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Evolution of Darwin’s finches and their beaks revealed by genome sequencing
Darwin’s finches, inhabiting the Galápagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin’s finch species and two close relatives. Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the
ALX1
gene that encodes a transcription factor affecting craniofacial development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (
Geospiza fortis
), a species that has undergone rapid evolution of beak shape in response to environmental changes. The
ALX1
haplotype has contributed to diversification of beak shapes among the Darwin’s finches and, thereby, to an expanded utilization of food resources.
Comprehensive genome sequencing of 120 individuals representing all of the Darwin’s finch species and two close relatives reveals important discrepancies with morphology-based taxonomy, widespread hybridization, and a gene,
ALX1
, underlying variation in beak shape.
Beak evolution genetics in Darwin's finches
Darwin's finches, from the Galápagos archipelago and nearby Cocos Island, are the iconic model for studies of evolution and particularly of speciation. Comprehensive genome sequencing of 120 individuals, including all Darwin's finch species and two close relatives, reveals important discrepancies with morphology-based taxonomy, including evidence that hybridization has given rise to species of mixed ancestry. Beak shape has traditionally featured prominently in discussions of finch adaptation. The study shows how a haplotype encompassing the
ALX1
gene — encoding a transcription factor affecting craniofacial development — is strongly associated with beak shape diversity across Darwin's finches and in the medium ground finch (a species that has undergone rapid evolution of beak shape in response to environmental changes).
Journal Article
The Vitamin A–Redox Hypothesis: A Biochemical Basis for Honest Signaling via Carotenoid Pigmentation
Trade-offs in resource allocation have been widely stated as the means by which the honesty of ornamental traits is maintained, but an alternative to this resource trade-off hypothesis is that production of ornamentation is linked to the biochemical efficiency of vital cellular processes. Carotenoids are antioxidants, potentially tying carotenoid-based coloration to the oxidative state of an organism, and some carotenoids are also precursors for vitamin A, which regulates numerous cellular processes. We present a biochemical model for regulation of ornamental coloration based on interdependencies of carotenoid and retinoid biochemistry. We propose that vitamin A regulatory mechanisms, redox systems, and carotenoid pigmentation pathways link carotenoid coloration to oxidative state and to a host of important aspects of performance, such as immune function. The activity of β-carotene ketolase, which catalyzes the oxidation of yellow carotenoids into red carotenoids, is responsive to the states of vitamin A pools and redox systems such that coloration is a direct reflection of the physiological state of an animal. According to the vitamin A–redox hypothesis, feather coloration is associated with a range of performance measures because performance emerges from functionality of the same basic cellular processes that regulate pigmentation. We present the vitamin A–redox hypothesis as a testable alternative hypothesis to the resource trade-off hypothesis for the maintenance of honesty of carotenoid pigmentation.
Journal Article
I am Henry Finch
This is a book about Henry Finch who strives for greatness, gets it all a bit wrong, then makes it right again in a very surprising way -- truly becoming great. -- From publisher.
Book
Hybridization increases population variation during adaptive radiation
Adaptive radiations are prominent components of the world’s biodiversity. They comprise many species derived from one or a small number of ancestral species in a geologically short time that have diversified into a variety of ecological niches. Several authors have proposed that introgressive hybridization has been important in the generation of new morphologies and even new species, but how that happens throughout evolutionary history is not known. Interspecific gene exchange is expected to have greatest impact on variation if it occurs after species have diverged genetically and phenotypically but before genetic incompatibilities arise. We use a dated phylogeny to infer that populations of Darwin’s finches in the Galápagos became more variable in morphological traits through time, consistent with the hybridization hypothesis, and then declined in variation after reaching a peak. Some species vary substantially more than others. Phylogenetic inferences of hybridization are supported by field observations of contemporary hybridization. Morphological effects of hybridization have been investigated on the small island of Daphne Major by documenting changes in hybridizing populations of Geospiza fortis and Geospiza scandens over a 30-y period. G. scandens showed more evidence of admixture than G. fortis. Beaks of G. scandens became progressively blunter, and while variation in length increased, variation in depth decreased. These changes imply independent effects of introgression on 2, genetically correlated, beak dimensions. Our study shows how introgressive hybridization can alter ecologically important traits, increase morphological variation as a radiation proceeds, and enhance the potential for future evolution in changing environments.
Journal Article
A beak size locus in Darwin's finches facilitated character displacement during a drought
Ecological character displacement is a process of morphological divergence that reduces competition for limited resources. We used genomic analysis to investigate the genetic basis of a documented character displacement event in Darwin's finches on Daphne Major in the Galápagos Islands: The medium ground finch diverged from its competitor, the large ground finch, during a severe drought. We discovered a genomic region containing the HMGA2 gene that varies systematically among Darwin's finch species with different beak sizes. Two haplotypes that diverged early in the radiation were involved in the character displacement event: Genotypes associated with large beak size were at a strong selective disadvantage in medium ground finches (selection coefficient s = 0.59). Thus, a major locus has apparently facilitated a rapid ecological diversification in the adaptive radiation of Darwin's finches.
Journal Article
Cranial shape evolution in adaptive radiations of birds: comparative morphometrics of Darwin's finches and Hawaiian honeycreepers
Adaptive radiation is the rapid evolution of morphologically and ecologically diverse species from a single ancestor. The two classic examples of adaptive radiation are Darwin's finches and the Hawaiian honeycreepers, which evolved remarkable levels of adaptive cranial morphological variation. To gain new insights into the nature of their diversification, we performed comparative three-dimensional geometric morphometric analyses based on X-ray microcomputed tomography (µCT) scanning of dried cranial skeletons. We show that cranial shapes in both Hawaiian honeycreepers and Coerebinae (Darwin's finches and their close relatives) are much more diverse than in their respective outgroups, but Hawaiian honeycreepers as a group display the highest diversity and disparity of all other bird groups studied. We also report a significant contribution of allometry to skull shape variation, and distinct patterns of evolutionary change in skull morphology in the two lineages of songbirds that underwent adaptive radiation on oceanic islands. These findings help to better understand the nature of adaptive radiations in general and provide a foundation for future investigations on the developmental and molecular mechanisms underlying diversification of these morphologically distinguished groups of birds.
This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.
Journal Article
Transgenic songbirds with suppressed or enhanced activity of CREB transcription factor
Songbirds postnatally develop their skill to utter and to perceive a vocal signal for communication. How genetic and environmental influences act in concert to regulate the development of such skill is not fully understood. Here, we report the phenotype of transgenic songbirds with altered intrinsic activity of cAMP response element-binding protein (CREB) transcription factor. By viral vector-mediated modification of genomic DNA, we established germ line-transmitted lines of zebra finches, which exhibited enhanced or suppressed activity of CREB. Although intrinsically acquired vocalizations or their hearing ability were not affected, the transgenic birds showed reduced vocal learning quality of their own songs and impaired audio-memory formation against conspecific songs. These results thus demonstrate that appropriate activity of CREB is necessary for the postnatal acquisition of learned behavior in songbirds, and the CREB transgenic birds offer a unique opportunity to separately manipulate both genetic and environmental factors that impinge on the postnatal song learning.
Significance In highly socialized animals such as humans or songbirds, individuals postnatally develop their skills to communicate with conspecifics under the social influence. Both genetic and environmental influences play a crucial role in the development of such abilities, but dissection of the influences has been difficult, because genetic manipulation of avian species is still a challenging issue. In this study, we applied transgenic technology to songbirds along with an experimental song-training paradigm to separately manipulate both genes and social environment, and found that appropriate activity of cAMP response element-binding protein (CREB) is necessary for the postnatal song learning in songbirds.
Journal Article