A Test of Phylogenetic Versus Biological Species Concepts in the Fungus Neurospora

与加州大学伯克利分校的同事David Jacobson博士合作，John Taylor博士的目标是通过利用多个基因谱系的一致性来诊断系统发育物种，挑战丝状真菌Neuropora(子囊菌)中现有的生物学和形态物种概念。同时，他们将通过在脉孢子虫物种之间进行实验配对来完善当前的生物物种概念(BSC)。泰勒实验室的基因谱系一致性诊断真菌物种的最新研究发现，在形态定义的物种中，遗传隔离的物种，就像实验配对一样。在一个案例中，由于交配行为而被放置在单一物种中的真菌至少分为四个在遗传上可区分的系统发育物种。因此，系统发育物种概念(PSC)诊断自然界中遗传隔离的物种，BSC应该如此，但它可以应用于所有真菌，无论它们是否表现出有性繁殖(许多没有)，形态物种概念也是如此。脉孢子虫是一种在发育和进化生物学中被广泛用作模式的生物，选择它是基于四个主要原因。1)这13个已知物种表现出在真菌中所见的生殖行为的范围，包括异交(异交)、自交(同源)以及两者的混合。2)近亲繁殖物种从一开始就被诊断为生物物种，NSF资助的真菌遗传学种群中心提供了4600多个个体，每个个体都通过交配测试被分配到物种。3)将个体分配给生物物种的交配测试并不总是明确的，而且需要一套以上的“测试器”来适应在粗毛拟青霉和中间拟青霉中发现的变异。这一变异表明，脉孢子菌的BSC可能聚集了遗传上孤立的群体(或谱系)。4)初步的分子系统发育研究表明，该属的一些生物物种之间可能存在基因流动，进一步质疑了基于交配测试的BSC的适用性。利用GenBank和Neuropora Genome Project中丰富的真菌DNA序列信息，研究人员将通过PCR扩增基因区域，检查有用的变异，并构建至少五个基因谱系，追踪五条主要染色体。然后可以分别为每个基因构建系统发育树，然后组合；对所有五个区域的同时分析显示，由于遗传分离后的谱系分类，所有五个单基因树的基本分支是共同的，而末端分支之间的冲突(在共识树中产生的多分割)揭示了遗传隔离物种中个体之间的重组。共有的分支和冲突的分支之间的界面代表物种边界，即世系分离的区域。

9981987Taylor Working with colleague Dr. David Jacobson at University of California-Berkeley, Dr. John Taylor aims to challenge the existing Biological and Morphological Species Concepts in the filamentous fungus Neurospora (Ascomycetes) by using concordance of multiple gene genealogies to diagnose phylogenetic species. In parallel, they will refine the current Biological Species Concept (BSC) via experimental matings among Neurospora species. Recent studies in Taylor's laboratory of gene genealogy concordance to diagnose fungal species have uncovered genetically isolated species within morphologically defined species, just as has been the case with experimental matings. In one case, fungi placed in a single species due to mating behavior sort into at least four genetically distinguishable phylogenetic species. Therefore, the phylogenetic species concept (PSC) diagnoses genetically isolated species in nature, as should the BSC, but it can be applied to all fungi, whether or not they exhibit sexual reproduction (many do not), as can the Morphological Species Concept. The choice of Neurospora, an organism used widely as a model in developmental and evolutionary biology, is based on four major reasons. 1) The 13 known species exhibit the range of reproductive behavior seen throughout fungi, including outbreeding (heterothallic), selfing (homothallic), and mixtures of the two. 2) The outbreeding species have been diagnosed as biological species from the start, and over 4,600 individuals are available from the NSF-funded Fungal Genetics Stock Center, each of them having been assigned to species by mating tests. 3) Mating tests to assign individuals to biological species are not always clear cut, and more than one set of "testers" has been required to accommodate variation found in N. crassa and N. intermedia. This variation suggests that the BSC for Neurospora may be lumping genetically isolated groups (or lineages). 4) Preliminary molecular phylogenetic studies indicate that gene flow may be occurring among some biological species in the genus, further questioning the applicability of the mating-test based BSC. Using the abundant DNA sequence information for fungi in GenBank and the Neurospora Genome Project, the researchers will PCR amplify gene regions, check for useful variation, and construct at least five gene genealogies, tracking the five major chromosomes. Phylogenetic trees can then be constructed for each of the genes individually and then combined; simultaneous analysis of all five regions reveals basal branches common to all five single gene trees due to lineage sorting following genetic isolation, while conflict among terminal branches (with resulting polytomies in the consensus tree) reveals recombination among individuals in genetically isolated species. The interface between the shared branches and the conflicting branches represents the species boundary, the zone of lineage separation.