Department of Zoology, University of Cambridge, UK.
BMC Evol Biol. 2010 Nov 29;10:368. doi: 10.1186/1471-2148-10-368.
Protein-coding change is one possible genetic mechanism underlying the evolution of adaptive wing colour pattern variation in Heliconius butterflies. Here we determine whether 38 putative genes within two major Heliconius patterning loci, HmYb and HmB, show evidence of positive selection. Ratios of nonsynonymous to synonymous nucleotide changes (ω) were used to test for selection, as a means of identifying candidate genes within each locus that control wing pattern.
Preliminary analyses using 454 transcriptome and Bacterial Artificial Chromosome (BAC) sequences from three Heliconius species highlighted a cluster of genes within each region showing relatively higher rates of sequence evolution. Other genes within the region appear to be highly constrained, and no ω estimates exceeded one. Three genes from each locus with the highest average pairwise ω values were amplified from additional Heliconius species and races. Two selected genes, fizzy-like (HmYb) and DALR (HmB), were too divergent for amplification across species and were excluded from further analysis. Amongst the remaining genes, HM00021 and Kinesin possessed the highest background ω values within the HmYb and HmB loci, respectively. After accounting for recombination, these two genes both showed evidence of having codons with a signature of selection, although statistical support for this signal was not strong in any case.
Tests of selection reveal a cluster of candidate genes in each locus, suggesting that weak directional selection may be occurring within a small region of each locus, but coding changes alone are unlikely to explain the full range of wing pattern diversity. These analyses pinpoint many of the same genes believed to be involved in the control of colour patterning in Heliconius that have been identified through other studies implementing different research methods.
蛋白质编码变化是导致食蚜蝇蝴蝶适应性翅膀颜色图案变异的一个可能的遗传机制。在这里，我们确定了两个主要的食蚜蝇图案基因座 HmYb 和 HmB 中的 38 个假定基因是否存在正选择的证据。非同义核苷酸与同义核苷酸变化的比值（ω）被用来检测选择，作为识别每个基因座中控制翅膀图案的候选基因的一种方法。
使用来自三个食蚜蝇物种的 454 转录组和细菌人工染色体（BAC）序列进行的初步分析突出了每个区域内的一组基因，这些基因显示出相对较高的序列进化率。该区域内的其他基因似乎受到高度限制，并且没有任何 ω 估计值超过 1。从每个基因座中具有最高平均成对 ω 值的三个基因从其他食蚜蝇物种和品种中扩增出来。由于两个选定的基因 fizzy-like（HmYb）和 DALR（HmB）在物种间的扩增过于发散，因此被排除在进一步分析之外。在其余基因中，HM00021 和 Kinesin 在 HmYb 和 HmB 基因座中分别具有最高的背景 ω 值。在考虑重组后，这两个基因都显示出具有选择特征的密码子的证据，尽管在任何情况下这种信号的统计支持都不是很强。
选择测试揭示了每个基因座中的一组候选基因，表明每个基因座的小区域内可能发生弱定向选择，但仅编码变化不太可能解释翅膀图案多样性的全部范围。这些分析确定了许多相同的基因，这些基因被认为参与了食蚜蝇的颜色图案控制，这些基因是通过其他采用不同研究方法的研究确定的。
