitic habits of the European Cuckoo Cuculus canorus have excited wonder, disbelief and speculation since the fourth century BC. Accurate knowledge of cuckoo biology, however, accumulated only slowly and mostly since 1700. The aim of this study is to review six main topics: (1) the placement of cuckoo eggs in host nests; (2) cuckoo ‘clutch’ size; (3) cuckoo egg characteristics, mimicry and rejection; (4) choice of hosts; (5) eviction of eggs and chicks; and (6) the reasons why cuckoos are brood parasites and are incapable of rearing their own young. Early errors in reporting cuckoo biology were often a consequence of poor or incomplete observations leading to erroneous interpretations. Many of the early observers were egg collectors who focussed almost exclusively on the egg-laying period, thus ignoring cuckoo chick biology. Major landmarks in cuckoo studies included the facts that: (1) cuckoo eggs often resembled those of their hosts (1760s) and that this mimicry was adaptive (1850s); (2) hosts sometimes evicted cuckoo eggs (1770s); (3) female cuckoos laid individually distinctive eggs and that specific cuckoo gentes may exist (1850s); and (4) although well recognised that cuckoo chicks were reared alone, prior to Jenner’s work in the 1780s female cuckoo parents were thought to either eat or evict the host eggs or young. Jenner’s results was more readily accepted in Britain than in Germany. Between 1700 and 1859, cuckoo brood parasitism was difficult to reconcile with the prevalent conceptual framework of physico-theology (later known as the argument from design). Thereafter, Darwin’s idea of natural selection provided a superior conceptual framework, which in conjunction with experimental testing of specific hypotheses has continued to advance our understanding of brood parasitism. Our knowledge of cuckoo biology is far from complete, however, and we predict that continuing research often incorporating new technologies will refine and extend our understanding of the cuckoo’s extraordinary biology.     

Genetic differences between the Chinese and European races of common carp

Summary Common carp of the Chinese and European races and their cross were tested in different environments. The test groups were either stocked together into the same pond, or each group was stocked separately. Mean growth, taken as a measure of the quality of the environment, varied widely between treatments. Genotype-environment interactions were estimated by the regression of growth of different genetic groups on this measure of environment. Proportional growth differences between the European and European X Chinese crossbreds, were several times higher in manured ponds than in ponds with artificial feed. The Chinese fish showed the fastest relative growth in poor conditions, with manure as the major nutrient input, while the European fish showed the fastest relative growth under improved conditions and irrespective of its source of food. The Chinese X European crossbred is heterotic over a range of intermediate conditions with manure as the principal nutrient.     

Identification of Differential Aberrations in Multiple‐Sample Array CGH Studies

Summary Most existing methods for identifying aberrant regions with array CGH data are confined to a single target sample. Focusing on the comparison of multiple samples from two different groups, we develop a new penalized regression approach with a fused adaptive lasso penalty to accommodate the spatial dependence of the clones. The nonrandom aberrant genomic segments are determined by assessing the significance of the differences between neighboring clones and neighboring segments. The algorithm proposed in this article is a first attempt to simultaneously detect the common aberrant regions within each group, and the regions where the two groups differ in copy number changes. The simulation study suggests that the proposed procedure outperforms the commonly used single‐sample aberration detection methods for segmentation in terms of both false positives and false negatives. To further assess the value of the proposed method, we analyze a data set from a study that identified the aberrant genomic regions associated with grade subgroups of breast cancer tumors.     

A multivariate and cladistic study of Vicia L. ser. Vicia (Fabaceae) based on analysis of morphological characters

 Vicia ser. Vicia, which includes the Vicia sativa aggregate, was studied by observing morphological variation. The study is an attempt to resolve the taxonomic relationships within the Vicia sativa aggregate by novel investigations along with a synthesis of the results obtained by previous researchers. The study has included some accessions and characters used previously, but has drawn accessions from a wider geographical range than has been attempted previously. Cluster analysis on the basis of 53 morphological characters justified the delimitation of four species within the series and six subspecies within the Vicia sativa aggregate. Accessions from South Asia could easily be incorporated in the classification, but some of the accessions from North Africa showed morphological differences. The morphometric data were coded using the gap weighting method of Thiele (1993) and used in a phylogenetic analysis to study the relationships between the taxa. The phylogenetic analysis, using 33 variables, showed Vicia pyrenaica closely related to Vicia sativa subsp. amphicarpa. A dichotomous key and a multi-access key to aid the identification of the taxa in the series are presented. Received January 21, 2002; accepted November 8, 2002 Published online: March 20, 2003     

Measuring the structural similarity of two communities composed of the same species

Summary The primary purpose of this paper is to propose empirical measures of the structural differences between two communities of plants or animals composed of the same species. Structure is defined to consist of; 1) the species in the community, 2) the pattern of interactions as represented by the covariance or correlation matrix of successive observations on each species, and 3) the mean abundances of each species in each of the two communities. Statistical tests are proposed for testing whether the covariance matrices and the vectors of mean densities for each community are equal and empirical measures of the differences between the covariance matrices and mean vectors are proposed. Given unequal covariance or correlation matrices the factor analysis model is used to derive empirical measures of the degree to which each variable of the ecosystem is responsible for the observed defferences in the pattern of interactions in each community. These tests and measures were applied to data gathered byHunter (1966) on the abundances of six species ofDrosophila censused monthly over a period of approximately two and a half years in two adjacent, but different habitats near Bogota, colombia. The two covariance matrices were significantly different indicating different patterns of interactions in the twoDrosophila communities.     

Abundance and population trends of mangrove landbirds in southwest Florida

ABSTRACT The avifauna of south Florida's mangrove forests is unique and relatively unstudied. The population status of landbirds that breed in these forests is currently unknown, and this lack of information is especially problematic for species that have North American ranges limited almost exclusively to Florida's mangroves. To address this information gap, we estimated trends in abundance using data generated during bird surveys conducted from 2000 to 2008 at 101 points in mangrove forests in southwestern Florida. We found that populations of two of three mangrove‐dependent species that breed in these forests, Black‐whiskered Vireos (Vireo altiloquus) and Mangrove Cuckoos (Coccyzus minor), declined significantly during our study. In contrast, only one of seven species with a broader North American range (Red‐bellied Woodpecker, Melanerpes carolinensis) declined in abundance. No species increased in abundance. The Mangrove Cuckoo population exhibited the greatest decline, with numbers declining 87.1% from 2000 to 2008. Numbers of Black‐whiskered Vireos declined 63.9%. These declines coincided with the outbreak of West Nile virus that has been linked to population declines of other North American birds, but we could not rule out other potential causes, including changes in the quality or extent of breeding or wintering habitat.     

Fragmentation causes rarity in common marmosets in the Atlantic forest of northeastern Brazil

The purpose of this study was to investigate the population status of the common marmosets, Callithrix jacchus, in one of their main habitats, the northeastern Atlantic forest of Brazil, where only 2% of its original area remains as small and isolated forest fragments, to determine long-term viable populations. The study was carried out in 15 forest fragments, measuring from 3,478.3 ha (the largest) to 6 ha, which were invariably subjected to high human impact. Line transect surveys were carried out between January 2002 and December 2004, along transects measuring from 350 to 4,000 m, between 0500 h and 0900 h. Common marmosets were registered in 73% (n = 11) of the forest fragments, were not recorded in the largest one, the Coimbra Forest, and group sizes varied from 1 to 4 individuals. A negative significant relationship was detected between the size of the fragment and the number of sightings of common marmosets. It is shown that the number of groups of common marmosets dwelling in this highly impacted landscape is nowadays lower than necessary for long-term survival. Additionally, smaller fragments having more groups suggests that they live in total association with humans, which assure their subsistence through the supply of introduced and exotic foods.