Chromosome evolution in the Salmonidae (Pisces): an update

The karyotypes of salmonid fishes including taxa in the three subfamilies Coregoninae, Thymallinae and Salmoninae are described. This review is an update of the (Hartley, 1987) review of the chromosomes of salmonid fishes. As described in the previous review, the karyotypes of salmonid fishes fall into two main categories based on chromosome numbers: the type A karyotypes have diploid numbers close to 80 with approximately 100 chromosome arms (2n = 80, NF = 100), and the type B karyotypes have diploid numbers close to 60 with approximately 100 chromosome arms (2n = 60, NF = 100). In this paper we have proposed additional sub categories based on variation in the number of chromosome arms: the A' type with NF = 110-120, the A" type with NF greater than 140, and the B' type with NF less than 80. Two modes of chromosome evolution are found in the salmonids: in the Coregoninae and the Salmoninae the chromosomes have evolved by centric fusions of the Robertsonian type decreasing chromosome numbers (2n) while retaining chromosome arm numbers (NF) close to that found in the hypothetical tetraploid ancestor so that most extant taxa have either type A or type B karyotypes. In the Thymallinae, the chromosomes have evolved by inversions so that chromosome arm numbers (NF) have increased but chromosome numbers (2n) close to the karyotype of the hypothetical tetraploid ancestor have been retained and all taxa have type A' karyotypes. Most of the taxa with type B karyotypes in the Coregoninae and Salmoninae are members of the genus Oncorhynchus, although at least one example of type B karyotypes is found in all of the other genera. These taxa either have an anadromous life history or are found in specialized lacustrine environments. Selection for increases or decreases in genetic recombination as proposed by Qumsiyeh, 1994 could have been involved in the evolution of chromosome number in salmonid fishes.     

Multifaceted genetic analysis of the “Critically Endangered” brush-tailed rock-wallaby Petrogale penicillata in Victoria, Australia: Implications for management

The use of molecular genetic techniques can aidwildlife managers in setting priorities anddevising management strategies for scatteredpopulations of threatened taxa. In this study,six remnant populations of the criticallyendangered brush-tailed rock-wallaby (Petrogale penicillata) in Victoria, Australia,were examined using karyotypic, microsatellite(11 loci) and mitochondrial DNA (mtDNA) controlregion sequence analysis. Each remnantpopulation was found to be genetically distinct(unique microsatellite alleles and controlregion haplotypes), but had low geneticdiversity. This distribution of geneticdiversity between, rather than withinpopulations, is most likely a consequence ofrecent severe reductions in population size anddispersal that have occurred since Europeansettlement. The six mtDNA control regionhaplotypes identified in the Victorianpopulations were all closely related (average1.3% sequence divergence), and only 2%divergence separated haplotypes from EastGippsland and the Grampians (550 km to thewest). In contrast there was considerablesequence divergence (7.7%) between theVictorian haplotypes and those found in P.penicillata from elsewhere in the speciesrange. In comparison, 8.8% divergenceseparates P. penicillata from the closelyrelated P. herberti. The Victorianhaplotypes also formed a distinct and wellsupported monophyletic group that excludedhaplotypes from other P. penicillata andP. herberti. In light of these data, werecommend that the remnant Victorianpopulations of P. penicillata be managedseparately from remaining populations in NewSouth Wales and Queensland; and thatindividuals be regularly exchanged amongst theVictorian populations to increase theirdiversity and reduce the likelihood ofinbreeding depression.     

Characterization of diploid,tetraploid and hexaploid Helianthus species by chromosome banding and FISH with 45S rDNA probe

Comparative karyotype analyses of five diploid, two tetraploid, and three hexaploid species of Helianthuswere performed using Feulgen staining, Giemsa C and CMA₃ (C-CMA) staining, and FISH with 45S rDNA probe. The karyotypes are composed by a basic number of x=17 with a predominance of meta- and submetacentric chromosome types. A polyploid series is associated with the basic number. Giemsa C- and C-CMA banding revealed terminal or interstitial heterochromatin according to the species, suggesting the existence of a mechanism that may be acting in the dispersion of heterochromatic segments in Helianthus. The nucleolar organizer regions were located at terminal chromosome positions by FISH with 45S rDNA probe. Diploid species presented four, six, and eight rDNA sites, tetraploid species showed eight sites and hexaploid species presented 12 rDNA sites. Karyomorphological differences include variation in number, size and chromosome morphology, suggesting that rearrangements involving small heterochromatic and rDNA segments played a major role in karyotype evolution.     

Polytene chromosomes of Simulium craigi (Diptera: Simuliidae)

Simulium craigi Adler and Currie is a polymorphic species based on polytene chromosome banding patterns in the long arm of chromosome III (IIIL). Three cytotypes are described based on the predominant IIIL sequences. These correspond to three broad geographic areas: cytotype CC from Pennsylvania; cytotype AF from Ontario and Manitoba; and cytotype ACF/BCF from New Hampshire. In the absence of sympatric populations, these cytotype differences are best explained by clinal variation within a single species. The relationship of S. craigi to other described members of the S. vernum group is discussed.     

Differential rates of evolution for the ZFY-related zinc finger genes,Zfy, Zfx,and Zfa in the mouse genus Mus

A comparative study of the last exon of the zinc finger genes Zfx, Zfy, and Zfa from species of mice in the genus Mus was conducted to assess the extent of gene-specific and chromosome-specific effects on the evolutionary patterns among related X-, Y-, and autosomal-linked genes. Phylogenetic analyses of 29 sequences from Zfx, Zfa, and Zfy from 10 taxa were performed to infer relatedness among the zinc finger loci, and codon-based maximum likelihood analyses were conducted to assess evolutionary pattern among genes. Five models of nucleotide sequence evolution were applied and compared using a likelihood ratio test. Estimates of nonsynonymous to synonymous changes (dN/dS) for these genes suggest that amino acid substitutions are occurring at a more rapid rate across the autosomal- and Y-specific lineages compared to the X-specific lineage, with the Y-specific lineage showing the highest rate under certain models. The data suggest the action of gene-specific effects on evolutionary pattern. In particular, Zfa and Zfy genes, both with presumed restricted expression, appear less functionally constrained relative to ubiquitously expressed Zfx. Slightly elevated dN/dS for Zfy genes in comparison to Zfa also suggest Y-specific effects.     

Genic mutation rates in mammals: local similarity,chromosomal heterogeneity,and X-versus-autosome disparity

The reduction of mutation rates on the mammalian X chromosome relative to autosomes is most often explained in the literature as evidence of male-driven evolution. This hypothesis attributes lowered mutation rates on the X chromosome to the fact that this chromosome spends less time in the germline of males than in the germline of females. In contrast to this majority view, two articles argued that the patterns of mutation rates across chromosomes are inconsistent with male-driven evolution. One article reported a 40% reduction in synonymous substitution rates (Ks) for X-linked genes relative to autosomes in the mouse-rat lineage. The authors argued that this reduction is too dramatic to be explained by male-driven evolution and concluded that selection has systematically reduced mutation rate on the X chromosome to a level optimal for this male-hemizygous chromosome. More recently, a second article found that chromosomal mutation rates in both the human-mouse and mouse-rat lineages were so heterogeneous that the X chromosome was not an outlier. Here again, the authors argued that this is at odds with male-driven evolution and suggested that selection has modulated chromosomal mutation rates to locally optimal levels, thus extending the argument of the first mentioned article to include autosomes. Here, we reexamine these conclusions using mouse-rat and human-mouse coding-region data. We find a more modest reduction of Ks on the X chromosome, but our results contradict the finding that the X chromosome is not distinct from autosomes. Multiple statistical tests show that Ks rates on the X chromosome differ systematically from the autosomes in both lineages. We conclude that the moderate reduction of mutation rate on the X chromosome of both lineages is consistent with male-driven evolution; however, the large variance in mutation rates across chromosomes suggests that mutation rates are affected by additional factors besides male-driven evolution. Investigation of mutation rates by synteny reveals that synteny blocks, rather than entire chromosomes, might represent the unit of mutation rate variation.     

Genomic studies of gene expression: regulation of the Wilson disease gene

Bacterial artificial chromosomes (BACs) have many advantages over other large-insert cloning vectors and have been used for a variety of genetic applications, including the final contigs of the human genome. We describe the utilization of a BAC construct to study gene regulation in a tissue culture-based system, using a 170-kb clone containing the entire Wilson disease (WND) locus as a model. A second BAC construct that lacked a putative negatively regulating promoter sequence was created. A nonviral method of gene delivery was applied to transfect three human cell lines stably with each construct. Our results show correct WND gene expression from the recombinant locus and quantification revealed significantly increased expression from the clone lacking the negative regulator. Comparison with conventional methods confirms the reliability of the genomic approach for thorough examination of gene expression. This experimental system illustrates the potential of BAC clones in genomic gene expression studies, new gene therapy strategies, and validation of potential molecular targets for drug discovery.     

“Chromosome Memory” of Parental Genomes in Embryonic Hybrid Cells

In the hybrid cells obtained by fusion of embryonic stem cells with adult differentiated cells, homologous chromosomes are in two ontogenetic configurations: pluripotent and differentiated. In order to assess the role of cis- and trans-regulation in the maintenance of these states, we studied a set of clones of hybrid cells of the type embryonic stem cells–splenocytes and used two approaches: segregation of parental chromosomes and comparison of pluripotency of the past hybrid cells and embryonic stem cells. The segregation test showed that the hybrid cells lost only the homologs of the somatic partner and this process was sharply accelerated when the cells were cultivated in nonselective conditions, thus suggesting the full or partial preservation of the initial differences in the organization of parental homologs. The descendants of the former hybrid cells, which had the karyotype similar to that of embryonic stem cells, demonstrated the level of pluripotency, comparable with that of embryonic stem cells despite the long-term effect of trans-acting factors from the somatic partner in the genome of hybrid cells. The data obtained are interpreted in the framework of the concept of chromosome memory, in the maintenance of which the key role is played bycis-regulatory factors.     

Temephos-resistant larvae of Simulium sanctipauli associated with a distinctive new chromosome inversion in untreated rivers of south-western Ghana

Larvae of the Simulium damnosum Theobald complex (Diptera: Simuliidae) were sampled in June 1996 from two sites in south-west Ghana where larviciding has not been applied: Sutri Rapids on the Tano river (05 degrees 23 minutes N 02 degrees 38 minures W) and Sekyere-Heman on the Pra river (05 degrees 11 minutes N 01 degrees 35 minutes W). All specimens were identified as Simulium sanctipauli Vajime & Dunbar sensu stricto (Diptera: Simuliidae). Bioassays with temephos (organophosphorus larvicide employed by the Onchocerciasis Programme for systematic treatment of most rivers across West Africa since the 1970s) showed about five-fold resistance in the Tano population (LC95 2.37-3.14 mg/L) and slight tolerance to temephos in the Pra population (LC95 0.67-0.76 mg/L), vs. the diagnostic concentration of 0.625 mg/L. Larval salivary polytene chromosomes of S. sanctipauli showed fixed inversions 1S-24/24, standard IIL-6 and a new inversion IL/36 polymorphism at Sutri on the Tano. These karyotype characteristics differ from those of temephos-resistant S. sanctipauli in rivers of C te d'Ivoire and other sites on the Tano in Ghana. Thus, temephos resistance in S. sanctipauli at Sutri is associated with distinct chromosomal configurations, showing that immigration was unlikely. This resistance could have been locally selected by exposure of S. sanctipauli larval populations to agrochemicals run-off from cocoa, coffee and oil plantations flanking the rivers.