Complex evolution of vitellogenin genes in salmonid fishes

Vitellogenins (Vtg) are usually encoded by small multigene families containing up to six genes. With 20 tandemly arranged genes, the rainbow trout ( Oncorhynchus mykiss) is an exception to this rule. PCR amplification, cloning and sequence analysis of Vtg genes in other salmonid species revealed the existence of two paralogous gene clusters, designated Vtg-A and Vtg-B. Southern hybridization showed that the number of genes varies from 2 to 30 copies from one species to another, as well as between the two gene clusters. All Coregonus, Thymallus, Salmo and Salvelinus species studied have both gene clusters, while Oncorhynchus species possess only the Vtg-A locus. Phylogenetic trees constructed from Vtg sequences revealed conflicting nodes with the consensus tree based on morphological and anatomical data. Vtg sequences support the grouping ( Salmo, ( Salvelinus, Oncorhynchus)) instead of the accepted consensus ( Salvelinus, ( Salmo, Oncorhynchus)). Structural data on gene organization also support the contention that Salvelinus and Oncorhynchus are sister taxa. Evolutionary implications for the Vtg gene clusters in salmonids are discussed.     

Mutation and evolution of microsatellite loci in Neurospora

The patterns of mutation and evolution at 13 microsatellite loci were studied in the filamentous fungal genus Neurospora. First, a detailed investigation was performed on five microsatellite loci by sequencing each microsatellite, together with its nonrepetitive flanking regions, from a set of 147 individuals from eight species of Neurospora. To elucidate the genealogical relationships among microsatellite alleles, repeat number was mapped onto trees constructed from flanking-sequence data. This approach allowed the potentially convergent microsatellite mutations to be placed in the evolutionary context of the less rapidly evolving flanking regions, revealing the complexities of the mutational processes that have generated the allelic diversity conventionally assessed in population genetic studies. In addition to changes in repeat number, frequent substitution mutations within the microsatellites were detected, as were substitutions and insertion/deletions within the flanking regions. By comparing microsatellite and flanking-sequence divergence, clear evidence of interspecific allele length homoplasy and microsatellite mutational saturation was observed, suggesting that these loci are not appropriate for inferring phylogenetic relationships among species. In contrast, little evidence of intraspecific mutational saturation was observed, confirming the utility of these loci for population-level analyses. Frequency distributions of alleles within species were generally consistent with the stepwise mutational model. By comparing variation within species at the microsatellites and the flanking-sequence, estimated microsatellite mutation rates were approximately 2500 times greater than mutation rates of flanking DNA and were consistent with estimates from yeast and fruit flies. A positive relationship between repeat number and variance in repeat number was significant across three genealogical depths, suggesting that longer microsatellite alleles are more mutable than shorter alleles. To test if the observed patterns of microsatellite variation and mutation could be generalized, an additional eight microsatellite loci were characterized and sequenced from a subset of the same Neurospora individuals.     

Conservation and evolution of microsatellite loci in primate taxa

Microsatellites are promising genetic markers for the study of demographic structure and phylogenetic history in populations. However, little information exists on the molecular nature of the repeats and their flanking sequences of a same microsatellite in a large range of species. In this study, we report polymorphism and consensus sequences of eight microsatellite loci using human primers in 20 primate species. The results show size polymorphism in almost all species and microsatellites. These loci are therefore useful markers for population genetic studies between populations of the same species. Insertion/deletion events are frequent in the flanking regions, the majority concerning several contiguous bases. This is in contrast with the more usual single base pair events in non-coding regions. The ranges of allele lengths in non-human primates often show no overlap with that of human, usually due to the deletion/insertion events in the flanking sequences, producing smaller allele lengths rather than smaller numbers of repeats. The use of length of PCR product will bias the inter-species interpretation reducing the number of observable alleles and treating as the same allele very divergent molecular sequences. Caution should be used when employing microsatellites in cross-species comparisons in which the species under study are separated by significant amounts of evolutionary time: in such cases allele comparison cannot be based on lengths alone.     

Minisatellite DNA fingerprints of salmonid fishes

The human minisatellite probes 33.6 and 33.15 cross-hybridized to DNA digests of Atlantic salmon, brown trout and rainbow trout revealing complex multi-banded patterns. These DNA fingerprints (in excess of 40 resolvable fragments in some cases) were highly polymorphic, individual specific and found to be stable, both somatically and in the germline. Pedigree analysis of an Atlantic salmon family confirmed that the minisatellite fragments showed Mendelian inheritance. With only a single occurrence of linkage and allelism being observed it is likely the minisatellite loci are widely distributed throughout the salmonid genome. The potential applications for both multi- and single locus minisatellite probes in salmonid research are discussed.     

Abnormal craniofacial development in cyclopic salmonid fishes

Different types and degrees of “spontaneous” and artificially induced cyclopic malformation in fishes are defined. Symmetrical cyclopia ranges from approximation of the eyes, to partial merger of the eyes in the midline, to complete cyclopia with a single median eye. It is always associated with dorsal displacement of the rostral-nasal apparatus to the top of the head. Skeletal reorganization associated with symmetrical cyclopia is described for the first time, using hatchery material of Salmo gairdneri and S. trutta. Development of the nasal capsule is essentially normal, except for position; the trabeculae cranii remain in the normal position but show modified shape corresponding to the degree of cyclopia. The jaw apparatus is modified through anterior foreshortening, especially the upper jaws. The branchial apparatus is unaffected. The condition demonstrates that later morphogenesis of the nasal capsule and trabeculae cranii are independent of each other. Cyclopia appears to result from alteration of relative position and timing in developmental events in the head, especially the prosencephalon.     

Polymorphic microsatellite loci in Allodapine bees for investigating the evolution of social behaviour

Allodapine bees provide extraordinary systems for investigating the evolution of cooperation and particularly the division of reproduction in animal societies. We present the first microsatellite primers for two native Australian species (Exoneura nigrescens and E. robusta; Hymenoptera: Apidae: Xylocopinae) which allow the accurate determination of pedigrees, reproductive skew and relatedness in colonies. Up to 55 different alleles were observed per locus.     

Complex evolution of a salmonid microsatellite locus and its consequences in inferring allelic divergence from size information

Sequence analysis of 78 alleles of a microsatellite locus was resolved atvarious taxonomic levels among salmonid fishes to test for congruencebetween size and sequence information. Allelic variability of this locusinvolved changes in number of dinucleotide repeats as expected formicrosatellite loci. However, additional mutational events involving largeindels and base substitutions also occurred frequently among and withinspecies. These caused the evolution of different imperfect microsatellitevariants, from an ancestral perfect one, which was undetectable fromallelic size information only. Alleles of the same length resulting fromdifferent mutational events were also observed among and within species.Altogether, these results revealed the incongruence between size and numberof mutation events, implying that it may be imprecise to interpretmutational rates and relationships on the basis of size information alonein interspecific comparisons and, to a lesser extent, within species.     

Immunochemical properties of erythrocyte-specific histone H5 in salmonid fishes

Comparative studies have been made on the immunochemical properties of histone H5 in Salmonidae species. High degree of homology between these histones and H5 histone from Oncorhynchus tschawytscha was demonstrated by microcomplement fixation. Properties of H5 histones in fish and birds are discussed.     

The salmonid MHC class I: more ancient loci uncovered

An unprecedented level of sequence diversity has been maintained in the salmonid major histocompatibility complex (MHC) class I UBA gene, with between lineage AA sequence identities as low as 34%. The derivation of deep allelic lineages may have occurred through interlocus exon shuffling or convergence of ancient loci with the UBA locus, but until recently, no such ancient loci were uncovered. Herein, we document the existence of eight additional MHC class I loci in salmon (UCA, UDA, UEA, UFA, UGA, UHA, ULA, and ZE), six of which share exon 2 and 3 lineages with UBA, and three of which have not been described elsewhere. Half of the UBA exon 2 lineages and all UBA exon 3 lineages are shared with other loci. Two loci, UGA and UEA, share only a single exon lineage with UBA, likely generated through exon shuffling. Based on sequence homologies, we hypothesize that most exchanges and duplications occurred before or during tetraploidization (50 to 100 Ma). Novel loci that share no relationship with other salmonid loci are also identified (UHA and ZE). Each locus is evaluated for its potential to function as a class Ia gene based on gene expression, conserved residues and polymorphism. UBA is the only locus that can indisputably be classified as a class Ia gene, although three of the eight loci (ZE, UCA, and ULA) conform in three out of four measures. We hypothesize that these additional loci are in varying states of degradation to class Ib genes.     

The evolution of sex-change mechanisms in fishes

Synopsis Five distinct sex-change mechanisms are identified among sequentially hermaphroditic fishes based on socio-ecological characteristics. The primary determinants of the sex-change mechanisms appear to be social organization and mating system, which in turn depend on resource distribution in space and time. The ability of a single individual to control all mating in the social unit, which is related to the size of the social unit, differentiates three suppression mechanisms from two induction mechanisms. Sex-change suppression, which is characteristic of species with small group size and rigid dominance hierarchies, refers to inevitable sex change in the absence of group dominance. Ability to migrate between resource patches differentiates protogynous suppression (e.g. inLabroides dimidiatus) from protandrous suppression (e.g. inAmphiprion spp.). Early sex change appears to have evolved from protogynous suppression under special conditions involving the loss of mating control by a single dominant individual in certain species (e.g.Centropyge spp. ). Sex-change induction, which is characteristic of species with large social groups lacking rigid dominance hierarchies, refers to the requirement that sex change must be induced by specific characteristics of (or changes in) the social group, regardless of dominance status. Ability to distinguish sex, or its importance, differentiates sex-ratio induction (e.g.Anthias squamipinnis) from size-ratio induction (e.g.Thalassoma spp.). Alternative models account for the possibility that all cases of sex change require stimulation from smaller conspecifics (universal induction-inhibition model) or that all fish have the genetic capacity to switch mechanisms, depending on changing ecological conditions and resulting changes in mating system (behavioral-scaling model). Neurophysiological models suggest that induction mechanisms, which require at least two categories of environmental stimuli, may have evolved from the simpler suppression mechanisms, which require only one kind of input from the environment.     

Redistribution of juvenile salmonid fishes after localized catastrophic depletion

Juvenile Atlantic salmon and brown trout were depleted at three sites ( c . 108–380 m²) of a natural stream during the summer months of 1991 and 1992. Local population changes and movements of fish marked in sections adjacent to each depleted area were monitored thereafter. There was very little movement of marked salmon parr into the central regions of the depleted areas following the immediate post-marking period. Upstream movement by young-of-the-year fish from high density sections in mid-late summer was noted for trout but not salmon. Unmarked 1-year-old salmon parr immigrated into depleted areas in June 1992, and the pattern of recolonization was consistent with migration upstream from the adjoining river. It is concluded that resident salmon were very strongly site-attached and resource tracking was of no functional significance as a compensatory mortality mechanism. The occurrence of a long distance migratory component in the population during early-mid summer indicates that this, rather than local resource tracking, constitutes a potential compensatory mechanism.     

Serological relationships of five herpesviruses isolated from salmonid fishes

The five herpesviruses isolated from salmonid fishes were compared for their serological relatedness by serum cross-neutralization studies with polyclonal rabbit serum. The five viruses fell into two major groups. The three viruses from fishes in Japan, Oncorbyncbus mason virus (OMV), yamame tumor virus (YTV) and nerka virus (NeVTA) were closely related. They however, differed considerably from two viruses from salmonid fishes in North America, Herpesvirus salmonis (HPV) and the steelhead herpesvirus (SHV). The latter two viruses were also closely related. This study indicated that the viruses in the two countries are serologically distinct and are not a result of transfers of infected fish or eggs between continents.     

Origins and evolution of the Europeans' genome: evidence from multiple microsatellite loci

There is general agreement that the current European gene pool is mainly derived from Palaeolithic hunting-gathering and Neolithic farming ancestors, but different studies disagree on the relative weight of these contributions. We estimated admixture rates in European populations from data on 377 autosomal microsatellite loci in 235 individuals, using five different numerical methods. On average, the Near Eastern (and presumably Neolithic) contribution was between 46 and 66%, and admixture estimates showed, with all methods, a strong and significant negative correlation with distance from the Near East. If the assumptions of the model are approximately correct, i.e. if the Basques' and Near Easterners' genomes represent a good approximation to the Palaeolithic and Neolithic settlers of Europe, respectively, these results imply that half or more of the Europeans' genes are descended from Near Eastern ancestors who immigrated in Europe 10000 years ago. If these assumptions are incorrect, our results show anyway that clinal variation is the rule in the Europeans' genomes and that lower estimates of Near Eastern admixture obtained from the analysis of single markers do not reflect the patterns observed at the genomic level.     

Polymorphic microsatellite loci in Linum usitatissimum

We report the characterization of 28 polymorphic microsatellite markers in Linum usitatissimum that allow distinguishing almost all cultivars of both flax and linseed. Polymorphism was low, ranging from two to 10 alleles per locus in the 93 cultivars screened. Linkage disequilibrium was found at about a third of the pairs of loci likely due to self‐fertilization and strong selection by breeders. We tested these loci for cross‐amplification in nine additional species of Linum and found that three species amplified a majority of loci.