Haldane's rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sex-linked loci across the Passerina bunting hybrid zone

Using cline fitting and divergence population genetics, we tested a prediction of Haldane's rule: autosomal alleles should introgress more than z-linked alleles or mitochondrial haplotypes across the Passerina amoena/Passerina cyanea (Aves: Cardinalidae) hybrid zone. We screened 222 individuals collected along a transect in the Great Plains of North America that spans the contact zone for mitochondrial (two genes), autosomal (four loci) and z-linked (two loci) markers. Maximum-likelihood cline widths estimated from the mitochondrial (223 km) and z-linked (309 km) datasets were significantly narrower on average than the autosomal cline widths (466 km). We also found that mean coalescent-based estimates of introgression were larger for the autosomal loci (0.63 genes/generation, scaled to the mutation rate mu) than for both the mitochondrial (0.27) and z-linked loci (0.59). These patterns are consistent with Haldane's rule, but the among-locus variation also suggests many independently segregating loci are required to investigate introgression patterns across the genome. These results provide the first comprehensive comparison of mitochondrial, sex-linked, and autosomal loci across an avian hybrid zone and add to the body of evidence suggesting that sex chromosomes play an important role in the formation and maintenance of reproductive isolation between closely related species.     

Insertional polymorphisms of endogenous feline leukemia viruses

The number, chromosomal distribution, and insertional polymorphisms of endogenous feline leukemia viruses (enFeLVs) were determined in four domestic cats (Burmese, Egyptian Mau, Persian, and nonbreed) using fluorescent in situ hybridization and radiation hybrid mapping. Twenty-nine distinct enFeLV loci were detected across 12 of the 18 autosomes. Each cat carried enFeLV at only 9 to 16 of the loci, and many loci were heterozygous for presence of the provirus. Thus, an average of 19 autosomal copies of enFeLV were present per cat diploid genome. Only five of the autosomal enFeLV sites were present in all four cats, and at only one autosomal locus, B4q15, was enFeLV present in both homologues of all four cats. A single enFeLV occurred in the X chromosome of the Burmese cat, while three to five enFeLV proviruses occurred in each Y chromosome. The X chromosome and nine autosomal enFeLV loci were telomeric, suggesting that ectopic recombination between nonhomologous subtelomeres may contribute to enFeLV distribution. Since endogenous FeLVs may affect the infectiousness or pathogenicity of exogenous FeLVs, genomic variation in enFeLVs represents a candidate for genetic influences on FeLV leukemogenesis in cats.     

Microsatellites in the Karoo scrub-robin, Cercotrichas coryphaeus (Passeriformes: Muscicapinae): isolation and characterization of 13 autosomal and two sex-linked loci

Fifteen polymorphic microsatellites were developed for the Karoo scrub-robin, Cercotrichas coryphaeus. Here we describe and characterize microsatellite variation of 13 autosomal loci and two Z-linked loci in 42 individuals from two distinct South African populations. The number of alleles per locus varied from three to 13 and values of observed heterozygosity ranged from 0.318 to 0.900. These loci will be used to test hypotheses relating to fine-scale social structure and mating strategies in this cooperatively breeding species.     

PERMANENT GENETIC RESOURCES: Isolation, characterization and multiplex genotyping of 11 autosomal and four sex-linked microsatellite loci in the reed bunting, Emberiza schoeniclus (Emberizidae, Aves)

Fifteen highly polymorphic microsatellite loci were characterized in the reed bunting, Emberiza schoeniclus. Eleven loci were autosomal and four linked to the Z chromosome. All loci were characterized and tested in 45 unrelated reed buntings from a Swiss population. Autosomal loci displayed seven to 17 and sex-linked loci displayed four to 13 alleles with heterozygosities ranging from 0.756 to 0.933 and from 0.478 to 0.957, respectively. These loci will be used in population genetic and mating system studies of reed buntings.     

Recombination and nucleotide diversity in the sex chromosomal pseudoautosomal region of the emu, Dromaius novaehollandiae

Pseudoautosomal regions (PARs) shared by avian Z and W sex chromosomes are typically small homologous regions within which recombination still occurs and are hypothesized to share the properties of autosomes. We capitalized on the unusual structure of the sex chromosomes of emus, Dromaius novaehollandiae, which consist almost entirely of PAR shared by both sex chromosomes, to test this hypothesis. We compared recombination, linkage disequilibrium (LD), GC content, and nucleotide diversity between pseudoautosomal and autosomal loci derived from 11 emu bacterial artificial chromosome (BAC) clones that were mapped to chromosomes by fluorescent in situ hybridization. Nucleotide diversity (pi = 4N(e)mu) was not significantly lower in pseudoautosomal loci (14 loci, 1.9 +/- 2.4 x 10(-3)) than autosomal loci (8 loci, 4.2 +/- 6.1 x 10(-3)). By contrast, recombination per site within BAC-end sequences (rho = 4Nc) (pseudoautosomal, 3.9 +/- 6.9 x 10(-2); autosomal, 2.3 +/- 3.7 x 10(-2)) was higher and average LD (D') (pseudoautosomal, 4.2 +/- 0.2 x 10(-1); autosomal, 4.7 +/- 0.5 x 10(-1)) slightly lower in pseudoautosomal sequences. We also report evidence of deviation from a simple neutral model in the PAR and in autosomal loci, possibly caused by departures from demographic equilibrium, such as population growth. This study provides a snapshot of the population genetics of avian sex chromosomes at an early stage of differentiation.     

Characterization of polymorphic microsatellite DNA markers in the black-tailed godwit (Limosa limosa: Aves)

We isolated and tested 16 microsatellite loci in black-tailed godwits from the Netherlands (Limosa limosa limosa), and from Australasia (subspecies melanuroides). One locus was monomorphic, two loci had null-alleles and one was significantly heterozygote deficient. The remaining 12 polymorphic loci had on average 7.9 alleles (range 5-11) and the mean expected heterozygosity was 0.69. No significant linkage disequilibrium between the loci was observed and all loci were autosomal. Fourteen loci were successfully cross-amplified in bar-tailed godwit (Limosa lapponica).     

Analysis of 31 STR loci in the genetic isolate of Carloforte (Sardinia, Italy)

The genotypes of 31 autosomal short tandem repeat loci in the population of Carloforte were analyzed, these representing a linguistic and genetic isolate located on the island of Sardinia (Italy). The markers span the entire length of chromosomes 19, 20, 21 and 22. Allele frequencies and statistical parameters were presented for all loci. Observed heterozygosity ranged from 0.279 to 0.884, and polymorphism information content from 0.552 to 0.886. All but two loci showed Hardy-Weinberg equilibrium after Bonferroni correction. The 31 short tandem repeat loci examined in the present work provide additional data on the genetic structure of the Carloforte population.     

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z‐linked sex chromosome loci. Between the two taxa, Z‐linked loci (Φ_ST = 0.088) were 5.2 times more differentiated than autosomal DNA (Φ_ST = 0.017) but comparable to mtDNA (Φ_ST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z‐linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (Φ_ST) and absolute (d_XY) estimates of divergence. In contrast, the ratio of Z‐linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (Φ_ST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.     

Novel locus for autosomal dominant hereditary spastic paraplegia, on chromosome 8q.

Hereditary spastic paraplegia (HSP) is a clinically and genetically heterogeneous group of disorders characterized by insidiously progressive spastic weakness in the legs. Genetic loci for autosomal dominant HSP exist on chromosomes 2p, 14q, and 15q. These loci are excluded in 45% of autosomal dominant HSP kindreds, indicating the presence of additional loci for autosomal dominant HSP. We analyzed a Caucasian kindred with autosomal dominant HSP and identified tight linkage between the disorder and microsatellite markers on chromosome 8q (maximum two-point LOD score 5.51 at recombination fraction 0). Our results clearly establish the existence of a locus for autosomal dominant HSP on chromosome 8q23-24. Currently this locus spans 6.2 cM between D8S1804 and D8S1774 and includes several potential candidate genes. Identifying this novel HSP locus on chromosome 8q23-24 will facilitate discovery of this HSP gene, improve genetic counseling for families with linkage to this locus, and extend our ability to correlate clinical features with different HSP loci.     

Haldane's sieve and adaptation from the standing genetic variation

We consider populations that adapt to a sudden environmental change by fixing alleles found at mutation-selection balance. In particular, we calculate probabilities of fixation for previously deleterious alleles, ignoring the input of new mutations. We find that "Haldane's sieve"--the bias against the establishment of recessive beneficial mutations--does not hold under these conditions. Instead probabilities of fixation are generally independent of dominance. We show that this result is robust to patterns of sex expression for both X-linked and autosomal loci. We further show that adaptive evolution is invariably slower at X-linked than autosomal loci when evolution begins from mutation-selection balance. This result differs from that obtained when adaptation uses new mutations, a finding that may have some bearing on recent attempts to distinguish between hitchhiking and background selection by contrasting the molecular population genetics of X-linked vs. autosomal loci. Last, we suggest a test to determine whether adaptation used new mutations or previously deleterious alleles from the standing genetic variation.     

Genetic data provided by 21 autosomal STR loci from Chinese Tujia ethnic group

The aim of this study was to investigate allelic frequency distribution and forensic genetic parameters of autosomal short tandem repeats (STR) loci of the population samples from 107 Tujia individuals from Chinese Hubei Province. Twenty-one autosomal STR genetic markers (D9S1122, D6S474, D6S1017, D5S2500, D4S2408, D3S4529, D2S441, D2S1776, D22S1045, D20S482, D1S1677, D1S1627, D1GATA113, D19S433, D18S853, D17S1301, D11S4463, D12ATA63, D10S1248, D10S1435 and D14S1434) were simultaneously amplified in a new multiplex polymerase chain reaction system. 155 alleles for all the STR loci from the Tujia population were observed and the corresponding allelic frequencies ranged from 0.005 to 0.589. Expected heterozygosity, polymorphic information content, power of discrimination and power of exclusion of the 21 STR loci in the Tujia population were from 0.579 to 0.824, from 0.525 to 0.802, from 0.773 to 0.945 and from 0.257 to 0.641, respectively. Our results indicate that the autosomal STRs multiplex system provides highly informative STR data and could be useful in forensic individual identification and parentage testing in this region.     

The Influence of Whole-Arm Trisomy on Gene Expression in Drosophila

The biochemical consequences of extensive aneuploidy in Drosophila have been examined by measuring the levels of specific proteins in larvae trisomic for entire chromosome arms. By far the most common effect is a reduction in gene product levels (per gene template) by one-third from the diploid quantity, consistent with the model that concentration-dependent repressors of these loci reside on the duplicated chromosome arms. Most loci appear sensitive to such repression in one or more of the trisomies examined, suggesting that such regulatory loci might be quite common. Repression of gene-product levels in trisomies may significantly contribute to their inviability. Few loci are activated in trisomies implying that most factors necessary for gene expression are in excess. While autosomal trisomies can repress the expression of both X-linked and autosomal loci, X-chromosomal trisomies have little effect on most autosomal genes. A family of genes coding for larval serum proteins do not respond similarly in trisomies, suggesting that regulation operates on a process which is not common to their coordinate regulation. Finally, Adh genes transposed to new chromosomal positions maintain their ability to be repressed in 3L trisomies suggesting that this response to regulation involves a closely linked cis-acting regulatory element.     

Population genetic analysis of 15 autosomal STR loci in the Russian population of northeastern Inner-Mongolia, China

In the present study, we investigated the genetic polymorphisms of 15 autosomal STR loci in the Russian population of northeastern Inner-Mongolia, China as well as its genetic relationships with other populations. DNA typing for 15 autosomal STR loci was performed on 148 randomly selected healthy individuals from the Russian population living in Eerguna, northeastern Inner-Mongolia. Allelic frequencies of these loci were calculated by direct counting. The genotype data of this Russian population was moreover compared to other populations using neighbor-joining method, as such constructing a phylogenic tree. A total of 143 alleles were found in the Russian population with corresponding allele frequencies in the range from 0.0034 to 0.5372. Among all the 15 loci, D18S51 had the highest polymorphism (PIC = 0.8632), whereas TPOX had the lowest (PIC = 0.5179). In the phylogenic tree, this Russian population has a close relationship with the populations of South Siberia and northeastern Asia. This study may increase our understanding of the genetic background of the Russian population in Eerguna, China as such providing useful information for anthropological research, forensic sciences as well as disease-association studies.     

Sex-linked markers facilitate genetic parentage analyses in knobbed whelk broods

To explore the potential of sex-linked polymorphisms for genetic parentage analyses in natural populations, we have employed a recently discovered "X-linked" microsatellite marker (in conjunction with polymorphic autosomal loci) to deduce biological paternity and maternity for large numbers of encapsulated embryos within individual broods of the knobbed whelk (Busycon carica). Empirical findings illustrate how such sex-linked genetic tags can in special instances find at least three novel utilities in genetic dissections of large-clutch species: clarification of paternity assignments that had remained ambiguous from di-locus autosomal data alone; elucidation of linkage relationships among pairs of autosomal loci; and illumination of maternity (and thereby paternity also) in broods for which neither biological parent was known from independent evidence.     

Characterization of 28 microsatellite loci in the European roller Coracias garrulus (Coracidae,AVES)

One hundred and forty-four existing microsatellite avian loci were tested for polymorphism in two to four unrelated European rollers. This allowed the identification of 28 unique polymorphic loci that we characterized in 34 unrelated individuals from a population in Guadix, Spain. The putative chromosomal locations of all the polymorphic loci in European rollers could be assigned based on the location of their orthologues in the assembled zebra finch and chicken genomes. All loci were assigned to autosomes based on predictive mapping and/or the presence of female heterozygotes, except CAM-11 that was assigned to the Z chromosome. By using a selected subset of 15 autosomal loci, the combined non-exclusion probability for identity was 4.7E-09.     

The genetics of hybrid male sterility between the allopatric species pair Drosophila persimilis and D. pseudoobscura bogotana: dominant sterility alleles in collinear autosomal regions

F(1) hybrid male sterility is thought to result from interactions between loci on the X chromosome and dominant-acting loci on the autosomes. While X-linked loci that contribute to hybrid male sterility have been precisely localized in many animal taxa, their dominant autosomal interactors have been more difficult to localize precisely and/or have been shown to be of relatively smaller effect. Here, we identified and mapped at least four dominant autosomal factors contributing to hybrid male sterility in the allopatric species pair Drosophila persimilis and D. pseudoobscura bogotana. Using these results, we tested predictions of reduced recombination models of speciation. Consistent with these models, three of the four QTL associated with hybrid male sterility occur in collinear (uninverted) regions of these genomes. Furthermore, these QTL do not contribute significantly to hybrid male sterility in crosses between the sympatric species D. persimilis and D. pseudoobscura pseudoobscura. The autosomal loci identified in this study provide the basis for introgression mapping and, ultimately, for molecular cloning of interacting genes that contribute to F(1) hybrid sterility.     

Contribution of DFNB1 and DFNB2 loci to neurosensory deafness in affected Tunisian families

Classical studies have demonstrated genetic heterogeneity for nonsyndromic autosomal recessive congenital neurosensory deafness. The first two DFNB1 and DFNB2 locations were found using two consanguineous Tunisian families respectively from north and south. We tested these loci for cosegregation with deafness in twenty four southern families with nonsyndromic presumed congenital sensorineural deafness and a pedigree structure consistent with autosomal recessive inheritance. Only in our families, did deafness cosegregate with DFNB1. Although our families are from the south, none of them showed linkage to DFNB2.     

Contrasting patterns of polymorphism and divergence on the Z chromosome and autosomes in two Ficedula flycatcher species

In geographic areas where pied and collared flycatchers (Ficedula hypoleuca and F. albicollis) breed in sympatry, hybridization occurs, leading to gene flow (introgression) between the two recently diverged species. Notably, while such introgression is observable at autosomal loci it is apparently absent at the Z chromosome, suggesting an important role for genes on the Z chromosome in creating reproductive isolation during speciation. To further understand the role of Z-linked loci in the formation of new species, we studied genetic variation of the two species from regions where they live in allopatry. We analyzed patterns of polymorphism and divergence in introns from 9 Z-linked and 23 autosomal genes in pied and collared flycatcher males. Average variation on the Z chromosome is greatly reduced compared to neutral expectations based on autosomal diversity in both species. We also observe significant heterogeneity between patterns of polymorphism and divergence at Z-linked loci and a relative absence of polymorphisms that are shared by the two species on the Z chromosome compared to the autosomes. We suggest that these observations may indicate the action of recurrent selective sweeps on the Z chromosome during the evolution of the two species, which may be caused by sexual selection acting on Z-linked genes. Alternatively, reduced variation on the Z chromosome could result from substantially higher levels of introgression at autosomal than at Z-linked loci or from a complex demographic history, such as a population bottleneck.     

A New Multiplex Assay of 17 Autosomal STRs and Amelogenin for Forensic Application

This paper describes a newly devised autosomal short tandem repeat (STR) multiplex polymerase chain reaction (PCR) systems for 17 autosomal loci (D1S1656, D2S441, D3S1358, D3S3045, D6S477, D7S3048, D8S1132, D10S1435, D10S1248, D11S2368, D13S325, D14S608, D15S659, D17S1290, D18S535, D19S253 and D22-GATA198B05) and Amelogenin. Primers for the loci were designed and optimized so that all of the amplicons were distributed from 50 base pairs (bp) to less than 500 bp within a five-dye chemistry design with the fifth dye reserved for the sizing standard. Strategies were developed to overcome challenges that encountered in creating the final assay. The limits of the multiplex were tested, resulting in the successful amplification of genomic DNA range from 0.25–4 ng with 30 PCR cycles. A total of 681 individuals from the Chinese Han population were studied and forensic genetic data were present. No significant deviations from Hardy–Weinberg equilibrium were observed. A total of 180 alleles were detected for the 17 autosomal STRs. The cumulative mean exclusion chance in duos (CMEC_D) was 0.999967, and cumulative mean exclusion chance in trios (CMEC_T) was 0.99999995. We conclude that the present 17plex autosomal STRs assay provides an additional powerful tool for forensic applications.