Phylogenetic relationships of finches and allies based on nuclear and mitochondrial DNA
Introduction
Within the Passeriformes the phylogenetic relationships between different groups of mostly granivorous species in the superfamily Passeroidea are still largely unclear. Groups containing emberizine, fringilline, passerine and estrildine species have been defined and redefined several times based on various anatomical and behavioural characteristics (Beecher, 1953, Hinde, 1956, Steiner, 1960, Sushkin, 1924, Tordoff, 1954). However, the characteristics used are often not exclusive for the groups proposed and it has been difficult to demonstrate monophyly for the various groups within the Passeroidea. It is generally assumed that these difficulties are the result of rapid radiation and the occurrence of character convergence (see also Ericson et al., 2003, Yuri and Mindell, 2002).
Many studies using molecular techniques suggest affinity between the fringillids and buntings (Klicka et al., 2000, Sibley and Ahlquist, 1990) and between the estrildids and weavers (Christidis, 1987a, Christidis, 1987b, Sibley and Ahlquist, 1990, Stempel, 1987). However, the results seem to depend on the number of taxa and characters used. A cytochrome b study by Groth (1998) showed that fringillids are sister taxa to a clade which included the emberizids as a terminal taxon, while a large study from Yuri and Mindell (2002) demonstrates monophyly of the Fringillidae and its two constituent subfamilies: the Fringillinae and the Emberizinae.
The fringillids can be divided into two groups, the Fringilla species and the cardueline finches (Sibley and Ahlquist, 1990, Stempel, 1987), but there have been many debates about the relationship of the genus Fringilla. They have been related to the carduelines (Beecher, 1953, Fiedler, 1951, Mayr et al., 1956), to the emberizines (Tordoff, 1954) and to the weavers (Sushkin, 1924), or are considered as intermediate between the emberizids and carduelines. Recent molecular studies place the Fringilla sp. basal to the carduelines (Groth, 1998, Yuri and Mindell, 2002). The phylogenetic relationships within the carduelini based on cytochrome b are well studied (Arnaiz-Villena et al., 2001). Most studies place Serinus within the carduelines (Arnaiz-Villena et al., 2001, Clement et al., 1993, Fehrer, 1996), but in the work of Sibley and Monroe, 1990, Sibley and Monroe, 1993 the genus Serinus is placed together with the genus Fringilla within the Fringillini.
Estrildids are often divided into three groups (Christidis, 1987a, Christidis, 1987b, Delacour, 1943, Goodwin, 1982, Mayr, 1968), the grassfinches of Australia, the manikins of Asia and Australasia and the waxbills, largely from Africa. However, Sibley and Ahlquist (1990) place part of the estrildids as the subfamily Estrildinae in the family Passeridae and some of the members of the African waxbills (Pytillia, Spermophaga, Pyrenestes) together with the weavers (Ploceinae). The relationships between estrildids, ploceids and sparrows have always been problematic. The passerine sparrows (Passeridae: Passerinae) are often placed together with the weavers (Bentz, 1979, Christidis, 1987b), but cytochrome b data supports separation of the sparrows and ploceids (Allende et al., 2001). The analysis of cytochrome b also suggests a position of the sparrows close to the fringillids and motacillids (Groth, 1998) although in this last study the bootstrap value is quite low.
The main objective of this study is to establish a monophyly of estrildids. Establishing the monophyly of an estrildid and a Fringilla-cardueline clade is a prerequisite to assess differences in husking performance and the morphology of the jaw apparatus, which are being investigated in separate studies.
We used the complete mitochondrial gene cytochrome b in combination with a second nuclear gene, β-fibrinogen intron 7. The combination of a mitochondrial and nuclear gene, is believed to yield more robust phylogenetic estimates (Ericson et al., 2003).
Section snippets
Taxon sampling
We focused our sampling on two groups of Passeriformes, the Estrildidae and Fringillidae and added buntings, weavers and passers to clarify the unresolved nodes. For this study we used sequences of mitochondrial cytochrome b (Cyt-b) and nuclear β-fibrinogen intron 7 (Fib-7) of 30 birds (Table 1): 12 estrildids (6 from Asia–Australia and 6 from Africa), three weavers, one Vidua, eight finches (6 Carduelini and 2 Fringillini), two sparrows, and two emberizids. The Great Tit (Parus major) and the
Phylogenetic analysis
The sequences were aligned with ClustalX 1.81 (Jeanmougin et al., 1998, Thompson et al., 1997) and saved as a nexus file. The alignment of Cyt-b was checked for stopcodons in MacClade 4 (D.R. Maddisson and W.P. Maddison, Sinauer Associates Inc., Sunderland, MA) using the mammalian mitochondrial DNA matrix to make the translation in amino-acids. After aligning with ClustalX the non-coding β-fibrinogen intron 7 sequences were checked in MacClade and partly realigned by eye. Trees were rooted
Alignment and sequence variation
The mean length of Fib-7 is 968.7 bp; the shortest length is 922 bp for the Lesser Masked Weaver (Ploceus intermedius) and the longest, 995 bp for the Brambling (Fringilla montifringilla). A 50 bp portion of the alignment is excised because it is impossible to align, mainly due to T repeats in a number of birds. After excising the not alignable part the mean sequence length is 955.3 bp with the Lesser Masked Weaver having the shortest length (913 bp) and the Gouldian Finch (Chloebia gouldiae) having
Data consideration
By far the most popular gene by zoologist to investigate phylogenetic relationships is cytochrome b, although the use of this gene does have some disadvantages such as the limited variation in the first and second codon, and the early saturation of the third codon. Because the analysis of the Cyt-b gene did not result in a well supported tree we have added a more conservative gene β-fibrinogen intron 7 to provide supplementary information. Both trees considered separately did not provide a
Acknowledgments
The authors are very thankful to Wouter van Gestel, University of Wageningen for his help to complete the species samples, Aurélie Plancke and Céline van der Putten for their help on Fib-7 data. Henk den Bakker of the National Herbarium of the Netherlands for advice on phylogenetic analyses and to Jim Vanden Berge for his comments on the manuscript.
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