Avian Phenotypic Convergence Is Subject to Low Genetic Constraints Based on Genomic Evidence Yu‑Chi Chen1 , Hao‑Chih Kuo1 , Wen‑Sui Lo2 and Chih‑Ming Hung1*
Total Page：16
File Type：pdf, Size：1020Kb
Chen et al. BMC Evol Biol (2020) 20:147 https://doi.org/10.1186/s12862-020-01711-7 RESEARCH ARTICLE Open Access Avian phenotypic convergence is subject to low genetic constraints based on genomic evidence Yu‑Chi Chen1 , Hao‑Chih Kuo1 , Wen‑Sui Lo2 and Chih‑Ming Hung1* Abstract Background: Phenotypic convergence between distinct species provides an opportunity to examine the predict‑ ability of genetic evolution. Unrelated species sharing genetic underpinnings for phenotypic convergence suggests strong genetic constraints, and thus high predictability of evolution. However, there is no clear big picture of the genomic constraints on convergent evolution. Genome‑based phylogenies have confrmed many cases of pheno‑ typic convergence in birds, making them a good system for examining genetic constraints in phenotypic conver‑ gence. In this study, we used hierarchical genomic approaches to estimate genetic constraints in three convergent avian traits: nocturnality, raptorial behavior and foot‑propelled diving. Results: Phylogeny‑based hypothesis tests and positive selection tests were applied to compare 16 avian genomes, representing 14 orders, and identify genes with strong convergence signals. We found 43 adaptively convergent genes (ACGs) associated with the three phenotypic convergence cases and assessed genetic constraints in all three cases, from (amino acid) site mutations to genetic pathways. We found that the avian orders shared few site mutations in the ACGs that contributed to the convergent phenotypes, and that these ACGs were not enriched in any genetic pathways. In addition, diferent pairs of orders with convergent foot‑propelled diving or raptorial behaviors shared few ACGs. We also found that closely related orders that shared foot‑propelled diving behavior did not share more ACGs than did distinct orders, suggesting that convergence among these orders could not be explained by their initial genomic backgrounds. Conclusions: Our analyses of three avian convergence events suggest low constraints for phenotypic convergence across multiple genetic levels, implying that genetic evolution is unpredictable at the phylogenetic level of avian order. Ours is one of frst studies to apply hierarchical genomic examination to multiple avian convergent cases to assess the genetic constraints in life history trait evolution. Keywords: Convergent evolution, Genomic comparison, Genetic constraint, Nocturnal birds, Foot‑propelled diving birds, Raptors Background of phenotypic convergence—distinct lineages indepen- Stephen Jay Gould argued that, if the tape of life could be dently reaching a similar phenotype [2]—have long fasci- replayed, the outcome would be diferent every time [1]. nated biologists because they seem to contradict Gould’s Tis suggests that evolution is unrepeatable, but cases hypothesis. While the genetic mechanism underlying phenotypic convergence is largely unclear, it is critical *Correspondence: [email protected] to understanding how evolution operates. For example, 1 Biodiversity Research Center, Academia Sinica, Taipei, Taiwan investigating how species converge genetically may Full list of author information is available at the end of the article help us evaluate whether evolution is subject to strong © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Chen et al. BMC Evol Biol (2020) 20:147 Page 2 of 15 constraints and is thus predictable [3–5], i.e., whether Avian lineages with each of the three convergent traits evolution is governed solely by probabilities or confned are widely distributed across all continents except the to a limited number of genetic variables rendering pre- Antarctic, where only a few species occur [20]. Tus, the dictable phenotypic outcomes [6, 7]. convergence of these traits occurs in lineages that are Te debate over the molecular underpinnings of phe- generally sympatric. Early molecular studies based on notypic convergence has lasted for decades [4]. Stayton DNA–DNA hybridization suggested that owls were sister [8] used a simulation to show that simple traits can con- to nightjars and their allies, all of which are active at night verge by chance. However, actual cases of convergence [21, 22]. More recent studies have shown that the noc- often involve traits that are coded by complex genetic turnality is convergent in owls (234 owl species constitut- pathways, making it unclear whether most examples of ing the order Strigiformes [20]) and nightjars (98 nightjar convergence occur by chance. On the other hand, one species and 34 species of their nocturnal allies consti- genetic mutation may impact multiple traits that have tuting fve families in the order Caprimulgiformes [20]) antagonistic efects on the organism’s ftness (i.e., pleio- because they belong to distinct lineages and thus evolved tropic efect), and thus the number of efective muta- the trait independently [23–25]. Owls are more closely tions could be restrained [9]. Terefore, authors argue related to Coraciimorphae birds such as woodpeckers that diferent species may fnd the same genetic solutions than to nightjars; nightjars are more closely related to in response to similar environmental pressures, causing hummingbirds, both of which are Caprimulgimorphae adaptive convergence [10, 11]. If this is the case, then birds, than to owls [17]. Tus, owls and nightjars rep- another question is whether genetic convergence tends to resent a typical case of convergent evolution [23]. Until occur at the level of (nucleotide or amino acid) site muta- around two decades ago, diurnal raptors—birds of prey tions, individual genes or genetic pathways. that generally have hooked beaks and taloned feet and are Te evolution of convergence in complex traits can- active in the daytime—were considered to be monophyl- not be fully understood using conventional candidate etic [26–28]; however, recent research suggests that diur- gene approaches, but instead requires genome-wide nal raptors should be divided into two non-sister groups: analyses [12]. Liu et al. [13] found that bats and toothed falcons (66 falcon species constituting the order Falconi- whales share 14 derived amino acids in one motor pro- formes [20]) and other diurnal raptors (252 eagle, hawk tein, Prestin, which is important for sensing ultrasound or kite species constituting the order Accipitriformes and and is assumed to be critical for the organisms’ conver- seven New World vulture species constituting its sister gent echolocation trait. However, Parker et al. [12] used order, Cathartiformes [20]) [25]. Falcons are more closely genome sequence data to show that signatures of con- related to parrots and passerines, all of which belong to vergence between bats and toothed whales are detected Australaves, than to other diurnal raptors, which belong in up to 200 genes, many of which are linked to hearing, to Afroaves [17]. Tus, the evidence suggests that rapto- deafness or vision. Terefore, genome-wide analyses pro- rial traits shared between falcons and other diurnal rap- vide a new avenue to examine the molecular mechanisms tors have evolved independently. of phenotypic convergence [14–16] and identify novel Grebes (22 species constituting the order Podicipedi- genes associated with complex traits, even for non-model formes [20]), loons (5 species constituting the order species. Gaviiformes [20]) and cormorants (40 cormorant spe- Te whole-genome sequences of many taxa, including cies and their foot-propelled diving allies, including four almost every avian order, were recently published [17, anhinga species, constituting two families in the order 18], making it possible to extensively test for genome- Suliformes [20]), also phylogenetically distinct, indepen- wide signatures of convergent evolution. Avian phylog- dently acquired similar foot-propelled diving traits [17, enies based on the above data [17] or genome-wide data 23]. Loons and grebes were once treated as each other’s from most avian families [19] confrm that there are closest relatives [29], partly because they both use feet many cases of phenotypic convergence in birds. Tus, instead of wings to propel through the water and have birds provide a good system to examine genomic con- rearward positioned legs; however, three decades ago, straints in phenotypic convergence. In this study, we genetic evidence revealed that the two groups are distinct explore the genomic bases of avian convergence on three [21]. Cormorants are another avian lineage characterized traits—nocturnality, raptorial