The rabbit alpha-like globin gene cluster is polymorphic both in the sizes of BamHI fragments and in the numbers of duplicated sets of genes

The alpha-like globin gene cluster in rabbits contains embryonic zeta- globin genes, an adult alpha-globin gene, and theta-globin genes of undetermined function. The basic arrangement of genes, deduced from analysis of cloned DNA fragments, is 5'-zeta 0-zeta 1-alpha 1-theta 1- zeta 2-zeta 3-theta 2-3'. However, the pattern of restriction fragments containing zeta- and theta-globin genes varies among individual rabbits. Analysis of BamHI fragments of genomic DNA from 24 New Zealand white rabbits revealed eight different patterns of fragments containing zeta-globin genes. The large BamHI fragments containing genes zeta 0 and zeta 1 are polymorphic in length, whereas a 1.9-kb fragment containing the zeta 2 gene and the 3.5-kb fragment containing the zeta 3 gene do not vary in size. In contrast to this constancy in the size of the restriction fragments, the copy number of the zeta 2 and zeta 3 genes does vary among different rabbits. No length polymorphism was detected in the BamHI fragments containing the theta-globin genes, but again the copy number varies for restriction fragments containing the theta 2 gene. The alpha 1- and theta 1-globin genes are located in a nonpolymorphic 7.2-kb BamHI fragment. The combined data from hybridization with both zeta and theta probes shows that the BamHI cleavage pattern does not vary within the region 5'-alpha 1-theta 1- zeta 2-zeta 3-theta 2-3', but the pattern genomic blot-hybridization patterns for the progeny of parental rabbits with different zeta-globin gene patterns shows that the polymorphic patterns are inherited in a Mendelian fashion. Two different haplotypes have been mapped based on the genomic blot-hybridization data. The variation in the alpha-like globin gene cluster in the rabbit population results both from differences in the copy number of the duplication block containing the zeta-zeta-theta gene set and from the presence or absence of polymorphic BamHI sites.      

Assignment of orthologous relationships among mammalian alpha-globin genes by examining flanking regions reveals a rapid rate of evolution

In order to study the relationships among mammalian alpha-globin genes, we have determined the sequence of the 3' flanking region of the human alpha 1 globin gene and have made pairwise comparisons between sequenced alpha-globin genes. The flanking regions were examined in detail because sequence matches in these regions could be interpreted with the least complication from the gene duplications and conversions that have occurred frequently in mammalian alpha-like globin gene clusters. We found good matches between the flanking regions of human alpha 1 and rabbit alpha 1, human psi alpha 1 and goat I alpha, human alpha 2 and goat II alpha, and horse alpha 1 and goat II alpha. These matches were used to align the alpha-globin genes in gene clusters from different mammals. This alignment shows that genes at equivalent positions in the gene clusters of different mammals can be functional or nonfunctional, depending on whether they corrected against a functional alpha-globin gene in recent evolutionary history. The number of alpha-globin genes (including pseudogenes) appears to differ among species, although highly divergent pseudogenes may not have been detected in all species examined. Although matching sequences could be found in interspecies comparisons of the flanking regions of alpha- globin genes, these matches are not as extensive as those found in the flanking regions of mammalian beta-like globin genes. This observation suggests that the noncoding sequences in the mammalian alpha-globin gene clusters are evolving at a faster rate than those in the beta-like globin gene clusters. The proposed faster rate of evolution fits with the poor conservation of the genetic linkage map around alpha-globin gene clusters when compared to that of the beta-like globin gene clusters. Analysis of the 3' flanking regions of alpha-globin genes has revealed a conserved sequence approximately 100-150 bp 3' to the polyadenylation site; this sequence may be involved in the expression or regulation of alpha-globin genes.      

Out of Africa and back again: nested cladistic analysis of human Y chromosome variation

We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of approximately 150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested cladistic analyses of human mtDNA and beta-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.      

Estimating western corn rootworm (Coleoptera: Chrysomelidae) larval susceptibility to event DAS‐59122‐7 maize

Susceptibility of Diabrotica virgifera virgifera (LeConte) larvae to DAS‐59122‐7 maize was evaluated using a laboratory technique that measures rootworm survival to adulthood on maize seedlings. This method produces direct measures of larval susceptibility using realistic exposure to the same range of insecticidal protein concentrations found in field‐grown DAS‐59122‐7 maize roots. First, second and third instars were reared to adulthood on DAS‐59122‐7 maize seedlings or a non‐transgenic, near‐isoline maize. Data on survival, adult gender ratio, adult weight and median emergence were collected. Overall, larval susceptibility to DAS‐59122‐7 maize was lower than earlier predictions ( Storer et al. 2006 ). Neonate survival on DAS‐59122‐7 maize was approximately 33% of isoline survival after 17 days, and the same 33% recovered and developed to adulthood when the isoline maize was substituted. Survival rate on DAS‐59122‐7 maize increased with instar. The mean survivorship was 0.5%, 26% and 65% when exposure to DAS‐59122‐7 maize began at the first, second and third instars, respectively. Exposure to DAS‐59122‐7 maize led to sub‐lethal effects on adult gender ratio, weight and median emergence. These effects decreased when exposure to DAS‐59122‐7 maize began at later instars. The killing effect of DAS‐59122‐7 maize on rootworm larvae appeared to result from the combined chronic effects and absence of a suitable host as perceived by the larvae. The relevance of these data and the methodology of estimating rootworm susceptibility to plant‐incorporated protectants are discussed in the context of the US Environmental Protection Agency’s functional definition of ‘high dose’ and use of refuge for resistance management ( EPA 1998a ). Based on these results it is evident that DAS‐59122‐7 maize does not meet the functional definitions of high dose as described by EPA (1998a,b) and ILSI (1999) , and the utility of refuge, refuge size and refuge placement for delaying rootworm resistance should be further investigated.     

Specialized morphology for a generalist diet: evidence for Liem's Paradox in a cichlid fish

The stable isotope ratio and seasonal changes in diet of Alluaud's haplo Astatoreochromis alluaudi, a cichlid fish with massive pharyngeal jaws well known for its ability to process hard‐bodied prey, are described. The diet of A. alluaudi was quantified in Lake Saka, Uganda, over a period of 30 months. Variation in physico‐chemical variables (mean monthly rainfall, water temperature, turbidity and dissolved oxygen), as well as potential competitor density and food abundance, was measured throughout the second half of the study (14 months). Stomach contents and isotope analysis revealed a diet comprised mainly of fishes and insects, with a low contribution of molluscs (0–33%) in any given month. No correlation was detected between diet and either macroinvertebrate abundance or competitor abundance. The running average rainfall was positively related to the percentage of fish consumed per month. Although A. alluaudi exhibits an apparent molluscivorous trophic morphology in Lake Saka, molluscs did not appear to compose a major portion of its diet. Gradients of rainfall seemed to be the most important environmental predictor of diet choice in Lake Saka. These results are discussed with reference to Liem's Paradox that apparently morphologically specialized fishes often function as generalist feeders in the wild.     

Localised intraspecific variation in the swimming phenotype of a coral reef fish across different wave exposures

Wave-driven water flow is a major force structuring marine communities. Species distributions are partly determined by the ability to cope with variation in water flow, such as differences in the assemblage of fish species found in a given water flow environment being linked to swimming ability (based on fin shape and mode of locomotion). It remains unclear, however, whether similar assembly rules apply within a species. Here we show phenotypic variation among sites in traits functionally linked to swimming ability in the damselfish Acanthochromis polyacanthus. These sites differ in wave energy and the observed patterns of phenotypic differences within A. polyacanthus closely mirrored those seen at the interspecific level. Fish from high-exposure sites had more tapered fins and higher maximum metabolic rates than conspecifics from sheltered sites. This translates to a 36 % larger aerobic scope and 33 % faster critical swimming speed for fish from exposed sites. Our results suggest that functional relationships among swimming phenotypes and water flow not only structure species assemblages, but can also shape patterns of phenotypic divergence within species. Close links between locomotor phenotype and local water flow conditions appear to be important for species distributions as well as phenotypic divergence across environmental gradients.