Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

Shapiro, Michael D.; Kronenberg, Zev; Cai, Li; Domyan, Eric T.; Pan, Hailin; Campbell, Michael S.; Tan, Hao; Huff, Chad; Hu, Haofu; Vickrey, Anna I.; Nielsen, Sandra C. A.; Stringham, Sydney A.; Hu, Hao; Willerslev, Eske; Gilbert, M. Thomas P.; Yandell, Mark; Zhang, Guojie; Wang, Jun

doi:10.1126/science.1230422

Cited by 237 publications

(223 citation statements)

References 75 publications

(30 reference statements)

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“…S2-S4 and Table S1-S3) by mapping sequence reads generated against the draft genome (1.09 Gb) of a domestic pigeon (Columba livia) (15). That is, we obtained between 68% and 91% of the maximum sequence length by mapping against this reference genome and recovered 57-75% of each passenger pigeon's genome, assuming that the sizes of the two pigeon species' complete genomes were similar (1.3 Gb) (15). To our knowledge, this is the longest genome sequence with the highest quality ever obtained for an extinct avian species.…”

Section: Resultsmentioning

confidence: 99%

“…Genomic sequences were generated applying the Illumina sequencing technology to aDNA extracted from toe pads of four passenger pigeons. Sequences of 90-bp paired-end reads were mapped to the draft genome of a domestic pigeon (15). We performed base quality recalibration, added several quality filters, and excluded Z-linked and mitochondrial genomes for the samples used for genetic diversity estimation and demographic analyses.…”

Section: Methodsmentioning

confidence: 99%

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Drastic population fluctuations explain the rapid extinction of the passenger pigeon

Hung¹,

Shaner²,

Zink

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

140

124

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To assess the role of human disturbances in species' extinction requires an understanding of the species population history before human impact. The passenger pigeon was once the most abundant bird in the world, with a population size estimated at 3-5 billion in the 1800s; its abrupt extinction in 1914 raises the question of how such an abundant bird could have been driven to extinction in mere decades. Although human exploitation is often blamed, the role of natural population dynamics in the passenger pigeon's extinction remains unexplored. Applying high-throughput sequencing technologies to obtain sequences from most of the genome, we calculated that the passenger pigeon's effective population size throughout the last million years was persistently about 1/10,000 of the 1800's estimated number of individuals, a ratio 1,000-times lower than typically found. This result suggests that the passenger pigeon was not always super abundant but experienced dramatic population fluctuations, resembling those of an "outbreak" species. Ecological niche models supported inference of drastic changes in the extent of its breeding range over the last glacial-interglacial cycle. An estimate of acorn-based carrying capacity during the past 21,000 y showed great year-to-year variations. Based on our results, we hypothesize that ecological conditions that dramatically reduced population size under natural conditions could have interacted with human exploitation in causing the passenger pigeon's rapid demise. Our study illustrates that even species as abundant as the passenger pigeon can be vulnerable to human threats if they are subject to dramatic population fluctuations, and provides a new perspective on the greatest human-caused extinction in recorded history

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Drastic population fluctuations explain the rapid extinction of the passenger pigeon

Hung¹,

Shaner²,

Zink

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

140

124

View full text Add to dashboard Cite

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“…This possibility is also supported by recent progress of genomic studies on domesticated mammals and birds (for example, dog, cat, cow, chicken, and pigeon) (Lindblad‐Toh et al, 2005; Wayne and Ostrander, 2007; Akey et al, 2010; Vonholdt et al, 2010; Shapiro et al, 2013). These studies explain the processes underlying fixation of genetic mutations through selective pressure on favorable morphological and/or physiological features, providing a more specific and promising framework for combined genomic and developmental biological approaches to investigate how fixed mutations altered ontogenetic processes to form the favorable morphological features in domestic animals in the context of evolutionary developmental biology (Cresko et al, 2007).…”

Section: Introductionmentioning

confidence: 85%

Postembryonic staging of wild‐type goldfish, with brief reference to skeletal systems

Chang

Liu

et al. 2015

Developmental Dynamics

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Background: Artificial selection of postembryonic features is known to have established morphological variation in goldfish (Carassius auratus). Although previous studies have suggested that goldfish and zebrafish are almost directly comparable at the embryonic level, little is known at the postembryonic level. Results: Here, we categorized the postembryonic developmental process in the wild‐type goldfish into 11 different stages. We also report certain differences between the postembryonic developmental processes of goldfish and zebrafish, especially in the skeletal systems (scales and median fin skeletons), suggesting that postembryonic development underwent evolutionary divergence in these two teleost species. Conclusions: Our postembryonic staging system of wild‐type goldfish paves the way for careful and appropriate comparison with other teleost species. The staging system will also facilitate comparative ontogenic analyses between wild‐type and mutant goldfish strains, allowing us to closely study the relationship between artificial selection and molecular developmental mechanisms in vertebrates. Developmental Dynamics 244:1485–1518, 2015. © 2015 Wiley Periodicals, Inc.

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“…Pigeon breeds can vary significantly in appearance with color, pattern, head crest, body shape, feathers, tails, vocalization, and flight display variations (Price 2002), inspiring considerable interest in identifying the genetic basis for these variations (Stringham et al 2012;Shapiro et al 2013). For the above reasons, both species' genomes were sequenced (Shapiro et al 2013;Zhan et al 2013); however, their assemblies are highly fragmented and chromosome-level assemblies are thus essential.…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

et al. 2016

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Most recent initiatives to sequence and assemble new species' genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE "deserts." This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.

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Genomic Diversity and Evolution of the Head Crest in the Rock Pigeon

Cited by 237 publications

References 75 publications

Drastic population fluctuations explain the rapid extinction of the passenger pigeon

Drastic population fluctuations explain the rapid extinction of the passenger pigeon

Postembryonic staging of wild‐type goldfish, with brief reference to skeletal systems

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

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