Data from: Is specialization an evolutionary dead-end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists.

Day E, Hua X, Bromham L

Date Published: March 23, 2016

DOI: http://dx.doi.org/10.5061/dryad.s6217

 

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Title Estimated tree using data from Fernandez et al., (2013)
Downloaded 4 times
Description Our estimated tree generated using data from Fernandez et al., (2013). The tree is based on the ITS DNA region (accession numbers from the supplementary material of Fernández-Mazuecos et al., (2013)) for 29 species of herbaceous plants in the genus Linaria and one outgroup, Antirrhinum graniticum. The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Fernández-Mazuecos et al., (2013). We used a GTR + Γ model of nucleotide evolution, separate partitions for each gene, a relaxed log-normal clock, and birth-death priors. Further information and full references can be found in the supplementary material of our paper.
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Title Estimated tree using data from Janz et al., (2001)
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Description Our estimated tree generated using data from Janz et al., (2001). The tree is based on the mitochondrial gene (nd1) and nuclear gene (wingless) for 25 species in the butterfly tribe Nymphalini and one outgroup, Argynnis paphia. The accession numbers were taken from Nylin et al., (2001). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Janz et al., (2001). We used a HKY + Γ model of nucleotide evolution with separate partitions for each gene, a relaxed log-normal clock, and a coalescent prior. Further information and full references can be found in the supplementary material of our paper.
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Title Estimated tree using data from Johnson et al., (2009)
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Description Our estimated tree generated using data from Johnson et al., (2009). The tree is based on the nuclear gene (EF-1α) and mitochondrial genes (12S and COI) for 38 species in the genus Columbicola and one outgroup, Oxyliperurus chiniri. The accession numbers were taken from Johnson et al., (2007). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014), allowing the topology to vary. We used a GTR + Γ model of nucleotide evolution with separate partitions for each gene and codon position, a relaxed log-normal clock, and a birth-death prior. Further information and full references can be found in the supplementary material of our paper.
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Title Estimated tree using data from Larkin et al., (2008)
Downloaded 5 times
Description Our estimated tree generated using data from Larkin et al., (2008). The tree is based on the mitochondrial genes (COI and COII including the intervening tRNA-leucine) and the nuclear gene (EF-1α) for 35 species of bees in the genus Andrena and one outgroup, Ancylandrena larreae. The accession numbers were taken from Larkin et al., (2006). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Larkin et al., (2008). We used a HKY + Γ model of nucleotide evolution, separate partitions for each gene, a relaxed log-normal clock, and a yule prior. Further information and full references can be found in the supplementary material of our paper.
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Title Estimated tree using data from Mendlová and Šimková (2014)
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Description Our estimated tree generated using data from Mendlová and Šimková (2014). The tree is based on two partial ribosomal RNA genes (SSU and LSU) and the entire ITS1 nuclear gene region for 25 species in the genus Cichlidogyrus and 3 species in the genus Scutogyrus. The accession numbers were taken from Mendlová et al. (2012) . The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Mendlová and Šimková (2014) . We used a GTR + Γ model of nucleotide evolution, separate partitions for each gene, a relaxed log-normal clock, and birth-death priors. Further information and full references can be found in the supplementary material of our paper.
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Title Estimated tree using data from Schweizer et al., (2014)
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Description Our estimated tree generated using data from Schweizer et al., (2014). The tree is based on three partial nuclear genes (c-mos, RAG-1 and Zenk) and one mitochondrial gene (ND2) for 78 parrot species within the order Psittaciformes and one outgroup, Falco tinnunculus. The accession numbers were taken from the supplementary material of Schweizer et al., (2014). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Schweizer et al., (2014). We used a HKY + Γ model of nucleotide evolution with separate partitions for each gene, a relaxed log-normal clock, and a coalescent prior. Further information and full references can be found in the supplementary material of our paper.
Download Schweizer_et_al_2014.tree (88.74 Kb)
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Title Estimated tree using data from Šimková et al., (2006)
Downloaded 5 times
Description Our estimated tree generated using data from Šimková et al., (2006). The tree is based on partial 18S rDNA and the entire nuclear ITS1 gene region for 51 species in the genus Dactylogyrus and two outgroups, Thaparocleidus vistulensis and Clediodiscus pricei. The accession numbers were taken from the Šimková et al., (2004). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Šimková et al., (2006). We used a GTR + Γ model of nucleotide evolution with separate partitions for each gene, a relaxed log-normal clock, and a birth-death prior. Further information and full references can be found in the supplementary material of our paper.
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Title Estimated tree using data from Tripp & Manos (2008)
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Description Our estimated tree generated using data from Tripp & Manos (2008). The tree is based on the nuclear ribosomal ITS + 5.8S region and the chloroplast trnG-trnR region for 115 species in the genus Ruellia and one outgroup, Sanchezia speciosa. We obtained the alignment of these genes from TreeBASE under study ID S1995. The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Tripp & Manos (2008). We used a GTR + Γ model of nucleotide evolution with separate partitions for each gene and codon position, a relaxed log-normal clock, and a birth-death prior. Further information and full references can be found in the supplementary material of our paper.
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Title Estimated tree using data from Stireman (2005)
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Description Our estimated tree generated using data from Stireman (2005). The tree is based on EF-1α and 28S rRNA genes for for 49 species of Tachinid flies in the subfamily Exoristinae and one outgroup, Metoposarcophaga sp. The accession numbers were taken from the Stireman (2002). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Stireman (2005). We used a GTR + Γ model of nucleotide evolution with separate partitions for each gene and codon position, a relaxed log-normal clock, and a birth-death prior. Further information and full references can be found in the supplementary material of our paper.
Download Stireman_2005.tree (55.57 Kb)
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When using this data, please cite the original publication:

Day E, Hua X, Bromham L (2016) Is specialization an evolutionary dead-end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists. Journal of Evolutionary Biology 29(6): 1257–1267. http://dx.doi.org/10.1111/jeb.12867

Additionally, please cite the Dryad data package:

Day E, Hua X, Bromham L (2016) Data from: Is specialization an evolutionary dead-end? Testing for differences in speciation, extinction and trait transition rates across diverse phylogenies of specialists and generalists. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.s6217
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