Tibayrenc M
UMR CNRS/ORSTOM 9926, ORSTOM, Montpellier, France.
Annu Rev Microbiol. 1996;50:401-29. doi: 10.1146/annurev.micro.50.1.401.
I propose here that evolutionary genetics, apart from improving our basic knowledge of the taxonomy and evolution of microbes (either eukaryotes or prokaryotes), can also greatly contribute to applied research in microbiology. Evolutionary genetics provides convenient guidelines for better interpreting genetic and molecular data dealing with microorganisms. The three main potential applications of evolutionary genetics in microbiology are (a) epidemiological follow-up (with the necessity of evaluating the stability of microbial genotypes over space and time); (b) taxonomy in the broad sense (better definition and sharper delimitation of presently described taxa, research of hidden genetic subdivisions); and (c) evaluation of the impact of the genetic diversity of microbes on their relevant properties (pathogenicity, resistance to drugs, etc). At present, two main kinds of population structure can be distinguished in natural microbial populations: (a) species that are not subdivided into discrete phylogenetic lineages (panmictic species or basically sexual species with occasional bouts of short-term clonality fall into this category); (b) species that are strongly subdivided by either cryptic speciation or clonal evolution. Improvements in available statistical methods are required to refine these distinctions and to better quantify the actual impact of gene exchange in natural microbial populations. Moreover, a codified selection of markers with appropriate molecular clocks (in other words: adapted levels of resolution) is sorely needed to answer distinct questions that address different scales of time and space: experimental, epidemic, and evolutionary. The problems raised by natural genetic diversity are very similar for all microbial species, in terms of both basic and applied science. Despite this fact, a regrettable compartmentalization among specialists has hampered progress in this field. I propose a synthetic approach, relying on the statistical improvements and technical standardizations called for above, to settle a unified evolutionary genetics of microorganisms, valid whatever the species studied, whether eukaryotic (parasitic protozoa and fungi) or prokaryotic (bacteria). Apart from benefits for basic evolutionary research, the anticipated payoff from this synthetic approach is to render routine and common-place the use of microbial evolutionary genetics in the fields of epidemiology, medicine, and agronomy.
我在此提出，进化遗传学除了能增进我们对微生物（真核生物或原核生物）分类学和进化的基础知识外，还能极大地促进微生物学的应用研究。进化遗传学为更好地解读与微生物相关的遗传和分子数据提供了便利的指导方针。进化遗传学在微生物学中的三个主要潜在应用是：（a）流行病学追踪（有必要评估微生物基因型在空间和时间上的稳定性）；（b）广义的分类学（对当前描述的分类单元进行更好的定义和更精确的界定，研究隐藏的遗传亚群）；以及（c）评估微生物遗传多样性对其相关特性（致病性、耐药性等）的影响。目前，在自然微生物群体中可区分出两种主要的群体结构：（a）未细分为离散系统发育谱系的物种（泛交物种或基本为有性繁殖、偶尔有短期克隆现象的物种属于此类）；（b）因隐秘物种形成或克隆进化而强烈细分的物种。需要改进现有的统计方法，以完善这些区分，并更好地量化基因交换在自然微生物群体中的实际影响。此外，迫切需要对具有适当分子钟（换句话说：适应的分辨率水平）的标记进行编码选择，以回答涉及不同时间和空间尺度的不同问题：实验性、流行性和进化性问题。就基础科学和应用科学而言，自然遗传多样性所引发的问题在所有微生物物种中都非常相似。尽管如此，专家之间令人遗憾的划分阻碍了该领域的进展。我提议采用一种综合方法，依靠上述所需的统计改进和技术标准化，来建立统一的微生物进化遗传学，无论所研究的物种是真核生物（寄生原生动物和真菌）还是原核生物（细菌），该方法都适用。除了对基础进化研究有益外，这种综合方法预期的回报是使微生物进化遗传学在流行病学、医学和农学领域的应用变得常规和普遍。
