Trees within trees: genes and species, molecules and morphology.

摘要: The construction and interpretation of gene trees is fundamental in molecular system- atics. If the defined a historical (coalescent) sense, there can be multiple within single contiguous set nucleotides, attempts to construct tree for such sequence must deal with homoplasy created by conflict among divergent histories. On larger scale, incongruence expected topologies at different loci individuals sexually reproducing species, it has been suggested that this discordance used delimit species. A practical concern topological methods polymorphisms may maintained through numerous cladogenic events; polymorphism problem less nontopological approaches species delimitation using data. Although central theoretical systematics between given true "species tree," primary empirical faced reconstructing taxic phylogeny inferred from sequences. Linkage relationships limit char- acter independence thus have important implications handling data sets phy- logenetic analysis, particularly level, where histori- cally associated expected. Gene also reconstructed influence phenotypic characters, but best tenuous relationship trees. Nevertheless, expression patterns orthology genes involved phenotypes theory provide criteria homology assessment morphological characters. (Gene trees; homoplasy; linkage; morphology; orthology; phylogeny; delimitation.) Page (1993, 1994) summarized several ways which one hierarchical level "include" historically lower level. lowest organizational lev- el, gene, are discussed here. systematics, i.e., generally. use trees, constructed DNA variation individual genetic loci, infer phylogenies taxa bearing those genes. As such, lit- tle more than collections nu- cleotides, each assumed an indepen- dent representative character organismal reconstruction. fact systematists speaking "gene trees" all distinguishing them rep- resents significant advance over earlier— not long past—ways thinking about mo- lecular systematics. full distinction, necessitated taxo- nomic often overlap- ping biological processes, still being elucidated remain incorporated into day-to-day work Two aspects "inclusion" involve explored first flow, organisms brings together lineages become his- torically as united combinations genomes organisms. levels involved: higher organism. presence al- leles locus provides substrate effective recombination. Within contigu- ous nucleotides composing struc- tural recombination produce new alleles phylogenetic mosaics, construction. Above el recombinational mecha- nisms (crossing over, conversion, in- dependent assortment) permit evolve independently poten- tially track An im-