A comparative description of mitochondrial DNA differentiation in selected avian and other vertebrate genera

Levels of mitochondrial DNA (mtDNA) sequence divergence between species within each of several avian (Anas, Aythya, Dendroica, Melospiza, and Zonotrichia) and nonavian (Lepomis and Hyla) vertebrate genera were compared. An analysis of digestion profiles generated by 13-18 restriction endonucleases indicates little overlap in magnitude of mtDNA divergence for the avian versus nonavian taxa examined. In 55 interspecific comparisons among the avian congeners, the fraction of identical fragment lengths (F) ranged from 0.26 to 0.96 (F = 0.46), and, given certain assumptions, these translate into estimates of nucleotide sequence divergence (p) ranging from 0.007 to 0.088; in 46 comparisons among the fish and amphibian congeners, F values ranged from 0.00 to 0.36 (F = 0.09), yielding estimates of P greater than 0.070. The small mtDNA distances among avian congeners are associated with protein-electrophoretic distances (D values) less than approximately 0.2, while the mtDNA distances among assayed fish and amphibian congeners are associated with D values usually greater than 0.4. Since the conservative pattern of protein differentiation previously reported for many avian versus nonavian taxa now appears to be paralleled by a conservative pattern of mtDNA divergence, it seems increasingly likely that many avian species have shared more recent common ancestors than have their nonavian taxonomic counterparts. However, estimates of avian divergence times derived from mtDNA- and protein-calibrated clocks cannot readily be reconciled with some published dates based on limited fossil remains. If the earlier paleontological interpretations are valid, then protein and mtDNA evolution must be somewhat decelerated in birds. The empirical and conceptual issues raised by these findings are highly analogous to those in the long-standing debate about rates of molecular evolution and times of separation of ancestral hominids from African apes.      

The relationship between fish assemblages and the helminth communities of a prey fish, in a group of small shallow lakes

Galaxias maculatus (small puyen) is an abundant native fish distributed in lakes and rivers of the Patagonia, and it is the frequent prey of other fishes, fish-eating birds, and mammals. Previous studies have shown that it is parasitized by 33 metazoan species and that the richness and composition of the parasite communities vary between lakes. The aim of the present work was to analyze the relationship between the composition of fish assemblages and the helminth component community structure of G. maculatus . Ten environmentally similar, small, shallow lakes, belonging to the Nahuel Huapi Lake basin, were chosen because of the differences in the native fish assemblages. Parasite community structure in G. maculatus varied according to the fish assemblage of each lake. The presence of the piscivorous fish Percichthys trucha regularly produced variations in the composition and richness at the component and infracommunity levels, as well as the percentage of autogenic parasite species in G. maculatus .     

Larval digenean community parasitizing the freshwater snail, Chilina dombeyana (Pulmonata: Chilinidae) in Patagonia, Argentina, with special reference to the notocotylid Catatropis chilinae

The objective of this research was to describe the structure of larval digenean communities in the freshwater snail Chilina dombeyana in Lake Mascardi, an oligotrophic Andean Patagonian lake. In total, 1,923 snails were collected during 2 sampling periods. Specimens were examined, and 8 digenean species were identified, all with allogenic life cycles. The snail infracommunities nearly always occurred as single-species infections, distributed mainly in the hepatopancreas. The double infections (0.2%) were always prepatent, and involved a schistosome and the notocotylid Catatropis chilinae. The overall prevalence, the prevalence of C. chilinae, and total species prevalence (without C. chilinae) significantly increased with snail size. Catatropis chilinae was the dominant species in all months and across all snail size classes. Maximum richness was reached in the size class between 16 and 18 mm. Diversity indices, i.e., the Shannon-Wiener Index and the reciprocal of the Simpson Index, increased with snail size only during the second sampling period. No robust evidence of antagonistic interactions was found in the digenean community of C. dombeyana from Lake Mascardi.     

Selection against genetic defects in conservation schemes while controlling inbreeding

We studied different genetic models and evaluation systems to select against a genetic disease with additive, recessive or polygenic inheritance in genetic conservation schemes. When using optimum contribution selection with a restriction on the rate of inbreeding (ΔF) to select against a disease allele, selection directly on DNA-genotypes is, as expected, the most efficient strategy. Selection for BLUP or segregation analysis breeding value estimates both need 1–2 generations more to halve the frequency of the disease allele, while these methods do not require knowledge of the disease mutation at the DNA level. BLUP and segregation analysis methods were equally efficient when selecting against a disease with single gene or complex polygene inheritance, i.e. knowledge about the mode of inheritance of the disease was not needed for efficient selection against the disease. Smaller schemes or schemes with a more stringent restriction on ΔF needed more generations to halve the frequency of the disease alleles or the fraction of diseased animals. Optimum contribution selection maintained ΔF at its predefined level, even when selection of females was at random. It is argued that in the investigated small conservation schemes with selection against a genetic defect, control of ΔF is very important.     

Effects of two acanthocephalan species on the reproduction of Hyalella patagonica (Amphipoda, Hyalellidae) in an Andean Patagonian Lake (Argentina)

The aim of the present study was to evaluate alterations in the reproduction induced by acanthellae and cystacanths of the acanthocephalans Acanthocephalus tumescens and Corynosoma sp. in the amphipod Hyalella patagonica from Lake Mascardi. Specimens of H. patagonica were separated in two categories: paired amphipods (joined specimens during precopulatory mate guarding period until fertilization) and unpaired amphipods (alone specimens). Different analyses were performed: first with paired (n = 406) and unpaired (n = 375) amphipods, and second only with female amphipods (n = 1949), that were classified into three categories (without internal oocytes and eggs, only with internal oocytes, and with eggs). Also, carotenoid extraction was performed of amphipods uninfected (n = 75) and infected (n = 105) by cystacanths of Corynosoma sp. Unpaired amphipods had significantly higher prevalence of cystacanths of both acanthocephalan species than paired ones; but such differences were not found in prevalence of acanthellae. Female amphipods without internal oocytes and eggs showed significantly higher prevalence of cystacanths of both acanthocephalan species than the two other female categories; while females with eggs had significantly higher prevalence of A. tumescens acanthellae. Amphipods infected by Corynosoma sp. showed lower carotenoid concentration than uninfected ones. In Lake Mascardi, there is indirect evidence of both reduced mating success and female fecundity of H. patagonica provoked by both cystacanths species (A. tumescens and Corynosoma sp.). However, infections by acanthellae seem to have no effects.     

Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae)

We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that are heterogeneity is correlated between loci at synonymous sites. At nonsynonymous sites, the pattern of rate heterogeneity is not correlated between loci, primarily due to an aberrant pattern of rate heterogeneity at nonsynonymous sites of rbcL. We compare patterns of synonymous rate heterogeneity to predictors based on the generation time effect and the speciation rate hypotheses. Although there is some evidence for generation time effects, neither generation time effects nor speciation rates appear to be sufficient to explain patterns of rate heterogeneity in the grass plastid sequences.      

Genomic aberrations in lung adenocarcinoma in never smokers

Background

Lung cancer in never smokers would rank as the seventh most common cause of cancer death worldwide.

Methods and Findings

We performed high-resolution array comparative genomic hybridization analysis of lung adenocarcinoma in sixty never smokers and identified fourteen new minimal common regions (MCR) of gain or loss, of which five contained a single gene (MOCS2, NSUN3, KHDRBS2, SNTG1 and ST18). One larger MCR of gain contained NSD1. One focal amplification and nine gains contained FUS. NSD1 and FUS are oncogenes hitherto not known to be associated with lung cancer. FISH showed that the amplicon containing FUS was joined to the next telomeric amplicon at 16p11.2. FUS was over-expressed in 10 tumors with gain of 16p11.2 compared to 30 tumors without that gain. Other cancer genes present in aberrations included ARNT, BCL9, CDK4, CDKN2B, EGFR, ERBB2, MDM2, MDM4, MET, MYC and KRAS. Unsupervised hierarchical clustering with adjustment for false-discovery rate revealed clusters differing by the level and pattern of aberrations and displaying particular tumor characteristics. One cluster was strongly associated with gain of MYC. Another cluster was characterized by extensive losses containing tumor suppressor genes of which RB1 and WRN. Tumors in that cluster frequently harbored a central scar-like fibrosis. A third cluster was associated with gains on 7p and 7q, containing ETV1 and BRAF, and displayed the highest rate of EGFR mutations. SNP array analysis validated copy-number aberrations and revealed that RB1 and WRN were altered by recurrent copy-neutral loss of heterozygosity.

Conclusions

The present study has uncovered new aberrations containing cancer genes. The oncogene FUS is a candidate gene in the 16p region that is frequently gained in never smokers. Multiple genetic pathways defined by gains of MYC, deletions of RB1 and WRN or gains on 7p and 7q are involved in lung adenocarcinoma in never smokers.     

Acanthocephalus tumescens (Acanthocephala, Echinorhynchidae) in Galaxias maculatus (Pisces, Galaxiidae) of Lake Gutiérrez, Patagonia, Argentina

The seasonal distribution of Acanthocephalus tumescens (Acanthocephala : Echinorhynchidae) among Galaxias maculatus (Pisces : Galaxiidae) in Lake Gutiérrez was studied from March 1994 to June 1996. Acanthocephalus tumescens always occurs in the intestine, has an overdispersed frequency distribution, a similar proportion of sexes, and females are larger than males. Mean intensity and prevalence are low and increase with host length. The pattern of the infection shows seasonality, with recruitment in winter and a reproductive period during spring-summer.     

Infection patterns of Tylodelphys barilochensis and T. crubensis (Trematoda: Diplostomatidae) metacercariae in Galaxias maculatus (Osmeriformes: Galaxiidae) from two Patagonian lakes and observations on their geographical distribution in the southern Andean region,Argentina

In the Patagonian Andean region, 2 species of diplostomatids parasitize the brains of Galaxias maculatus.The purpose of this study was to evaluate seasonal variation, spatial variation, and association with host age in the transmission of Tylodelphys barilochensis and T. crubensis in several oligotrophic lakes in Argentinian Patagonia. Fishes were captured monthly in Lake Gutiérrez and bimonthly in Lake Escondido. One summer or autumn sample was also taken in several other Patagonian lakes. Infection parameters were calculated and compared using nonparametric tests. The 2 species co-occurred in most of the sampled lakes, with high values of prevalence and mean intensity. In Lake Gutiérrez and Lake Escondido, the intensity of both diplostomatid species did not show significant differences between sexes and co-varied with host length. All age classes were infected; maximum prevalence values were reached before maximum mean intensity values in the 1-yr age class. A seasonal pattern of prevalence and mean intensity of the 2 parasite species with autumn mean intensity values differing significantly from those of the other seasons was evident only in Lake Gutiérrez.     

Parasite volume as an indicator of competition: the case of Acanthocephalus tumescens and Pseudocorynosoma sp. (Acanthocephala) in their intermediate host

In Lake Mascardi (Patagonia), 2 acanthocephalan species, Acanthocephalus tumescens and Pseudocorynosoma sp., share an amphipod intermediate host but have different definitive hosts. Because both acanthocephalan species are potentially capable of manipulating amphipod behavior, one of the parasites may, therefore, have no opportunity to complete its life cycle; accordingly, negative interactions between them can be expected. The purpose of the present work was to examine the possibility of competition in the intermediate host through a comparison of A. tumescens and Pseudocorynosoma sp. cystacanth volume. Specimens of the amphipod Hyalella patagonica were collected monthly over almost 2 yr. Amphipods were measured (total length), necropsied, and cystacanths collected. Cystacanths were also measured, and their volume was calculated. Size of both acanthocepalan species was positively associated with amphipod total length. Competition, during 3 different infection periods, was assessed: high level of Pseudocorynosoma sp. infection (HP), high level of A. tumescens infection (HA), and high level of mixed infection (HM). In Pseudocorynosoma sp., intra-specific competition in HM was the only interaction found. In contrast, in A. tumescens, inter-specific competition in HP, intra-specific competion in HA, and intra- and inter-specific competition in HM were found. We suggest that Pseudocorynosoma sp. is a non-plastic species mostly found in single infections, while A. tumescens is a more variable species occurring more frequently in co-infections.