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

John Taylor博士与加州大学伯克利分校的同事David Jacobson博士合作，旨在通过使用多基因谱系的一致性来诊断系统发育物种，从而挑战丝状真菌神经孢子菌（子囊菌）中现有的生物学和形态学物种概念。同时，他们将通过神经孢子虫物种之间的实验交配来完善目前的生物物种概念（BSC）。最近在Taylor的基因谱系一致性实验室进行的诊断真菌物种的研究发现，在形态学上确定的物种中，遗传上孤立的物种，就像实验交配的情况一样。在一种情况下，真菌由于交配行为被划分为至少四个遗传上可区分的系统发育物种。因此，系统发育物种概念（PSC）诊断自然界中遗传孤立的物种，BSC也是如此，但它可以应用于所有真菌，无论它们是否有性生殖（许多没有），形态学物种概念也可以。神经孢子虫是一种在发育和进化生物学中被广泛用作模型的生物，选择它是基于四个主要原因。1)已知的13种真菌表现出在真菌中所见的生殖行为范围，包括近亲繁殖（异thallic）、自交（homothallic）以及两者的混合。2)外交种从一开始就被诊断为生物物种，在nsf资助的真菌遗传资源中心有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，并且需要不止一组“测试者”来适应在草丛和中间媒介中发现的变异。这种变异表明神经孢子虫的BSC可能集中了遗传上分离的群体（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，这进一步质疑了基于交配测试的平衡计分卡的适用性。利用GenBank和Neurospora Genome Project中丰富的真菌DNA序列信息，研究人员将对基因区域进行PCR扩增，检查有用的变异，并构建至少五个基因谱系，跟踪五个主要染色体。然后可以为每个基因单独构建系统发育树，然后将它们组合起来；同时对所有五个区域的分析显示，由于遗传隔离后的谱系分类，所有五个单基因树的基支都是共同的，而终端分支之间的冲突（在共识树中导致多裂）揭示了遗传隔离物种中个体之间的重组。共享分支和冲突分支之间的界面代表物种边界，即谱系分离区。

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.