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Whittle CA, Extavour CG. Gene Protein Sequence Evolution Can Predict the Rapid Divergence of Ovariole Numbers in the Drosophila melanogaster Subgroup. Genome Biol Evol 2024; 16:evae118. [PMID: 38848313 PMCID: PMC11272079 DOI: 10.1093/gbe/evae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/01/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
Ovaries play key roles in fitness and evolution: they are essential female reproductive structures that develop and house the eggs in sexually reproducing animals. In Drosophila, the mature ovary contains multiple tubular egg-producing structures known as ovarioles. Ovarioles arise from somatic cellular structures in the larval ovary called terminal filaments (TFs), formed by TF cells and subsequently enclosed by sheath (SH) cells. As in many other insects, ovariole number per female varies extensively in Drosophila. At present, however, there is a striking gap of information on genetic mechanisms and evolutionary forces that shape the well-documented rapid interspecies divergence of ovariole numbers. To address this gap, here we studied genes associated with Drosophila melanogaster ovariole number or functions based on recent experimental and transcriptional datasets from larval ovaries, including TFs and SH cells, and assessed their rates and patterns of molecular evolution in five closely related species of the melanogaster subgroup that exhibit species-specific differences in ovariole numbers. From comprehensive analyses of protein sequence evolution (dN/dS), branch-site positive selection, expression specificity (tau), and phylogenetic regressions (phylogenetic generalized least squares), we report evidence of 42 genes that showed signs of playing roles in the genetic basis of interspecies evolutionary change of Drosophila ovariole number. These included the signaling genes upd2 and Ilp5 and extracellular matrix genes vkg and Col4a1, whose dN/dS predicted ovariole numbers among species. Together, we propose a model whereby a set of ovariole-involved gene proteins have an enhanced evolvability, including adaptive evolution, facilitating rapid shifts in ovariole number among Drosophila species.
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Affiliation(s)
- Carrie A Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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2
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Cantlay JC, Martin GR, McClelland SC, Potier S, O'Brien MF, Fernández-Juricic E, Bond AL, Portugal SJ. Binocular vision and foraging in ducks, geese and swans (Anatidae). Proc Biol Sci 2023; 290:20231213. [PMID: 37670586 PMCID: PMC10510447 DOI: 10.1098/rspb.2023.1213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Wide variation in visual field configuration across avian species is hypothesized to be driven primarily by foraging ecology and predator detection. While some studies of selected taxa have identified relationships between foraging ecology and binocular field characteristics in particular species, few have accounted for the relevance of shared ancestry. We conducted a large-scale, comparative analysis across 39 Anatidae species to investigate the relationship between the foraging ecology traits of diet or behaviour and binocular field parameters, while controlling for phylogeny. We used phylogenetic models to examine correlations between traits and binocular field characteristics, using unidimensional and morphometric approaches. We found that foraging behaviour influenced three parameters of binocular field size: maximum binocular field width, vertical binocular field extent, and angular separation between the eye-bill projection and the direction of maximum binocular field width. Foraging behaviour and body mass each influenced two descriptors of binocular field shape. Phylogenetic relatedness had minimal influence on binocular field size and shape, apart from vertical binocular field extent. Binocular field differences are associated with specific foraging behaviours, as related to the perceptual challenges of obtaining different food items from aquatic and terrestrial environments.
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Affiliation(s)
- Jennifer C. Cantlay
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Graham R. Martin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Stephanie C. McClelland
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Simon Potier
- Department of Biology, Faculty of Science, Lund University, Sölvegatan 35, 223 62 Lund, Sweden
| | | | | | - Alexander L. Bond
- Bird Group, Department of Life Sciences, The Natural History Museum, Akeman Street, Tring, Hertfordshire HP23 6AP, UK
| | - Steven J. Portugal
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- Bird Group, Department of Life Sciences, The Natural History Museum, Akeman Street, Tring, Hertfordshire HP23 6AP, UK
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Richardson R, Feigin CY, Bano-Otalora B, Johnson MR, Allen AE, Park J, McDowell RJ, Mereby SA, Lin IH, Lucas RJ, Mallarino R. The genomic basis of temporal niche evolution in a diurnal rodent. Curr Biol 2023; 33:3289-3298.e6. [PMID: 37480852 PMCID: PMC10529858 DOI: 10.1016/j.cub.2023.06.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 05/05/2023] [Accepted: 06/26/2023] [Indexed: 07/24/2023]
Abstract
Patterns of diel activity-how animals allocate their activity throughout the 24-h daily cycle-play key roles in shaping the internal physiology of an animal and its relationship with the external environment.1,2,3,4,5 Although shifts in diel activity patterns have occurred numerous times over the course of vertebrate evolution,6 the genomic correlates of such transitions remain unknown. Here, we use the African striped mouse (Rhabdomys pumilio), a species that transitioned from the ancestrally nocturnal diel niche of its close relatives to a diurnal one,7,8,9,10,11 to define patterns of naturally occurring molecular variation in diel niche traits. First, to facilitate genomic analyses, we generate a chromosome-level genome assembly of the striped mouse. Next, using transcriptomics, we show that the switch to daytime activity in this species is associated with a realignment of daily rhythms in peripheral tissues with respect to the light:dark cycle and the central circadian clock. To uncover selection pressures associated with this temporal niche shift, we perform comparative genomic analyses with closely related rodent species and find evidence of relaxation of purifying selection on striped mouse genes in the rod phototransduction pathway. In agreement with this, electroretinogram measurements demonstrate that striped mice have functional differences in dim-light visual responses compared with nocturnal rodents. Taken together, our results show that striped mice have undergone a drastic change in circadian organization and provide evidence that the visual system has been a major target of selection as this species transitioned to a novel temporal niche.
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Affiliation(s)
- Rose Richardson
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Beatriz Bano-Otalora
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Diabetes, Endocrinology, & Gastroenterology, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Matthew R Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Annette E Allen
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jongbeom Park
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Richard J McDowell
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Sarah A Mereby
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - I-Hsuan Lin
- Bioinformatics Core Facility, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Robert J Lucas
- Centre for Biological Timing, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK; Division of Neuroscience, Faculty of Biology Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA.
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Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
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Luo H, Luo S, Fang W, Lin Q, Chen X, Zhou X. Genomic insight into the nocturnal adaptation of the black-crowned night heron (Nycticorax nycticorax). BMC Genomics 2022; 23:683. [PMID: 36192687 PMCID: PMC9531477 DOI: 10.1186/s12864-022-08904-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The black-crowned night heron (Nycticorax nycticorax) is an ardeid bird successfully adapted to the nocturnal environment. Previous studies had indicated that the eyes of the night herons have evolved several specialized morphological traits favoring nocturnal vision. However, the molecular mechanisms of the nocturnal vision adaptation of night herons remained inattentions. In this study, the whole genome of N. nycticorax was sequenced and comparative analyses were performed on the vision-related and olfactory receptor (OR) genes to understand the molecular mechanisms of the visual and olfactory adaptation of night herons. RESULTS The results indicated that a number of vision genes were under positive or relaxed selection in N. nycticorax, whereas a number of other vision genes were under relaxed or intensified selection in the boat-billed heron (Cochlearius cochlearius), which suggested that the two species adapt to nocturnality with different genetic mechanisms. The different selections acting on vision genes are probably associated with the enlargement of eye size and the enhancement of visual sensitivity in night herons. The analyses on olfactory receptor (OR) genes indicated that the total number of OR genes in the genomes of N. nycticorax and C. cochlearius were about half those in the little egret (Egretta garzetta), whereas the diversity of their OR genes was not remarkably different. Additionally, the number of expressed OR genes in the transcriptomes of N. nycticorax was also fewer than that in E. garzetta. These results suggest a reduced olfactory capability in night herons compared with E. garzetta. CONCLUSIONS Our results provided evidence that several vision genes of the night herons were subjected to different natural selections, which can contribute to a better understanding of the genetic mechanisms of visual adaptions of the night heron. In addition, the finding of the reduced number of total and expressed OR genes in night herons may reflect a trade-off between olfaction and vision.
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Affiliation(s)
- Haoran Luo
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Site Luo
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China.
| | - Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China.
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Keirnan A, Worthy TH, Smaers JB, Mardon K, Iwaniuk AN, Weisbecker V. Not like night and day: the nocturnal letter-winged kite does not differ from diurnal congeners in orbit or endocast morphology. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220135. [PMID: 35620001 PMCID: PMC9128852 DOI: 10.1098/rsos.220135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/29/2022] [Indexed: 05/03/2023]
Abstract
Nocturnal birds display diverse adaptations of the visual system to low-light conditions. The skulls of birds reflect many of these and are used increasingly to infer nocturnality in extinct species. However, it is unclear how reliable such assessments are, particularly in cases of recent evolutionary transitions to nocturnality. Here, we investigate a case of recently evolved nocturnality in the world's only nocturnal hawk, the letter-winged kite Elanus scriptus. We employed phylogenetically informed analyses of orbit, optic foramen and endocast measurements from three-dimensional reconstructions of micro-computed tomography scanned skulls of the letter-winged kite, two congeners, and 13 other accipitrid and falconid raptors. Contrary to earlier suggestions, the letter-winged kite was not unique in any of our metrics. However, all species of Elanus have significantly higher ratios of orbit versus optic foramen diameter, suggesting high visual sensitivity at the expense of acuity. In addition, visual system morphology varies greatly across accipitrid species, likely reflecting hunting styles. Overall, our results suggest that the transition to nocturnality can occur rapidly and without changes to key hard-tissue indicators of vision, but also that hard-tissue anatomy of the visual system may provide a means of inferring a range of raptor behaviours, well beyond nocturnality.
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Affiliation(s)
- Aubrey Keirnan
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Trevor H. Worthy
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | | | - Karine Mardon
- Centre of Advanced Imaging, The University of Queensland, St. Lucia, QLD, Australia
| | - Andrew N. Iwaniuk
- Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Vera Weisbecker
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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Espíndola-Hernández P, Mueller JC, Carrete M, Boerno S, Kempenaers B. Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls. Genome Biol Evol 2020; 12:1895-1908. [PMID: 32770228 PMCID: PMC7566403 DOI: 10.1093/gbe/evaa166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
Owls (Strigiformes) evolved specific adaptations to their nocturnal predatory lifestyle, such as asymmetrical ears, a facial disk, and a feather structure allowing silent flight. Owls also share some traits with diurnal raptors and other nocturnal birds, such as cryptic plumage patterns, reversed sexual size dimorphism, and acute vision and hearing. The genetic basis of some of these adaptations to a nocturnal predatory lifestyle has been studied by candidate gene approaches but rarely with genome-wide scans. Here, we used a genome-wide comparative analysis to test for selection in the early history of the owls. We estimated the substitution rates in the coding regions of 20 bird genomes, including 11 owls of which five were newly sequenced. Then, we tested for functional overrepresentation across the genes that showed signals of selection. In the ancestral branch of the owls, we found traces of positive selection in the evolution of genes functionally related to visual perception, especially to phototransduction, and to chromosome packaging. Several genes that have been previously linked to acoustic perception, circadian rhythm, and feather structure also showed signals of an accelerated evolution in the origin of the owls. We discuss the functions of the genes under positive selection and their putative association with the adaptation to the nocturnal predatory lifestyle of the owls.
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Affiliation(s)
- Pamela Espíndola-Hernández
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Martina Carrete
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Sevilla, Spain
| | - Stefan Boerno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
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Hadden PW, Pas AE, Cassidy SB, Ober WC. The eye of the takahe, Porphyrio hochstetteri. NEW ZEALAND JOURNAL OF ZOOLOGY 2020. [DOI: 10.1080/03014223.2020.1792945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Peter W. Hadden
- Department of Ophthalmology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | | | | | - William C. Ober
- Cornell University – Shoals Marine Laboratory, Ithaca, NY, USA
- University of New Hampshire – Shoals Marine Laboratory, Durham, NH, USA
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Baldwin MW, Ko MC. Functional evolution of vertebrate sensory receptors. Horm Behav 2020; 124:104771. [PMID: 32437717 DOI: 10.1016/j.yhbeh.2020.104771] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022]
Abstract
Sensory receptors enable animals to perceive their external world, and functional properties of receptors evolve to detect the specific cues relevant for an organism's survival. Changes in sensory receptor function or tuning can directly impact an organism's behavior. Functional tests of receptors from multiple species and the generation of chimeric receptors between orthologs with different properties allow for the dissection of the molecular basis of receptor function and identification of the key residues that impart functional changes in different species. Knowledge of these functionally important sites facilitates investigation into questions regarding the role of epistasis and the extent of convergence, as well as the timing of sensory shifts relative to other phenotypic changes. However, as receptors can also play roles in non-sensory tissues, and receptor responses can be modulated by numerous other factors including varying expression levels, alternative splicing, and morphological features of the sensory cell, behavioral validation can be instrumental in confirming that responses observed in heterologous systems play a sensory role. Expression profiling of sensory cells and comparative genomics approaches can shed light on cell-type specific modifications and identify other proteins that may affect receptor function and can provide insight into the correlated evolution of complex suites of traits. Here we review the evolutionary history and diversity of functional responses of the major classes of sensory receptors in vertebrates, including opsins, chemosensory receptors, and ion channels involved in temperature-sensing, mechanosensation and electroreception.
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Affiliation(s)
| | - Meng-Ching Ko
- Max Planck Institute for Ornithology, Seewiesen, Germany
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