Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): patterns of variation consistent with reticulate evolution

The ITS sequences of Acropora spp. are the shortest so far identified in any metazoan and are among the shortest seen in eukaryotes; ITS1 was 70-80 bases, and ITS2 was 100-112 bases. The ITS sequences were also highly variable, but base composition and secondary structure prediction indicate that divergent sequence variants are unlikely to be pseudogenes. The pattern of variation was unusual in several other respects: (1) two distinct ITS2 types were detected in both A. hyacinthus and A. cytherea, species known to hybridize in vitro with high success rates, and a putative intermediate ITS2 form was also detected in A. cytherea; (2) A. valida was found to contain highly (29%) diverged ITS1 variants; and (3) A. longicyathus contained two distinct 5.8S rDNA types. These data are consistent with a reticulate evolutionary history for the genus Acropora.      

Factors predicting coroners�� decisions to hold discretionary inquests

Background:

Coroners in Australia, Canada, New Zealand and other countries in the Commonwealth hold inquests into deaths in two situations. Mandatory inquests are held when statutory rules dictate they must be; discretionary inquests are held based on the decisions of individual coroners. Little is known as to how and why coroners select particular deaths for discretionary inquests.

Methods:

We analyzed the deaths investigated by Australian coroners for a period of seven and one-half years in five jurisdictions. We classified inquests as mandatory or discretionary. After excluding mandatory inquests, we used logistic regression analysis to identify the factors associated with coroners’ decisions to hold discretionary inquests.

Results:

Of 20 379 reported deaths due to external causes, 1252 (6.1%) proceeded to inquest. Of these inquests, 490 (39.1%) were mandatory and 696 (55.6%) were discretionary. In unadjusted analyses, the rates of discretionary inquests varied widely in terms of age of the decedent and cause of death. In adjusted analyses, the odds of discretionary inquests declined with the age of the decedent; the odds were highest for children (odds ratio [OR] 2.17, 95% confidence interval [CI] 1.54–3.06) and lowest for people aged 65 years and older (OR 0.38, 95% CI 0.28–0.51). Using poisoning as a reference cause of death, the odds of discretionary inquests were highest for fatal complications of medical care (OR 12.83, 95% CI 8.65–19.04) and lowest for suicides (OR 0.44, 95% CI 0.30–0.65).

Interpretation:

Deaths that coroners choose to take to inquest differ systematically from those they do not. Although this vetting process is invisible, it may influence the public’s understanding of safety risks, fatal injury and death.In Anglo-American legal systems, coroners operate as an inquisitorial branch of the judiciary, investigating the cause and circumstances of deaths reported to them.^1,2 For most of the deaths investigated, coroners’ findings follow an administrative review of documentary evidence, including reports of postmortem examinations, police reports and witness statements.² However, a small selection of cases proceed to an inquest — formal public hearings in which witnesses testify and parties connected to the death may retain lawyers. Many inquests draw public attention and coverage by media.³ They are arguably the most visible aspect of the work of coroners.For coroners in Australia, Canada, New Zealand and many other countries in the Commonwealth, inquests are held for two main reasons. Statutes governing coroners’ courts dictate that inquests must be held in certain specified circumstances (mandatory inquests). For cases that fall outside the mandatory criteria, coroners may choose to hold an inquest (discretionary inquests). A great deal of variation in the rates of inquests is evident between and within countries (1^,4–6

Table 1:

Rates of coroners’ inquests in selected jurisdictions of Australia, the United Kingdom, New Zealand, the Republic of Ireland and Canada^*

Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans

Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we present sequence data for the ND3 and ND5 genes from 59 lines of Drosophila melanogaster and 29 lines of D. simulans. Of interest are the frequency spectra of silent and replacement polymorphisms, and potential variation among genes and taxa in the departures from neutral expectations. The Drosophila ND3 and ND5 data show no significant excess of replacement polymorphism using the McDonald-Kreitman test. These data are in contrast to significant departures from neutrality for the ND3 gene in mammals and other genes in Drosophila mtDNA (cytochrome b and ATPase 6). Pooled across genes, however, both Drosophila and human mtDNA show very significant excesses of amino acid polymorphism. Silent polymorphisms at ND5 show a significantly higher variance in frequency than replacement polymorphisms, and the latter show a significant skew toward low frequencies (Tajima's D = -1.954). These patterns are interpreted in light of the nearly neutral theory where mildly deleterious amino acid haplotypes are observed as ephemeral variants within species but do not contribute to divergence. The patterns of polymorphism and divergence at charge-altering amino acid sites are presented for the Drosophila ND5 gene to examine the evolution of functionally distinct mutations. Excess charge-altering polymorphism is observed at the carboxyl terminal and excess charge-altering divergence is detected at the amino terminal. While the mildly deleterious model fits as a net effect in the evolution of nonrecombining mitochondrial genomes, these data suggest that opposing evolutionary pressures may act on different regions of mitochondrial genes and genomes.      

Evolution of the 28S ribosomal RNA gene in anurans: regions of variability and their phylogenetic implications

Fifteen restriction sites were mapped to the 28S ribosomal RNA gene of individuals representing 54 species of frogs, two species of salamanders, a caecilian, and a lungfish. Eight of these sites were present in all species examined, and two were found in all but one species. Alignment of these conserved restriction sites revealed, among anuran 28S rRNA genes, five regions of major length variation that correspond to four of 12 previously identified divergent domains of this gene. One of the divergent domains (DD8) consists of two regions of length variation separated by a short segment that is conserved at least throughout tetrapods. Most of the insertions, deletions, and restriction-site variations identified in the 28S gene will require sequence-level analysis for a detailed reconstruction of their history. However, an insertion in DD9 that is coextensive with frogs in the suborder Neobatrachia, a BstEII site that is limited to representatives of two leptodactylid subfamilies, and a deletion in DD10 that is found only in three ranoid genera are probably synapomorphies.      

Mathematical and computational modeling in biology at multiple scales

A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy as an inference tool in the fields of biology and drug discovery is discussed. Mathematical and computational methods and models in the areas of epidemiology, cell physiology and cancer are surveyed. The technique of molecular dynamics is covered, with special attention to force fields for protein simulations and methods for the calculation of solvation free energies. The utility of quantum mechanical methods in biophysical and biochemical modeling is explored. The field of computational enzymology is examined.