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Ma G, Zuo Z, Li H, Zhai X, Wang T, Wang J. Comparative analysis of the liver transcriptome in the red-eared slider (Trachemys scripta elegans) post exposure to noise. PLoS One 2024; 19:e0305858. [PMID: 39088466 PMCID: PMC11293744 DOI: 10.1371/journal.pone.0305858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/05/2024] [Indexed: 08/03/2024] Open
Abstract
Exposure to noise can cause non-auditory health problems and has been widely studied in mammals such as rats and rabbits. However, the non-auditory effects of noise exposure on reptiles (such as red-eared sliders) remain unclear. In this study, we determined the noise exposure-induced transcriptomic changes in the liver of red-eared slider (Trachemys scripta elegans) using Illumina Novaseq6000 sequencing technology. The transcriptome analysis identified 176 differentially expressed genes (DEGs), which were mainly enriched in lipid metabolism. KEGG analysis showed that by affecting the peroxisome proliferator activated receptor (PPAR) signaling pathway these DEGs increased lipid synthesis and decreased lipid oxidation. The Oil Red O staining results validated our data that noise exposure increased hepatic lipid deposition. Thus, noise exposure may lead to lipid accumulation and toxicity, mitochondrial damage, and accelerated oxidative stress. Our findings provide insights into the molecular process underlying non-auditory damage caused by noise exposure in T. scripta elegans.
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Affiliation(s)
- Guangwei Ma
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Ziye Zuo
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Handong Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xiaofei Zhai
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Tongliang Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jichao Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
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2
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Guo R, Ma G, Zhai X, Shi H, Wang J. Single-cell transcriptomic landscape of peripheral blood cells provides insights into adaptation of red-eared sliders (Trachemys scripta elegans). Integr Zool 2024; 19:468-479. [PMID: 37226359 DOI: 10.1111/1749-4877.12725] [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] [Indexed: 05/26/2023]
Abstract
Red-eared sliders (Trachemys scripta elegans), as one of the 100 most threatening aliens, have stronger immunity than the native species in response to environmental stress. Blood cells are an important component of immunity in the body. However, the blood cell researches of turtle are still in the traditional blood cell classification and morphological structure observation. Furthermore, turtle granulocytes cannot be accurately identified using traditional methods. Single-cell RNA sequencing techniques have been successfully implemented to study cells based on the mRNA expression patterns of each cell. The present study profiled the transcriptomes of peripheral blood cells in red-eared sliders to construct a single-cell transcriptional landscape of the different cell types and explored environmental adaptation mechanism from the perspective of hematology. All 14 transcriptionally distinct clusters (platelets, erythrocytes1, erythrocytes2, CSF1R monocytes, POF1B monocytes, neutrophils, GATA2high basophils, GATA2low basophils, CD4 T cells, CD7 T cells, B cells, ACKR4 cells, serotriflin cells, and ficolin cells) were identified in the peripheral blood cells of the red-eared sliders. In particular, a subtype of erythrocytes (erythrocytes1) that expressed immune signals was identified. Peripheral blood cells were grouped into three lineages: platelet, erythroid/lymphoid, and myeloid cell lineages. Furthermore, based on differentiation trajectory and up-regulated gene expression, ACKR4 cells were newly identified as lymphocytes, and serotriflin and ficolin cells as granulocytes. The single-cell transcriptional atlas of the peripheral blood cells in red-eared sliders provided in the present study will offer a comprehensive transcriptome reference for the exploration of physiological and pathological hematology in this species.
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Affiliation(s)
- Rui Guo
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Guangwei Ma
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xiaofei Zhai
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Haitao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jichao Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
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3
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Comparison of the Single-Cell Immune Landscape of Testudines from Different Habitats. Cells 2022; 11:cells11244023. [PMID: 36552787 PMCID: PMC9816942 DOI: 10.3390/cells11244023] [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: 10/08/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022] Open
Abstract
Testudines, also known as living fossils, have evolved diversely and comprise many species that occupy a variety of ecological niches. However, the immune adaptation of testudines to the different ecological niches remains poorly understood. This study compared the composition, function, and differentiation trajectories of peripheral immune cells in testudines (Chelonia mydas, Trachemys scripta elegans, Chelonoidis carbonaria, and Pelodiscus sinensis) from different habitats using the single-cell RNA sequencing (scRNA-seq) technique. The results showed that T. scripta elegans, which inhabits freshwater and brackish environments, had the most complex composition of peripheral immune cells, with 11 distinct immune cell subsets identified in total. The sea turtle C. mydas, had the simplest composition of peripheral immune cells, with only 5 distinct immune cell clusters. Surprisingly, neither basophils were found in C. mydas nor T cells in C. carbonaria. Basophil subsets in peripheral blood were identified for the first time; two basophil subtypes (GATA2-high-basophils and GATA2-low-basophils) were observed in the peripheral blood of T. scripta elegans. In addition, ACKR4 cells, CD4 T cells, CD7 T cells, serotriflin cells, and ficolin cells were specifically identified in the peripheral blood of T. scripta elegans. Furthermore, LY6G6C cells, SPC24 cells, and NKT cells were specifically observed in C. carbonaria. Moreover, there were differences in the functional status and developmental trajectory of peripheral immune cells among the testudine species. The identification of specific features of peripheral immune cells in testudines from different habitats may enable elucidation of the adaptation mechanism of testudines to various ecological niches.
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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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Welt RS, Raxworthy CJ. Dispersal, not vicariance, explains the biogeographic origin of iguanas on Madagascar. Mol Phylogenet Evol 2021; 167:107345. [PMID: 34748875 DOI: 10.1016/j.ympev.2021.107345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 09/23/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022]
Abstract
Lizards of the clade Iguanidae (sensu lato) are primarily a New World group. Thus, the remarkable presence of an endemic lineage of iguanas (family Opluridae) on the isolated Indian Ocean island of Madagascar has long been considered a biogeographic anomaly. Previous work attributed this disjunct extant distribution to: (1) vicariance at about 140-165 Ma, caused by the breakup of Gondwana and the separation of South America, Africa, and Madagascar (with subsequent extinction of iguanas on Africa, and potentially other Gondwanan landmasses), (2) vicariance at about 80-90 Ma, caused by the sundering of hypothesized land-bridge connections between South America, Antarctica, India, and Madagascar, or (3) long-distance overwater dispersal from South America to Madagascar. Each hypothesis has been supported with molecular divergence dating analyses, and thus the biogeographic origin of the Opluridae is not yet well resolved. Here we utilize genetic sequences of ultraconserved elements for all Iguania families and the majority of Iguanidae (s.l.) genera, and morphological data for extant and fossil taxa (used for divergence dating analyses), to produce the most comprehensive dataset applied to date to test these origin hypotheses. We find strong support for a sister relationship between the Opluridae (Madagascar) and Leiosauridae (South America). Divergence of the Opluridae from Leiosauridae is dated to between the late Cretaceous and mid-Paleogene, at a time when Madagascar was already an island and was isolated from all other Gondwanan landmasses. Consequently, our results support a hypothesis of long-distance overwater dispersal of the Opluridae lineage, either directly from South America to Madagascar or potentially via Antarctica or Africa, leading to this radiation of iguanas in the Indian Ocean.
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Affiliation(s)
- Rachel S Welt
- Department of Herpetology, American Museum of Natural History, USA.
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6
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A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins. Proc Natl Acad Sci U S A 2021; 118:2012215118. [PMID: 33558231 DOI: 10.1073/pnas.2012215118] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities.
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7
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Short-term impacts of a record-shattering flood and dam removal on a river turtle assemblage and population placed within the context of a 50 year study. ACTA OECOLOGICA 2021. [DOI: 10.1016/j.actao.2020.103699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Ryu G, Moon JI, Song YJ, Park J, Park SM, Choi JH, Sung HC, Lee DH. Complete mitochondrial genome of the Cumberland slider ( Trachemys scripta troostii, Testudienes: Emydidae) in Korea. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1131-1133. [PMID: 33796765 PMCID: PMC7995875 DOI: 10.1080/23802359.2021.1902410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complete mitochondrial (mt) genome of Trachemys scripta troostii was sequenced and was characterized, which comprised 37 genes (13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs) and a non-coding control region. Phylogenetic analysis based on the full mt genome indicated that T. s. troostii was more closely related to T. scripta from Canada than to T. s. elegans from China or T. s. scripta fom China. This is the first complete mt genome from T. s. troostii, which provides data for further study of phylogeny in Emydidae.
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Affiliation(s)
- Gayeon Ryu
- School of Biological Sciences and Biotechnology Graduate School, Chonnam National University, Gwangju, Korea
| | - Jae-I Moon
- School of Biological Sciences and Biotechnology Graduate School, Chonnam National University, Gwangju, Korea
| | - Yun-Ju Song
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Korea
| | - Jaehong Park
- School of Biological Sciences and Biotechnology Graduate School, Chonnam National University, Gwangju, Korea
| | - Seung-Min Park
- School of Biological Sciences and Biotechnology Graduate School, Chonnam National University, Gwangju, Korea
| | - Jae Hyeok Choi
- School of Biological Sciences and Biotechnology Graduate School, Chonnam National University, Gwangju, Korea
| | - Ha-Cheol Sung
- Research Center of Ecomimetics, Chonnam National University, Gwangju, Korea.,Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Korea
| | - Dong-Hyun Lee
- Research Center of Ecomimetics, Chonnam National University, Gwangju, Korea.,Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju, Korea
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9
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Riley JL, Hudson S, Frenette-Ling C, Davy CM. All together now! Hatching synchrony in freshwater turtles. Behav Ecol Sociobiol 2020. [DOI: 10.1007/s00265-020-2800-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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10
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Rajpoot A, Bahuguna A, Kumar VP. Molecular study of globally threatened turtle species (families Trionychidae and Geoemydidae) of Uttarakhand and their relationship with other Indian populations: A wildlife forensic and conservation genetic approach. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2019. [DOI: 10.1016/j.fsir.2019.100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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11
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Bullard SA, Roberts JR, Warren MB, Dutton HR, Whelan NV, Ruiz CF, Platt TR, Tkach VV, Brant SV, Halanych KM. Neotropical Turtle Blood Flukes: Two New Genera and Species from the Amazon River Basin with a Key to Genera and Comments on a Marine-Derived Parasite Lineage in South America. J Parasitol 2019. [DOI: 10.1645/19-27] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Stephen A. Bullard
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama 36849
| | - Jackson R. Roberts
- Louisiana State University Museum of Natural Sciences, Biological Sciences Department, Louisiana State University, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Micah B. Warren
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama 36849
| | - Haley R. Dutton
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama 36849
| | - Nathan V. Whelan
- Southeastern Conservation Genetics Laboratory, Auburn University, Auburn, Alabama 36849
| | - Carlos F. Ruiz
- Aquatic Parasitology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, Auburn, Alabama 36849
| | - Thomas R. Platt
- Department of Biology, Saint Mary's College, Notre Dame, Indiana 46556
| | - Vasyl V. Tkach
- Department of Biology, University of North Dakota, Grand Forks, North Dakota 58202
| | - Sara V. Brant
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Kenneth M. Halanych
- Molette Biology Laboratory for Environmental and Climate Change Studies (MBL), Department of Biological Sciences, Auburn University, Auburn, Alabama 36849
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Abstract
Improved understanding of tick phylogeny has allowed testing of some biogeographical patterns. On the basis of both literature data and a meta-analysis of available sequence data, there is strong support for a Gondwanan origin of Ixodidae, and probably Ixodida. A particularly strong pattern is observed for the genus Amblyomma, which appears to have originated in Antarctica/southern South America, with subsequent dispersal to Australia. The endemic Australian lineages of Ixodidae (no other continent has such a pattern) appear to result from separate dispersal events, probably from Antarctica. Minimum ages for a number of divergences are determined as part of an updated temporal framework for tick evolution. Alternative hypotheses for tick evolution, such as a very old Pangean group, a Northern hemisphere origin, or an Australian origin, fit less well with observed phylogeographic patterns.
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Affiliation(s)
- Lorenza Beati
- Institute for Coastal Plain Science and US National Tick Collection, Georgia Southern University, Statesboro, Georgia 30460, USA;
| | - Hans Klompen
- Department of Evolution, Ecology, and Organismal Biology and Museum of Biological Diversity, The Ohio State University, Columbus, Ohio 43212, USA
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13
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Amori G, Luiselli L. A Review of the Mono- and Bispecific Genera of Turtles and Tortoises Worldwide, with an Assessment of the Island Endemics: Implications for Conservation. CHELONIAN CONSERVATION AND BIOLOGY 2018. [DOI: 10.2744/ccb-1296.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Giovanni Amori
- CNR-—Institute for Ecosystem Study, viale dell'Università 32, 00185 Rome, Italy [giovanni.amori@unir
| | - Luca Luiselli
- Department of Applied and Environmental Biology, Rivers State University of Science and Technology,
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14
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Cano Garcia M, Nesbit SC, Le CC, Dearworth JR. Ocular Kinematics Measured by In Vitro Stimulation of the Cranial Nerves in the Turtle. J Vis Exp 2018. [PMID: 29912183 DOI: 10.3791/56864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
After animals are euthanized, their tissues begin to die. Turtles offer an advantage because of a longer survival time of their tissues, especially when compared to warm-blooded vertebrates. Because of this, in vitro experiments in turtles can be performed for extended periods of time to investigate the neural signals and control of their target actions. Using an isolated head preparation, we measured the kinematics of eye movements in turtles, and their modulation by electrical signals carried by cranial nerves. After the brain was removed from the skull, leaving the cranial nerves intact, the dissected head was placed in a gimbal to calibrate eye movements. Glass electrodes were attached to cranial nerves (oculomotor, trochlear, and abducens) and stimulated with currents to evoke eye movements. We monitored eye movements with an infrared video tracking system and quantified rotations of the eyes. Current pulses with a range of amplitudes, frequencies, and train durations were used to observe effects on responses. Because the preparation is separated from the brain, the efferent pathway going to muscle targets can be examined in isolation to investigate neural signaling in the absence of centrally processed sensory information.
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Affiliation(s)
| | - Steven C Nesbit
- Department of Biology and Neuroscience Program, Lafayette College
| | - Chi C Le
- Department of Information Technology, Computer Science, and Digital Media, Juniata College
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15
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Zhang Y, Sun J, Rouse GW, Wiklund H, Pleijel F, Watanabe HK, Chen C, Qian PY, Qiu JW. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol Phylogenet Evol 2018; 125:220-231. [PMID: 29625228 DOI: 10.1016/j.ympev.2018.04.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/16/2018] [Accepted: 04/02/2018] [Indexed: 01/07/2023]
Abstract
Next-generation sequencing (NGS) has become a powerful tool in phylogenetic and evolutionary studies. Here we applied NGS to recover two ribosomal RNA genes (18S and 28S) from 16 species and 15 mitochondrial genomes from 16 species of scale worms representing six families in the suborder Aphroditiformia (Phyllodocida, Annelida), a complex group of polychaetes characterized by the presence of dorsal elytra or scales. The phylogenetic relationship of the several groups of scale worms remains unresolved due to insufficient taxon sampling and low resolution of individual gene markers. Phylogenetic tree topology based on mitochondrial genomes is comparable with that based on concatenated sequences from two mitochondrial genes (cox1 and 16S) and two ribosomal genes (18S and 28S) genes, but has higher statistical support for several clades. Our analyses show that Aphroditiformia is monophyletic, indicating the presence of elytra is an apomorphic trait. Eulepethidae and Aphroditidae together form the sister group to all other families in this suborder, whereas Acoetidae is sister to Iphionidae. Polynoidae is monophyletic, but within this family the deep-sea subfamilies Branchinotogluminae and Macellicephalinae are paraphyletic. Mitochondrial genomes in most scale-worm families have a conserved gene order, but within Polynoidae there are two novel arrangement patterns in the deep-sea clade. Mitochondrial protein-coding genes in polynoids as a whole have evolved under strong purifying selection, but substitution rates in deep-sea species are much higher than those in shallow-water species, indicating that purifying selection is relaxed in deep-sea polynoids. There are positive selected amino acids for some mitochondrial genes of the deep-sea clade, indicating they may involve in the adaption of deep-sea polynoids. Overall, our study (1) provided more evidence for reconstruction of the phylogeny of Aphroditiformia, (2) provided evidence to refute the assumption that mitochondrial gene order in Errantia is conserved, and (3) indicated that the deep-sea extreme environment may have affected the mitochondrial genome evolution rate and gene order arrangement in Polynoidae.
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Affiliation(s)
- Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Hong Kong, China.
| | - Jin Sun
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay Road, Hong Kong, China
| | - Greg W Rouse
- Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Helena Wiklund
- Zoology Department, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Fredrik Pleijel
- Department of Marine Sciences, University of Gothenburg, Tjärnö, SE-452 96 Strömstad, Sweden.
| | - Hiromi K Watanabe
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Chong Chen
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Pei-Yuan Qian
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay Road, Hong Kong, China.
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Hong Kong, China.
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16
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Ferreira GS, Bronzati M, Langer MC, Sterli J. Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira). ROYAL SOCIETY OPEN SCIENCE 2018; 5:171773. [PMID: 29657780 PMCID: PMC5882704 DOI: 10.1098/rsos.171773] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/26/2018] [Indexed: 05/13/2023]
Abstract
Pleurodires or side-necked turtles are today restricted to freshwater environments of South America, Africa-Madagascar and Australia, but in the past they were distributed much more broadly, being found also on Eurasia, India and North America, and marine environments. Two hypotheses were proposed to explain this distribution; in the first, vicariance would have shaped the current geographical distribution and, in the second, extinctions constrained a previously widespread distribution. Here, we aim to reconstruct pleurodiran biogeographic history and diversification patterns based on a new phylogenetic hypothesis recovered from the analysis of the largest morphological dataset yet compiled for the lineage, testing which biogeographical process prevailed during its evolutionary history. The resulting topology generally agrees with previous hypotheses of the group and shows that most diversification shifts were related to the exploration of new niches, e.g. littoral or marine radiations. In addition, as other turtles, pleurodires do not seem to have been much affected by either the Cretaceous-Palaeogene or the Eocene-Oligocene mass extinctions. The biogeographic analyses highlight the predominance of both anagenetic and cladogenetic dispersal events and support the importance of transoceanic dispersals as a more common driver of area changes than previously thought, agreeing with previous studies with other non-turtle lineages.
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Affiliation(s)
- Gabriel S. Ferreira
- Biology Department, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil
- Senckenberg Center for Human Evolution and Palaeoenvironment (HEP) at Eberhard Karls Universität, Sigwartstraße 10, 72076 Tübingen, Germany
- Fachbereich Geowissenschaften der Eberhard Karls Universität Tübingen, Hölderlinstraße 12, 72074 Tübingen, Germany
| | - Mario Bronzati
- Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Strasse 10, 80333 Munich, Germany
- Department of Earth and Enviromental Sciences, Ludwig–Maximilians–Universität, Richard-Wagner-Strasse 10, 80333 Munich, Germany
| | - Max C. Langer
- Biology Department, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Juliana Sterli
- CONICET-Museo Paleontológico Egidio Feruglio, Fontana 140, 9100 Trelew, Chubut, Argentina
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17
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Thomson RC, Spinks PQ, Shaffer HB. Molecular phylogeny and divergence of the map turtles (Emydidae: Graptemys). Mol Phylogenet Evol 2017; 121:61-70. [PMID: 29242165 DOI: 10.1016/j.ympev.2017.11.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 10/13/2017] [Accepted: 11/27/2017] [Indexed: 11/30/2022]
Abstract
The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well as timing of their divergence. We present a phylogeny for the group that includes geographically representative sampling for all described species and subspecies. We make use of an empirical prior on rates of molecular evolution to estimate divergence times with a molecular clock under a coalescent framework. Together, the phylogeny and divergence time estimates suggest that diversification has been both more recent and more rapid than has so far been suspected. We provide a well-supported evolutionary framework for Graptemys that is necessary for understanding map turtle diversity, biogeography, and for conservation of this threatened clade of turtles.
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Affiliation(s)
- Robert C Thomson
- Department of Biology, University of Hawai'i, Honolulu, HI 96822, USA.
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, and La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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18
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Multilocus phylogeny and statistical biogeography clarify the evolutionary history of major lineages of turtles. Mol Phylogenet Evol 2017; 113:59-66. [DOI: 10.1016/j.ympev.2017.05.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/13/2017] [Accepted: 05/09/2017] [Indexed: 11/19/2022]
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19
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Li H, Liu J, Xiong L, Zhang H, Zhou H, Yin H, Jing W, Li J, Shi Q, Wang Y, Liu J, Nie L. Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes. J Evol Biol 2017; 30:1011-1023. [PMID: 28294452 DOI: 10.1111/jeb.13070] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 02/22/2017] [Accepted: 03/10/2017] [Indexed: 11/30/2022]
Abstract
The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea + Pelodiscus + Dogania + Nilssonia + Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108 million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous-Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India-Asia collision and opening of the Bering Strait, which provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group.
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Affiliation(s)
- H Li
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - J Liu
- The College of Life Sciences, Beijing Normal University, Beijing, China
| | - L Xiong
- Wannan medical college, Wuhu, Anhui, China
| | - H Zhang
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - H Zhou
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - H Yin
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - W Jing
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - J Li
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - Q Shi
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - Y Wang
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - J Liu
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - L Nie
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
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20
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Joyce WG. A Review of the Fossil Record of Turtles of the CladePan-Chelydridae. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2016. [DOI: 10.3374/014.057.0103] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Joyce WG, Bourque JR. A Review of the Fossil Record of Turtles of the CladePan-Kinosternoidea. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2016. [DOI: 10.3374/014.057.0104] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Zhou CF, Rabi M. A sinemydid turtle from the Jehol Biota provides insights into the basal divergence of crown turtles. Sci Rep 2015; 5:16299. [PMID: 26553740 PMCID: PMC4639786 DOI: 10.1038/srep16299] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/09/2015] [Indexed: 11/09/2022] Open
Abstract
Morphological phylogenies stand in a major conflict with molecular hypotheses regarding the phylogeny of Cryptodira, the most diverse and widely distributed clade of extant turtles. However, molecular hypotheses are often considered a better estimate of phylogeny given that it is more consistent with the stratigraphic and geographic distribution of extinct taxa. That morphology fails to reproduce the molecular topology partly originates from problematic character polarization due to yet another contradiction around the composition of the cryptodiran stem lineage. Extinct sinemydids are one of these problematic clades: they have been either placed among stem-cryptodires, stem-chelonioid sea turtles, or even stem-turtles. A new sinemydid from the Early Cretaceous Jehol Biota (Yixian Formation, Barremian-Early Aptian) of China, Xiaochelys ningchengensis gen. et sp. nov., allows for a reassessment of the phylogenetic position of Sinemydidae. Our analysis indicates that sinemydids mostly share symplesiomorphies with sea turtles and their purported placement outside the crown-group of turtles is an artefact of previous datasets. The best current phylogenetic estimate is therefore that sinemydids are part of the stem lineage of Cryptodira together with an array of other Jurassic to Cretaceous taxa. Our study further emphasises the importance of using molecular scaffolds in global turtle analyses.
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Affiliation(s)
- Chang-Fu Zhou
- Paleontological Institute, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Márton Rabi
- Institut für Geowissenschaften, University of Tübingen, Hölderlinstraße 12, 72074 Tübingen, Germany
- Department of Paleontology & MTA – ELTE Lendület Dinosaur Research Group, Eötvös Loránd University, Budapest, Hungary
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23
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Anquetin J, Püntener C, Billon-Bruyat JP. Portlandemys gracilis n. sp., a New Coastal Marine Turtle from the Late Jurassic of Porrentruy (Switzerland) and a Reconsideration of Plesiochelyid Cranial Anatomy. PLoS One 2015; 10:e0129193. [PMID: 26106888 PMCID: PMC4480851 DOI: 10.1371/journal.pone.0129193] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/05/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Several groups of stem cryptodires became adapted to coastal marine environments as early as the Late Jurassic, 40 million years before the Pan-Chelonioidea. The Plesiochelyidae are a major component of this first radiation of crown-group turtles into marine habitats. They are abundant in many European localities, but their systematics is still greatly confused. Only three species are represented by cranial material: Plesiochelys etalloni, Plesiochelys planiceps, and Portlandemys mcdowelli. METHODOLOGY/PRINCIPAL FINDINGS In the present study, we describe a cranium and a mandible from the Kimmeridgian of Porrentruy (Switzerland), which we refer to a new species, Portlandemys gracilis n. sp. This new taxon differs from Portlandemys mcdowelli in several aspects of the cranium and mandible, notably in being generally more gracile, but the two species share a narrow skull, a more acute angle between the labial ridges on the mandible, and a unique configuration of the anterodorsal part of the basicranium. The cranial anatomy of plesiochelyid turtles is discussed in details based primarily on these new specimens and new cranial material of Plesiochelys etalloni from Solothurn, Switzerland. CONCLUSIONS/SIGNIFICANCE Several characters (e.g., the contribution of the parietal to the foramen nervi trigemini, the configuration of the dorsum sellae and sella turcica, the presence of an infolding ridge on the posterior surface of the quadrate) appear as potential candidates to help elucidate plesiochelyid relationships. Some of these characters are included in a previously published phylogenetic dataset and help to stabilize the relationships of plesiochelyid turtles and closely related taxa. For the first time, our results suggest that plesiochelyids, 'Thalassemys' moseri, and Solnhofia parsonsi (representing the Eurysternidae) form a clade at the base of Eucryptodira.
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Affiliation(s)
- Jérémy Anquetin
- Section d'archéologie et paléontologie, Office de la culture, République et Canton du Jura, 2900 Porrentruy, Switzerland
| | - Christian Püntener
- Section d'archéologie et paléontologie, Office de la culture, République et Canton du Jura, 2900 Porrentruy, Switzerland
| | - Jean-Paul Billon-Bruyat
- Section d'archéologie et paléontologie, Office de la culture, République et Canton du Jura, 2900 Porrentruy, Switzerland
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24
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Crawford NG, Parham JF, Sellas AB, Faircloth BC, Glenn TC, Papenfuss TJ, Henderson JB, Hansen MH, Simison WB. A phylogenomic analysis of turtles. Mol Phylogenet Evol 2015; 83:250-7. [DOI: 10.1016/j.ympev.2014.10.021] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/16/2014] [Accepted: 10/28/2014] [Indexed: 11/25/2022]
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25
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Angielczyk KD, Burroughs RW, Feldman CR. Do turtles follow the rules? Latitudinal gradients in species richness, body size, and geographic range area of the world's turtles. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:270-94. [DOI: 10.1002/jez.b.22602] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 09/10/2014] [Accepted: 09/29/2014] [Indexed: 11/11/2022]
Affiliation(s)
| | - Robert W. Burroughs
- Jackson School of Geosciences; The University of Texas at Austin; Austin Texas
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26
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Spinks PQ, Thomson RC, Shaffer HB. The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle. Mol Ecol 2014; 23:2228-41. [PMID: 24673803 DOI: 10.1111/mec.12736] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 11/29/2022]
Abstract
As the field of phylogeography has matured, it has become clear that analyses of one or a few genes may reveal more about the history of those genes than the populations and species that are the targets of study. To alleviate these concerns, the discipline has moved towards larger analyses of more individuals and more genes, although little attention has been paid to the qualitative or quantitative gains that such increases in scale and scope may yield. Here, we increase the number of individuals and markers by an order of magnitude over previously published work to comprehensively assess the phylogeographical history of a well-studied declining species, the western pond turtle (Emys marmorata). We present a new analysis of 89 independent nuclear SNP markers and one mitochondrial gene sequence scored for rangewide sampling of >900 individuals, and compare these to smaller-scale, rangewide genetic and morphological analyses. Our enlarged SNP data fundamentally revise our understanding of evolutionary history for this lineage. Our results indicate that the gains from greatly increasing both the number of markers and individuals are substantial and worth the effort, particularly for species of high conservation concern such as the pond turtle, where accurate assessments of population history are a prerequisite for effective management.
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Affiliation(s)
- Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, University of California, 621 Charles E. Young Dr. South, Los Angeles, CA, 90095-1606, USA; La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, La Kretz Hall, Suite 300, 619 Charles E. Young Dr. South, Los Angeles, CA, 90095-14966, USA
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27
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Dearworth JR, Ashworth AL, Kaye JM, Bednarz DT, Blaum JF, Vacca JM, McNeish JE, Higgins KA, Michael CL, Skrobola MG, Jones MS, Ariel M. Role of the trochlear nerve in eye abduction and frontal vision of the red-eared slider turtle (Trachemys scripta elegans). J Comp Neurol 2014; 521:3464-77. [PMID: 23681972 DOI: 10.1002/cne.23361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 01/09/2023]
Abstract
Horizontal head rotation evokes significant responses from trochlear motoneurons of turtle that suggests they have a functional role in abduction of the eyes like that in frontal-eyed mammals. The finding is unexpected given that the turtle is generally considered lateral-eyed and assumed to have eye movements instead like that of lateral-eyed mammals, in which innervation of the superior oblique muscle by the trochlear nerve (nIV) produces intorsion, elevation, and adduction (not abduction). Using an isolated turtle head preparation with the brain removed, glass suction electrodes were used to stimulate nIV with trains of current pulses. Eyes were monitored via an infrared camera with the head placed in a gimble to quantify eye rotations and their directions. Stimulations of nIV evoked intorsion, elevation, and abduction. Dissection of the superior oblique muscle identified lines of action and a location of insertion on the eye, which supported kinematics evoked by nIV stimulation. Eye positions in alert behaving turtles with their head extended were compared with that when their heads were retracted in the carapace. When the head was retracted, there was a reduction in interpupillary distance and an increase in binocular overlap. Occlusion of peripheral fields by the carapace forces the turtle to a more frontal-eyed state, perhaps the reason for the action of abduction by the superior oblique muscle. These findings support why trochlear motoneurons in turtle respond in the same way as abducens motoneurons to horizontal rotations, an unusual characteristic of vestibulo-ocular physiology in comparison with other mammalian lateral-eyed species.
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Affiliation(s)
- J R Dearworth
- Department of Biology and Neuroscience Program, Lafayette College, Easton, Pennsylvania, 18042
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28
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Zhou CF, Rabi M, Joyce WG. A new specimen of Manchurochelys manchoukuoensis from the Early Cretaceous Jehol Biota of Chifeng, Inner Mongolia, China and the phylogeny of Cretaceous basal eucryptodiran turtles. BMC Evol Biol 2014; 14:77. [PMID: 24707892 PMCID: PMC4021230 DOI: 10.1186/1471-2148-14-77] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 03/24/2014] [Indexed: 11/27/2022] Open
Abstract
Background Manchurochelys manchoukuoensis is an emblematic turtle from the Cretaceous Yixian Formation of Liaoning, China, a geological rock unit that is famous for yielding perfectly preserved skeletons of fossil vertebrates, including that of feathered dinosaurs. Manchurochelys manchoukuoensis was one of the first vertebrates described from this fauna, also known as the Jehol Biota. The holotype was lost during World War II and only one additional specimen has been described since. Manchurochelys manchoukuoensis is a critical taxon for unraveling the phylogenetic relationships of Cretaceous pancryptodires from Asia, a group that is considered to be of key importance for the origin of crown-group hidden-neck turtles (Cryptodira). Results A new specimen of Manchurochelys manchoukuoensis is described here from the Jiufotang Formation of Qilinshan, Chifeng, Inner Mongolia, China. This is the third specimen described and expands the range of this taxon from the Yixian Formation of the Fuxin-Yixian Basin in Liaoning to the Jiufotang Formation of the Chifeng-Yuanbaoshan Basin. A possible temporal extension of the range is less certain. The new finding adds to our understanding of the morphology of this taxon and invites a thorough revision of the phylogeny of Macrobaenidae, Sinemydidae, and closely allied forms. Conclusions Our comprehensive phylogenetic analyses of Cretaceous Asian pancryptodires yielded two main competing hypotheses: in the first these taxa form a paraphyletic grade, whereas in the second they form a monophyletic clade. The inclusion of problematic tree changing taxa, such as Panpleurodires (stem + crown side-neck turtles) has a major influence on the phylogenetic relationships of Sinemydidae and closely allied forms. Manchurochelys manchoukuoensis nests within Sinemydidae together with Sinemys spp. and Dracochelys bicuspis in the majority of our analyses.
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Affiliation(s)
- Chang-Fu Zhou
- Paleontological Institute, Shenyang Normal University, 253 North Huanghe Street, Shenyang, Liaoning 110034, People's Republic of China.
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Le M, Duong HT, Dinh LD, Nguyen TQ, Pritchard PCH, McCormack T. A phylogeny of softshell turtles (Testudines: Trionychidae) with reference to the taxonomic status of the critically endangered, giant softshell turtle, Rafetus swinhoei. ORG DIVERS EVOL 2014. [DOI: 10.1007/s13127-014-0169-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Iverson JB, Le M, Ingram C. Molecular phylogenetics of the mud and musk turtle family Kinosternidae. Mol Phylogenet Evol 2013; 69:929-39. [DOI: 10.1016/j.ympev.2013.06.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 05/15/2013] [Accepted: 06/18/2013] [Indexed: 11/24/2022]
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Rabi M, Zhou CF, Wings O, Ge S, Joyce WG. A new xinjiangchelyid turtle from the Middle Jurassic of Xinjiang, China and the evolution of the basipterygoid process in Mesozoic turtles. BMC Evol Biol 2013; 13:203. [PMID: 24053145 PMCID: PMC3852240 DOI: 10.1186/1471-2148-13-203] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/16/2013] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Most turtles from the Middle and Late Jurassic of Asia are referred to the newly defined clade Xinjiangchelyidae, a group of mostly shell-based, generalized, small to mid-sized aquatic froms that are widely considered to represent the stem lineage of Cryptodira. Xinjiangchelyids provide us with great insights into the plesiomorphic anatomy of crown-cryptodires, the most diverse group of living turtles, and they are particularly relevant for understanding the origin and early divergence of the primary clades of extant turtles. RESULTS Exceptionally complete new xinjiangchelyid material from the ?Qigu Formation of the Turpan Basin (Xinjiang Autonomous Province, China) provides new insights into the anatomy of this group and is assigned to Xinjiangchelys wusu n. sp. A phylogenetic analysis places Xinjiangchelys wusu n. sp. in a monophyletic polytomy with other xinjiangchelyids, including Xinjiangchelys junggarensis, X. radiplicatoides, X. levensis and X. latiens. However, the analysis supports the unorthodox, though tentative placement of xinjiangchelyids and sinemydids outside of crown-group Testudines. A particularly interesting new observation is that the skull of this xinjiangchelyid retains such primitive features as a reduced interpterygoid vacuity and basipterygoid processes. CONCLUSIONS The homology of basipterygoid processes is confidently demonstrated based on a comprehensive review of the basicranial anatomy of Mesozoic turtles and a new nomenclatural system is introduced for the carotid canal system of turtles. The loss of the basipterygoid process and the bony enclosure of the carotid circulation system occurred a number of times independently during turtle evolution suggesting that the reinforcement of the basicranial region was essential for developing a rigid skull, thus paralleling the evolution of other amniote groups with massive skulls.
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Affiliation(s)
- Márton Rabi
- Institut für Geowissenschaften, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany
- Department of Paleontology & MTA–ELTE Lendület Dinosaur Research Group, Eötvös Loránd University, Budapest, Hungary
| | - Chang-Fu Zhou
- Paleontological Institute, Shenyang Normal University, 253 North Huanghe Street, Shenyang 110034, China
| | - Oliver Wings
- Niedersächsisches Landesmuseum Hannover, 5 Willy-Brandt-Allee, Hannover 530169, Germany
| | - Sun Ge
- Paleontological Institute, Shenyang Normal University, 253 North Huanghe Street, Shenyang 110034, China
| | - Walter G Joyce
- Institut für Geowissenschaften, University of Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany
- Yale Peabody Museum of Natural History, 170 Whitney Avenue, New Haven, Connecticut 06511, USA
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Soylemez O, Kondrashov FA. Estimating the rate of irreversibility in protein evolution. Genome Biol Evol 2013; 4:1213-22. [PMID: 23132897 PMCID: PMC3542581 DOI: 10.1093/gbe/evs096] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Whether or not evolutionary change is inherently irreversible remains a controversial
topic. Some examples of evolutionary irreversibility are known; however, this question has
not been comprehensively addressed at the molecular level. Here, we use data from 221
human genes with known pathogenic mutations to estimate the rate of irreversibility in
protein evolution. For these genes, we reconstruct ancestral amino acid sequences along
the mammalian phylogeny and identify ancestral amino acid states that match known
pathogenic mutations. Such cases represent inherent evolutionary irreversibility because,
at the present moment, reversals to these ancestral amino acid states are impossible for
the human lineage. We estimate that approximately 10% of all amino acid
substitutions along the mammalian phylogeny are irreversible, such that a return to the
ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes
with high rates of irreversibility, as much as 40% of all amino acid evolution was
estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral
phenotypes, the molecular nature of the high rate of irreversibility in proteins is best
explained by evolution with a high prevalence of compensatory, epistatic interactions
between amino acid sites. Under such mode of protein evolution, once an amino acid
substitution is fixed, the probability of its reversal declines as the protein sequence
accumulates changes that affect the phenotypic manifestation of the ancestral state. The
prevalence of epistasis in evolution indicates that the observed high rate of
irreversibility in protein evolution is an inherent property of protein structure and
function.
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Affiliation(s)
- Onuralp Soylemez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
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Bradley Shaffer H, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning APJ, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol 2013; 14:R28. [PMID: 23537068 PMCID: PMC4054807 DOI: 10.1186/gb-2013-14-3-r28] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/15/2013] [Accepted: 03/28/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. RESULTS Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. CONCLUSIONS Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-1496, USA
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Daniel E Warren
- Department of Biology, Saint Louis University, St Louis, MO 63103, USA
| | - Andrew M Shedlock
- College of Charleston Biology Department and Grice Marine Laboratory, Charleston, SC 29424, USA
- Medical University of South Carolina College of Graduate Studies and Center for Marine Biomedicine and Environmental Sciences, Charleston, SC 29412, USA
| | - Robert C Thomson
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - John Abramyan
- Faculty of Dentistry, Life Sciences Institute University of British Columbia, Vancouver BC, Canada
| | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101 USA
| | - Daleen Badenhorst
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Kyle K Biggar
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada K1S 5B6, Canada
| | - Glen M Borchert
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
- Department of Biological Sciences, Life Sciences Building, University of South Alabama, Mobile, AL 36688-0002, USA
| | | | - Rachel M Bowden
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
| | - Anne M Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
- Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leslie T Buck
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5, Canada
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Todd A Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Mike Czerwinski
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kim D Delehaunty
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Catrina C Fronick
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lucinda Fulton
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Tina A Graves
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Richard E Green
- Baskin School of Engineering University of California, Santa Cruz Santa Cruz, CA 95064, USA
| | - Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Ramkumar Hariharan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud P.O, Thiruvananthapuram, Kerala 695014, India
| | - Omar Hernandez
- FUDECI, Fundación para el Desarrollo de las Ciencias Físicas, Matemáticas y Naturales. Av, Universidad, Bolsa a San Francisco, Palacio de Las Academias, Caracas, Venezuela
| | - LaDeana W Hillier
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Alisha K Holloway
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Daniel Janes
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Fredric J Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Cyriac Kandoth
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Lesheng Kong
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - AP Jason de Koning
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Yang Li
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | | | - Lindsey Mork
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Ryan T Paitz
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Srihari Radhakrishnan
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Joy M Richman
- Faculty of Dentistry, Life Sciences Institute University of British Columbia, Vancouver BC, Canada
| | - John St John
- Baskin School of Engineering University of California, Santa Cruz Santa Cruz, CA 95064, USA
| | - Tonia Schwartz
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Arun Sethuraman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-1496, USA
| | - Kenneth B Storey
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada K1S 5B6, Canada
| | - Nay Thane
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Tomas Vinar
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska Dolina, Bratislava 84248, Slovakia
| | - Laura M Zimmerman
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
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Assessing DNA barcoding as a tool for species identification and data quality control. PLoS One 2013; 8:e57125. [PMID: 23431400 PMCID: PMC3576373 DOI: 10.1371/journal.pone.0057125] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 01/17/2013] [Indexed: 11/19/2022] Open
Abstract
In recent years, the number of sequences of diverse species submitted to GenBank has grown explosively and not infrequently the data contain errors. This problem is extensively recognized but not for invalid or incorrectly identified species, sample mixed-up, and contamination. DNA barcoding is a powerful tool for identifying and confirming species and one very important application involves forensics. In this study, we use DNA barcoding to detect erroneous sequences in GenBank by evaluating deep intraspecific and shallow interspecific divergences to discover possible taxonomic problems and other sources of error. We use the mitochondrial DNA gene encoding cytochrome b (Cytb) from turtles to test the utility of barcoding for pinpointing potential errors. This gene is widely used in phylogenetic studies of the speciose group. Intraspecific variation is usually less than 2.0% and in most cases it is less than 1.0%. In comparison, most species differ by more than 10.0% in our dataset. Overlapping intra- and interspecific percentages of variation mainly involve problematic identifications of species and outdated taxonomies. Further, we detect identical problems in Cytb from Insectivora and Chiroptera. Upon applying this strategy to 47,524 mammalian CoxI sequences, we resolve a suite of potentially problematic sequences. Our study reveals that erroneous sequences are not rare in GenBank and that the DNA barcoding can serve to confirm sequencing accuracy and discover problems such as misidentified species, inaccurate taxonomies, contamination, and potential errors in sequencing.
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Desantis LM, Delehanty B, Weir JT, Boonstra R. Mediating free glucocorticoid levels in the blood of vertebrates: are corticosteroid-binding proteins always necessary? Funct Ecol 2013. [DOI: 10.1111/1365-2435.12038] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lanna M. Desantis
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto; Ontario; M1C 1A4; Canada
| | - Brendan Delehanty
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto; Ontario; M1C 1A4; Canada
| | - Jason T. Weir
- Department of Biological Sciences; University of Toronto Scarborough; Toronto; Ontario; M1C 1A4; Canada
| | - Rudy Boonstra
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto; Ontario; M1C 1A4; Canada
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Mulcahy DG, Noonan BP, Moss T, Townsend TM, Reeder TW, Sites JW, Wiens JJ. Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles. Mol Phylogenet Evol 2012; 65:974-91. [PMID: 22982760 DOI: 10.1016/j.ympev.2012.08.018] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Revised: 08/21/2012] [Accepted: 08/22/2012] [Indexed: 11/16/2022]
Abstract
Recently, phylogenetics has expanded to routinely include estimation of clade ages in addition to their relationships. Various dating methods have been used, but their relative performance remains understudied. Here, we generate and assemble an extensive phylogenomic data set for squamate reptiles (lizards and snakes) and evaluate two widely used dating methods, penalized likelihood in r8s (r8s-PL) and Bayesian estimation with uncorrelated relaxed rates among lineages (BEAST). We obtained sequence data from 25 nuclear loci (∼500-1,000 bp per gene; 19,020bp total) for 64 squamate species and nine outgroup taxa, estimated the phylogeny, and estimated divergence dates using 14 fossil calibrations. We then evaluated how well each method approximated these dates using random subsets of the nuclear loci (2, 5, 10, 15, and 20; replicated 10 times each), and using ∼1 kb of the mitochondrial ND2 gene. We find that estimates from r8s-PL based on 2, 5, or 10 loci can differ considerably from those based on 25 loci (mean absolute value of differences between 2-locus and 25-locus estimates were 9.0 Myr). Estimates from BEAST are somewhat more consistent given limited sampling of loci (mean absolute value of differences between 2 and 25-locus estimates were 5.0 Myr). Most strikingly, age estimates using r8s-PL for ND2 were ∼68-82 Myr older (mean=73.1) than those using 25 nuclear loci with r8s-PL. These results show that dates from r8s-PL with a limited number of loci (and especially mitochondrial data) can differ considerably from estimates derived from a large number of nuclear loci, whereas estimates from BEAST derived from fewer nuclear loci or mitochondrial data alone can be surprisingly similar to those from many nuclear loci. However, estimates from BEAST using relatively few loci and mitochondrial data could still show substantial deviations from the full data set (>50 Myr), suggesting the benefits of sampling many nuclear loci. Finally, we found that confidence intervals on ages from BEAST were not significantly different when sampling 2 vs. 25 loci, suggesting that adding loci decreased errors but did not increase confidence in those estimates.
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Affiliation(s)
- Daniel G Mulcahy
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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39
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Geometric and Developmental Perspectives on the Evolution of the Skull and Internal Carotid Circulation in Turtles. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/978-94-007-4309-0_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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40
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Spinks PQ, Thomson RC, Zhang Y, Che J, Wu Y, Shaffer HB. Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora. Mol Phylogenet Evol 2012; 63:656-67. [PMID: 22649793 DOI: 10.1016/j.ympev.2012.02.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Turtles are currently the most endangered major clade of vertebrates on earth, and Asian box turtles (Cuora) are in catastrophic decline. Effective management of this diverse turtle clade has been hampered by human-mediated, and perhaps natural hybridization, resulting in discordance between mitochondrial and nuclear markers and confusion regarding species boundaries and phylogenetic relationships among hypothesized species of Cuora. Here, we present analyses of mitochondrial and nuclear DNA data for all 12 currently hypothesized species to resolve both species boundaries and phylogenetic relationships. Our 15-gene, 40-individual nuclear data set was frequently in conflict with our mitochondrial data set; based on its general concordance with published morphological analyses and the strength of 15 independent estimates of evolutionary history, we interpret the nuclear data as representing the most reliable estimate of species boundaries and phylogeny of Cuora. Our results strongly reiterate the necessity of using multiple nuclear markers for phylogeny and species delimitation in these animals, including any form of DNA "barcoding", and point to Cuora as an important case study where reliance on mitochondrial DNA can lead to incorrect species identification.
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Affiliation(s)
- Phillip Q Spinks
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA.
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41
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Sparkman AM, Schwartz TS, Madden JA, Boyken SE, Ford NB, Serb JM, Bronikowski AM. Rates of molecular evolution vary in vertebrates for insulin-like growth factor-1 (IGF-1), a pleiotropic locus that regulates life history traits. Gen Comp Endocrinol 2012; 178:164-73. [PMID: 22569170 DOI: 10.1016/j.ygcen.2012.04.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 03/24/2012] [Accepted: 04/23/2012] [Indexed: 11/20/2022]
Abstract
Insulin-like growth factor-1 (IGF-1) is a member of the vertebrate insulin/insulin-like growth factor/relaxin gene family necessary for growth, reproduction, and survival at both the cellular and organismal level. Its sequence, protein structure, and function have been characterized in mammals, birds, and fish; however, a notable gap in our current knowledge of the function of IGF-1 and its molecular evolution is information in ectothermic reptiles. To address this disparity, we sequenced the coding region of IGF-1 in 11 reptile species-one crocodilian, three turtles, three lizards, and four snakes. Complete sequencing of the full mRNA transcript of a snake revealed the Ea-isoform, the predominant isoform of IGF-1 also reported in other vertebrate groups. A gene tree of the IGF-1 protein-coding region that incorporated sequences from diverse vertebrate groups showed similarity to the species phylogeny, with the exception of the placement of Testudines as sister group to Aves, due to their high nucleotide sequence similarity. In contrast, long-branch lengths indicate more rapid divergence in IGF-1 among lizards and snakes. Additionally, lepidosaurs (i.e., lizards and snakes) had higher rates of non-synonymous:synonymous substitutions (dN/dS) relative to archosaurs (i.e., birds and crocodilians) and turtles. Tests for positive selection on specific codons within branches and evaluation of the changes in the amino acid properties, suggested positive selection in lepidosaurs on the C domain of IGF-1, which is involved in binding affinity to the IGF-1 receptor. Predicted structural changes suggest that major alterations in protein structure and function may have occurred in reptiles. These data propose new insights into the molecular co-evolution of IGF-1 and its receptors, and ultimately the evolution of IGF-1's role in regulating life-history traits across vertebrates.
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Affiliation(s)
- Amanda M Sparkman
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA 50011, USA
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Vilaça ST, Vargas SM, Lara-Ruiz P, Molfetti É, Reis EC, Lôbo-Hajdu G, Soares LS, Santos FR. Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast. Mol Ecol 2012; 21:4300-12. [PMID: 22780882 DOI: 10.1111/j.1365-294x.2012.05685.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surprisingly, a high frequency of interspecific sea turtle hybrids has been previously recorded in a nesting site along a short stretch of the Brazilian coast. Mitochondrial DNA data indicated that as much as 43% of the females identified as Eretmochelys imbricata are hybrids in this area (Bahia State of Brazil). It is a remarkable find, because most of the nesting sites surveyed worldwide, including some in northern Brazil, presents no hybrids, and rare Caribbean sites present no more than 2% of hybrids. Thus, a detailed understanding of the hybridization process is needed to evaluate natural or anthropogenic causes of this regional phenomenon in Brazil, which could be an important factor affecting the conservation of this population. We analysed a set of 12 nuclear markers to investigate the pattern of hybridization involving three species of sea turtles: hawksbill (E. imbricata), loggerhead (Caretta caretta) and olive ridley (Lepidochelys olivacea). Our data indicate that most of the individuals in the crossings L. olivacea × E. imbricata and L. olivacea × C. caretta are F1 hybrids, whereas C. caretta × E. imbricata crossings present F1 and backcrosses with both parental species. In addition, the C. caretta × E. imbricata hybridization seems to be gender and species biased, and we also found one individual with evidence of multispecies hybridization among C. caretta × E. imbricata × Chelonia mydas. The overall results also indicate that hybridization in this area is a recent phenomenon, spanning at least two generations or ~40 years.
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Affiliation(s)
- Sibelle T Vilaça
- Laboratório de Biodiversidade e Evolução Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, 31.270-010 Belo Horizonte, MG, Brazil
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Shen XX, Liang D, Zhang P. The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR. PLoS One 2012; 7:e39256. [PMID: 22720083 PMCID: PMC3375249 DOI: 10.1371/journal.pone.0039256] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/22/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Universal nuclear protein-coding locus (NPCL) markers that are applicable across diverse taxa and show good phylogenetic discrimination have broad applications in molecular phylogenetic studies. For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups. However, such markers with broad working range and high phylogenetic performance are still scarce. It is necessary to develop more universal NPCL markers comparable to RAG1 for osteichthyan phylogenetics. METHODOLOGY/PRINCIPAL FINDINGS We developed three long universal NPCL markers (>1.6 kb each) based on single-copy nuclear genes (KIAA1239, SACS and TTN) that possess large exons and exhibit the appropriate evolutionary rates. We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species. In comparison with RAG1, each of the three long universal markers yielded similar topologies and branch supports, all in congruence with the currently accepted osteichthyan phylogeny. To compare their phylogenetic performance visually, we also estimated the phylogenetic informativeness (PI) profile for each of the four long universal NPCL markers. The PI curves indicated that SACS performed best over the whole timescale, while RAG1, KIAA1239 and TTN exhibited similar phylogenetic performances. In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments. The amplification success rate and efficiency of the nested PCR were overwhelmingly higher than those of standard PCR. CONCLUSIONS/SIGNIFICANCE Our work clearly demonstrates the superiority of nested PCR over the conventional PCR in phylogenetic studies and develops three long universal NPCL markers (KIAA1239, SACS and TTN) with the nested PCR strategy. The three markers exhibit high phylogenetic utilities in osteichthyan phylogenetics and can be widely used as pilot genes for phylogenetic questions of osteichthyans at different taxonomic levels.
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Affiliation(s)
- Xing-Xing Shen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Dan Liang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Peng Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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Du WG, Ye H, Zhao B, Pizzatto L, Ji X, Shine R. Patterns of interspecific variation in the heart rates of embryonic reptiles. PLoS One 2011; 6:e29027. [PMID: 22174948 PMCID: PMC3236780 DOI: 10.1371/journal.pone.0029027] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/18/2011] [Indexed: 11/18/2022] Open
Abstract
New non-invasive technologies allow direct measurement of heart rates (and thus, developmental rates) of embryos. We applied these methods to a diverse array of oviparous reptiles (24 species of lizards, 18 snakes, 11 turtles, 1 crocodilian), to identify general influences on cardiac rates during embryogenesis. Heart rates increased with ambient temperature in all lineages, but (at the same temperature) were faster in lizards and turtles than in snakes and crocodilians. We analysed these data within a phylogenetic framework. Embryonic heart rates were faster in species with smaller adult sizes, smaller egg sizes, and shorter incubation periods. Phylogenetic changes in heart rates were negatively correlated with concurrent changes in adult body mass and residual incubation period among the lizards, snakes (especially within pythons) and crocodilians. The total number of embryonic heart beats between oviposition and hatching was lower in squamates than in turtles or the crocodilian. Within squamates, embryonic iguanians and gekkonids required more heartbeats to complete development than did embryos of the other squamate families that we tested. These differences plausibly reflect phylogenetic divergence in the proportion of embryogenesis completed before versus after laying.
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Affiliation(s)
- Wei-Guo Du
- Key Laboratory of Animal Ecology and Conservational Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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Dating cryptodiran nodes: origin and diversification of the turtle superfamily Testudinoidea. Mol Phylogenet Evol 2011; 62:496-507. [PMID: 22100825 DOI: 10.1016/j.ympev.2011.10.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 10/19/2011] [Accepted: 10/25/2011] [Indexed: 11/20/2022]
Abstract
The superfamily Testudinoidea is the most diverse and widely distributed clade of extant turtles. Surprisingly, despite an extensive fossil record, and increasing amount of molecular data available, the temporal origin of this group is still largely unknown. To address this issue, we used a comprehensive molecular dataset to perform phylogenetic and molecular dating analyses, as well as seven fossil constraints to calibrate the ages of the nodes in the phylogeny. The molecular dataset includes the complete mitochondrial genomes of 37 turtle species, including newly sequenced mitochondrial genomes of Phrynops hilarii, Emys orbicularis, Rhinoclemmys punctularia, and Chelonoidis nigra, and four nuclear markers. Our results revealed that the earliest divergences within crown testudinoids occurred around 95.0 Mya, in the early Late Cretaceous, earlier than previously reported, raising new questions about the historical biogeography of this group.
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Townsend TM, Mulcahy DG, Noonan BP, Sites JW, Kuczynski CA, Wiens JJ, Reeder TW. Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation. Mol Phylogenet Evol 2011; 61:363-80. [DOI: 10.1016/j.ympev.2011.07.008] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Revised: 07/06/2011] [Accepted: 07/08/2011] [Indexed: 11/29/2022]
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The complete mitochondrial genome sequences of Chelodina rugosa and Chelus fimbriata (Pleurodira: Chelidae): implications of a common absence of initiation sites (OL) in pleurodiran turtles. Mol Biol Rep 2011; 39:2097-107. [DOI: 10.1007/s11033-011-0957-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
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Reid BN, LE M, McCord WP, Iverson JB, Georges A, Bergmann T, Amato G, Desalle R, Naro-Maciel E. Comparing and combining distance-based and character-based approaches for barcoding turtles. Mol Ecol Resour 2011; 11:956-67. [PMID: 21635698 DOI: 10.1111/j.1755-0998.2011.03032.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Molecular barcoding can serve as a powerful tool in wildlife forensics and may prove to be a vital aid in conserving organisms that are threatened by illegal wildlife trade, such as turtles (Order Testudines). We produced cytochrome oxidase subunit one (COI) sequences (650 bp) for 174 turtle species and combined these with publicly available sequences for 50 species to produce a data set representative of the breadth of the order. Variability within the barcode region was assessed, and the utility of both distance-based and character-based methods for species identification was evaluated. For species in which genetic material from more than one individual was available (n = 69), intraspecific divergences were 1.3% on average, although divergences greater than the customary 2% barcode threshold occurred within 15 species. High intraspecific divergences could indicate species with a high degree of internal genetic structure or possibly even cryptic species, although introgression is also probable in some of these taxa. Divergences between species of the same genus were 6.4% on average; however, 49 species were <2% divergent from congeners. Low levels of interspecific divergence could be caused by recent evolutionary radiations coupled with the low rates of mtDNA evolution previously observed in turtles. Complementing distance-based barcoding with character-based methods for identifying diagnostic sets of nucleotides provided better resolution in several cases where distance-based methods failed to distinguish species. An online identification engine was created to provide character-based identifications. This study constitutes the first comprehensive barcoding effort for this seriously threatened order.
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Affiliation(s)
- B N Reid
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA.
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Dornburg A, Beaulieu JM, Oliver JC, Near TJ. Integrating Fossil Preservation Biases in the Selection of Calibrations for Molecular Divergence Time Estimation. Syst Biol 2011; 60:519-27. [DOI: 10.1093/sysbio/syr019] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alex Dornburg
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Jeremy M. Beaulieu
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Jeffrey C. Oliver
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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