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Sharma S, Kumar S. Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning. Mol Biol Evol 2024; 41:msae131. [PMID: 38916040 PMCID: PMC11247346 DOI: 10.1093/molbev/msae131] [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: 01/02/2024] [Revised: 05/30/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024] Open
Abstract
Phylogenomic analyses of long sequences, consisting of many genes and genomic segments, reconstruct organismal relationships with high statistical confidence. But, inferred relationships can be sensitive to excluding just a few sequences. Currently, there is no direct way to identify fragile relationships and the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance and clade probability derived from evolutionary sparse learning models. We validated these metrics using fungi, plant, and animal phylogenomic datasets, highlighting the ability of the new metrics to pinpoint fragile clades and the sequences responsible. The new approach does not necessitate the investigation of alternative phylogenetic hypotheses, substitution models, or repeated data subset analyses. Our methodology offers a streamlined approach to evaluating major inferred clades and identifying sequences that may distort reconstructed phylogenies using large datasets.
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Affiliation(s)
- Sudip Sharma
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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2
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Iijima M, Mayerl CJ, Munteanu VD, Blob RW. Forelimb muscle activation patterns in American alligators: Insights into the evolution of limb posture and powered flight in archosaurs. J Anat 2024; 244:943-958. [PMID: 38242862 PMCID: PMC11095314 DOI: 10.1111/joa.14011] [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: 08/08/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/21/2024] Open
Abstract
The evolution of archosaurs provides an important context for understanding the mechanisms behind major functional transformations in vertebrates, such as shifts from sprawling to erect limb posture and the acquisition of powered flight. While comparative anatomy and ichnology of extinct archosaurs have offered insights into musculoskeletal and gait changes associated with locomotor transitions, reconstructing the evolution of motor control requires data from extant species. However, the scarcity of electromyography (EMG) data from the forelimb, especially of crocodylians, has hindered understanding of neuromuscular evolution in archosaurs. Here, we present EMG data for nine forelimb muscles from American alligators during terrestrial locomotion. Our aim was to investigate the modulation of motor control across different limb postures and examine variations in motor control across phylogeny and locomotor modes. Among the nine muscles examined, m. pectoralis, the largest forelimb muscle and primary shoulder adductor, exhibited significantly smaller mean EMG amplitudes for steps in which the shoulder was more adducted (i.e., upright). This suggests that using a more adducted limb posture helps to reduce forelimb muscle force and work during stance. As larger alligators use a more adducted shoulder and hip posture, the sprawling to erect postural transition that occurred in the Triassic could be either the cause or consequence of the evolution of larger body size in archosaurs. Comparisons of EMG burst phases among tetrapods revealed that a bird and turtle, which have experienced major musculoskeletal transformations, displayed distinctive burst phases in comparison to those from an alligator and lizard. These results support the notion that major shifts in body plan and locomotor modes among sauropsid lineages were associated with significant changes in muscle activation patterns.
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Affiliation(s)
- Masaya Iijima
- Structure and Motion Lab, Department of Comparative Biomedical SciencesThe Royal Veterinary CollegeHertfordshireUK
- Nagoya University MuseumNagoyaJapan
| | | | - V. David Munteanu
- Department of Biological SciencesClemson UniversityClemsonSouth CarolinaUSA
| | - Richard W. Blob
- Department of Biological SciencesClemson UniversityClemsonSouth CarolinaUSA
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3
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Hassan NT, Galbraith JD, Adelson DL. Multiple horizontal transfer events of a DNA transposon into turtles, fishes, and a frog. Mob DNA 2024; 15:7. [PMID: 38605364 PMCID: PMC11008031 DOI: 10.1186/s13100-024-00318-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Horizontal transfer of transposable elements (HTT) has been reported across many species and the impact of such events on genome structure and function has been well described. However, few studies have focused on reptilian genomes, especially HTT events in Testudines (turtles). Here, as a consequence of investigating the repetitive content of Malaclemys terrapin terrapin (Diamondback turtle) we found a high similarity DNA transposon, annotated in RepBase as hAT-6_XT, shared between other turtle species, ray-finned fishes, and a frog. hAT-6_XT was notably absent in reptilian taxa closely related to turtles, such as crocodiles and birds. Successful invasion of DNA transposons into new genomes requires the conservation of specific residues in the encoded transposase, and through structural analysis, these residues were identified indicating some retention of functional transposition activity. We document six recent independent HTT events of a DNA transposon in turtles, which are known to have a low genomic evolutionary rate and ancient repeats.
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Affiliation(s)
- Nozhat T Hassan
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - James D Galbraith
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, Australia.
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4
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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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5
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Garg KM, Gwee CY, Chattopadhyay B, Ng NS, Prawiradilaga DM, David G, Fuchs J, Hung Le Manh, Martinez J, Olsson U, Vuong Tan Tu, Chhin S, Alström P, Lei F, Rheindt FE. When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae). Mol Phylogenet Evol 2024; 193:107999. [PMID: 38160993 DOI: 10.1016/j.ympev.2023.107999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace's Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.
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Affiliation(s)
- Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat, India; Department of Biology, Ashoka University, Sonipat, India
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Department of Biology, Ashoka University, Sonipat, India; Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Nathaniel S Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Dewi M Prawiradilaga
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Bogor-Cibinong, West Java, Indonesia
| | - Gabriel David
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, 22 S U, EPHE, UA CP51, Paris, France
| | - Hung Le Manh
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Center, Göteborg, Sweden
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Sophea Chhin
- Department of Biodiversity, General Directorate of Policy and Strategy, Ministry of Environment, Phnom Penh, Cambodia
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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6
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Gônet J, Laurin M, Hutchinson JR. Evolution of posture in amniotes-Diving into the trabecular architecture of the femoral head. J Evol Biol 2023; 36:1150-1165. [PMID: 37363887 DOI: 10.1111/jeb.14187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/29/2023] [Accepted: 04/16/2023] [Indexed: 06/28/2023]
Abstract
Extant amniotes show remarkable postural diversity. Broadly speaking, limbs with erect (strongly adducted, more vertically oriented) posture are found in mammals that are particularly heavy (graviportal) or show good running skills (cursorial), while crouched (highly flexed) limbs are found in taxa with more generalized locomotion. In Reptilia, crocodylians have a "semi-erect" (somewhat adducted) posture, birds have more crouched limbs and lepidosaurs have sprawling (well-abducted) limbs. Both synapsids and reptiles underwent a postural transition from sprawling to more erect limbs during the Mesozoic Era. In Reptilia, this postural change is prominent among archosauriforms in the Triassic Period. However, limb posture in many key Triassic taxa remains poorly known. In Synapsida, the chronology of this transition is less clear, and competing hypotheses exist. On land, the limb bones are subject to various stresses related to body support that partly shape their external and internal morphology. Indeed, bone trabeculae (lattice-like bony struts that form the spongy bone tissue) tend to orient themselves along lines of force. Here, we study the link between femoral posture and the femoral trabecular architecture using phylogenetic generalized least squares. We show that microanatomical parameters measured on bone cubes extracted from the femoral head of a sample of amniote femora depend strongly on body mass, but not on femoral posture or lifestyle. We reconstruct ancestral states of femoral posture and various microanatomical parameters to study the "sprawling-to-erect" transition in reptiles and synapsids, and obtain conflicting results. We tentatively infer femoral posture in several hypothetical ancestors using phylogenetic flexible discriminant analysis from maximum likelihood estimates of the microanatomical parameters. In general, the trabecular network of the femoral head is not a good indicator of femoral posture. However, ancestral state reconstruction methods hold great promise for advancing our understanding of the evolution of posture in amniotes.
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Affiliation(s)
- Jordan Gônet
- Centre de recherche en paléontologie - Paris, UMR 7207, Sorbonne Université, Muséum national d'histoire naturelle, Centre national de la recherche scientifique, Paris, France
| | - Michel Laurin
- Centre de recherche en paléontologie - Paris, UMR 7207, Sorbonne Université, Muséum national d'histoire naturelle, Centre national de la recherche scientifique, Paris, France
| | - John R Hutchinson
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hatfield, UK
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Reiner A. Could theropod dinosaurs have evolved to a human level of intelligence? J Comp Neurol 2023; 531:975-1006. [PMID: 37029483 PMCID: PMC10106414 DOI: 10.1002/cne.25458] [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: 08/09/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 04/09/2023]
Abstract
Noting that some theropod dinosaurs had large brains, large grasping hands, and likely binocular vision, paleontologist Dale Russell suggested that a branch of these dinosaurs might have evolved to a human intelligence level, had dinosaurs not become extinct. I offer reasons why the likely pallial organization in dinosaurs would have made this improbable, based on four assumptions. First, it is assumed that achieving human intelligence requires evolving an equivalent of the about 200 functionally specialized cortical areas characteristic of humans. Second, it is assumed that dinosaurs had an avian nuclear type of pallial organization, in contrast to the mammalian cortical organization. Third, it is assumed that the interactions between the different neuron types making up an information processing unit within pallium are critical to its role in analyzing information. Finally, it is assumed that increasing axonal length between the neuron sets carrying out this operation impairs its efficacy. Based on these assumptions, I present two main reasons why dinosaur pallium might have been unable to add the equivalent of 200 efficiently functioning cortical areas. First, a nuclear pattern of pallial organization would require increasing distances between the neuron groups corresponding to the separate layers of any given mammalian cortical area, as more sets of nuclei equivalent to a cortical area are interposed between the existing sets, increasing axon length and thereby impairing processing efficiency. Second, because of its nuclear organization, dinosaur pallium could not reduce axon length by folding to bring adjacent areas closer together, as occurs in cerebral cortex.
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Affiliation(s)
- Anton Reiner
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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Motoshima T, Nagashima A, Ota C, Oka H, Hosono K, Braasch I, Nishihara H, Kato A. Na +/Cl - cotransporter 2 is not fish-specific and is widely found in amphibians, non-avian reptiles, and select mammals. Physiol Genomics 2023; 55:113-131. [PMID: 36645671 PMCID: PMC9988527 DOI: 10.1152/physiolgenomics.00143.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/28/2022] [Accepted: 01/12/2023] [Indexed: 01/17/2023] Open
Abstract
Solute carrier 12 (Slc12) is a family of electroneutral cation-coupled chloride (Cl-) cotransporters. Na+/K+/2Cl- (Nkcc) and Na+/Cl- cotransporters (Ncc) belong to the Nkcc/Ncc subfamily. Human and mouse possess one gene for the Na+/Cl- cotransporter (ncc gene: slc12a3), whereas teleost fishes possess multiple ncc genes, slc12a3 (ncc1) and slc12a10 (ncc2), in addition to their species-specific paralogs. Amphibians and squamates have two ncc genes: slc12a3 (ncc1) and ncc3. However, the evolutionary relationship between slc12a10 and ncc3 remains unresolved, and the presence of slc12a10 (ncc2) in mammals has not been clarified. Synteny and phylogenetic analyses of vertebrate genome databases showed that ncc3 is the ortholog of slc12a10, and slc12a10 is present in most ray-finned fishes, coelacanths, amphibians, reptiles, and a few mammals (e.g., platypus and horse) but pseudogenized or deleted in birds, most mammals, and some ray-finned fishes (pufferfishes). This shows that slc12a10 is widely present among bony vertebrates and pseudogenized or deleted independently in multiple lineages. Notably, as compared with some fish that show varied slc12a10 tissue expression profile, spotted gar, African clawed frog, red-eared slider turtle, and horse express slc12a10 in the ovaries or premature gonads. In horse tissues, an unexpectedly large number of splicing variants for Slc12a10 have been cloned, many of which encode truncated forms of Slc12a10, suggesting that the functional constraints of horse slc12a10 are weakened, which may be in the process of becoming a pseudogene. Our results elaborate on the evolution of Nkcc/Ncc subfamily of Slc12 in vertebrates.NEW & NOTEWORTHY slc12a10 is not a fish-specific gene and is present in a few mammals (e.g., platypus and horse), non-avian reptiles, amphibians, but was pseudogenized or deleted in most mammals (e.g., human, mouse, cat, cow, and rhinoceros), birds, and some ray-finned fishes (pufferfishes).
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Affiliation(s)
- Toya Motoshima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ayumi Nagashima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Chihiro Ota
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Haruka Oka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kohei Hosono
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ingo Braasch
- Department of Integrative Biology, College of Natural Science, Michigan State University, East Lansing, Michigan, United States
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Akira Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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Pedro Selvatti A, Romero Rebello Moreira F, Cardoso de Carvalho D, Prosdocimi F, Augusta de Moraes Russo C, Carolina Martins Junqueira A. Phylogenomics reconciles molecular data with the rich fossil record on the origin of living turtles. Mol Phylogenet Evol 2023; 183:107773. [PMID: 36977459 DOI: 10.1016/j.ympev.2023.107773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 02/07/2023] [Accepted: 03/21/2023] [Indexed: 03/28/2023]
Abstract
Although a consensus exists that all living turtles fall within either Pleurodira or Cryptodira clades, estimating when these lineages split is still under debate. Most molecular studies date the split in the Triassic Period, whereas a Jurassic age is unanimous among morphological studies. Each hypothesis implies different paleobiogeographical scenarios to explain early turtle evolution. Here we explored the rich turtle fossil record with the Fossilized Birth-Death (FBD) and the traditional node dating (ND) methods using complete mitochondrial genomes (147 taxa) and a set of nuclear orthologs with over 10 million bp (25 taxa) to date the major splits in Testudines. Our results support an Early Jurassic split (191-182 Ma) for the crown Testudines with great consistency across different dating methods and datasets, with a narrow confidence interval. This result is independently supported by the oldest fossils of Testudines that postdate the Middle Jurassic (174 Ma), which were not used for calibration in this study. This age coincides with the Pangaea fragmentation and the formation of saltwater barriers such as the Atlantic Ocean and the Turgai Strait, supporting that diversification in Testudines was triggered by vicariance. Our ages of the splits in Pleurodira coincide with the geologic events of the Late Jurassic and Early Cretaceous. Conversely, the early Cryptodira radiation remained in Laurasia, and its diversification ensued as all its major lineages expanded their distribution into every continent during the Cenozoic. We provide the first detailed hypothesis of the evolution of Cryptodira in the Southern Hemisphere, in which our time estimates are correlated with each contact between landmasses derived from Gondwana and Laurasia. Although most South American Cryptodira arrived through the Great American Biotic Interchange, our results indicate that the Chelonoidis ancestor probably arrived from Africa through the chain islands of the South Atlantic during the Paleogene. Together, the presence of ancient turtle diversity and the vital role that turtles occupy in marine and terrestrial ecosystems underline South America as a chief area for conservation.
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10
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An ankylosaur larynx provides insights for bird-like vocalization in non-avian dinosaurs. Commun Biol 2023; 6:152. [PMID: 36792659 PMCID: PMC9932143 DOI: 10.1038/s42003-023-04513-x] [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: 07/24/2022] [Accepted: 01/20/2023] [Indexed: 02/17/2023] Open
Abstract
A voice box (larynx) is unique for tetrapods and plays functional roles in respiration, airway protection, and vocalization. However, in birds and other reptiles, the larynx fossil is extremely rare, and the evolution of this structure remains largely unknown. Here we report the fossil larynx found in non-avian dinosaurs from ankylosaur Pinacosaurus grangeri. The larynx of Pinacosaurus is composed of the cricoid and arytenoid like non-avian reptiles, but specialized with the firm and kinetic cricoid-arytenoid joint, prominent arytenoid process, long arytenoid, and enlarged cricoid, as a possible vocal modifier like birds rather than vocal source like non-avian reptiles. Although bird-unique vocal source (syrinx) have never been reported in non-avian dinosaurs, Pinacosaurus could have employed bird-like vocalization with the bird-like large, kinetic larynx. This oldest laryngeal fossil from the Cretaceous dinosaur provides the first step for understanding the vocal evolution in non-avian dinosaurs toward birds.
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11
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Wirth W, Forzán MJ, Schwarzkopf L, Ariel E. Pathogenesis of Bohle iridovirus infection in Krefft's freshwater turtle hatchlings ( Emydura macquarii krefftii). Vet Pathol 2023; 60:139-150. [PMID: 36086869 DOI: 10.1177/03009858221122591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ranaviruses have been detected in over 12 families of reptiles including many genera of turtles, tortoises, and terrapins, but the pathogenesis of these infections is still poorly understood. Krefft's river turtle hatchlings (N = 36; Emydura macquarii krefftii) were inoculated intramuscularly with Bohle iridovirus (BIV, Ranavirus, isolate) or saline, and euthanized at 9 timepoints (3 infected and 1 control per timepoint) over a 24-day period. Samples of lung, liver, kidney, and spleen were collected for quantitative polymerase chain reaction (PCR); internal organs, skin, and oral cavity samples were fixed for histopathological examination. The earliest lesions, at 8 days postinoculation (dpi), were lymphocytic inflammation of the skin and fibrinoid necrosis of regional vessels at the site of inoculation, and mild ulcerative necrosis with lymphocytic and heterophilic inflammation in the oral, nasal, and tongue mucosae. Fibrinonecrotic foci with heterophilic inflammation were detected in spleen and gonads at 16 dpi. Multifocal hepatic necrosis, heterophilic inflammation, and occasional basophilic intracytoplasmic inclusion bodies were observed at 20 dpi, along with ulcerative lymphocytic and heterophilic tracheitis and bronchitis. Tracheitis, bronchitis, and rare bone marrow necrosis were present at 24 dpi. Of the viscera tested for ranaviral DNA by PCR, the liver and spleen had the highest viral loads throughout infection, and thus appeared to be major targets of viral replication. Testing of whole blood by qPCR was the most-effective ante-mortem method for detecting ranaviral infection compared with oral swabs. This study represents the first time-dependent pathogenesis study of a ranaviral infection in turtles.
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Affiliation(s)
| | | | | | - Ellen Ariel
- James Cook University, Townsville, QLD, Australia
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12
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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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13
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van der Geest N, Garcia L, Nates R, Godoy DA. New insight into the swimming kinematics of wild Green sea turtles (Chelonia mydas). Sci Rep 2022; 12:18151. [PMID: 36316441 PMCID: PMC9622894 DOI: 10.1038/s41598-022-21459-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/27/2022] [Indexed: 12/31/2022] Open
Abstract
Biomechanically, sea turtles could be perceived as birds of the ocean as they glide and flap their forelimbs to produce the necessary forces required for locomotion, making sea turtles an interesting animal to study. However, being an endangered species makes studying the sea turtle's biomechanics a complex problem to solve, both technically and ethically, without causing disturbance. This work develops a novel, non-invasive procedure to develop full three-dimensional kinematics for wild sea turtles by filming the animals in Australia's Great Barrier Reef using underwater drones without disturbing them. We found that the wild animals had very different swimming patterns than previous studies on juveniles in captivity. Our findings show that the flipper goes through a closed-loop trajectory with extended sweeping of the flipper tip towards the centre of the carapace to create a clapping motion. We have named this the "sweep stroke" and in contrast to previously described four-stage models, it creates a five-stage cycle swimming locomotion model. The model presented here could lead to a better comprehension of the sea turtle propulsion methods and their fluid-structure interaction.
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Affiliation(s)
- Nick van der Geest
- BioDesign Lab, Auckland University of Technology, Auckland, 1010, New Zealand
| | - Lorenzo Garcia
- BioDesign Lab, Auckland University of Technology, Auckland, 1010, New Zealand.
| | - Roy Nates
- BioDesign Lab, Auckland University of Technology, Auckland, 1010, New Zealand
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14
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Romanenko SA, Prokopov DY, Proskuryakova AA, Davletshina GI, Tupikin AE, Kasai F, Ferguson-Smith MA, Trifonov VA. The Cytogenetic Map of the Nile Crocodile ( Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs. Int J Mol Sci 2022; 23:13063. [PMID: 36361851 PMCID: PMC9656864 DOI: 10.3390/ijms232113063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 01/16/2024] Open
Abstract
Tandemly arranged and dispersed repetitive DNA sequences are important structural and functional elements that make up a significant portion of vertebrate genomes. Using high throughput, low coverage whole genome sequencing followed by bioinformatics analysis, we have identified seven major tandem repetitive DNAs and two fragments of LTR retrotransposons in the genome of the Nile crocodile (Crocodylus niloticus, 2n = 32). The repeats showed great variability in structure, genomic organization, and chromosomal distribution as revealed by fluorescence in situ hybridization (FISH). We found that centromeric and pericentromeric heterochromatin of C. niloticus is composed of previously described in Crocodylus siamensis CSI-HindIII and CSI-DraI repetitive sequence families, a satellite revealed in Crocodylus porosus, and additionally contains at least three previously unannotated tandem repeats. Both LTR sequences identified here belong to the ERV1 family of endogenous retroviruses. Each pericentromeric region was characterized by a diverse set of repeats, with the exception of chromosome pair 4, in which we found only one type of satellite. Only a few repeats showed non-centromeric signals in addition to their centromeric localization. Mapping of 18S-28S ribosomal RNA genes and telomeric sequences (TTAGGG)n did not demonstrate any co-localization of these sequences with revealed centromeric and pericentromeric heterochromatic blocks.
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Affiliation(s)
- Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Dmitry Yu. Prokopov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Anastasia A. Proskuryakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Guzel I. Davletshina
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Fumio Kasai
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, The National Institute of Biomedical Innovation, Health and Nutrition, Saito-Asagi, Ibaraki 567-0085, Osaka, Japan
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | | | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia
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15
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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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16
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Ecay TW, Stewart JR, Khambaty M. Functional complexity in the chorioallantoic membrane of an oviparous snake: Specializations for calcium uptake from the eggshell. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:331-341. [PMID: 35652464 DOI: 10.1002/jez.b.23146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/15/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
The chorioallantoic membrane of oviparous reptiles forms a vascular interface with the eggshell. The eggshell contains calcium, primarily as calcium carbonate. Extraction and mobilization of this calcium by the chorioallantoic membrane contributes importantly to embryonic nutrition. Development of the chorioallantoic membrane is primarily known from studies of squamates and birds. Although there are pronounced differences in eggshell structure, squamate and bird embryos each mobilize calcium from eggshells. Specialized cells in the chicken chorionic epithelium transport calcium from the eggshell aided by a second population of cells that secrete protons generated by the enzyme carbonic anhydrase. Calcium transporting cells also are present in the chorioallantoic membrane of corn snakes, although these cells function differently than those of chickens. We used histology and immunohistology to characterize the morphology and functional attributes of the chorioallantoic membrane of corn snakes. We identified two populations of cells in the outer layer of the chorionic epithelium. Calbindin-D28K , a cellular marker for calcium transport expressed in squamate chorioallantoic membranes, is localized in large, flattened cells that predominate in the chorionic epithelium. Smaller cells, interspersed among the large cells, express carbonic anhydrase 2, an enzyme not previously localized in the chorionic epithelium of an oviparous squamate. These findings indicate that differentiation of chorionic epithelial cells contributes to extraction and transport of calcium from the eggshell. The presence of specializations of chorioallantoic membranes for calcium uptake from eggshells in chickens and corn snakes suggests that eggshell calcium was a source of embryonic nutrition early in the evolution of Sauropsida.
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Affiliation(s)
- Tom W Ecay
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson, Tennessee, USA
| | - James R Stewart
- Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee, USA
| | - Maleka Khambaty
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson, Tennessee, USA
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17
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Chromosome-level genome assembly of Asian yellow pond turtle (Mauremys mutica) with temperature-dependent sex determination system. Sci Rep 2022; 12:7905. [PMID: 35550586 PMCID: PMC9098631 DOI: 10.1038/s41598-022-12054-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022] Open
Abstract
Knowledge of sex determination has important implications in physiology, ecology and genetics, but the evolutionary mechanisms of sex determination systems in turtles have not been fully elucidated, due to a lack of reference genomes. Here, we generate a high-quality genome assembly of Asian yellow pond turtle (Mauremys mutica) using continuous long-read (PacBio platform), Illumina, and high-throughput chromatin conformation capture (Hi-C) technologies. The M. mutica haplotype has a genome size of 2.23 Gb with a contig N50 of 8.53 Mb and scaffold N50 of 141.98 Mb. 99.98% sequences of the total assembly are anchored to 26 pseudochromosomes. Comparative genomics analysis indicated that the lizard-snake-tuatara clade diverged from the bird-crocodilian-turtle clade at approximately 267.0-312.3 Mya. Intriguingly, positive selected genes are mostly enriched in the calcium signaling pathway and neuroactive ligand-receptor interaction, which are involved in the process of temperature-dependent sex determination. These findings provide important evolutionary insights into temperature-dependent sex determination system.
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18
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Pavón-Vázquez CJ, Esquerré D, Fitch AJ, Maryan B, Doughty P, Donnellan SC, Scott Keogh J. Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex). Mol Phylogenet Evol 2022; 173:107516. [DOI: 10.1016/j.ympev.2022.107516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
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The Two Domains of the Avian Double-β-Defensin AvBD11 Have Different Ancestors, Common with Potential Monodomain Crocodile and Turtle Defensins. BIOLOGY 2022; 11:biology11050690. [PMID: 35625418 PMCID: PMC9138766 DOI: 10.3390/biology11050690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/08/2022] [Accepted: 04/16/2022] [Indexed: 12/12/2022]
Abstract
Simple Summary Vertebrate defensins are a multigene family of antimicrobial peptides that evolved following a series of gene duplication and divergence events during the expansion of vertebrates. In birds, the repertoire of avian defensins contains an atypical defensin, namely AvBD11 (avian beta-defensin 11), which consists of two repeated but divergent defensin units (or domains) while most vertebrate defensins only possess one unit. In this study, we investigated the evolutionary scenario leading to the formation of this double defensin in birds by comparing each defensin unit of AvBD11 with other defensins from birds and closely related reptiles (crocodile, turtles) predicted to have a single defensin unit. Our most outstanding results suggest that the double defensin AvBD11 probably appeared following a fusion of two ancestral genes or from an ancestral double defensin, but not from a recent internal duplication as it can be observed in other types of proteins with domain repeats. Abstract Beta-defensins are an essential group of cysteine-rich host-defence peptides involved in vertebrate innate immunity and are generally monodomain. Among bird defensins, the avian β-defensin 11 (AvBD11) is unique because of its peculiar structure composed of two β-defensin domains. The reasons for the appearance of such ‘polydefensins’ during the evolution of several, but not all branches of vertebrates, still remain an open question. In this study, we aimed at exploring the origin and evolution of the bird AvBD11 using a phylogenetic approach. Although they are homologous, the N- and C-terminal domains of AvBD11 share low protein sequence similarity and possess different cysteine spacing patterns. Interestingly, strong variations in charge properties can be observed on the C-terminal domain depending on bird species but, despite this feature, no positive selection was detected on the AvBD11 gene (neither on site nor on branches). The comparison of AvBD11 protein sequences in different bird species, however, suggests that some amino acid residues may have undergone convergent evolution. The phylogenetic tree of avian defensins revealed that each domain of AvBD11 is distant from ovodefensins (OvoDs) and may have arisen from different ancestral defensins. Strikingly, our phylogenetic analysis demonstrated that each domain of AvBD11 has common ancestors with different putative monodomain β-defensins from crocodiles and turtles and are even more closely related with these reptilian defensins than with their avian paralogs. Our findings support that AvBD11′s domains, which differ in their cysteine spacing and charge distribution, do not result from a recent internal duplication but most likely originate from a fusion of two different ancestral genes or from an ancestral double-defensin arisen before the Testudines-Archosauria split.
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20
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Scanes CG, Witt J, Ebeling M, Schaller S, Baier V, Bone AJ, Preuss TG, Heckmann D. Quantitative Morphometric, Physiological, and Metabolic Characteristics of Chickens and Mallards for Physiologically Based Kinetic Model Development. Front Physiol 2022; 13:858283. [PMID: 35464078 PMCID: PMC9019682 DOI: 10.3389/fphys.2022.858283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/17/2022] [Indexed: 11/25/2022] Open
Abstract
Physiologically based kinetic (PBK) models are a promising tool for xenobiotic environmental risk assessment that could reduce animal testing by predicting in vivo exposure. PBK models for birds could further our understanding of species-specific sensitivities to xenobiotics, but would require species-specific parameterization. To this end, we summarize multiple major morphometric and physiological characteristics in chickens, particularly laying hens (Gallus gallus) and mallards (Anas platyrhynchos) in a meta-analysis of published data. Where such data did not exist, data are substituted from domesticated ducks (Anas platyrhynchos) and, in their absence, from chickens. The distribution of water between intracellular, extracellular, and plasma is similar in laying hens and mallards. Similarly, the lengths of the components of the small intestine (duodenum, jejunum, and ileum) are similar in chickens and mallards. Moreover, not only are the gastrointestinal absorptive areas similar in mallard and chickens but also they are similar to those in mammals when expressed on a log basis and compared to log body weight. In contrast, the following are much lower in laying hens than mallards: cardiac output (CO), hematocrit (Hct), and blood hemoglobin. There are shifts in ovary weight (increased), oviduct weight (increased), and plasma/serum concentrations of vitellogenin and triglyceride between laying hens and sexually immature females. In contrast, reproductive state does not affect the relative weights of the liver, kidneys, spleen, and gizzard.
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Affiliation(s)
- Colin G. Scanes
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
- Department of Biological Science, University of Wisconsin Milwaukee, Milwaukee, WI, United States
- *Correspondence: Colin G. Scanes,
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21
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Dutton HR, DuPreez LH, Urabe M, Bullard SA. Paraharmotrema karinganiense n. gen., n. sp. (Digenea: Liolopidae) infecting the intestine of serrated hinged terrapin ( Pelusios sinuatus), east African black mud turtle ( Pelusios subniger), and South African helmeted turtle ( Pelomedusa galeata) and a phylogenetic hypothesis for liolopid genera. Int J Parasitol Parasites Wildl 2022; 17:43-52. [PMID: 34976724 PMCID: PMC8688888 DOI: 10.1016/j.ijppaw.2021.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 06/14/2023]
Abstract
We herein describe Paraharmotrema karinganiense n. gen., n. sp. Dutton & Bullard (Liolopidae Dollfus, 1934) from specimens infecting the intestine of the serrated hinged terrapin (Pelusios sinuatus), east African black mud turtle (Pelusios subniger) (both Nwanedzi River, Mozambique), and South African helmeted terrapin (Pelomedusa galeata) (North-western Zululand, KwaZulu-Natal Province, South Africa). The new genus can be easily differentiated from the other accepted liolopid genera (Liolope Cohn, 1902; Helicotrema Odhner, 1912; Harmotrema Nicoll, 1914; Dracovermis Brooks & Overstreet, 1978) by the combination of having a linguliform body approximately 6-9 × longer than wide, tegumental spines/scales, a minute ventral sucker located in the anterior 1/7-1/8 of the body, deeply lobed testes that are transverse and abut the caeca (spanning the intercaecal space), a uterus that is lateral to the anterior testis (not ventral to the anterior testis), a lobed ovary that is dextral and nearest the posterior testis, and a vitellarium that does not extend anteriad to the level of the ventral sucker and that does not fill the intercaecal space. Nucleotide sequences of large subunit ribosomal DNA (28S) and internal transcribed space region (ITS2) from all analyzed specimens of the new species were identical, respectively; the 28S sequences differed from that of Liolope copulans Cohn, 1902 and from that of Harmotrema laticaudae Yamaguti, 1933 by 103 (8%) and 105 (8%) nucleotides, respectively. The 28S phylogenetic analysis recovered the new genus sister to a clade comprising L. copulans and H. laticaudae. A key to liolopid genera is provided herein. The present study comprises the first nucleotide-based phylogenetic placement of Harmotrema and first record of a liolopid from South Africa or Mozambique. It is the first proposal of a new liolopid genus in 43 yrs, and it documents a second liolopid genus from P. subniger while tripling the number of liolopid turtle hosts reported from the continent of Africa.
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Affiliation(s)
- Haley R. Dutton
- Aquatic Parasitology Laboratory and Southeastern Cooperative Fish Parasite and Disease Laboratory, School of Fisheries, Aquaculture, & Aquatic Sciences, College of Agriculture, Auburn University, 559 Devall Dr., Auburn, AL, 36832, USA
| | - Louis H. DuPreez
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Private Bag ×6001, Potchefstroom, 2520, South Africa
- South African Institute for Aquatic Biodiversity, Somerset Street, Grahamstown 6139, South Africa
| | - Misako Urabe
- University Shiga Prefecture, Department of Ecosystem Studies, Faculty of Environmental Science, 2500 Hassaka, Hikone, Shiga, 5228533, Japan
| | - Stephen A. Bullard
- Aquatic Parasitology Laboratory and Southeastern Cooperative Fish Parasite and Disease Laboratory, School of Fisheries, Aquaculture, & Aquatic Sciences, College of Agriculture, Auburn University, 559 Devall Dr., Auburn, AL, 36832, USA
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22
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Gable SM, Byars MI, Literman R, Tollis M. A Genomic Perspective on the Evolutionary Diversification of Turtles. Syst Biol 2022; 71:1331-1347. [DOI: 10.1093/sysbio/syac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies based on annotated regions from the western painted turtle (Chrysemys picta bellii) genome (coding regions, introns, untranslated regions, intergenic, and others). We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for temporal patterns in phylogenomic conflict across turtle evolution. We found strong and consistent support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa. Our results suggest that gene tree-species tree discordance in these datasets is likely driven by population-level processes such as incomplete lineage sorting. We found very little effect of substitutional saturation on species tree topologies, and no clear phylogenetic patterns in codon usage bias and compositional heterogeneity. There was no correlation between gene and site concordance, node age, and DNA substitution rate across most annotated genomic regions. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible in order to obtain accurate phylogenies for assessing conservation priorities in turtles.
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Affiliation(s)
- Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA
| | - Michael I Byars
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA
| | - Robert Literman
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingstown, RI, 0288, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, PO Box 5693, Flagstaff, AZ 8601, USA
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23
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Clulow S, Clulow J, Marcec-Greaves R, Della Togna G, Calatayud NE. Common goals, different stages: the state of the ARTs for reptile and amphibian conservation. Reprod Fertil Dev 2022; 34:i-ix. [PMID: 35275052 DOI: 10.1071/rdv34n5_fo] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Amphibians and reptiles are highly threatened vertebrate taxa with large numbers of species threatened with extinction. With so many species at risk, conservation requires the efficient and cost-effective application of all the tools available so that as many species as possible are assisted. Biobanking of genetic material in genetic resource banks (GRBs) in combination with assisted reproductive technologies (ARTs) to retrieve live animals from stored materials are two powerful, complementary tools in the conservation toolbox for arresting and reversing biodiversity decline for both amphibians and reptiles. However, the degree of development of the ARTs and cryopreservation technologies differ markedly between these two groups. These differences are explained in part by different perceptions of the taxa, but also to differing reproductive anatomy and biology between the amphibians and reptiles. Artificial fertilisation with cryopreserved sperm is becoming a more widely developed and utilised technology for amphibians. However, in contrast, artificial insemination with production of live progeny has been reported in few reptiles, and while sperm have been successfully cryopreserved, there are still no reports of the production of live offspring generated from cryopreserved sperm. In both amphibians and reptiles, a focus on sperm cryopreservation and artificial fertilisation or artificial insemination has been at the expense of the development and application of more advanced technologies such as cryopreservation of the female germline and embryonic genome, or the use of sophisticated stem cell/primordial germ cell cryopreservation and transplantation approaches. This review accompanies the publication of ten papers on amphibians and twelve papers on reptiles reporting advances in ARTs and biobanking for the herpetological taxa.
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Affiliation(s)
- Simon Clulow
- Centre for Conservation Ecology & Genomics, Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - John Clulow
- University of Newcastle, Conservation Biology Research Group, University Drive, Callaghan, NSW 2308, Australia
| | | | - Gina Della Togna
- Universidad Interamericana de Panama, Direccion de Investigacion, Campus Central, Avenida Ricardo J. Alfaro, Panama City, Panama; and Smithsonian Tropical Research Institute, Panama Amphibian Rescue and Conservation Project, Panama
| | - Natalie E Calatayud
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, 15600 San Pasqual valley Road, Escondido, CA 92025, USA; and Conservation Science Network, 24 Thomas Street, Mayfield, NSW 2304, Australia
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24
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OUP accepted manuscript. Syst Biol 2022; 71:973-985. [DOI: 10.1093/sysbio/syac014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 11/12/2022] Open
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25
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Davidian AG, Dyomin AG, Galkina SA, Makarova NE, Dmitriev SE, Gaginskaya ER. 45S rDNA Repeats of Turtles and Crocodiles Harbor a Functional 5S rRNA Gene Specifically Expressed in Oocytes. Mol Biol Evol 2021; 39:6432055. [PMID: 34905062 PMCID: PMC8789306 DOI: 10.1093/molbev/msab324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In most eukaryotic genomes, tandemly repeated copies of 5S rRNA genes are clustered outside the nucleolus organizer region (NOR), which normally encodes three other major rRNAs: 18S, 5.8S, and 28S. Our analysis of turtle rDNA sequences has revealed a 5S rDNA insertion into the NOR intergenic spacer in antisense orientation. The insertion (hereafter called NOR-5S rRNA gene) has a length of 119 bp and coexists with the canonical 5S rDNA clusters outside the NOR. Despite the ∼20% nucleotide difference between the two 5S gene sequences, their internal control regions for RNA polymerase III are similar. Using the turtle Trachemys scripta as a model species, we showed the NOR-5S rDNA specific expression in oocytes. This expression is concurrent with the NOR rDNA amplification during oocyte growth. We show that in vitellogenic oocytes, the NOR-5S rRNA prevails over the canonical 5S rRNA in the ribosomes, suggesting a role of modified ribosomes in oocyte-specific translation. The orders Testudines and Crocodilia seem to be the only taxa of vertebrates with such a peculiar rDNA organization. We speculate that the amplification of the 5S rRNA genes as a part of the NOR DNA during oogenesis provides a dosage balance between transcription of all the four ribosomal RNAs while producing a maternal pool of extra ribosomes. We further hypothesize that the NOR-5S rDNA insertion appeared in the Archelosauria clade during the Permian period and was lost later in the ancestors of Aves.
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Affiliation(s)
- Asya G Davidian
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexander G Dyomin
- Laboratory of Cell Technologies, Saratov State Medical University, Saratov, Russia
| | - Svetlana A Galkina
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
| | - Nadezhda E Makarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Elena R Gaginskaya
- Biological Faculty, Saint Petersburg State University, Saint Petersburg, Russia
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26
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Sex Chromosomes and Master Sex-Determining Genes in Turtles and Other Reptiles. Genes (Basel) 2021; 12:genes12111822. [PMID: 34828428 PMCID: PMC8622242 DOI: 10.3390/genes12111822] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022] Open
Abstract
Among tetrapods, the well differentiated heteromorphic sex chromosomes of birds and mammals have been highly investigated and their master sex-determining (MSD) gene, Dmrt1 and SRY, respectively, have been identified. The homomorphic sex chromosomes of reptiles have been the least studied, but the gap with birds and mammals has begun to fill. This review describes our current knowledge of reptilian sex chromosomes at the cytogenetic and molecular level. Most of it arose recently from various studies comparing male to female gene content. This includes restriction site-associated DNA sequencing (RAD-Seq) experiments in several male and female samples, RNA sequencing and identification of Z- or X-linked genes by male/female comparative transcriptome coverage, and male/female transcriptomic or transcriptome/genome substraction approaches allowing the identification of Y- or W-linked transcripts. A few putative master sex-determining (MSD) genes have been proposed, but none has been demonstrated yet. Lastly, future directions in the field of reptilian sex chromosomes and their MSD gene studies are considered.
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How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae). Mol Phylogenet Evol 2021; 167:107342. [PMID: 34785384 DOI: 10.1016/j.ympev.2021.107342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/05/2021] [Accepted: 10/29/2021] [Indexed: 12/24/2022]
Abstract
Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed.
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28
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Dunton AD, Göpel T, Ho DH, Burggren W. Form and Function of the Vertebrate and Invertebrate Blood-Brain Barriers. Int J Mol Sci 2021; 22:ijms222212111. [PMID: 34829989 PMCID: PMC8618301 DOI: 10.3390/ijms222212111] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 12/25/2022] Open
Abstract
The need to protect neural tissue from toxins or other substances is as old as neural tissue itself. Early recognition of this need has led to more than a century of investigation of the blood-brain barrier (BBB). Many aspects of this important neuroprotective barrier have now been well established, including its cellular architecture and barrier and transport functions. Unsurprisingly, most research has had a human orientation, using mammalian and other animal models to develop translational research findings. However, cell layers forming a barrier between vascular spaces and neural tissues are found broadly throughout the invertebrates as well as in all vertebrates. Unfortunately, previous scenarios for the evolution of the BBB typically adopt a classic, now discredited 'scala naturae' approach, which inaccurately describes a putative evolutionary progression of the mammalian BBB from simple invertebrates to mammals. In fact, BBB-like structures have evolved independently numerous times, complicating simplistic views of the evolution of the BBB as a linear process. Here, we review BBBs in their various forms in both invertebrates and vertebrates, with an emphasis on the function, evolution, and conditional relevance of popular animal models such as the fruit fly and the zebrafish to mammalian BBB research.
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Affiliation(s)
- Alicia D. Dunton
- Developmental Integrative Biology Group, Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; (T.G.); (W.B.)
- Correspondence:
| | - Torben Göpel
- Developmental Integrative Biology Group, Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; (T.G.); (W.B.)
| | - Dao H. Ho
- Department of Clinical Investigation, Tripler Army Medical Center, Honolulu, HI 96859, USA;
| | - Warren Burggren
- Developmental Integrative Biology Group, Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; (T.G.); (W.B.)
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29
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Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ' sexomics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200426. [PMID: 34247497 PMCID: PMC8293304 DOI: 10.1098/rstb.2020.0426] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
| | - Michail Rovatsos
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ben J. Evans
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université de Montpellier/IRD/EPHE), Montpellier, France
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Neuroscience and Developmental Biology, University of Vienna, A-1090 Vienna, Austria
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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30
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Walker JF, Smith SA, Hodel RGJ, Moyroud E. Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets. Syst Biol 2021; 71:943-958. [PMID: 34240209 DOI: 10.1093/sysbio/syab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.
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Affiliation(s)
- Joseph F Walker
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607 U.S.A
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Edwige Moyroud
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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31
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de Bakker MAG, van der Vos W, de Jager K, Chung WY, Fowler DA, Dondorp E, Spiekman SNF, Chew KY, Xie B, Jiménez R, Bickelmann C, Kuratani S, Blazek R, Kondrashov P, Renfree MB, Richardson MK. Selection on phalanx development in the evolution of the bird wing. Mol Biol Evol 2021; 38:4222-4237. [PMID: 34164688 PMCID: PMC8476175 DOI: 10.1093/molbev/msab150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 05/03/2021] [Indexed: 11/12/2022] Open
Abstract
The frameshift hypothesis is a widely-accepted model of bird wing evolution. This hypothesis postulates a shift in positional values, or molecular-developmental identity, that caused a change in digit phenotype. The hypothesis synthesised developmental and palaeontological data on wing digit homology. The 'most anterior digit' (MAD) hypothesis presents an alternative view based on changes in transcriptional regulation in the limb. The molecular evidence for both hypotheses is that the most anterior digit expresses Hoxd13 but not Hoxd11 and Hoxd12. This digit I 'signature' is thought to characterise all amniotes. Here, we studied Hoxd expression patterns in a phylogenetic sample of 18 amniotes. Instead of a conserved molecular signature in digit I, we find wide variation of Hoxd11, Hoxd12 and Hoxd13 expression in digit I. Patterns of apoptosis, and Sox9 expression, a marker of the phalanx-forming region, suggest that phalanges were lost from wing digit IV because of early arrest of the phalanx-forming region followed by cell death. Finally, we show that multiple amniote lineages lost phalanges with no frameshift. Our findings suggest that the bird wing evolved by targeted loss of phalanges under selection. Consistent with our view, some recent phylogenies based on dinosaur fossils eliminate the need to postulate a frameshift in the first place. We suggest that the phenotype of the Archaeopteryx lithographica wing is also consistent with phalanx loss. More broadly, our results support a gradualist model of evolution based on tinkering with developmental gene expression.
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Affiliation(s)
- Merijn A G de Bakker
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Wessel van der Vos
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72.,Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstrasse 43, 10115 Berlin, Germany
| | - Kaylah de Jager
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Wing Yu Chung
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Donald A Fowler
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Esther Dondorp
- Naturalis Biodiversity Center, 2300 RA Leiden, PO Box 9517, The Netherlands
| | - Stephan N F Spiekman
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland
| | - Keng Yih Chew
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Bing Xie
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Rafael Jiménez
- Departamento de Genética, Universidad de Granada, Lab 127 Centro de Investigación Biomédica, Avenida del Conocimiento S/N, 1810018016 Armilla, Granada, Spain
| | - Constanze Bickelmann
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstrasse 43, 10115 Berlin, Germany
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,RIKEN Cluster for Pioneering Research, Kobe, Japan
| | - Radim Blazek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna, 603 65, Czech Republic 8, Brno
| | - Peter Kondrashov
- Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences, Kirksville, 63501, MO USA)
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Michael K Richardson
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
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32
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Mahbub M, Wahab Z, Reaz R, Rahman MS, Bayzid MS. wQFM: Highly Accurate Genome-scale Species Tree Estimation from Weighted Quartets. Bioinformatics 2021; 37:3734-3743. [PMID: 34086858 DOI: 10.1093/bioinformatics/btab428] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree-species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree can allow for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging. RESULTS We propose wQFM, a highly accurate method for species tree estimation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. wQFM was assessed on a collection of simulated and real biological datasets, including the avian phylogenomic dataset which is one of the largest phylogenomic datasets to date. We compared wQFM with wQMC, which is the best alternate method for weighted quartet amalgamation, and with ASTRAL, which is one of the most accurate and widely used coalescent-based species tree estimation methods. Our results suggest that wQFM matches or improves upon the accuracy of wQMC and ASTRAL. AVAILABILITY wQFM is available in open source form at https://github.com/Mahim1997/wQFM-2020. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mahim Mahbub
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Zahin Wahab
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Rezwana Reaz
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - M Saifur Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka-1205, Bangladesh
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33
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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: 15] [Impact Index Per Article: 5.0] [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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34
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Hekkala E, Gatesy J, Narechania A, Meredith R, Russello M, Aardema ML, Jensen E, Montanari S, Brochu C, Norell M, Amato G. Paleogenomics illuminates the evolutionary history of the extinct Holocene "horned" crocodile of Madagascar, Voay robustus. Commun Biol 2021; 4:505. [PMID: 33907305 PMCID: PMC8079395 DOI: 10.1038/s42003-021-02017-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300-1400 year old specimens (n = 2) of the extinct "horned" crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.
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Affiliation(s)
- E Hekkala
- Department of Biological Sciences, Fordham University, Bronx, NY, USA.
- American Museum of Natural History, New York, NY, USA.
| | - J Gatesy
- American Museum of Natural History, New York, NY, USA
| | - A Narechania
- American Museum of Natural History, New York, NY, USA
| | - R Meredith
- American Museum of Natural History, New York, NY, USA
- Montclair State University, Montclair, NJ, USA
| | - M Russello
- University of British Columbia, Department of Biology, Kelowna, BC, Canada
| | - M L Aardema
- American Museum of Natural History, New York, NY, USA
- Montclair State University, Montclair, NJ, USA
| | - E Jensen
- University of British Columbia, Department of Biology, Kelowna, BC, Canada
- Newcastle University, School of Natural and Environmental Sciences Ecology Group, Newcastle, UK
| | - S Montanari
- American Museum of Natural History, New York, NY, USA
| | - C Brochu
- University of Iowa, Department of Geosciences, Iowa City, IA, USA
| | - M Norell
- American Museum of Natural History, New York, NY, USA
| | - G Amato
- American Museum of Natural History, New York, NY, USA
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35
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D'Alba L, Goldenberg J, Nallapaneni A, Parkinson DY, Zhu C, Vanthournout B, Shawkey MD. Evolution of eggshell structure in relation to nesting ecology in non-avian reptiles. J Morphol 2021; 282:1066-1079. [PMID: 33713039 DOI: 10.1002/jmor.21347] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/01/2021] [Accepted: 02/21/2021] [Indexed: 12/14/2022]
Abstract
Amniotic eggs are multifunctional structures that enabled early tetrapods to colonize the land millions of years ago, and are now the reproductive mode of over 70% of all terrestrial amniotes. Eggshell morphology is at the core of animal survival, mediating the interactions between embryos and their environment, and has evolved into a massive diversity of forms and functions in modern reptiles. These functions are critical to embryonic survival and may serve as models for new antimicrobial and/or breathable membranes. However, we still lack critical data on the basic structural and functional properties of eggs, particularly of reptiles. Here, we first characterized egg shape, shell thickness, porosity, and mineralization of eggs from 91 reptile species using optical images, scanning electron microscopy, and micro computed tomography, and collected data on nesting ecology from the literature. We then used comparative analyses to test hypotheses on the selective pressures driving their evolution. We hypothesized that eggshell morphology has evolved to protect shells from physical damage and desiccation, and, in support, found a positive relationship between thickness and precipitation, and a negative relationship between porosity and temperature. Although mineralization varied extensively, it was not correlated with nesting ecology variables. Ancestral state reconstructions show thinning and increased porosity over evolutionary time in squamates, but the opposite in turtles and crocodilians. Egg shape, size, porosity and calcification were correlated, suggesting potential structural or developmental tradeoffs. This study provides new data and insights into the morphology and evolution of reptile eggs, and raises numerous questions for additional research.
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Affiliation(s)
- Liliana D'Alba
- Department of Biology, EON-Unit, Universiteit Gent, Ghent, Belgium
| | | | - Asritha Nallapaneni
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dilworth Y Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Chenhui Zhu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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36
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Farah IT, Islam MM, Zinat KT, Rahman AH, Bayzid MS. Species tree estimation from gene trees by minimizing deep coalescence and maximizing quartet consistency: a comparative study and the presence of pseudo species tree terraces. Syst Biol 2021; 70:1213-1231. [PMID: 33844023 DOI: 10.1093/sysbio/syab026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 11/14/2022] Open
Abstract
Species tree estimation from multi-locus datasets is extremely challenging, especially in the presence of gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Summary methods have been developed which estimate gene trees and then combine the gene trees to estimate a species tree by optimizing various optimization scores. In this study, we have extended and adapted the concept of phylogenetic terraces to species tree estimation by "summarizing" a set of gene trees, where multiple species trees with distinct topologies may have exactly the same optimality score (i.e., quartet score, extra lineage score, etc.). We particularly investigated the presence and impacts of equally optimal trees in species tree estimation from multi-locus data using summary methods by taking ILS into account. We analyzed two of the most popular ILS-aware optimization criteria: maximize quartet consistency (MQC) and minimize deep coalescence (MDC). Methods based on MQC are provably statistically consistent, whereas MDC is not a consistent criterion for species tree estimation. We present a comprehensive comparative study of these two optimality criteria. Our experiments, on a collection of datasets simulated under ILS, indicate that MDC may result in competitive or identical quartet consistency score as MQC, but could be significantly worse than MQC in terms of tree accuracy - demonstrating the presence and impacts of equally optimal species trees. This is the first known study that provides the conditions for the datasets to have equally optimal trees in the context of phylogenomic inference using summary methods.
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Affiliation(s)
- Ishrat Tanzila Farah
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh
| | - Md Muktadirul Islam
- Applied Statistics and Data Science (ASDS), Department of Statistics Jahangirnagar University Dhaka-1342, Bangladesh
| | - Kazi Tasnim Zinat
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh.,Department of Computer Science University of Maryland, College Park, Maryland, USA
| | - Atif Hasan Rahman
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology Dhaka-1205, Bangladesh
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37
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Abstract
Many species from diverse and often distantly related animal groups (e.g. monkeys, crows, fish and bees) have a sense of number. This means that they can assess the number of items in a set - its 'numerosity'. The brains of these phylogenetically distant species are markedly diverse. This Review examines the fundamentally different types of brains and neural mechanisms that give rise to numerical competence across the animal tree of life. Neural correlates of the number sense so far exist only for specific vertebrate species: the richest data concerning explicit and abstract number representations have been collected from the cerebral cortex of mammals, most notably human and nonhuman primates, but also from the pallium of corvid songbirds, which evolved independently of the mammalian cortex. In contrast, the neural data relating to implicit and reflexive numerical representations in amphibians and fish is limited. The neural basis of a number sense has not been explored in any protostome so far. However, promising candidate regions in the brains of insects, spiders and cephalopods - all of which are known to have number skills - are identified in this Review. A comparative neuroscientific approach will be indispensable for identifying evolutionarily stable neuronal circuits and deciphering codes that give rise to a sense of number across phylogeny.
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Affiliation(s)
- Andreas Nieder
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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38
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Freitas FV, Branstetter MG, Griswold T, Almeida EAB. Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae). Mol Biol Evol 2021; 38:1090-1100. [PMID: 33179746 PMCID: PMC7947843 DOI: 10.1093/molbev/msaa277] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g., incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here, we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 ultraconserved element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with >1,200 species. We sampled representatives of all tribes within the group and >80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.
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Affiliation(s)
- Felipe V Freitas
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT
| | - Terry Griswold
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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39
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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: 7] [Impact Index Per Article: 2.3] [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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40
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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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41
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Andreu-Sánchez S, Chen W, Stiller J, Zhang G. Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles. Gigascience 2021; 10:giaa161. [PMID: 33463679 PMCID: PMC7814300 DOI: 10.1093/gigascience/giaa161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/05/2020] [Accepted: 12/18/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND During evolutionary history, molecular mechanisms have emerged to cope with deleterious mutations. Frameshift insertions in protein-coding sequences are extremely rare because they disrupt the reading frame. There are a few known examples of their correction through translational frameshifting, a process that enables ribosomes to skip nucleotides during translation to regain proper reading frame. Corrective frameshifting has been proposed to act on the single base pair insertion at position 174 of the mitochondrial NADH dehydrogenase subunit 3 gene (ND3) that has been observed in several turtles and birds. However, the relatively sparse taxonomic representation has hampered our understanding of the evolution of this insertion in vertebrates. RESULTS Here, we analyzed 87,707 ND3 sequences from 10,309 vertebrate taxa to reveal the evolutionary history of this insertion and its common genomic characteristics. We confirmed that the insertion only appears in turtles and birds and reconstructed that it evolved independently in both groups with complex patterns of gains and losses. The insertion was observed in almost all bird orders but was absent in all members of the diverse Passeriformes. We found strong conservation in the nucleotides surrounding the insertion in both turtles and birds, which implies that the insertion enforces structural constraints that could be involved in its correction. CONCLUSIONS Our study demonstrates that frameshifts can be widespread and can be retained for millions of years if they are embedded in a conserved sequence theme.
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Affiliation(s)
- Sergio Andreu-Sánchez
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Present Address: University of Groningen, University Medical Center Groningen, Department of Pediatrics, 9700 RB Groningen, Netherlands
| | - Wanjun Chen
- China National Genebank, BGI-Shenzhen, Beishan Industrial Zone, 518083 Shenzhen, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Beishan Industrial Zone, 518083 Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, 650223 Kunming, China
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42
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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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43
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Friesen CR, Kahrl AF, Olsson M. Sperm competition in squamate reptiles. Philos Trans R Soc Lond B Biol Sci 2020; 375:20200079. [PMID: 33070739 DOI: 10.1098/rstb.2020.0079] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multiple paternity is ubiquitous within the polyphyletic group called 'reptiles', especially within the lizards and snakes. Therefore, the probability of sperm competition occurring, and being intense, is high. Squamates exhibit a diversity of tactics to ensure fertilization success in the face of sperm competition. The duration of female sperm storage, which can be many months and even years in some species, remains an enigma. Here, we emphasize some mechanisms that might affect patterns of paternity, the source and function of ejaculates and features of the female reproductive tract that may aid in long-term sperm storage. In doing so, we present a new analysis of the relationship between sperm size, the strength of sperm competition and the duration of female sperm storage. Lizards and snakes are a diverse group that has provided many excellent models for the study of an array of life-history strategies. However, when it comes to postcopulatory sexual selection, there is much left to discover. This article is part of the theme issue 'Fifty years of sperm competition'.
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Affiliation(s)
- Christopher R Friesen
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia.,Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Ariel F Kahrl
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Mats Olsson
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia.,Department of Biological and Environmental Science, University of Gothenburg, Goteborg, Sweden
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44
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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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45
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Kvasilova A, Olejnickova V, Jensen B, Christoffels VM, Kolesova H, Sedmera D, Gregorovicova M. The formation of the atrioventricular conduction axis is linked in development to ventricular septation. ACTA ACUST UNITED AC 2020; 223:223/19/jeb229278. [PMID: 33046580 DOI: 10.1242/jeb.229278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/09/2020] [Indexed: 12/22/2022]
Abstract
During development, the ventricles of mammals and birds acquire a specialized pattern of electrical activation with the formation of the atrioventricular conduction system (AVCS), which coincides with the completion of ventricular septation. We investigated whether AVCS formation coincides with ventricular septation in developing Siamese crocodiles (Crocodylus siamensis). Comparisons were made with Amazon toadhead turtle (Mesoclemmys heliostemma) with a partial septum only and no AVCS (negative control) and with chicken (Gallus gallus) (septum and AVCS, positive control). Optical mapping of the electrical impulse in the crocodile and chicken showed a similar developmental specialization that coincided with full ventricular septation, whereas in the turtle the ventricular activation remained primitive. Co-localization of neural marker human natural killer-1 (HNK-1) and cardiomyocyte marker anti-myosin heavy chain (MF20) identified the AVCS on top of the ventricular septum in the crocodile and chicken only. AVCS formation is correlated with ventricular septation in both evolution and development.
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Affiliation(s)
- Alena Kvasilova
- Charles University, First Faculty of Medicine, Institute of Anatomy, U Nemocnice 3, 128 00 Prague, Czech Republic
| | - Veronika Olejnickova
- Charles University, First Faculty of Medicine, Institute of Anatomy, U Nemocnice 3, 128 00 Prague, Czech Republic.,Czech Academy of Sciences, Institute of Physiology, Department of Developmental Cardiology, Videnska 1083, 142 20 Prague, Czech Republic
| | - Bjarke Jensen
- University of Amsterdam, Amsterdam UMC, Department of Medical Biology, Amsterdam Cardiovascular Sciences, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
| | - Vincent M Christoffels
- University of Amsterdam, Amsterdam UMC, Department of Medical Biology, Amsterdam Cardiovascular Sciences, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
| | - Hana Kolesova
- Charles University, First Faculty of Medicine, Institute of Anatomy, U Nemocnice 3, 128 00 Prague, Czech Republic
| | - David Sedmera
- Charles University, First Faculty of Medicine, Institute of Anatomy, U Nemocnice 3, 128 00 Prague, Czech Republic .,Czech Academy of Sciences, Institute of Physiology, Department of Developmental Cardiology, Videnska 1083, 142 20 Prague, Czech Republic
| | - Martina Gregorovicova
- Charles University, First Faculty of Medicine, Institute of Anatomy, U Nemocnice 3, 128 00 Prague, Czech Republic .,Czech Academy of Sciences, Institute of Physiology, Department of Developmental Cardiology, Videnska 1083, 142 20 Prague, Czech Republic
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46
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Masila NM, Ross KE, Gardner MG, Whiley H. Zoonotic and Public Health Implications of Campylobacter Species and Squamates (Lizards, Snakes and Amphisbaenians). Pathogens 2020; 9:pathogens9100799. [PMID: 32998205 PMCID: PMC7601876 DOI: 10.3390/pathogens9100799] [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: 08/26/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 11/24/2022] Open
Abstract
Campylobacter spp. is one of the most widespread infectious diseases of veterinary and public health significance. Globally, the incidence of campylobacteriosis has increased over the last decade in both developing and developed countries. Squamates (lizards, snakes and amphisbaenians) are a potential reservoir and source of transmission of campylobacteriosis to humans. This systematic review examined studies from the last 20 years that have reported squamate-associated human campylobacteriosis. It was found that C. fetus subsp. testudinum and C. fetus subsp. fetus were the most common species responsible for human campylobacteriosis from a squamate host. The common squamate hosts identified included bearded dragons (Pogona vitticeps), green iguana (Iguana iguana), western beaked gecko (Rhynchoedura ornate) and blotched blue-tongued skink (Tiliqua nigrolutea). People with underlying chronic illnesses, the immunocompromised and the elderly were identified as the most vulnerable population. Exposure to pet squamates, wild animals, consumption of reptilian cuisines and cross contamination with untreated water were risk factors associated with Campylobacter infections. Proper hand hygiene practices, responsible pet ownership, ‘One Health’ education and awareness on zoonotic diseases will help reduce the public health risks arising from Campylobacter exposure through squamates. Continued surveillance using molecular diagnostic methods will also enhance detection and response to squamate-linked campylobacteriosis.
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Affiliation(s)
- Nicodemus M Masila
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
- Kenya Tsetse and Trypanosomiasis Eradication Council (KENTTEC), P.O. BOX 66290, Westlands, Nairobi 00800, Kenya
| | - Kirstin E Ross
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Michael G Gardner
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - Harriet Whiley
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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Davidian A, Koshel E, Dyomin A, Galkina S, Saifitdinova A, Gaginskaya E. On some structural and evolutionary aspects of rDNA amplification in oogenesis of Trachemys scripta turtles. Cell Tissue Res 2020; 383:853-864. [PMID: 32897424 DOI: 10.1007/s00441-020-03282-x] [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] [Received: 03/21/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
The features of rDNA amplification have been studied in oocytes of the red-eared slider Trachemys scripta using a number of specific histochemical and cytomolecular methods. A single nucleolus in early diplotene oocytes is associated with the nucleolus organizer region (NOR). With oocyte growth, the number of nucleoli increases dramatically and reaches hundreds by the lampbrush chromosome stage (pre-vitellogenesis). RNA-polymerase I, fibrillarin, and PCNA immunodetection in the amplified nucleoli and FISH of the 5'ETS probe to the oocyte nuclear content suggest pre-rRNA and rDNA synthesis in the nucleoli at all stages studied. This implies a continuous reproduction of the nucleoli during oocyte development from early diplotene up to vitellogenesis. The data obtained offer a different way for rDNA amplification and formation of extrachromosomal nucleoli in turtle oocytes compared with the amplified nucleoli formation in amphibian and fish oocytes. In the Sauropsida clade of Archelosauria, which includes turtles, crocodiles, and birds, rDNA function is known to be suppressed in avian oogenesis during the lampbrush stage (Gaginskaya et al. in Cytogenet Genome Res 124:251-267, 2009).
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Affiliation(s)
- Asya Davidian
- St Petersburg University, St Petersburg, 199034, Russia
| | | | - Alexander Dyomin
- St Petersburg University, St Petersburg, 199034, Russia.,Saratov State Medical University, Saratov, 410000, Russia
| | | | - Alsu Saifitdinova
- Herzen State Pedagogical University of Russia, St Petersburg, 191186, Russia
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48
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Straková B, Rovatsos M, Kubička L, Kratochvíl L. Evolution of Sex Determination in Amniotes: Did Stress and Sequential Hermaphroditism Produce Environmental Determination? Bioessays 2020; 42:e2000050. [DOI: 10.1002/bies.202000050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 07/15/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Barbora Straková
- Department of Ecology, Faculty of Science Charles University Viničná 7 Praha 2 12844 Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science Charles University Viničná 7 Praha 2 12844 Czech Republic
| | - Lukáš Kubička
- Department of Ecology, Faculty of Science Charles University Viničná 7 Praha 2 12844 Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science Charles University Viničná 7 Praha 2 12844 Czech Republic
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Iijima M, Kubo T. Intervertebral joint polarity reversions in extant and extinct crocodylians. ACTA ZOOL-STOCKHOLM 2020. [DOI: 10.1111/azo.12346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Masaya Iijima
- Department of Biological Sciences Clemson University Clemson SC USA
- Nagoya University Museum Nagoya Aichi Japan
- Engineering Research Center for Mineral Resources and Mine Environments, School of Resource and Environmental Engineering Hefei University of Technology Hefei China
| | - Tai Kubo
- The University Museum The University of Tokyo Tokyo Japan
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Zhu W, He Y, Ruan Z, Zhang X, Liao L, Gao Y, Lin N, Chen X, Liang R, Liu WS. Identification of the cDNA Encoding the Growth Hormone Receptor ( GHR) and the Regulation of GHR and IGF-I Gene Expression by Nutritional Status in Reeves' Turtle ( Chinemys reevesii). Front Genet 2020; 11:587. [PMID: 32582298 PMCID: PMC7296147 DOI: 10.3389/fgene.2020.00587] [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: 08/22/2019] [Accepted: 05/14/2020] [Indexed: 11/19/2022] Open
Abstract
Chinemys reevesii (Reeves’ turtle) is a slow-growing reptile that is distributed widely across China. Prior to this study, the cDNA sequence of the growth hormone receptor (GHR) in the Reeve’s turtle, or how periods of starvation might influence the gene expression of GHR and insulin-like growth factor I (IGF-I) in this species, were unknown. Here, we identified the full-length sequence of the cDNA encoding GHR in Reeves’ turtle by using RT-PCR and RACE. The full-length GHR cDNA was identified to be 3936 base-pairs in length, with a 1848 base-pair open reading frame (ORF) that encodes a 615 amino acid protein. Analysis showed that GHR mRNA was detectable in a wide range of tissues; the highest and lowest levels of expression were detected in the liver and the gonad, respectively. IGF-I was also expressed in a range of tissues, but not in the gonad; the highest levels of IGF-I expression were detected in the liver. After 4 weeks of fasting, the expression levels of GHR and IGF-I in the liver had decreased significantly; however, these gradually returned to normal after refeeding. We report the first cloned cDNA sequence for the GHR gene in the Reeve’s turtle. Our findings provide a foundation from which to investigate the specific function of the GHR in Reeve’s turtle, and serve as a reference for studying the effects of different nutrient levels on GHR expression in this species.
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Affiliation(s)
- Wenlu Zhu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Yuhui He
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Zhuohao Ruan
- College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Province Key Laboratory for Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Xiquan Zhang
- Guangdong Province Key Laboratory for Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Liangyuan Liao
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Yicong Gao
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Nani Lin
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xiancan Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Rui Liang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Wen-Sheng Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Province Engineering Research Centre of Aquatic Immunization and Aquaculture Health Techniques, South China Agricultural University, Guangzhou, China
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