101
|
Leslie AB, Losada JM. Reproductive Ontogeny and the Evolution of Morphological Diversity in Conifers and Other Plants. Integr Comp Biol 2019; 59:548-558. [DOI: 10.1093/icb/icz062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Biologists often study morphological evolution through form and function relationships. But biological structures can perform multiple functional roles, complicating efforts to understand the evolutionary significance of any one relationship. Plant reproductive organs perform multiple roles in a sequence, however, which provides a unique opportunity to understand how structures evolve to meet multiple functional demands. Using conifers as a study group, we discuss how a shared developmental trajectory links the performance of sequential functional roles. Variation in development among lineages can underlie morphological diversity; pollination-stage seed cones in Pinaceae conifers function similarly but show diverse forms reflecting differences in developmental rate. As cones develop further, the morphologies that they use to perform later functional roles are influenced by the specific developmental patterns used to meet earlier demands, which may ultimately limit morphological diversity. However, we also show how selective pressures relating to the final functional stage (seed dispersal) may influence cone anatomy and morphology over all previous stages, highlighting the complex linkages among form, function, and development. We end by discussing the potential relationships between functional ontogeny and morphological disparity in plant reproductive structures more broadly, suggesting that the complex functional roles associated with seed plant reproduction probably underlie the high disparity in this group.
Collapse
Affiliation(s)
- A B Leslie
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, RI 02912, USA
| | - J M Losada
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC). Avda. Dr. Wienberg s/n, Algarrobo-Costa, Málaga 29750, Spain
| |
Collapse
|
102
|
Gutierrez EDA, Castiglione GM, Morrow JM, Schott RK, Loureiro LO, Lim BK, Chang BSW. Functional Shifts in Bat Dim-Light Visual Pigment Are Associated with Differing Echolocation Abilities and Reveal Molecular Adaptation to Photic-Limited Environments. Mol Biol Evol 2019; 35:2422-2434. [PMID: 30010964 DOI: 10.1093/molbev/msy140] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a nonecholocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis. We also found that these rates of decay were remarkably slower compared with those of other mammals, likely indicating an adaptation to dim light. To examine whether functional changes in rhodopsin are associated with shifts in selection intensity upon bat Rh1 sequences, we implemented selection analyses using codon-based likelihood clade models. While no shifts in selection were identified in response to diverse echolocation abilities of bats, we detected a significant increase in the intensity of evolutionary constraint accompanying the diversification of Chiroptera. Taken together, this suggests that substitutions that modulate the stability of the light-activated rhodopsin state were likely maintained through intensified constraint after bats diversified, being finely tuned in response to novel sensory specializations. Our study demonstrates the power of combining experimental and computational approaches for investigating functional mechanisms underlying the evolution of complex sensory adaptations.
Collapse
Affiliation(s)
- Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, ON, Canada.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James M Morrow
- Department of Cell and Systems Biology, University of Toronto, ON, Canada.,Centre of Forensic Sciences, Toronto, ON, Canada
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Livia O Loureiro
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, ON, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
103
|
Nyakatura JA. Early primate evolution: insights into the functional significance of grasping from motion analyses of extant mammals. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- John A Nyakatura
- AG Morphologie und Formengeschichte, Institut für Biologie, Humboldt Universität, Philippstraße, Berlin, Germany
| |
Collapse
|
104
|
Adams RH, Schield DR, Castoe TA. Recent Advances in the Inference of Gene Flow from Population Genomic Data. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s40610-019-00120-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
105
|
Nordeen CA, Martin SL. Engineering Human Stasis for Long-Duration Spaceflight. Physiology (Bethesda) 2019; 34:101-111. [PMID: 30724130 DOI: 10.1152/physiol.00046.2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Suspended animation for deep-space travelers is moving out of the realm of science fiction. Two approaches are considered: the first elaborates the current medical practice of therapeutic hypothermia; the second invokes the cascade of metabolic processes naturally employed by hibernators. We explore the basis and evidence behind each approach and argue that mimicry of natural hibernation will be critical to overcome the innate limitations of human physiology for long-duration space travel.
Collapse
Affiliation(s)
- Claire A Nordeen
- Department of Emergency Medicine, Harborview Medical Center, University of Washington , Seattle, Washington
| | - Sandra L Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine , Aurora, Colorado
| |
Collapse
|
106
|
de Sá ALA, Breaux B, Burlamaqui TCT, Deiss TC, Sena L, Criscitiello MF, Schneider MPC. The Marine Mammal Class II Major Histocompatibility Complex Organization. Front Immunol 2019; 10:696. [PMID: 31019512 PMCID: PMC6459222 DOI: 10.3389/fimmu.2019.00696] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/13/2019] [Indexed: 12/17/2022] Open
Abstract
Sirenians share with cetaceans and pinnipeds several convergent traits selected for the aquatic lifestyle. Living in water poses new challenges not only for locomotion and feeding but also for combating new pathogens, which may render the immune system one of the best tools aquatic mammals have for dealing with aquatic microbial threats. So far, only cetaceans have had their class II Major Histocompatibility Complex (MHC) organization characterized, despite the importance of MHC genes for adaptive immune responses. This study aims to characterize the organization of the marine mammal class II MHC using publicly available genomes. We located class II sequences in the genomes of one sirenian, four pinnipeds and eight cetaceans using NCBI-BLAST and reannotated the sequences using local BLAST search with exon and intron libraries. Scaffolds containing class II sequences were compared using dotplot analysis and introns were used for phylogenetic analysis. The manatee class II region shares overall synteny with other mammals, however most DR loci were translocated from the canonical location, past the extended class II region. Detailed analysis of the genomes of closely related taxa revealed that this presumed translocation is shared with all other living afrotherians. Other presumptive chromosome rearrangements in Afrotheria are the deletion of DQ loci in Afrosoricida and deletion of DP in E. telfairi. Pinnipeds share the main features of dog MHC: lack of a functional pair of DPA/DPB genes and inverted DRB locus between DQ and DO subregions. All cetaceans share the Cetartiodactyla inversion separating class II genes into two subregions: class IIa, with DR and DQ genes, and class IIb, with non-classic genes and a DRB pseudogene. These results point to three distinct and unheralded class II MHC structures in marine mammals: one canonical organization but lacking DP genes in pinnipeds; one bearing an inversion separating IIa and IIb subregions lacking DP genes found in cetaceans; and one with a translocation separating the most diverse class II gene from the MHC found in afrotherians and presumptive functional DR, DQ, and DP genes. Future functional research will reveal how these aquatic mammals cope with pathogen pressures with these divergent MHC organizations.
Collapse
Affiliation(s)
- André Luiz Alves de Sá
- Laboratory of Applied Genetics, Socio-Environmental and Water Resources Institute, Federal Rural University of the Amazon, Belém, Brazil.,Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
| | - Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | | | - Thaddeus Charles Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Leonardo Sena
- Center of Biodiversity Advanced Studies, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
| | - Michael Frederick Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Maria Paula Cruz Schneider
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará, Belém, Brazil
| |
Collapse
|
107
|
Carter AM. Hans Bluntschli in Berne: Researching reproduction in hedgehog tenrecs (Afrosoricida, Tenrecidae). J Morphol 2019; 280:841-848. [DOI: 10.1002/jmor.20988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Anthony M. Carter
- Cardiovascular and Renal ResearchInstitute of Molecular Medicine, University of Southern Denmark Odense Denmark
| |
Collapse
|
108
|
Laurin-Lemay S, Philippe H, Rodrigue N. Multiple Factors Confounding Phylogenetic Detection of Selection on Codon Usage. Mol Biol Evol 2019; 35:1463-1472. [PMID: 29596640 DOI: 10.1093/molbev/msy047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Detecting selection on codon usage (CU) is a difficult task, since CU can be shaped by both the mutational process and selective constraints operating at the DNA, RNA, and protein levels. Yang and Nielsen (2008) developed a test (which we call CUYN) for detecting selection on CU using two competing mutation-selection models of codon substitution. The null model assumes that CU is determined by the mutation bias alone, whereas the alternative model assumes that both mutation bias and/or selection act on CU. In applications on mammalian-scale alignments, the CUYN test detects selection on CU for numerous genes. This is surprising, given the small effective population size of mammals, and prompted us to use simulations to evaluate the robustness of the test to model violations. Simulations using a modest level of CpG hypermutability completely mislead the test, with 100% false positives. Surprisingly, a high level of false positives (56.1%) resulted simply from using the HKY mutation-level parameterization within the CUYN test on simulations conducted with a GTR mutation-level parameterization. Finally, by using a crude optimization procedure on a parameter controlling the CpG hypermutability rate, we find that this mutational property could explain a very large part of the observed mammalian CU. Altogether, our work emphasizes the need to evaluate the potential impact of model violations on statistical tests in the field of molecular phylogenetic analysis. The source code of the simulator and the mammalian genes used are available as a GitHub repository (https://github.com/Simonll/LikelihoodFreePhylogenetics.git).
Collapse
Affiliation(s)
- Simon Laurin-Lemay
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Center for Bioinformatics and Genomics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Hervé Philippe
- Department of Biochemistry and Molecular Medicine, Robert-Cedergren Center for Bioinformatics and Genomics, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.,Centre de Théorisation et de Modélisation de la Biodiversité, Station d'Écologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, Ariège, France
| | - Nicolas Rodrigue
- Department of Biology, Institute of Biochemistry, and School of Mathematics and Statistics, Carleton University, Ottawa, ON, Canada
| |
Collapse
|
109
|
McKee CD, Krawczyk AI, Sándor AD, Görföl T, Földvári M, Földvári G, Dekeukeleire D, Haarsma AJ, Kosoy MY, Webb CT, Sprong H. Host Phylogeny, Geographic Overlap, and Roost Sharing Shape Parasite Communities in European Bats. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00069] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
110
|
Halliday TJD, dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z, Goswami A. Rapid morphological evolution in placental mammals post-dates the origin of the crown group. Proc Biol Sci 2019; 286:20182418. [PMID: 30836875 PMCID: PMC6458320 DOI: 10.1098/rspb.2018.2418] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/12/2019] [Indexed: 12/28/2022] Open
Abstract
Resolving the timing and pattern of early placental mammal evolution has been confounded by conflict among divergence date estimates from interpretation of the fossil record and from molecular-clock dating studies. Despite both fossil occurrences and molecular sequences favouring a Cretaceous origin for Placentalia, no unambiguous Cretaceous placental mammal has been discovered. Investigating the differing patterns of evolution in morphological and molecular data reveals a possible explanation for this conflict. Here, we quantified the relationship between morphological and molecular rates of evolution. We show that, independent of divergence dates, morphological rates of evolution were slow relative to molecular evolution during the initial divergence of Placentalia, but substantially increased during the origination of the extant orders. The rapid radiation of placentals into a highly morphologically disparate Cenozoic fauna is thus not associated with the origin of Placentalia, but post-dates superordinal origins. These findings predict that early members of major placental groups may not be easily distinguishable from one another or from stem eutherians on the basis of skeleto-dental morphology. This result supports a Late Cretaceous origin of crown placentals with an ordinal-level adaptive radiation in the early Paleocene, with the high relative rate permitting rapid anatomical change without requiring unreasonably fast molecular evolutionary rates. The lack of definitive Cretaceous placental mammals may be a result of morphological similarity among stem and early crown eutherians, providing an avenue for reconciling the fossil record with molecular divergence estimates for Placentalia.
Collapse
Affiliation(s)
- Thomas J. D. Halliday
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
- School of Geography, Earth, and Environmental Science, University of Birmingham, Edgbaston B15 2TT, UK
| | - Mario dos Reis
- School of Biological and Chemical Sciences, Queen Mary University London, Mile End Road, London E1 4NS, UK
| | - Asif U. Tamuri
- Research IT Services, University College London, Gower Street, London WC1E 6BT, UK
- European Molecular Biology Laboratory, European Bioinformatics, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Henry Ferguson-Gow
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ziheng Yang
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Anjali Goswami
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, UK
- Faculty of Life Sciences, Natural History Museum, Cromwell Road, London SW9 5DJ, UK
| |
Collapse
|
111
|
Grunstra NDS, Zachos FE, Herdina AN, Fischer B, Pavličev M, Mitteroecker P. Humans as inverted bats: A comparative approach to the obstetric conundrum. Am J Hum Biol 2019; 31:e23227. [PMID: 30810261 PMCID: PMC6492174 DOI: 10.1002/ajhb.23227] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVES The narrow human birth canal evolved in response to multiple opposing selective forces on the pelvis. These factors cannot be sufficiently disentangled in humans because of the limited range of relevant variation. Here, we outline a comparative strategy to study the evolution of human childbirth and to test existing hypotheses in primates and other mammals. METHODS We combined a literature review with comparative analyses of neonatal and female body and brain mass, using three existing datasets. We also present images of bony pelves of a diverse sample of taxa. RESULTS Bats, certain non-human primates, seals, and most ungulates, including whales, have much larger relative neonatal masses than humans, and they all differ in their anatomical adaptations for childbirth. Bats, as a group, are particularly interesting in this context as they give birth to the relatively largest neonates, and their pelvis is highly dimorphic: Whereas males have a fused symphysis, a ligament bridges a large pubic gap in females. The resulting strong demands on the widened and vulnerable pelvic floor likely are relaxed by roosting head-down. CONCLUSIONS Parturition has constituted a strong selective force in many non-human placentals. We illustrated how the demands on pelvic morphology resulting from locomotion, pelvic floor stability, childbirth, and perhaps also erectile function in males have been traded off differently in mammals, depending on their locomotion and environment. Exploiting the power of a comparative approach, we present new hypotheses and research directions for resolving the obstetric conundrum in humans.
Collapse
Affiliation(s)
- Nicole D. S. Grunstra
- Department of Theoretical BiologyUniversity of ViennaViennaAustria
- Mammal CollectionNatural History Museum ViennaViennaAustria
| | - Frank E. Zachos
- Mammal CollectionNatural History Museum ViennaViennaAustria
- Department of Integrative ZoologyUniversity of ViennaViennaAustria
| | | | - Barbara Fischer
- Konrad Lorenz Institute for Evolution and Cognition ResearchKlosterneuburgAustria
| | - Mihaela Pavličev
- Cincinnati Children's Hospital Medical CenterCincinnatiOhio
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhio
- Department of PhilosophyUniversity of CincinnatiCincinnatiOhio
| | - Philipp Mitteroecker
- Department of Theoretical BiologyUniversity of ViennaViennaAustria
- Konrad Lorenz Institute for Evolution and Cognition ResearchKlosterneuburgAustria
| |
Collapse
|
112
|
Youlatos D, Widayati KA, Tsuji Y. Foot postures and grasping of free-ranging Sunda colugos (Galeopterus variegatus) in West Java, Indonesia. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
113
|
Rasche A, Sander AL, Corman VM, Drexler JF. Evolutionary biology of human hepatitis viruses. J Hepatol 2019; 70:501-520. [PMID: 30472320 PMCID: PMC7114834 DOI: 10.1016/j.jhep.2018.11.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/09/2018] [Accepted: 11/10/2018] [Indexed: 02/06/2023]
Abstract
Hepatitis viruses are major threats to human health. During the last decade, highly diverse viruses related to human hepatitis viruses were found in animals other than primates. Herein, we describe both surprising conservation and striking differences of the unique biological properties and infection patterns of human hepatitis viruses and their animal homologues, including transmission routes, liver tropism, oncogenesis, chronicity, pathogenesis and envelopment. We discuss the potential for translation of newly discovered hepatitis viruses into preclinical animal models for drug testing, studies on pathogenesis and vaccine development. Finally, we re-evaluate the evolutionary origins of human hepatitis viruses and discuss the past and present zoonotic potential of their animal homologues.
Collapse
Affiliation(s)
- Andrea Rasche
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany,German Center for Infection Research (DZIF), Germany
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - Victor Max Corman
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany,German Center for Infection Research (DZIF), Germany
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany; German Center for Infection Research (DZIF), Germany.
| |
Collapse
|
114
|
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: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
115
|
Dell L, Innocenti GM, Hilgetag CC, Manger PR. Cortical and thalamic connectivity of posterior parietal visual cortical areas PPc and PPr of the domestic ferret (
Mustela putorius furo
). J Comp Neurol 2019; 527:1315-1332. [DOI: 10.1002/cne.24630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Leigh‐Anne Dell
- Institute of Computational NeuroscienceUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Giorgio M. Innocenti
- Department of NeuroscienceKarolinska Institute Stockholm Sweden
- Brain and Mind InstituteÉcole Polytechnique Fédérale de Lausanne Lausanne Switzerland
| | - Claus C. Hilgetag
- Institute of Computational NeuroscienceUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
- Department of Health SciencesBoston University Boston Massachusetts
| | - Paul R. Manger
- School of Anatomical Sciences, Faculty of Health SciencesUniversity of the Witwatersrand Johannesburg South Africa
| |
Collapse
|
116
|
Bird DJ, Murphy WJ, Fox-Rosales L, Hamid I, Eagle RA, Van Valkenburgh B. Olfaction written in bone: cribriform plate size parallels olfactory receptor gene repertoires in Mammalia. Proc Biol Sci 2019. [PMID: 29540522 DOI: 10.1098/rspb.2018.0100] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolution of mammalian olfaction is manifested in a remarkable diversity of gene repertoires, neuroanatomy and skull morphology across living species. Olfactory receptor genes (ORGs), which initiate the conversion of odorant molecules into odour perceptions and help an animal resolve the olfactory world, range in number from a mere handful to several thousand genes across species. Within the snout, each of these ORGs is exclusively expressed by a discrete population of olfactory sensory neurons (OSNs), suggesting that newly evolved ORGs may be coupled with new OSN populations in the nasal epithelium. Because OSN axon bundles leave high-fidelity perforations (foramina) in the bone as they traverse the cribriform plate (CP) to reach the brain, we predicted that taxa with larger ORG repertoires would have proportionately expanded footprints in the CP foramina. Previous work found a correlation between ORG number and absolute CP size that disappeared after accounting for body size. Using updated, digital measurement data from high-resolution CT scans and re-examining the relationship between CP and body size, we report a striking linear correlation between relative CP area and number of functional ORGs across species from all mammalian superorders. This correlation suggests strong developmental links in the olfactory pathway between genes, neurons and skull morphology. Furthermore, because ORG number is linked to olfactory discriminatory function, this correlation supports relative CP size as a viable metric for inferring olfactory capacity across modern and extinct species. By quantifying CP area from a fossil sabertooth cat (Smilodon fatalis), we predicted a likely ORG repertoire for this extinct felid.
Collapse
Affiliation(s)
- Deborah J Bird
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA
| | - Lester Fox-Rosales
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| | - Iman Hamid
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| | - Robert A Eagle
- Department of Atmospheric and Oceanic Sciences, Institute of the Environment and Sustainability, University of California Los Angeles, 520 Portola Plaza, Math Sciences Building 7127, Los Angeles, CA 90095, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| |
Collapse
|
117
|
Imam A, Bhagwandin A, Ajao MS, Ihunwo AO, Manger PR. The brain of the tree pangolin (Manis tricuspis). IV. The hippocampal formation. J Comp Neurol 2019; 527:2393-2412. [PMID: 30592043 DOI: 10.1002/cne.24620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 01/06/2023]
Abstract
Employing a range of standard and immunohistochemical stains we provide a description of the hippocampal formation in the brain of the tree pangolin. For the most part, the architecture, chemical neuroanatomy, and topological relationships of the component parts of the hippocampal formation of the tree pangolin were consistent with that observed in other mammalian species. Within the hippocampus proper fields CA1, 3, and 4 could be identified with certainty, while CA2 was tentatively identified as a small transitional zone between the CA1 and CA3 fields. Within the dentate gyrus evidence for adult hippocampal neurogenesis at a rate comparable to other mammals was observed. The subicular complex and entorhinal cortex also exhibited divisions typically observed in other mammalian species. In contrast to many other mammals, an architecturally and neurochemically distinct CA4 field was observed, supporting Lorente de Nó's proposed CA4 field, at least in some mammalian species. In addition, up to seven laminae were evident in the dentate gyrus. Calretinin immunostaining revealed the three sublamina of the molecular layer, while immunostaining for vesicular glutamate transporter 2 and neurofilament H indicate that the granule cell layer was composed of two sublamina. The similarities and differences observed in the tree pangolin indicate that the hippocampal formation is an anatomically and neurochemically conserved neural unit in mammalian evolution, but minor changes may relate to specific life history features and habits of species.
Collapse
Affiliation(s)
- Aminu Imam
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa.,Department of Anatomy, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Adhil Bhagwandin
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Moyosore S Ajao
- Department of Anatomy, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | - Amadi O Ihunwo
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Paul R Manger
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
| |
Collapse
|
118
|
Simões BF, Foley NM, Hughes GM, Zhao H, Zhang S, Rossiter SJ, Teeling EC. As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats. Mol Biol Evol 2019; 36:54-68. [PMID: 30476197 PMCID: PMC6340466 DOI: 10.1093/molbev/msy192] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Through their unique use of sophisticated laryngeal echolocation bats are considered sensory specialists amongst mammals and represent an excellent model in which to explore sensory perception. Although several studies have shown that the evolution of vision is linked to ecological niche adaptation in other mammalian lineages, this has not yet been fully explored in bats. Recent molecular analysis of the opsin genes, which encode the photosensitive pigments underpinning color vision, have implicated high-duty cycle (HDC) echolocation and the adoption of cave roosting habits in the degeneration of color vision in bats. However, insufficient sampling of relevant taxa has hindered definitive testing of these hypotheses. To address this, novel sequence data was generated for the SWS1 and MWS/LWS opsin genes and combined with existing data to comprehensively sample species representing diverse echolocation types and niches (SWS1 n = 115; MWS/LWS n = 45). A combination of phylogenetic analysis, ancestral state reconstruction, and selective pressure analyses were used to reconstruct the evolution of these visual pigments in bats and revealed that although both genes are evolving under purifying selection in bats, MWS/LWS is highly conserved but SWS1 is highly variable. Spectral tuning analyses revealed that MWS/LWS opsin is tuned to a long wavelength, 555-560 nm in the bat ancestor and the majority of extant taxa. The presence of UV vision in bats is supported by our spectral tuning analysis, but phylogenetic analyses demonstrated that the SWS1 opsin gene has undergone pseudogenization in several lineages. We do not find support for a link between the evolution of HDC echolocation and the pseudogenization of the SWS1 gene in bats, instead we show the SWS1 opsin is functional in the HDC echolocator, Pteronotus parnellii. Pseudogenization of the SWS1 is correlated with cave roosting habits in the majority of pteropodid species. Together these results demonstrate that the loss of UV vision in bats is more widespread than was previously considered and further elucidate the role of ecological niche specialization in the evolution of vision in bats.
Collapse
Affiliation(s)
- Bruno F Simões
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
- School of Earth Science, University of Bristol, Bristol, United Kingdom
- School of Biological Science, The University of Adelaide, South Australia, Australia
| | - Nicole M Foley
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Graham M Hughes
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Huabin Zhao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
119
|
Valeri MP, Dias GB, Pereira VDS, Campos Silva Kuhn G, Svartman M. An eutherian intronic sequence gave rise to a major satellite DNA in Platyrrhini. Biol Lett 2018; 14:rsbl.2017.0686. [PMID: 29386361 DOI: 10.1098/rsbl.2017.0686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/08/2018] [Indexed: 11/12/2022] Open
Abstract
Satellite DNAs (satDNAs) are major components of eukaryote genomes. However, because of their quick divergence, the evolutionary origin of a given satDNA family can rarely be determined. Herein we took advantage of available primate sequenced genomes to determine the origin of the CapA satDNA (approx. 1500 bp long monomers), first described in the tufted capuchin monkey Sapajus apella We show that CapA is an abundant satDNA in Platyrrhini, whereas in the genomes of most eutherian mammals, including humans, this sequence is present only as a single copy located within a large intron of the NOS1AP (nitric oxide synthase 1 adaptor protein) gene. Our data suggest that this intronic CapA-like sequence gave rise to the CapA satDNA and we discuss possible mechanisms implicated in this event. This is the first report to our knowledge of a single copy intronic sequence giving origin to a satDNA that reaches up to 100 000 copies in some genomes.
Collapse
Affiliation(s)
- Mirela Pelizaro Valeri
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Guilherme Borges Dias
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | | | - Gustavo Campos Silva Kuhn
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Marta Svartman
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| |
Collapse
|
120
|
Sander AL, Corman VM, Lukashev AN, Drexler JF. Evolutionary Origins of Enteric Hepatitis Viruses. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031690. [PMID: 29610146 DOI: 10.1101/cshperspect.a031690] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The enterically transmitted hepatitis A (HAV) and hepatitis E viruses (HEV) are the leading causes of acute viral hepatitis in humans. Despite the discovery of HAV and HEV 40-50 years ago, their evolutionary origins remain unclear. Recent discoveries of numerous nonprimate hepatoviruses and hepeviruses allow revisiting the evolutionary history of these viruses. In this review, we provide detailed phylogenomic analyses of primate and nonprimate hepatoviruses and hepeviruses. We identify conserved and divergent genomic properties and corroborate historical interspecies transmissions by phylogenetic comparisons and recombination analyses. We discuss the likely non-recent origins of human HAV and HEV precursors carried by mammals other than primates, and detail current zoonotic HEV infections. The novel nonprimate hepatoviruses and hepeviruses offer exciting new possibilities for future research focusing on host range and the unique biological properties of HAV and HEV.
Collapse
Affiliation(s)
- Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany.,German Center for Infection Research (DZIF), Germany
| | - Victor Max Corman
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany.,German Center for Infection Research (DZIF), Germany
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119991 Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations, 142782 Moscow, Russia
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin 10117, Germany.,German Center for Infection Research (DZIF), Germany
| |
Collapse
|
121
|
Cascini M, Mitchell KJ, Cooper A, Phillips MJ. Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence. Syst Biol 2018; 68:520-537. [DOI: 10.1093/sysbio/syy080] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Manuela Cascini
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
| |
Collapse
|
122
|
Hüppi E, Sánchez-Villagra MR, Tzika AC, Werneburg I. Ontogeny and phylogeny of the mammalian chondrocranium: the cupula nasi anterior and associated structures of the anterior head region. ZOOLOGICAL LETTERS 2018; 4:29. [PMID: 30505462 PMCID: PMC6260904 DOI: 10.1186/s40851-018-0112-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/26/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND The study of chondrocrania has a long tradition with a focus on single specimens and stages. It revealed great interspecific diversity and a notion of intraspecific variation. As an embryonic structure, the chondrocranium is subject to major changes in ontogeny with resorption and ossification of different cartilaginous structures. The cupula nasi anterior is the anteriormost portion of the cartilaginous nasal capsule and is expected to mirror much of the animal's life history and lifestyle. Its diversity in mammals is reflected in the external nasal anatomy of newborns. Marsupials and placentals show marked differences, likely related to breathing and suckling behavior. RESULTS We examined histological sections of five marsupial and three placentals species and traced the development of the cupula nasi anterior and the anterior nasal capsule. We found ontogenetic variation for nearly 50% of the 43 characters defined herein. By comparing to the literature and considering ontogenetic variation, we performed an analysis of character evolution in 70 mammalian species and reconstructed the nasal anatomy of the therian ancestor. CONCLUSIONS At birth, marsupials have a complete but simple cupula nasi anterior, whereas placentals display a more diverse morphology due to reductions and variations of chondrocranial elements. The more compact nasal capsule in marsupials is related to a long and strong fixation to the mother's teat after birth. Within marsupials and placentals, several derived characters distinguish major taxa, probably related to developmental and functional constraints. The reconstructed ancestral anatomy of the cupula nasi anterior supports the hypothesis that the therian ancestor was placental-like and that the marsupial lifestyle is more derived.
Collapse
Affiliation(s)
- Evelyn Hüppi
- Paläontologisches Institut und Museum der Universität Zürich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland
| | - Marcelo R. Sánchez-Villagra
- Paläontologisches Institut und Museum der Universität Zürich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland
| | - Athanasia C. Tzika
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Quai E. Ansermet 30, 1205 Genève, Switzerland
| | - Ingmar Werneburg
- Senckenberg Center for Human Evolution and Palaeoenvironment (HEP) at Eberhard Karls Universität, Sigwartstraße 10, 72076 Tübingen, Germany
- Fachbereich Geowissenschaften der Eberhard-Karls-Universität Tübingen, Hölderlinstraße 12, 72074 Tübingen, Germany
- Museum für Naturkunde, Leibniz-Institut für Evolutions- & Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstraße 43, 10115 Berlin, Germany
| |
Collapse
|
123
|
Abstract
This study investigated long-term substitution rate differences using three calibration points, divergences between lobe-finned vertebrates and ray-finned fish, between mammals and sauropsids, and between holosteans (gar and bowfin) and teleost fish with amino acid sequence data of 625 genes for 25 bony vertebrates. The result showed that the substitution rate was two to three times higher in the stem branches of lobe-finned vertebrates before the mammal-sauropsid divergence than in amniotes. The rate in the stem branch of ray-finned fish before the holostean-teleost fish divergence was also a few times higher than the holostean rate, whereas it was similar to or somewhat slower than the teleost fish rate. The phylogenetic relationship of coelacanth and lungfish with tetrapod was difficult to determine because of the short interval of the divergences. Considering the high rate in the stem branches, the divergences of coelacanth and lungfish from the stem branch were estimated as 408–427 Ma and 399–414 Ma, respectively, with the interval of 9–13 Myr. With the external calibration of the mammal-sauropsid split, the estimated times for ordinal divergences within eutherian mammals tend to be smaller than those in previous studies that used the calibration points within the lineage, with deeper divergences before the Cretaceous–Paleogene boundary and shallower ones after the boundary. In contrast the estimated times within birds were larger than those of previous studies, with the divergence between Galliformes and Anseriformes ∼80 Ma and that between Galloanserae and Neoaves 110 Ma.
Collapse
Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Kitagun, Kagawa, Japan
| |
Collapse
|
124
|
Pinheiro C, Venter ML, Sahd L, Bronner GN, Kotzé SH. Comparative gastrointestinal morphology of seven golden mole species (Mammalia: Chrysochloridae) from South Africa. J Morphol 2018; 279:1776-1786. [DOI: 10.1002/jmor.20900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/17/2018] [Accepted: 09/04/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Cassandra Pinheiro
- Division of Anatomy and Histology, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences; Stellenbosch University; Cape Town South Africa
| | - Michaela L. Venter
- Division of Anatomy and Histology, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences; Stellenbosch University; Cape Town South Africa
| | - Lauren Sahd
- Division of Anatomy and Histology, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences; Stellenbosch University; Cape Town South Africa
| | - Gary N. Bronner
- Department of Biological Sciences; University of Cape Town; Rondebosch South Africa
| | - Sanet H. Kotzé
- Division of Anatomy and Histology, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences; Stellenbosch University; Cape Town South Africa
| |
Collapse
|
125
|
Positive Selection in the Evolution of Mammalian CRISPs. J Mol Evol 2018; 86:635-645. [DOI: 10.1007/s00239-018-9872-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/20/2018] [Indexed: 11/24/2022]
|
126
|
Castiglione GM, Chang BS. Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision. eLife 2018; 7:35957. [PMID: 30362942 PMCID: PMC6203435 DOI: 10.7554/elife.35957] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/09/2018] [Indexed: 12/11/2022] Open
Abstract
Trade-offs between protein stability and activity can restrict access to evolutionary trajectories, but widespread epistasis may facilitate indirect routes to adaptation. This may be enhanced by natural environmental variation, but in multicellular organisms this process is poorly understood. We investigated a paradoxical trajectory taken during the evolution of tetrapod dim-light vision, where in the rod visual pigment rhodopsin, E122 was fixed 350 million years ago, a residue associated with increased active-state (MII) stability but greatly diminished rod photosensitivity. Here, we demonstrate that high MII stability could have likely evolved without E122, but instead, selection appears to have entrenched E122 in tetrapods via epistatic interactions with nearby coevolving sites. In fishes by contrast, selection may have exploited these epistatic effects to explore alternative trajectories, but via indirect routes with low MII stability. Our results suggest that within tetrapods, E122 and high MII stability cannot be sacrificed-not even for improvements to rod photosensitivity.
Collapse
Affiliation(s)
- Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Belinda Sw Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| |
Collapse
|
127
|
Imam A, Bhagwandin A, Ajao MS, Spocter MA, Ihunwo AO, Manger PR. The brain of the tree pangolin (Manis tricuspis
). II. The olfactory system. J Comp Neurol 2018; 526:2548-2569. [DOI: 10.1002/cne.24510] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/27/2018] [Accepted: 07/27/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Aminu Imam
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
- Department of Anatomy, Faculty of Basic Medical Sciences; College of Health Sciences, University of Ilorin; Ilorin Nigeria
| | - Adhil Bhagwandin
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
| | - Moyosore S. Ajao
- Department of Anatomy, Faculty of Basic Medical Sciences; College of Health Sciences, University of Ilorin; Ilorin Nigeria
| | - Muhammed A. Spocter
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
- Department of Anatomy; Des Moines University; Iowa
| | - Amadi O. Ihunwo
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
| | - Paul R. Manger
- Faculty of Health Sciences, University of the Witwatersrand; School of Anatomical Sciences; Republic of South Africa
| |
Collapse
|
128
|
Imam A, Bhagwandin A, Ajao MS, Ihunwo AO, Fuxe K, Manger PR. Brain of the tree pangolin (Manis tricuspis
). III. The unusual locus coeruleus complex. J Comp Neurol 2018; 526:2570-2684. [DOI: 10.1002/cne.24519] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Aminu Imam
- Faculty of Health Sciences, School of Anatomical Sciences; University of the Witwatersrand; Parktown Johannesburg Republic of South Africa
- Faculty of Basic Medical Sciences, Department of Anatomy; College of Health Sciences, University of Ilorin; Ilorin Nigeria
| | - Adhil Bhagwandin
- Faculty of Health Sciences, School of Anatomical Sciences; University of the Witwatersrand; Parktown Johannesburg Republic of South Africa
| | - Moyosore S. Ajao
- Faculty of Basic Medical Sciences, Department of Anatomy; College of Health Sciences, University of Ilorin; Ilorin Nigeria
| | - Amadi O. Ihunwo
- Faculty of Health Sciences, School of Anatomical Sciences; University of the Witwatersrand; Parktown Johannesburg Republic of South Africa
| | - Kjell Fuxe
- Department of Neuroscience; Karolinska Institutet; Stockholm Sweden
| | - Paul R. Manger
- Faculty of Health Sciences, School of Anatomical Sciences; University of the Witwatersrand; Parktown Johannesburg Republic of South Africa
| |
Collapse
|
129
|
Cong Q, Li W, Borek D, Otwinowski Z, Grishin NV. The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots. Mol Genet Genomics 2018; 294:211-226. [PMID: 30293092 DOI: 10.1007/s00438-018-1494-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
Abstract
Giant-Skippers (Megathymini) are unusual thick-bodied, moth-like butterflies whose caterpillars feed inside Yucca roots and Agave leaves. Giant-Skippers are attributed to the subfamily Hesperiinae and they are endemic to southern and mostly desert regions of the North American continent. To shed light on the genotypic determinants of their unusual phenotypic traits, we sequenced and annotated a draft genome of the largest Giant-Skipper species, the Bear (Megathymus ursus violae). The Bear skipper genome is the least heterozygous among sequenced Lepidoptera genomes, possibly due to much smaller population size and extensive inbreeding. Their lower heterozygosity helped us to obtain a high-quality genome with an N50 of 4.2 Mbp. The ~ 430 Mb genome encodes about 14000 proteins. Phylogenetic analysis supports placement of Giant-Skippers with Grass-Skippers (Hesperiinae). We find that proteins involved in odorant and taste sensing as well as in oxidative reactions have diverged significantly in Megathymus as compared to Lerema, another Grass-Skipper. In addition, the Giant-Skipper has lost several odorant and gustatory receptors and possesses many fewer (1/3-1/2 of other skippers) anti-oxidative enzymes. Such differences may be related to the unusual life style of Giant-Skippers: they do not feed as adults, and their caterpillars feed inside Yuccas and Agaves, which provide a source of antioxidants such as polyphenols.
Collapse
Affiliation(s)
- Qian Cong
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8816, USA
| | - Wenlin Li
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8816, USA
| | - Dominika Borek
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8816, USA
| | - Zbyszek Otwinowski
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8816, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9050, USA. .,Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8816, USA.
| |
Collapse
|
130
|
Breaux B, Hunter ME, Cruz-Schneider MP, Sena L, Bonde RK, Criscitiello MF. The Florida manatee (Trichechus manatus latirostris) T cell receptor loci exhibit V subgroup synteny and chain-specific evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 85:71-85. [PMID: 29649552 DOI: 10.1016/j.dci.2018.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/06/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
The Florida manatee (Trichechus manatus latirostris) has limited diversity in the immunoglobulin heavy chain. We therefore investigated the antigen receptor loci of the other arm of the adaptive immune system: the T cell receptor. Manatees are the first species from Afrotheria, a basal eutherian superorder, to have an in-depth characterization of all T cell receptor loci. By annotating the genome and expressed transcripts, we found that each chain has distinct features that correlates to their individual functions. The genomic organization also plays a role in modulating sequence conservation between species. There were extensive V subgroup synteny blocks in the TRA and TRB loci between T. m. latirostris and human. Increased genomic locus complexity correlated to increased locus synteny. We also identified evidence for a VHD pseudogene for the first time in a eutherian mammal. These findings emphasize the value of including species within this basal eutherian radiation in comparative studies.
Collapse
Affiliation(s)
- Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Margaret E Hunter
- Sirenia Project, Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | | | - Leonardo Sena
- Laboratory of Medical and Human Genetics, Federal University of Pará, Belém, Pará, Brazil.
| | - Robert K Bonde
- Sirenia Project, Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
131
|
Azab W, Dayaram A, Greenwood AD, Osterrieder N. How Host Specific Are Herpesviruses? Lessons from Herpesviruses Infecting Wild and Endangered Mammals. Annu Rev Virol 2018; 5:53-68. [PMID: 30052491 DOI: 10.1146/annurev-virology-092917-043227] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Herpesviruses are ubiquitous and can cause disease in all classes of vertebrates but also in animals of lower taxa, including molluscs. It is generally accepted that herpesviruses are primarily species specific, although a species can be infected by different herpesviruses. Species specificity is thought to result from host-virus coevolutionary processes over the long term. Even with this general concept in mind, investigators have recognized interspecies transmission of several members of the Herpesviridae family, often with fatal outcomes in non-definitive hosts-that is, animals that have no or only a limited role in virus transmission. We here summarize herpesvirus infections in wild mammals that in many cases are endangered, in both natural and captive settings. Some infections result from herpesviruses that are endemic in the species that is primarily affected, and some result from herpesviruses that cause fatal disease after infection of non-definitive hosts. We discuss the challenges of such infections in several endangered species in the absence of efficient immunization or therapeutic options.
Collapse
Affiliation(s)
- Walid Azab
- Institut für Virologie, Zentrum für Infektionsmedizin, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Anisha Dayaram
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany;
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany;
| | - Nikolaus Osterrieder
- Institut für Virologie, Zentrum für Infektionsmedizin, Freie Universität Berlin, 14163 Berlin, Germany;
| |
Collapse
|
132
|
Pfeffer PL. Building Principles for Constructing a Mammalian Blastocyst Embryo. BIOLOGY 2018; 7:biology7030041. [PMID: 30041494 PMCID: PMC6164496 DOI: 10.3390/biology7030041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022]
Abstract
The self-organisation of a fertilised egg to form a blastocyst structure, which consists of three distinct cell lineages (trophoblast, epiblast and hypoblast) arranged around an off-centre cavity, is unique to mammals. While the starting point (the zygote) and endpoint (the blastocyst) are similar in all mammals, the intervening events have diverged. This review examines and compares the descriptive and functional data surrounding embryonic gene activation, symmetry-breaking, first and second lineage establishment, and fate commitment in a wide range of mammalian orders. The exquisite detail known from mouse embryogenesis, embryonic stem cell studies and the wealth of recent single cell transcriptomic experiments are used to highlight the building principles underlying early mammalian embryonic development.
Collapse
Affiliation(s)
- Peter L Pfeffer
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand.
| |
Collapse
|
133
|
Sharma V, Lehmann T, Stuckas H, Funke L, Hiller M. Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals. PLoS Biol 2018; 16:e2005293. [PMID: 29953435 PMCID: PMC6023123 DOI: 10.1371/journal.pbio.2005293] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 05/24/2018] [Indexed: 01/13/2023] Open
Abstract
Descent of testes from a position near the kidneys into the lower abdomen or into the scrotum is an important developmental process that occurs in all placental mammals, with the exception of five afrotherian lineages. Since soft-tissue structures like testes are not preserved in the fossil record and since key parts of the placental mammal phylogeny remain controversial, it has been debated whether testicular descent is the ancestral or derived condition in placental mammals. To resolve this debate, we used genomic data of 71 mammalian species and analyzed the evolution of two key genes (relaxin/insulin-like family peptide receptor 2 [RXFP2] and insulin-like 3 [INSL3]) that induce the development of the gubernaculum, the ligament that is crucial for testicular descent. We show that both RXFP2 and INSL3 are lost or nonfunctional exclusively in four afrotherians (tenrec, cape elephant shrew, cape golden mole, and manatee) that completely lack testicular descent. The presence of remnants of once functional orthologs of both genes in these afrotherian species shows that these gene losses happened after the split from the placental mammal ancestor. These “molecular vestiges” provide strong evidence that testicular descent is the ancestral condition, irrespective of persisting phylogenetic discrepancies. Furthermore, the absence of shared gene-inactivating mutations and our estimates that the loss of RXFP2 happened at different time points strongly suggest that testicular descent was lost independently in Afrotheria. Our results provide a molecular mechanism that explains the loss of testicular descent in afrotherians and, more generally, highlight how molecular vestiges can provide insights into the evolution of soft-tissue characters. While fossils of whales with legs demonstrate that these species evolved from legged ancestors, the ancestral state of nonfossilizing soft-tissue structures can only be indirectly inferred. This difficulty is also confounded by uncertainties in the phylogenetic relationships between the animals concerned. A prime example is the case of testicular descent, a developmental process that determines the final position of testes, which occurs in most placental mammals but is absent from several afrotherian lineages. Here, we discovered that afrotherians possess remnants of genes known to be required for testicular descent. These “molecular vestiges” show that testicular descent was already present in the placental ancestor and was subsequently lost in Afrotheria. Our study highlights the potential of molecular vestiges in resolving contradictory ancestral states of soft-tissue characters.
Collapse
Affiliation(s)
- Virag Sharma
- 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, Germany
| | - Thomas Lehmann
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | | | - Liane Funke
- Max Planck Institute of Molecular Cell Biology and Genetics, 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, Germany
- * E-mail:
| |
Collapse
|
134
|
|
135
|
Usui K, Tokita M. Creating diversity in mammalian facial morphology: a review of potential developmental mechanisms. EvoDevo 2018; 9:15. [PMID: 29946416 PMCID: PMC6003202 DOI: 10.1186/s13227-018-0103-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022] Open
Abstract
Mammals (class Mammalia) have evolved diverse craniofacial morphology to adapt to a wide range of ecological niches. However, the genetic and developmental mechanisms underlying the diversification of mammalian craniofacial morphology remain largely unknown. In this paper, we focus on the facial length and orofacial clefts of mammals and deduce potential mechanisms that produced diversity in mammalian facial morphology. Small-scale changes in facial morphology from the common ancestor, such as slight changes in facial length and the evolution of the midline cleft in some lineages of bats, could be attributed to heterochrony in facial bone ossification. In contrast, large-scale changes of facial morphology from the common ancestor, such as a truncated, widened face as well as the evolution of the bilateral cleft possessed by some bat species, could be brought about by changes in growth and patterning of the facial primordium (the facial processes) at the early stages of embryogenesis.
Collapse
Affiliation(s)
- Kaoru Usui
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510 Japan
| | - Masayoshi Tokita
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510 Japan
| |
Collapse
|
136
|
A Novel Marsupial Hepatitis A Virus Corroborates Complex Evolutionary Patterns Shaping the Genus Hepatovirus. J Virol 2018; 92:JVI.00082-18. [PMID: 29695421 PMCID: PMC6002732 DOI: 10.1128/jvi.00082-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 11/30/2022] Open
Abstract
The discovery of highly diverse nonprimate hepatoviruses illuminated the evolutionary origins of hepatitis A virus (HAV) ancestors in mammals other than primates. Marsupials are ancient mammals that diverged from other Eutheria during the Jurassic. Viruses from marsupials may thus provide important insight into virus evolution. To investigate Hepatovirus macroevolutionary patterns, we sampled 112 opossums in northeastern Brazil. A novel marsupial HAV (MHAV) in the Brazilian common opossum (Didelphis aurita) was detected by nested reverse transcription-PCR (RT-PCR). MHAV concentration in the liver was high, at 2.5 × 109 RNA copies/g, and at least 300-fold higher than those in other solid organs, suggesting hepatotropism. Hepatovirus seroprevalence in D. aurita was 26.6% as determined using an enzyme-linked immunosorbent assay (ELISA). Endpoint titers in confirmatory immunofluorescence assays were high, and marsupial antibodies colocalized with anti-HAV control sera, suggesting specificity of serological detection and considerable antigenic relatedness between HAV and MHAV. MHAV showed all genomic hallmarks defining hepatoviruses, including late-domain motifs likely involved in quasi-envelope acquisition, a predicted C-terminal pX extension of VP1, strong avoidance of CpG dinucleotides, and a type 3 internal ribosomal entry site. Translated polyprotein gene sequence distances of at least 23.7% from other hepatoviruses suggested that MHAV represents a novel Hepatovirus species. Conserved predicted cleavage sites suggested similarities in polyprotein processing between HAV and MHAV. MHAV was nested within rodent hepatoviruses in phylogenetic reconstructions, suggesting an ancestral hepatovirus host switch from rodents into marsupials. Cophylogenetic reconciliations of host and hepatovirus phylogenies confirmed that host-independent macroevolutionary patterns shaped the phylogenetic relationships of extant hepatoviruses. Although marsupials are synanthropic and consumed as wild game in Brazil, HAV community protective immunity may limit the zoonotic potential of MHAV. IMPORTANCE Hepatitis A virus (HAV) is a ubiquitous cause of acute hepatitis in humans. Recent findings revealed the evolutionary origins of HAV and the genus Hepatovirus defined by HAV in mammals other than primates in general and in small mammals in particular. The factors shaping the genealogy of extant hepatoviruses are unclear. We sampled marsupials, one of the most ancient mammalian lineages, and identified a novel marsupial HAV (MHAV). The novel MHAV shared specific features with HAV, including hepatotropism, antigenicity, genome structure, and a common ancestor in phylogenetic reconstructions. Coevolutionary analyses revealed that host-independent evolutionary patterns contributed most to the current phylogeny of hepatoviruses and that MHAV was the most drastic example of a cross-order host switch of any hepatovirus observed so far. The divergence of marsupials from other mammals offers unique opportunities to investigate HAV species barriers and whether mechanisms of HAV immune control are evolutionarily conserved.
Collapse
|
137
|
Hughes GM, Boston ESM, Finarelli JA, Murphy WJ, Higgins DG, Teeling EC. The Birth and Death of Olfactory Receptor Gene Families in Mammalian Niche Adaptation. Mol Biol Evol 2018; 35:1390-1406. [PMID: 29562344 PMCID: PMC5967467 DOI: 10.1093/molbev/msy028] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The olfactory receptor (OR) gene families, which govern mammalian olfaction, have undergone extensive expansion and contraction through duplication and pseudogenization. Previous studies have shown that broadly defined environmental adaptations (e.g., terrestrial vs. aquatic) are correlated with the number of functional and non-functional OR genes retained. However, to date, no study has examined species-specific gene duplications in multiple phylogenetically divergent mammals to elucidate OR evolution and adaptation. Here, we identify the OR gene families driving adaptation to different ecological niches by mapping the fate of species-specific gene duplications in the OR repertoire of 94 diverse mammalian taxa, using molecular phylogenomic methods. We analyze >70,000 OR gene sequences mined from whole genomes, generated from novel amplicon sequencing data, and collated with data from previous studies, comprising one of the largest OR studies to date. For the first time, we demonstrate statistically significant patterns of OR species-specific gene duplications associated with the presence of a functioning vomeronasal organ. With respect to dietary niche, we uncover a novel link between a large number of duplications in OR family 5/8/9 and herbivory. Our results also highlight differences between social and solitary niches, indicating that a greater OR repertoire expansion may be associated with a solitary lifestyle. This study demonstrates the utility of species-specific duplications in elucidating gene family evolution, revealing how the OR repertoire has undergone expansion and contraction with respect to a number of ecological adaptations in mammals.
Collapse
Affiliation(s)
- Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Emma S M Boston
- AECOM, 9th Floor Clarence West Building, Clarence Street West, Belfast, BT2 7GP, United Kingdom
| | - John A Finarelli
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Desmond G Higgins
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
138
|
A novel hepatitis B virus species discovered in capuchin monkeys sheds new light on the evolution of primate hepadnaviruses. J Hepatol 2018; 68:1114-1122. [PMID: 29428874 DOI: 10.1016/j.jhep.2018.01.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 01/19/2018] [Accepted: 01/27/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS All known hepatitis B virus (HBV) genotypes occur in humans and hominoid Old World non-human primates (NHPs). The divergent woolly monkey HBV (WMHBV) forms another orthohepadnavirus species. The evolutionary origins of HBV are unclear. METHODS We analysed sera from 124 Brazilian monkeys collected during 2012-2016 for hepadnaviruses using molecular and serological tools, and conducted evolutionary analyses. RESULTS We identified a novel orthohepadnavirus species in capuchin monkeys (capuchin monkey hepatitis B virus [CMHBV]). We found CMHBV-specific antibodies in five animals and high CMHBV concentrations in one animal. Non-inflammatory, probably chronic infection was consistent with an intact preCore domain, low genetic variability, core deletions in deep sequencing, and no elevated liver enzymes. Cross-reactivity of antisera against surface antigens suggested antigenic relatedness of HBV, CMHBV, and WMHBV. Infection-determining CMHBV surface peptides bound to the human HBV receptor (human sodium taurocholate co-transporting polypeptide), but preferentially interacted with the capuchin monkey receptor homologue. CMHBV and WMHBV pseudotypes infected human hepatoma cells via the human sodium taurocholate co-transporting polypeptide, and were poorly neutralised by HBV vaccine-derived antibodies, suggesting that cross-species infections may be possible. Ancestral state reconstructions and sequence distance comparisons associated HBV with humans, whereas primate hepadnaviruses as a whole were projected to NHP ancestors. Co-phylogenetic analyses yielded evidence for co-speciation of hepadnaviruses and New World NHP. Bayesian hypothesis testing yielded strong support for an association of the HBV stem lineage with hominoid ancestors. Neither CMHBV nor WMHBV was likely the ancestor of the divergent human HBV genotypes F/H found in American natives. CONCLUSIONS Our data suggest ancestral co-speciation of hepadnaviruses and NHP, and an Old World origin of the divergent HBV genotypes F/H. The identification of a novel primate hepadnavirus offers new perspectives for urgently needed animal models of chronic hepatitis B. LAY SUMMARY The origins of HBV are unclear. The new orthohepadnavirus species from Brazilian capuchin monkeys resembled HBV in elicited infection patterns and could infect human liver cells using the same receptor as HBV. Evolutionary analyses suggested that primate HBV-related viruses might have emerged in African ancestors of New World monkeys millions of years ago. HBV was associated with hominoid primates, including humans and apes, suggesting evolutionary origins of HBV before the formation of modern humans. HBV genotypes found in American natives were divergent from those found in American monkeys, and likely introduced along prehistoric human migration. Our results elucidate the evolutionary origins and dispersal of primate HBV, identify a new orthohepadnavirus reservoir, and enable new perspectives for animal models of hepatitis B.
Collapse
|
139
|
Springer MS, Murphy WJ, Roca AL. Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Mol Phylogenet Evol 2018; 121:158-165. [PMID: 29331683 DOI: 10.1016/j.ympev.2018.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 12/27/2017] [Accepted: 01/09/2018] [Indexed: 11/30/2022]
Abstract
The mammalian order Eulipotyphla includes four extant families of insectivorans: Solenodontidae (solenodons); Talpidae (moles); Soricidae (shrews); and Erinaceidae (hedgehogs). Of these, Solenodontidae includes only two extant species, which are endemic to the largest islands of the Greater Antilles: Cuba and Hispaniola. Most molecular studies suggest that eulipotyphlan families diverged from each other across several million years, with the basal split between Solenodontidae and other families occurring in the Late Cretaceous. By contrast, Sato et al. (2016) suggest that eulipotyphlan families diverged from each other in a polytomy ∼58.6 million years ago (Mya). This more recent divergence estimate for Solenodontidae versus other extant eulipotyphlans suggests that solenodons must have arrived in the Greater Antilles via overwater dispersal rather than vicariance. Here, we show that the young timetree estimates for eulipotyphlan families and the polytomy are due to an inverted ingroup-outgroup arrangement of the tree, the result of using Tracer rather than TreeAnnotator to compile interfamilial divergence times, and of not enforcing the monophly of well-established clades such as Laurasiatheria and Eulipotyphla. Finally, Sato et al.'s (2016) timetree includes several zombie lineages where estimated divergence times are much younger than minimum ages that are implied by the fossil record. We reanalyzed Sato et al.'s (2016) original data with enforced monophyly for well-established clades and updated fossil calibrations that eliminate the inference of zombie lineages. Our resulting timetrees, which were compiled with TreeAnnotator rather than Tracer, produce dates that are in good agreement with other recent studies and place the basal split between Solenodontidae and other eulipotyphlans in the Late Cretaceous.
Collapse
Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA.
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| |
Collapse
|
140
|
Springer MS, Gatesy J. Evolution of the MC5R gene in placental mammals with evidence for its inactivation in multiple lineages that lack sebaceous glands. Mol Phylogenet Evol 2017; 120:364-374. [PMID: 29277542 DOI: 10.1016/j.ympev.2017.12.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/09/2017] [Indexed: 12/30/2022]
Abstract
MC5R is one of five melanocortin receptor genes found in placental mammals. MC5R plays an important role in energy homeostasis and is also expressed in the terminal differentiation of sebaceous glands. Among placental mammals there are multiple lineages that either lack or have degenerative sebaceous glands including Cetacea (whales, dolphins, and porpoises), Hippopotamidae (hippopotamuses), Sirenia (manatees and dugongs), Proboscidea (elephants), Rhinocerotidae (rhinos), and Heterocephalus glaber (naked mole rat). Given the loss or diminution of sebaceous glands in these taxa, we procured MC5R sequences from publicly available genomes and transcriptomes, supplemented by a newly generated sequence for Choeropsis liberiensis (pygmy hippopotamus), to determine if this gene remains intact or is inactivated in association with loss/reduction of sebaceous glands. Our data set includes complete MC5R sequences for 114 placental mammal species including two individuals of Mammuthus primigenius (woolly mammoth) from Oimyakon and Wrangel Island. Complete loss or inactivation of the MC5R gene occurs in multiple placental lineages that have lost sebaceous glands (Cetacea, West Indian manatee, African elephant, white rhinoceros) or are characterized by unusual skin (pangolins, aardvarks). Both M. primigenius individuals share inactivating mutations with the African elephant even though sebaceous glands have been reported in the former. MC5R remains intact in hippopotamuses and the naked mole rat, although slightly elevated dN/dS ratios in these lineages allow for the possibility that the accumulation of inactivating mutations in MC5R may lag behind the relaxation of purifying selection. For Cetacea and Hippopotamidae, the absence of shared inactivating mutations in two different skin genes (MC5R, PSORS1C2) is consistent with the hypothesis that semi-aquatic lifestyles were acquired independently in these clades following divergence from a common ancestor.
Collapse
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.
| |
Collapse
|
141
|
Abstract
Fungi must meet four criteria to infect humans: growth at human body temperatures, circumvention or penetration of surface barriers, lysis and absorption of tissue, and resistance to immune defenses, including elevated body temperatures. Morphogenesis between small round, detachable cells and long, connected cells is the mechanism by which fungi solve problems of locomotion around or through host barriers. Secretion of lytic enzymes, and uptake systems for the released nutrients, are necessary if a fungus is to nutritionally utilize human tissue. Last, the potent human immune system evolved in the interaction with potential fungal pathogens, so few fungi meet all four conditions for a healthy human host. Paradoxically, the advances of modern medicine have made millions of people newly susceptible to fungal infections by disrupting immune defenses. This article explores how different members of four fungal phyla use different strategies to fulfill the four criteria to infect humans: the Entomophthorales, the Mucorales, the Ascomycota, and the Basidiomycota. Unique traits confer human pathogenic potential on various important members of these phyla: pathogenic Onygenales comprising thermal dimorphs such as Histoplasma and Coccidioides; the Cryptococcus spp. that infect immunocompromised as well as healthy humans; and important pathogens of immunocompromised patients-Candida, Pneumocystis, and Aspergillus spp. Also discussed are agents of neglected tropical diseases important in global health such as mycetoma and paracoccidiomycosis and common pathogens rarely implicated in serious illness such as dermatophytes. Commensalism is considered, as well as parasitism, in shaping genomes and physiological systems of hosts and fungi during evolution.
Collapse
|
142
|
Deler-Hernández A, Sýkora V, Seidel M, Cala-Riquelme F, Fikáček M. Multiple origins of the Phaenonotum beetles in the Greater Antilles (Coleoptera: Hydrophilidae): phylogeny, biogeography and systematics. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Albert Deler-Hernández
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná, Praha, Czech Republic
| | - Vít Sýkora
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná, Praha, Czech Republic
| | - Matthias Seidel
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná, Praha, Czech Republic
- Department of Entomology, National Museum, Cirkusová, Praha – Horní Počernice, CZ, Czech Republic
| | - Franklyn Cala-Riquelme
- Programa de postgrado, Departamento de Biología, Universidad Nacional de Colombia, Carrera, Bogota D. C., Colombia
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera, Bogota D. C. Colombia
| | - Martin Fikáček
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná, Praha, Czech Republic
- Department of Entomology, National Museum, Cirkusová, Praha – Horní Počernice, CZ, Czech Republic
| |
Collapse
|
143
|
Affiliation(s)
- Mark S. Springer
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - John Gatesy
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| |
Collapse
|
144
|
Kacprzyk J, Hughes GM, Palsson-McDermott EM, Quinn SR, Puechmaille SJ, O'Neill LAJ, Teeling EC. A Potent Anti-Inflammatory Response in Bat Macrophages May Be Linked to Extended Longevity and Viral Tolerance. ACTA CHIROPTEROLOGICA 2017. [DOI: 10.3161/15081109acc2017.19.2.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eva M. Palsson-McDermott
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Susan R. Quinn
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Sébastien J. Puechmaille
- Zoological Institute and Museum, Greifswald University, Soldmann-Straβe 14, D-17489, Greifswald, Germany
| | - Luke A. J. O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
145
|
Teeling EC, Vernes SC, Dávalos LM, Ray DA, Gilbert MTP, Myers E. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species. Annu Rev Anim Biosci 2017; 6:23-46. [PMID: 29166127 DOI: 10.1146/annurev-animal-022516-022811] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.
Collapse
Affiliation(s)
- Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, 6500 AH, The Netherlands.,Donders Centre for Cognitive Neuroimaging, Nijmegen, 6525 EN, The Netherlands
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Eugene Myers
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | -
- *Full list of Bat1K Consortium members in Supplemental Appendix
| |
Collapse
|
146
|
Springer MS, Gatesy J. Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree. J Hered 2017; 109:297-307. [DOI: 10.1093/jhered/esx089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/07/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY
| |
Collapse
|
147
|
Nascimento FF, Reis MD, Yang Z. A biologist's guide to Bayesian phylogenetic analysis. Nat Ecol Evol 2017; 1:1446-1454. [PMID: 28983516 PMCID: PMC5624502 DOI: 10.1038/s41559-017-0280-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/17/2017] [Indexed: 11/09/2022]
Abstract
Bayesian methods have become very popular in molecular phylogenetics due to the availability of user-friendly software implementing sophisticated models of evolution. However, Bayesian phylogenetic models are complex, and analyses are often carried out using default settings, which may not be appropriate. Here, we summarize the major features of Bayesian phylogenetic inference and discuss Bayesian computation using Markov chain Monte Carlo (MCMC), the diagnosis of an MCMC run, and ways of summarising the MCMC sample. We discuss the specification of the prior, the choice of the substitution model, and partitioning of the data. Finally, we provide a list of common Bayesian phylogenetic software and provide recommendations as to their use.
Collapse
Affiliation(s)
- Fabrícia F Nascimento
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
148
|
Georgieva AY, Gordon ER, Weirauch C. Sylvatic host associations of Triatominae and implications for Chagas disease reservoirs: a review and new host records based on archival specimens. PeerJ 2017; 5:e3826. [PMID: 28948106 PMCID: PMC5609523 DOI: 10.7717/peerj.3826] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/29/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The 152 extant species of kissing bug include important vectors of the debilitating, chronic, and often fatal Chagas disease, which affects several million people mainly in Central and South America. An understanding of the natural hosts of this speciose group of blood-feeding insects has and will continue to aid ongoing efforts to impede the spread of Chagas disease. However, information on kissing bug biology is piecemeal and scattered, developed using methods with varying levels of accuracy over more than 100 years. Existing host records are heavily biased towards well-studied primary vector species and are derived from primarily three different types of observations, associational, immunological or DNA-based, with varying reliability. METHODS We gather a comprehensive and unparalleled number of sources reporting host associations via rigorous targeted searches of publication databases to review all known natural, or sylvatic, host records including information on how each record was collected. We integrate this information with novel host records obtained via attempted amplification and sequencing of a ∼160 base pair (bp) region of the vertebrate 12S mitochondrial gene from the gastrointestinal tract of 64 archival specimens of Triatominae representing 19 species collected primarily in sylvatic habitats throughout the southern United States and Central and South America during the past 10 years. We show the utility of this method for uncovering novel and under-studied groups of Triatominae hosts, as well as detecting the presence of the Chagas disease pathogen via Polymerase Chain Reaction (PCR) of a ∼400 bp sequence of the trypanosome 18S gene. RESULTS New host associations for several groups of arboreal mammals were determined including sloths, New World monkeys, coatis, arboreal porcupines and, for the first time as a host of any Triatominae, tayras. A thorough review of previously documented sylvatic hosts, organized by triatomine species and the type of observation (associational, antibody-based, or DNA-based), is presented in a phylogenetic context and highlights large gaps in our knowledge of Triatominae biology. CONCLUSION The application of DNA-based methods of host identification towards additional species of Triatominae, including rarely collected species that may require use of archival specimens, is the most efficient and promising way to resolve recognized shortfalls.
Collapse
Affiliation(s)
- Anna Y. Georgieva
- Department of Entomology, University of California, Riverside, CA, United States of America
| | - Eric R.L. Gordon
- Department of Entomology, University of California, Riverside, CA, United States of America
| | - Christiane Weirauch
- Department of Entomology, University of California, Riverside, CA, United States of America
| |
Collapse
|
149
|
Yang Z, Donoghue PCJ. Dating species divergences using rocks and clocks. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0126. [PMID: 27325825 DOI: 10.1098/rstb.2015.0126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| |
Collapse
|
150
|
Esselstyn JA, Oliveros CH, Swanson MT, Faircloth BC. Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements. Genome Biol Evol 2017; 9:2308-2321. [PMID: 28934378 PMCID: PMC5604124 DOI: 10.1093/gbe/evx168] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2017] [Indexed: 12/21/2022] Open
Abstract
The phylogeny of eutherian mammals contains some of the most recalcitrant nodes in the tetrapod tree of life. We combined comprehensive taxon and character sampling to explore three of the most debated interordinal relationships among placental mammals. We performed in silico extraction of ultraconserved element loci from 72 published genomes and invitro enrichment and sequencing of ultraconserved elements from 28 additional mammals, resulting in alignments of 3,787 loci. We analyzed these data using concatenated and multispecies coalescent phylogenetic approaches, topological tests, and exploration of support among individual loci to identify the root of Eutheria and the sister groups of tree shrews (Scandentia) and horses (Perissodactyla). Individual loci provided weak, but often consistent support for topological hypotheses. Although many gene trees lacked accepted species-tree relationships, summary coalescent topologies were largely consistent with inferences from concatenation. At the root of Eutheria, we identified consistent support for a sister relationship between Xenarthra and Afrotheria (i.e., Atlantogenata). At the other nodes of interest, support was less consistent. We suggest Scandentia is the sister of Primatomorpha (Euarchonta), but we failed to reject a sister relationship between Scandentia and Glires. Similarly, we suggest Perissodactyla is sister to Cetartiodactyla (Euungulata), but a sister relationship between Perissodactyla and Chiroptera remains plausible.
Collapse
Affiliation(s)
- Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Carl H. Oliveros
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Mark T. Swanson
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge
| | - Brant C. Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge
| |
Collapse
|