Abstract
Large data sets, with several hundred terminal taxa, are becoming increasingly common in phylogenetic studies, but are proving very difficult to analyze because existing algorithms cannot explore the enormous number of trees efficiently. This article presents the results of an ongoing project to carry out phylogenetic analyses on a data base with 760 terminal taxa, the genera of the grass family (Gramineae), initially scored for more than 400 morphological and anatomical characters. The approach consists of three steps: (1) Using a small number of highly consistent characters, determine which large groups are demonstrably monophyletic and which may be polyphyletic. Treat the large monophyletic groups as single terminal taxa, and focus on the overall structure of the entire group. This results in a tree that links the large monophyletic “black boxes” with smaller basal groups; the latter can then be taken as provisional outgroups. (2) Use the outgroups defined in step 1 to analyze the cladistic structure of the big monophyletic groups, with a much larger set of characters. (3) Use a cladistically-guided sample of basal taxa from each large clade to redo the family-level analysis. Kellogg and Campbell (1987) carried out step 1 for the grass family and defined four monophyletic groups (subfamilies) that were derived from within a highly polyphyletic assemblage of genera. This article reports on step 2, analyses of three of the four monophyletic groups, the pooid clade (184 genera), the bambusoid clade (166 genera), and the Andropogonodae plus Arundinelleae (121 genera). 150–220 characters per clade, a much larger number than commonly used in morphological studies, were chosen from the comprehensive database. The initial descriptions of characters, their division into states, and their application to particular genera were the result of 20 years of work on the family by one of us (LW). Subsequent choice of characters for cladistic analysis was done by the other author (EAK) using only the pattern of variation of the character rather than the morphological descriptor, thus eliminating possible bias from a priori ideas of a character’s value. Each clade was analyzed in two ways, (1) with all terminal taxa for which there were adequate data, and (2) for only mono- and ditypic taxa; the latter analysis was to minimize the effect of possibly polyphyletic genera. In all cases, the reduced data set produced groups similar to those of the entire data set. The bambusoid clade consists of several well-defined subclades corresponding approximately to previously-recognized tribes. The relationships among the subclades are not resolved by these data. The Andro-pogonodae is made up of two major groups, an awned group and an awnless group; the latter includes taxa previously included in the Maydeae and also genera conventionally assigned to the Rottboelliinae. The pooid clade exhibits high homoplasy and no robust cladistic relationships. This is not likely to be caused by problems with generic circumscription, but may reflect extensive lateral gene flow (hybridization), rapid radiation followed by extensive anagenetic change, or true parallelism in morphological characters. The traditional tribes of the Pooideae are, with the exception of the Triticeae, apparently not monophyletic. Morphological cladograms are evaluated in light of data from molecular characters; while the results are generally consistent, there are too few molecular data yet to make meaningful comparisons.
Resumen
Grupos de datos grandes, con varios cientos de taxones terminales, son cada día más comunes en estudios filogenéticos. Sin embargo su análisis ha resultado ser muy difícil dado que los algoritmos existentes no pueden explorar eficientemente el enorme número de árboles. Este artículo presenta los resultados de un proyecto en progreso encaminado a realizar análisis filogenéticos en una base de datos de 760 taxones terminales, los géneros de la familia de las gramíneas, evaluados inicialmente en más de 400 caracteres morfológicos y anatómicos. El procedimiento consiste en tres pasos: (1) Usando un pequeño número de caracteres áltamente consistentes, determinar para cuales grupos grandes existe fuerte evidencia de que estos sean monofiléticos y cuales puedan ser polifiléticos. Considerar los grandes grupos monofiléticos como taxones terminales unitarios, y hacer énfasis en la estructura general del grupo entero. El resultado es un árbol que une las “cajas negras” monofiléticas con grupos basales más pequeños; estos últimos pueden entonces tomarse como grupos externos provisionales. (2) Utilizar los grupos externos definidos en el paso 1 para analizar la estructura cladística de los grupos monofiléticos grandes con un número de caracteres mucho mayor. (3) Utilizar una muestra de taxones basales, inferida cladísticamente, de cada uno de los clados grandes para rehacer el análisis a nivel de familia. Kellogg y Campbell (1987) realizaron el paso 1 para la familia de las gramíneas y definieron cuatro grupos monofiléticos (subfamilias), derivados a partir de un ensamblaje de géneros áltamente polifilético. Este articulo presenta un reporte del paso 2, los análisis de tres de los cuatro grupos monofiléticos: el clado pooide (184 géneros), el bambusoide (166 géneros) y juntas la supertribu Andropogonodae y la tribu Arundinelleae (121 géneros). Unos 150–220 caracteres por clado, un número mucho mayor de lo comúnmente usado en estudios morfológicos, fueron escogidos de la base de datos completa. La description inicial de los caracteres, su división en dos atributos y su aplicación a cada género fue el resultado de 20 años de trabajo en la familia por parte del segundo autor (LW). La subsiguiente selección de caracteres para el análisis cladístico fue llevada a cabo por la primera autora (EAK) utilizando únicamente el patrón de variación del carácter envés de su significado morfológico, eliminando así el posible sesgo proveniente de ideas a priori acerca del valor de un determinado carácter. Cada clado fue analizado de dos maneras, (1) con todos los taxones terminales para los cuales existían datos adecuados, y (2) únicamente con taxones mono- y ditípicos; este ultimo análisis, con el fin de minimizar el efecto de géneros que puedan ser polifiléticos. En todos los casos, la muestra reducida de datos produjo grupos similares a aquellos obtenidos con el juego completo. El clado bambusoide esta compuesto por varios subclados bien definidos, correspondiendo aproximadamente a las subtribus reconocidas en el pasado. No fue posible resolver las relaciones entre los subclados con estos datos. La supertribu Andropogonodae esta compuesta por dos grandes grupos, uno aristado y otro sin aristas; este último incluye taxones anteriormente incluidos en la tribu Maydeae, además de géneros convencionalmente asignados a la subtribu Rottboelliinae. El clado pooide demuestra alta homoplasia y relaciones cladfsticas no robustas. Es muy probable que lo anterior no sea el producto de problemas de circunscripción genérica, sino que puede reflejar, bien sea, un gran flujo genético lateral (hibridización), radiación rápida seguida de cambio genético anagénico extenso, o verdadero paralelismo en caracteres morfológicos. Las tribus tradicionales de la subfamilia Pooideae, exceptuando la tribu Triticeae, aparentemente no son monofiléticas. Los cladogramas morfológicos fueron evaluados a la luz de información proveniente de caracteres moleculares; mientras los resultados son generalmente consistentes, por lo pronto existen muy pocos datos moleculares como para hacer comparaciones significativas. (Translation kindly provided by S. Madriñan.)
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Kellogg, E.A., Watson, L. Phylogenetic studies of a large data set. I. Bambusoideae, Andropogonodae, and Pooideae (Gramineae). Bot. Rev 59, 273–343 (1993). https://doi.org/10.1007/BF02857419
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DOI: https://doi.org/10.1007/BF02857419