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Hautier L, Gomes Rodrigues H, Ferreira-Cardoso S, Emerling CA, Porcher ML, Asher RJ, Portela Miguez R, Delsuc F. From teeth to pad: tooth loss and development of keratinous structures in sirenians. Proc Biol Sci 2023; 290:20231932. [PMID: 38018114 PMCID: PMC10685118 DOI: 10.1098/rspb.2023.1932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023] Open
Abstract
Sirenians are a well-known example of morphological adaptation to a shallow-water grazing diet characterized by a modified feeding apparatus and orofacial morphology. Such adaptations were accompanied by an anterior tooth reduction associated with the development of keratinized pads, the evolution of which remains elusive. Among sirenians, the recently extinct Steller's sea cow represents a special case for being completely toothless. Here, we used μ-CT scans of sirenian crania to understand how motor-sensor systems associated with tooth innervation responded to innovations such as keratinized pads and continuous dental replacement. In addition, we surveyed nine genes associated with dental reduction for signatures of loss of function. Our results reveal how patterns of innervation changed with modifications of the dental formula, especially continuous replacement in manatees. Both our morphological and genomic data show that dental development was not completely lost in the edentulous Steller's sea cows. By tracing the phylogenetic history of tooth innervation, we illustrate the role of development in promoting the innervation of keratinized pads, similar to the secondary use of dental canals for innervating neomorphic keratinized structures in other tetrapod groups.
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Affiliation(s)
- Lionel Hautier
- Institut des Sciences de l’Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
- Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, London, UK
| | - Helder Gomes Rodrigues
- Centre de Recherche en Paléontologie—Paris (CR2P), UMR CNRS 7207, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France
| | - Sérgio Ferreira-Cardoso
- Institut des Sciences de l’Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | | | - Marie-Lou Porcher
- Institut des Sciences de l’Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Robert J. Asher
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Roberto Portela Miguez
- Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, London, UK
| | - Frédéric Delsuc
- Institut des Sciences de l’Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
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2
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Springer MS, Emerling CA, Gatesy J. Three Blind Moles: Molecular Evolutionary Insights on the Tempo and Mode of Convergent Eye Degeneration in Notoryctes typhlops (Southern Marsupial Mole) and Two Chrysochlorids (Golden Moles). Genes (Basel) 2023; 14:2018. [PMID: 38002961 PMCID: PMC10671557 DOI: 10.3390/genes14112018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Golden moles (Chrysochloridae) and marsupial moles (Notoryctidae) are textbook examples of convergent evolution. Both taxa are highly adapted to subterranean lifestyles and have powerful limbs for digging through the soil/sand, ears that are adapted for low-frequency hearing, vestigial eyes that are covered by skin and fur, and the absence of optic nerve connections between the eyes and the brain. The eyes of marsupial moles also lack a lens as well as retinal rods and cones. Two hypotheses have been proposed to account for the greater degeneracy of the eyes of marsupial moles than golden moles. First, marsupial moles may have had more time to adapt to their underground habitat than other moles. Second, the eyes of marsupial moles may have been rapidly and recently vestigialized to (1) reduce the injurious effects of sand getting into the eyes and (2) accommodate the enlargement of lacrimal glands that keep the nasal cavity moist and prevent the entry of sand into the nasal passages during burrowing. Here, we employ molecular evolutionary methods on DNA sequences for 38 eye genes, most of which are eye-specific, to investigate the timing of relaxed selection (=neutral evolution) for different groups of eye-specific genes that serve as proxies for distinct functional components of the eye (rod phototransduction, cone phototransduction, lens/cornea). Our taxon sampling included 12 afrothere species, of which two are golden moles (Amblysomus hottentotus, Chrysochloris asiatica), and 28 marsupial species including two individuals of the southern marsupial mole (Notoryctes typhlops). Most of the sequences were mined from databases, but we also provide new genome data for A. hottentotus and one of the two N. typhlops individuals. Even though the eyes of golden moles are less degenerate than the eyes of marsupial moles, there are more inactivating mutations (e.g., frameshift indels, premature stop codons) in their cone phototransduction and lens/cornea genes than in orthologous genes of the marsupial mole. We estimate that cone phototransduction recovery genes were inactivated first in each group, followed by lens/cornea genes and then cone phototransduction activation genes. All three groups of genes were inactivated earlier in golden moles than in marsupial moles. For the latter, we estimate that lens/cornea genes were inactivated ~17.8 million years ago (MYA) when stem notoryctids were burrowing in the soft soils of Australian rainforests. Selection on phototransduction activation genes was relaxed much later (5.38 MYA), during the early stages of Australia's aridification that produced coastal sand plains and eventually sand dunes. Unlike cone phototransduction activation genes, rod phototransduction activation genes are intact in both golden moles and one of the two individuals of N. typhlops. A second marsupial mole individual has just a single inactivating mutation in one of the rod phototransduction activation genes (PDE6B). One explanation for this result is that some rod phototransduction activation genes are pleiotropic and are expressed in extraocular tissues, possibly in conjunction with sperm thermotaxis.
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Affiliation(s)
- Mark S. Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | | | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA;
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3
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Manzoor H, Zahid H, Emerling CA, Kumar KR, Hussain HMJ, Seo GH, Wajid M, Naz S. A biallelic variant of DCAF13 implicated in a neuromuscular disorder in humans. Eur J Hum Genet 2023; 31:629-637. [PMID: 36797467 PMCID: PMC10250411 DOI: 10.1038/s41431-023-01319-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Neuromuscular disorders encompass a broad range of phenotypes and genetic causes. We investigated a consanguineous family in which multiple patients had a neuromuscular disorder characterized by a waddling gait, limb deformities, muscular weakness and facial palsy. Exome sequencing was completed on the DNA of three of the four patients. We identified a novel missense variant in DCAF13, ENST00000612750.5, NM_015420.7, c.907 G > A;p.(Asp303Asn), ENST00000616836.4, NM_015420.6, c.1363 G > A:p.(Asp455Asn) (rs1209794872) segregating with this phenotype; being homozygous in all four affected patients and heterozygous in the unaffected individuals. The variant was extremely rare in the public databases (gnomAD allele frequency 0.000007081); was absent from the DNA of 300 ethnically matched controls and affected an amino acid which has been conserved across 1-2 billion years of evolution in eukaryotes. DCAF13 contains three WD40 domains and is hypothesized to have roles in both rRNA processing and in ubiquitination of proteins. Analysis of DCAF13 with the p.(Asp455Asn) variant predicted that the amino acid change is deleterious and affects a β-hairpin turn, within a WD40 domain of the protein which may decrease protein stability. Previously, a heterozygous variant of DCAF13 NM_015420.6, c.20 G > C:p.(Trp7Ser) with or without a heterozygous missense variant in CCN3, was suggested to cause inherited cortical myoclonic tremor with epilepsy. In addition, a heterozygous DCAF13 variant has been associated with autism spectrum disorder. Our study indicates a potential role of biallelic DCAF13 variants in neuromuscular disorders. Screening of additional patients with similar phenotype may broaden the allelic and phenotypic spectrum due to DCAF13 variants.
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Affiliation(s)
- Humera Manzoor
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
| | - Hafsa Zahid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | | | - Kishore R Kumar
- Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Concord Clinical School Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | | | - Muhammad Wajid
- Department of Zoology, University of Okara, Punjab, Pakistan
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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Fiddaman SR, Vinkler M, Spiro SG, Levy H, Emerling CA, Boyd AC, Dimopoulos EA, Vianna JA, Cole TL, Pan H, Fang M, Zhang G, Hart T, Frantz LAF, Smith AL. Adaptation and cryptic pseudogenization in penguin Toll-like Receptors. Mol Biol Evol 2021; 39:6460345. [PMID: 34897511 PMCID: PMC8788240 DOI: 10.1093/molbev/msab354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.
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Affiliation(s)
- Steven R Fiddaman
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University Prague, Czech Republic
| | - Simon G Spiro
- Wildlife Health Services, Zoological Society of London Regent's Park, London, UK
| | - Hila Levy
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | | | - Amy C Boyd
- Jenner Institute, University of Oxford Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford Oxford, UK
| | - Juliana A Vianna
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ecosistemas y Medio Ambiente Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Theresa L Cole
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen DK2100, Copenhagen, Denmark
| | - Hailin Pan
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China
| | - Miaoquan Fang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen DK2100, Copenhagen, Denmark.,BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Tom Hart
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Fogg Building, Queen Mary University of London Mile End Rd, Bethnal Green, London E1 4DQ, UK.,Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Germany
| | - Adrian L Smith
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
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5
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Emerling CA, Springer MS, Gatesy J, Jones Z, Hamilton D, Xia-Zhu D, Collin M, Delsuc F. Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals. Open Res Eur 2021; 1:75. [PMID: 35967080 PMCID: PMC7613276 DOI: 10.12688/openreseurope.13795.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 11/20/2022]
Abstract
Background: The study of regressive evolution has yielded a wealth of examples where the underlying genes bear molecular signatures of trait degradation, such as pseudogenization or deletion. Typically, it appears that such disrupted genes are limited to the function of the regressed trait, whereas pleiotropic genes tend to be maintained by natural selection to support their myriad purposes. One such set of pleiotropic genes is involved in the synthesis ( AANAT, ASMT) and signaling ( MTNR1A, MTNR1B) of melatonin, a hormone secreted by the vertebrate pineal gland. Melatonin provides a signal of environmental darkness, thereby influencing the circadian and circannual rhythmicity of numerous physiological traits. Therefore, the complete loss of a pineal gland and the underlying melatonin pathway genes seems likely to be maladaptive, unless compensated by extrapineal sources of melatonin. Methods: We examined AANAT, ASMT, MTNR1A and MTNR1B in 123 vertebrate species, including pineal-less placental mammals and crocodylians. We searched for inactivating mutations and modelled selective pressures (dN/dS) to test whether the genes remain functionally intact. Results: We report that crocodylians retain intact melatonin genes and express AANAT and ASMT in their eyes, whereas all four genes have been repeatedly inactivated in the pineal-less xenarthrans, pangolins, sirenians, and whales. Furthermore, colugos have lost these genes, and several lineages of subterranean mammals have partial melatonin pathway dysfunction. These results are supported by the presence of shared inactivating mutations across clades and analyses of selection pressure based on the ratio of non-synonymous to synonymous substitutions (dN/dS), suggesting extended periods of relaxed selection on these genes. Conclusions: The losses of melatonin synthesis and signaling date to tens of millions of years ago in several lineages of placental mammals, raising questions about the evolutionary resilience of pleiotropic genes, and the causes and consequences of losing melatonin pathways in these species.
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Affiliation(s)
- Christopher A. Emerling
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
- Biology Department, Reedley College, Reedley, CA, 93654, USA
| | - Mark S. Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Zachary Jones
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Deana Hamilton
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - David Xia-Zhu
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Matt Collin
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, 92521, USA
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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6
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Blanquart S, Borowiec AS, Delcourt P, Figeac M, Emerling CA, Meseguer AS, Roudbaraki M, Prevarskaya N, Bidaux G. Evolution of the human cold/menthol receptor, TRPM8. Mol Phylogenet Evol 2019; 136:104-118. [PMID: 30980935 DOI: 10.1016/j.ympev.2019.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 10/27/2022]
Abstract
Genes showing versatile functions or subjected to fast expansion and contraction during the adaptation of species to specific ecological conditions, like sensory receptors for odors, pheromones and tastes, are characterized by a great plasticity through evolution. One of the most fascinating sensory receptors in the family of TRP channels, the cold and menthol receptor TRPM8, has received significant attention in the literature. Recent studies have reported the existence of TRPM8 channel isoforms encoded by alternative mRNAs transcribed from alternative promoters and processed by alternative splicing. Since the first draft of the human genome was accomplished in 2000, alternative transcription, alternative splicing and alternative translation have appeared as major sources of gene product diversity and are thought to participate in the generation of complexity in higher organisms. In this study, we investigate whether alternative transcription has been a driving force in the evolution of the human forms of the cold receptor TRPM8. We identified 33 TRPM8 alternative mRNAs (24 new sequences) and their associated protein isoforms in human tissues. Using comparative genomics, we described the evolution of the human TRPM8 sequences in eight ancestors since the origin of Amniota, and estimated in which ancestors the new TRPM8 variants originated. In order to validate the estimated origins of this receptor, we performed experimental validations of predicted exons in mouse tissues. Our results suggest a first diversification event of the cold receptor in the Boreoeutheria ancestor, and a subsequent divergence at the origin of Simiiformes.
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Affiliation(s)
| | - Anne-Sophie Borowiec
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France
| | - Philippe Delcourt
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France
| | - Martin Figeac
- Université de Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France; CHRU de Lille, Cellule de bioinformatique du plateau commun de séquençage du CHRU de Lille, F-59000 Lille, France
| | - Christopher A Emerling
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Université Montpellier, UMR5554, Montpellier, France
| | - Andrea S Meseguer
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, EPHE, Université Montpellier, UMR5554, Montpellier, France
| | - Morad Roudbaraki
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France
| | - Natalia Prevarskaya
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France
| | - Gabriel Bidaux
- Inserm, U-1003, Equipe labellisée par la Ligue Nationale contre le cancer, Villeneuve d'Ascq F-59655, France; Université des Sciences et Technologies de Lille (USTL), Villeneuve d'Ascq F-59655, France; Univ Lyon, CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, 69550 Bron, France; Hospices Civils de Lyon, Groupement Hospitalier EST, Département de Cardiologie, IHU-OPERA Bâtiment B13, 69550 Bron, France.
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Abstract
Regressive evolution involves the degradation of formerly useful traits as organisms invade novel ecological niches. In animals, committing to a strict subterranean habit can lead to regression of the eyes, likely due to a limited exposure to light. Several lineages of subterranean mammals show evidence of such degeneration, which can include decreased organization of the retina, malformation of the lens, and subcutaneous positioning of the eye. Advances in DNA sequencing have revealed that this regression co-occurs with a degradation of genomic loci encoding visual functions, including protein-coding genes. Other dim light-adapted vertebrates with normal ocular anatomy, such as nocturnal and aquatic species, also demonstrate evidence of visual gene loss, but the absence of comparative studies has led to the untested assumption that subterranean mammals are special in the degree of this genomic regression. Additionally, previous studies have shown that not all vision genes have been lost in subterranean mammals, but it is unclear whether they are under relaxed selection and will ultimately be lost, are maintained due to pleiotropy or if natural selection is favoring the retention of the eye and certain critical underlying loci. Here I report that vision gene loss in subterranean mammals tends to be more extensive in quantity and differs in distribution from other dim light-adapted mammals, although some committed subterranean mammals demonstrate significant overlap with nocturnal microphthalmic species. In addition, blind subterranean mammals retain functional orthologs of non-pleiotropic visual genes that are evolving at rates consistent with purifying selection. Together, these results suggest that although living underground tends to lead to major losses of visual functions, natural selection is maintaining genes that support the eye, perhaps as an organ for circadian and/or circannual entrainment.
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Affiliation(s)
- Christopher A Emerling
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Institut des Sciences de l'Evolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, 34090 Montpellier, France
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8
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Delsuc F, Emerling CA, Nachman MW. [Chitinase genes provide insights into the radiation of placental mammals]. Med Sci (Paris) 2019; 35:12-15. [PMID: 30672452 DOI: 10.1051/medsci/2018317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frédéric Delsuc
- Institut des sciences de l'évolution de Montpellier (ISEM), CNRS, IRD, EPHE, université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Christopher A Emerling
- Institut des sciences de l'évolution de Montpellier (ISEM), CNRS, IRD, EPHE, université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France - Museum of vertebrate zoology, university of California, Berkeley, Californie, États-Unis
| | - Michael W Nachman
- Museum of vertebrate zoology, university of California, Berkeley, Californie, États-Unis
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Springer MS, Emerling CA, Gatesy J, Randall J, Collin MA, Hecker N, Hiller M, Delsuc F. Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales. BMC Evol Biol 2019; 19:31. [PMID: 30674270 PMCID: PMC6343362 DOI: 10.1186/s12862-019-1359-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we leverage the power of natural selection to test competing hypotheses that ODAM is tooth-specific versus pleiotropic. Specifically, we compiled and screened complete protein-coding sequences, plus sequences for flanking intronic regions, for ODAM in 165 placental mammals to determine if this gene contains inactivating mutations in lineages that either lack teeth (baleen whales, pangolins, anteaters) or lack enamel on their teeth (aardvarks, sloths, armadillos), as would be expected if the only essential functions of ODAM are related to tooth development and the adhesion of the gingival junctional epithelium to the enamel tooth surface. Results We discovered inactivating mutations in all species of placental mammals that either lack teeth or lack enamel on their teeth. A surprising result is that ODAM is also inactivated in a few additional lineages including all toothed whales that were examined. We hypothesize that ODAM inactivation is related to the simplified outer enamel surface of toothed whales. An alternate hypothesis is that ODAM inactivation in toothed whales may be related to altered antimicrobial functions of the junctional epithelium in aquatic habitats. Selection analyses on ODAM sequences revealed that the composite dN/dS value for pseudogenic branches is close to 1.0 as expected for a neutrally evolving pseudogene. DN/dS values on transitional branches were used to estimate ODAM inactivation times. In the case of pangolins, ODAM was inactivated ~ 65 million years ago, which is older than the oldest pangolin fossil (Eomanis, 47 Ma) and suggests an even more ancient loss or simplification of teeth in this lineage. Conclusion Our results validate the hypothesis that the only essential functions of ODAM that are maintained by natural selection are related to tooth development and/or the maintenance of a healthy junctional epithelium that attaches to the enamel surface of teeth. Electronic supplementary material The online version of this article (10.1186/s12862-019-1359-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA.
| | - Christopher A Emerling
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.,Department of Biology, Whittier College, Whittier, CA, 90602, USA
| | - John Gatesy
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Jason Randall
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Matthew A Collin
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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Maheepala DC, Emerling CA, Rajewski A, Macon J, Strahl M, Pabón-Mora N, Litt A. Evolution and Diversification of FRUITFULL Genes in Solanaceae. Front Plant Sci 2019; 10:43. [PMID: 30846991 PMCID: PMC6394111 DOI: 10.3389/fpls.2019.00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 01/11/2019] [Indexed: 05/12/2023]
Abstract
Ecologically and economically important fleshy edible fruits have evolved from dry fruit numerous times during angiosperm diversification. However, the molecular mechanisms that underlie these shifts are unknown. In the Solanaceae there has been a major shift to fleshy fruits in the subfamily Solanoideae. Evidence suggests that an ortholog of FRUITFULL (FUL), a transcription factor that regulates cell proliferation and limits the dehiscence zone in the silique of Arabidopsis, plays a similar role in dry-fruited Solanaceae. However, studies have shown that FUL orthologs have taken on new functions in fleshy fruit development, including regulating elements of tomato ripening such as pigment accumulation. FUL belongs to the core eudicot euFUL clade of the angiosperm AP1/FUL gene lineage. The euFUL genes fall into two paralogous clades, euFULI and euFULII. While most core eudicots have one gene in each clade, Solanaceae have two: FUL1 and FUL2 in the former, and MBP10 and MBP20 in the latter. We characterized the evolution of the euFUL genes to identify changes that might be correlated with the origin of fleshy fruit in Solanaceae. Our analyses revealed that the Solanaceae FUL1 and FUL2 clades probably originated through an early whole genome multiplication event. By contrast, the data suggest that the MBP10 and MBP20 clades are the result of a later tandem duplication event. MBP10 is expressed at weak to moderate levels, and its atypical short first intron lacks putative transcription factor binding sites, indicating possible pseudogenization. Consistent with this, our analyses show that MBP10 is evolving at a faster rate compared to MBP20. Our analyses found that Solanaceae euFUL gene duplications, evolutionary rates, and changes in protein residues and expression patterns are not correlated with the shift in fruit type. This suggests deeper analyses are needed to identify the mechanism underlying the change in FUL ortholog function.
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Affiliation(s)
- Dinusha C. Maheepala
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Christopher A. Emerling
- Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, École Pratique des Hautes Études, Montpellier, France
| | - Alex Rajewski
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Jenna Macon
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Maya Strahl
- The New York Botanical Garden, Bronx, NY, United States
| | | | - Amy Litt
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Amy Litt,
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Ain NU, Iqbal M, Valta H, Emerling CA, Ahmed S, Makitie O, Naz S. Novel variants in natriuretic peptide receptor 2 in unrelated patients with acromesomelic dysplasia type Maroteaux. Eur J Med Genet 2018; 62:103554. [PMID: 30359775 DOI: 10.1016/j.ejmg.2018.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/05/2018] [Accepted: 10/20/2018] [Indexed: 11/29/2022]
Abstract
Acromesomelic dysplasia are a heterogeneous group of disorders with variable spectrum and severity of skeletal anomalies in the affected individuals. Acromesomelic dysplasia type Maroteaux (AMDM) is characterized by extreme shortening of the forelimbs and disproportionate short stature. Several homozygous inactivating mutations in NPR2 have been identified in different AMDM patients. We report five novel variants in affected individuals in four different families. These include two nonsense and three missense variants. This study broadens the genotypic spectrum of NPR2 mutations in individuals with AMDM and also describes the intra- and inter-familial phenotypic variability due to NPR2 variants.
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Affiliation(s)
- Noor Ul Ain
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan; Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Muddassar Iqbal
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Helena Valta
- Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Christopher A Emerling
- Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sufian Ahmed
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Outi Makitie
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Folkhälsan Institute of Genetics and University of Helsinki, Helsinki, Finland; Department of Clinical Genetics, HUSLAB, Helsinki University Hospital, Helsinki, Finland; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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Emerling CA, Delsuc F, Nachman MW. Chitinase genes ( CHIAs) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals. Sci Adv 2018; 4:eaar6478. [PMID: 29774238 PMCID: PMC5955627 DOI: 10.1126/sciadv.aar6478] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/30/2018] [Indexed: 05/21/2023]
Abstract
The end-Cretaceous extinction led to a massive faunal turnover, with placental mammals radiating in the wake of nonavian dinosaurs. Fossils indicate that Cretaceous stem placentals were generally insectivorous, whereas their earliest Cenozoic descendants occupied a variety of dietary niches. It is hypothesized that this dietary radiation resulted from the opening of niche space, following the extinction of dinosaurian carnivores and herbivores. We provide the first genomic evidence for the occurrence and timing of this dietary radiation in placental mammals. By comparing the genomes of 107 placental mammals, we robustly infer that chitinase genes (CHIAs), encoding enzymes capable of digesting insect exoskeletal chitin, were present as five functional copies in the ancestor of all placental mammals, and the number of functional CHIAs in the genomes of extant species positively correlates with the percentage of invertebrates in their diets. The diverse repertoire of CHIAs in early placental mammals corroborates fossil evidence of insectivory in Cretaceous eutherians, with descendant lineages repeatedly losing CHIAs beginning at the Cretaceous/Paleogene (K/Pg) boundary as they radiated into noninsectivorous niches. Furthermore, the timing of gene loss suggests that interordinal diversification of placental mammals in the Cretaceous predates the dietary radiation in the early Cenozoic, helping to reconcile a long-standing debate between molecular timetrees and the fossil record. Our results demonstrate that placental mammal genomes, including humans, retain a molecular record of the post-K/Pg placental adaptive radiation in the form of numerous chitinase pseudogenes.
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Affiliation(s)
- Christopher A. Emerling
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Institut des Sciences de l’Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
- Corresponding author.
| | - Frédéric Delsuc
- Institut des Sciences de l’Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Michael W. Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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Emerling CA, Widjaja AD, Nguyen NN, Springer MS. Their loss is our gain: regressive evolution in vertebrates provides genomic models for uncovering human disease loci. J Med Genet 2017; 54:787-794. [PMID: 28814606 DOI: 10.1136/jmedgenet-2017-104837] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/07/2017] [Accepted: 07/10/2017] [Indexed: 12/20/2022]
Abstract
Throughout Earth's history, evolution's numerous natural 'experiments' have resulted in a diverse range of phenotypes. Though de novo phenotypes receive widespread attention, degeneration of traits inherited from an ancestor is a very common, yet frequently neglected, evolutionary path. The latter phenomenon, known as regressive evolution, often results in vertebrates with phenotypes that mimic inherited disease states in humans. Regressive evolution of anatomical and/or physiological traits is typically accompanied by inactivating mutations underlying these traits, which frequently occur at loci identical to those implicated in human diseases. Here we discuss the potential utility of examining the genomes of vertebrates that have experienced regressive evolution to inform human medical genetics. This approach is low cost and high throughput, giving it the potential to rapidly improve knowledge of disease genetics. We discuss two well-described examples, rod monochromacy (congenital achromatopsia) and amelogenesis imperfecta, to demonstrate the utility of this approach, and then suggest methods to equip non-experts with the ability to corroborate candidate genes and uncover new disease loci.
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Affiliation(s)
- Christopher A Emerling
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Biology, University of California, Riverside, California, USA
| | - Andrew D Widjaja
- Department of Biochemistry, University of California, Riverside, California, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, USA
| | - Nancy N Nguyen
- Department of Bioengineering, University of California, Riverside, California, USA
- Department of Bioengineering, University of California, Los Angeles, California, USA
| | - Mark S Springer
- Department of Biology, University of California, Riverside, California, USA
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Abstract
Vertebrate color vision has evolved partly through the modification of five ancestral visual opsin proteins via gene duplication, loss, and shifts in spectral sensitivity. While many vertebrates, particularly mammals, birds, and fishes, have had their visual opsin repertoires studied in great detail, testudines (turtles) and crocodylians have largely been neglected. Here I examine the genomic basis for color vision in four species of turtles and four species of crocodylians, and demonstrate that while turtles appear to vary in their number of visual opsins, crocodylians experienced a reduction in their color discrimination capacity after their divergence from Aves. Based on the opsin sequences present in their genomes and previous measurements of crocodylian cones, I provide evidence that crocodylians have co-opted the rod opsin (RH1) for cone function. This suggests that some crocodylians might have reinvented trichromatic color vision in a novel way, analogous to several primate lineages. The loss of visual opsins in crocodylians paralleled the loss of various anatomical features associated with photoreception, attributed to a "nocturnal bottleneck" similar to that hypothesized for Mesozoic mammals. I further queried crocodylian genomes for nonvisual opsins and genes associated with protection from ultraviolet light, and found evidence for gene inactivation or loss for several of these genes. Two genes, encoding parietopsin and parapinopsin, were additionally inactivated in birds and turtles, likely co-occurring with the loss of the parietal eye in these lineages.
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Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP. Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. Genome Biol Evol 2017; 9:2522-2545. [PMID: 28992302 PMCID: PMC5629816 DOI: 10.1093/gbe/evx158] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/20/2022] Open
Abstract
We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106 nt. We calculated the genome-wide fixation index (FST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.
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Affiliation(s)
- Zachary R. Hanna
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, California, USA
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, California, USA
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, USA
| | - James B. Henderson
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, California, USA
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, USA
| | - Jeffrey D. Wall
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, California, USA
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, USA
- Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Christopher A. Emerling
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Jérôme Fuchs
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, California, USA
- UMR 7205 Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Charles Runckel
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Howard Hughes Medical Institute, Bethesda, Maryland, USA
- Runckel & Associates, Portland, Oregon, USA
| | - David P. Mindell
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Howard Hughes Medical Institute, Bethesda, Maryland, USA
| | - John P. Dumbacher
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, California, USA
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California, USA
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Emerling CA. Genomic regression of claw keratin, taste receptor and light-associated genes provides insights into biology and evolutionary origins of snakes. Mol Phylogenet Evol 2017; 115:40-49. [PMID: 28739369 DOI: 10.1016/j.ympev.2017.07.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 06/16/2017] [Accepted: 07/13/2017] [Indexed: 01/11/2023]
Abstract
Regressive evolution of anatomical traits often corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The evolutionary origins of snakes involved the regression of a number of anatomical traits, including limbs, taste buds and the visual system, and by analyzing serpent genomes, I was able to test three hypotheses associated with the regression of these features. The first concerns two keratins that are putatively specific to claws. Both genes that encode these keratins are pseudogenized/deleted in snake genomes, providing additional evidence of claw-specificity. The second hypothesis is that snakes lack taste buds, an issue complicated by conflicting results in the literature. I found evidence that different snakes have lost one or more taste receptors, but all snakes examined retained at least one gustatory channel. The final hypothesis addressed is that the earliest snakes were adapted to a dim light niche. I found evidence of deleted and pseudogenized genes with light-associated functions in snakes, demonstrating a pattern of gene loss similar to other dim light-adapted clades. Molecular dating estimates suggest that dim light adaptation preceded the loss of limbs, providing some bearing on interpretations of the ecological origins of snakes.
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Springer MS, Emerling CA, Meredith RW, Janečka JE, Eizirik E, Murphy WJ. Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification. Mol Phylogenet Evol 2016; 106:86-102. [PMID: 27659724 DOI: 10.1016/j.ympev.2016.09.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 09/15/2016] [Accepted: 09/18/2016] [Indexed: 02/06/2023]
Abstract
The explosive, long fuse, and short fuse models represent competing hypotheses for the timing of placental mammal diversification. Support for the explosive model, which posits both interordinal and intraordinal diversification after the KPg mass extinction, derives from morphological cladistic studies that place Cretaceous eutherians outside of crown Placentalia. By contrast, most molecular studies favor the long fuse model wherein interordinal cladogenesis occurred in the Cretaceous followed by intraordinal cladogenesis after the KPg boundary. Phillips (2016) proposed a soft explosive model that allows for the emergence of a few lineages (Xenarthra, Afrotheria, Euarchontoglires, Laurasiatheria) in the Cretaceous, but otherwise agrees with the explosive model in positing the majority of interordinal diversification after the KPg mass extinction. Phillips (2016) argues that rate transference errors associated with large body size and long lifespan have inflated previous estimates of interordinal divergence times, and further suggests that most interordinal divergences are positioned after the KPg boundary when rate transference errors are avoided through the elimination of calibrations in large-bodied and/or long lifespan clades. Here, we show that rate transference errors can also occur in the opposite direction and drag forward estimated divergence dates when calibrations in large-bodied/long lifespan clades are omitted. This dragging forward effect results in the occurrence of more than half a billion years of 'zombie lineages' on Phillips' preferred timetree. By contrast with ghost lineages, which are a logical byproduct of an incomplete fossil record, zombie lineages occur when estimated divergence dates are younger than the minimum age of the oldest crown fossils. We also present the results of new timetree analyses that address the rate transference problem highlighted by Phillips (2016) by deleting taxa that exceed thresholds for body size and lifespan. These analyses recover all interordinal divergence times in the Cretaceous and are consistent with the long fuse model of placental diversification. Finally, we outline potential problems with morphological cladistic analyses of higher-level relationships among placental mammals that may account for the perceived discrepancies between molecular and paleontological estimates of placental divergence times.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
| | | | - Robert W Meredith
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA
| | - Jan E Janečka
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Eduardo Eizirik
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS 90619-900, Brazil
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
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Springer MS, Emerling CA, Fugate N, Patel R, Starrett J, Morin PA, Hayashi C, Gatesy J. Inactivation of Cone-Specific Phototransduction Genes in Rod Monochromatic Cetaceans. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00061] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Emerling CA, Springer MS. Genomic evidence for rod monochromacy in sloths and armadillos suggests early subterranean history for Xenarthra. Proc Biol Sci 2016; 282:20142192. [PMID: 25540280 DOI: 10.1098/rspb.2014.2192] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rod monochromacy is a rare condition in vertebrates characterized by the absence of cone photoreceptor cells. The resulting phenotype is colourblindness and low acuity vision in dim-light and blindness in bright-light conditions. Early reports of xenarthrans (armadillos, sloths and anteaters) suggest that they are rod monochromats, but this has not been tested with genomic data. We searched the genomes of Dasypus novemcinctus (nine-banded armadillo), Choloepus hoffmanni (Hoffmann's two-toed sloth) and Mylodon darwinii (extinct ground sloth) for retinal photoreceptor genes and examined them for inactivating mutations. We performed PCR and Sanger sequencing on cone phototransduction genes of 10 additional xenarthrans to test for shared inactivating mutations and estimated the timing of inactivation for photoreceptor pseudogenes. We concluded that a stem xenarthran became an long-wavelength sensitive-cone monochromat following a missense mutation at a critical residue in SWS1, and a stem cingulate (armadillos, glyptodonts and pampatheres) and stem pilosan (sloths and anteaters) independently acquired rod monochromacy early in their evolutionary history following the inactivation of LWS and PDE6C, respectively. We hypothesize that rod monochromacy in armadillos and pilosans evolved as an adaptation to a subterranean habitat in the early history of Xenarthra. The presence of rod monochromacy has major implications for understanding xenarthran behavioural ecology and evolution.
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Affiliation(s)
- Christopher A Emerling
- Department of Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Mark S Springer
- Department of Biology, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
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Emerling CA, Huynh HT, Nguyen MA, Meredith RW, Springer MS. Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution. Proc Biol Sci 2015; 282:20151817. [PMID: 26582021 PMCID: PMC4685808 DOI: 10.1098/rspb.2015.1817] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/09/2015] [Indexed: 11/12/2022] Open
Abstract
Retinal opsin photopigments initiate mammalian vision when stimulated by light. Most mammals possess a short wavelength-sensitive opsin 1 (SWS1) pigment that is primarily sensitive to either ultraviolet or violet light, leading to variation in colour perception across species. Despite knowledge of both ultraviolet- and violet-sensitive SWS1 classes in mammals for 25 years, the adaptive significance of this variation has not been subjected to hypothesis testing, resulting in minimal understanding of the basis for mammalian SWS1 spectral tuning evolution. Here, we gathered data on SWS1 for 403 mammal species, including novel SWS1 sequences for 97 species. Ancestral sequence reconstructions suggest that the most recent common ancestor of Theria possessed an ultraviolet SWS1 pigment, and that violet-sensitive pigments evolved at least 12 times in mammalian history. We also observed that ultraviolet pigments, previously considered to be a rarity, are common in mammals. We then used phylogenetic comparative methods to test the hypotheses that the evolution of violet-sensitive SWS1 is associated with increased light exposure, extended longevity and longer eye length. We discovered that diurnal mammals and species with longer eyes are more likely to have violet-sensitive pigments and less likely to possess UV-sensitive pigments. We hypothesize that (i) as mammals evolved larger body sizes, they evolved longer eyes, which limited transmittance of ultraviolet light to the retina due to an increase in Rayleigh scattering, and (ii) as mammals began to invade diurnal temporal niches, they evolved lenses with low UV transmittance to reduce chromatic aberration and/or photo-oxidative damage.
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Affiliation(s)
- Christopher A Emerling
- Department of Biology, University of California Riverside, Riverside, CA, USA Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
| | - Hieu T Huynh
- Department of Biology, University of California Riverside, Riverside, CA, USA School of Pharmacy, Loma Linda University, Loma Linda, CA, USA
| | - Minh A Nguyen
- Department of Biology, University of California Riverside, Riverside, CA, USA School of Pharmacy, Loma Linda University, Loma Linda, CA, USA
| | - Robert W Meredith
- Department of Biology, University of California Riverside, Riverside, CA, USA Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ, USA
| | - Mark S Springer
- Department of Biology, University of California Riverside, Riverside, CA, USA
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Westerman M, Krajewski C, Kear BP, Meehan L, Meredith RW, Emerling CA, Springer MS. Phylogenetic relationships of dasyuromorphian marsupials revisited. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12323] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Michael Westerman
- Genetics Department; LaTrobe University; Melbourne Vic. 3086 Australia
| | - Carey Krajewski
- Zoology Department; Southern Illinois University; Carbondale IL 62901 USA
| | - Benjamin P. Kear
- Paleobiology Programme; Department of Earth Sciences; Uppsala University; Villavagen 16 SE-752 36 Uppsala Sweden
| | - Lucy Meehan
- Genetics Department; LaTrobe University; Melbourne Vic. 3086 Australia
| | | | | | - Mark S. Springer
- Department of Biology; University of California; Riverside CA 92521 USA
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Emerling CA, Springer MS. Eyes underground: regression of visual protein networks in subterranean mammals. Mol Phylogenet Evol 2014; 78:260-70. [PMID: 24859681 DOI: 10.1016/j.ympev.2014.05.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 04/26/2014] [Accepted: 05/05/2014] [Indexed: 11/26/2022]
Abstract
Regressive evolution involves the degeneration of formerly useful structures in a lineage over time, and may be accompanied by the molecular decay of phenotype-specific genes. The mammalian eye has repeatedly undergone degeneration in taxa that occupy dim-light environments including subterranean habitats. Here we assess whether a decrease in the amount of light that reaches the retina is associated with increased regression of retinal genes, whether the phototransduction and visual cycle pathways degrade in a predictable pattern, and if the timing of retinal gene loss is associated with the entrance of mammalian lineages into subterranean environments. Sequence data were obtained from the publically available genomes of the Cape golden mole (Chrysochloris asiatica), naked mole-rat (Heterocephalus glaber) and star-nosed mole (Condylura cristata) for 65 genes associated with phototransduction, the visual cycle, and other retinal functions. Gene sequences were inspected for inactivating mutations and, when present, pseudogene sequences were compared to sequences from subaerial outgroup species. To test whether retinal degeneration is correlated with historical entrances into subterranean environments, estimated dates of retinal gene inactivation were compared to the fossil record and phylogenetic inferences of ancestral fossoriality. Our results show that (1) lower levels of light available to the retina correspond with an increase in the number of retinal pseudogenes, (2) retinal protein networks generally degrade in a predictable manner, although the extensive loss of cone phototransduction genes in Heterocephalus raises further questions regarding SWS1-cone monochromacy versus functional rod monochromacy in this species, and (3) inactivation dates of retinal genes usually post-date inferred entrances into subterranean habitats.
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Affiliation(s)
- Christopher A Emerling
- Department of Biology, University of California Riverside, 900 University Ave, Riverside, CA 92521, United States.
| | - Mark S Springer
- Department of Biology, University of California Riverside, 900 University Ave, Riverside, CA 92521, United States.
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Meredith RW, Gatesy J, Emerling CA, York VM, Springer MS. Rod monochromacy and the coevolution of cetacean retinal opsins. PLoS Genet 2013; 9:e1003432. [PMID: 23637615 PMCID: PMC3630094 DOI: 10.1371/journal.pgen.1003432] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/15/2013] [Indexed: 01/02/2023] Open
Abstract
Cetaceans have a long history of commitment to a fully aquatic lifestyle that extends back to the Eocene. Extant species have evolved a spectacular array of adaptations in conjunction with their deployment into a diverse array of aquatic habitats. Sensory systems are among those that have experienced radical transformations in the evolutionary history of this clade. In the case of vision, previous studies have demonstrated important changes in the genes encoding rod opsin (RH1), short-wavelength sensitive opsin 1 (SWS1), and long-wavelength sensitive opsin (LWS) in selected cetaceans, but have not examined the full complement of opsin genes across the complete range of cetacean families. Here, we report protein-coding sequences for RH1 and both color opsin genes (SWS1, LWS) from representatives of all extant cetacean families. We examine competing hypotheses pertaining to the timing of blue shifts in RH1 relative to SWS1 inactivation in the early history of Cetacea, and we test the hypothesis that some cetaceans are rod monochomats. Molecular evolutionary analyses contradict the "coastal" hypothesis, wherein SWS1 was pseudogenized in the common ancestor of Cetacea, and instead suggest that RH1 was blue-shifted in the common ancestor of Cetacea before SWS1 was independently knocked out in baleen whales (Mysticeti) and in toothed whales (Odontoceti). Further, molecular evidence implies that LWS was inactivated convergently on at least five occasions in Cetacea: (1) Balaenidae (bowhead and right whales), (2) Balaenopteroidea (rorquals plus gray whale), (3) Mesoplodon bidens (Sowerby's beaked whale), (4) Physeter macrocephalus (giant sperm whale), and (5) Kogia breviceps (pygmy sperm whale). All of these cetaceans are known to dive to depths of at least 100 m where the underwater light field is dim and dominated by blue light. The knockout of both SWS1 and LWS in multiple cetacean lineages renders these taxa rod monochromats, a condition previously unknown among mammalian species.
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Affiliation(s)
- Robert W. Meredith
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology and Molecular Biology, Montclair State University, Montclair, New Jersey, United States of America
| | - John Gatesy
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Christopher A. Emerling
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Vincent M. York
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Mark S. Springer
- Department of Biology, University of California Riverside, Riverside, California, United States of America
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24
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Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janečka JE, Fisher CA, Murphy WJ. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS One 2012; 7:e49521. [PMID: 23166696 PMCID: PMC3500307 DOI: 10.1371/journal.pone.0049521] [Citation(s) in RCA: 270] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 10/09/2012] [Indexed: 01/24/2023] Open
Abstract
Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ("Grande Coupure") at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.
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Affiliation(s)
- Mark S. Springer
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert W. Meredith
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology and Molecular Biology, Montclair State University, Montclair, New Jersey, United States of America
| | - John Gatesy
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Christopher A. Emerling
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Jong Park
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Rabosky
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tanja Stadler
- Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zurich, Zurich, Switzerland
| | - Cynthia Steiner
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Oliver A. Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Jan E. Janečka
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Colleen A. Fisher
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
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