Proportionate spatial sampling and equal‐time sampling of mobile animals: A dilemma for inferring areal dependence

Abstract Patch or island area is one of the most frequently used variables for inference in conservation biology and biogeography, and is often used in ecological applications. Given that all of these disciplines deal with large spatial scales, exhaustive censusing is not often possible, especially when there are large numbers of patches (e.g. for replication and control purposes). Therefore, data for patches or islands are usually collected by sampling. We argue that if area is to be used as an inferential factor, then the objects under study (i.e. the patches) must be characterized on an areal basis. This necessarily means that fixed‐area sampling is inadequate (e.g. a single standard quadrat or transect set within patches irrespective of the patch area) and that some form of area‐proportionate sampling is needed (e.g. a fixed areal proportion of each patch is surveyed by random allocation of standard quadrats across each patch). However, use of area‐proportionate sampling is not usually dissociated from the increased temporal intensity of sampling that arises from using this approach. The dilemma we see is deciding how much of the area‐specificity of variables such as species richness, rare‐species indices or probabilities of occurrence of individual species is related to the area‐proportionate survey protocol and how much is due to the temporal intensity of surveys. We undertook a study in which we balanced temporal and spatial effects by increasing the time spent surveying smaller patches of vegetation to account for the area‐ratio difference. The estimated species richness of birds of the box–ironbark system of central Victoria, Australia, was found to depend strongly upon area when area‐proportionate sampling alone was performed. When time‐balancing was imposed upon area‐proportionate sampling, the differences between smaller (10‐ha) and larger (40‐ha) areas were much reduced or effectively disappeared. We show that species found in the additional surveys used to conduct the time‐balancing were significantly less abundant than species recorded in area‐proportionate sampling. This effect is probably most severe for mobile animals, but may emerge in other forms of sampling.     

Frequent non-reciprocal exchange in microsatellite-containing-DNA-regions of vertebrates

Microsatellites are DNA-fragments containing short repetitive motifs with 2–10 bp. They are highly variable in most species and distributed throughout the whole genome. It is broadly accepted that their high degree of variability is closely associated with mispairing of DNA-strands during the replication phase, termed slippage, although recombination is also observed. The aim of this study is to demonstrate evidence that non-reciprocal recombination processes changing the total genomic structure are common in microsatellites and flanking regions. We sequenced DNA fragments from birds in which microsatellites are located, and analyzed the structure of the microsatellites and their flanking regions. Additionally, other data and those from literature of three microsatellite regions of primates coding for the Ataxin-2, the Huntingtin and the TATA-box binding protein were analyzed. The structures of seven avian and three primate microsatellites support the hypothesis that non-reciprocal recombination is a common process that may also contribute considerably to the variation at microsatellite loci. We conclude that results of population genetic studies that are analyzed statistically with methods based on stepwise mutation models should be interpreted with caution if no detailed information on the allelic variation of microsatellites is available.     

The tendency of lentiviral open reading frames to become A-rich: constraints imposed by viral genome organization and cellular tRNA availability

Human immunodeficiency virus type 1 (HIV-1) and other lentiviridae demonstrate a strong preference for the A-nucleotide, which can account for up to 40% of the viral RNA genome. The biological mechanism responsible for this nucleotide bias is currently unknown. The increased A-content of these viral genomes corresponds to the typical use of synonymous codons by all members of the lentiviral family (HIV, SIV, BIV, FIV, CAEV, EIAV, visna) and the human spuma retrovirus, but not by other retroviruses like the human T-cell leukemia viruses HTLV-I and HTLV-II. In this article, we analyzed A-bias for all codon groups in all open reading frames of several lentiviruses. The extent of lentiviral codon bias could be related to host cellular translation. By calculating codon bias indices (CBIs), we were able to demonstrate an inverse correlation between the extent of codon bias and the rate of translation of individual reading frames in these viruses. Specifically, the shift toward A-rich codons is more pronounced in pol than in gag lentiviral genes. Since it is known that Gag synthesis exceeds Pol synthesis by a factor of 20 due to infrequent ribosomal frame-shifting during translation of the gap-pol mRNA molecule, we propose that the aminoacyl-tRNA availability in the host cell restricts the lentiviral preference for A-rich codons. In addition, less A-nucleotides were found in regions of the viral genome encoding multiple functions; e.g., overlapping reading frames (tat-rev-env) or in genes that overlap regulatory sequences (nef-LTR region). Finally, the characteristics of lentiviral codon usage are presented as a phylogenetic tree without the need for prior sequence alignment.Correspondence to: B. Berkhout     

ASSESSMENT OF POTENTIAL BIAS WITH SNOWSHOE HARE FECAL PELLET-PLOT COUNTS

Abstract: The fecal pellet-plot method has been used extensively for snowshoe hare (Lepus americanus) population studies across the species' range, but potential biases associated with the technique have not been addressed adequately. We studied hare pellet-plots in northern Idaho to quantify pellet decomposition rates across environmental gradients, and conducted feeding trials on captive hares to assess the role of diet on pellet production rates. We found that across our study area pellet numbers tended to be higher on plots with high vegetative cover, which likely was a reflection of hare habitat choice rather than lesser pellet decomposition in such habitat. A pellet decomposition experiment indicated that pellet persistence was negatively related to moisture level, and that pellets produced by hares during summer decomposed more quickly than those from winter. We found that only 19% of fecal pellets collected from plots located across northern Idaho were produced by hares during winter. There was a correlation between pellet numbers from plots that were pre-cleared 1 year earlier and estimated numbers of hares on 6 study areas. A similar correlation was lacking for pellet counts from uncleared plots, implying that hare population estimation via pellet-plot counts should involve plot pre-clearing. In captive studies, juvenile hares produced slightly fewer pellets per day per gram of food ingested than adults, but pellet production was similar across diets comprised of 10 different browse species. We conclude that for our study area the fecal pellet-plot method may be subject to notable pellet decomposition bias, and therefore recommend that use of the method elsewhere across the species' range be preceded by assessment of both the pellet-hare density relationship and pellet decomposition rates across habitats.     

A Combined Product Estimator in Sample Survey

For the estimation of the population mean in stratified random sampling a ‘Combined Product Estimator’ is proposed which is more efficient than the ‘Combined Ratio’ and ‘Separate Ratio’ estimators. Also, the proposed estimator have exact expressions for bias and mean square error. An empirical illustration is given to compare the efficiencies of different estimators.     

A journey through time: exploring temporal patterns amongst digitized plant specimens from Australia

Online access to species occurrence records has opened new windows into investigating biodiversity patterns across multiple scales. The value of these records for research depends on their spatial, temporal, and taxonomic quality. We assessed temporal patterns in records from the Australasian Virtual Herbarium, asking: (1) How temporally consistent has collecting been across Australia? (2) Which areas of Australia have the most reliable records, in terms of temporal consistency and inventory completeness? (3) Are there temporal trends in the completeness of attribute information associated with records? We undertook a multi-step filtering procedure, then estimated temporal consistency and inventory completeness for sampling units (SUs) of 50?km ×?50?km. We found temporal bias in collecting, with 80% of records collected over the period 1970–1999. South-eastern Australia, the Wet Tropics in north-east Queensland, and parts of Western Australia have received the most consistent sampling effort over time, whereas much of central Australia has had low temporal consistency. Of the SUs, 18% have relatively complete inventories with high temporal consistency in sampling. We also determined that 25% of digitized records had missing attribute information. By identifying areas with low reliability, we can limit erroneous inferences about distribution patterns and identify priority areas for future sampling.     

Lineage-Biased Hematopoietic Stem Cells Are Regulated by Distinct Niches

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STRUCTURAL FEATURES OF NUCLEAR GENES IN THE CENTRIC DIATOM THALASSIOSIRA WEISSFLOGII (BACILLARIOPHYCEAE)

Thalassiosira weissflogii (Grun.) Fryxell et Hasle is one of the more commonly studied centric diatoms, and yet molecular studies of this organism are still in their infancy. The ability to identify open reading frames and thus distinguish between introns and exons, coding and noncoding sequence is essential to move from nuclear DNA sequences to predicted amino acid sequences. To facilitate the identification of open reading frames in T. weissflogii , two newly identified nuclear genes encoding β-tubulin and t  -complex polypeptide (TCP)-γ, along with six previously published nuclear DNA sequences, were examined for general structural features. The coding region of the nuclear open reading frames had a G + C content of about 49% and could readily be distinguished from noncoding sequence due to a significant difference in G + C content. The introns were uniformly small, about 100 base pairs in size. Furthermore, the 5' and 3' splice sites of introns displayed the canonical GT/AG sequence, further facilitating recognition of noncoding regions. Six of the nuclear open reading frames displayed relatively little bias in the use of synonymous codons, as exemplified by the cDNAs encoding β-tubulin and TCP-γ. Two open reading frames displayed strong bias in the use of particular codons (although the codons used were different), as exemplified by the cDNA encoding fucoxanthin chlorophyll a/c binding protein. Knowledge of codon bias should facilitate, for example, design of degenerate PCR primers and potential heterologous reporter gene constructs.     

The study of neighboring nucleotide composition and transition/transversion bias

Base substitution is one of the raw fuels that produce genetic variation and drive evolution. Recent studies have shown that the genome components affect mutation patterns to some extent. In order to infer the correlation between the Transition/Transversion ratio (Ts/Tv) and the number of immediately adjacent A&T nucleotides, we investigated 3611007 Oryza sativa SNPs (including 45462 coding SNPs, and 242811 intronic SNPs) and 32019 Arabidopsis SNPs. The results show that Ts/Tv is negatively correlated with the number of immediately adjacent A&T in O. Sativa and Arabidopsis. We further calculated AT₂ (the number of SNPs whose immediately adjacent nucleotides are either A or T) and AT₀ (the number of SNPs whose immediately adjacent nucleotides are either C or G) for all 6 types of SNPs. C/G SNP of O. sativa and Arabidopsis has the highest AT₂/AT₀, which denotes C/G SNP may be influenced by the adjacent A&T nucleotides mostly. For SNPs in O. sativa, the neighboring effect of A&T nucleotides is limited to 2 nucleotides on both sides; for SNPs in Arabidopsis, the effect extends no more than 4 nucleotides on both sides.     

Bias in the development of health and ecological assessments and potential solutions

The effectiveness and credibility of environmental decisions depend on the information provided by scientific assessments. However, the conflicting assessments provided by government agencies, industries, and environmental advocacy groups suggest that biases occur during assessment processes. Sources of bias include personal bias, regulatory capture, advocacy, reliance on volunteer assessors, biased stakeholder and peer review processes, literature searches, standardization of data, inappropriate standards of proof, misinterpretation, and ambiguity. Assessors can adopt practices to increase objectivity, transparency, and clarity. Decision-makers, managers of assessors, and institutions that commission assessments can adopt other practices that reduce pressures on assessors and reduce opportunities for expression of the personal biases of assessors. Environmental assessment should be recognized as a discipline with its own technical and ethical best practices.