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Miller E, Lee HW, Abzhanov A, Evers SW. The topological organization of the turtle cranium is constrained and conserved over long evolutionary timescales. Anat Rec (Hoboken) 2024; 307:2713-2748. [PMID: 38102921 DOI: 10.1002/ar.25356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023]
Abstract
The cranium of turtles (Testudines) is characterized by the secondary reduction of temporal fenestrae and loss of cranial joints (i.e., characteristics of anapsid, akinetic skulls). Evolution and ontogeny of the turtle cranium are associated with shape changes. Cranial shape variation among Testudines can partially be explained by dietary and functional adaptations (neck retraction), but it is unclear if cranial topology shows similar ecomorphological signal, or if it is decoupled from shape evolution. We assess the topological arrangement of cranial bones (i.e., number, relative positioning, connections), using anatomical network analysis. Non-shelled stem turtles have similar cranial arrangements to archosauromorph outgroups. Shelled turtles (Testudinata) evolve a unique cranial organization that is associated with bone losses (e.g., supratemporal, lacrimal, ectopterygoid) and an increase in complexity (i.e., densely and highly interconnected skulls with low path lengths between bones), resulting from the closure of skull openings and establishment of unusual connections such as a parietal-pterygoid contact in the secondary braincase. Topological changes evolutionarily predate many shape changes. Topological variation and taxonomic morphospace discrimination among crown turtles are low, indicating that cranial topology may be constrained. Observed variation results from repeated losses of nonintegral bones (i.e., premaxilla, nasal, epipterygoid, quadratojugal), and changes in temporal emarginations and palate construction. We observe only minor ontogenetic changes. Topology is not influenced by diet and habitat, contrasting cranial shape. Our results indicate that turtles have a unique cranial topology among reptiles that is conserved after its initial establishment, and shows that cranial topology and shape have different evolutionary histories.
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Affiliation(s)
- Eve Miller
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Berkshire, UK
- Natural History Museum, London, UK
| | - Hiu Wai Lee
- Department of Earth Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Arkhat Abzhanov
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Berkshire, UK
- Natural History Museum, London, UK
| | - Serjoscha W Evers
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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2
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Jiménez S, Santos-Álvarez I, Fernández-Valle E, Castejón D, Villa-Valverde P, Rojo-Salvador C, Pérez-Llorens P, Ruiz-Fernández MJ, Ariza-Pastrana S, Martín-Orti R, González-Soriano J, Moreno N. Comparative MRI analysis of the forebrain of three sauropsida models. Brain Struct Funct 2024; 229:1349-1364. [PMID: 38546870 PMCID: PMC11176103 DOI: 10.1007/s00429-024-02788-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/12/2024] [Indexed: 06/15/2024]
Abstract
The study of the brain by magnetic resonance imaging (MRI) allows to obtain detailed anatomical images, useful to describe specific encephalic structures and to analyze possible variabilities. It is widely used in clinical practice and is becoming increasingly used in veterinary medicine, even in exotic animals; however, despite its potential, its use in comparative neuroanatomy studies is still incipient. It is a technology that in recent years has significantly improved anatomical resolution, together with the fact that it is non-invasive and allows for systematic comparative analysis. All this makes it particularly interesting and useful in evolutionary neuroscience studies, since it allows for the analysis and comparison of brains of rare or otherwise inaccessible species. In the present study, we have analyzed the prosencephalon of three representative sauropsid species, the turtle Trachemys scripta (order Testudine), the lizard Pogona vitticeps (order Squamata) and the snake Python regius (order Squamata) by MRI. In addition, we used MRI sections to analyze the total brain volume and ventricular system of these species, employing volumetric and chemometric analyses together. The raw MRI data of the sauropsida models analyzed in the present study are available for viewing and downloading and have allowed us to produce an atlas of the forebrain of each of the species analyzed, with the main brain regions. In addition, our volumetric data showed that the three groups presented clear differences in terms of total and ventricular brain volumes, particularly the turtles, which in all cases presented distinctive characteristics compared to the lizards and snakes.
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Affiliation(s)
- S Jiménez
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), Leioa, Bilbao, 48940, Spain
| | - I Santos-Álvarez
- Departament Section of Anatomy and Embriology, Faculty of Veterinary, Complutense University, Avenida Puerta de Hierro s/n, Madrid, 28040, Spain
| | - E Fernández-Valle
- ICTS Bioimagen Complutense, Complutense University, Paseo de Juan XXIII 1, Madrid, 28040, Spain
| | - D Castejón
- ICTS Bioimagen Complutense, Complutense University, Paseo de Juan XXIII 1, Madrid, 28040, Spain
| | - P Villa-Valverde
- ICTS Bioimagen Complutense, Complutense University, Paseo de Juan XXIII 1, Madrid, 28040, Spain
| | - C Rojo-Salvador
- Departament Section of Anatomy and Embriology, Faculty of Veterinary, Complutense University, Avenida Puerta de Hierro s/n, Madrid, 28040, Spain
| | - P Pérez-Llorens
- Departament Section of Anatomy and Embriology, Faculty of Veterinary, Complutense University, Avenida Puerta de Hierro s/n, Madrid, 28040, Spain
| | - M J Ruiz-Fernández
- Departament Section of Anatomy and Embriology, Faculty of Veterinary, Complutense University, Avenida Puerta de Hierro s/n, Madrid, 28040, Spain
| | - S Ariza-Pastrana
- Palmitos Park Canarias, Barranco de los Palmitos, s/n, Maspalomas, Las Palmas, 35109, Spain
| | - R Martín-Orti
- Departament Section of Anatomy and Embriology, Faculty of Veterinary, Complutense University, Avenida Puerta de Hierro s/n, Madrid, 28040, Spain
| | - Juncal González-Soriano
- Departament Section of Anatomy and Embriology, Faculty of Veterinary, Complutense University, Avenida Puerta de Hierro s/n, Madrid, 28040, Spain.
| | - Nerea Moreno
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University, Avenida José Antonio Nováis 12, Madrid, 28040, Spain.
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3
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Werneburg I, Preuschoft H. Evolution of the temporal skull openings in land vertebrates: A hypothetical framework on the basis of biomechanics. Anat Rec (Hoboken) 2024; 307:1559-1593. [PMID: 38197580 DOI: 10.1002/ar.25371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
The complex constructions of land vertebrate skulls have inspired a number of functional analyses. In the present study, we provide a basic view on skull biomechanics and offer a framework for more general observations using advanced modeling approaches in the future. We concentrate our discussion on the cranial openings in the temporal skull region and work out two major, feeding-related factors that largely influence the shape of the skull. We argue that (1) the place where the most forceful biting is conducted and (2) the handling of resisting food (sideward movements) constitute the formation and shaping of either one or two temporal arcades surrounding these openings. Diversity in temporal skull anatomy among amniotes can be explained by specific modulations of these factors with different amounts of acting forces which inevitably lead to deposition or reduction of bone material. For example, forceful anterior bite favors an infratemporal bar, whereas forceful posterior bite favors formation of an upper temporal arcade. Transverse forces (inertia and resistance of seized objects) as well as neck posture also influence the shaping of the temporal region. Considering their individual skull morphotypes, we finally provide hypotheses on the feeding adaptation in a variety of major tetrapod groups. We did not consider ligaments, internal bone structure, or cranial kinesis in our considerations. Involving those in quantitative tests of our hypotheses, such as finite element system synthesis, will provide a comprehensive picture on cranial mechanics and evolution in the future.
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Affiliation(s)
- Ingmar Werneburg
- Paläontologische Sammlung, Fachbereich Geowissenschaften, Eberhard Karls Universität, Tübingen, Germany
- Senckenberg Center for Human Evolution and Palaeoenvironment, Eberhard Karls Universität, Tübingen, Germany
| | - Holger Preuschoft
- Funktionelle Morphologie im Anatomischen Institut, Ruhr-Universität Bochum, Bochum, Germany
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Wu HJ, Tseng YC, Tsao SH, Chiang PL, Tai WY, Hsieh HI, Yu HT, Juang JY. A Comparative Study on the Microstructures, Mineral Content, and Mechanical Properties of Non-Avian Reptilian Eggshells. BIOLOGY 2023; 12:688. [PMID: 37237502 PMCID: PMC10215611 DOI: 10.3390/biology12050688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/25/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
We analyze 214 freshly laid eggs belonging to 16 species across three orders of Class Reptilia. Using mechanical compression tests, we measure each egg's absolute stiffness (K, unit: N m-1) and relative stiffness (C number). The effective Young's modulus, E, was obtained by combining experimental and numerical methods. The mineral (CaCO3) content was measured by acid-base titration, the microstructures by scanning electron microscopy (SEM), and the crystallography by electron backscatter diffraction (EBSD). We find that the C number of reptilian eggs is, on average, higher than that of bird eggs, indicating that reptilian eggs are stiffer with respect to the egg mass than birds. However, Young's moduli of the reptilian eggshells (32.85 ± 3.48 GPa) are similar to those of avian eggshells (32.07 ± 5.95 GPa), even though those eggshells have different crystal forms, microstructures, and crystallography. Titration measurement shows that the reptilian eggshells are highly mineralized (>89% for nine Testudines species and 96% for Caiman crocodilus). Comparing the species with aragonite and calcite crystals, we find that calcite shells, including those of the Kwangsi gecko (inner part) and spectacled caiman (outer part), generally have larger grains than the aragonite ones. However, the grain size is not correlated to the effective Young's modulus. Also, as measured by the C number, the aragonite shells are, on average, stiffer than the calcite ones (except for the Kwangsi gecko), primarily due to their thicker shells.
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Affiliation(s)
- Hsio-Jou Wu
- Department of Mechanical Engineering, National Taiwan University, Taipei 10617, Taiwan; (H.-J.W.); (Y.-C.T.); (S.-H.T.); (P.-L.C.)
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan;
| | - Yu-Chien Tseng
- Department of Mechanical Engineering, National Taiwan University, Taipei 10617, Taiwan; (H.-J.W.); (Y.-C.T.); (S.-H.T.); (P.-L.C.)
| | - Shu-Han Tsao
- Department of Mechanical Engineering, National Taiwan University, Taipei 10617, Taiwan; (H.-J.W.); (Y.-C.T.); (S.-H.T.); (P.-L.C.)
| | - Pei-Lin Chiang
- Department of Mechanical Engineering, National Taiwan University, Taipei 10617, Taiwan; (H.-J.W.); (Y.-C.T.); (S.-H.T.); (P.-L.C.)
| | - Wei-Yu Tai
- Taipei Zoo, Taipei 11656, Taiwan; (W.-Y.T.); (H.-I.H.)
| | - Hsin-I Hsieh
- Taipei Zoo, Taipei 11656, Taiwan; (W.-Y.T.); (H.-I.H.)
| | - Hon-Tsen Yu
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan;
- Degree Program of Genome and Systems Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Jia-Yang Juang
- Department of Mechanical Engineering, National Taiwan University, Taipei 10617, Taiwan; (H.-J.W.); (Y.-C.T.); (S.-H.T.); (P.-L.C.)
- Program in Nanoengineering and Nanoscience, Graduate School of Advanced Technology, National Taiwan University, Taipei 10617, Taiwan
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McCarthy CGP, Mulhair PO, Siu-Ting K, Creevey CJ, O’Connell MJ. Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny. Mol Biol Evol 2023; 40:6989790. [PMID: 36649189 PMCID: PMC9848061 DOI: 10.1093/molbev/msac276] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023] Open
Abstract
There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of model selection, taxon sampling, and outgroup selection. The influence of dataset construction is comparatively understudied. We re-examine five animal phylogeny datasets that have supported either root hypothesis using an approach designed to enrich orthologous signal in phylogenomic datasets. We find that many component orthogroups in animal datasets fail to recover major lineages as monophyletic with the exception of Ctenophora, regardless of the supported root. Enriching these datasets to retain orthogroups recovering ≥3 major lineages reduces dataset size by up to 50% while retaining underlying phylogenetic information and taxon sampling. Site-heterogeneous phylogenomic analysis of these enriched datasets recovers both Porifera-sister and Ctenophora-sister positions, even with additional constraints on outgroup sampling. Two datasets which previously supported Ctenophora-sister support Porifera-sister upon enrichment. All enriched datasets display improved model fitness under posterior predictive analysis. While not conclusively rooting animals at either Porifera or Ctenophora, we do see an increase in signal for Porifera-sister and a decrease in signal for Ctenophore-sister when data are filtered for orthologous signal. Our results indicate that dataset size and construction as well as model fit influence animal root inference.
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Affiliation(s)
| | | | - Karen Siu-Ting
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, United Kingdom
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The quest for a generic bird target to detect the presence of bird in food products and considerations for paleoprotein analysis. PLoS One 2022; 17:e0279369. [PMID: 36538508 PMCID: PMC9767367 DOI: 10.1371/journal.pone.0279369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
It can be important for consumers to know whether food products contain animal material and, if so, of which species. Food products with animal material as an ingredient often contain collagen type 1. LC-MS/MS (Liquid Chromatography-tandem Mass Spectrometry) was applied as technique to generically detect bird. Unlike for example fish, that have experienced longer divergence times, it is still possible to find generic LC-MS targets for avian type 1 collagen. After theoretical target selection using 83 collagen 1α2 bird sequences of 33 orders and construction of a common ancestor sequence of birds, experimental evidence was provided by analyzing extracts from 10 extant bird species. Two suitable options have been identified. The combination of VGPIGPAGNR and VGPIGAAGNR (pheasant only) covers all investigated birds and was not found in other species. The peptide EGPVGFpGADGR covers all investigated birds, but also occurs in several species of crocodiles and turtles. The presence of the generic peptide (combination) was confirmed in food products, proving the principle, and can therefore be used to detect the presence of bird. Furthermore, it is shown how the use of constructed ancestor sequences could benefit the field of paleoproteomics, in the interpretation of collagen MS/MS spectra of ancient species. Our theoretical analysis and assessment of reported Brachylophosaurus canadensis collagen 1α2 MS/MS data provided support for several previous peptide sequence assignments, but we also propose that our constructed ancestral bird sequence GPpGESGAVGPAGPIGSR may fit the MS/MS data better than the original assignment GLPGESGAVGPAGPpGSR.
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Wang P, Xiong G, Zeng D, Zhang J, Ge L, Liu L, Wang X, Hu Y. Comparative transcriptome and miRNA analysis of skin pigmentation during embryonic development of Chinese soft-shelled turtle (Pelodiscus sinensis). BMC Genomics 2022; 23:801. [PMID: 36471254 PMCID: PMC9721069 DOI: 10.1186/s12864-022-09029-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/21/2022] [Indexed: 12/10/2022] Open
Abstract
BACKGROUND Aquatic animals show diverse body coloration, and the formation of animal body colour is a complicated process. Increasing evidence has shown that microRNAs (miRNAs) play important regulatory roles in many life processes. The role of miRNAs in pigmentation has been investigated in some species. However, the regulatory patterns of miRNAs in reptile pigmentation remain to be elucidated. In this study, we performed an integrated analysis of miRNA and mRNA expression profiles to explore corresponding regulatory patterns in embryonic body colour formation in the soft-shelled turtle Pelodiscus sinensis. RESULTS We identified 8 866 novel genes and 9 061 mature miRNAs in the skin of Chinese soft-shelled turtles in three embryonic stages (initial period: IP, middle period: MP, final period: FP). A total of 16 563 target genes of the miRNAs were identified. Furthermore, we identified 2 867, 1 840 and 4 290 different expression genes (DEGs) and 227, 158 and 678 different expression miRNAs (DEMs) in IP vs. MP, MP vs. FP, and IP vs. FP, respectively. Among which 72 genes and 25 miRNAs may be related to turtle pigmentation in embryonic development. Further analysis of the novel miRNA families revealed that some novel miRNAs related to pigmentation belong to the miR-7386, miR-138, miR-19 and miR-129 families. Novel_miR_2622 and novel_miR_2173 belong to the miR-19 family and target Kit and Gpnmb, respectively. The quantification of novel_miR_2622 and Kit revealed negative regulation, indicating that novel_miR_2622 may participate in embryonic pigmentation in P. sinensis by negatively regulating the expression of Kit. CONCLUSIONS miRNA act as master regulators of biological processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs and their target genes in Chinese soft-shelled turtle might be useful for investigating the molecular processes involved in pigmentation. All the results of this study may aid in the improvement of P. sinensis breeding traits for aquaculture.
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Affiliation(s)
- Pei Wang
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
| | - Gang Xiong
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127 Hunan China
| | - Dan Zeng
- grid.440778.80000 0004 1759 9670College of Life and Environmental Science, Hunan University of Arts and Science, Changde, 415000 Hunan China
| | - Jianguo Zhang
- Hunan Biological and Electromechanical Polytechnic, Changsha, 410127 Hunan China
| | - Lingrui Ge
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China ,Hunan Biological and Electromechanical Polytechnic, Changsha, 410127 Hunan China
| | - Li Liu
- grid.449642.90000 0004 1761 026XSchool of Medical Technology, Shaoyang University, Shaoyang, 422000 Hunan China
| | - Xiaoqing Wang
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
| | - Yazhou Hu
- grid.257160.70000 0004 1761 0331College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
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8
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Shiels HA. Avian cardiomyocyte architecture and what it reveals about the evolution of the vertebrate heart. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210332. [PMID: 36189815 PMCID: PMC9527935 DOI: 10.1098/rstb.2021.0332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/02/2022] [Indexed: 11/17/2022] Open
Abstract
Bird cardiomyocytes are long, thin and lack transverse (t)-tubules, which is akin to the cardiomyocyte morphology of ectothermic non-avian reptiles, who are typified by low maximum heart rates and low pressure development. However, birds can achieve greater contractile rates and developed pressures than mammals, whose wide cardiomyocytes contain a dense t-tubular network allowing for uniform excitation-contraction coupling and strong contractile force. To address this apparent paradox, this paper functionally links recent electrophysiological studies on bird cardiomyocytes with decades of ultrastructure measurements. It shows that it is the strong transsarcolemmal Ca2+ influx via the L-type Ca2+ current (ICaL) and the high gain of Ca2+-induced Ca2+ release from the sarcoplasmic reticulum (SR), coupled with an internal SR Ca2+ release relay system, that facilitates the strong fast contractions in the long thin bird cardiomyocytes, without the need for t-tubules. The maintenance of an elongated myocyte morphology following the post-hatch transition from ectothermy to endothermy in birds is discussed in relation to cardiac load, myocyte ploidy, and cardiac regeneration potential in adult cardiomyocytes. Overall, the paper shows how little we know about cellular Ca2+ dynamics in the bird heart and suggests how increased research efforts in this area would provide vital information in our quest to understand the role of myocyte architecture in the evolution of the vertebrate heart. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'. Please see glossary at the end of the paper for definitions of specialized terms.
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Affiliation(s)
- Holly A. Shiels
- Division of Cardiovascular Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
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9
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Hermanson G, Benson RBJ, Farina BM, Ferreira GS, Langer MC, Evers SW. Cranial ecomorphology of turtles and neck retraction as a possible trigger of ecological diversification. Evolution 2022; 76:2566-2586. [PMID: 36117268 PMCID: PMC9828723 DOI: 10.1111/evo.14629] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 01/22/2023]
Abstract
Turtles have a highly modified body plan, including a rigid shell that constrains postcranial anatomy. Skull morphology and neck mobility may therefore be key to ecological specialization in turtles. However, the ecological signal of turtle skull morphologies has not been rigorously evaluated, leaving uncertainties about the roles of ecological adaptation and convergence. We evaluate turtle cranial ecomorphology using three-dimensional geometric morphometrics and phylogenetic comparative methods. Skull shape correlates with allometry, neck retraction capability, and different aquatic feeding ecologies. We find that ecological variables influence skull shape only, whereas a key functional variable (the capacity for neck retraction) influences both shape and size. Ecology and functional predictions from three-dimensional shape are validated by high success rates for extant species, outperforming previous two-dimensional approaches. We use this to infer ecological and functional traits of extinct species. Neck retraction evolved among crownward stem-turtles by the Late Jurassic, signaling functional decoupling of the skull and neck from the shell, possibly linked to a major episode of ecomorphological diversification. We also find strong evidence for convergent ecological adaptations among marine groups. This includes parallel loss of neck retraction, evidence for active hunting, possible grazing, and suction feeding in extinct marine groups. Our large-scale assessment of dietary and functional adaptation throughout turtle evolution reveals the timing and origin of their distinct ecomorphologies, and highlights the potential for ecology and function to have distinct effects on skull form.
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Affiliation(s)
- Guilherme Hermanson
- Department of GeosciencesUniversity of FribourgFribourgCH‐1700Switzerland,Department of Earth SciencesUniversity of OxfordOxfordOX1 3ANUnited Kingdom,Laboratório de Paleontologia de Ribeirão PretoUniversidade de São PauloRibeirão Preto14040‐091Brazil
| | - Roger B. J. Benson
- Department of Earth SciencesUniversity of OxfordOxfordOX1 3ANUnited Kingdom
| | - Bruna M. Farina
- Laboratório de Paleontologia de Ribeirão PretoUniversidade de São PauloRibeirão Preto14040‐091Brazil,Department of BiologyUniversity of FribourgFribourgCH‐1700Switzerland
| | - Gabriel S. Ferreira
- Senckenberg Centre for Human Evolution and Palaeoenvironment (HEP)Eberhard Karls Universität Tübingen72076TübingenGermany,Fachbereich GeowissenschaftenUniversität Tübingen72074TübingenGermany
| | - Max C. Langer
- Laboratório de Paleontologia de Ribeirão PretoUniversidade de São PauloRibeirão Preto14040‐091Brazil
| | - Serjoscha W. Evers
- Department of GeosciencesUniversity of FribourgFribourgCH‐1700Switzerland
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10
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Common evolutionary origin of acoustic communication in choanate vertebrates. Nat Commun 2022; 13:6089. [PMID: 36284092 PMCID: PMC9596459 DOI: 10.1038/s41467-022-33741-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Acoustic communication, broadly distributed along the vertebrate phylogeny, plays a fundamental role in parental care, mate attraction and various other behaviours. Despite its importance, comparatively less is known about the evolutionary roots of acoustic communication. Phylogenetic comparative analyses can provide insights into the deep time evolutionary origin of acoustic communication, but they are often plagued by missing data from key species. Here we present evidence for 53 species of four major clades (turtles, tuatara, caecilian and lungfish) in the form of vocal recordings and contextual behavioural information accompanying sound production. This and a broad literature-based dataset evidence acoustic abilities in several groups previously considered non-vocal. Critically, phylogenetic analyses encompassing 1800 species of choanate vertebrates reconstructs acoustic communication as a homologous trait, and suggests that it is at least as old as the last common ancestor of all choanate vertebrates, that lived approx. 407 million years before present.
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11
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Abel P, Pommery Y, Ford DP, Koyabu D, Werneburg I. Skull Sutures and Cranial Mechanics in the Permian Reptile Captorhinus aguti and the Evolution of the Temporal Region in Early Amniotes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.841784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While most early limbed vertebrates possessed a fully-roofed dermatocranium in their temporal skull region, temporal fenestrae and excavations evolved independently at least twice in the earliest amniotes, with several different variations in shape and position of the openings. Yet, the specific drivers behind this evolution have been only barely understood. It has been mostly explained by adaptations of the feeding apparatus as a response to new functional demands in the terrestrial realm, including a rearrangement of the jaw musculature as well as changes in strain distribution. Temporal fenestrae have been retained in most extant amniotes but have also been lost again, notably in turtles. However, even turtles do not represent an optimal analog for the condition in the ancestral amniote, highlighting the necessity to examine Paleozoic fossil material. Here, we describe in detail the sutures in the dermatocranium of the Permian reptile Captorhinus aguti (Amniota, Captorhinidae) to illustrate bone integrity in an early non-fenestrated amniote skull. We reconstruct the jaw adductor musculature and discuss its relation to intracranial articulations and bone flexibility within the temporal region. Lastly, we examine whether the reconstructed cranial mechanics in C. aguti could be treated as a model for the ancestor of fenestrated amniotes. We show that C. aguti likely exhibited a reduced loading in the areas at the intersection of jugal, squamosal, and postorbital, as well as at the contact between parietal and postorbital. We argue that these “weak” areas are prone for the development of temporal openings and may be treated as the possible precursors for infratemporal and supratemporal fenestrae in early amniotes. These findings provide a good basis for future studies on other non-fenestrated taxa close to the amniote base, for example diadectomorphs or other non-diapsid reptiles.
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12
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Knaus PL, van Heteren AH, Lungmus JK, Sander PM. High Blood Flow Into the Femur Indicates Elevated Aerobic Capacity in Synapsids Since the Synapsida-Sauropsida Split. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.751238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Varanids are the only non-avian sauropsids that are known to approach the warm-blooded mammals in stamina. Furthermore, a much higher maximum metabolic rate (MMR) gives endotherms (including birds) higher stamina than crocodiles, turtles, and non-varanid lepidosaurs. This has led researchers to hypothesize that mammalian endothermy evolved as a second step after the acquisition of elevated MMR in non-mammalian therapsids from a plesiomorphic state of low metabolic rates. In recent amniotes, MMR correlates with the index of blood flow into the femur (Qi), which is calculated from femoral length and the cross-sectional area of the nutrient foramen. Thus, Qi may serve as an indicator of MMR range in extinct animals. Using the Qi proxy and phylogenetic eigenvector maps, here we show that elevated MMRs evolved near the base of Synapsida. Non-mammalian synapsids, including caseids, edaphosaurids, sphenacodontids, dicynodonts, gorgonopsids, and non-mammalian cynodonts, show Qi values in the range of recent endotherms and varanids, suggesting that raised MMRs either evolved in synapsids shortly after the Synapsida-Sauropsida split in the Mississippian or that the low MMR of lepidosaurs and turtles is apomorphic, as has been postulated for crocodiles.
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13
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Dudgeon TW, Livius MCH, Alfonso N, Tessier S, Mallon JC. A new model of forelimb ecomorphology for predicting the ancient habitats of fossil turtles. Ecol Evol 2021; 11:17071-17079. [PMID: 34938493 PMCID: PMC8668755 DOI: 10.1002/ece3.8345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022] Open
Abstract
Various morphological proxies have been used to infer habitat preferences among fossil turtles and their early ancestors, but most are tightly linked to phylogeny, thereby minimizing their predictive power. One particularly widely used model incorporates linear measurements of the forelimb (humerus + ulna + manus), but in addition to the issue of phylogenetic correlation, it does not estimate the likelihood of habitat assignment. Here, we introduce a new model that uses intramanual measurements (digit III metacarpal + non-ungual phalanges + ungual) to statistically estimate habitat likelihood and that has greater predictive strength than prior estimators. Application of the model supports the hypothesis that stem-turtles were primarily terrestrial in nature and recovers the nanhsiungchelyid Basilemys (a fossil crown-group turtle) as having lived primarily on land, despite some prior claims to the contrary.
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Affiliation(s)
- Thomas W. Dudgeon
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Natural HistoryRoyal Ontario MuseumTorontoOntarioCanada
| | - Marissa C. H. Livius
- Ottawa‐Carleton Geoscience Centre and Department of Earth SciencesCarleton UniversityOttawaOntarioCanada
| | - Noel Alfonso
- Beaty Centre for Species Discovery and Zoology SectionCanadian Museum of NatureOttawaOntarioCanada
| | - Stéphanie Tessier
- Beaty Centre for Species Discovery and Zoology SectionCanadian Museum of NatureOttawaOntarioCanada
| | - Jordan C. Mallon
- Ottawa‐Carleton Geoscience Centre and Department of Earth SciencesCarleton UniversityOttawaOntarioCanada
- Beaty Centre for Species Discovery and Palaeobiology SectionCanadian Museum of NatureOttawaOntarioCanada
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14
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Fromm B, Høye E, Domanska D, Zhong X, Aparicio-Puerta E, Ovchinnikov V, Umu SU, Chabot PJ, Kang W, Aslanzadeh M, Tarbier M, Mármol-Sánchez E, Urgese G, Johansen M, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ. MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Res 2021; 50:D204-D210. [PMID: 34850127 PMCID: PMC8728216 DOI: 10.1093/nar/gkab1101] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 11/23/2021] [Indexed: 12/03/2022] Open
Abstract
We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.
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Affiliation(s)
- Bastian Fromm
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Eirik Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Diana Domanska
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.,Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Xiangfu Zhong
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Ernesto Aparicio-Puerta
- Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.,Biotechnology Institute, CIBM, Granada, Spain.,Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain
| | - Vladimir Ovchinnikov
- Computational and Molecular Evolutionary Biology Research Group, School of life sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
| | - Sinan U Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Peter J Chabot
- Department of Biological Sciences, Dartmouth College, Hanover, USA
| | - Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Morteza Aslanzadeh
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | | | - Morten Johansen
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Michael Hackenberg
- Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.,Biotechnology Institute, CIBM, Granada, Spain.,Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, USA
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15
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Callender-Crowe LM, Sansom RS. Osteological characters of birds and reptiles are more congruent with molecular phylogenies than soft characters are. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Despite increased use of genomic data in phylogenetics, morphological information remains vital for resolving evolutionary relationships, particularly for fossil taxa. The properties and models of evolution of molecular sequence data are well characterized and mature, relative to those of morphological data. Furthermore, heterogeneity, integration and relative homoplasy of empirical morphological data could prove problematic for phylogenetic reconstruction. Here we compare osteological and non-osteological characters of 28 morphological datasets of extant saurians in terms of their homoplasy relative to molecular trees. Analysis of individual avian datasets finds osteological characters to be significantly more consistent with molecular data than soft characters are. Significant differences between morphological partitions were also observed in the age at which characters resolved on molecular trees. Osteological character changes occur relatively earlier in deep branches, whilst soft-tissue character transitions are more recent in shallow branches. The combined results demonstrate differences in evolutionary dynamics between morphological partitions. This may reflect evolutionary constraints acting on osteological characters, compared with the relative lability of soft characters. Furthermore, it provides some support to phylogenetic interpretations of fossil data, including dinosaurs, which are predominately osteological. Recent advances in amphibian and mammal phylogenetics may make these patterns possible to test for all tetrapods.
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Affiliation(s)
- Leah M Callender-Crowe
- The University of Manchester, Department of Earth and Environmental Sciences, Manchester, UK
- School of Biological Sciences, University of Reading, Reading, UK
| | - Robert S Sansom
- The University of Manchester, Department of Earth and Environmental Sciences, Manchester, UK
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16
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Starck JM, Stewart JR, Blackburn DG. Phylogeny and evolutionary history of the amniote egg. J Morphol 2021; 282:1080-1122. [PMID: 33991358 DOI: 10.1002/jmor.21380] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 01/02/2023]
Abstract
We review morphological features of the amniote egg and embryos in a comparative phylogenetic framework, including all major clades of extant vertebrates. We discuss 40 characters that are relevant for an analysis of the evolutionary history of the vertebrate egg. Special attention is given to the morphology of the cellular yolk sac, the eggshell, and extraembryonic membranes. Many features that are typically assigned to amniotes, such as a large yolk sac, delayed egg deposition, and terrestrial reproduction have evolved independently and convergently in numerous clades of vertebrates. We use phylogenetic character mapping and ancestral character state reconstruction as tools to recognize sequence, order, and patterns of morphological evolution and deduce a hypothesis of the evolutionary history of the amniote egg. Besides amnion and chorioallantois, amniotes ancestrally possess copulatory organs (secondarily reduced in most birds), internal fertilization, and delayed deposition of eggs that contain an embryo in the primitive streak or early somite stage. Except for the amnion, chorioallantois, and amniote type of eggshell, these features evolved convergently in almost all major clades of aquatic vertebrates possibly in response to selective factors such as egg predation, hostile environmental conditions for egg development, or to adjust hatching of young to favorable season. A functionally important feature of the amnion membrane is its myogenic contractility that moves the (early) embryo and prevents adhering of the growing embryo to extraembryonic materials. This function of the amnion membrane and the liquid-filled amnion cavity may have evolved under the requirements of delayed deposition of eggs that contain developing embryos. The chorioallantois is a temporary embryonic exchange organ that supports embryonic development. A possible evolutionary scenario is that the amniote egg presents an exaptation that paved the evolutionary pathway for reproduction on land. As shown by numerous examples from anamniotes, reproduction on land has occurred multiple times among vertebrates-the amniote egg presenting one "solution" that enabled the conquest of land for reproduction.
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Affiliation(s)
- J Matthias Starck
- Department of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - James R Stewart
- Department of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.,Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee, USA
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17
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Laurentino TG, Xavier M, Ronco F, Pina-Martins F, Domingues I, Penha B, Dias M, de Sousa A, Carrilho T, Rodrigues LR, Pinheiro C, Rato D, Balata D, Ayala-Botto G, Matos M, Campelo M, Botelho R. evALLution: making basic evolution concepts accessible to people with visual impairment through a multisensory tree of life. Evolution 2021; 14:5. [PMID: 33786157 PMCID: PMC7952356 DOI: 10.1186/s12052-021-00143-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/07/2021] [Indexed: 11/10/2022]
Abstract
Background People with visual impairment have benefitted from recent developments of assistive technology that aim to decrease socio-economic inequality. However, access to post-secondary education is still extremelly challenging, especially for scientific areas. The under representation of people with visual impairment in the evolution research community is connected with the vision-based communication of evolutionary biology knowledge and the accompanying lack of multisensory alternatives for learning. Results Here, we describe the development of an inclusive outreach activity based on a multisensory phylogeny representing 20 taxonomic groups. We provide a tool kit of materials and ideas that allow both the replication of this activity and the adaptation of others, to include people with visual impairment. Furthermore, we provide activity evaluation data, a discussion of the lessons learned and an inclusive description of all figures and visual data presented. The presented baseline data show that people with visual impairment indeed have lack of access to education but are interested in and apt to understand evolutionary biology concepts and predict evolutionary change when education is inclusive. Conclusions We show that, with creative investment, basic evolutionary knowledge is perfectly possible to be transmitted through multisensory activities, which everyone can benefit from. Ultimately, we hope this case study will provide a baseline for future initiatives and a more inclusive outreach community.
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Affiliation(s)
- Telma G Laurentino
- Zoology, University of Basel, Basel, Switzerland.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720 USA
| | | | | | - Francisco Pina-Martins
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa (ULisboa), Campo Grande, 1749-016 Lisbon, Portugal
| | - Iolanda Domingues
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Bruno Penha
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa (ULisboa), Campo Grande, 1749-016 Lisbon, Portugal
| | - Marta Dias
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa (ULisboa), Campo Grande, 1749-016 Lisbon, Portugal
| | - Alexandra de Sousa
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK.,Centre for Health and Cognition, Bath Spa University, Bath, UK.,Crossmodal Cognition Laboratory, University of Bath, Bath, UK
| | - Tiago Carrilho
- Centro Pedagógico Do Jardim Zoológico de Lisboa, Lisbon, Portugal
| | - Leonor R Rodrigues
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa (ULisboa), Campo Grande, 1749-016 Lisbon, Portugal
| | - Carlota Pinheiro
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa (ULisboa), Campo Grande, 1749-016 Lisbon, Portugal
| | - Daniela Rato
- Centro Pedagógico Do Jardim Zoológico de Lisboa, Lisbon, Portugal
| | - Duarte Balata
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa (ULisboa), Campo Grande, 1749-016 Lisbon, Portugal
| | | | - Margarida Matos
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa (ULisboa), Campo Grande, 1749-016 Lisbon, Portugal
| | | | - Rafael Botelho
- Centro Pedagógico Do Jardim Zoológico de Lisboa, Lisbon, Portugal
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18
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Nachtigall PG, Bovolenta LA, Patton JG, Fromm B, Lemke N, Pinhal D. A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks. BMC Genomics 2021; 22:153. [PMID: 33663371 PMCID: PMC7931589 DOI: 10.1186/s12864-021-07441-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/12/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND During vertebrate evolution, the heart has undergone remarkable changes that lead to morphophysiological differences in the fully formed heart of these species, such as chamber septation, heart rate frequency, blood pressure, and cardiac output volume. Despite these differences, the heart developmental process is guided by a core gene set conserved across vertebrates. Nonetheless, the regulatory mechanisms controlling the expression of genes involved in heart development and maintenance are largely uncharted. MicroRNAs (miRNAs) have been described as important regulatory elements in several biological processes, including heart biology. These small RNA molecules are broadly conserved in sequence and genomic context in metazoans. Mutations may occur in miRNAs and/or genes that contribute to the establishment of distinct repertoires of miRNA-target interactions, thereby favoring the differential control of gene expression and, consequently, the origin of novel phenotypes. In fact, several studies showed that miRNAs are integrated into genetic regulatory networks (GRNs) governing specific developmental programs and diseases. However, studies integrating miRNAs in vertebrate heart GRNs under an evolutionary perspective are still scarce. RESULTS We comprehensively examined and compared the heart miRNome of 20 species representatives of the five major vertebrate groups. We found 54 miRNA families with conserved expression and a variable number of miRNA families with group-specific expression in fishes, amphibians, reptiles, birds, and mammals. We also detected that conserved miRNAs present higher expression levels and a higher number of targets, whereas the group-specific miRNAs present lower expression levels and few targets. CONCLUSIONS Both the conserved and group-specific miRNAs can be considered modulators orchestrating the core and peripheral genes of heart GRNs of vertebrates, which can be related to the morphophysiological differences and similarities existing in the heart of distinct vertebrate groups. We propose a hypothesis to explain evolutionary differences in the putative functional roles of miRNAs in the heart GRNs analyzed. Furthermore, we present new insights into the molecular mechanisms that could be helping modulate the diversity of morphophysiology in the heart organ of vertebrate species.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório Especial de Toxinologia Aplicada (LETA), CeTICS, Instituto Butantan, São Paulo, Brazil. .,Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil.
| | - Luiz A Bovolenta
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute (MBW), Stockholm University, Stockholm, Sweden
| | - Ney Lemke
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Danillo Pinhal
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
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19
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Santana FL, Estrada K, Ortiz E, Corzo G. Reptilian β-defensins: Expanding the repertoire of known crocodylian peptides. Peptides 2021; 136:170473. [PMID: 33309943 DOI: 10.1016/j.peptides.2020.170473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 01/31/2023]
Abstract
One of the major families of host defense peptides (HDPs) in vertebrates are β-defensins. They constitute important components of innate immunity and have remained an interesting topic of research for more than two decades. While many β-defensin sequences in mammals and birds have been identified and their properties and functions characterized, β-defensin peptides from other groups of vertebrates, particularly reptiles, are still largely unexplored. In this review, we focus on reptilian β-defensins and summarize different aspects of their biology, such as their genomic organization, evolution, structure, and biological activities. Reptilian β-defensin genes exhibit similar genomic organization to birds and their number and gene structure are variable among different species. During the evolution of reptiles, several gene duplication and deletion events have occurred and the functional diversification of β-defensins has been mainly driven by positive selection. These peptides display broad antimicrobial activity in vitro, but a deeper understanding of their mechanisms of action in vivo, including their role as immunomodulators, is still lacking. Reptilian β-defensins constitute unique polypeptide sequences to expand our current understanding of innate immunity in these animals and elucidate core biological functions of this family of HDPs across amniotes.
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Affiliation(s)
- Felix L Santana
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca Mor., 62250, Mexico.
| | - Karel Estrada
- Unidad de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ernesto Ortiz
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca Mor., 62250, Mexico
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca Mor., 62250, Mexico.
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20
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Heading for higher ground: Developmental origins and evolutionary diversification of the amniote face. Curr Top Dev Biol 2021; 141:241-277. [PMID: 33602490 DOI: 10.1016/bs.ctdb.2020.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amniotes, a clade of terrestrial vertebrates, which includes all of the descendants of the last common ancestor of the reptiles (including dinosaurs and birds) and mammals, is one of the most successful group of animals on our planet. In addition to having an egg equipped with an amnion, an adaptation to lay eggs on land, amniotes possess a number of other major morphological characteristics. Chief among them is the amniote skull, which can be classified into several major types distinguished by the presence and number of temporal fenestrae (windows) in the posterior part. Amniotes evolved from ancestors who possessed a skull composed of a complex mosaic of small bones separated by sutures. Changes in skull composition underlie much of the large-scale evolution of amniotes with many lineages showing a trend in reduction of cranial elements known as the "Williston's Law." The skull of amniotes is also arranged into a set of modules of closely co-evolving bones as revealed by modularity and integration tests. One of the most consistently recovered and at the same time most versatile modules is the "face," anatomically defined as the anterior portion of the head. The faces of amniotes display extraordinary amount of variation, with many adaptive radiations showing parallel tendencies in facial scaling, e.g., changes in length or width. This review explores the natural history of the amniote face and discusses how a better understanding of its anatomy and developmental biology helps to explain the outstanding scale of adaptive facial diversity. We propose a model for facial evolution in the amniotes, based on the differential rate of cranial neural crest cell proliferation and the timing of their skeletal differentiation.
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21
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Lyson TR, Bever GS. Origin and Evolution of the Turtle Body Plan. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-024746] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The origin of turtles and their uniquely shelled body plan is one of the longest standing problems in vertebrate biology. The unfulfilled need for a hypothesis that both explains the derived nature of turtle anatomy and resolves their unclear phylogenetic position among reptiles largely reflects the absence of a transitional fossil record. Recent discoveries have dramatically improved this situation, providing an integrated, time-calibrated model of the morphological, developmental, and ecological transformations responsible for the modern turtle body plan. This evolutionary trajectory was initiated in the Permian (>260 million years ago) when a turtle ancestor with a diapsid skull evolved a novel mechanism for lung ventilation. This key innovation permitted the torso to become apomorphically stiff, most likely as an adaption for digging and a fossorial ecology. The construction of the modern turtle body plan then proceeded over the next 100 million years following a largely stepwise model of osteological innovation.
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Affiliation(s)
- Tyler R. Lyson
- Department of Earth Sciences, Denver Museum of Nature & Science, Denver, Colorado 80205, USA
| | - Gabriel S. Bever
- Department of Earth Sciences, Denver Museum of Nature & Science, Denver, Colorado 80205, USA
- Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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22
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Pardo JD, Lennie K, Anderson JS. Can We Reliably Calibrate Deep Nodes in the Tetrapod Tree? Case Studies in Deep Tetrapod Divergences. Front Genet 2020; 11:506749. [PMID: 33193596 PMCID: PMC7596322 DOI: 10.3389/fgene.2020.506749] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Recent efforts have led to the development of extremely sophisticated methods for incorporating tree-wide data and accommodating uncertainty when estimating the temporal patterns of phylogenetic trees, but assignment of prior constraints on node age remains the most important factor. This depends largely on understanding substantive disagreements between specialists (paleontologists, geologists, and comparative anatomists), which are often opaque to phylogeneticists and molecular biologists who rely on these data as downstream users. This often leads to misunderstandings of how the uncertainty associated with node age minima arises, leading to inappropriate treatments of that uncertainty by phylogeneticists. In order to promote dialogue on this subject, we here review factors (phylogeny, preservational megabiases, spatial and temporal patterns in the tetrapod fossil record) that complicate assignment of prior node age constraints for deep divergences in the tetrapod tree, focusing on the origin of crown-group Amniota, crown-group Amphibia, and crown-group Tetrapoda. We find that node priors for amphibians and tetrapods show high phylogenetic lability and different phylogenetic treatments identifying disparate taxa as the earliest representatives of these crown groups. This corresponds partially to the well-known problem of lissamphibian origins but increasingly reflects deeper instabilities in early tetrapod phylogeny. Conversely, differences in phylogenetic treatment do not affect our ability to recognize the earliest crown-group amniotes but do affect how diverse we understand the earliest amniote faunas to be. Preservational megabiases and spatiotemporal heterogeneity of the early tetrapod fossil record present unrecognized challenges in reliably estimating the ages of tetrapod nodes; the tetrapod record throughout the relevant interval is spatially restricted and disrupted by several major intervals of minimal sampling coincident with the emergence of all three crown groups. Going forward, researchers attempting to calibrate the ages for these nodes, and other similar deep nodes in the metazoan fossil record, should consciously consider major phylogenetic uncertainty, preservational megabias, and spatiotemporal heterogeneity, preferably examining the impact of working hypotheses from multiple research groups. We emphasize a need for major tetrapod collection effort outside of classic European and North American sections, particularly from the southern hemisphere, and suggest that such sampling may dramatically change our timelines of tetrapod evolution.
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Affiliation(s)
- Jason D. Pardo
- Department of Comparative and Experimental Biology, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
| | - Kendra Lennie
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jason S. Anderson
- Department of Comparative and Experimental Biology, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
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23
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Blackburn DG. Functional morphology, diversity, and evolution of yolk processing specializations in embryonic reptiles and birds. J Morphol 2020; 282:995-1014. [PMID: 32960458 DOI: 10.1002/jmor.21267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/24/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022]
Abstract
Evolution of the terrestrial, amniotic egg of vertebrates required new mechanisms by which yolk material could be processed for embryonic use. Recent studies on each of the major extant reptile groups have revealed elaborate morphological specializations for yolk processing, features that differ dramatically from those of birds. In the avian pattern, liquid yolk is housed in a yolk sac whose endodermal lining absorbs and digests yolk material and sends resultant nutrients into the blood circulation. In snakes, lizards, turtles, and crocodilians, as documented herein, the yolk sac becomes invaded by endodermal cells that proliferate and phagocytose yolk material. Blood vessels then invade, and the endodermal cells become arranged around them, forming elongated "spaghetti-like" strands that fill the yolk sac cavity. This pattern provides an effective means by which yolk material is cellularized, digested, and transported by vitelline vessels to the developing embryo. Phylogenetically, the (non-avian) "reptilian" pattern was ancestral for sauropsids and was modified or replaced in ancestors to birds. This review postulates that evolution of the "avian" pattern involved increased reliance on extracellular digestion of yolk, allowing embryonic development to occur more rapidly than in typical reptiles. Comparative studies of yolk processing that draw on morphological, biochemical, molecular approaches are needed to explain how and why the "reptilian" pattern was replaced in birds or their archosaurian ancestors.
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Affiliation(s)
- Daniel G Blackburn
- Department of Biology, Electron Microscopy Center, Trinity College, Hartford, Connecticut, USA
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24
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Smith Paredes D, Lord A, Meyer D, Bhullar BS. A developmental staging system and musculoskeletal development sequence of the common musk turtle (
Sternotherus odoratus
). Dev Dyn 2020; 250:111-127. [DOI: 10.1002/dvdy.210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 01/02/2023] Open
Affiliation(s)
- Daniel Smith Paredes
- Department of Earth and Planetary Science, Peabody Museum of Natural History Yale University New Haven Connecticut USA
| | - Arianna Lord
- Department of Earth and Planetary Science, Peabody Museum of Natural History Yale University New Haven Connecticut USA
| | - Dalton Meyer
- Department of Earth and Planetary Science, Peabody Museum of Natural History Yale University New Haven Connecticut USA
| | - Bhart‐Anjan S. Bhullar
- Department of Earth and Planetary Science, Peabody Museum of Natural History Yale University New Haven Connecticut USA
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25
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Carlson BE, Klein K, Rhodes C. First report of rapid eye color change in a non‐avian tetrapod. Ethology 2020. [DOI: 10.1111/eth.13068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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26
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Janis CM, Napoli JG, Warren DE. Palaeophysiology of pH regulation in tetrapods. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190131. [PMID: 31928199 DOI: 10.1098/rstb.2019.0131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The involvement of mineralized tissues in acid-base homeostasis was likely important in the evolution of terrestrial vertebrates. Extant reptiles encounter hypercapnia when submerged in water, but early tetrapods may have experienced hypercapnia on land due to their inefficient mode of lung ventilation (likely buccal pumping, as in extant amphibians). Extant amphibians rely on cutaneous carbon dioxide elimination on land, but early tetrapods were considerably larger forms, with an unfavourable surface area to volume ratio for such activity, and evidence of a thick integument. Consequently, they would have been at risk of acidosis on land, while many of them retained internal gills and would not have had a problem eliminating carbon dioxide in water. In extant tetrapods, dermal bone can function to buffer the blood during acidosis by releasing calcium and magnesium carbonates. This review explores the possible mechanisms of acid-base regulation in tetrapod evolution, focusing on heavily armoured, basal tetrapods of the Permo-Carboniferous, especially the physiological challenges associated with the transition to air-breathing, body size and the adoption of active lifestyles. We also consider the possible functions of dermal armour in later tetrapods, such as Triassic archosaurs, inferring palaeophysiology from both fossil record evidence and phylogenetic patterns, and propose a new hypothesis relating the archosaurian origins of the four-chambered heart and high systemic blood pressures to the perfusion of the osteoderms. This article is part of the theme issue 'Vertebrate palaeophysiology'.
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Affiliation(s)
- Christine M Janis
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.,School of Earth Sciences, University of Bristol, Bristol BS8 1RL, UK
| | - James G Napoli
- Richard Gilder Graduate School and Division of Paleontology, American Museum of Natural History, New York, NY 10024-5102, USA
| | - Daniel E Warren
- Department of Biology, Saint Louis University, St Louis, MO 63103, USA
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27
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Murray CM, Crother BI, Doody JS. The evolution of crocodilian nesting ecology and behavior. Ecol Evol 2020; 10:131-149. [PMID: 31993116 PMCID: PMC6972877 DOI: 10.1002/ece3.5859] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 11/12/2022] Open
Abstract
Crocodilians comprise an ancient and successful lineage of archosaurs that repeatedly raises questions on how they survived a mass extinction and remained relatively unchanged for ~100 million years. Was their success due to the change-resistant retention of a specific set of traits over time (phylogenetic conservatism) or due to flexible, generalist capabilities (e.g., catholic diets, phenotypic plasticity in behavior), or some combination of these? We examined the evolution of reproductive ecology and behavior of crocodilians within a phylogenetic perspective, using 14 traits for all 24 species to determine whether these traits were phylogenetically constrained versus (ecologically) convergent. Our analysis revealed that the ancestral crocodilian was a mound nester that exhibited both nest attendance and defense. Nesting mode exhibited 4-5 transformations from mound to hole nesting, a convergence of which habitat may have been a driving factor. Hole nesters were more likely to nest communally, but this association may be biased by scale. Although there were exceptions, mound nesters typically nested during the wet season and hole nesters during the dry season; this trait was relatively conserved, however. About two-thirds of species timed their nesting with the wet season, while the other third timed their hatching with the onset of the wet season. Nest attendance and defense were nearly ubiquitous and thus exhibited phylogenetic conservatism, but attendance lodging was diverse among species, showing multiple reversals between water and burrows. Collectively, our analysis reveals that reproductive trait evolution in crocodilians reflects phylogenetic constraint (nest attendance, nest defense), ecological convergence (seasonal timing of nesting, nest attendance lodging), or both (mode of nesting). Some traits (e.g., communal nesting and mode of nesting) were autocorrelated. Our analysis provides a framework for addressing hypotheses raised for why there has been trait convergence in reproductive ecology and behavior in crocodilians and why some traits remained phylogenetically conserved.
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Affiliation(s)
- Christopher M. Murray
- Department of BiologyTennessee Technological UniversityCookevilleTNUSA
- Department of BiologySoutheastern Louisiana UniversityHammondLAUSA
| | - Brian I. Crother
- Department of BiologySoutheastern Louisiana UniversityHammondLAUSA
| | - J. Sean Doody
- Department of Biological SciencesUniversity of South Florida ‐ St. PetersburgSt. PetersburgFLUSA
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28
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Goldberg S, Venkatesh A, Martinez J, Dombroski C, Abesamis J, Campbell C, Mccalipp M, de Bellard ME. The development of the trunk neural crest in the turtle Trachemys scripta. Dev Dyn 2020; 249:125-140. [PMID: 31587387 PMCID: PMC7293771 DOI: 10.1002/dvdy.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The neural crest is a group of multipotent cells that give rise to a wide variety of cells, especially portion of the peripheral nervous system. Neural crest cells (NCCs) show evolutionary conserved fate restrictions based on their axial level of origin: cranial, vagal, trunk, and sacral. While much is known about these cells in mammals, birds, amphibians, and fish, relatively little is known in other types of amniotes such as snakes, lizards, and turtles. We attempt here to provide a more detailed description of the early phase of trunk neural crest cell (tNCC) development in turtle embryos. RESULTS In this study, we show, for the first time, migrating tNCC in the pharyngula embryo of Trachemys scripta by vital-labeling the NCC with DiI and through immunofluorescence. We found that (a) tNCC form a line along the sides of the trunk NT; (b) The presence of late migrating tNCC on the medial portion of the somite; (c) The presence of lateral mesodermal migrating tNCC in pharyngula embryos; (d) That turtle embryos have large/thick peripheral nerves. CONCLUSIONS The similarities and differences in tNCC migration and early PNS development that we observe across sauropsids (birds, snake, gecko, and turtle) suggests that these species evolved some distinct NCC pathways.
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Affiliation(s)
| | | | | | - Catherine Dombroski
- California State University Northridge, Biology Dept., MC 8303. 18111 Nordhoff Street. Northridge, CA 91330
| | - Jessica Abesamis
- California State University Northridge, Biology Dept., MC 8303. 18111 Nordhoff Street. Northridge, CA 91330
| | - Catherine Campbell
- California State University Northridge, Biology Dept., MC 8303. 18111 Nordhoff Street. Northridge, CA 91330
| | - Mialishia Mccalipp
- California State University Northridge, Biology Dept., MC 8303. 18111 Nordhoff Street. Northridge, CA 91330
| | - Maria Elena de Bellard
- California State University Northridge, Biology Dept., MC 8303. 18111 Nordhoff Street. Northridge, CA 91330
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29
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Ford DP, Benson RBJ. The phylogeny of early amniotes and the affinities of Parareptilia and Varanopidae. Nat Ecol Evol 2019; 4:57-65. [DOI: 10.1038/s41559-019-1047-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022]
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30
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Botha AE, Botha J. Ontogenetic and inter-elemental osteohistological variability in the leopard tortoise Stigmochelys pardalis. PeerJ 2019; 7:e8030. [PMID: 31871831 PMCID: PMC6924341 DOI: 10.7717/peerj.8030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/14/2019] [Indexed: 11/20/2022] Open
Abstract
Testudines are a group of reptiles characterized by the presence of a shell covered by keratinous shields. Stigmochelys pardalis is the most widely distributed terrestrial testudine in southern Africa. Although relatively common with some life history traits being well known, the growth of this species has yet to be studied in any detail. The bone microanatomy of this clade differs from that found in other amniotes, where terrestrial species tend to display characteristics normally seen in aquatic species and vice versa. A detailed histological analysis of the limb bones of S. pardalis reveals extensive variation through ontogeny. Cortical bone becomes increasingly thicker through ontogeny and is finally resorbed in the late sub-adult stage, resulting in a thin cortex and a large infilled medullary cavity. The predominant bone tissues are parallel-fibred and lamellar-zonal for the forelimbs and hind limbs respectively. The oldest individual displayed an External Fundamental System indicating that the growth rate had decreased substantially by this stage. Variability is prevalent between the forelimb and hind limb as well as between early and late sub-adults Forelimb elements exhibit characteristics such as faster growing parallel-fibered bone tissue, slightly higher vascularization and a predominance of annuli over Lines of Arrested Growth (LAG) compared to the hind limb which exhibits poorly vascularized, slower growing lamellar-zonal bone interrupted by LAGs. These differences indicate that the forelimb grew more rapidly than the hind limb, possibly due to the method of locomotion seen in terrestrial species. The extensive bone resorption that occurs from the early sub-adult stage destroys much of the primary cortex and results in a significantly different ratio of inner and outer bone diameter (p = 3.59 × 10--5; df = 28.04) as well as compactness (p = 2.91 × 10--5; df = 31.27) between early and late sub-adults. The extensive bone resorption seen also destroys the ecological signal and infers an aquatic lifestyle for this species despite it being clearly terrestrial. This supports the results of other studies that have found that using bone microanatomy to determine lifestyle in testudines does not produce accurate results.
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Affiliation(s)
- Alexander Edward Botha
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, Free State, South Africa
| | - Jennifer Botha
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, Free State, South Africa.,Department of Karoo Palaeontology, National Museum, Bloemfontein, Free State, South Africa
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31
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Jensen MF, Nedergaard S, Nielsen HN, Skovgaard N, Stevnsner TV, Wang T. Endothelin-1 induces a strong pressor effect in ball pythons (Python regius). Comp Biochem Physiol A Mol Integr Physiol 2019; 241:110620. [PMID: 31770594 DOI: 10.1016/j.cbpa.2019.110620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/19/2019] [Accepted: 11/19/2019] [Indexed: 11/18/2022]
Abstract
Endothelin-1 (ET-1) is a very potent vasoactive peptide released from endothelial cells, and ET-1 plays an important role in the maintenance and regulation of blood pressure in mammals. ET-1 signaling is mediated by two receptors: ETA and ETB. In mammals, ETA receptors are located on vascular smooth muscle where they mediate vasoconstriction. ETB receptors located on the endothelium mediate vasodilatation through the release of nitric oxide, whereas stimulation of ETB receptors placed on vascular smooth muscle leads to vasoconstriction. Less is known about ET-1 signaling in reptiles. In anaesthetized alligators, ET-1 elicits a biphasic blood pressure with a long-lasting initial decrease followed by a smaller increase in systemic blood pressure. In anaesthetized freshwater turtles, ET-1 causes a dose-dependent systemic vasodilatation mediated through ETB receptors. In the present study, we investigated the cardiovascular effects of ET-1 on the systemic and pulmonary vasculature of pythons. The presence of ETA and ETB receptors in the vasculature of pythons was verified by means of immunoblotting. Myography on isolated vessels revealed a dose-dependent vasoconstrictory response to ET-1 in both mesenteric and pulmonary arteries. Pressure measurements in recovered specimens revealed an ET-1-induced rise in systemic blood pressure supporting our in vitro findings. In conclusion, our study shows that ET-1 induces a strong pressor effect in the systemic circulation.
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Affiliation(s)
- Maja Fuhlendorff Jensen
- Zoophysiology, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.
| | - Signe Nedergaard
- Zoophysiology, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | | | - Nini Skovgaard
- Zoophysiology, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
| | - Tinna V Stevnsner
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Tobias Wang
- Zoophysiology, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark; Aarhus Institute of Advanced Studies, 8000 Aarhus C, Denmark
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32
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Aboitiz F, Montiel JF. Morphological evolution of the vertebrate forebrain: From mechanical to cellular processes. Evol Dev 2019; 21:330-341. [DOI: 10.1111/ede.12308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Francisco Aboitiz
- Departamento de Psiquiatría, Escuela de MedicinaPontificia Universidad Católica de Chile Santiago Chile
- Centro Interdisciplinario de NeurocienciasPontificia Universidad Católica de Chile Santiago Chile
| | - Juan F. Montiel
- Centro de Investigación Biomédica, Facultad de MedicinaUniversidad Diego Portales Santiago Chile
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33
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Ultrastructural analysis of the yolk processing pattern in embryonic pond slider turtles (Trachemys scripta: Emydidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:187-197. [DOI: 10.1002/jez.b.22894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/19/2019] [Accepted: 06/27/2019] [Indexed: 01/19/2023]
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34
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Alzugaray ME, Bruno MC, Villalobos Sambucaro MJ, Ronderos JR. The Evolutionary History of The Orexin/Allatotropin GPCR Family: from Placozoa and Cnidaria to Vertebrata. Sci Rep 2019; 9:10217. [PMID: 31308431 PMCID: PMC6629687 DOI: 10.1038/s41598-019-46712-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
Peptidic messengers constitute a highly diversified group of intercellular messengers widely distributed in nature that regulate a great number of physiological processes in Metazoa. Being crucial for life, it seem that they have appeared in the ancestral group from which Metazoa evolved, and were highly conserved along the evolutionary process. Peptides act mainly through G-protein coupled receptors (GPCRs), a family of transmembrane molecules. GPCRs are also widely distributed in nature being present in metazoan, but also in Choanoflagellata and Fungi. Among GPCRs, the Allatotropin/Orexin (AT/Ox) family is particularly characterized by the presence of the DRW motif in the second intracellular loop (IC Loop 2), and seems to be present in Cnidaria, Placozoa and in Bilateria, suggesting that it was present in the common ancestor of Metazoa. Looking for the evolutionary history of this GPCRs we searched for corresponding sequences in public databases. Our results suggest that AT/Ox receptors were highly conserved along evolutionary process, and that they are characterized by the presence of the E/DRWYAI motif at the IC Loop 2. Phylogenetic analyses show that AT/Ox family of receptors reflects evolutionary relationships that agree with current phylogenetic understanding in Actinopterygii and Sauropsida, including also the largely discussed position of Testudines.
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Affiliation(s)
- María Eugenia Alzugaray
- Cátedra de Histología y Embriología Animal, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (FCNyM-UNLP), La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Cecilia Bruno
- Cátedra de Histología y Embriología Animal, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (FCNyM-UNLP), La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María José Villalobos Sambucaro
- Cátedra de Histología y Embriología Animal, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (FCNyM-UNLP), La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jorge Rafael Ronderos
- Cátedra de Histología y Embriología Animal, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (FCNyM-UNLP), La Plata, Argentina.
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35
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Iulianella A, Wingate RJ, Moens CB, Capaldo E. The generation of granule cells during the development and evolution of the cerebellum. Dev Dyn 2019; 248:506-513. [PMID: 31131952 DOI: 10.1002/dvdy.64] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/10/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022] Open
Abstract
The cerebellum coordinates vestibular input into the hindbrain to control balance and movement, and its anatomical complexity is increasingly viewed as a high-throughput processing center for sensory and cognitive functions. Cerebellum development however is relatively simple, and arises from a specialized structure in the anterior hindbrain called the rhombic lip, which along with the ventricular zone of the rostral-most dorsal hindbrain region, give rise to the distinct cell types that constitute the cerebellum. Granule cells, being the most numerous cell types, arise from the rhombic lip and form a dense and distinct layer of the cerebellar cortex. In this short review, we describe the various strategies used by amniotes and anamniotes to generate and diversify granule cell types during cerebellar development.
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Affiliation(s)
- Angelo Iulianella
- Department of Medical Neuroscience and Brain Repair Centre, Life Science Research Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Richard J Wingate
- MRC Centre of Neurodevelopmental Disorders, King's College London, London, UK
| | - Cecilia B Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Emily Capaldo
- Department of Medical Neuroscience and Brain Repair Centre, Life Science Research Institute, Dalhousie University, Halifax, Nova Scotia, Canada
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36
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Stein K, Prondvai E, Huang T, Baele JM, Sander PM, Reisz R. Structure and evolutionary implications of the earliest (Sinemurian, Early Jurassic) dinosaur eggs and eggshells. Sci Rep 2019; 9:4424. [PMID: 30872623 PMCID: PMC6418122 DOI: 10.1038/s41598-019-40604-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/14/2019] [Indexed: 11/08/2022] Open
Abstract
One of the fossil record's most puzzling features is the absence of preserved eggs or eggshell for the first third of the known 315 million year history of amniote evolution. Our meagre understanding of the origin and evolution of calcareous eggshell and amniotic eggs in general, is largely based on Middle Jurassic to Late Cretaceous fossils. For dinosaurs, the most parsimonious inference yields a thick, hard shelled egg, so richly represented in the Late Cretaceous fossil record. Here, we show that a thin calcareous layer (≤100 µm) with interlocking units of radiating crystals (mammillae) and a thick shell membrane already characterize the oldest known amniote eggs, belonging to three coeval, but widely distributed Early Jurassic basal sauropodomorph dinosaurs. This thin shell layer strongly contrasts with the considerably thicker calcareous shells of Late Jurassic dinosaurs. Phylogenetic analyses and their Sinemurian age indicate that the thin eggshell of basal sauropodomorphs represents a major evolutionary innovation at the base of Dinosauria and that the much thicker eggshell of sauropods, theropods, and ornithischian dinosaurs evolved independently. Advanced mineralization of amniote eggshell (≥150 µm in thickness) in general occurred not earlier than Middle Jurassic and may correspond with a global trend of increase in atmospheric oxygen.
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Affiliation(s)
- Koen Stein
- Earth System Science - AMGC, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Royal Belgian Institute of Natural Sciences, Directorate 'Earth and History of Life', Rue Vautier 29, 1000, Brussels, Belgium.
| | - Edina Prondvai
- Evolutionary Morphology of Vertebrates, Ghent University, K.L. Ledeganckstraat 35, 9000, Gent, Belgium
- MTA-ELTE Lendület Dinosaur Research Group, Eötvös Loránd University, Pázmány P. s. 1/C, 1117, Budapest, Hungary
| | - Timothy Huang
- International Center of Future Science, and Dinosaur Evolution Research Center of Jilin University, Changchun, Jilin Province, China
- National Chung Hsing University, Taichung, 402, Taiwan
| | - Jean-Marc Baele
- Department of Geology and Applied Geology, Faculty of Engineering, University of Mons, Place du Parc 20, 7000, Mons, Belgium
| | - P Martin Sander
- Steinmann Institute of Geology, Mineralogy, and Paleontology, Division of Paleontology, University of Bonn, Nussallee 8, 53115, Bonn, Germany
- Natural History Museum of Los Angeles County, Dinosaur Institute, 900 Exposition Boulevard, Los Angeles, CA, 90007, USA
| | - Robert Reisz
- International Center of Future Science, and Dinosaur Evolution Research Center of Jilin University, Changchun, Jilin Province, China.
- National Chung Hsing University, Taichung, 402, Taiwan.
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
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37
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Cuff AR, Daley MA, Michel KB, Allen VR, Lamas LP, Adami C, Monticelli P, Pelligand L, Hutchinson JR. Relating neuromuscular control to functional anatomy of limb muscles in extant archosaurs. J Morphol 2019; 280:666-680. [PMID: 30847966 DOI: 10.1002/jmor.20973] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 12/21/2022]
Abstract
Electromyography (EMG) is used to understand muscle activity patterns in animals. Understanding how much variation exists in muscle activity patterns in homologous muscles across animal clades during similar behaviours is important for evaluating the evolution of muscle functions and neuromuscular control. We compared muscle activity across a range of archosaurian species and appendicular muscles, including how these EMG patterns varied across ontogeny and phylogeny, to reconstruct the evolutionary history of archosaurian muscle activation during locomotion. EMG electrodes were implanted into the muscles of turkeys, pheasants, quail, guineafowl, emus (three age classes), tinamous and juvenile Nile crocodiles across 13 different appendicular muscles. Subjects walked and ran at a range of speeds both overground and on treadmills during EMG recordings. Anatomically similar muscles such as the lateral gastrocnemius exhibited similar EMG patterns at similar relative speeds across all birds. In the crocodiles, the EMG signals closely matched previously published data for alligators. The timing of lateral gastrocnemius activation was relatively later within a stride cycle for crocodiles compared to birds. This difference may relate to the coordinated knee extension and ankle plantarflexion timing across the swing-stance transition in Crocodylia, unlike in birds where there is knee flexion and ankle dorsiflexion across swing-stance. No significant effects were found across the species for ontogeny, or between treadmill and overground locomotion. Our findings strengthen the inference that some muscle EMG patterns remained conservative throughout Archosauria: for example, digital flexors retained similar stance phase activity and M. pectoralis remained an 'anti-gravity' muscle. However, some avian hindlimb muscles evolved divergent activations in tandem with functional changes such as bipedalism and more crouched postures, especially M. iliotrochantericus caudalis switching from swing to stance phase activity and M. iliofibularis adding a novel stance phase burst of activity.
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Affiliation(s)
- Andrew R Cuff
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, AL9 7TA, United Kingdom
| | - Monica A Daley
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, AL9 7TA, United Kingdom
| | - Krijn B Michel
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, AL9 7TA, United Kingdom
| | - Vivian R Allen
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, AL9 7TA, United Kingdom
| | - Luis Pardon Lamas
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, AL9 7TA, United Kingdom
| | - Chiara Adami
- Queen Mother Hospital, Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, United Kingdom
| | - Paolo Monticelli
- Queen Mother Hospital, Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, United Kingdom
| | - Ludo Pelligand
- Queen Mother Hospital, Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, United Kingdom
| | - John R Hutchinson
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, AL9 7TA, United Kingdom
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38
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Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Mol Phylogenet Evol 2019; 131:80-92. [DOI: 10.1016/j.ympev.2018.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023]
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Bower DS, Brannelly LA, McDonald CA, Webb RJ, Greenspan SE, Vickers M, Gardner MG, Greenlees MJ. A review of the role of parasites in the ecology of reptiles and amphibians. AUSTRAL ECOL 2018. [DOI: 10.1111/aec.12695] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Deborah S. Bower
- College of Science and Engineering; James Cook University; Townsville Queensland 4811 Australia
- School of Environmental and Rural Science; University of New England; Armidale New South Wales Australia
| | - Laura A. Brannelly
- Department of Biological Sciences; University of Pittsburgh; Pittsburgh Pennsylvania USA
| | - Cait A. McDonald
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca New York USA
| | - Rebecca J. Webb
- College of Public Health, Medical and Veterinary Sciences; James Cook University; Townsville Queensland Australia
| | - Sasha E. Greenspan
- Department of Biological Sciences; University of Alabama; Tuscaloosa Alabama USA
| | - Mathew Vickers
- College of Science and Engineering; James Cook University; Townsville Queensland 4811 Australia
| | - Michael G. Gardner
- College of Science and Engineering; Flinders University; Adelaide South Australia Australia
- Evolutionary Biology Unit; South Australian Museum; Adelaide South Australia Australia
| | - Matthew J. Greenlees
- School of Life and Environmental Sciences; University of Sydney; Sydney New South Wales Australia
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40
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Betancur-R R, Arcila D, Vari RP, Hughes LC, Oliveira C, Sabaj MH, Ortí G. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution 2018; 73:329-345. [PMID: 30426469 DOI: 10.1111/evo.13649] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022]
Abstract
Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non-monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.
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Affiliation(s)
- Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico, 00931.,Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013
| | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Richard P Vari
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Lily C Hughes
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Mark H Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, 19103
| | - Guillermo Ortí
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
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41
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A comparative study of eggshells of Gekkota with morphological, chemical compositional and crystallographic approaches and its evolutionary implications. PLoS One 2018; 13:e0199496. [PMID: 29933400 PMCID: PMC6014675 DOI: 10.1371/journal.pone.0199496] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/10/2018] [Indexed: 01/30/2023] Open
Abstract
The Gekkota is an important clade in the evolution of calcified eggshells in that some of its families lay rigid eggshells like archosaurs. However, the fundamental differences and similarities between the mechanism of rigid eggshell formation of the Gekkota and Archosauria have not been investigated thoroughly due to the lack of knowledge of gekkotan eggshells. Here, we report for the first time a comprehensive analysis of morphological, chemical compositional, and crystallographic features of rigid and soft gekkotan eggshells. Exhaustive morphological description provided common characters for gekkotan eggshells, as well as unique features of each species. We found that elemental distribution of rigid gekkotan eggshells is different from that of avian eggshells, especially in the case of Mg and P. In addition, the crystallographic features (size, shape, and alignment of calcite grains) of gekkotan eggshells are completely different from those of archosaur eggshells. The result of this study suggests that soft gekkotan eggshells are morphologically more similar to tuatara eggshells rather than soft eggshells of derived squamates. The chemical compositional analysis suggests that the eggshell may act as a mineral reservoir for P and F as well as Ca. More importantly, all chemical compositions and crystallographic features imply that the gekkotan eggshell formation may begin at the outer surface and growing down to the inner surface, which is opposite to the direction of the archosaur eggshell formation. This character would be crucial for identifying fossil gekkotan eggs, which are poorly known in paleontology. All these lines of evidence support that soft gekkotan and tuatara eggshells share the primitive characters of all lepidosaurid eggshells. Finally, gekkotan and archosaur rigid eggshells represent a typical example of convergent evolution in the lineage of the Sauropsida.
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Tarver JE, Taylor RS, Puttick MN, Lloyd GT, Pett W, Fromm B, Schirrmeister BE, Pisani D, Peterson KJ, Donoghue PCJ. Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss. Genome Biol Evol 2018; 10:1457-1470. [PMID: 29788279 PMCID: PMC6007596 DOI: 10.1093/gbe/evy096] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Richard S Taylor
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Mark N Puttick
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
- Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Graeme T Lloyd
- School of Earth and Environment, University of Leeds, United Kingdom
| | - Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Bettina E Schirrmeister
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Davide Pisani
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Philip C J Donoghue
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
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43
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Myhrvold NP. Response to formal comment on Myhrvold (2016) submitted by Griebeler and Werner (2017). PLoS One 2018; 13:e0192912. [PMID: 29489880 PMCID: PMC5831047 DOI: 10.1371/journal.pone.0192912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/20/2018] [Indexed: 11/19/2022] Open
Abstract
Griebeler and Werner offer a formal comment on Myhrvold, 2016 defending the conclusions of Werner and Griebeler, 2014. Although the comment criticizes several aspects of methodology in Myhrvold, 2016, all three papers concur on a key conclusion: the metabolism of extant endotherms and ectotherms cannot be reliably classified using growth-rate allometry, because the growth rates of extant endotherms and ectotherms overlap. A key point of disagreement is that the 2014 paper concluded that despite this general case, one can nevertheless classify dinosaurs as ectotherms from their growth rate allometry. The 2014 conclusion is based on two factors: the assertion (made without any supporting arguments) that the comparison with dinosaurs must be restricted only to extant sauropsids, ignoring other vertebrate groups, and that extant sauropsid endotherm and ectotherm growth rates in a data set studied in the 2014 work do not overlap. The Griebeler and Werner formal comment presents their first arguments in support of the restriction proposition. In this response I show that this restriction is unsupported by established principles of phylogenetic comparison. In addition, I show that the data set studied in their 2014 work does show overlap, and that this is visible in one of its figures. I explain how either point effectively invalidates the conclusion of their 2014 paper. I also address the other methodological criticisms of Myhrvold 2016, and find them unsupported.
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44
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Lautenschlager S, Ferreira GS, Werneburg I. Sensory Evolution and Ecology of Early Turtles Revealed by Digital Endocranial Reconstructions. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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45
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Werneburg I, Laurin M, Koyabu D, Sánchez-Villagra MR. Evolution of organogenesis and the origin of altriciality in mammals. Evol Dev 2017; 18:229-44. [PMID: 27402569 DOI: 10.1111/ede.12194] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mammals feature not only great phenotypic disparity, but also diverse growth and life history patterns, especially in maturity level at birth, ranging from altriciality to precocity. Gestation length, morphology at birth, and other markers of life history are fundamental to our understanding of mammalian evolution. Based on the first synthesis of embryological data and the study of new ontogenetic series, we reconstructed estimates of the ancestral chronology of organogenesis and life-history modes in placental mammals. We found that the ancestor of marsupial and placental mammals was placental-like at birth but had a long, marsupial-like infancy. We hypothesize that mammalian viviparity might have evolved in association with the extension of growth after birth, enabled through lactation, and that mammalian altriciality is inherited from the earliest amniotes. The precocial lifestyle of extant sauropsids and that of many placental mammals were acquired secondarily. We base our conclusions on the best estimates and provide a comprehensive discussion on the methods used and the limitations of our dataset. We provide the most comprehensive embryological dataset ever published, "rescue" old literature sources, and apply available methods and illustrate thus an approach on how to investigate comparatively organogenesis in macroevolution.
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Affiliation(s)
- Ingmar Werneburg
- Paläontologisches Institut und Museum der Universität Zürich, Karl Schmid Strasse 4, 8006 Zürich, Switzerland.,Senckenberg Center for Human Evolution and Palaeoenvironment (HEP) at Eberhard Karls Universität, Sigwartstraße 10, 72074 Tübingen, Germany.,Fachbereich Geowissenschaften, Eberhard Karls Universität, Hölderlinstraße 12, D-72076 Tübingen, Germany.,Museum für Naturkunde, Leibniz-Institut für Evolutions- and Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstraße 43, 10115 Berlin, Germany
| | - Michel Laurin
- Sorbonne Universités, CR2P, CNRS/MNHN/UPMC (U. Paris 6), Muséum National d'Histoire Naturelle, Batiment de Géologie, Case postale 48, 43 rue Buffon, F-75231 Paris Cedex 05, France
| | - Daisuke Koyabu
- University Museum, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Marcelo R Sánchez-Villagra
- Paläontologisches Institut und Museum der Universität Zürich, Karl Schmid Strasse 4, 8006 Zürich, Switzerland
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46
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Tong C, Tian F, Zhang C, Zhao K. The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau. PLoS One 2017; 12:e0174534. [PMID: 28358922 PMCID: PMC5373569 DOI: 10.1371/journal.pone.0174534] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/11/2017] [Indexed: 12/12/2022] Open
Abstract
Tibetan naked carp Gymnocypris przewalskii is an ideal model system to study highland adaptation of fish, because it evolved specific genetic and phenotypic characteristics to adapt to chronic cold and alkaline environments in Lake Qinghai. MicroRNAs (miRNAs) are small noncoding RNAs that regulating gene expression post-transcriptionally in a wide range of biological processes. In this study, we focus on the role of miRNAs in adaptation of G. przewalskii to extreme conditions in Lake Qinghai. We generate the first miRNAome of G. przewalskii in Schizothoracinae fish. Using several genomic resources, we inferred 341 conserved miRNAs belonged to 152 miRNA families and 43 novel miRNAs in G. przewalskii, and also identified 15 teleost-specific miRNAs. Using a large scale of conserved miRNAs, we constructed a high-confidence phylogenetic tree between teleost and mammals than mitochondria and nuclear genes. In addition, we found that several miRNA family (e.g. miR-10 and let-7) members highly expressed in G. przewalskii, which may function in multiple biological processes. Finally, we predicted a total of 34,258 miRNA targets genes. Conserved miRNAs target genes participating in signal transduction, cell differentiation and biosynthetic process, and showed signature of functional constraint. While novel miRNAs in a species displayed species-specific targets and involved in ion binding, transport and oxidoreductase activity, may affect the expression patterns of targets with signature of gene family expansion or positive selection under extreme environment. Taken together, this study demonstrated that miRNAs may involve into roles of adaptation of G. przewalskii to highland aquatic environment, and also provide insights into miRNA regulatory network in Schizothoracinae fish as a case study.
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Affiliation(s)
- Chao Tong
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Tian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Cunfang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Kai Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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47
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Schroeter ER, DeHart CJ, Cleland TP, Zheng W, Thomas PM, Kelleher NL, Bern M, Schweitzer MH. Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein. J Proteome Res 2017; 16:920-932. [PMID: 28111950 PMCID: PMC5401637 DOI: 10.1021/acs.jproteome.6b00873] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the previous study with substantially less sample material. Data are available via ProteomeXchange with identifier PXD005087.
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Affiliation(s)
- Elena R. Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Caroline J. DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Timothy P. Cleland
- Department of Chemistry, University of Texas-Austin, Austin, Texas 78712, United States
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul M. Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Marshall Bern
- Protein Metrics, San Carlos, California 94070, United States
| | - Mary H. Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, United States
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48
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Melstrom KM. The relationship between diet and tooth complexity in living dentigerous saurians. J Morphol 2017; 278:500-522. [PMID: 28145089 DOI: 10.1002/jmor.20645] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 11/28/2016] [Accepted: 12/09/2016] [Indexed: 11/07/2022]
Abstract
Living saurian reptiles exhibit a wide range of diets, from carnivores to strict herbivores. Previous research suggests that the tooth shape in some lizard clades correlates with diet, but this has not been tested using quantitative methods. I investigated the relationship between phenotypic tooth complexity and diet in living reptiles by examining the entire dentary tooth row in over 80 specimens comprising all major dentigerous saurian clades. I quantified dental complexity using orientation patch count rotated (OPCR), which discriminates diet in living and extinct mammals, where OPCR-values increase with the proportion of dietary plant matter. OPCR was calculated from high-resolution CT-scans, and I standardized OPCR-values by the total number of teeth to account for differences in tooth count across taxa. In contrast with extant mammals, there appears to be greater overlap in tooth complexity values across dietary groups because multicusped teeth characterize herbivores, omnivores, and insectivores, and because herbivorous skinks have relatively simple teeth. In particular, insectivorous lizards have dental complexities that are very similar to omnivores. Regardless, OPCR-values for animals that consume significant amounts of plant material are higher than those of carnivores, with herbivores having the highest average dental complexity. These results suggest reptilian tooth complexity is related to diet, similar to extinct and extant mammals, although phylogenetic history also plays a measurable role in dental complexity. This has implications for extinct amniotes that display a dramatic range of tooth morphologies, many with no modern analogs, which inhibits detailed dietary reconstructions. These data demonstrate that OPCR, when combined with additional morphological data, has the potential to be used to reconstruct the diet of extinct amniotes. J. Morphol. 278:500-522, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Keegan M Melstrom
- Department of Geology and Geophysics, University of Utah, 115 S 1460 E, Salt Lake City, Utah, 84112-0102
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49
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Bever G, Lyson TR, Field DJ, Bhullar BAS. The amniote temporal roof and the diapsid origin of the turtle skull. ZOOLOGY 2016; 119:471-473. [DOI: 10.1016/j.zool.2016.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 12/01/2022]
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50
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Foth C, Ezcurra MD, Sookias RB, Brusatte SL, Butler RJ. Unappreciated diversification of stem archosaurs during the Middle Triassic predated the dominance of dinosaurs. BMC Evol Biol 2016; 16:188. [PMID: 27628503 PMCID: PMC5024528 DOI: 10.1186/s12862-016-0761-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/05/2016] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Archosauromorpha originated in the middle-late Permian, radiated during the Triassic, and gave rise to the crown group Archosauria, a highly successful clade of reptiles in terrestrial ecosystems over the last 250 million years. However, scientific attention has mainly focused on the diversification of archosaurs, while their stem lineage (i.e. non-archosaurian archosauromorphs) has often been overlooked in discussions of the evolutionary success of Archosauria. Here, we analyse the cranial disparity of late Permian to Early Jurassic archosauromorphs and make comparisons between non-archosaurian archosauromorphs and archosaurs (including Pseudosuchia and Ornithodira) on the basis of two-dimensional geometric morphometrics. RESULTS Our analysis recovers previously unappreciated high morphological disparity for non-archosaurian archosauromorphs, especially during the Middle Triassic, which abruptly declined during the early Late Triassic (Carnian). By contrast, cranial disparity of archosaurs increased from the Middle Triassic into the Late Triassic, declined during the end-Triassic extinction, but re-expanded towards the end of the Early Jurassic. CONCLUSIONS Our study indicates that non-archosaurian archosauromorphs were highly diverse components of terrestrial ecosystems prior to the major radiation of archosaurs, including dinosaurs, while disparity patterns of the Ladinian and Carnian indicate a gradual faunal replacement of stem archosaurs by the crown group, including a short interval of partial overlap in morphospace during the Ladinian.
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Affiliation(s)
- Christian Foth
- Department of Geosciences, University of Fribourg/Freiburg, Fribourg, Switzerland.
- SNSB, Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany.
- Department of Earth and Environmental Sciences and GeoBio-Center, Ludwig-Maximilians-Universität, München, Germany.
| | - Martín D Ezcurra
- CONICET, Sección Paleontología de Vertebrados, Museo Argentino de Ciencias Naturales, Buenos Aires, Argentina
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Roland B Sookias
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | | | - Richard J Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
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