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PubMed2024

Repeated evolution on oceanic islands: comparative genomics reveals species-specific processes in birds.

Understanding the interplay between genetic drift, natural selection, gene flow, and demographic history in driving phenotypic and genomic differentiation of insular populations can help us gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study repeated evolution and identify shared patterns in their genomic landscapes of differentiation. We selected four species of passerine birds (Common Chaffinch Fringilla coelebs/canariensis, Red-billed Chough Pyrrhocorax pyrrhocorax, House Finch  Haemorhous mexicanus and Dark-eyed/island Junco Junco hyemalis/insularis) that have both mainland and insular populations. Changes in body size between island and mainland populations were consistent with the island rule. For each species, we sequenced whole genomes from mainland and insular individuals to infer their demographic history, characterize their genomic differentiation, and identify the factors shaping them. We estimated the relative (Fst) and absolute (dxy) differentiation, nucleotide diversity (π), Tajima's D, gene density and recombination rate. We also searched for selective sweeps and chromosomal inversions along the genome. All species shared a marked reduction in effective population size (Ne) upon island colonization. We found diverse patterns of differentiated genomic regions relative to the genome average in all four species, suggesting the role of selection in island-mainland differentiation, yet the lack of congruence in the location of these regions indicates that each species evolved differently in insular environments. Our results suggest that the genomic mechanisms involved in the divergence upon island colonization-such as chromosomal inversions, and historical factors like recurrent selection-differ in each species, despite the highly conserved structure of avian genomes and the similar selective factors involved. These differences are likely influenced by factors such as genetic drift, the polygenic nature of fitness traits and the action of case-specific selective pressures.

Animals↗
PubMed1976

The frequency and allelism of lethal chromosomes in isolated desert populations of Drosophila pseudoobscura.

Second-chromosome lethals were extracted from four populations of Drosophila pseudoobscura in Southern California. Two of the populations were from desert oases and two from the classic habitat on Mt. San Jacinto, previously studied by Dobzhansky. Allelism tests were made on the lethals within and between all locations. The frequency of lethal second-chromosomes in each location was 0.18, and this was not different from the results of other workers for samples throughout the species range. Interpopulational allelism rates were about 0.005, and not different from earlier results of Dobzhansky. Intrapopulational rates in this study were, with one exception, the same as the interpopulational rates, and significantly lower than Dobzhansky found using the third chromosome. This may be due to lethals being linked with heterotic third-chromosome inversions. The allelism rate of the exceptional population (about 0.03 and equal to Dobzhansky's intrapopulational results) may be due to heterotic lethals, or a founder effect. Two lethals were found in three populations each, possibly due to migration among these populations, which are up to 334 km apart.

Alleles↗
PubMed2001

Chromosomal distribution of the transposable elements Osvaldo and blanco in original and colonizer populations of Drosophila buzzatii.

Chromosomal distribution of transposable elements (TEs) Osvaldo and blanco in D. buzzatii was studied in three original natural populations from Argentina (Berna, Puerto Tirol and La Nostalgia) and a colonizer population from the Iberian Peninsula (Carboneras). The Spanish population showed significant differences for Osvaldo and blanco copy numbers when we compared the X chromosome and the autosomes; but it is mainly the accumulation of copies in chromosome 2, where most sites with high insertion frequency were located, that causes the discrepancy with the negative selection model. We found no significant differences in TE frequency between chromosomal regions with different exchange rates, and no evident accumulation of TE was detected within chromosomal inversions where recombination rate is reduced. The Carboneras population shows euchromatic sites of Osvaldo and blanco with high occupancy and others with low copy number. On the contrary, Argentinian populations show only a generalized low occupancy per insertion site. Moreover, the mean copy number of both elements is higher in Spain than in Argentina. All these results suggest an important role of the colonization process in the distribution of TEs. The increase in the copy number of the TEs analysed and their elevated frequency in some chromosomal sites in Carboneras is, most probably, a sequel of the founder event and drift that took place at the time of the colonization of the Old World by D. buzzatii from the New World some 300 years ago.

Animals↗
PubMed1999

Paracentric inversion of the X chromosome [inv(X)(q12q28)] in familial FG syndrome.

FG syndrome is an X-linked incomplete recessive condition comprising mental retardation, congenital hypotonia, macrocephaly, a distinctive facial appearance, and constipation or anal malformations. Here, we report on a chromosome X inversion [inv(X)(q12q28)] in a boy with FG syndrome and in his mentally retarded maternal uncle, and we discuss the possible involvement of this paracentric inversion in the FG syndrome.

Abnormalities, Multiple↗
PubMed2001

Drosophila bipectinata species complex.

The Drosophila bipectinata species complex belongs to the ananassae subgroup of the melanogaster species group (Genus Drosophila, Subgenus Sophophora). The members of the complex are: D. bipectinata, D. parabipectinata, D. malerkotliana, and D. pseudoananassae. Of the four species, D. bipectinata is most widely distributed. Females are indistinguishable, but males are distinguishable by their sex-comb teeth number and pattern and by abdominal colouration. Chromosomal inversions have been detected in these species. In natural populations of D. bipectinata the frequency of inversions and the level of inversion heterozygosity were found to be very low but in laboratory stocks inversions persisted for more than 20 generations due to heterotic buffering. On an average 9.3 fixed interspecific inversions separate each species pair. Non-random association between linked inversions indicated epistatic interaction in natural populations of D. bipectinata. Certain spontaneous mutations were detected and mapped for the first time in D. bipectinata. Low frequency of spontaneous male recombination has also been reported in D. bipectinata. Sexual isolation study in the complex indicated strong preference for homogamic mating. The results also indicated incomplete sexual isolation among different members of this complex. The isolation estimate among six different geographic populations of D. bipectinata ranged from 0.54 - 0.92 representing positive assortative mating which is an evidence for incipient sexual isolation. Incipient sexual isolation was also found within D. malerkotliana and D. parabipectinata . Chromosomal, hybridization and allozyme studies revealed close phylogenetic relationship among the four species of the bipectinata complex. Mitochondrial DNA study revealed net nucleotide difference (delta) between these species to be very small (0.0002 +/- 0.0008) reflecting closeness. Evidence for genetic control of sexual activity and existence of sexual selection in D. bipectinata has been shown on the basis of mating propensity tests carried out on geographic strains, their hybrids and diallel crosses. Significant variation was found among the strains tested with respect to courtship time, duration of copulation and fertility. A positive correlation between duration of copulation and fertility in D. bipectinata was found. Evidence for rare-male mating advantage was also found in D. bipectinata. A positive response to selection for high and low mating activity provided evidence for polygenic control of this phenomenon in D. bipectinata. Bilateral outgrowths on thorax, a unique phenotype, reported for the first time in D. bipectinata has been shown to affect mate recognition ability. Results of the study on pupation site preference (larval behaviour) and oviposition site preference (non-sexual behaviour) have also been included.

Animals↗
PubMed1993

Inversion (X)(p11.4q22) associated with Norrie disease in a four generation family.

We report on a 4-generation family in which Norrie disease occurs together with a pericentric inversion of the X chromosome in all affected males and carrier females. The breakpoint in the short arm of the X chromosome appears to be at the purported location of the Norrie disease gene. This is the second report of an association between Norrie disease and a chromosome aberration involving Xp11, and the first report of a specific gene disruption, thus physical gene location, due to a pericentric chromosome inversion.

Blindness↗
PubMed1990

Inversion polymorphism in Indian natural populations of Drosophila melanogaster.

Six natural populations (three urban and three rural) of Drosophila melanogaster from India were analysed for chromosome inversions, revealing the presence of 19 different paracentric autosomal inversions. One new inversion has also been detected in a laboratory stock established from flies collected from Kerala. In total 20 different paracentric inversions in Indian D. melanogaster have been detected during the present study, and of these, 4 are common cosmopolitans; 2 are rare cosmopolitans; 7 are recurrent endemics; and 7 are unique endemics. The quantitative data clearly show that the urban populations are different from the rural ones with respect to inversion polymorphism.

Animals↗
PubMed2005

Descriptions of members of the Simulium damnosum complex (Diptera: Simuliidae) from southern Africa, Ethiopia and Tanzania.

This paper presents cytotaxonomic details of five populations of the Simulium damnosum complex from South Africa, Swaziland and Ethiopia. The 'Nkusi SW' and 'Pienaars' forms are newly designated members of the complex from South Africa, but the taxonomic rank of an isolate indistinguishable chromosomally from the 'Nkusi' cytoform remains unclear. From Ethiopia two cytoforms were identified, one of which shares two diagnostic chromosome inversions with the cytoform 'Kisiwani' from Tanzania. The second form belongs to S. kaffaense, and is the suspected local vector of Onchocerca volvulus. In addition, a re-analysis of the cytoform 'Kibwezi' from north-eastern Tanzania provided further insights into its population subdivision, and its genetic and morphological characteristics. Cytotaxonomic similarities between 'Kibwezi', S. mengense and S. pandanophilum, along with their biogeography, indicate a relict status of each of these taxa.

Animals↗
PubMed2002

Dose-dependent increase or decrease of somatic intrachromosomal recombination produced by etoposide.

Chromosomal inversions and deletions can occur via somatic intrachromosomal recombination (SICR), a mechanism known to be important in mutagenesis and carcinogenesis. Here, we demonstrate a dose-dependent increase or decrease in SICR inversion frequency both in vivo and in vitro after treatment with etoposide, using the pKZ1 mouse mutagenesis model. pKZ1 mice received a single intraperitoneal injection of etoposide dose ranging from 0.0005 to 50mg/kg. Animals were sacrificed 3 days after treatment and the spleen was analysed for SICR. A significant 1.4-3.1-fold induction of SICR inversion events was detected in pKZ1 mice after treatment with etoposide doses ranging from 0.05 to 50 mg/kg etoposide. However, inversion frequencies after treatment with 0.0005 and 0.005 mg/kg etoposide decreased significantly to 0.67 and 0.43 of the levels observed in control animals, respectively. A pKZ1 mouse hybridoma cell line was exposed to etoposide (1-1000 nM) and a similar pattern of SICR response to that detected in vivo was observed. A significant 2.3-4.6-fold induction of SICR inversions was observed in pKZ1 cells treated with 100 and 1000 nM etoposide. Inversion frequencies after treatment with 1 and 10nM etoposide decreased significantly to 0.31 and 0.5 of the level observed in control cell lines. Our in vitro studies complement our in vivo studies and exclude a kinetic phenomenon as the responsible mechanism of reduction in SICR in response to low dose etoposide. Determination of the exact mechanism and significance of recombination suppression at low doses of etoposide treatment requires further investigation.

Animals↗
PubMed2007

The role of RELN in lissencephaly and neuropsychiatric disease.

Reelin is an extracellular matrix-associated protein important in the regulation of neuronal migration during cerebral cortical development. Point mutations in the RELN gene have been shown to cause an autosomal recessive human brain malformation termed lissencephaly with cerebellar hypoplasia (LCH). Recent work has raised the possibility that reelin may also play a pathogenic role in other neuropsychiatric disorders. We sought, therefore, to define more precisely the phenotype of RELN gene disruption. To do this, we performed a clinical, radiological, and molecular study of a family in whom multiple individuals carry a chromosomal inversion that disrupts the RELN locus. A 6-year-old girl homozygous for the pericentric inversion 46,XX,inv7(p11.2q22) demonstrated the same clinical features that have been previously described in association with RELN point mutations. The girl's brain magnetic resonance imaging (MRI) findings, including pachygyria and severe cerebellar hypoplasia, were identical to those seen with RELN point mutations. Fluorescence in situ hybridization confirmed that one of the breakpoints of this inversion mapped to within the RELN gene, and Western blotting revealed an absence of detectable serum reelin protein. Several relatives who were heterozygous for this inversion were neurologically normal and had no signs of psychotic illness. Our findings demonstrate the distinctive phenotype of LCH, which is easily distinguishable from other forms of lissencephaly. Although RELN appears to be critical for normal cerebral and cerebellar development, its role, if any, in the pathogenesis of psychiatric disorders remains unclear.

Brain↗
PubMed1989

Genomic organization of the human asparagine transfer RNA genes: localization to the U1 RNA gene and class I pseudogene repeat units.

Previously isolated human DNA clones containing asparagine transfer RNA (tRNAAsn) genes have been used to determine the genomic organization of this multigene family in man. One clone also contained a gene for U1 RNA, and so the organization of the two multigene families could be directly compared. The majority, and perhaps all, of the human tRNAAsn genes map to the same chromosome bands as do the U1 RNA true genes and class I pseudogenes located on the short and long arms, respectively, of chromosome 1. These two gene clusters were independently isolated using a somatic-cell hybrid minipanel, and use of repeat-unit DNA polymorphisms showed that one tRNA gene clone maps to the short-arm gene cluster and the other to the long-arm gene cluster. Electron microscopy of heteroduplexes between these two clones showed duplex formation along the proposed region of overlap between them, indicating that the short- and long-arm gene clusters are structurally related. I suggest that the split into two distinct loci was facilitated by a pericentric chromosome inversion. This would have had the effect of positioning the genes currently on the long arm adjacent to the centromeric heterochromatin, perhaps resulting in a "position effect" on transcription of these genes. Restriction fragments of different sizes were found that were common to a majority of repeat units, depending on the restriction enzyme being used. Pulsed-field electrophoresis revealed that fragments of molecular weight of 180 kb were common to each unit (or multiples of units). These fragments also contained U1 RNA gene sequences. I therefore propose that these two gene families are closely linked on repeat units (or multiples of units) of 180 kb in size, which are probably organized in tandem arrays.

Chromosome Inversion↗
PubMed1997

Fusion of splicing factor genes PSF and NonO (p54nrb) to the TFE3 gene in papillary renal cell carcinoma.

We demonstrate that the cytogenetically defined translocation t(X;1)(p11.2;p34) observed in papillary renal cell carcinomas results in the fusion of the splicing factor gene PSF located at 1p34 to the TFE3 helix-loop-helix transcription factor gene at Xp11.2. In addition we define an X chromosome inversion inv(X)(p11.2;q12) that results in the fusion of the NonO (p54nrb) gene to TFE3. NonO (p54nrb), the human homologue of the Drosophila gene NonAdiss which controls the male courtship song, is closely related to PSF and also believed to be involved in RNA splicing. In each case the rearrangement results in the fusion of almost the entire splicing factor protein to the TFE3 DNA-binding domain. These observations suggest the possibility of intriguing links between the processes of RNA splicing, DNA transcription and oncogenesis.

Adolescent↗
PubMed2006

Hyperphagia, severe obesity, impaired cognitive function, and hyperactivity associated with functional loss of one copy of the brain-derived neurotrophic factor (BDNF) gene.

The neurotrophin brain-derived neurotrophic factor (BDNF) inhibits food intake, and rodent models of BDNF disruption all exhibit increased food intake and obesity, as well as hyperactivity. We report an 8-year-old girl with hyperphagia and severe obesity, impaired cognitive function, and hyperactivity who harbored a de novo chromosomal inversion, 46,XX,inv(11)(p13p15.3), a region encompassing the BDNF gene. We have identified the proximal inversion breakpoint that lies 850 kb telomeric of the 5' end of the BDNF gene. The patient's genomic DNA was heterozygous for a common coding polymorphism in BDNF, but monoallelic expression was seen in peripheral lymphocytes. Serum concentration of BDNF protein was reduced compared with age- and BMI-matched subjects. Haploinsufficiency for BDNF was associated with increased ad libitum food intake, severe early-onset obesity, hyperactivity, and cognitive impairment. These findings provide direct evidence for the role of the neurotrophin BDNF in human energy homeostasis, as well as in cognitive function, memory, and behavior.

Adult↗
PubMed1991

Four decades of inversion polymorphism in Drosophila pseudoobscura.

We report data that continue the studies of Dobzhansky and others on the frequencies of third-chromosome inversions in natural populations of Drosophila pseudoobscura in North America. The common gene arrangements continue to be present in frequencies similar to those described four decades ago, and the broad geographic patterns also remain unchanged. There is only one pronounced trend over time: the increase in frequency of the Tree Line inversion in Pacific coast populations.

Animals↗
PubMed1998

Chromosome 18q paracentric inversion in a family with mental retardation and hearing loss.

We report on a mother and child with a paracentric inversion of the long arm of chromosome 18: 46,XX,inv(18)(q21.1q23). The child had findings in common with those seen in 18q- syndrome including: microcephaly, epicanthal folds, midface hypoplasia, and abnormally modeled ears, dermatoglyphic whorls on fingertips, clubfeet, hearing loss, and developmental delay. The mother and several maternal relatives had mild mental retardation and hearing loss. Magnetic resonance imaging of the child's brain showed abnormal myelination. Molecular studies including PCR-based markers for the MBP locus and fluorescent in situ hybridization with a P1 genomic clone on mother and child demonstrated only one copy of the MBP locus (18q23) with the deletion extending beyond the MBP locus. Therefore, the deletion in the MBP region may account for the abnormal myelination seen in the patient. The other clinical findings, including mental retardation and hearing loss in this family, may reflect disruption of distal or proximal genes within the deleted MBP region or at the more proximal breakpoint 18q21.1, and may represent a contiguous gene syndrome. Further study of this family may help define those genes functioning in the MBP region that contribute to the phenotype of 18q- syndrome.

Adult↗