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PubMed2006

A molecular cytogenetic study of chromosome evolution in chimpanzee.

We applied multitude multicolor banding (mMCB) in combination with a novel FISH DNA probe set including subcentromeric, subtelomeric and whole chromosome painting probes (subCTM) to characterize a Pan paniscus (PPA) cell line. These powerful techniques allowed us to refine the breakpoints of a pericentric inversion on chimpanzee chromosome 4, and discovered a novel cryptic pericentric inversion in chimpanzee chromosome 11. mMCB provided a starting point for mapping and high resolution analysis of breakpoints on PPA chromosome 4, which are within a long terminal repeat (LTR) and surrounded by segmental duplications, as well as the integration/expansion sites of the interstitial heterochromatin on chimpanzee chromosomes 6 and 14. Moreover, we found evidence at hand for different types of heterochromatin in the chimpanzee genome. Finally, shedding new light on the human/chimpanzee speciation, karyotypes of three members of the genus Pan were studied by mMCB and no cytogenetic differences were found although the phylogenetic distance between these subspecies is suggested to be 2.5 million years.

Animals↗
PubMed2002

Intranuclear virus-like particles of a Drosophila hybrid.

Intranuclear virus-like particles (VLPs) have been observed in different cell lines and adult tissues of Drosophila. In the present study, intranuclear VLPs have been found in larval tissues (salivary glands, midgut, fat body) as well as in adult tissues (midgut, genitals, fat body) of a rare interspecific hybrid (D. mauritiana x D. melanogaster) called 'mame'. The intranuclear VLPs were round or slightly elliptical with a diameter of 30 nm, and they were found mainly in highly organised clusters, forming large crystalline arrays, near the nucleolus and the polycene chromosomes. These particles were never observed in the cytoplasm of any mame's tissue. A few VLPs were also seen in the corresponding tissues of D. melanogaster, but they were never observed in any tissue of D. mauritiana. There is the intriguing possibility that these VLPs are related to transposable elements and probably contribute to the speciation process, in an unknown, so far, manner.

Animals↗
PubMed2005

Genome evolution of allopolyploids: a process of cytological and genetic diploidization.

Allopolyploidy is a prominent mode of speciation in higher plants. Due to the coexistence of closely related genomes, a successful allopolyploid must have the ability to invoke and maintain diploid-like behavior, both cytologically and genetically. Recent studies on natural and synthetic allopolyploids have raised many discrepancies. Most species have displayed non-Mendelian behavior in the allopolyploids, but others have not. Some species have demonstrated rapid genome changes following allopolyploid formation, while others have conserved progenitor genomes. Some have displayed directed, non-random genome changes, whereas others have shown random changes. Some of the genomic changes have appeared in the F1 hybrids, which have been attributed to the union of gametes from different progenitors, while other changes have occurred during or after genome doubling. Although these observations provide significant novel insights into the evolution of allopolyploids, the overall mechanisms of the event are still elusive. It appears that both genetic and epigenetic operations are involved in the diploidization process of allopolyploids. Overall, genetic and epigenetic variations are often associated with the activities of repetitive sequences and transposon elements. Specifically, genomic sequence elimination and chromosome rearrangement are probably the major forces guiding cytological diploidization. Gene non-functionalization, sub-functionalization, neo-functionalization, as well as other kinds of epigenetic modifications, are likely the leading factors promoting genetic diploidization.

Chromosomes, Plant↗
PubMed1984

Identification of species, strains and clones of Leishmania by characterization of kinetoplast DNA minicircles.

Molecular analysis of kinetoplast deoxyribonucleic acid (kDNA) minicircles has permitted the genotypic characterization of pathogenic isolates of Leishmania species. The apparent size in agarose gels of unit-length minicircles released by EcoRI digestion of kDNA networks is not conserved during speciation in this genus since the minicircles of strains and clones of L. major are smaller (710 base pairs, bp) than those found in certain strains of L. mexicana subspecies (820 bp), L. donovani (825, 865 bp) or L. tropica (900, 930 bp). EcoRI-cut minicircles within any one species of Leishmania are heterogeneous in mobility during electrophoresis in acrylamide gels. Schizodeme analysis of minicircles reveals a high degree of sequence divergence in kDNA with the degree of microheterogeneity varying between species. This sequence divergence allows the discrimination of closely related clones and strains within a given species. Southern blot hybridization reveals that overall minicircle sequence homology is conserved among clones and strains of one species (L. major or L. tropica) but not between different species. This property of minicircle DNA permits the use of kDNA probes as a species-specific diagnostic test for the identification of Leishmania isolates. The analysis of kDNA from two L. tropica strains isolated at 14 year intervals from a patient with leishmaniasis recidivans has shown that the two strains are closely related, suggesting that the individual suffered the cutaneous disease as a result of a resurgence of the same parasite which caused the initial infection. The differences in the properties of kDNA from the L. tropica and L. major strains studied support the taxonomic separation of L. tropica and L. major into distinct species.

Animals↗
PubMed1997

Variable expression of myoglobin among the hemoglobinless Antarctic icefishes.

The important intracellular oxygen-binding protein, myoglobin (Mb), is thought to be absent from oxidative muscle tissues of the family of hemoglobinless Antarctic icefishes, Channichthyidae. Within this family of fishes, which is endemic to the Southern Ocean surrounding Antarctica, there exist 15 known species and 11 genera. To date, we have examined eight species of icefish (representing seven genera) using immunoblot analyses. Results indicate that Mb is present in heart ventricles from five of these species of icefish. Mb is absent from heart auricle and oxidative skeletal muscle of all species. We have identified a 0.9-kb mRNA in Mb-expressing species that hybridizes with a Mb cDNA probe from the closely related red-blooded Antarctic nototheniid fish, Notothenia coriiceps. In confirmation that the 0.9-kb mRNA encodes Mb, we report the full-length Mb cDNA sequence of the ocellated icefish, Chionodraco rastrospinosus. Of the eight icefish species examined, three lack Mb polypeptide in heart ventricle, although one of these expresses the Mb mRNA. All species of icefish retain the Mb gene in their genomic DNA. Based on phylogeny of the icefishes, loss of Mb expression has occurred independently at least three times and by at least two distinct molecular mechanisms during speciation of the family.

Amino Acid Sequence↗
PubMed2005

Effect of seminal fluids in mating between M and S forms of Anopheles gambiae.

Previous studies have shown that sympatric populations of M and S molecular forms of Anopheles gambiae sensu stricto exhibit strong assortative mating. In the few documented cases of cross-mating between M and S forms, females that mated with amale of the alternative form were often also mated with a male of their own form. A potential explanation for the association between cross-mating and double mating could be that male accessory gland or sperm proteins that are responsible for inducing refractoriness to further mating by females have diverged between the M and S forms. This mechanism of postmating reproductive isolation would have important implications for our understanding of the speciation processes in the An. gambiae complex. We tested for this mechanism, by comparing the likelihood of mating, feeding, and laying eggs, as well as the fertility of females presented with males of their own form or the alternate form in the laboratory. We also compared the likelihood of remating in cross-mated and assortatively-mated females, and we analyzed their progeny to unravel patterns of sperm precedence. We found that cross-mated females differed from assortatively-mated females only in terms of egg-hatching rate and larval survival but that these effects could be attributed to hybrid vigor rather than differential response to seminal products. Cross-mating between forms was not associated with remating behavior. These results indicate that the sex proteins responsible for inhibiting further insemination and triggering the gonotrophic cycle in females have not diverged between these M and S populations. We discuss alternative explanations for the patterns of cross-mating and multiple mating observed in the field.

Animals↗
PubMed2003

Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci.

Genome duplications may have played a role in the early stages of vertebrate evolution, near the time of divergence of the lamprey lineage. Additional genome duplication, specifically in ray-finned fish, may have occurred before the divergence of the teleosts. The common carp (Cyprinus carpio) has been considered tetraploid because of its chromosome number (2n = 100) and its high DNA content. We studied variation using 59 microsatellite primer pairs to better understand the ploidy level of the common carp. Based on the number of PCR amplicons per individual, about 60% of these primer pairs are estimated to amplify duplicates. Segregation patterns in families suggested a partially duplicated genome structure and disomic inheritance. This could suggest that the common carp is tetraploid and that polyploidy occurred by hybridization (allotetraploidy). From sequences of microsatellite flanking regions, we estimated the difference per base between pairs of alleles and between pairs of paralogs. The distribution of differences between paralogs had two distinct modes suggesting one whole-genome duplication and a more recent wave of segmental duplications. The genome duplication was estimated to have occurred about 12 MYA, with the segmental duplications occurring between 2.3 and 6.8 MYA. At 12 MYA, this would be one of the most recent genome duplications among vertebrates. Phylogenetic analysis of several cyprinid species suggests an evolutionary model for this tetraploidization, with a role for polyploidization in speciation and diversification.

Animals↗
PubMed1985

Comparison of gram stain, DNA probe, and culture for the identification of species of Mobiluncus in female genital specimens.

The detection of species of Mobiluncus in female genital specimens by DNA probe (with whole-chromosomal bacterial DNA), culture, and gram stain were compared by using specimens obtained from hospital patients, college students, and women attending a sexually transmitted disease clinic. Culture purification and speciation required an average of 37 days to complete, whereas the DNA-probe assay required five days. Gram stain was also rapid but did not allow speciation. There was 100% correlation between species identification by DNA probe and by conventional biochemical tests. Gram stain alone detected 90% of the samples that were positive by any method, whereas culture detected 77%-83% and DNA probe detected 52%-83%.

Bacteria, Anaerobic↗
PubMed1996

Genetic divergence and speciation in an extremely young species flock in Mexico formed by the genus Cyprinodon (Cyprinodontidae, Teleostei).

The lake Laguna Chichancanab contains one of the evolutionarily youngest species flocks known, composed of five endemic species of the genus Cyprinodon. The presumed sister species Cyprinodon artifrons still exists in marine coastal habitats. Sequences of the mitochondrial control region were obtained for C. artifrons (genes of 17 individuals sequenced) and for all five endemic species (genes of 32 individuals sequenced). While nine different haplotypes were found in C. artifrons, only a single haplotype was shared with the species from the laguna. Four additional haplotypes were found among the endemics. These four were most closely related to that single haplotype shared with C. artifrons. The deprivation in haplotypes among the endemics points to a small founder population or to bottlenecking. The distribution pattern of overlapping haplotypes in four of the five species suggests incomplete lineage sorting or hybridization among them. Complete reproductive isolation is only assumed for one species, C. maya, in which a single and unique haplotype was found.

Animals↗
PubMed2005

Phylogenetic analysis of Petunia sensu Jussieu (Solanaceae) using chloroplast DNA RFLP.

BACKGROUND AND AIMS: The phylogenetic relationships of Petunia sensu Jussieu (Petunia sensu Wijsman plus Calibrachoa) are unclear. This study aimed to resolve this uncertainty using molecular evidence. METHODS: Phylogenetic trees of 52 taxa of Petunia sensu Jussieu were constructed using restriction fragment length polymorphism (RFLP) of chloroplast DNA digested with 19 restriction enzymes and hybridized with 12 cloned Nicotiana chloroplast DNA fragments as probes. KEY RESULTS: In all, 89 phylogenetically informative RFLPs were detected and one 50 % majority consensus tree was obtained, using the maximum parsimony method, and one distance matrix tree, using the neighbour joining method. Petunia sensu Wijsman and Calibrachoa were monophyletic sister clades in both trees. Calibrachoa parviflora and C. pygmaea, previously thought to differ from the other species in terms of their cross-compatibility, seed morphology, and nuclear DNA content, formed a basal clade that was sister to the remainder of Calibrachoa. Several clades found in the phylogenetic trees corresponded to their distribution ranges, suggesting that recent speciation in the genus Petunia sensu Jussieu occurred independently in several different regions. CONCLUSIONS: The separation of Petunia sensu Wijsman and Calibrachoa was supported by chloroplast DNA analysis. Two groups in the Calibrachoa were also recognized with a high degree of confidence.

DNA, Chloroplast↗
PubMed2001

Cross-fertility in two tropical tree species: evidence of inbreeding depression within populations and genetic divergence among populations.

Knowing the spatial patterns of cross-fertility in natural plant populations yields key insight into biparental inbreeding depression, isolation by distance, and, ultimately, speciation. Three adults each of two tropical tree species (Syzygium rubicundum and Shorea cordifolia) were each crossed with five conspecific pollen donors ranging from self to trees occurring in separate forest reserves (12 and 35 km distance for S. rubicundum and Sh. cordifolia, respectively). Cross-fertility was estimated as fruit set, seed germination, and seedling survivorship and height at 1 yr. Means of most cross-fertility measures increased steadily with outcrossing distance, peaking at 1-2 km for S. rubicundum and 1-10 km for Sh. cordifolia, and then declining at the between-forest crosses. However, seed germination and seedling height for Sh. cordifolia suggested hybrid vigor in between-forest crosses. The mean fitness cost of nearest-neighbor mating relative to crossing with more distant neighbors was 45% for S. rubicundum and 0% for Sh. cordifolia. The mean fitness cost of between-forest crosses was 52% and 70% for the two species. Crossing effects on fitness diminished between the stages of fruit set and 1-yr-old seedlings. Results indicate a strong potential for inbreeding depression within forest tree populations and partial reproductive isolation among forests in Sri Lanka's wet zone.

Journal Article↗
PubMed1988

Structure and pre-B lymphocyte restricted expression of the VpreB in humans and conservation of its structure in other mammalian species.

DNA from several mammals, including humans, was found to contain one or more restriction enzyme digested DNA fragments which hybridized to the mouse VpreB gene under stringencies demonstrating at least 70% nucleotide sequence homologies, indicating that the VpreB locus may be widespread and highly conserved among mammals. A human VpreB genomic clone was isolated and sequenced. Two exons and the intervening intron are spaced almost identically as in the mouse VpreB1 gene, and show 76% sequence homology to the mouse gene. As in the mouse VpreB1 gene, the 5' end of the human VpreB gene contains characteristic features of Ig domains, while the 3' end is Ig non-related. This 3' Ig non-related structure of the VpreB gene(s) may, therefore, have existed before the speciation of humans and mice over 65 million years ago. Sequences encoding the entire putative second framework region and a stretch in the third framework region are identical in human and mouse VpreB. the human VpreB gene appears to be selectively expressed in human pre-B cell lines as an 0.85 kb poly(A)+ RNA. Its expression promises to be a useful marker for the detection of normal and malignant human pre-B lymphocytes.

Amino Acid Sequence↗
PubMed2002

Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera).

Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

Animals↗
PubMed2002

Evolution and structure of 5S rDNA loci in allotetraploid Nicotiana tabacum and its putative parental species.

Nicotiana tabacum (tobacco) is an allotetraploid derived from ancestors of the modern diploids, N. sylvestris and N. tomentosiformis. We identified and characterized two distinct families of 5S ribosomal DNA (rDNA) in N. tabacum; one family had an average 431 bp unit length and the other a 646 bp unit length. In the diploid species, N. sylvestris and N. tomentosiformis, the 5S rDNA unit lengths are 431 bp and 644 bp respectively. The non-coding spacer sequence of the short unit in tobacco had high sequence homology to the spacer of N. sylvestris5S rDNA, while the longer spacer of tobacco had high homology with the 5S spacer of N. tomentosiformis. This suggests that the two 5S families in tobacco have their origin in the diploid ancestors. The longer spacer sequence had a GC rich sub-region (called the T-genome sub-region) that was absent in the short spacer. Pulsed field gel analysis and fluorescent in situ hybridization to tobacco metaphase chromosomes showed that the two families of 5S rDNA units are spatially separate at two chromosomal loci, on chromosomes S8 (short family) and T8 (long family). The repeat copy number at each chromosomal locus showed heterogeneity between different tobacco cultivars, with a tendency for a decrease in the copy number of one family to be compensated by an increase in the copy number of the second family. Sequence analysis reveals there is as much diversity in 5S family units within the diploid species as there is within the T and S-genome 5S family units respectively, suggesting 5S diversification within each family had occurred before tobacco speciation. There is no evidence of interlocus homogenization of the two 5S families in tobacco. This is therefore substantially different to 18-26S rDNA where interlocus gene conversion has substantially influenced most sequences of S and T genome origin; possible reasons are discussed.

DNA, Intergenic↗
PubMed1997

MHC-DRB allelic sequences incorporate distinct intragenic trans-specific segments.

The second exon of primate MHC-DRB genes encodes discrete areas of allelic hypervariability (HVR), which are used as the basis for lineage assignments to determine genetic and evolutionary relationships. Comparisons of these regions have led to the "trans-species hypothesis", which proposes that certain MHC alleles from one species are more closely related to those from other species than they are to each other; i.e., that allelic lineages are ancestral in origin. We evaluated this paradigm in an analysis of macaque and baboon MHC-DRB genes using oligotyping and sequencing of 87 new nonhuman primate DRB alleles. A remarkable conservation of sequence motifs in the HVRIII region (codon 60-79) was observed, detected both by hybridization and by sequencing; some of these motifs were found in species such as prosimians that have diverged from the human lineage 50 MYA. However, these fixed HVRIII motif sequences nevertheless occur on a background of diverse lineages suggesting that it is the segmental motif, rather than the allele per se which is trans-specific in origin. Sequences within the first hypervariable region (codons 7-14) identified lineage assignments to several DRB loci (DRB1, DRB3, DRB4, DRB5, DRB6 and DRB7), although a large number of DRB nucleotide sequences did not correspond to a defined allelic motif, suggesting that many of the nonhuman sequences lack human HVRI homologs and have accumulated additional intraspecies variation subsequent to speciation. While there are certain allelic lineages in HVRI that show trans-species conservation, other sequence motifs seem purely species-specific. These differences suggest that HVRI and HVRIII regions have distinct mechanisms for maintenance of trans-specific sequence elements, with different evolutionary histories for segmental nucleotide conservation.

Alleles↗
PubMed1992

Major-histocompatibility-complex DRB genes of a New-World monkey, the cottontop tamarin (Saguinus oedipus).

The DRB region of the human and great-ape major histocompatibility complex displays not only gene but also haplotype polymorphism. The number of genes in the human DRB region can vary from one to four, and even greater variability exists among the DRB haplotypes of chimpanzees, gorillas, and orangutans. Accumulating evidence indicates that, like gene polymorphism, part of the haplotype polymorphism predates speciation. In an effort to determine when the gene haplotype polymorphisms emerged in the primate lineage, we sequenced three cDNA clones of the New-World monkey, the cottontop tamarin (Saguinus oedipus). We could identify two DRB loci in this species, one (Saoe-DRB1) occupied by apparently functional alleles (*0101 and *0102) which differ by only two nucleotide substitutions and the other (Saoe-DRB2) occupied by an apparent pseudogene. The Saoe-DRB2 gene contains an extra sequence derived from the 3' portion of exon 2 and placed 5' to this exon. This sequence contains a stop codon which makes the translation of the bulk of the Saoe-DRB2 gene unlikely. Preliminary Southern blot hybridization analysis with probes derived from these two genes suggests that both the DRB gene polymorphism and the haplotype polymorphism in the cottontop tamarin may be low. In most individuals the DRB region of this species probably consists of three genes. Comparisons of the Saoe-DRB sequences with those of other primates suggest that probably all of the DRB genes found until now in the Catarrhini were derived from a common ancestor after the separation of the Catarrhini and Platyrrhini lineages. The extant DRB gene and haplotype polymorphism may therefore have been founded in the mid-Oligocene some 33 Mya.

Amino Acid Sequence↗
PubMed2004

Speciation in the large-spored Metschnikowia clade and establishment of a new species, Metschnikowia borealis comb. nov.

The reproductive boundaries among species in the large-spored Metschnikowia clade were studied by prototrophic recombinant selection, electrophoretic karyotyping, mitochondrial DNA restriction analysis, and DNA sequence analysis. Inviable ascospores arose from crosses between the two varieties of Metschnikowia continentalis, indicating that they should be recognized as separate species. Prototrophic recombinants were recovered from crosses between auxotrophic mutants of Metschnikowia borealis, M. continentalis, Metschnikowia lochheadii, Metschnikowia sp. UWO(PS)00-154.1, and Candida ipomoeae, showing that some genetic exchange is possible in spite of the sterility of the asci formed in interspecific crosses. Metschnikowia hawaiiensis, although capable of ascus formation when its h(-) mating type is crossed with the h(+) mating type of the other species, did not give rise to recombinants. In the other species, some recombinants acquired the ability to form asci directly from single cells. These often contained the chromosomes of both parents, suggesting formation of allodiploid hybrids. Other recombinants behaved as haploids and were similar to one parent except for having inherited the selectable wild-type allele from the other parent. In most, but not all cases, inheritance of the mitochondrial genome was uniparental and correlated with the inheritance of the nuclear chromosome complement. In some cases, what appeared to be a recombinant mitochondrial genome was observed. Phylogenies derived from the sequences of various DNA regions were not congruent, indicating that hybridization may have taken place in nature as the large-spored species diverged from their common ancestor. Further evidence that C. ipomoeae arose from a natural recombination event was obtained, but a pair of Metschnikowia species that might represent derived forms of the parents could not be identified conclusively. C. ipomoeae and most of its closely related Metschnikowia species contained a group-II intron in the mitochondrial small-subunit ribosomal gene. The intron was absent in M. borealis, M. hawaiiensis, and other species in the genus Metschnikowia.

Candida↗
PubMed2025

Strong but diffuse genetic divergence underlies differentiation in an incipient species of marine stickleback.

Understanding how lineages proceed along the "speciation continuum" and how species boundaries are maintained over time remain central questions in evolutionary biology. Populations early in the speciation process can give us detailed insight into the reproductive barriers that first initiate speciation. In this study, we explore the nature of genomic divergence between two sympatric marine stickleback ecotypes from Atlantic Canada, "whites" and "commons". Males of each ecotype exhibit distinct nuptial colorations, nesting habits, and parental care strategies. Using population genomic analyses of SNPs and copy number variants (CNVs; deletions and duplications) we show that whites and commons consistently form distinct populations. We uncover genomic differentiation in the white ecotype characteristic of an incipient species, showing extremely low genome-wide differentiation (FST) and very recent divergence (~1 kya). Demographic analysis detected very low levels of ongoing gene flow between populations. Our results and prior genomic studies suggest that reproductive isolation is being maintained between ecotypes despite recent evidence that hybridization in nature does occur. Contrary to other systems, we found many small, but dispersed regions of high differentiation throughout the genome rather than explicitly within chromosomal inversions or the sex chromosomes. On chromosomes VII and XVI, we identified CNVs overlapping genes enriched for olfaction, which may play a role in differences in reproductive strategies between ecotypes. Ultimately, our results demonstrate that genome-wide rather than localized differences can underlie the early stages of divergence, and that this pattern is corroborated by both SNPs and CNVs.

Copy Number Variation↗