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Color and W-chromosome sequence data from study on maternal inheritance of egg mimicry

Citation

Spottiswoode, Claire N. et al. (2022), Color and W-chromosome sequence data from study on maternal inheritance of egg mimicry, Dryad, Dataset, https://doi.org/10.5061/dryad.rn8pk0pck

Abstract

This dataset supports a study demonstrating that host-specific egg mimicry in the brood-parasitic African cuckoo finch Anomalospiza imberbis is maternally inherited. It includes egg reflectance spectra for the background colour of 188 cuckoo finch eggs from four host species in Zambia, and consensus sequences for 68 W-linked ddRAD-seq loci derived from 80 female cuckoo finches belonging to four different host-specific maternal lineages from three host species in Zambia. These data derive from two partially overlapping samples of eggs: some eggs with genetic data lacked egg spectral data, and vice versa. W-linked genetic data were all of offspring origin as they derived from embryonic or nestling tissue. Additional phenotypic data (host nest species and descriptions of egg phenotype), date and location data associated with each egg spectrum are provided in a separate file. Data on the origin of the individuals contributing to the W-linked loci are provided in Table S1 of the associated publication.

Methods

cuckoo_finch_egg_color_spectra.txt
Reflectance spectra of the background color of 188 cuckoo finch (Anomalospiza imberbis) eggs over the bird-visible spectrum (300–700 nm). Spectra were taken using Ocean Optics USB2000 and USB4000 spectrometers following methods in Spottiswoode & Stevens 2010 (PNAS 107: 8672-8676). Values for each egg are means of five measurements per egg, and processed using the R package pavo to apply smoothing and remove negative values by setting the minimum value to zero and scaling other values accordingly. Spectra describe seven different cuckoo finch egg phenotypes, each of which mimics a different host species or different colour variant within a host species (plotted in Fig S2 of the associated paper). Where more than one cuckoo finch egg was present in a host nest, one was selected for analysis, since multiple eggs in the same host nest were typically laid by the same host female (one exception was a nest containing two parasitic eggs of different color phenotypes, presumably laid by different females). Note that some eggs from different host nests were laid by the same parasitic female (as confirmed by sibship of offspring from a subset of eggs with ddRAD-seq data) and so are non-independent. All eggs are from our study site in Zambia (detailed in the associated paper) during 2007–2009 and 2012–2014. 
 
cuckoo_finch_egg_color_spectra_metadata.txt
Additional data relating to cuckoo finch (Anomalospiza imberbis) eggs with reflectance spectra: geographical coordinates, dates, host nest species, descriptions of mimetic egg phenotypes, and notes on four eggs that mimicked a different host species to the host nest they were found in.
 
cuckoo_finch_W-linked_ddRAD-seq_loci.nex
NEXUS file comprising 68 ddRAD-seq loci recovered in some or all female cuckoo finches (Anomalospiza imberbis) but not in males. The consensus sequence for each W-linked locus is shown for each of four host-specific maternal lineages. Samples sizes for the four host-specific lineages were: “erythrops” = 5 females; “juncidis" = 16; “prinia_blue" = 34; “prinia_red" = 25. Only one position at one locus was variable within a given maternal lineage (see locus C1617.d). At all other loci the females in each matriline had identical sequences. Loci are numbered arbitrarily, as output by the ddRAD-seq analysis pipeline. In some cases, two or more similar loci were initially clustered together into a single putative locus, but were then separated manually based on careful examination of the raw data, including read depths. These separated loci are indicated by letter suffixes. Loci not recovered from females in a particular matriline are indicated by a string of "N"s. The data set includes 68 loci, 8,604 alignment positions plus 25 indel and locus presence-absence characters.

Usage Notes

Details are provided in ReadMe files.

Also see GenBank (BioProject ID: PRJNA809323) for additional cuckoo finch genetic data associated with this study.

Funding

BBSRC, Award: BB/J014109/1

DST-NRF Centre of Excellence at the FitzPatrick Institute

National Science Foundation, Award: DEB 0640759

The Royal Society, Award: Dorothy Hodgkin Research Fellowship