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

9981987泰勒与加州大学伯克利分校的同事大卫雅各布森博士合作，约翰泰勒博士旨在通过使用多个基因谱系的一致性来诊断系统发育物种，从而挑战丝状真菌脉孢菌（子囊菌）中现有的生物学和形态学物种概念。同时，他们将通过脉孢菌属物种之间的实验交配来完善当前的生物物种概念（BSC）。最近在泰勒的基因系谱一致性诊断真菌物种的实验室的研究发现，在形态学定义的物种遗传隔离的物种，就像已经与实验交配的情况。在一种情况下，由于交配行为而被置于单个物种中的真菌分类成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）诊断自然界中遗传隔离的物种，BSC也是如此，但它可以适用于所有真菌，无论它们是否表现出有性生殖（许多不），形态学物种概念也是如此。选择脉孢菌作为发育和进化生物学中广泛使用的模式生物，是基于四个主要原因。1)这13个已知的物种表现出在整个真菌中看到的生殖行为的范围，包括远系繁殖（异宗配合），自交（同宗配合），以及两者的混合物。2)这些远系繁殖的物种从一开始就被诊断为生物物种，美国国家科学基金会资助的真菌遗传学储备中心有4,600多个个体，每个个体都通过交配测试被分配到物种中。3)将个体分配到生物物种的交配测试并不总是明确的，并且需要一组以上的“测试者”来适应在N. crassa和N.中间的这种变化表明脉孢菌的BSC可能是将遗传隔离的群体（或谱系）集中在一起。4)初步的分子系统发育研究表明，基因流可能发生在该属的一些生物物种，进一步质疑的交配测试为基础的BSC的适用性。利用GenBank和脉孢菌基因组计划中丰富的真菌DNA序列信息，研究人员将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，跟踪五个主要染色体。系统发生树可以分别为每个基因构建，然后组合;所有五个区域的同时分析揭示了由于遗传隔离后的谱系排序而导致的所有五个单基因树共有的基底分支，而末端分支之间的冲突（在共识树中产生多分裂）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了物种边界，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.