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Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage

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Recent publication by MVZ alumnus Zach Hanna (PhD 2017), MVZ staff curator and researcher Carla Cicero, and MVZ faculty Rauri Bowie: https://t.co/TtUYWVxGwM #mvzucb #mvzpubs https://t.co/TtUYWVxGwM
Recent publication by MVZ alumnus Zach Hanna (PhD 2017), MVZ staff curator and researcher Carla Cicero, and MVZ faculty Rauri Bowie: https://t.co/TtUYWVxGwM #mvzucb #mvzpubs https://t.co/TtUYWVxGwM
101 days ago
RT @IBIS_journal: Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passerif…
101 days ago
Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage https://t.co/FntpmqKjdX | Preprint @thePeerJ | #ornithology
107 days ago
Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage https://t.co/0bOUSQk9Cu
peerJ: Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage https://t.co/PXwuMX1cxM
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Supplemental Information

Specimen data

We provide the identifying codes and taxon of each Oreothlypis sample used in this study (including the O. ruficapilla samples used as outgroups). The institution and collection codes that precede the specimen number in each specimen identifier match those of the National Center for Biotechnology Information (NCBI) BioCollections database. We list the collections that archive each sample as well as additional information for each sample, including specific location, county, state, country, and date of collection. For the O. celata samples, we also provide a number to denote the ND2 haplotype in the column “ND2 Hap Num”, which matches the numbers used in the haplotype network figures. We list the subspecies of O. celata in the column “Ssp” and the population designation of the sample within the “8 populations” schema in the column “Population”. We provide the NCBI GenBank Accession numbers for all of the ND2 sequences we produced.

DOI: 10.7287/peerj.preprints.27418v1/supp-1

Subspecies pairwise divergence statistics

This table presents divergence statistics for pairwise subspecies comparisons calculated using ND2 mitochondrial DNA sequence (ΦST above diagonal) and microsatellite data (RST below diagonal). Values followed by asterisks are significant after applying a Bonferroni correction (p ≤ 0.008). See Table S1 for the samples included in each population.

DOI: 10.7287/peerj.preprints.27418v1/supp-2

Coastal and interior pairwise divergence statistics

This table presents divergence statistics for pairwise coastal and interior population comparisons calculated using ND2 mitochondrial DNA sequence (ΦST above diagonal) and microsatellite data (RST below diagonal). Values followed by asterisks are significant after applying a Bonferroni correction (p ≤ 0.008).

DOI: 10.7287/peerj.preprints.27418v1/supp-3

Microsatellite statistics

This table presents the statistics regarding the variability of the microsatellite loci in each population. “Nis the number of individuals genotyped. “A” is the number of alleles in the population followed by the number of private alleles in parentheses. "RS" is allelic richness, "HO" is observed heterozygosity, "HE" is expected heterozygosity, and “p-val” is the p-value resulting from a test of Hardy-Weinberg Equilibrium. P-values followed by asterisks indicate significant difference between the observed and expected heterozygosities after applying a Bonferroni correction (p < 0.005). See Table S1 for the samples included in each population.

DOI: 10.7287/peerj.preprints.27418v1/supp-4

Microsatellite genotypes

We present here the genotype values of all successfully genotyped individuals. The first row gives the names of the loci. The first column gives the sample codes of the individuals (see Table S1 for the specimens corresponding to each of these sample codes). There are two rows for each individual with a single column providing the two alleles for each individual at a locus.

DOI: 10.7287/peerj.preprints.27418v1/supp-5

Ventral specimen photos

This is a ventral view of five Oreothlypis celata museum skins. From left to right, the specimens are MVZ:Bird:177025, MVZ:Bird:177011, MVZ:Bird:179458, MVZ:Bird:173505, and MVZ:Bird:173962. These represent the four recognized subspecies with representatives of O. c. sordida from both the southern and northern Channel Islands. From left to right, the specimens are an O. c. sordida from Santa Catalina Island; an O. c. sordida from Santa Cruz Island; an O. c. lutescens from interior northern California; an O. c. orestera from Nevada; and an O. c. celata from Fairbanks, Alaska. Image taken by Anand Varma, reproduced with permission.

DOI: 10.7287/peerj.preprints.27418v1/supp-6

Dorsal specimen photos

This is a dorsal-view of the same five specimens seen in Figure S1. Image taken by Anand Varma, reproduced with permission.

DOI: 10.7287/peerj.preprints.27418v1/supp-7

ND2 haplotype network with subspecies population grouping

This is the ND2 haplotype network colored by the subspecies designations of samples. The haplotype numbers correspond with the numbers in Table S1. The size of each circle is proportional to the number of individuals with that haplotype. Lines connect haplotypes that differ by one mutation. Dots represent inferred haplotypes. Hash marks indicate the number of mutations between haplotypes separated by more than one mutation.

DOI: 10.7287/peerj.preprints.27418v1/supp-8

ND2 haplotype network with coast-interior population grouping

This is the ND2 haplotype network colored by samples’ grouping into coast and interior populations. See Figure S3 for the haplotype numbers that correspond with the numbers in Table S1. The size of each circle is proportional to the number of individuals with that haplotype. Lines connect haplotypes that differ by one mutation. Dots represent inferred haplotypes. Hash marks indicate the number of mutations between haplotypes separated by more than one mutation.

DOI: 10.7287/peerj.preprints.27418v1/supp-9

Mismatch distributions

Depicted here are mismatch distributions for ten populations. Square points connected by smooth lines represent observed distributions. Circular points connected by dotted lines represent expected distributions for a growing population with the same mean.

DOI: 10.7287/peerj.preprints.27418v1/supp-10

Structure plot for K=2 with Channel Islands population excluded

This figure depicts the ancestry of each individual in the two genetic clusters identified by Structure within the seven labeled populations after we excluded the Channel Islands population. Different colors represent the two genetic clusters identified by Structure. Each vertical bar represents an individual Oreothlypis celata. The height of each color in a given bar illustrates the proportion of ancestry derived from each genetic cluster for that individual.

DOI: 10.7287/peerj.preprints.27418v1/supp-11

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Zachary R Hanna performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Carla Cicero conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Rauri CK Bowie conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

UC Berkeley Animal Care and Use Committee provided approval for sample collection and this research under Animal Use Protocols R285 and R317.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

We collected samples under California Department of Fish and Game scientific collecting permit numbers SC-458 and SC-10109 as well as U.S. Fish and Wildlife Service permit number MB153526.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The ND2 sequences are available from NCBI (GenBank accession numbers MG686636 to MG686821 and MH543328 to MH543332). We provide the microsatellite genotypes in Table S5.

Data Deposition

The following information was supplied regarding data availability:

We provide further methodology details and scripts on GitHub.

https://github.com/zacharyhanna/ocwa-popgen

Funding

Funds were provided by the Sponsored Projects for Undergraduate Research Program (SPUR), College of Natural Resources, University of California, Berkeley to Zachary R. Hanna. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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