miércoles, 12 de marzo de 2008

The phylogeny of Falconidae ¿morphological or molecular? A view from PBS


The phylogenetic analyses are subject to inherent factors related to the nature of the data. Among them, incongruence is found in the obtained topologies because different kinds of data used in the analysis. About clade quality, there are two aspects that are frequently mentioned: support and stability (Brower, 2006).

A measure of node support frequently used is the Bremer support or BS (Bremer, 1994). BS is a statistical parameter of a particular data set and it is quantified as the extra length needed to lose a branch in the consensus of near most parsimonious trees. This approach is based solely on the original data, opposed to the data permutation used in the bootstrap procedures (Bremer, 1994).

There are two forms of calculate BS, the first approach is to find the most parsimonious tree(s) for a given data set, and then examining sets of trees of increasing length (referred to as the ‘‘tree decay’’ method). The second method is by the employment of anticonstraint trees (Bremer, 1994).

An extension based in the Bremer's method is the Partitioned Branch Support or PBS (Baker & DeSalle, 1997; Baker et al., 1998), this approach is used when a data set is divided into partitions (morphological-molecular, gene-gene). PBS first estimates the support to each partition and combined data, and after is possible to estimate incongruence between partitions. So, the overall BS for a given branch is the sum of the BS derived from each of the data partitions for the most parsimonious tree(s).

Falconidae (diurnal raptors) is a family within Falconiformes groups. The phylogenetic relationships of Falconidae have been debated along time because morphological and molecular characters generate different results (Griffiths, 1994, 1997, 1999; Griffiths et al., 2004). The objective of this study is to elucidate the phylogenetic relationships within Falconidae using PBS to estimate the support of different data (morphological and molecular).


15 species representing of Falconidae and two outgroups (Pelecanus onocrotalus and Gampsonyx swainsonii) were chosen. The morphological data were collected from Griffiths (1994, 1999) and molecular sequences from Griffiths (1999) and Griffiths et al. (2004). The RAG-1 sequences were downloaded from GenBank (AY461396 – AY461410, DQ881819 and EF078725). The sequences of specimens were alignment using the software MUSCLE 3.6 (Edgar, 2005). The matrices of costs used in the alignments were generates using TTG version 1.0 (Villabona-Arenas, 2008), available by the author.

The phylogenetic analysis were developed using the software T.N.T. version 1.1 (Goloboff, Farris & Nixon, 2001). Heuristic searches, Bremer Support, and Partitioned Bremer Support were elaborated following the methodologies from Hovenkamp (2005) and Arias et al. (2007). The Partitioned Bremer Support was made using a T.N.T. macro created by Pablo Goloboff (available in http://tux.uis.edu.co/labsist/intro.html). TreeView version 1.6.6 (Page, 1996) was used to view the tree generated.


The phylogenetic analysis using morphological data generates 60 most parsimonious trees of length 45 (Fig. 1), the strict consensus tree is shown in Fig. 2. Nodes that define the various morphological species groups are generally supported by low Bremer support values.

In molecular data (Rag-1) is found one tree (Fig. 3). The resulting groups of this topology were monophyletic, and they were supported in BS. The nodes in molecular topology were different to the results of Griffiths et al. (2004) because the different species (outgroups) used in this analysis. However, the Falco group is recovered in the topology (F. sparverius is not within of Falco group).

In combined analysis generates one most parsimonious tree (Fig. 4). Here, the groups appear supported with a high Bremer Support. In molecular and combined analysis the same nodes were recovered.

There is high incongruence between these two data partitions (Table 1). The results using PBS to estimate the support of partitions indicates that the nodes generated by morphological data were not supported (the PBS in whole nodes of morphological analysis were negatives), so, the Falconid group is collapsed totally. On the other hand, the nodes have a high support in the molecular topology.


The measures of support in Phylogenetic Systematics are appropriates to estimate the fit of different kinds of data in phylogenetic analysis. There are several methods to estimate support, Bremer Support among them. A advantage of BS is a statistical parameter of a particular data set, rather than being an estimate based on pseudoreplicated subsamples of the data (like bootstrapping and jackknifing), and thus is not dependent on the data matching a particular assumed distribution (Brower, 2006).

The poor support in nodes of morphological analysis shows that the syringeal data are not posses phylogenetic signal sufficiently, this phenomenon is due to the amount characters that supported a node are not high related to the characters that are not supported this. So, the node is supported for few characters within matrix. I disagree with Griffiths (1994) who stated that the syringeal characters “can be used to resolve phylogenetic questions at the generic and family levels of the Falconidae”. Also, the syringeal morphology is relatively conservative within genera and there may not be enough variation within speciose genera to resolve relationships (Griffiths, 1994). So, these characters were not highly informative in this study.

In molecular and combined analysis, the recovered nodes show high BS. Also, the PBS for molecular partition is high (1-812). The very high values in PBS in the nodes (Milvago chimachima, Polihierax semitorquatus), and (Daptrius americanus, Falco sparverius) is due the great phylogenetic signal of molecular data against the morphological data.

The implementation of PBS in phylogenetic analysis is extensive in literature (Baker & DeSalle, 1997; DeSalle & Brower, 1997; Baker et al., 1998; Gatesy et al., 1999). Brower (2006) reviewed the advantages and disadvantages of Bremer Support (BS) and Partitioned Bremer Support (PBS). PBS posses some disadvantages in some issues. For example, if the size of the partitions are different. In this study, the morphologic matrix contains 23 characters and the molecular matrix 2936 characters. So, the different size in the data set could influence in the results of analysis. Also, PBS also appears to be sensitive to missing data, and can shift dramatically among partitions as missing data are filled into the matrix. In morphological analysis, Falco vespertinus not posses syringeal characters, because is taxon is not sampled. However, preliminary runs without F. vespertinus were not affecting the results.

I agree with Brower (2006) who stated that PBS is a efficient tools to estimate the support degree in data sets because it is a more direct and less sophisticated way to document the accumulation of character support for a particular branch in a particular phylogenetic hypothesis. In the same way, the phylogenetic relationships within Falconidae are more supported for molecular data than morphological data. A interesting point may be study more morphological characters (osteological).


Arias, J. S., Garzón, I. J., & Miranda, R. D. (2007) Sistemática Filogenética: Introducción a la práctica. División Editorial y de Publicaciones UIS. Colombia.

Baker, R. H., & DeSalle, R. (1997) Multiple sources of character information and the phylogeny of Hawaiian Drosophila. Systematic Biology, 46, 654–673.

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1 comentario:

Salva dijo...

Hola Sergio

Hay un par de cositas que vale la pena resaltar. En primer lugar, y como tus resultados muestran, la suma de los PBS NO SON iguales al BS! Ese es un mal mito que se a colado en la literatura sobre soporte.

Por otro lado, ni jack ni boot asumen ninguna distribución de los datos si se toman desde el punto de vista de apoyo (es decir cantidad de información y en contra)

Side notes: no se si nuestro manual sea una forma adecuada de citar como hacer BS xD... y pues si el script de TNT lo escribió Pablo, no creo que este en la pag del lab! (es más probable que este en )