Pigeonetics takes flight: Evolution, development, and genetics of intraspecific variation

Domyan, Eric T.; Shapiro, Michael D.

doi:10.1016/j.ydbio.2016.11.008

Cited by 56 publications

(48 citation statements)

References 145 publications

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“…The domestic pigeon (Columba livia) is an outstanding model to study the evolution of genetic and developmental programs that underlie limb diversification. Pigeons display striking variation in HL morphology within a single species and are amenable to genetic crosses, genomic analyses, and embryonic studies , Domyan and Shapiro, 2017. While most pigeons have scaled HLs, in some breeds scaled epidermis is replaced by skin with a range of feather morphologies ( Figure 1A-C).…”

Section: Introductionmentioning

confidence: 99%

Pigeon foot feathering reveals conserved limb identity networks

Boer

Hollebeke

Park

et al. 2019

Preprint

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statementIn feather-footed pigeons, mutant alleles of PITX1 and TBX5 drive the partial redeployment of an evolutionarily conserved forelimb genetic program in the hindlimb. AbstractThe tetrapod limb is a stunning example of evolutionary diversity, with dramatic variation not only among distantly related species, but also between the serially homologous forelimbs (FLs) and hindlimbs (HLs) within species. Despite this variation, highly conserved genetic and developmental programs underlie limb development and identity in all tetrapods, raising the question of how limb diversification is generated from a conserved toolkit. In some breeds of domestic pigeon, shifts in the expression of two conserved limb identity transcription factors, PITX1 and TBX5, are associated with the formation of feathered HLs with partial FL identity. To determine how modulation of PITX1 and TBX5 expression affects downstream gene expression, we compared the transcriptomes of embryonic limb buds from pigeons with scaled and feathered HLs. We identified a set of differentially expressed genes enriched for genes encoding transcription factors, extracellular matrix proteins, and components of developmental signaling pathways with important roles in limb development. A subset of the genes that distinguish scaled and feathered HLs are also differentially expressed between FL and scaled HL buds in pigeons, pinpointing a set of gene expression changes downstream of PITX1 and TBX5 in the partial transformation from HL to FL identity. We extended our analyses by comparing pigeon limb bud transcriptomes to chicken, anole lizard, and mammalian datasets to identify deeply conserved PITX1-and TBX5-regulated components of the limb identity program. Our analyses reveal a suite of predominantly low-level gene expression changes that are conserved across amniotes to regulate the identity of morphologically distinct limbs.

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Section: Introductionmentioning

confidence: 99%

Pigeon foot feathering reveals conserved limb identity networks

Boer

Hollebeke

Park

et al. 2019

Preprint

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“…However, depending on the life-history characters and evolutionary history, intraspecific genetic diversity can be regionally heterogeneous and may vary widely between taxa (e.g. Alonso-Blanco et al 2016;Domyan and Shapiro 2017).…”

Section: Introductionmentioning

confidence: 99%

Highly variable COI haplotype diversity between three species of invasive pest fruit fly reflects remarkably incongruent demographic histories

Doorenweerd

Jose

Barr

et al. 2019

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AbstractDistance decay principles predict that species with larger geographic ranges would have greater intraspecific genetic diversity than more restricted species. However, invasive pest species may not follow this prediction, with confounding implications for tracking phenomena including original ranges, invasion pathways and source populations. We sequenced an 815 base-pair section of the COI gene for 441 specimens of Bactrocera correcta, 214 B. zonata and 372 Zeugodacus cucurbitae; three invasive pest fruit fly species with overlapping hostplants. For each species, we explored how many individuals would need to be included in a study to sample the majority of their haplotype diversity. We also tested for phylogeographic signal and used demographic estimators as a proxy for invasion potency. We find contrasting patterns of haplotype diversity amongst the species, where B. zonata has the highest diversity but most haplotypes were represented by singletons; B. correcta has ∼7 dominant haplotypes more evenly distributed; Z. cucurbitae has a single dominant haplotype with closely related singletons in a ‘star-shape’ surrounding it. We discuss how these differing patterns relate to their invasion histories. None of the species showed meaningful phylogeographic patterns, possibly due to gene-flow between areas across their distributions, obscuring or eliminating substructuring.

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“…The domestic rock pigeon (Columba livia) displays enormous phenotypic 42 diversity within and among over 350 breeds, including a wide variety of plumage 43 pigmentation patterns (Shapiro and Domyan 2013;Domyan and Shapiro 2017). Some of 44 these pattern phenotypes are found in feral and wild populations as well (Johnston and 45 Janiga 1995).…”

Section: Introduction 29mentioning

confidence: 99%

Protein-coding variation and introgression of regulatory alleles drive plumage pattern diversity in the rock pigeon

Bruders

Kronenberg

et al. 2018

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15Birds and other vertebrates display stunning variation in pigmentation patterning, yet the 16 genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) 17 are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: 18 T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified 19 NDP as a candidate gene for this variation. Allele-specific expression differences in NDP 20indicate cis-regulatory differences between ancestral and melanistic alleles. Sequence 21 comparisons suggest that derived alleles originated in the speckled pigeon (Columba 22 guinea), providing a striking example of introgression of alleles that are favored by 23 breeders and are potentially advantageous in the wild. In contrast, barless rock pigeons 24have an increased incidence of vision defects and, like two human families with 25 hereditary blindness, carry start-codon mutations in NDP. In summary, we find 26 unexpected links between color pattern, introgression, and vision defects associated with 27 regulatory and coding variation at a single locus. 28

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Pigeonetics takes flight: Evolution, development, and genetics of intraspecific variation

Cited by 56 publications

References 145 publications

Pigeon foot feathering reveals conserved limb identity networks

Pigeon foot feathering reveals conserved limb identity networks

Highly variable COI haplotype diversity between three species of invasive pest fruit fly reflects remarkably incongruent demographic histories

Protein-coding variation and introgression of regulatory alleles drive plumage pattern diversity in the rock pigeon

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