Recombination rate in Drosophila species shapes the impact of selection in the genome and is positively correlated with nucleotide diversity.

The proximal or core promoter of a typical eukaryotic protein coding gene comprises distinct elements, TATA and/or initiator (Inr). The existence of TATA or Inr at the core promoter suggests that the mechanism of transcription initiation mediated by these two genetic elements may be different. Accordingly, it has been demonstrated that the transcriptional requirements for the TATA-containing, Inr-less ( Transcription initiation of protein coding genes is brought about by RNA polymerase II and a set of general transcription initiation factors (1-3). These factors, in a combinatorial fashion, can direct transcription initiation of a variety of eukaryotic promoters in an in vitro assay (1-3). The core promoter region of a typical eukaryotic gene consists of a TATA box and/or an Inr 1 element (4, 5). The presence of distinct core promoter elements in different genes suggests distinct transcriptional strategies. However, the differences in mechanism of transcriptional initiation mediated by TATA or Inr elements have yet to be elucidated. Biochemical complementation assays employing heat-treated nuclear extracts have demonstrated that the transcription factor requirements for a TATA ϩ InrϪ promoter are different from a TATA Ϫ Inr ϩ promoter (6). The TATA-binding transcription factor complex TFIID is required for both promoters (7), and heat treatment of nuclear extracts (at 49°C for 15 min) renders the TFIID inactive (6, 8). Hence, a heat-treated nuclear extract was incapable of transcribing either a TATAcontaining or a TATA-less promoter unless supplemented with exogenous TFIID (6). Exogenously added TFIID could restore only a TATA ϩ Inr Ϫ promoter activity but not a TATA Ϫ Inr ϩ promoter activity, suggesting that in addition to TFIID, another heat-sensitive component(s) was required for the TATA Ϫ Inr ϩ promoter (6). The mechanism of action of this component is unclear. Because TFIID is required for a TATAless promoter, it is possible that such a factor may serve to anchor TFIID to a TATA (16), and a member of the TBP-associated factors (TAF;6,(17)(18)(19)(20), although other studies have suggested that a TAF may not bind directly to an Inr element (21). However, these observations may not be mutually exclusive. The differences possibly indicate redundancy in Inr element-mediated interactions, which may be condition-and/or promoter context-dependent. In addition, it is possibile that structurally (and perhaps functionally) different classes of Inr elements exist.We wish to elucidate the molecular mechanisms of transcription initiation mediated via an Inr element in TATA Ϫ Inr ϩ promoters. Here, we report that TFII-I (10 -12) is necessary for transcription of a naturally occurring TATA Ϫ Inr ϩ but not for a TATA ϩ Inr Ϫ promoter. For our analyses, we have used the T cell receptor variable region-derived (V␤) promoter (22) Inrϩ V␤ promoter. In each case we have selectively blocked the transcription of the V␤ promoter and subsequently restored its transcriptional activity by exogenous addition of purified TFII-I. We ...

While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of Drosophila pseudoobscura from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape.Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a QST-FST analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read wholegenome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations (2) interpopulation differences in recombination rate may be the result of local adaptation, and (3) the observed variation among individuals in recombination rate is primarily driven by global regulators of crossover rate, with little detected variation in recombination rate among strains across specific tracts of individual chromosomes.

25One of the most influential observations in molecular evolution has been a strong association between 26 regional recombination rate and amount of nucleotide polymorphism in those genomic regions, 27 interpreted as evidence for ubiquitous natural selection. The alternative explanation, that recombination is 28 mutagenic, has been rejected by the absence of a similar association between regional recombination rate 29 and nucleotide divergence between species. However, many recent studies show that recombination rates 30 are often very different even in closely related species, questioning whether an association between 31 recombination rate and divergence between species has been tested satisfactorily. To circumvent this 32 problem, we directly surveyed recombination across approximately 43% of the D. pseudoobscura 33 physical genome in two separate recombination maps, and 31.3% of the D. miranda physical genome, 34 and we identified both global and local differences in recombination rate between these two closely 35 related species. Using only regions with conserved recombination rates between and within species and 36 accounting for multiple covariates, our data support the conclusion that recombination is positively 37 related to diversity because recombination modulates hitchhiking in the genome. Finally, our data show 38 that diversity around nonsynonymous substitutions is recovered at closer distances in areas of higher 39 recombination than in areas of lower recombination -empirically demonstrating that recombination rate 40 can limit the size and severity of potential selective sweeps. 41 42 Nature Precedings :

Fine scale meiotic recombination maps have uncovered a large amount of variation in crossover rate across the genomes of many species, and such variation in mammalian and yeast genomes is concentrated to <5kb regions of highly elevated recombination rates (10–100x the background rate) called “hotspots.” Drosophila exhibit substantial recombination rate heterogeneity across their genome, but evidence for these highly-localized hotspots is lacking. We assayed recombination across a 40Kb region of Drosophila pseudoobscura chromosome 2, with one 20kb interval assayed every 5Kb and the adjacent 20kb interval bisected into 10kb pieces. We found that recombination events across the 40kb stretch were relatively evenly distributed across each of the 5kb and 10kb intervals, rather than concentrated in a single 5kb region. This, in combination with other recent work, indicates that the recombination landscape of Drosophila may differ from the punctate recombination pattern observed in many mammals and yeast. Additionally, we found no correlation of average pairwise nucleotide diversity and divergence with recombination rate across the 20kb intervals, nor any effect of maternal age in weeks on recombination rate in our sample.