Data from: Passerine sister clade comparisons reveal variable macroevolutionary outcomes of interhemispheric dispersal
Data files
Oct 18, 2023 version files 295.66 MB
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1_WHEH_Oscine_Analyses.R
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1.5_WHEH_mvMORPH_Distribution.R
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2_OscineSuboscine_Analyses.R
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All_OscSub_Simulations.RData
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All_WHEH_Simulations.RData
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AppendixTable1.csv
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HackettS2_Trees.RData
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IOCJetzNames_AgeWork.csv
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JetzTree_SequenceList.csv
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PasseriformesMCC.tre
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README.md
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WHEH_CladeData.csv
Abstract
Dispersal events offer a unique window into macroevolutionary processes. While several hypotheses predict alternative outcomes from such events, many empirical studies have been limited in geographic and phylogenetic scale. Here, we tested some of these hypotheses by comparing an assemblage of 16 oscine passerine clades, representing independent dispersal events into the Western Hemisphere, to their sister clades in the Eastern Hemisphere. We also compared the diversity of this assemblage of clades to an older, incumbent passerine clade in the Western Hemisphere, the suboscines. We tested for ecological opportunity and incumbency-mediated constraints versus neutrality by integrating estimates of clade-specific morphological disparities with models of multivariate regimes of trait evolution. While there was no consistent outcome of oscine dispersal and macroevolution in the Western Hemisphere relative to their Eastern Hemisphere sister groups, most clades supported a role for ecological opportunity or incumbency effects, and such effects were better explained by differences in species accumulation than by differences in rates of trait evolution or colonization timing. However, we found that this general pattern was not evident when comparing the entire oscine assemblage of the Western Hemisphere to the incumbent suboscine clade. Oscines and suboscines occupy comparable regions of functional trait diversity and, despite oscines possessing higher rates of trait evolution, these observations were consistent with simulated null expectations. This result suggests that oscine and suboscine assemblages most likely evolved in relative isolation until 5-10 million years ago, with oscines primarily in North America and suboscines in South America, which limited incumbency effects of the autochthonous suboscine radiation on subsequent oscine diversification.
README
DATA FOR:
Macroevolutionary outcomes of repeated transcontinental dispersal by passerines into the Americas
Tyler S. Imfeld and F. Keith Barker
DATA FILES:
- IOCJetzNames_AgeWork.csv A csv file containing a list of species with their IOC checklist name, their name in the Jetz et al. 2012 phylogeny, and to what clade they belong to as part of this study. Species with values of "NA" in the 'Jetz Name' column are recognized on the IOC checklist but are not included in the Jetz et al. 2012 phylogeny.
- JetzTree_SequenceList.csv A csv file containing a list of the species included in the Jetz et al. 2012 phylogeny, whether each species is represented by sequence data, and GenBank accession numbers for each sequence used for these species.
- AppendixTable1.csv A csv file containing the raw morphometric data measured from study skins used in this study, including the measurements from Imfeld and Barker 2022. Complete methods for data collection are included in the manuscript and appendix. But, briefly, columns contain the following data: 'Species' is that species' scientific name. 'Lineage' is the clade to which that species belongs in this study. 'SpecimenID' contains two pieces of information: the abbreviation of the museum collection (as in the main manuscript) and the actual specimen number. 'Mass' was recorded in grams exactly as it appeared on the specimen's tag; NA indicates that mass was not recorded. The remaining columns contain linear measurements following Baldwin et al. 1931 and are explained at greater length in the manuscript text. All measurements of the bill and hindlimb (tarsus & hallux) were taken with Mitutoyo digital calipers, and the wing and tail length were taken with a standard wing rule. These measurements are recorded in millimeters. Full measurement names, in order, as follows: Length of Exposed Culmen, Length of Bill from Nares, Width of Bill at Nares, Depth of Bill at Nares, Width of Bill at Base, Depth of Bill at Base, Length of Tarsus, Length of Hallux, Length of Closed Wing, Length of Tail.
- WHEH_CladeData.csv A csv file containing clade-specific information about age and functional trait diversity. In all columns, 'WH' and 'EH' represent the Western and Eastern Hemisphere clades, respectively. 'Clade' conlumns contain the names of the = clades, respectively. 'Hyp' columns contain the 4-dimensional kernel density hypervolume disparities calculated for each clade on PC1-4. 'Overlap' contains the shared hypervolume occupied by the clade pair and 'Sum' contains the total hypervolume (union) occupied by the pair. 'ScaledDiff' contains the scaled difference in hypervolume occupied between the WH and EH clades. 'Unique' columns contain the hypervolume disparity uniquely occupied by either clade in the clade pair. 'PropOL' columns contain proportion of clade-specific hypervolume that's shared between each clade's sister clade, calculated as the hypervolume overlap between clades divided by each clade-specific hypervolume. 'Spp' columns contain the species richness of each clade. 'Crown' contains the crown age of the WH clade in millions of years, and 'Stem' contains the stem age of the sister clade pair in millions of years. 'SppDiff' contains the difference in species richness between the WH and EH clades.
TREE FILES:
- PasseriformesMCC.tre A NEWICK formatted tree file containing an MCC tree that was generated from a distribution of 1,000 Stage II Hackett et al. backbone trees downloaded from birdtree.org. Code in the R scripts below prune the tree to contain only species placed with sequence data (Stage I).
- HackettS2_Trees.RData An .RData file that will load the original distribution of 1,000 Stage II Hackett et al. backbone trees downloaded from birdtree.org. Code in R script 1.5 will prune the tree to contain only species placed with sequence data (Stage I).
R SCRIPTS AND RDATA FILES:
- 1_WHEH_Oscine_Analyses.R An R script containing all of the morphometric data analysis, model fitting, and simulations for comparing Western and Eastern hemisphere oscine sister clades.
- 1.5_WHEH_mvMORPH_Distribution.R An R script that will fit the mvMORPH models to a distribution of Jetz et al. trees to assess how robust model fitting results are to phylogenetic uncertainty.
- 2_OscineSuboscine_Analyses.R An R script containing all of the morphometric data analysis, model fitting, and simulations for comparing the Western Hemisphere oscine assemblage and the Western Hemisphere suboscine clade.
- All_OscSub_Simulations.RData An RData file containing the cumulative simulated posterior from parallelized cluster runs for comparing Western and Eastern Hemisphere oscine sister clades.
- All_WHEH_Simulations.RData An RData file containing the cumulative simulated posterior from parallelized cluster runs for comparing the oscine assemblage and suboscine clade in the Western Hemisphere.