Convergent regulatory evolution and loss of flight in paleognathous birds

Sackton, Timothy B.; Grayson, Phil; Cloutier, Alison; Hu, Zhirui; Wheeler, Nicole E.; Gardner, Paul P.; Clarke, Julia A.; Baker, Allan J.; Clamp, Michele; Edwards, Scott V.

doi:10.1126/science.aat7244

Cited by 237 publications

(335 citation statements)

References 115 publications

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“…Therefore, homoplasy of pelvic reduction in sticklebacks is more likely to be caused by different selective pressures, low calcium ion concentration and lack of native predatory fishes, in different lakes (Bell, 1987). Furthermore, homoplasy is common with reduced characters especially for complex characters, which may have low probability of origin but can be lost or reduced by the action of a few genes (Culver & Pipan, 2016;Cunningham, Omland, & Oakley, 1998;Maddison, 1994;Sackton et al, 2019). In this study, …”

Section: Character Evolution and Morphological Homoplasymentioning

confidence: 77%

Evolution and losses of spines in slug caterpillars (Lepidoptera: Limacodidae)

Lin

Braby

et al. 2019

Ecology and Evolution

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Larvae of the cosmopolitan family Limacodidae, commonly known as “slug” caterpillars, are well known because of the widespread occurrence of spines with urticating properties, a morpho‐chemical adaptive trait that has been demonstrated to protect the larvae from natural enemies. However, while most species are armed with rows of spines (“nettle” caterpillars), slug caterpillars are morphologically diverse with some species lacking spines and thus are nonstinging. It has been demonstrated that the evolution of spines in slug caterpillars may have a single origin and that this trait is possibly derived from nonstinging slug caterpillars, but these conclusions were based on limited sampling of mainly New World taxa; thus, the evolution of spines and other traits within the family remains unresolved. Here, we analyze morphological variation in slug caterpillars within an evolutionary framework to determine character evolution of spines with samples from Asia, Australia, North America, and South America. The phylogeny of the Limacodidae was reconstructed based on a multigene dataset comprising five molecular markers (5.6 Kbp: COI, 28S, 18S, EF‐1α, and wingless) representing 45 species from 40 genera and eight outgroups. Based on this phylogeny, we infer that limacodids evolved from a common ancestor in which the larval type possessed spines, and then slug caterpillars without spines evolved independently multiple times in different continents. While larvae with spines are well adapted to avoiding generalist predators, our results imply that larvae without spines may be suited to different ecological niches. Systematic relationships of our dataset indicate six major lineages, several of which have not previously been identified.

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Section: Character Evolution and Morphological Homoplasymentioning

confidence: 77%

Evolution and losses of spines in slug caterpillars (Lepidoptera: Limacodidae)

Lin

Braby

et al. 2019

Ecology and Evolution

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“…1B). Although a single loss of flight followed by a regain of flight in T. patachonicus is a theoretical possibility, such an evolutionary transition has been deemed unlikely (Sackton et al 2019) and is not supported by the genetic data in this study.…”

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confidence: 60%

mentioning

confidence: 99%

“…Evidence for convergent molecular evolution exists in ratites, the lineage that includes ostriches and kiwis, which lost their ability to fly in the distant past (Sackton et al 2019). Studying a lineage with multiple recent losses of flight allowed Campagna et al (2019) to determine the genomic regions associated with the flightless phenotype with great precision, providing insight…”

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confidence: 99%

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Digest: A single genetic origin and a role for bone development pathways in repeated losses of flight in steamer ducks*

Lele

Ottenburghs

2019

Evolution

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Is there evidence for convergence in the molecular mechanisms underlying the loss of flight in the avian evolutionary tree? Campagna et al. used genomic data to investigate the genetic basis of flightlessness in steamer ducks, a recently diverged clade that is polymorphic with respect to flight. They found an association between morphological changes related to flightlessness and several genes, one of which is involved in growth and bone development, providing evidence for a single genetic origin for flightlessness.

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“…While previous studies have explored the genetic basis of other key avian traits (e.g. song, flight), such studies are typically targeted towards candidate genes, or incorporated clade-specific features (Whitney et al 2014;Wirthlin et al 2014;Machado et al 2016;Sackton et al 2019). Thus, relatively little is currently known about the genetics underpinning the macroevolution of beak shape (Wirthlin et al 2014;Machado et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Noncoding regions underpin avian bill shape diversification at macroevolutionary scales

Yusuf

Heatley

Palmer

et al. 2019

Preprint

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AbstractRecent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1,434 protein coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cells pathways, including BMP and Wnt signalling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome wide scale over macroevolutionary time is feasible. While the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.

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Convergent regulatory evolution and loss of flight in paleognathous birds

Cited by 237 publications

References 115 publications

Evolution and losses of spines in slug caterpillars (Lepidoptera: Limacodidae)

Evolution and losses of spines in slug caterpillars (Lepidoptera: Limacodidae)

Digest: A single genetic origin and a role for bone development pathways in repeated losses of flight in steamer ducks*

Noncoding regions underpin avian bill shape diversification at macroevolutionary scales

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