Sampling bias in the determination of first and last occurrences

Background: Past studies of first and last occurrence dates of phenological events have revealed close associations with climatic parameters. Consequently, it is widely acknowledged that recent shifts in the beginning, duration or ending of such events are a response to present climate change. In addition, in recent times, there have tended to be many more observers than in earlier times, especially in urban areas. Furthermore, the number of individuals (plants or animals) observed has often changed markedly. In many situations it is not possible to obtain the average first or last occurrence date of a group of individuals, and only the most extreme occurrence is recorded. This common observational difficulty leads to sampling bias that needs to be taken into account.

Aim: Our aim is to use statistical models to quantify the sampling bias and its dependence on sample size and the variability and correlation amongst the individuals under consideration.

Methods: n-dimensional multivariate normal distribution and two-way fixed-effects analysis of variance models were developed to examine the dependence of the sampling bias on the above factors. Our results are compared with real data.

Results: For first and last occurrence observations, which are the most common index in many phenological studies, we found that changes in observational practice and sample size can, in certain circumstances, easily produce changes in bias that can swamp (or indeed reverse) any climatic change effects.

Conclusions: Our new, realistic statistical models allow the sampling bias to be quantified and calculated in terms of the number of individuals under observation, their variability and the degree of correlation between individuals.     

An examination of observer bias as a source of error in surveys of seagrass shoots

Abstract Mensurative experiments investigated the effects of different observers on estimates of the density of shoots of two species of seagrass: Posidonia australis Hook and Zostera capricorni Aschers. Balanced programmes of sampling were used to examine variation in counts of seagrass shoots attributable to different observers, sizes of quadrats, depths and locations within large beds of each species of seagrass. A separate experiment examined differences between novice observers and a more experienced observer, when an ‘optimal’ size of sampling unit was used. Estimated densities of Zostera shoots varied inconsistently among observers, quadrats, depths and locations. Differences between observers were not affected by the size of quadrat used to count Posidonia shoots, but varied between locations in the seagrass bed. Experience had only a minor impact on biases. Only two of 12 novices produced counts that were different from the experienced observer. These results emphasize the importance of considering both accuracy and precision in the design of field studies of seagrasses.     

On the Estimation of Population Mean in Stratified Sampling

When stratified random sampling is used for the estimation of population mean, use of ‘Combined ratio estimator’ is well known. Some improved estimators for population mean are proposed which are better than ‘Combined ratio estimator’ and some other well known existing ones, from the point of view of bias and mean square error. An empirical illustration is given.     

Intragenic codon bias in a set of mouse and human genes

To better conceptualize the mechanism underlying the evolution of synonymous codons, we have analysed intragenic codon usage in chosen "regions" of some mouse and human genes. We divided a given gene into two regions: one consisting of a trinucleotide repeat (TNR) and the other consisting of the "rest of the coding region" (RCR). Usually, a TNR is composed of a repetitive single codon, which may reflect its frequency in a gene. In contrast, a non-random frequency of a codon in the RCR versus TNR (or vice versa) of a gene should indicate a bias for that codon within the TNR. We examined this scenario by comparing codon frequency between the RCR and the cognate TNR(s) for a set of human and mouse genes. A TNR length of six amino acids or more was used to identify genes from the Genbank database. Twenty nine human and twenty one mouse genes containing TNRs coding for nine different amino acid runs were identified. The ratio of codon frequency in a TNR versus the corresponding RCR was expressed as "fold change" which was also regarded as a measure of codon bias (defined as preferential use either in TNR or in RCR). Chi-square values were then determined from the distribution of codon frequency in a TNR vs. the cognate RCR. At p<0.001, 22% and 27%, respectively, of human and mouse TNRs showed codon bias. Greater than 40% of the TNRs (29 out of 69 in human, and 18 of 42 in mouse) showed codon bias at p<0.05. In addition, we identify eight single-codon TNRs in mouse and ten in human genes. Thus, our results show intragenic codon bias in both mouse and human genes expressed in diverse tissue types. Since our results are independent of the Codon Adaptation Index (CAI) and starvation CAI, and since the tRNA repertoire in a cell or in a tissue is constant, our data suggest that other constraints besides tRNA abundance played a role in creating intragenic codon bias in these genes.     

Evidence of partial anadromy and resident-form dispersal bias on a fine scale in populations of Oncorhynchus mykiss

We examine sympatric anadromous (steelhead) and nonanadromous (resident) rainbow trout (Oncorhynchus mykiss) from neighboring locations to test three hypotheses: (1) the sympatric life history types are not genetically different; (2) fine-scale dispersal is the same for both sexes, and (3) fine-scale dispersal is the same for steelhead and resident individuals. Data from 13 microsatellite loci reveal no genetic difference between sympatric steelhead and resident O. mykiss but moderate population structure (F _ST=0.019–0.028) between adjacent samples, regardless of life history type. Our results provide further evidence of partial anadromy and suggest that geographic proximity and genetic history, more than migratory type, should be considered when identifying populations for use in restoration of local genetic diversity. We find evidence of resident-form dispersal bias on a fine spatial scale, however, we find no evidence that fine-scale dispersal varies by gender. Conservation strategies should aim to maintain resident and anadromous forms when they occur in sympatry, as they may be important in facilitating gene flow on small and large spatial scales, respectively.     

Mortality rate, reproductive output, and trap response bias in populations of the blowfly Lucilia sericata

1. The ages of 877 females of the blowfly Lucilia sericata, collected from two farms in south-west England between May and September 1996, were determined using a combination of ovarian dissection and wing fray analysis. 2. Using survivorship analysis, the mortality rates over the entire field season were estimated to be 2.2 and 1.9% per day-degree at the two farms, respectively. These gave a mean life expectancy of 46 and 53 day-degrees, and a lifetime reproductive output of 130 and 172 eggs per female. 3. The mortality rate remained relatively constant over time, with one exception, the first sample of the season when no older flies were present, indicating that underlying changes in demography (emergence and senescence of generations) over the field season were not sufficient to affect the rates calculated by survivorship analysis. 4. The response of L. sericata to liver-baited traps was affected strongly by age and reproductive status, with gravid females and females in the early stages of ovarian development being most markedly over-represented relative to other age categories.     

Retrieving chronological age from dental remains of early fossil hominins to reconstruct human growth in the past

A chronology of dental development in Pan troglodytes is arguably the best available model with which to compare and contrast reconstructed dental chronologies of the earliest fossil hominins. Establishing a time scale for growth is a requirement for being able to make further comparative observations about timing and rate during both dento-skeletal growth and brain growth. The absolute timing of anterior tooth crown and root formation appears not to reflect the period of somatic growth. In contrast, the molar dentition best reflects changes to the total growth period. Earlier initiation of molar mineralization, shorter crown formation times, less root length formed at gingival emergence into functional occlusion are cumulatively expressed as earlier ages at molar eruption. Things that are similar in modern humans and Pan, such as the total length of time taken to form individual teeth, raise expectations that these would also have been the same in fossil hominins. The best evidence there is from the youngest fossil hominin specimens suggests a close resemblance to the model for Pan but also hints that Gorilla may be a better developmental model for some. A mosaic of great ape-like features currently best describes the timing of early hominin dental development.     

DNA degradation in avian faecal samples and feasibility of non-invasive genetic studies of threatened capercaillie populations

We evaluated the feasibility of using faeces as a non-invasively collected DNA source for the genetic study of an endangered bird population (capercaillie; Tetrao urogallus). We used a multitube approach, and for our panel of 11 microsatellites genotyping reliability was estimated at 98% with five repetitions. Experiments showed that free DNases in faecal material were the major cause of DNA degradation. Our results demonstrate that using avian faeces as a source of DNA, reliable microsatellite genotyping can be obtained with a reasonable number of PCR replicates.     

DNA diversity in the studies of genetic distance among isolated human populations in bosnia

Different degrees of isolation found in various part of Bosnia and Herzegovina may be induced by various factors. Bjelasnica-Treskavica region, located around 40 kilometers southwest from Sarajevo — capital of Bosnia and Herzegovina, is highly specific in that way. We chose three isolated communities: Dejcici, Bobovica and Lukomir for the study of genetic structure of isolated human populations. Based on general data three relative degrees of isolation/openness among the villages have been presumed as follows: first (lower-Dejcici), second (middle — Bobovica) and third (higher — Lukomir) 15 short tandem repeat (STR) loci and hypervariable region of mtDNA were chosen as a markers for study of population structure. Microsatellite allele frequencies, and mtDNA molecular diversity of Heterozigosity and coefficient of gene differentiation across all observed STR loci were estimated. Also, gene and nucleotide diversity of observed mtDNA regions were obtained. Genetic distance between three populations was calculated using method of Reynolds et al. (1983). For analysis of interpopulation relationship based on polymorphism of HV I and HV II region, estimation of pairwise differences was used. results of this research showed consistence with initial hypothesis on divergence based on socio-cultural factors.     

Palaeopathology and genes: Investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations

The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future.