Systematics within Gyps vultures: a clade at risk

Background  

Populations of the Oriental White-backed Vulture (Gyps bengalensis) have declined by over 95% within the past decade. This decline is largely due to incidental consumption of the non-steroidal anti-inflammatory veterinary pharmaceutical diclofenac, commonly used to treat domestic livestock. The conservation status of other Gyps vultures in southern Asia is also of immediate concern, given the lack of knowledge regarding status of their populations and the continuing existence of taxonomic uncertainties. In this study, we assess phylogenetic relationships for all recognized species and the majority of subspecies within the genus Gyps. The continuing veterinary use of diclofenac is an unknown but potential risk to related species with similar feeding habits to Gyps bengalensis. Therefore, an accurate assessment of the phylogenetic relationships among Gyps vultures should aid in their conservation by clarifying taxonomic uncertainties, and enabling inference of their respective relatedness to susceptible G. bengalensis.     

Patterns of divergence during evolution of alpha 1-proteinase inhibitors in mammals

alpha 1-Proteinase inhibitor (alpha 1-PI), a member of the serine proteinase inhibitor superfamily, has a primary role in controlling neutrophil elastase activity within the mammalian circulation. Several studies have indicated that the reactive center region of alpha 1-PI, the amino acid sequence of which is critical to recognition of and binding to target proteinases, is highly divergent within and among species. This appears to be a consequence of accelerated rates of evolution that may have been driven by positive Darwinian selection. In order to examine this and other features of alpha 1-PI evolution in more detail, we have isolated and sequenced cDNAs representing alpha 1- PI mRNAs of the mouse species Mus saxicola and Mus minutoides and have compared these with a number of other mammalian alpha 1-PI mRNAs. Relative to other mammalian mRNAs, the extent of nonsynonymous substitution is generally high throughout the alpha 1-PI mRNA molecule, indicating greater overall rates of amino acid substitution. Within and among mouse species, the 5'-half of the mRNA, but not the 3'-half, has been homogenized by concerted evolution. Finally, the reactive center is under diversifying or positive Darwinian selection in murid rodents (rats, mice) and guinea pigs yet is under purifying selection in primates and artiodactyls. The significance of these findings to alpha 1-PI function and the possible selective forces driving evolution of serpins in general are discussed.      

Mitochondrial DNA polymorphisms in subterranean mole-rats of the Spalax ehrenbergi superspecies in Israel, and its peripheral isolates

Patterns of mitochondrial DNA (mtDNA) variation were examined in 133 mole-rats constituting all four chromosomal species (2n = 52, 2n = 54, 2n = 58, and 2n = 60) of the Spalax ehrenbergi superspecies in Israel, as well as the peripheral isolates of 2n = 60. In the main range of the complex, a total of 28 mtDNA haplotypes were found in 64 mole-rats, with most haplotypes being unique to either a single chromosomal species or population. mtDNA divergence increased from low to high diploid number in a north-to-south direction in Israel. Overall levels of mtDNA diversity were unexpectedly the highest in the 2n = 60, the youngest species of the complex. The mtDNA haplotypes can be separated into two major groups, 2n = 52-54 and 2n = 58-60, and a phylogenetic analysis for each group revealed evidence of a few haplotypes not sorted by diploid number. The overall patterns of mtDNA divergence seen within and among the four chromosomal species are consistent with the parapatric mode of speciation as suggested from previous studies of allozyme and DNA hybridization. In a separate data set the patterns of mtDNA variation were examined across the main geographic range and across peripheral semi-isolates and isolates of the 2n = 60 chromosomal species. Fifteen haplotypes were found in 69 mole-rats. High levels of mtDNA diversity characterized the main range, semi-isolated, and even some desert isolated populations. The peripheral isolates contain much mtDNA diversity, including novel haplotypes.      

Cranial morphology and adaptations in Eocene Adapidae. II. The Cambridge skull of Adapis parisiensis

One of the most complete skulls of the early primate Adapis parisiensis is in the collection of the Department of Zoology, Cambridge University. This exceptionally well-preserved male skull, from Quercy in southern France, is important in showing relatively small orbits that are highly convergent, a distinct ethmoid component in the medial orbital wall, very small infraorbital foramina, a well-preserved auditory region with the stapedial canal about twice the diameter of the canal for the promontory artery, and a well-preserved braincase 8.8 cm³ in endocranial volume. The frontal lobe of the brain in the Cambridge skull described here is less expanded than that reported previously in a British Museum skull. The average body weight of Adapis parisiensis is estimated to have been about 2.0 kg, and that of Adapis magnus is estimated to have been about 8.4 to 9.0 kg. The encephalization quotient (EQ) of Adapis parisiensis is estimated to have been 0.45, which is well below the range found in modern prosimians. There is some indication that the size of the foramen magnum has increased with increasing brain size during primate evolution. Adapis parisiensis appears to have been a medium-sized, visually oriented, diurnal, sexually dimorphic arboreal folivore.     

Arithmetic or geometric normality of biological variation: an empirical test of theory

Variation of biological populations is required for evolution by natural selection, and variance is a fundamental component in quantitative characterization of evolutionary differences and rates of change. Biological variation is widely understood to be normally distributed because of a general theoretical law of error. The law of error has two forms, and resulting normality may be arithmetic-where equivalent positive and negative deviations from expectation differ by equal amounts, or normality may be geometric-where equivalent deviations differ by equal proportions. Which law of error applies in biology can only be determined empirically, and this is surprisingly difficult. A new likelihood approach is developed here using data from anthropometric surveys of humans in two states in India: Maharashtra and Uttar Pradesh. Each state sample is large, but more importantly, each includes a large number of smaller subsamples. Likelihood support is additive, and subsamples are advantageous because (1) they are more homogeneous, (2) they yield probabilities and support scores in every case, and (3) significance can be evaluated first by tracing signs of the subsample support scores and then by comparing subsample support sums. Sign traces that fluctuate randomly show arithmetic and geometric normality to be indistinguishable. Two of 14 measurement variables studied here have subsample support sign traces differing from random, and one is significant in having a subsample support sum falling outside a 95% prediction interval for the 12 fluctuating traces: geometric normality is favored by a factor of ca. 10(60). Six of 14 index variables have support sign traces differing from random, and all are significant in having subsample support sums falling outside a 95 % prediction interval for the 8 fluctuating traces: geometric normality is favored by factors of 10(8) or more. Arithmetic and geometric normality cannot be distinguished for 21 of 28 variables studied here, but whenever alternatives are distinguishable geometric normality is consistently and strongly favored. This means that the applicable law of errors is proportional. In practical terms, arithmetic measurements must be transformed using logarithms to represent both the geometric normality of biological variation and the relative functional significance of measurements appropriately.     

Phylogenetic utility of the nuclear gene arginine decarboxylase: an example from Brassicaceae

Arginine decarboxylase (ADC) is an important enzyme in the production of putrescine and polyamines in plants. It is encoded by a single or low-copy nuclear gene that lacks introns in sequences studied to date. The rate of Adc amino acid sequence evolution is similar to that of ndhF for the angiosperm family studied. Highly conserved regions provide several target sites for PCR priming and sequencing and aid in nucleotide and amino acid sequence alignment across a range of taxonomic levels, while a variable region provides an increased number of potentially informative characters relative to ndhF for the taxa surveyed. The utility of the Adc gene in plant molecular systematic studies is demonstrated by analysis of its partial nucleotide sequences obtained from 13 representatives of Brassicaceae and 3 outgroup taxa, 2 from the mustard oil clade (order Capparales) and 1 from the related order Malvales. Two copies of the Adc gene, Adc1 and Adc2, are found in all members of the Brassicaceae studied to data except the basal genus Aethionema. The resulting Adc gene tree provides robust phylogenetic data regarding relationships within the complex mustard family, as well as independent support for proposed tribal realignments based on other molecular data sets such as those from chloroplast DNA.      

Ultrastructural localization of pancreatic polypeptide in the F cell of the dog pancreas.

The F cell of the dog pancreas has been identified as the specific cell type containing pancreatic polypeptide. This localization of pnacreatic polypeptide was accomplished by immunocytochemical staining of ultrathin sections and direct electron microscopic identification. Verification of the specificity of the reaction was obtained by blocking experiments on serial sections of the same cell. It is proposed that the name F cell be used for defining in all species the islet cell that contains pancreatic polypeptide.     

Large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice

Selective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or E3s) in plants. One important type uses Cullin-3 as a scaffold to assemble multisubunit E3 complexes containing one of a multitude of bric-a-brac/tramtrack/broad complex (BTB) proteins that function as substrate recognition factors. We previously described the 80-member BTB gene superfamily in Arabidopsis thaliana. Here, we describe the complete BTB superfamily in rice (Oryza sativa spp japonica cv Nipponbare) that contains 149 BTB domain-encoding genes and 43 putative pseudogenes. Amino acid sequence comparisons of the rice and Arabidopsis superfamilies revealed a near equal repertoire of putative substrate recognition module types. However, phylogenetic comparisons detected numerous gene duplication and/or loss events since the rice and Arabidopsis BTB lineages split, suggesting possible functional specialization within individual BTB families. In particular, a major expansion and diversification of a subset of BTB proteins containing Meprin and TRAF homology (MATH) substrate recognition sites was evident in rice and other monocots that likely occurred following the monocot/dicot split. The MATH domain of a subset appears to have evolved significantly faster than those in a smaller core subset that predates flowering plants, suggesting that the substrate recognition module in many monocot MATH-BTB E3s are diversifying to ubiquitinate a set of substrates that are themselves rapidly changing. Intriguing possibilities include pathogen proteins attempting to avoid inactivation by the monocot host.