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PubMed2002

Incipient speciation across a depth gradient in a scleractinian coral?

A few marine cases have demonstrated morphological and genetic divergence in the absence of spatial barriers to gene flow, suggesting that the initial phase of speciation is possible without geographic isolation. In the Bocas del Toro Archipelago of the Atlantic Coast of Panama, we found two morphotypes of the scleractinian coral Favia fragum with opposing depth distributions. One morphotype fit the classical description of F. fragum and was most abundant at 3 m depth. A second morphotype was distinguished by raised corallites and was restricted to < or = 1 m depth. The two morphotypes overlapped in distribution at 1 m depth. Multivariate analysis of polyp-level characters (shape and distribution of septa within corallites) divided samples into two groups corresponding to initial qualitative observations of colony shape and corallite relief. To determine whether reduced gene flow maintains morphological variation, we measured the frequencies of alleles at five allozyme loci in both morphotypes at three sites 1-2 km distant. While there were significant differences in allele frequencies between morphotypes within sites, there were also frequency differences among sites at most loci, with the exception of nearly fixed alleles at the PGM locus. Extremely low heterozygosity permitted us to use haplotypes to compare genetic distance between morphotypes and among sites. Comparisons between haplotype data and a null model assuming gene flow between morphotypes showed that the two morphotypes shared significantly fewer haplotypes than expected, and average genetic distance between morphotypes was significantly greater than expected. Partitioning haplotype variation with analysis of molecular variance demonstrated that 35% of the variation was explained by morphotype, whereas 28% of the variation was explained by site. Two PGM heterozygotes and several individuals homozygous for rare PGM alleles are consistent with hybridization, and perhaps introgression by selfing within morphotypes. We consider three hypotheses for this morphological and genetic divergence in F. fragum: (1) intraspecific polymorphism, (2) incipient species, (3) biological species; and discuss the role of reproductive characters in a divergence-with-gene flow mechanism of speciation.

Animals↗

PubMed2005

Detection of transferrin isoforms in human serum: comparison of UV and ICP-MS detection after CZE and HPLC separations.

Two methods for separation of transferrin (Tf) sialoforms, capillary electrophoresis (CE) and high performance liquid chromatography (HPLC) with conventional UV absorbance detection, have been investigated and compared. First, conditions affecting the separation of the Tf isoforms by capillary zone electrophoresis and HPLC were carefully optimized. The use of 15 mmol L(-1) borate buffer (pH 8.4) containing 3 mmol L(-1) diaminobutane (DAB) as additive enabled good separation of the Tf isoforms by CE (75 cm x 50 microm i.d. fused silica capillary) at 25 kV. In HPLC, a gradient of ammonium acetate (from 0 to 250 mmol L(-1) in 45 min) buffered at pH 6 (Tris-HCl) proved suitable for separation of Tf isoforms on a Mono-Q HR 5/5 anion-exchange column. On-line specific detection of the iron associated with the different Tf isoforms, after Fe saturation, by inductively coupled plasma mass spectrometry (ICP-MS) was studied in detail to compare its analytical performance with UV detection. For both CE and HPLC an octapole reaction system (ORS) ICP-MS instrument was used to minimize polyatomic interferences on the (56)Fe major isotope. Limits of detection of the different isoforms were in the range of 0.02-0.04 micromol L(-1) Tf for HPLC-ICP (ORS)-MS. This hybrid technique proved more selective and reliable detection of transferrin isoforms with 2, 3, 4, 5, and 6 sialic acid residues (S(2), S(3), S(4), S(5), and S(6)) in real serum samples. Interesting results from iron speciation of Tf in serum from healthy individuals and from pregnant women are given.

Chromatography, High Pressure Liquid↗

PubMed1999

Chromosome evolution in kangaroos (Marsupialia: Macropodidae): cross species chromosome painting between the tammar wallaby and rock wallaby spp. with the 2n = 22 ancestral macropodid karyotype.

Marsupial mammals show extraordinary karyotype stability, with 2n = 14 considered ancestral. However, macropodid marsupials (kangaroos and wallabies) exhibit a considerable variety of karyotypes, with a hypothesised ancestral karyotype of 2n = 22. Speciation and karyotypic diversity in rock wallabies (Petrogale) is exceptional. We used cross species chromosome painting to examine the chromosome evolution between the tammar wallaby (2n = 16) and three 2n = 22 rock wallaby species groups with the putative ancestral karyotype. Hybridization of chromosome paints prepared from flow sorted chromosomes of the tammar wallaby to Petrogale spp., showed that this ancestral karyotype is largely conserved among 2n = 22 rock wallaby species, and confirmed the identity of ancestral chromosomes which fused to produce the bi-armed chromosomes of the 2n = 16 tammar wallaby. These results illustrate the fission-fusion process of karyotype evolution characteristic of the kangaroo group.

Animals↗

PubMed1992

[Genetic evidence of a species complex in Anopheles pseudopunctipennis pseudopunctipennis].

In light of inconsistencies in the pattern of malaria transmission within geographical areas inhabited by Anopheles pseudopunctipennis pseudopunctipennis, a study was carried out to investigate the possibility that this vector constitutes a species complex. Hybrid crossing studies, electrophoretic analysis of enzyme loci, and DNA restriction analysis were conducted on mosquitoes captured at nine sites in Mexico, Bolivia, and Peru. The sterility of generations resulting from cross-mating of Mexican female mosquitoes and South American male mosquitoes; the results of electrophoretic analysis, which showed differences at two loci; and a genetic distance value of 0.13 confirmed the existence of a species complex, probably produced by allopatric speciation. It is concluded that the geographic distribution of this newly discovered species complex should be defined, in view of its potential effect on malaria control.

Animals↗

PubMed2006

Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment.

The availability of the whole-genome sequence from the 2 known varieties of the human pathogenic fungus Cryptococcus neoformans provides an opportunity to study the relative contribution of divergence and introgression during the process of speciation in a genetically tractable organism. At the genomic level, these varieties are nearly completely syntenic, share approximately 85-90% nucleotide identity, and are believed to have diverged approximately 18 MYA. Via a comparative genomic approach, we identified a 14-gene region (approximately 40 kb) that is nearly identical between the 2 varieties that resulted from a nonreciprocal transfer event from var. grubii to var. neoformans approximately 2 MYA. The majority of clinical and environmental var. neoformans strains from around the world contain this sequence obtained from var. grubii. This introgression event likely occurred via an incomplete intervarietal sexual cycle, creating a hybrid intermediate where mobile elements common to both lineages mediated the exchange. The subsequent duplication in laboratory strains of a fragment of this same genomic region supports evolutionary theories that instabilities in subtelomeric regions promote adaptive evolution through gene amplification and subsequent adaptation. Along with a more ancient predicted transfer event in C. neoformans and a recently reported example from Saccharomyces cerevisiae, these data indicate that DNA exchange between closely related sympatric varieties or species may be a recurrent theme in the evolution of fungal species. It further suggests that although evolutionary divergence is the primary force driving speciation, rare introgression events also play a potentially important role.

Chromosome Mapping↗

PubMed2006

Molecular phylogeny of silkmoths reveals the origin of domesticated silkmoth, Bombyx mori from Chinese Bombyx mandarina and paternal inheritance of Antheraea proylei mitochondrial DNA.

Molecular phylogeny of some of the economically important silkmoths was derived using three mitochondrial genes, 12S rRNA, 16S rRNA, and COI, and the control region (CR). Maximum likelihood (ML) analyses showed two distinct clades, one consisting of moths from Bombycidae family and the other from Saturniidae family. The mitochondrial CR showed length polymorphisms with indels. The ML analyses for complete mitochondrial genome sequences of Bombyx mori (strains Aojuku, C108, Backokjam, and Xiafang), Japanese and Chinese strains of B. mandarina (Japanese mandarina and Chinese mandarina) and, Antheraea pernyi revealed two distinct clades, one comprising of B. mori strains and the other with B. mandarina, and A. pernyi forming an outgroup. Pairwise distances revealed that all of the strains of B. mori studied are closer to Chinese than to Japanese mandarina. Phylogenetic analyses based on whole mitochondrial genome sequences, the finding of a tandem triplication of a 126bp repeat element only in Japanese mandarina, and chromosome number variation in B. mandarina suggest that B. mori must have shared its recent common ancestor with Chinese mandarina. Another wild species of the Bombycidae family, Theophila religiosa, whose phylogenetic status was not clear, clustered together with the other bombycid moths in the study. Analysis of the interspecific hybrid, A. proylei gave evidence for paternal inheritance of mitochondrial DNA.

Animals↗

PubMed2006

Anion-exchange high performance liquid chromatography hyphenated to inductively coupled plasma-isotope dilution-time-of-flight mass spectrometry for speciation analysis of metal complexes with metallothionein isoforms in gibel carp (Carassius auratus gibelio) exposed to environmental metal pollution.

The capability of post-column isotope dilution (ID) combined with anion-exchange HPLC-ICP-time-of-flight (TOF)-MS was for the first time investigated for environmental quality assessment through metal speciation analysis of metallothionein (MT) isoforms in cytosols of gibel carp (Carassius auratus gibelio), used as biomarkers for environmental metal exposure. A full spectral scanning of the biological sample (with 50 microl injection volume) using ICP-TOF-MS in transient mode allowed fast multi-isotope screening of cytosolic metal-containing fractions and to investigate the presence of matrix-induced interferences. The MT cytosolic fraction of liver and kidney of the carp, sampled at three different sampling sites in Belgium, was partially purified using size-exclusion (SE) HPLC. Quantification of the elements Cd (toxic) and Zn and Cu (essential) associated with MT isoforms in this fraction was addressed using an hybrid approach based on post-column addition of the enriched isotopes 65Cu, 67Zn, 106Cd and monitoring on-line the isotope ratios 63Cu/65Cu, 64Zn/67Zn and 114Cd/106Cd by ICP-MS with a time of flight instrument, which was coupled to anion-exchange HPLC. With this separation method, baseline separation of up to five MT isoforms, which is required for quantitative metal speciation by HPLC-ICP-IDMS, was achieved within a run of 15 min. The MT fraction of the cytosols was also analysed for the total metal content using IDMS with size-exclusion HPLC-ICP-MS and species-unspecific calibration. Results showed significant differences between speciation results and total MT concentrations of control fish and fish from the most contaminated sampling sites, revealing the potential of gibel carp MT for sequestering excess intracellular free-ions (essential and toxic elements) and for its protection against metal toxicity. Preferences for metal sequestration of metal complexes with MT isoforms were also found to be tissue-specific: excess of Cd was found preferably bound to a major MT isoform (tR = 8.0 min) in kidney, whereas excess intracellular Zn appeared to be mostly sequestered by four MT isoforms (tR=7.3, 8.0, 12.2 and 14.4 min) in liver, the MT form with tR = 8.0 min being the main Zn scavenger form. Such kind of quantitative speciation information on the preferences of MT isoforms in different fish organs for sequestering heavy metals, reported here for the first time, is important to elucidate the role of isoform-specific induction of vertebrate fish MT in metal detoxification and the use of MT as biomarker.

Animals↗

PubMed1996

Chromosomal and molecular divergence in the Indian pygmy field mice Mus booduga-terricolor lineage of the subgenus Mus.

Mus booduga and Mus terricolor both have 2n = 40. Unlike M. booduga, with all acrocentric chromosomes, M. terricolor invariably has large submetacentric X and acrocentric Y due to an increase of heterochromatin. In contrast to the conservative karyotype of the co-existing sibling species booduga, three chromosome types of terricolor are found in different populations and their divergent karyotypes have autosomal heterochromatin variations established in the homozygous condition. The average genetic distance determined from electrophoretic study of 20 protein loci ranges from lowest (D = 0.106) between chromosome types I & II to highest (D = 0.185) between types II & III. In terricolor, booduga and M. m. tytleri high mean values of variations per locus (range A = 1.604 to 1.928) and heterozygosity per individual per locus (range H = 0.180 to 0.336) have been observed. Sequence divergence of 0.39 to 1.2%, calculated from restriction profiles of mtDNA, shows that the terricolor chromosome types have diverged recently. Hybridizations between type I females and type III males gave a preponderance of males in the F1 with varying degrees of sterility. The 'terricolor complex' is an interesting system for critical probing for the role of heterochromatin in the process of speciation. MtDNA, protein loci and AT-rich musculus-related major and minor satellite DNA data indicate that progenitors of the booduga-terricolor lineage might have evolved simultaneously with the caroli-cookii-cervicolor lineage in the evolution of the subgenus Mus.

Animals↗

PubMed2006

Plasmodium falciparum: worldwide sequence diversity and evolution of the malaria vaccine candidate merozoite surface protein-2 (MSP-2).

We examined patterns and putative mechanisms of sequence diversification in the merozoite surface protein-2 (MSP-2) of Plasmodium falciparum, a major dimorphic malaria vaccine candidate antigen, by analyzing 448 msp-2 alleles from all continents. We describe several nucleotide replacements, insertion and deletion events, frameshift mutations, and proliferations of repeat units that generate the extraordinary diversity found in msp-2 alleles. We discuss the role of positive selection exerted by naturally acquired type- and variant-specific immunity in maintaining the observed levels of polymorphism and suggest that this is the most likely explanation for the significant excess of nonsynonymous nucleotide replacements found in dimorphic msp-2 domains. Hybrid sequences created by meiotic recombination between alleles of different dimorphic types were observed in few (3.1%) isolates, mostly from Africa. We found no evidence for an extremely ancient origin of allelic dimorphism at the msp-2 locus, predating P. falciparum speciation, in contrast with recent findings for other surface malarial antigens.

Alleles↗

PubMed2005

Reinforcement of pre-zygotic isolation and karyotype evolution in Agrodiaetus butterflies.

The reinforcement model of evolution argues that natural selection enhances pre-zygotic isolation between divergent populations or species by selecting against unfit hybrids or costly interspecific matings. Reinforcement is distinguished from other models that consider the formation of reproductive isolation to be a by-product of divergent evolution. Although theory has shown that reinforcement is a possible mechanism that can lead to speciation, empirical evidence has been sufficiently scarce to raise doubts about the importance of reinforcement in nature. Agrodiaetus butterflies (Lepidoptera: Lycaenidae) exhibit unusual variability in chromosome number. Whereas their genitalia and other morphological characteristics are largely uniform, different species vary considerably in male wing colour, and provide a model system to study the role of reinforcement in speciation. Using comparative phylogenetic methods, we show that the sympatric distribution of 15 relatively young sister taxa of Agrodiaetus strongly correlates with differences in male wing colour, and that this pattern is most likely the result of reinforcement. We find little evidence supporting sympatric speciation: rather, in Agrodiaetus, karyotypic changes accumulate gradually in allopatry, prompting reinforcement when karyotypically divergent races come into contact.

Animals↗

PubMed1992

Relatedness of strains of methicillin-resistant coagulase-negative Staphylococcus colonizing hospital personnel and producing bacteremias in a neonatal intensive care unit.

The emergence of methicillin-resistant coagulase-negative Staphylococcus as a major bacterial pathogen in neonatal intensive care units has stimulated interest in the epidemiology of spread of the organism. During a 12-month "epidemic" of bacteremias with methicillin-resistant coagulase-negative Staphylococcus we compared the characteristics of bacteremic and personnel nasally-carried strains by traditional and biomolecular methods. Sixty-two percent of neonatal intensive care unit nurses were colonized with methicillin-resistant coagulase-negative Staphylococcus with similar speciation to bacteremic strains. Inspection of plasmid profiles revealed a moderate degree of similarity between bacteremic and colonizing strains although genomic DNA restriction patterns showed diversity. Ribotype patterns were highly conserved (90%) in personnel strains. A 2.6-kilobase plasmid DNA probe hybridized to similarly sized plasmids and larger plasmids in one-half of the strains. We hypothesize that related methicillin-resistant strains may be transferred among personnel and neonates in the neonatal intensive care unit. Epidemiologic studies of coagulase-negative staphylococci should consider multiple molecular techniques to relate strains.

Bacteremia↗

PubMed1993

Genetic evidence of a species complex in Anopheles pseudopunctipennis sensu lato.

This preliminary report provides information concerning genetic variation in the vector mosquito Anopheles pseudopunctipennis sensu lato that could have malaria control implications. Because of inconsistencies in malaria transmission patterns within geographic zones inhabited by this vector, the possibility that it represents a species complex was investigated. Hybrid crossing studies, electrophoretic analysis of enzyme variation, and DNA restriction studies were carried out in mosquitoes captured in nine areas of Mexico, Bolivia, and Peru. The findings demonstrated the existence of a species complex believed to have resulted from allopatric speciation. This research points to a need for establishing the geographic distribution of the newly recognized species because of their potential influence on malaria control.

Animals↗

PubMed2001

Population structure and speciation in tropical seas: global phylogeography of the sea urchin Diadema.

The causes of speciation in the sea are rarely obvious, because geographical barriers are not conspicuous and dispersal abilities or marine organisms, particularly those of species with planktonic larvae, are hard to determine. The phylogenetic relations of species in cosmopolitan genera can provide information on the likely mode of their formation. We reconstructed the phylogeny of the pantropical and subtropical sea urchin genus Diadema, using sequences of mitochondrial DNA from 482 individuals collected around the world, to determine the efficacy of barriers to gene flow and to ascertain the history of possible dispersal and vicariance events that led to speciation. We also compared 22 isozyme loci between all described species except D. palmeri. The mitochondrial DNA data show that the two deepest lineages are found in the Indian and West Pacific Oceans. (Indo-Pacific) Diadema setosum diverged first from all other extant Diadema, probably during the initiation of wide fluctuations in global sea levels in the Miocene. The D. setosum clade then split 3-5 million years ago into two clades, one found around the Arabian Peninsula and the other in the Indo-West Pacific. On the lineage leading to the other species of Diadema, the deepest branch is composed of D. palmeri, apparently separated when the climate of New Zealand became colder and other tropical echinoids at these islands went extinct. The next lineage to separate is composed of a currently unrecognized species of Diadema that is found at Japan and the Marshall Islands. Diadema mexicanum in the eastern Pacific separated next, whereas D. paucispinum, D. savignyi, and D. antillarum from the western and central Atlantic, and (as a separate clade) D. antillarum from the eastern Atlantic form a shallow polytomy. Apparently, Indo-Pacific populations of Diadema maintained genetic contact with Atlantic ones around the southern tip of Africa for some time after the Isthmus of Panama was complete. Diadema paucispinum contains two lineages: D. paucispinum sensu stricto is not limited to Hawaii as previously thought, but extends to Easter Island, Pitcairn, and Okinawa; A second mitochondrial clade of D. paucispinum extends from East Africa and Arabia to the Philippines and New Guinea. A more recent separation between West Indian Ocean and West Pacific populations was detected in D. setosum. Presumably, these genetic discontinuities are the result of water flow restrictions in the straits between northern Australia and Southeast Asia during Pleistocene episodes of low sea level. Diadema savignyi is characterized by high rates of gene flow from Kiribati in the central Pacific all the way to the East African Coast. In the Atlantic, there is a biogeographic barrier between the Caribbean and Brazil, possibly caused by fresh water outflow from the Amazon and the Orinoco Rivers. Diadema antillarum populations of the central Atlantic islands of Ascension and St. Helena are genetically isolated and phylogenetically derived from Brazil. Except for its genetic separation by the mid-Atlantic barrier, Diadema seems to have maintained connections through potential barriers to dispersal (including the Isthmus of Panama) more recently than did Eucidaris or Echinometra, two other genera of sea urchins in which phylogeography has been studied. Nevertheless, the mtDNA phylogeography of Diadema includes all stages expected from models of allopatric differentiation. There are anciently separated clades that now overlap in their geographic distribution, clades isolated in the periphery of the genus range that have remained in the periphery, clades that may have been isolated in the periphery but have since spread towards the center, closely related clades on either side of an existing barrier, and closely related monophyletic entities on either side of an historical barrier that have crossed the former barrier line, but have not attained genetic equilibrium. Except for D. paucispinum and D. savignyi, in which known hybridization may have lodged mtDNA from one species into the genome of the other, closely related clades are always allopatric, and only distantly related ones overlap geographically. Thus, the phylogenetic history and distribution of extant species of Diadema is by and large consistent with allopatric speciation.

Adenosine Triphosphatases↗

PubMed2001

Characterization of the rbcS multigene family in wheat: subfamily classification, determination of chromosomal location and evolutionary analysis.

To elucidate the evolution of a multigene family in plants, nucleotide sequences of members of the rbcS multigene family encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase in wheat were determined. Five genomic clones containing rbcS sequences were isolated. The known members of the rbcS family of common wheat, including the clones reported here, were categorized into two Classes (I and II), which, in turn, were classified into three (A, B and E) and two (C and D) subtypes, respectively. The sequences of the intron and the 3' flanking region were divergent between the classes but not among the types within a class. The differences among the types within a class were caused by large indels (about 100-350 bp) in the intron. The members of Classes I and II were located on homeologous group 2 and 5 chromosomes, respectively. The Southern hybridization data indicated that all types of rbcS were present in the ancestral species of wheat. Thus, it is concluded that the divergence between the classes originated from an interchromosomal duplication and that several intrachromosomal duplications followed; these events occurred before the speciation of diploids. The detection of nonfunctional genes and the elimination of fragments suggests that several mechanisms were involved in reducing the copy number of rbcS during the evolution of wheat.

Base Sequence↗

PubMed1980

Metabolic interference and the + - heterozygote. a hypothetical form of simple inheritance which is neither dominant nor recessive.

Another form of simple inheritance is possible which is neither dominant nor recessive and in which the heterozygote alone is affected. In this system, homozygosity for the normal allele AA, and the mutant allele A'A', give a normal phenotype. Only the heterozygous condition AA' (+ - heterozygote) produces an abnormal phenotype because the two alleles, when present together, interact to produce a harmful effect. This metabolic interference may occur because the two allelic genes code for different subunits of a multisubunit enzyme or structural protein. The two genes may interact in other ways and need not be allelic. The various matings result in pedigrees, which in some cases resemble those of dominant or recessive inheritance, and in other cases are unique. Certain unusual pedigrees in the literature are compatible with the predictions of metabolic interference and are difficult to explain by other means. Metabolic interference is most likely to be recognized as: (1) a disorder limited to females, apparently dominant or recessive, especially a disorder passed to affected females through unaffected males; (2) a disorder occurring in all members of a large sibship with normal parents; (3) a disorder occurring in all members of a large sibship with one parent similarly affected; (4) an apparently dominant disorder with females more severely affected than males; (5) an apparently X-linked dominant disorder in which males are not more severely affected; or (6) any autosomal dominant disorder. Examples of possible metabolic interference exist among disorders of animals, and the mechanism could be a factor in speciation. Tissue culture methods could be used to demonstrate metabolic interference.

Alleles↗

PubMed1979

The distribution of endogenous chicken retrovirus sequences in the DNA of galliform birds does not coincide with avian phylogenetic relationships.

The chicken is a domesticated form of Red Jungle-fowl (Gallus gallus), which belongs to the Pheasant family (Phasianidae) within the order Galliformes. Domestic chickens carry the genome of the endogenous retrovirus RAV-O as DNA sequences integrated into host chromosomes transmitted through the germ line. We have examined the presence and distribution of RAV-O-related sequences in the DNA of Red Junglefowl and other closely related species of Junglefowl, as well as more distantly related Pheasants and Quail. DNA sequences homologous to RAV-O were analyzed by molecular hybridization in liquid and after electrophoresis of restriction endonuclease fragments. The presence of RAV-O-related sequences in avian DNA does not correlate with phylogenetic relationships. Under stringent conditions of hybridization in liquid, DNA sequences homologous to RAV-O cDNA were detected at high levels (greater than 80% homology( only in the genomes of the domestic chicken and its phylogenetic ancestor, the Red Junglefowl (Gallus gallus). The DNA of two other species of Gallus (G. sonnerati, Sonnerat's Junglefowl and G. varius, Green Junglefowl), of Ring-necked Pheasant and of Japanese Quail contained sequences with less than 10% homology to RAV-O cDNA. Under conditions permitting mismatching, however, Ring-necked Pheasant DNA hybridized up to 50% of the RAV-O cDNA, and Quail DNA 24%, whereas the extent of hybridization to Sonnerat's and Green Junglefowl DNA was not markedly increased. Analysis of restriction enzyme digests revealed several distinct fragments of DNA hybridizing to chick retrovirus cDNA in both Red Junglefowl and domestic chicken, and multiple fragments in DNA from two species of Phasianus. No fragments with sequences related to chicken retroviruses were found, however, in digests of DNA prepared from Sonnerat's, Ceylonese and Green Junglefowl, from two other Pheasant genera (Chrysolophus and Lophura), or from one Quail genus (Coturnix). Thus the DNA of three Junglefowl species closely related to Gallus gallus lacked RAV-O sequences while the DNA of more distantly related Phasianus species showed significant homology. These results show that RAV-O-related sequences have not diverged together with the normal host genes during the evolution of the Phasianidae. Although RAV-O sequences are endogenous in all domestic chickens and Red Junglefowl studied thus far, it appears that the RAV-O genome has been introduced relatively recently into the germ line of Gallus gallus, following speciation but before domestication, and independently of the related sequences found in members of the genus Phasianus.

Alpharetrovirus↗

PubMed2006

Contrast between extensive variation of 28S rDNA and stability of 5S rDNA and telomeric repeats in the diploid-polyploid Squalius alburnoides complex and in its maternal ancestor Squalius pyrenaicus (Teleostei, Cyprinidae).

The diploid-polyploid Squalius alburnoides complex resulted from interspecific hybridization. The chromosomal mapping of 28S and 5S ribosomal genes and of (TTAGGG)n telomeric repeats was performed on specimens from the complex and from the sympatric bisexual species S. pyrenaicus (the complex maternal ancestor) as part of an investigation of the evolutionary relationships between genomic constitutions and the consequences of the ongoing polyploidization process in terms of chromosome reshaping. Contrasting results were obtained. While results with 5S rDNA and telomeric probes gave an impression of genomic stability, the variability detected with 28S rDNA probe suggested quite the opposite. The 5S rDNA probe mapped constantly to three chromosomes per haploid genome with apparently conserved locations in morphologically similar chromosomes; conversely, prominent intra- and inter-individual variations of 28S rDNA and of syntenic sites with 5S rDNA were detected with regard to number, size and location. Hypotheses for the causes of such polymorphisms are discussed. The terminal position of most 28S rDNA sites and the absence of detectable interstitial telomeric sequences suggest a mechanism that does not involve major chromosomal rearrangements. These fishes share similar patterns for the studied cytogenetic markers which may be taken as evidence of an apparent stability that may be hiding extensive and subtle genome variations that are possibly related to an ongoing evolutionary process of genome tetraploidization and speciation.

Alleles↗

PubMed2026

Polyploidy Arithmetic.

Polyploidy occurs in plants and animals, and is an important force in speciation and genome evolution. The main focus of this paper is the following fundamental question that was recently posed by Huber and Maher: Given the ploidy numbers of a collection of extant species, or their ploidy profile, what is the smallest number of hybridizations needed in any evolutionary history for these species to completely represent these numbers? In this paper, we shall show that this question can be rephrased in terms of addition chains and the closely related addition sequences, which have been studied for over a century in mathematics and computer science. These are sequences of natural numbers that start with 1, so that each number in the sequence larger than 1 is the sum of two other numbers arising earlier in the sequence. In our first main result, we show that finding the smallest number of hybridization events to explain a ploidy profile, or the hybrid number, is equivalent to solving the so-called addition sequence problem. This immediately implies that computing the hybridization number is computationally intractable. Even so, it also leads to new connections to representing polyploid evolution using networks. More specifically, in our second main result we show that ploidy profiles representable by tree-child networks are exactly the addition chains, implying a polynomial-time algorithm for identifying these profiles. We then consider beaded tree-child networks, which permit the representation of autopolyploidy events, and in our third main result we provide a greedy polynomial-time algorithm to decide whether a given profile can be realized by such a network. We expect that our results can be leveraged in future work through, for example, making use of known algorithms for computing short addition sequences to give bounds for the hybrid number, and in guiding network reconstruction for polyploid species.

Polyploidy↗