Speciational history of North American Haemorhous finches (Aves: Fringillidae) inferred from multilocus data

Smith, Brian Tilston; Bryson, Robert W.; Chua, Vivien L.; Africa, Lia A.; Klicka, John

doi:10.1016/j.ympev.2012.11.016

Cited by 11 publications

(5 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…; Smith et al. ). Fringillids are the most likely ancestral hosts of the pinnatus + Joubertophyllodes group because these birds harbor its greatest diversity (Fig.…”

Section: Discussionmentioning

confidence: 97%

Detecting ancient codispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds

2017

View full text Add to dashboard Cite

Inferring cophylogeographic events requires matching the timing of these events on both host and symbiont (e.g., parasites) phylogenies because divergences of hosts and their symbionts may not temporally coincide, and host switches may occur. We investigate a large radiation of birds (Passeriformes) and their permanent symbionts, the proctophyllodid feather mites (117 species from 116 bird species; six genes, 11,468 nt aligned) using two time-calibration strategies for mites: fossils only and host phylogeography only. Out of 10 putative cophylogeographic events 4 agree in timing for both symbiont and host events being synchronous co-origins or codispersals; three were based on host shifts, but agree in timing being very close to the origin of modern hosts; two disagree; and one large basal mite split was seemingly independent from host phylogeography. Among these events was an ancient (21-25.3 Mya), synchronous codispersal from the Old World leading to the origin and diversifications of New World emberizoid passerids and their mites, the thraupis + quadratus species groups of Proctophyllodes. Our framework offers a more robust detection of host and symbiont cophylogeographic events (as compared to host-symbiont reconciliation analysis and using host phylogeography for time-calibration) and provides independent data for testing alternative hypotheses on timing of host diversification and dispersal.

show abstract

“…; Smith et al. ). Fringillids are the most likely ancestral hosts of the pinnatus + Joubertophyllodes group because these birds harbor its greatest diversity (Fig.…”

Section: Discussionmentioning

confidence: 97%

Detecting ancient codispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds

2017

View full text Add to dashboard Cite

show abstract

“…To identify derived alleles within the frontalis subspecies, we also sampled individuals from the griscomi ( n = 6) subspecies (square, Fig. B; Table ) and two closely related sister species as outgroups, the Purple Finch ( H. purpurus ; n = 3) and the Cassin's Finch ( H. cassinii ; n = 3) (Smith, Bryson, Chua, Africa, & Klicka, ; Table ). Blood samples were preserved in Queen's lysis buffer (Seutin, White, & Boag, ) and stored at −80 ° C. Tissue samples were frozen in liquid nitrogen following collection, and stored at −80 ° C, and transferred between laboratories in 100% ethanol at room temperature.…”

Section: Methodsmentioning

confidence: 99%

SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)

Shultz

Baker

Hill

et al. 2016

Ecology and Evolution

View full text Add to dashboard Cite

Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen‐induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre‐epizootic western US birds, introduced birds from Hawaii and the eastern United States, post‐epizootic eastern birds, and western birds sampled across a similar time span. We found 14% and 7% reductions in nucleotide diversity, respectively, in Hawaiian and pre‐epizootic eastern birds relative to pre‐epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre‐epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.

show abstract

“…The inversion haplotype was found in all three species in the genus Haemorhous -- the House Finch, Cassin’s Finch, and Purple Finch -- suggesting pre-existing genetic variation in prior to the origin of House Finches. Thus, the minimum age of the derived inversion is approximately 10 million years (My), which is the time to the most recent common ancestor (TMRCA) of the genus Haemorhous (64, 65, 80).…”

Section: Resultsmentioning

confidence: 99%

Fitness consequences of structural variation inferred from a House Finch pangenome

Fang,

Edwards

2024

Preprint

View full text Add to dashboard Cite

Genomic structural variants (SVs) play a crucial role in adaptive evolution, yet their average fitness effects and characterization with pangenome tools are understudied in wild animal populations. We constructed a pangenome for House Finches, a model for studies of hostpathogen coevolution, using long-read sequence data on 16 individuals (32 de novo-assembled haplotypes) and one outgroup. We identified 643,207 SVs larger than 50 base pairs, mostly (60%) involving repetitive elements, with reduced SV diversity in the eastern US as a result of its introduction by humans. The distribution of fitness effects of genome-wide SVs was estimated using maximum likelihood approaches and showed SVs in both coding and non-coding regions to be on average more deleterious than smaller indels or single nucleotide polymorphisms. The reference-free pangenome facilitated discovery of a 10-million-year-old, 11-megabase-long pericentric inversion on chromosome 1. We found that the genotype frequencies of the inversion, estimated from 135 birds widely sampled geographically and temporally, increased steadily over the 25 years since House Finches were first exposed to the bacterial pathogen Mycoplasma gallispecticum and showed signatures of balancing selection, capturing genes related to immunity and telomerase activity. We also observed shorter telomeres in populations with a greater number of years exposure to Mycoplasma. Our study illustrates the utility of applying pangenome methods to wild animal populations, helps estimate fitness effects of genome-wide SVs, and advances our understanding of adaptive evolution through structural variation.

show abstract

Speciational history of North American Haemorhous finches (Aves: Fringillidae) inferred from multilocus data

Cited by 11 publications

References 24 publications

Detecting ancient codispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds

Detecting ancient codispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds

SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)

Fitness consequences of structural variation inferred from a House Finch pangenome

Contact Info

Product

Resources

About