Periodic Reporting for period 1 - Finch Evo-Devo (Developmental Basis of Beak Shape Variation in Darwin’s Finches)
Periodo di rendicontazione: 2016-05-01 al 2018-04-30
Context and overall objectives
Today on our planet we see an enormous variety of living creatures, including ourselves. But how did this remarkable plethora of diverse forms come into existance? According to the integrative field of evolutionary developmental biology (evo-devo), the morphological changes seen in adult organisms first appear during their embryonic development, as a result of molecular modifications. Therefore, revealing which particular developmental program is responsible for a specific evolutionary change is pivotal to our understanding of the origin of diversity. Of all land vertebrates, birds are the most species-rich and, arguably, most diverse group with about 10,000 species. Much of this success can be attributed to their toothless beaks, a novelty of the bird lineage. The astonishing variation in shape and size of bird beaks reflects a wide range of dietary specializations, and hence of ecological niches they occupy. This makes birds an interesting model to study general evolutionary principles by focusing on mechanisms underlying their craniofacial development.
The iconic Darwin’s finches inhabit Galápagos and Cocos Islands. They are a group of about 15 songbird species all of whom arose from a single colonizing ancestor and now occupy ecological niches normally filled by representatives of multiple bird families. While very similar in overall appearance, Darwin’s finches are strikingly distinct in the size and shape of their beaks and in feeding behaviours (Figure 1). Hence, they represent a classical example of, and an inviting model for studying factors underlying rapid morphological evolution and adaptive radiation. Darwin’s finches have been extensively studied but knowledge on the molecular mechanisms controlling their embryonic development has been lacking and was provided by Dr. Abzhanov, the supervisor of this project. His team has used a combination of morphometrics, comparative developmental genetic and functional tests to reveal basic principles underlying beak shape morphogenesis. The team discovered several signaling pathways that during embryonic development control independently the three axes of beak morphology (length, depth and width). The three axes represent separate developmental modules which allow for independent variability among them, thus increasing overall variation in beak shape in the course of evolution. The team showed that the enormous beak diversity in Darwin’s finches could be reduced to three “group shapes” (A, B, and C) where group members are related by scaling, and revealed specific molecular mechanisms controlling the variation within group “A”. Within-group variation is due to scaling but the difference between groups is determined by beak curvature. The main objective of this project was to identify the developmental programs underlying the leaps of beak shape diversification during Darwin’s finches’ adaptive radiation – the variation between “group shapes” (Figure 2).
Today on our planet we see an enormous variety of living creatures, including ourselves. But how did this remarkable plethora of diverse forms come into existance? According to the integrative field of evolutionary developmental biology (evo-devo), the morphological changes seen in adult organisms first appear during their embryonic development, as a result of molecular modifications. Therefore, revealing which particular developmental program is responsible for a specific evolutionary change is pivotal to our understanding of the origin of diversity. Of all land vertebrates, birds are the most species-rich and, arguably, most diverse group with about 10,000 species. Much of this success can be attributed to their toothless beaks, a novelty of the bird lineage. The astonishing variation in shape and size of bird beaks reflects a wide range of dietary specializations, and hence of ecological niches they occupy. This makes birds an interesting model to study general evolutionary principles by focusing on mechanisms underlying their craniofacial development.
The iconic Darwin’s finches inhabit Galápagos and Cocos Islands. They are a group of about 15 songbird species all of whom arose from a single colonizing ancestor and now occupy ecological niches normally filled by representatives of multiple bird families. While very similar in overall appearance, Darwin’s finches are strikingly distinct in the size and shape of their beaks and in feeding behaviours (Figure 1). Hence, they represent a classical example of, and an inviting model for studying factors underlying rapid morphological evolution and adaptive radiation. Darwin’s finches have been extensively studied but knowledge on the molecular mechanisms controlling their embryonic development has been lacking and was provided by Dr. Abzhanov, the supervisor of this project. His team has used a combination of morphometrics, comparative developmental genetic and functional tests to reveal basic principles underlying beak shape morphogenesis. The team discovered several signaling pathways that during embryonic development control independently the three axes of beak morphology (length, depth and width). The three axes represent separate developmental modules which allow for independent variability among them, thus increasing overall variation in beak shape in the course of evolution. The team showed that the enormous beak diversity in Darwin’s finches could be reduced to three “group shapes” (A, B, and C) where group members are related by scaling, and revealed specific molecular mechanisms controlling the variation within group “A”. Within-group variation is due to scaling but the difference between groups is determined by beak curvature. The main objective of this project was to identify the developmental programs underlying the leaps of beak shape diversification during Darwin’s finches’ adaptive radiation – the variation between “group shapes” (Figure 2).
Work performed and main results achieved
Genomic studies provide information about the genetic composition of each species, but they do not give any spatial (tissue where particular genes are active), temporal (time when these genes are active – e.g. during development or adult life, at which stage of development, etc.), or dosage (how much is a gene expressed) information. While many genomic studies on Darwin’s finches exist, we are the first team to compare their transcriptomes in this project – the composition of mRNA in a particular tissue (the developing beak primordium) and particular moment during embryonic development (when beak curvature forms). This extensive comparison (based on RNA-seq technology, Figure 3) revealed a list of candidate developmental genes that are active during beak curvature formation, and relative levels of their gene expression during beak development. The differences in expression between species, representatives of the three “beak shapes” of Darwin’s finches, and the existing knowledge about gene interactions and networks, allowed us to start uncovering the complex regulation of beak curvature formation. To date, we validated some of the best candidate genes by in situ hybridization (Figure 3) – an assay that allows us to detect the exact location of gene expression in sections of Darwin’s finch embryos. We are currently validating a subset of these candidates by gain- and loss-of-function tests using genetically engineered viruses carrying the gene of interest on developing chicken embryos, to reveal their roles in beak morphogenesis. The tests in chicken embryos aim at mimicking the beak shape of different Darwin’s finch embryos in chicken after manipulation with a particular gene, confirming its role in beak shape morphogenesis.
Darwin’s finches live only on Galapagos. Ecuadorian authorities do not allow the establishment of colonies of these birds away from their native environment. This project involved two annual field trips to the islands to collect eggs of different species. During fieldwork, we collected the third egg from each nest and incubated them in a field incubator until the embryos reach the desired stage of development. The embryos were then dissected and preserved in fixative and brought back to the laboratory, where we process them for different experiments. The fieldwork we carried out during this project resulted in optimizing the existing administrative and logistics procedure, training of new researchers and successful collection of embryonic material (Figure 4).
Genomic studies provide information about the genetic composition of each species, but they do not give any spatial (tissue where particular genes are active), temporal (time when these genes are active – e.g. during development or adult life, at which stage of development, etc.), or dosage (how much is a gene expressed) information. While many genomic studies on Darwin’s finches exist, we are the first team to compare their transcriptomes in this project – the composition of mRNA in a particular tissue (the developing beak primordium) and particular moment during embryonic development (when beak curvature forms). This extensive comparison (based on RNA-seq technology, Figure 3) revealed a list of candidate developmental genes that are active during beak curvature formation, and relative levels of their gene expression during beak development. The differences in expression between species, representatives of the three “beak shapes” of Darwin’s finches, and the existing knowledge about gene interactions and networks, allowed us to start uncovering the complex regulation of beak curvature formation. To date, we validated some of the best candidate genes by in situ hybridization (Figure 3) – an assay that allows us to detect the exact location of gene expression in sections of Darwin’s finch embryos. We are currently validating a subset of these candidates by gain- and loss-of-function tests using genetically engineered viruses carrying the gene of interest on developing chicken embryos, to reveal their roles in beak morphogenesis. The tests in chicken embryos aim at mimicking the beak shape of different Darwin’s finch embryos in chicken after manipulation with a particular gene, confirming its role in beak shape morphogenesis.
Darwin’s finches live only on Galapagos. Ecuadorian authorities do not allow the establishment of colonies of these birds away from their native environment. This project involved two annual field trips to the islands to collect eggs of different species. During fieldwork, we collected the third egg from each nest and incubated them in a field incubator until the embryos reach the desired stage of development. The embryos were then dissected and preserved in fixative and brought back to the laboratory, where we process them for different experiments. The fieldwork we carried out during this project resulted in optimizing the existing administrative and logistics procedure, training of new researchers and successful collection of embryonic material (Figure 4).
Progress beyond the state of the art and expected potential impact
The transcriptomic analysis (RNA-seq) we applied during this project is definitely beyond the state of the art in Darwin’s finches research. It is difficult to obtain a permit for collection of Darwin’s finch eggs, and the collection procedure is difficult and expensive. Therefore, it is not surprising that we are the only team in the world allowed to collect and export Darwin’s finch embryos. Therefore, we expect the publications resulting from this project to keep expanding the state of the art in the field, in similar way as the previous publications on the team have.
After publication, the results of this project will be widely used and cited by fellow evolutionary, developmental biology, and evo-devo researchers. The results are expected to be valuable to the scientific community in general. Furthermore, previous research by the team has been widely cited in textbooks and reviews. Our group’s earlier discoveries on Darwin’s finches and other birds have been featured in multiple popular science books and documentaries. Birds are among the most charismatic animals on our planet and the story of bird evolution always attracts a lot of public and academic interest. Darwin’s finches, moreover, are among the most interesting bird groups with their exceptional and striking adaptive radiation. Therefore, we expect this project to attract a lot of attention on completion. Overall, when the scientific publications are ready, this project will provide novel insights on intrinsic mechanisms that facilitate adaptive morphological diversity, will offer an opportunity for interdisciplinary research interactions and will generate resources valuable to the entire biological community.
The transcriptomic analysis (RNA-seq) we applied during this project is definitely beyond the state of the art in Darwin’s finches research. It is difficult to obtain a permit for collection of Darwin’s finch eggs, and the collection procedure is difficult and expensive. Therefore, it is not surprising that we are the only team in the world allowed to collect and export Darwin’s finch embryos. Therefore, we expect the publications resulting from this project to keep expanding the state of the art in the field, in similar way as the previous publications on the team have.
After publication, the results of this project will be widely used and cited by fellow evolutionary, developmental biology, and evo-devo researchers. The results are expected to be valuable to the scientific community in general. Furthermore, previous research by the team has been widely cited in textbooks and reviews. Our group’s earlier discoveries on Darwin’s finches and other birds have been featured in multiple popular science books and documentaries. Birds are among the most charismatic animals on our planet and the story of bird evolution always attracts a lot of public and academic interest. Darwin’s finches, moreover, are among the most interesting bird groups with their exceptional and striking adaptive radiation. Therefore, we expect this project to attract a lot of attention on completion. Overall, when the scientific publications are ready, this project will provide novel insights on intrinsic mechanisms that facilitate adaptive morphological diversity, will offer an opportunity for interdisciplinary research interactions and will generate resources valuable to the entire biological community.