DNA hybridization evidence for the principal lineages of hummingbirds (Aves:Trochilidae)

The spectacular evolutionary radiation of hummingbirds (Trochilidae) has served as a model system for many biological studies. To begin to provide a historical context for these investigations, we generated a complete matrix of DNA hybridization distances among 26 hummingbirds and an outgroup swift (Chaetura pelagica) to determine the principal hummingbird lineages. FITCH topologies estimated from symmetrized delta TmH-C values and subjected to various validation methods (bootstrapping, weighted jackknifing, branch length significance) indicated a fundamental split between hermit (Eutoxeres aquila, Threnetes ruckeri; Phaethornithinae) and nonhermit (Trochilinae) hummingbirds, and provided strong support for six principal nonhermit clades with the following branching order: (1) a predominantly lowland group comprising caribs (Eulampis holosericeus) and relatives (Androdon aequatorialis and Heliothryx barroti) with violet-ears (Colibri coruscans) and relatives (Doryfera ludovicae); (2) an Andean-associated clade of highly polytypic taxa (Eriocnemis, Heliodoxa, and Coeligena); (3) a second endemic Andean clade (Oreotrochilus chimborazo, Aglaiocercus coelestis, and Lesbia victoriae) paired with thorntails (Popelairia conversii); (4) emeralds and relatives (Chlorostilbon mellisugus, Amazilia tzacatl, Thalurania colombica, Orthorhyncus cristatus and Campylopterus villaviscensio); (5) mountain-gems (Lampornis clemenciae and Eugenes fulgens); and (6) tiny bee-like forms (Archilochus colubris, Myrtis fanny, Acestrura mulsant, and Philodice mitchellii). Corresponding analyses on a matrix of unsymmetrized delta values gave similar support for these relationships except that the branching order of the two Andean clades (2, 3 above) was unresolved. In general, subsidiary relationships were consistent and well supported by both matrices, sometimes revealing surprising associations between forms that differ dramatically in plumage and bill morphology. Our results also reveal some basic aspects of hummingbird ecologic and morphologic evolution. For example, most of the diverse endemic Andean assemblage apparently comprises two genetically divergent clades, whereas the majority of North American hummingbirds belong a single third clade. Genetic distances separating some morphologically distinct genera (Oreotrochilus, Aglaiocercus, Lesbia; Myrtis, Acestrura, Philodice) were no greater than among congeneric (Coeligena) species, indicating that, in hummingbirds, morphological divergence does not necessarily reflect level of genetic divergence.      

Loss of phylogenetic information in chorion gene families of Bombyx mori gene conversion

The silkmoth chorion has provided a stimulating model for the study of evolution and developmental regulation of gene families. Previous attempts at inferring relationships among chorion sequences have been based on pairwise comparisons of overall similarity, a potentially problematic approach. To remedy this, we identified the alignable regions of low sequence variability and then analyzed this restricted database by parsimony and neighbor-joining methods. At the deepest level, the chorion sequence tree is split into two branches, called "alpha" and "beta." Within each branch, early- and late-expressing genes each constitute monophyletic groups, while the situation with middle-expressing genes remains uncertain. The HcB gene family appears to be the most basal beta-branch group, but this conclusion is qualified because the effect of gene conversion on branching order is unknown. Previous studies by Eickbush and colleagues have strongly suggested that ErA, HcA, and HcB families undergo gene conversion within a gene family, whereas the ErB family does not. The occurrence of conversion correlates with a particular tree structure; namely, branch lengths are much greater at the base of the family than at higher internodes and terminal branches. These observations raise the possibility that chorion gene families are defined by gene conversion events (reticulate evolution) rather than by descent with modification (synapomorphy).      

First record of a spiral form of Aulacoseira,A. ambigua f. japonica (F.Meister) Tuji & D.M.Williams,in South African fresh waters

Water quality and algal populations in the Vaal River Barrage Reservoir have been monitored extensively for many decades, because of its importance as a water source for the most densely populated area in South Africa. Although Aulacoseira granulata (Ehrenberg) Simonsen is frequently found and at it times dominates algal assemblages in the Barrage, Aulacoseira ambigua (F.Meister) Tuji & D.M.Williams has never before been recorded at this locality. During a countrywide proficiency-testing scheme for algae counting, coordinated by Rand Water, spiral-shaped diatom colonies with distinctly curved cells were detected during May 2015. Upon investigation, it was found that the spiral colonies were Aulacoseira ambigua f. japonica, its presence in the fresh waters of South Africa being recorded for the first time. Since their first appearance during May 2015, colonies of Aulacoseira ambigua f. japonica have been constantly present in the surface waters of the Barrage. Their presence at this site can be linked to increasing eutrophication in the Vaal River, because the spiral form is known to prefer eutrophic conditions. Centric diatoms rarely form spiral colonies and there is some confusion in the literature as to the identity of this particular form, therefore in this paper we discuss this taxon, its nomenclature and ecological significance.     

Chromosomal similarities and differences between tamarins,Leontopithecusand Saguinus (Platyrrhini,Primates)

The karyotypes of two taxa of genus Leontopithecus(rosalia and chrysomelas) are studied. Their G-, C- and NOR-banding patterns are compared with those of representatives of the genus Saguinus to determine chromosomal similarities and differences between the two genera and thus contribute to explaining phylogenetic relations between the tamarins. Leontopithecus, like the Saguinus, presents 2n = 46, 14 autosomes plus the Y acrocentric and 30 autosomes plus the X biarmed. No chromosomal rearrangement distinguishes the karyotypes of the representatives of genus Leontopithecus or genus Saguinus. The two genera are distinguished from each other by a paracentric inversion and pericentric inversions on at least four pairs of acrocentric autosomes, displacing the NORs of the small short arms in Leontopithecus to the proximal region of the long arms in Saguinus or vice versa. The tamarins are also distinguished by the distribution of noncentromeric constitutive heterochromatin. The data obtained indicate that the two tamarin genera are closely related chromosomally, suggesting that they probably originated from the same ancestral branch. Am. J. Primatol. 43:265–276, 1997. © 1997 Wiley-Liss, Inc.     

Bioresponsive matrices in drug delivery

For years, the field of drug delivery has focused on (1) controlling the release of a therapeutic and (2) targeting the therapeutic to a specific cell type. These research endeavors have concentrated mainly on the development of new degradable polymers and molecule-labeled drug delivery vehicles. Recent interest in biomaterials that respond to their environment have opened new methods to trigger the release of drugs and localize the therapeutic within a particular site. These novel biomaterials, usually termed "smart" or "intelligent", are able to deliver a therapeutic agent based on either environmental cues or a remote stimulus. Stimuli-responsive materials could potentially elicit a therapeutically effective dose without adverse side effects. Polymers responding to different stimuli, such as pH, light, temperature, ultrasound, magnetism, or biomolecules have been investigated as potential drug delivery vehicles. This review describes the most recent advances in "smart" drug delivery systems that respond to one or multiple stimuli.     

Karyotypic comparison among Cebuella pygmaea,Callithrix jacchus and C. emiliae (Callitrichidae,Primates) and its taxonomic implications

The karyotype of Cebuella pygmaea (2n=44) obtained by G-, C-banding, and NOR-staining is described. This species presents a heteromorphic C band in the intersticial region of the short arm of chromosome 2. The data obtained were compared with those previously described for the karyotypes of Callithrix jacchus and Callithrix emiliae. The three species differ in the amount and distribution of non-centromeric constitutive heterochromatin. The importance of the variation in constitutive heterochromatin for the phylogeny of the group is discussed. Comparison of the karyotypes in terms of G-banding patterns showed that C. pygmaea and C. emiliae differ from C. jacchus by a Robertsonian translocation and a paracentric inversion, whereas C. pygmaea and C. emiliae differ from each other by a reciprocal translocation between an acrocentric autosome and the short arm of the submetacentric chromosomes that distinguishes their karyotypes from that of C. jacchus. The possible evolutionary paths followed by the karyotypes of the three species are discussed.     

Reproductive ecology of the female pink cusk-eel (Genypterus blacodes): evaluating differences between fishery management zones in the Chilean austral zone

The pink cusk-eel (Genypterus blacodes), a benthic-demersal fish confined to the southern hemisphere, supports an important commercial fishery in Chile where it is exploited over an extensive geographic area. Although the fishery was originally divided into a northern (41º28′–47º00′S) and southern (47º00′–57º00′S) zone for the purposes of fisheries management, recent studies have reported significant differences in life history parameters between these zones. Individuals from the southern zone reached larger asymptotic sizes and possessed higher survival rates compared to the northern zone. We estimate and compare the gonadosomatic index (GSI), shape of the maturity ogive, and length at 50 % maturity (L _50%) of female G. blacodes between management zones and across time using biological data collected from the industrial fleet between 1985 and 2009. Females in the northern zone had higher monthly mean GSI than females in the southern zone. Our analyses also revealed L _50% to be significantly higher in the southern zone than in the northern zone from 1985 to 2009. The significant differences in life-history traits between fishery management zones agree with the trade-offs predicted by Charnov’s life history theory. Together these results provide additional support for the hypothesis that two separate stocks exist and suggest that females from the northern zone have developed a life-history strategy, which favours early maturation and a proportionally greater investment in reproduction than females from the southern zone.     

Efficient linkage mapping using exome capture and extreme QTL in schistosome parasites

Background

Identification of parasite genes that underlie traits such as drug resistance and host specificity is challenging using classical linkage mapping approaches. Extreme QTL (X-QTL) methods, originally developed by rodent malaria and yeast researchers, promise to increase the power and simplify logistics of linkage mapping in experimental crosses of schistosomes (or other helminth parasites), because many 1000s of progeny can be analysed, phenotyping is not required, and progeny pools rather than individuals are genotyped. We explored the utility of this method for mapping a drug resistance gene in the human parasitic fluke Schistosoma mansoni.

Results

We staged a genetic cross between oxamniquine sensitive and resistant parasites, then between two F1 progeny, to generate multiple F2 progeny. One group of F2s infecting hamsters was treated with oxamniquine, while a second group was left untreated. We used exome capture to reduce the size of the genome (from 363 Mb to 15 Mb) and exomes from pooled F2 progeny (treated males, untreated males, treated females, untreated females) and the two parent parasites were sequenced to high read depth (mean = 95-366×) and allele frequencies at 14,489 variants compared. We observed dramatic enrichment of alleles from the resistant parent in a small region of chromosome 6 in drug-treated male and female pools (combined analysis: = 11.07, p = 8.74 × 10^-29). This region contains Smp_089320 a gene encoding a sulfotransferase recently implicated in oxamniquine resistance using classical linkage mapping methods.

Conclusions

These results (a) demonstrate the utility of exome capture for generating reduced representation libraries in Schistosoma mansoni, and (b) provide proof-of-principle that X-QTL methods can be successfully applied to an important human helminth. The combination of these methods will simplify linkage analysis of biomedically or biologically important traits in this parasite.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-617) contains supplementary material, which is available to authorized users.