"Genetics of development, fitness, and life-history variability in salmonid fishes"

全基因组复制（WGD）事件（每个细胞中的所有染色体经历完全加倍以产生一组完全相同的基因）现在被认为是动物和植物进化变化的潜在加速器。由WGD产生的新基因的命运各不相同，但大多数复制的拷贝似乎注定了基因沉默。最近的证据表明，这一过程不是随机的，因为调节早期发育的基因具有多功能特性，而那些参与疾病防御的基因可能更不易丢失。我的研究考察了一类被称为保守非编码元件（CNE）的DNA元件的分布。CNE调节早期发育基因的表达，并且在所有脊椎动物物种中高度保守。因此，这些可能是启动和影响脊椎动物发育程序的一些最重要的因素。我研究了CNE和功能基因在鲑科鱼类（鳟鱼、鲑鱼、鲑）基因组中重复染色体的分布和保留。我这样做是因为鲑科是最近在其祖先中经历过WGD事件的脊椎动物群体，我们有可用的基因组资源来研究WGD事件的后果。在鲑科鱼类体内的所有染色体中，我们发现有一对祖先染色体对它们的生活史和生长有很大的影响。由于这些鱼的WGD事件，我们可以确定这对鱼的“A”和“B”组。在某些物种中，染色体组A似乎对生活史变异（即雌性产卵的时间、雄性成熟的时间以及鱼类发育的速度等）具有更大的调节作用，而染色体组B在其他物种中则更强大。我的研究通过检查基因和CNE在这些重复染色体上的保留和分布，以及每个重复组是否对研究物种中的基因表达有不同的影响，来询问为什么会这样。这项研究将从根本上增强我们对多倍体作为一种塑造进化和物种形成的力量的认识。

Whole genome duplication (WGD) events (where all the chromosomes in each cell undergo a complete doubling to give rise to a completely identical set of genes) are now recognized as being potential accelerators of evolutionary change in animals and plants. The fates of new genes that arise from WGD are varied, but most duplicated copies appear destined for gene silencing. Recent evidence suggests that this process is not random, in that genes regulating early development, with multifunctional properties, and those involved in disease defense may be more refractory to gene loss. My research examines the distribution of a class of DNA elements known as conserved non-coding elements (CNE). CNE regulate the expression of early development genes and are highly conserved across all vertebrate species. Hence these may be some of the most important elements that initiate and influence the developmental programs of vertebrates. I study the distribution and retention of CNE and functional genes across the duplicated chromosomes in the genomes of salmonid fishes (trout, salmon, charr). I do this because salmonids are the most recent vertebrate group to have undergone a WGD event in their ancestry, and for which we have the genomic resources available to study the consequences of WGD events. Of all the chromosomes in the bodies of salmonid fishes, there is one ancestral chromosome pair we have discovered that strongly influences their life-history and growth. Because of the WGD event in these fishes we can identify an 'A' and 'B' group for this pair. Chromosome set A appears to have greater regulatory effects on life-history variation (i.e., the timing of when females spawn, males mature, and how fast fish develop, etc.) in some species, while chromosome set B is more powerful in other species. My research asks why this should be so, by examining the retention and distribution of genes and CNE on these duplicated chromosomes, and whether each duplicated set differentially influences gene expression among the study species. This research will fundamentally enhance our knowledge of polyploidy as a force shaping evolution and speciation.