Divergence of X-linked trans regulatory proteins and the misexpression of gene targets in sterile Drosophila pseudoobscura hybrids

Background The genetic basis of hybrid incompatibilities is characterized by pervasive cases of gene interactions. Sex chromosomes play a major role in speciation and X-linked hybrid male sterility (HMS) genes have been identified. Interestingly, some of these genes code for proteins with DNA binding domains, suggesting a capability to act as trans-regulatory elements and disturb the expression of a large number of gene targets. To understand how interactions between trans- and cis-regulatory elements contribute to speciation, we aimed to map putative X-linked trans-regulatory elements and to identify gene targets with disrupted gene expression in sterile hybrids between the subspecies Drosophila pseudoobscura pseudoobscura and D. p. bogotana. Results We find six putative trans-regulatory proteins within previously mapped X chromosome HMS loci with sequence changes that differentiate the two subspecies. Among them, the previously characterized HMS gene Overdrive (Ovd) had the largest number of amino acid changes between subspecies, with some substitutions localized within the protein’s DNA binding domain. Using an introgression approach, we detected transcriptional responses associated with a sterility/fertility Ovd allele swap. We found a network of 52 targets of Ovd and identified cis-regulatory effects among target genes with disrupted expression in sterile hybrids. However, a combined analysis of polymorphism and divergence in non-coding sequences immediately upstream of target genes found no evidence of changes in candidate regulatory proximal cis-elements. Finally, peptidases were over-represented among target genes. Conclusions We provide evidence of divergence between subspecies within the DNA binding domain of the HMS protein Ovd and identify trans effects on the expression of 52 gene targets. Our results identify a network of trans-cis interactions with possible effects on HMS. This network provides molecular evidence of gene × gene incompatibilities as contributors to hybrid dysfunction.

Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila

Y chromosomes of many species are gene poor and show low levels of nucleotide variation, yet often display high amounts of structural diversity. Dobzhansky cataloged several morphologically distinct Y chromosomes in Drosophila pseudoobscura that differ in size and shape, but the molecular causes of their dramatic size differences are unclear. Here we use cytogenetics and long-read sequencing to study the sequence content of polymorphic Y chromosomes in D. pseudoobscura. We show that Y chromosomes differ by almost 2-fold in size, ranging from 30 to 60 Mb. Most of this size difference is caused by a handful of active transposable elements (TEs) that have recently expanded on the largest Y chromosome, with different elements being responsible for Y expansion on differently sized D. pseudoobscura Ys. We show that Y chromosomes differ in their heterochromatin enrichment, expression of Y-enriched TEs, and also influence expression of dozens of autosomal and X-linked genes. Intriguingly, the same helitron element that showed the most drastic amplification on the largest Y in D. pseudoobscura independently amplified on a polymorphic large Y chromosome in D. affinis, suggesting that some TEs are inherently more prone to become deregulated on Y chromosomes.

Testing potential mechanisms of conspecific sperm precedence in Drosophila pseudoobscura

Drosophila pseudoobscura females that co-occur with sister species D. persimilis show elevated fertilization by conspecific sperm when they mate with both a heterospecific and a conspecific male. This phenomenon, known as conspecific sperm precedence (CSP), has evolved as a mechanism to avoid maladaptive hybridization with D. persimilis. In this study, we assessed pericopulatory (during mating) and postcopulatory (after mating) traits in crosses with sympatric or allopatric D. pseudoobscura females and conspecific or heterospecific males to evaluate potential mechanisms of CSP in this system. We observed shorter copulation duration in crosses with sympatric females, but found no difference in quantity of sperm transferred or female reproductive tract toxicity between sympatry and allopatry. Our data also support the hypothesis that parasperm, a short, sterile sperm morph, can protect fertile eusperm from the D. pseudoobscura female reproductive tract, though it is unclear how this might affect patterns of sperm use in sympatry vs. allopatry. Overall, these results suggest that copulation duration could potentially contribute to the elevated CSP observed in sympatry.

“…this Brazilian venture…” A brief biography of Theodosius Dobzhansky before he arrived in Brazil

This paper describes life and career of Theodosius Dobzhansky (1900-1975) until he arrived in Brazil in 1943. During his years in Russia, Dobzhansky began his entomology studies and undertook research expeditions to Central Asia to study livestock, which focused on speciation biology. Once he arrived in the United States Dobzhansky began working with Drosophila melanogaster with Thomas Hunt Morgan (1866-1945) at Columbia University. Once Morgan relocated to the California Institute of Technology (Caltech), Dobzhansky started collaborating with his colleague, Alfred Henry Sturtevant (1891-1970), on studies of a wild cousin of Drosophila melanogaster, Drosophila pseudoobscura. Dobzhansky and Sturtevant’s friendship and collaboration suffered due to several factors, including most importantly, their differing approaches to Drosophila pseudoobscura as influenced by their different conceptions of the purpose of their work. While Sturtevant studied the flies using the same techniques as his studies of the domestic Drosophila melanogaster, Dobzhansky studied Drosophila pseudoobscura in the field considering his broader dictum that “Nothing in biology makes sense except in the light of evolution.”

Cambios en las frecuencias de inversiones cromosómicas en poblaciones experimentales de Drosophila pseudoobscura

Se determinaron las fluctuaciones temporales en cuatro poblaciones experimentales de Drosophila pseudoobscura; a partir de cromosomas politénicos se determinaron los genotipos y frecuencias relativas durante 4-6 muestreos mensuales Poblaciones de ésta especie muestran 2-3 inversiones principales con frecuencias conjuntas del 90% del total y de 4-7 secundarias que completan la muestra. Los cambios se presentan fundamentalmente en los componentes principales, provocando oscilaciones a través del tiempo. Se obtuvieron los cambios siguientes: población Tulancingo, la inversión TL (Tree Line) pasa de 54 a 70% y su contraparte CU (Cuernavaca) de 34 a 17%. Población Zirahuén, SC (Santa Cruz) de 34 a 36%, TL de 25 a 30% y CU de 23 a 5% y de los secundarios OA (Oaxaca) de 10 a 5% y EP (Estes Park) de 3 a 12%. Población Xochimilco CU de 51 a 16%, TL de 33 a 44%, EP de 8 a 10% con un máximo intermedio de 17% y OL (Olympic) de 1 a 18%. Población Nevado de Colima SC de 65 a 45% con oscilación máxima de 74%, TL de 20 a 29% y un mínimo de 16%, OL de 5 a 17%. En general en las cuatro poblaciones el resto de las inversiones secundarias fluctuaron en promedio dos por ciento.

Identifying genomic markers associated with female re-mating rate in Drosophila pseudoobscura by replicated bulk segregant analysis

ABSTRACTIdentifying loci associated with a phenotype is a critical step in many evolutionary studies. Most methods require large sample sizes or breeding designs that can be prohibitively difficult. Here we apply a rarely used approach to identify SNP loci associated with a complex phenotype. We mate siblings from isofemale lines isolate genotypes from three wild populations. After phenotyping we perform whole genome sequencing of isofemale lines from the extremes of the phenotypic distribution of each population and identify SNPs that are consistently fixed for alternative alleles across line pairs. The focal phenotype is female remating rate in the fly Drosophila pseudoobscura, defined as the willingness of a female to mate with a second male after her first mating. This is an integral part of mating system evolution, sexual selection and sexual conflict, and is a quantitative polygenic trait.About 200 SNPs are consistently fixed for alternate alleles in the three pairs of isofemale lines. We use different simulation approaches to explore how many SNPs would be expected to be fixed. We find the surprising result that we uncover fewer observed fixed SNPs than are expected by either simulation approach. We also complete functional analyses of these SNPs. Many lie near genes or regulatory regions known to be involved in Drosophila courtship and mating behaviours, and some have previously been associated with re-mating rates in Genome-Wide Association Studies. Given the small sample size, these results should be treated with caution. Nevertheless, this study suggests that even from a relatively small number of isofemale lines established from wild populations, it is possible to identify candidate loci potentially associated with a complex quantitative trait. However, further work is required to understand modelling the expected distribution of differences.