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Wang JY, Zhang LH, Hong YH, Cai LN, Storey KB, Zhang JY, Zhang SS, Yu DN. How Does Mitochondrial Protein-Coding Gene Expression in Fejervarya kawamurai (Anura: Dicroglossidae) Respond to Extreme Temperatures? Animals (Basel) 2023; 13:3015. [PMID: 37835622 PMCID: PMC10571990 DOI: 10.3390/ani13193015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Unusual climates can lead to extreme temperatures. Fejervarya kawamurai, one of the most prevalent anurans in the paddy fields of tropical and subtropical regions in Asia, is sensitive to climate change. The present study focuses primarily on a single question: how do the 13 mitochondrial protein-coding genes (PCGs) respond to extreme temperature change compared with 25 °C controls? Thirty-eight genes including an extra tRNA-Met gene were identified and sequenced from the mitochondrial genome of F. kawamurai. Evolutionary relationships were assessed within the Dicroglossidae and showed that Dicroglossinae is monophyletic and F. kawamurai is a sister group to the clade of (F. multistriata + F. limnocharis). Transcript levels of mitochondrial genes in liver were also evaluated to assess responses to 24 h exposure to low (2 °C and 4 °C) or high (40 °C) temperatures. Under 2 °C, seven genes showed significant changes in liver transcript levels, among which transcript levels of ATP8, ND1, ND2, ND3, ND4, and Cytb increased, respectively, and ND5 decreased. However, exposure to 4 °C for 24 h was very different in that the expressions of ten mitochondrial protein-coding genes, except ND1, ND3, and Cytb, were significantly downregulated. Among them, the transcript level of ND5 was most significantly downregulated, decreasing by 0.28-fold. Exposure to a hot environment at 40 °C for 24 h resulted in a marked difference in transcript responses with strong upregulation of eight genes, ranging from a 1.52-fold increase in ND4L to a 2.18-fold rise in Cytb transcript levels, although COI and ND5 were reduced to 0.56 and 0.67, respectively, compared with the controls. Overall, these results suggest that at 4 °C, F. kawamurai appears to have entered a hypometabolic state of hibernation, whereas its mitochondrial oxidative phosphorylation was affected at both 2 °C and 40 °C. The majority of mitochondrial PCGs exhibited substantial changes at all three temperatures, indicating that frogs such as F. kawamurai that inhabit tropical or subtropical regions are susceptible to ambient temperature changes and can quickly employ compensating adjustments to proteins involved in the mitochondrial electron transport chain.
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Affiliation(s)
- Jing-Yan Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Li-Hua Zhang
- Taishun County Forestry Bureau, Wenzhou 325000, China
| | - Yue-Huan Hong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ling-Na Cai
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Shu-Sheng Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Wuyanling National Nature Reserve, Wenzhou 325500, China
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Tran DV, Vu TT, Fukutani K, Nishikawa K. Demographic and ecological niche dynamics of the Vietnam warty newt, Paramesotriton deloustali: Historical climate influences. PLoS One 2023; 18:e0290044. [PMID: 37594998 PMCID: PMC10437943 DOI: 10.1371/journal.pone.0290044] [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: 03/08/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023] Open
Abstract
Quaternary climatic cycles strongly affected the genetic diversification and ranges of organisms, shaping current genetic structures and distribution patterns. Urodeles provide ideal examples for exploring these dynamics over time and across space. In this study, we integrated a phylogeographic approach and ensemble species distribution modeling (eSDM) to infer the historical demography and distribution patterns of the Vietnam warty newt, Paramesotriton deloustali. Mitochondrial data revealed two groups, West and East, which diverged approximately 1.92 million years ago (Mya). Diversification was likely driven by change in the climate during early stages of the Pleistocene, with increasing monsoon and drought intensities. Biogeographic analysis indicated that the newt's current distribution formed as a result of vicariance events. In addition, the two groups occupy distinct ecological niches. Demographic reconstruction showed signs of expansion in the effective population sizes of the two major groups beginning around 0.11 and 0.15 Mya, respectively. However, eSDM showed fluctuating predicted distributions during the last interglacial, last glacial maximum, mid-Holocene, and present. Mountain systems in northern Vietnam are likely to have served as climatic refuges and to have played a crucial role in safeguarding species from the effects of climate change.
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Affiliation(s)
- Dung Van Tran
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Wildlife Department, Vietnam National University of Forestry, Ha Noi, Vietnam
| | - Thinh Tien Vu
- Wildlife Department, Vietnam National University of Forestry, Ha Noi, Vietnam
| | - Kazumi Fukutani
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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Phung TM, Pham CT, Nguyen TQ, Ninh HT, Nguyen HQ, Bernardes M, Le ST, Ziegler T, Nguyen TT. Southbound - the southernmost record of Tylototriton (Amphibia, Caudata, Salamandridae) from the Central Highlands of Vietnam represents a new species. Zookeys 2023; 1168:193-218. [PMID: 38328626 PMCID: PMC10848839 DOI: 10.3897/zookeys.1168.96091] [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: 10/07/2022] [Accepted: 05/29/2023] [Indexed: 02/09/2024] Open
Abstract
A new species of the genus Tylototriton is described from Ngoc Linh Mountain, Kon Tum Province, in the Central Highlands of Vietnam based on integrative taxonomy, namely by combining molecular and morphological evidence. Tylototritonngoclinhensissp. nov. differs from all other congeners based on morphological data, allopatric distribution, and molecular divergence. In terms of genetic divergence, Tylototritonngoclinhensissp. nov. distinctly differs from the sister species T.panhai (6.77%) and from T.ngarsuensis (12.36%) based on the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. Tylototritonngoclinhensissp. nov. is a moderate sized and robust salamander species with large cephalic edges, parotoids, and vertebral ridge orange in coloration. The new taxon differs from its congeners by a combination of the following morphological characteristics: size medium (SVL 60.8-66.5 mm, TL 57.6-61.8 mm in males, and SVL 72.5-75.6 mm, TL 62.9-67.9 mm in females); head longer than wide; parotoids very prominent and enlarged, projecting backwards; tail length shorter than snout-vent length; vertebral ridge large, high and glandular in appearance; 14 large and distinct dorsolateral glandular warts; gular fold present; tips of fore and hind limbs overlapping when adpressed along the body; tips of fingers reaching between eye and nostril when foreleg is laid forward; dorsal surface and lateral sides of the head, upper and lower lips, dorsolateral glandular warts, vertebral ridge, the peripheral area of the cloaca and the ventral edge of the tail orange in coloration; the presence of a distinct black line extending from the posterior end of the eye towards the shoulder. Tylototritonngoclinhensissp. nov. is restricted to evergreen montane forests near water bodies on Ngoc Linh Mountain. We suggest that the new species should be classified as Endangered (EN) in the IUCN Red List. This new important discovery represents the eighth Tylototriton taxon described from Vietnam, and at the same time constitutes the southernmost distributional record for the whole genus in Asia.
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Affiliation(s)
- Trung My Phung
- Dong Khoi 9A, Tam Hiep, Bien Hoa, Dong Nai Province, VietnamUnaffiliatedBien HoaVietnam
| | - Cuong The Pham
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi 10072, VietnamInstitute of Ecology and Biological Resources, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10072, VietnamGraduate University of Science and TechnologyHanoiVietnam
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi 10072, VietnamInstitute of Ecology and Biological Resources, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10072, VietnamGraduate University of Science and TechnologyHanoiVietnam
| | - Hoa Thi Ninh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi 10072, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Huy Quoc Nguyen
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi 10072, VietnamVietnam National Museum of Nature, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Marta Bernardes
- Cologne Zoo, Riehler Str. 173, D–50735 Cologne, GermanyCologne ZooCologneGermany
- Institute of Zoology, University of Cologne, Zülpicher Str. 47b, D–50674 Cologne, GermanyUniversity of CologneCologneGermany
| | - Son Thanh Le
- National Institute of Medicinal Materials, 43 Đinh Tien Hoang, Ben Nghe, Ho Chi Minh city, VietnamNational Institute of Medicinal MaterialsHo Chi Minh CityVietnam
| | - Thomas Ziegler
- Cologne Zoo, Riehler Str. 173, D–50735 Cologne, GermanyCologne ZooCologneGermany
- Institute of Zoology, University of Cologne, Zülpicher Str. 47b, D–50674 Cologne, GermanyUniversity of CologneCologneGermany
| | - Tao Thien Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi 10072, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
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Gaczorek TS, Marszałek M, Dudek K, Arntzen JW, Wielstra B, Babik W. Interspecific introgression of MHC genes in Triturus newts: Evidence from multiple contact zones. Mol Ecol 2023; 32:867-880. [PMID: 36458894 PMCID: PMC10108261 DOI: 10.1111/mec.16804] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 11/03/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
Abstract
The major histocompatibility complex (MHC) genes are central to the adaptive immune response in vertebrates. Selection generally maintains high MHC variation because the spectrum of recognized pathogens depends on MHC polymorphism. Novel alleles favoured by selection originate by interallelic recombination or de novo mutations but may also be acquired by introgression from related species. However, the extent and prevalence of MHC introgression remain an open question. In this study, we tested for MHC introgression in six hybrid zones formed by six Triturus newt species. We sequenced and genotyped the polymorphic second exons of the MHC class I and II genes and compared their interspecific similarity at various distances from the centre of the hybrid zone. We found evidence for introgression of both MHC classes in the majority of examined hybrid zones, with support for a more substantial class I introgression. Furthermore, the overall MHC allele sharing outside of hybrid zones was elevated between pairs of Triturus species with abutting ranges, regardless of the phylogenetic distance between them. No effect of past hybrid zone movement on MHC allele sharing was found. Finally, using previously published genome-wide data, we demonstrated that MHC introgression was more extensive than genome-wide introgression, supporting its adaptive potential. Our study thus provides evidence for the prevalence of MHC introgression across multiple Triturus hybrid zones, indicating that MHC introgression between divergent hybridizing species may be widespread and adaptive.
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Affiliation(s)
- Tomasz S Gaczorek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Marzena Marszałek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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5
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Fieschi-Méric L, Van Leeuwen P, Hopkins K, Bournonville M, Denoël M, Lesbarrères D. Strong restructuration of skin microbiota during captivity challenges ex-situ conservation of amphibians. Front Microbiol 2023; 14:1111018. [PMID: 36891392 PMCID: PMC9986596 DOI: 10.3389/fmicb.2023.1111018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/31/2023] [Indexed: 02/22/2023] Open
Abstract
In response to the current worldwide amphibian extinction crisis, conservation instances have encouraged the establishment of ex-situ collections for endangered species. The resulting assurance populations are managed under strict biosecure protocols, often involving artificial cycles of temperature and humidity to induce active and overwintering phases, which likely affect the bacterial symbionts living on the amphibian skin. However, the skin microbiota is an important first line of defense against pathogens that can cause amphibian declines, such as the chytrid Batrachochytrium dendrobatidis (Bd). Determining whether current husbandry practices for assurance populations might deplete amphibians from their symbionts is therefore essential to conservation success. Here, we characterize the effect of the transitions from the wild to captivity, and between aquatic and overwintering phases, on the skin microbiota of two newt species. While our results confirm differential selectivity of skin microbiota between species, they underscore that captivity and phase-shifts similarly affect their community structure. More specifically, the translocation ex-situ is associated with rapid impoverishment, decrease in alpha diversity and strong species turnover of bacterial communities. Shifts between active and overwintering phases also cause changes in the diversity and composition of the microbiota, and on the prevalence of Bd-inhibitory phylotypes. Altogether, our results suggest that current husbandry practices strongly restructure the amphibian skin microbiota. Although it remains to be determined whether these changes are reversible or have deleterious effects on their hosts, we discuss methods to limit microbial diversity loss ex-situ and emphasize the importance of integrating bacterial communities to applied amphibian conservation.
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Affiliation(s)
- Léa Fieschi-Méric
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and OCeanic science Unit of reSearch (FOCUS), Université de Liège, Liège, Belgium.,Biology Department, Laurentian University, Sudbury, ON, Canada
| | | | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London (ZSL), London, United Kingdom
| | - Marie Bournonville
- Aquarium-Muséum de l'Université de Liège, Freshwater and OCeanic science Unit of reSearch (FOCUS), Liège, Belgium
| | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and OCeanic science Unit of reSearch (FOCUS), Université de Liège, Liège, Belgium
| | - David Lesbarrères
- Biology Department, Laurentian University, Sudbury, ON, Canada.,Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, ON, Canada
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6
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Dufresnes C, Mahony S, Prasad VK, Kamei RG, Masroor R, Khan MA, Al-Johany AM, Gautam KB, Gupta SK, Borkin LJ, Melnikov DA, Rosanov JM, Skorinov DV, Borzée A, Jablonski D, Litvinchuk SN. Shedding light on taxonomic chaos: Diversity and distribution of South Asian skipper frogs (Anura, Dicroglossidae, Euphlyctis). SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2102686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
| | - Stephen Mahony
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Vishal Kumar Prasad
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, People’s Republic of China
- Wildlife Institute of India, Chandrabani, Uttarakhand, India
| | - Rachunliu G. Kamei
- Department of Life Sciences, The Natural History Museum, London, UK
- 566 Kohima-Meriema Road (AH1), Meriema, Kohima, 797001, Nagaland, India
| | - Rafaqat Masroor
- Zoological Sciences Division, Pakistan Museum of Natural History, Garden Avenue, Shakarparian, 44000, Islamabad Pakistan
| | - Muazzam Ali Khan
- Department of Botany, Bacha Khan University Charsadda, Charsadda, KP, Pakistan
| | - Awadh M. Al-Johany
- Department of Zoology, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | | | | | - Leo J. Borkin
- Laboratory of Herpetology, Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Daniel A. Melnikov
- Laboratory of Herpetology, Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Juriy M. Rosanov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Dmitriy V. Skorinov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, People’s Republic of China
| | - Daniel Jablonski
- Department of Zoology, Comenius University, in Bratislava, Mlynská dolina, Ilkovičova 6, Bratislava, 842 15, Slovakia
| | - Spartak N. Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
- Dagestan State University, Makhachkala, Russia
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Milec LJM, Vanhove MPM, Bukinga FM, De Keyzer ELR, Kapepula VL, Masilya PM, Mulimbwa N, Wagner CE, Raeymaekers JAM. Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation. BMC Ecol Evol 2022; 22:127. [PMID: 36329403 PMCID: PMC9635120 DOI: 10.1186/s12862-022-02085-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Background The hydrogeological history of Lake Tanganyika paints a complex image of several colonization and adaptive radiation events. The initial basin was formed around 9–12 million years ago (MYA) from the predecessor of the Malagarasi–Congo River and only 5–6 MYA, its sub-basins fused to produce the clear, deep waters of today. Next to the well-known radiations of cichlid fishes, the lake also harbours a modest clade of only two clupeid species, Stolothrissatanganicae and Limnothrissamiodon. They are members of Pellonulini, a tribe of clupeid fishes that mostly occur in freshwater and that colonized West and Central-Africa during a period of high sea levels during the Cenozoic. There is no consensus on the phylogenetic relationships between members of Pellonulini and the timing of the colonization of Lake Tanganyika by clupeids. Results We use short-read next generation sequencing of 10X Chromium libraries to sequence and assemble the full mitochondrial genomes of S.tanganicae and L.miodon. We then use Maximum likelihood and Bayesian inference to place them into the phylogeny of Pellonulini and other clupeiforms, taking advantage of all available full mitochondrial clupeiform genomes. We identify Potamothrissaobtusirostris as the closest living relative of the Tanganyika sardines and confirm paraphyly for Microthrissa. We estimate the divergence of the Tanganyika sardines around 3.64 MYA [95% CI: 0.99, 6.29], and from P.obtusirostris around 10.92 MYA [95% CI: 6.37–15.48]. Conclusions These estimates imply that the ancestor of the Tanganyika sardines diverged from a riverine ancestor and entered the proto-lake Tanganyika around the time of its formation from the Malagarasi–Congo River, and diverged into the two extant species at the onset of deep clearwater conditions. Our results prompt a more thorough examination of the relationships within Pellonulini, and the new mitochondrial genomes provide an important resource for the future study of this tribe, e.g. as a reference for species identification, genetic diversity, and macroevolutionary studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02085-8.
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Affiliation(s)
- Leona J. M. Milec
- grid.465487.cFaculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway ,grid.12155.320000 0001 0604 5662Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Maarten P. M. Vanhove
- grid.12155.320000 0001 0604 5662Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium ,grid.5596.f0000 0001 0668 7884Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Charles Déberiotstraat 32, 3000 Leuven, Belgium
| | - Fidel Muterezi Bukinga
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo
| | - Els L. R. De Keyzer
- grid.5596.f0000 0001 0668 7884Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Charles Déberiotstraat 32, 3000 Leuven, Belgium ,grid.5284.b0000 0001 0790 3681Evolutionary Ecology Group (EVECO), Universiteit Antwerpen, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Vercus Lumami Kapepula
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo ,grid.7942.80000 0001 2294 713XUniversité Catholique de Louvain, Place Sainte Barbe 2, 1348 Louvain-la-Neuve, Belgium
| | - Pascal Mulungula Masilya
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo ,Unité d’Enseignement et de Recherche en Hydrobiologie Appliquée (UERHA)-ISP/Bukavu, Bukavu, Sud-Kivu Democratic Republic of Congo
| | - N’Sibula Mulimbwa
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo
| | - Catherine E. Wagner
- grid.135963.b0000 0001 2109 0381University of Wyoming, 1000 E University Ave, Laramie, WY 82071 USA
| | - Joost A. M. Raeymaekers
- grid.465487.cFaculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway
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Characterization, Comparison of Two New Mitogenomes of Crocodile Newts Tylototriton (Caudata: Salamandridae), and Phylogenetic Implications. Genes (Basel) 2022; 13:genes13101878. [PMID: 36292763 PMCID: PMC9601590 DOI: 10.3390/genes13101878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) are valuable resources in molecular and evolutionary studies, such as phylogeny and population genetics. The complete mitogenomes of two crocodile newts, Tylototriton broadoridgus and Tylototriton gaowangjienensis, were sequenced, assembled, and annotated for the first time using next-generation sequencing. The complete mitogenomes of T. broadoridgus and T. gaowangjienensis were 16,265 bp and 16,259 bp in lengths, which both composed of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 1 control region. The two mitogenomes had high A + T content with positive AT-skew and negative GC-skew patterns. The ratio of non-synonymous and synonymous substitutions showed that, relatively, the ATP8 gene evolved the fastest and COI evolved the slowest among the 13 PCGs. Phylogenetic trees from BI and ML analyses resulted in identical topologies, where the Tylototriton split into two groups corresponding to two subgenera. Both T. broadoridgus and T. gaowangjienensis sequenced here belonged to the subgenus Yaotriton, and these two species shared a tentative sister group relationship. The two mitogenomes reported in this study provided valuable data for future molecular and evolutionary studies of the genus Tylotoriton and other salamanders.
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Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
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Hanifin CT, Kudo Y, Yotsu-Yamashita M. Chemical Ecology of the North American Newt Genera Taricha and Notophthalmus. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2022; 118:101-130. [PMID: 35416518 DOI: 10.1007/978-3-030-92030-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The North American newt genera Taricha and Notophthalmus (order Caudata) are well known for the combination of potent toxicity, aposematic coloration, and striking defense postures that protects these animals from predation. This suite of traits is centered around the neurotoxin tetrodotoxin, which causes paralysis and death in metazoans by disrupting the initiation and propagation of electrical signals in the nerves and muscles. Tetrodotoxin defends newts from predation across multiple life history stages and its role in generating arms-race coevolution between Taricha newts and garter snake (genus Thamnophis) predators is well studied. However, understanding the broader picture of chemical defenses in Taricha and Notophthalmus requires an expanded comprehension of the defensive chemical ecology of tetrodotoxin that includes possible coevolutionary interactions with insect egg predators, protection against parasites, as well as mimicry complexes associated with tetrodotoxin and aposematic coloration in both genera. Herein the authors review what is known about the structure, function, and pharmacology of tetrodotoxin to explore its evolution and chemical ecology in the North American newt. Focus is made specifically on the origin and possible biosynthesis of tetrodotoxin in these taxa as well as providing an expanded picture of the web of interactions that contribute to landscape level patterns of toxicity and defense in Taricha and Notophthalmus.
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Affiliation(s)
- Charles T Hanifin
- Department of Biology, Utah State University, 320 N. Aggie Blvd, Vernal, UT, 84078, USA.
| | - Yuta Kudo
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Mari Yotsu-Yamashita
- Graduate School of Agricultural Science & Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
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11
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Vasconcelos IAD, Souza JOD, de Castro JS, Santana CJCD, Magalhães ACM, Castro MDS, Pires Júnior OR. Salamanders and caecilians, neglected from the chemical point of view. TOXIN REV 2021. [DOI: 10.1080/15569543.2021.1977326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | | | | | - Carlos José Correia de Santana
- Department of Physiological Sciences, University of Brasilia, Brasilia, Brazil
- Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | | | - Mariana de Souza Castro
- Department of Physiological Sciences, University of Brasilia, Brasilia, Brazil
- Department of Cell Biology, University of Brasilia, Brasilia, Brazil
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12
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Bai Y, Gao X, Chen J, Li G, Luo J, Wang H, Yang Y, Liang S, Ouyang B. The complete mitochondrial genome of Pachytriton granulosus (Chang, 1933) (Amphibia: Caudata: Salamandridae). Mitochondrial DNA B Resour 2021; 6:2131-2133. [PMID: 34263035 PMCID: PMC8253190 DOI: 10.1080/23802359.2021.1944368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Complete mitochondrial genome (GenBank accession number MN073499) for Pachytriton granulosus (Amphibia: Caudata: Salamandridae) was obtained with Sanger sequencing and assembled manually. The mitogenome consists of a circular DNA molecule of 16,288 bp, with 68.51% AT content. It comprises 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The protein-coding genes have typical ATN (Met) start codons, except cox1 (GTG as start codon), and are terminated by typical TAN stop codons, except nad6 (AGA as start codon).
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Affiliation(s)
- Yu Bai
- College of Mathematics & Information Science, Guiyang University, Guiyang, China
| | - Xuyuan Gao
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jing Chen
- College of Mathematics & Information Science, Guiyang University, Guiyang, China
| | - Guoyong Li
- S&T Park Management Center, Guiyang University, Guiyang, China
| | - Jianlin Luo
- S&T Park Management Center, Guiyang University, Guiyang, China
| | - Hui Wang
- S&T Park Management Center, Guiyang University, Guiyang, China
| | - Yang Yang
- College of Mathematics & Information Science, Guiyang University, Guiyang, China
| | - Sheng Liang
- College of Mathematics & Information Science, Guiyang University, Guiyang, China
| | - Bocheng Ouyang
- College of Mathematics & Information Science, Guiyang University, Guiyang, China
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13
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Karyological Diversification in the Genus Lyciasalamandra (Urodela: Salamandridae). Animals (Basel) 2021; 11:ani11061709. [PMID: 34201034 PMCID: PMC8228943 DOI: 10.3390/ani11061709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The Lycian salamanders of the genus Lyciasalamandra are characterized by a debated taxonomy and phylogenetic relationships. They have been the subject of various molecular and phylogenetic analyses, but their chromosomal diversity is completely unknown. We here present a comparative cytogenetic analysis on five out of the seven described species and seven subspecies of Lyciasalamandra, providing the first karyological assessment on the genus and comparing them to closely related representatives of the genus Salamandra. We analyzed the occurrence and distribution of different conserved (chromosome number and morphology) and highly variable karyological features. We found an impressive diversity in the configuration of nucleolus organizing regions (NORs), which alternatively occur either as heteromorphic or homomorphic loci on distinct regions of different chromosome pairs. We highlight that the observed peculiar taxon-specific pattern of chromosome markers supports the taxonomic validity of the different studied evolutionary lineages and is consistent with a scenario of synchronous evolution in the Lycian salamanders. Abstract We performed the first cytogenetic analysis on five out of the seven species of the genus Lyciasalamandra, including seven subspecies, and representatives of its sister genus Salamandra. All the studied species have a similar karyotype of 2n = 24, mostly composed of biarmed elements. C-bands were observed on all chromosomes, at centromeric, telomeric and interstitial position. We found a peculiar taxon-specific NOR configuration, including either heteromorphic and homomorphic NORs on distinct regions of different chromosomes. Lyciasalamandra a.antalyana and L. helverseni showed two homomorphic NORs (pairs 8 and 2, respectively), while heteromorphic NORs were found in L. billae (pairs 6, 12), L. flavimembris (pairs 2, 12), L. l. luschani (pairs 2, 12), L. l. basoglui (pairs 6, 12), L. l. finikensis (pairs 2, 6) and S. lanzai (pairs 8, 10). Homomorphic NORs with an additional supernumerary site were shown by S. s. salamandra (pairs 2, 8) and S. s. gigliolii (pairs 2, 10). This unexpected highly variable NOR configuration is probably derived from multiple independent NOR translocations and paracentric inversions and correlated to lineage divergence in Lyciasalamandra. These results support the taxonomic validity of the studied taxa and are consistent with a hypothesized scenario of synchronous evolution in the genus.
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Vaissi S. Historic range dynamics in Kaiser's mountain newt ( Neurergus kaiseri): Insights from phylogeographic analyses and species distribution modeling. Ecol Evol 2021; 11:7622-7633. [PMID: 34188839 PMCID: PMC8216884 DOI: 10.1002/ece3.7595] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 11/20/2022] Open
Abstract
Vulnerable Kaiser's mountain newt, Neurergus kaiseri, is endemic to highland streams, springs, and pools of the southwestern Zagros mountain, Iran. The present study aimed to use an integration of phylogeographical and species distribution modeling (SDM) approaches to provide new insights into the evolutionary history of the species throughout Quaternary climate oscillations. The phylogeographical analysis was followed by analyzing two mitochondrial DNA (mt-DNA) markers including 127 control region (D-loop) and 72 NADH dehydrogenase 2 (ND2) sequences from 15 populations in the entire species range that were obtained from GenBank. Potential recent and past distribution (the Last Glacial Maximum, LGM, 21 Kya and the Mid-Holocene, 6 Kya) reconstructed by ensemble SDM using nine algorithms with CCSM4, MIROC-ESM, and MPI-ESM-P models. N. kaiseri displayed two distinct lineages in the northern and southern regions that diverged in the Early-Pleistocene. The demographics analysis showed signs of a slight increase in effective population size for both northern and southern populations in the Mid-Pleistocene. Biogeography analysis showed that both vicariance and dispersal events played an important role in the formation of recent species distribution of N. kaiseri. Based on SDM projection onto paleoclimatic data, N. kaiseri displayed a scenario of past range expansion that followed by postglacial contraction. The models showed that the distribution range of the species may have shifted to a lower altitude during LGM while with amelioration of climatic during Mid-Holocene to recent conditions caused the species to shift to the higher altitude. The findings of the current study support the hypothesis that the Zagros mountains may be acting as climatic refugia and play an important role in the protection of isolated populations during climate oscillations.
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Affiliation(s)
- Somaye Vaissi
- Department of BiologyFaculty of ScienceRazi UniversityKermanshahIran
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15
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Hoang CV, Nguyen TT, Ninh HT, Luong AM, Pham CT, Nguyen TQ, Orlov NL, Chen Y, Wang B, Ziegler T, Jiang J. Two new cryptic species of Microhyla Tschudi, 1838 (Amphibia, Anura, Microhylidae) related to the M. heymonsi group from central Vietnam. Zookeys 2021; 1036:47-74. [PMID: 34017214 PMCID: PMC8116321 DOI: 10.3897/zookeys.1036.56919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 02/26/2021] [Indexed: 12/02/2022] Open
Abstract
The Microhyla heymonsi species complex from central Vietnam was examined, and based upon morphological and molecular evidence, two new species are described. The discovery of Microhyla daklakensis sp. nov. and Microhyla ninhthuanensis sp. nov. brings the total number of known species in the genus to 46 and the species number of Microhyla in Vietnam to 13. The Truong Son Range harbors the highest diversity of the genus Microhyla with 11 recorded species so far. However, this apparent micro-endemic diversity is at risk because of habitat loss by deforestation, which highlights the necessity of further research leading to improved conservation measures.
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Affiliation(s)
- Chung Van Hoang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
- University of Chinese Academy of Sciences, Beijing 810000, ChinaUniversity of Chinese Academy of SciencesBeijingChina
- Forest Resources and Environment Center, 300 Ngoc Hoi Road, Thanh Tri, Hanoi, VietnamUniversity of CologneCologneGermany
| | - Tao Thien Nguyen
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamForest Resources and Environment CenterHanoiVietnam
| | - Hoa Thi Ninh
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamForest Resources and Environment CenterHanoiVietnam
| | - Anh Mai Luong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamVietnam National Museum of Nature, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Cuong The Pham
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamVietnam National Museum of Nature, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi, VietnamInstitute of Ecology and Biological Resources, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Hanoi, VietnamVietnam National Museum of Nature, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi, VietnamInstitute of Ecology and Biological Resources, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Nikolai L. Orlov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab 1, St. Petersburg 199034, RussiaGraduate University of Science and TechnologyHanoiVietnam
| | - Youhua Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
| | - Bin Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
| | - Thomas Ziegler
- AG Zoologischer Garten Köln, Riehler Strasse 173, D-50735 Cologne, GermanyZoological Institute, Russian Academy of SciencesSt. PetersburgRussia
- Institute of Zoology, University of Cologne, Zülpicher Strasse 47b, D-50674 Cologne, GermanyAG Zoologischer Garten KölnCologneGermany
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, ChinaChengdu Institute of Biology, Chinese Academy of SciencesChengduChina
- University of Chinese Academy of Sciences, Beijing 810000, ChinaUniversity of Chinese Academy of SciencesBeijingChina
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Velo-Antón G, Lourenço A, Galán P, Nicieza A, Tarroso P. Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander. Sci Rep 2021; 11:9259. [PMID: 33927228 PMCID: PMC8085075 DOI: 10.1038/s41598-021-88349-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023] Open
Abstract
Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.
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Affiliation(s)
- Guillermo Velo-Antón
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.6312.60000 0001 2097 6738Universidade de Vigo, Grupo de Ecoloxía Animal, Departamento de Ecoloxía e Bioloxía Animal, Torre Cacti (Lab 97), 36310 Vigo, Spain
| | - André Lourenço
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.5808.50000 0001 1503 7226Departamento de Biologia da Faculdade de Ciências, Universidade do Porto. Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro Galán
- grid.8073.c0000 0001 2176 8535Grupo de Investigación en Bioloxía Evolutiva (GIBE), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n, 15071 A Coruña, Spain
| | - Alfredo Nicieza
- grid.10863.3c0000 0001 2164 6351Departamento de Biologıa de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain ,grid.10863.3c0000 0001 2164 6351Unidad Mixta de Investigacion en Biodiversidad (UMIB), CSIC-Universidad de Oviedo-Principado de Asturias, Mieres, Spain
| | - Pedro Tarroso
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal
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17
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Kakehashi R, Kurabayashi A. Patterns of Natural Selection on Mitochondrial Protein-Coding Genes in Lungless Salamanders: Relaxed Purifying Selection and Presence of Positively Selected Codon Sites in the Family Plethodontidae. Int J Genomics 2021; 2021:6671300. [PMID: 33928143 PMCID: PMC8053045 DOI: 10.1155/2021/6671300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/12/2021] [Accepted: 03/26/2021] [Indexed: 11/18/2022] Open
Abstract
There are two distinct lungless groups in caudate amphibians (salamanders and newts) (the family Plethodontidae and the genus Onychodactylus, from the family Hynobiidae). Lunglessness is considered to have evolved in response to environmental and/or ecological adaptation with respect to oxygen requirements. We performed selection analyses on lungless salamanders to elucidate the selective patterns of mitochondrial protein-coding genes associated with lunglessness. The branch model and RELAX analyses revealed the occurrence of relaxed selection (an increase of the dN/dS ratio = ω value) in most mitochondrial protein-coding genes of plethodontid salamander branches but not in those of Onychodactylus. Additional branch model and RELAX analyses indicated that direct-developing plethodontids showed the relaxed pattern for most mitochondrial genes, although metamorphosing plethodontids had fewer relaxed genes. Furthermore, aBSREL analysis detected positively selected codons in three plethodontid branches but not in Onychodactylus. One of these three branches corresponded to the most recent common ancestor, and the others corresponded with the most recent common ancestors of direct-developing branches within Hemidactyliinae. The positive selection of mitochondrial protein-coding genes in Plethodontidae is probably associated with the evolution of direct development.
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Affiliation(s)
- Ryosuke Kakehashi
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga 526-0829, Japan
| | - Atsushi Kurabayashi
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga 526-0829, Japan
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
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18
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Hu HL, Zhong JJ, Ma L, Lin ZH, Ding GH. Two complete mitochondrial genomes of the black-spotted stout newt ( Pachytriton brevipes) and their relative phylogenetics relationship with other Salamandridae. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:106-107. [PMID: 33659645 PMCID: PMC7872577 DOI: 10.1080/23802359.2020.1847619] [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: 12/02/2022]
Abstract
The black-spotted stout newt (Pachytriton brevipes) is widely distributed in the mountains of southeastern China. In this study, we sequenced and determined the complete mitochondrial genome (mitogenomes) of two P. brevipes samples collected in Mount Wuyi. The assembled mitogenomes were 16,298 bp and 16,301 bp in length, and contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, one non-coding region, and one control region. The phylogenetic analysis indicated the two samples of black-spotted stout newt grouped together and are the sister group of P. feii.
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Affiliation(s)
- Hua-Li Hu
- College of Ecology, Laboratory of Amphibian Diversity Investigation, Lishui University, Lishui, China
| | - Jun-Jie Zhong
- College of Ecology, Laboratory of Amphibian Diversity Investigation, Lishui University, Lishui, China
| | - Li Ma
- College of Ecology, Laboratory of Amphibian Diversity Investigation, Lishui University, Lishui, China
| | - Zhi-Hua Lin
- College of Ecology, Laboratory of Amphibian Diversity Investigation, Lishui University, Lishui, China
| | - Guo-Hua Ding
- College of Ecology, Laboratory of Amphibian Diversity Investigation, Lishui University, Lishui, China
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19
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Korábek O, Kosová T, Dolejš P, Petrusek A, Neubert E, Juřičková L. Geographic isolation and human-assisted dispersal in land snails: a Mediterranean story of Helix borealis and its relatives (Gastropoda: Stylommatophora: Helicidae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The Mediterranean basin is a major centre for land-snail diversity, with many localized endemics, but there are also species widely spread by humans. Both endemics and introductions can be found in the snail genus Helix, which comprises many large-bodied species used for human consumption in the past and present. The Mediterranean clade of Helix is currently distributed throughout this region, but the phylogenetic and biogeographic relationships among its forms from different parts of the basin remain enigmatic. The reasons include insufficient sampling, taxa with unclear taxonomy and a significant impact of human-assisted transport obscuring the natural distribution of phylogenetic lineages. We provide evidence that European and Anatolian populations of H. cincta and its relatives are not native to those regions, but originate from the northern Levant. These results have implications for taxonomy of the genus, but also for the understanding of its evolutionary history. We posit that the Mediterranean clade consists of four geographically separated groups, which diversified in Northern Africa, the Apennine Peninsula and Corsica, the Aegean and Greece, and the northern Levant. This geographic pattern has been subsequently blurred by multiple instances of human-assisted dispersal. However, revealing the founding populations with certainty requires thorough sampling in currently inaccessible countries.
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Affiliation(s)
- Ondřej Korábek
- Department of Ecology, Faculty of Science, Charles University, Viničná, Praha, CZ, Czechia
| | - Tereza Kosová
- Department of Zoology, Faculty of Science, Charles University, Viničná, Praha, CZ, Czechia
| | - Petr Dolejš
- Department of Zoology, Natural History Museum, National Museum, Cirkusová, Praha 9-Horní Počernice, CZ, Czechia
| | - Adam Petrusek
- Department of Ecology, Faculty of Science, Charles University, Viničná, Praha, CZ, Czechia
| | - Eike Neubert
- Natural History Museum of the Burgergemeinde Bern, Bernastrasse, Bern, CH, Switzerland
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse, Bern, CH, Switzerland
| | - Lucie Juřičková
- Department of Zoology, Faculty of Science, Charles University, Viničná, Praha, CZ, Czechia
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20
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Borzée A, Min MS. Disentangling the Impacts of Speciation, Sympatry and the Island Effect on the Morphology of Seven Hynobius sp. Salamanders. Animals (Basel) 2021; 11:187. [PMID: 33466897 PMCID: PMC7830202 DOI: 10.3390/ani11010187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 11/16/2022] Open
Abstract
Closely related individuals from different areas can see their morphologies change based on differences between clades, but also ecological variables such as the island effect or sympatry. This is the case of salamanders, which have adapted to a broad range of ecological niches, ranging from underground dwellers in xeric landscape to tropical arboreal habitats. On the Korean Peninsula, salamanders from the Hynobius clade are widespread on the mainland and islands, with several partially sympatric clades and candidate species. Currently, seven lineages have been identified based on mtDNA, four of them matching named species and three others for which the species status remains untested. While the morphology of Korean Hynobius is known to be variable between genetically segregated clades, we hypothesise that (1) the candidate species are morphologically different, and that (2) the island effect and (3) the sympatric status have significant impacts on the morphology of individuals within the genus. Here we measured 329 Hynobius salamanders from all seven clades, in areas of sympatry and allopatry, and on islands and on the mainland (Graphical Abstract A). We determined that the island effect had a significant impact on the morphology of the genus, with mainland individuals generally displaying a broader range of morphology than islandic individuals (Graphical Abstract B). We also determined that sympatry had an impact on morphology, with the sizes of individuals from clades in sympatric areas diverging from each other (Graphical Abstract C). Finally, we demonstrated that all seven clades have significantly different morphologies, and we described the three candidate species that had already been isolated based on mtDNA and microsatellite data: Hynobius notialis sp. nov., Hynobius geojeensis sp. nov. and Hynobius perplicatus sp. nov. We conclude that looking at morphology alone would be misleading about the true diversity of Hynobius species, and species in general, because of the island and patry effects.
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Affiliation(s)
- Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Mi-Sook Min
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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21
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Rancilhac L, Irisarri I, Angelini C, Arntzen JW, Babik W, Bossuyt F, Künzel S, Lüddecke T, Pasmans F, Sanchez E, Weisrock D, Veith M, Wielstra B, Steinfartz S, Hofreiter M, Philippe H, Vences M. Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders. Mol Phylogenet Evol 2020; 155:106967. [PMID: 33031928 DOI: 10.1016/j.ympev.2020.106967] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 07/09/2020] [Accepted: 09/28/2020] [Indexed: 11/18/2022]
Abstract
Hybridization can leave genealogical signatures in an organism's genome, originating from the parental lineages and persisting over time. This potentially confounds phylogenetic inference methods that aim to represent evolution as a strictly bifurcating tree. We apply a phylotranscriptomic approach to study the evolutionary history of, and test for inter-lineage introgression in the Salamandridae, a Holarctic salamanders group of interest in studies of toxicity and aposematism, courtship behavior, and molecular evolution. Although the relationships between the 21 currently recognized salamandrid genera have been the subject of numerous molecular phylogenetic studies, some branches have remained controversial and sometimes affected by discordances between mitochondrial vs. nuclear trees. To resolve the phylogeny of this family, and understand the source of mito-nuclear discordance, we generated new transcriptomic (RNAseq) data for 20 salamandrids and used these along with published data, including 28 mitochondrial genomes, to obtain a comprehensive nuclear and mitochondrial perspective on salamandrid evolution. Our final phylotranscriptomic data set included 5455 gene alignments for 40 species representing 17 of the 21 salamandrid genera. Using concatenation and species-tree phylogenetic methods, we find (1) Salamandrina sister to the clade of the "True Salamanders" (consisting of Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), (2) Ichthyosaura sister to the Near Eastern genera Neurergus and Ommatotriton, (3) Triturus sister to Lissotriton, and (4) Cynops paraphyletic with respect to Paramesotriton and Pachytriton. Combining introgression tests and phylogenetic networks, we find evidence for introgression among taxa within the clades of "Modern Asian Newts" and "Modern European Newts". However, we could not unambiguously identify the number, position, and direction of introgressive events. Combining evidence from nuclear gene analysis with the observed mito-nuclear phylogenetic discordances, we hypothesize a scenario with hybridization and mitochondrial capture among ancestral lineages of (1) Lissotriton into Ichthyosaura and (2) Triturus into Calotriton, plus introgression of nuclear genes from Triturus into Lissotriton. Furthermore, both mitochondrial capture and nuclear introgression may have occurred among lineages assigned to Cynops. More comprehensive genomic data will, in the future, allow testing this against alternative scenarios involving hybridization with other, extinct lineages of newts.
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Affiliation(s)
- Loïs Rancilhac
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
| | - Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | | | - Jan W Arntzen
- Naturalis Biodiversity Center, 2300 RA Leiden, the Netherlands
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Franky Bossuyt
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels Belgium
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Tim Lüddecke
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchesterstr. 2, 35394 Gießen, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Eugenia Sanchez
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - David Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Michael Veith
- Biogeography Department, Trier University, 54286 Trier, Germany
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, 2300 RA Leiden, the Netherlands
| | - Sebastian Steinfartz
- Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, Talstrasse 33, 04103, Leipzig, Germany
| | - Michael Hofreiter
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, UMR CNRS 5321, Station of Theoretical and Experimental Ecology, 2 route du CNRS, 09200 Moulis, France
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
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22
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Parra Olea G, Garcia-Castillo MG, Rovito SM, Maisano JA, Hanken J, Wake DB. Descriptions of five new species of the salamander genus Chiropterotriton (Caudata: Plethodontidae) from eastern Mexico and the status of three currently recognized taxa. PeerJ 2020; 8:e8800. [PMID: 32518712 PMCID: PMC7258950 DOI: 10.7717/peerj.8800] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/25/2020] [Indexed: 11/20/2022] Open
Abstract
The genus Chiropterotriton is endemic to Mexico with a geographical distribution along the Sierra Madre Oriental, the Trans Mexican Volcanic Belt and the Sierra de Juárez. The recent use of molecular tools has shown that Mexico's amphibian diversity is highly underestimated, including a large number of cryptic, unnamed species. Chiropterotriton has 18 described species including terrestrial, arboreal and cave-dwelling species. In previous molecular studies, the presence of multiple undescribed species was evident. We present a phylogenetic hypothesis based on mitochondrial data, which includes all described species and six undescribed taxa. Based on the morphological analyses and, when available, combined with molecular data, we describe five new species of the genus; Chiropterotriton casasi sp. nov., C. ceronorum sp. nov., C. melipona sp. nov., C. perotensis sp. nov. and C. totonacus sp. nov. In addition, we redescribe two others: Chiropterotriton chiropterus and C. orculus, and provide a comparable account of one additional sympatric congener. This increases the number of species in the genus to 23, which represent a considerable component of Mexican plethodontid richness.
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Affiliation(s)
- Gabriela Parra Olea
- Zoology, Instituto de Biología, Universidad Nacional Autonoma de México, Mexico city, México
| | - Mirna G Garcia-Castillo
- Zoology, Instituto de Biología, Universidad Nacional Autonoma de México, Mexico city, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sean M Rovito
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato, Guanajuato, México
| | - Jessica A Maisano
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - David B Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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23
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Mahony S, Kamei RG, Teeling EC, Biju SD. Taxonomic review of the Asian Horned Frogs (Amphibia: Megophrys Kuhl & Van Hasselt) of Northeast India and Bangladesh previously misidentified as M. parva (Boulenger), with descriptions of three new species. J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1736679] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Stephen Mahony
- School of Biology and Environmental Science, University College Dublin, Belfield, Ireland
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Rachunliu G. Kamei
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Ireland
| | - S. D. Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
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24
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Pogoda P, Zuber M, Baumbach T, Schoch RR, Kupfer A. Cranial shape evolution of extant and fossil crocodile newts and its relation to reproduction and ecology. J Anat 2020; 237:285-300. [PMID: 32297321 PMCID: PMC7369190 DOI: 10.1111/joa.13201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/19/2020] [Accepted: 03/19/2020] [Indexed: 01/22/2023] Open
Abstract
The diversity of the vertebrate cranial shape of phylogenetically related taxa allows conclusions on ecology and life history. As pleurodeline newts (the genera Echinotriton, Pleurodeles and Tylototriton) have polymorphic reproductive modes, they are highly suitable for following cranial shape evolution in relation to reproduction and environment. We investigated interspecific differences externally and differences in the cranial shape of pleurodeline newts via two‐dimensional geometric morphometrics. Our analyses also included the closely related but extinct genus Chelotriton to better follow the evolutionary history of cranial shape. Pleurodeles was morphologically distinct in relation to other phylogenetically basal salamanders. The subgenera within Tylototriton (Tylototriton and Yaotriton) were well separated in morphospace, whereas Echinotriton resembled the subgenus Yaotriton more than Tylototriton. Oviposition site choice correlated with phylogeny and morphology. Only the mating mode, with a random distribution along the phylogenetic tree, separated crocodile newts into two morphologically distinct groups. Extinct Chelotriton likely represented several species and were morphologically and ecologically more similar to Echinotriton and Yaotriton than to Tylototriton subgenera. Our data also provide the first comprehensive morphological support for the molecular phylogeny of pleurodeline newts.
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Affiliation(s)
- Peter Pogoda
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany.,Comparative Zoology, Institute of Evolution and Ecology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Marcus Zuber
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.,Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.,Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Rainer R Schoch
- Department of Paleontology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Alexander Kupfer
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany.,Institute of Zoology, University of Hohenheim, Stuttgart, Germany
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25
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Mebs D, Yotsu-Yamashita M, Hartmann K, Elbert C, Zehner R, Toennes SW. Revisited - Failure of tetrodotoxin to protect red-spotted newts, Notophthalmus viridescens, from endoparasites. Toxicon 2020; 178:77-81. [PMID: 32250750 DOI: 10.1016/j.toxicon.2020.02.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 02/23/2020] [Accepted: 02/29/2020] [Indexed: 11/17/2022]
Abstract
Red-spotted newts, Notophthalmus viridescens, contain tetrodotoxin (TTX) and its analogue 6-epiTTX in variable concentrations. In a follow-up study, newts were sampled from a pond in Pennsylvania, USA, in 2010, 2014, and 2018. Their toxin levels were assayed by liquid-chromatography-fluorescence detection (LC-FLD), and assessment of their infection with endoparasites such as nematodes and helminths was performed by histological examination of internal organs. In the 2010 and 2014 samples, average prevalence of parasite infection was 53 and 60%, respectively, but reached 100% in the 2018 sample, where metacercaria stages of the digenean trematode genus Australapatemon/Apatemon (family: Strigeidae) were predominant causing severe tissue damage in liver and kidney. Mean values of TTX and 6-epiTTX were not significantly different in parasitized or parasite-free newts over the study period, confirming previous findings that host toxicity and parasite load are not negatively correlated. Whereas the role of TTX in defence against predators is undisputed, its efficacy to prevent parasitic infections is less obvious. Toxin-resistance of various metazoan parasites may promote their widespread occurrence in poisonous newts.
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Affiliation(s)
- Dietrich Mebs
- Institute of Legal Medicine, University of Frankfurt, Kennedyallee 104, D-60596, Frankfurt, Germany.
| | - Mari Yotsu-Yamashita
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - Katharina Hartmann
- Institute of Legal Medicine, University of Frankfurt, Kennedyallee 104, D-60596, Frankfurt, Germany
| | - Christine Elbert
- Institute of Legal Medicine, University of Frankfurt, Kennedyallee 104, D-60596, Frankfurt, Germany
| | - Richard Zehner
- Institute of Legal Medicine, University of Frankfurt, Kennedyallee 104, D-60596, Frankfurt, Germany
| | - Stefan W Toennes
- Institute of Legal Medicine, University of Frankfurt, Kennedyallee 104, D-60596, Frankfurt, Germany
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26
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Li H, Cui L, Li D, Fan X, Yang M, Yang D, Ni Q, Li Y, Yao Y, Xu H, Zeng B, Li Y, Sun F, Zhang M. The complete mitochondrial genome of Cynops cyanurus cyanurus (Caudata: Salamandridae) and its phylogenetics analysis. Mitochondrial DNA B Resour 2020; 5:824-825. [PMID: 33366768 PMCID: PMC7748605 DOI: 10.1080/23802359.2020.1715887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete mitochondrial of Cynops cyanurus cyanurus was determined by using Sanger sequencing and the mitogenome size of C. c. cyanurus was 16,465 bp. It contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, 1 control region (D-loop) and a non-coding region (NC). In addition, the phylogenetic tree shows that C. c. cyanurus has the closest relationship with C. c. chuxiongensis. Hoping this study can improve our understanding of the species evolutionary relationship of Cynops.
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Affiliation(s)
- Hao Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lin Cui
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Diyan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaolan Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingyao Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Sichuan, P. R. China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Sichuan, P. R. China
| | - Bo Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Feida Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, P. R. China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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27
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Matsui T, Komamoto K, Igarashi H, Kurohmaru M. Characterization of glycoconjugates and sialic acid modification in the olfactory bulb of the Chinese fire-bellied newt (Cynops orientalis). Anat Histol Embryol 2019; 49:260-269. [PMID: 31854005 DOI: 10.1111/ahe.12524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/27/2019] [Accepted: 12/04/2019] [Indexed: 01/12/2023]
Abstract
Diverse glycoconjugates are expressed in the vertebrate olfactory bulb and serve as guidance cues for axons of nasal receptor neurons. Although the involvement of glycoconjugates in the segregation of the olfactory pathway has been suggested, it is poorly understood in salamanders. In this study, lectin histochemistry was used to determine glycoconjugate distribution in the olfactory bulb of the Chinese fire-bellied newt (Cynops orientalis). Succinylated wheat germ agglutinin (sWGA), Ricinus communis agglutinin-I and Lens culinaris agglutinin showed different bindings in the nerve fibre layer or glomerular layer, or both, between the main and accessory olfactory bulbs. We then investigated the lectin-binding pattern after the removal of terminal sialic acids using neuraminidase. Desialylation resulted in a change in the binding reactivities with seven lectins. Wheat germ agglutinin, sWGA, soybean agglutinin (SBA) and peanut agglutinin showed different degrees of binding between the main and accessory olfactory bulbs. In addition, SBA showed a heterogeneous labelling of glomeruli in the rostral region of the main olfactory bulb. Our results suggest that terminal sialic acids mask the heterogeneity of glycoconjugates in the olfactory bulb of C. orientalis.
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Affiliation(s)
- Toshiyasu Matsui
- Laboratory of Veterinary Anatomy, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Kazuyuki Komamoto
- Laboratory of Veterinary Anatomy, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Hitomi Igarashi
- Laboratory of Veterinary Anatomy, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Masamichi Kurohmaru
- Laboratory of Veterinary Anatomy, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
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28
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Cui L, Han F, Li D, Fan X, Yang M, Yang D, Ni Q, Li Y, Yao Y, Xu H, Zeng B, Li Y, Sun F, Zhang D, Zhang M. The complete mitochondrial genome of Cynops cyanurus chuxiongensis (Caudata: Salamandridae). Mitochondrial DNA B Resour 2019; 5:231-232. [PMID: 33366500 PMCID: PMC7748774 DOI: 10.1080/23802359.2019.1698987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 11/23/2019] [Indexed: 11/28/2022] Open
Abstract
Cynops cyanurus chuxiongensis is distributed in Yunnan plateau. In this paper, we sequenced and determined the complete mitochondrial genome of C. c. chuxiongensis. The assembled mitogenome is 16,465 bp in length and encoding 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), and one control region (D-loop). The phylogenetic trees indicated C. c. chuxiongensis (KY418068) has the closest relationship with C. orientalis + C. orphicus, and clustered within the clade of genus Cynops.
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Affiliation(s)
- Lin Cui
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Fuyao Han
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Diyan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Xiaolan Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Mingyao Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya’an, PR China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya’an, PR China
| | - Bo Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Ying Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
| | - Feida Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
| | - Dongru Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
- Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, PR China
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29
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Lourenço A, Gonçalves J, Carvalho F, Wang IJ, Velo‐Antón G. Comparative landscape genetics reveals the evolution of viviparity reduces genetic connectivity in fire salamanders. Mol Ecol 2019; 28:4573-4591. [DOI: 10.1111/mec.15249] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/22/2019] [Accepted: 09/16/2019] [Indexed: 01/07/2023]
Affiliation(s)
- André Lourenço
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão Vairão Portugal
| | - João Gonçalves
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão Vairão Portugal
| | - Filipe Carvalho
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão Vairão Portugal
- Department of Zoology and Entomology School of Biological and Environmental Sciences University of Fort Hare Alice South Africa
| | - Ian J. Wang
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
| | - Guillermo Velo‐Antón
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão Vairão Portugal
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30
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Huang W, Luo H, Luo S, Huang A, Ni Q, Yao Y, Xu H, Zeng B, Li Y, Wei Z, Zhang M. The complete mitogenome of the splendid japalure Japalura splendida (Squamata, Agamidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2641-2642. [PMID: 33365662 PMCID: PMC7706609 DOI: 10.1080/23802359.2019.1643797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The complete mitogenome of Japalura splendida (16,673 bp in length) is determined and analyzed in this study. It contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and one non-coding regions. All the genes in J. splendida are distributed on the H-strand, except for the ND6 gene and seven tRNA genes which are encoded on the L-strand. The phylogenetic tree suggests that J. splendida and Japalura flaviceps formed a sister group and reveals the order ((((Acanthosaura lepidogaster, Acanthosaura armata), ((J. splendida, J. flaviceps), Pseudocalotes microlepis))), Calotes versicolor) with substantial support for the monophyly.
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Affiliation(s)
- Weiyi Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongdi Luo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Sangdawa Luo
- Forestry and Grassland Administration of Qushui County, Lhasa, China
| | - An Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhimin Wei
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.,College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, China
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31
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Liu J, Yu J, Zhou M, Yang J. Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species. Int J Biol Macromol 2019; 125:423-431. [DOI: 10.1016/j.ijbiomac.2018.12.068] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
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32
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Kálmán M, Lőrincz DL, Sebők OM, Ari C, Oszwald E, Somiya H, Jancsik V. Cerebrovascular β-dystroglycan immunoreactivity in vertebrates: not detected in anurans and in the teleosts Ostariophysi and Euteleostei. Integr Zool 2019; 15:16-31. [PMID: 30811839 DOI: 10.1111/1749-4877.12384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The aim of the present paper was to check for the presence of cerebrovascular dystroglycan in vertebrates, because dystroglycan, which is localized in the vascular astroglial end-feet, has a pivotal function in glio-vascular connections. In mammalian brains, the immunoreactivity of β-dystroglycan subunit delineates the vessels. The results of the present study demonstrate similar patterns in other vertebrates, except for anurans and the teleost groups Ostariophysi and Euteleostei. In this study, we investigated 1 or 2 representative species of the main groups of Chondrichthyes, teleost and non-teleost ray-finned fishes, urodeles, anurans, and reptiles. We also investigated 5 mammalian and 3 bird species. Animals were obtained from breeders or fishermen. The presence of β-dystroglycan was investigated immunohistochemically in free-floating sections. Pre-embedding electron microscopical immunohistochemistry on Heterodontus japonicus shark brains demonstrated that in Elasmobranchii, β-dystroglycan is also localized in the perivascular glial end-feet despite the different construction of their blood-brain barrier. The results indicated that the cerebrovascular β-dystroglycan immunoreactivity disappeared separately in anurans, and in teleosts, in the latter group before its division to Ostariophysi and Euteleostei. Immunohistochemistry in muscles and western blots from brain homogenates, however, detected the presence of β-dystroglycan, even in anurans and all teleosts. A possible explanation is that in the glial end-feet, β-dystroglycan is masked in these animals, or disappeared during adaptation to the freshwater habitat.
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Affiliation(s)
- Mihály Kálmán
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - David L Lőrincz
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary.,University of Leicester, Dept. of Neuroscience, Psychology and Behaviour, Leicester, United Kingdom
| | - Olivér M Sebők
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Csilla Ari
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary.,Hyperbaric Neuroscience Research Lab., Dept of Psychology, University of South Florida, Tampa, Florida, USA
| | - Erzsébet Oszwald
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Hiroaki Somiya
- Department of Environmental Biology, Chubu University, Chubu, Japan
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33
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Rancilhac L, Goudarzi F, Gehara M, Hemami MR, Elmer KR, Vences M, Steinfarz S. Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis. Mol Phylogenet Evol 2019; 133:189-197. [PMID: 30659915 DOI: 10.1016/j.ympev.2019.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/01/2019] [Accepted: 01/01/2019] [Indexed: 10/27/2022]
Abstract
We reconstruct the molecular phylogeny of Near Eastern mountain brook newts of the genus Neurergus (family Salamandridae) based on newly determined RADseq data, and compare the outcomes of concatenation-based phylogenetic reconstruction with species-tree inference. Furthermore, we test the current taxonomy of Neurergus (with four species: Neurergus strauchii, N. crocatus, N. kaiseri, and N. derjugini) against coalescent-based species-delimitation approaches of our genome-wide genetic data set. While the position of N. strauchii as sister species to all other Neurergus species was consistent in all of our analyses, the phylogenetic relationships between the three remaining species changed depending on the applied method. The concatenation approach, as well as quartet-based species-tree inference, supported a topology with N. kaiseri as the closest relative to N. derjugini, while full-coalescent species-tree inference approaches supported N. crocatus as sister species of N. derjugini. Investigating the individual signal of gene trees highlighted an extensive variation among gene histories, most likely resulting from incomplete lineage sorting. Coalescent-based species-delimitation models suggest that the current taxonomy might underestimate the species richness within Neurergus and supports seven species. Based on the current sampling, our analysis suggests that N. strauchii, N. derjugini and N. kaiseri might each be subdivided into further species. However, as amphibian species are known to be composed of deep conspecific lineages that do not always warrant species status, these results need to be cautiously interpreted in an integrative taxonomic framework. We hypothesize that the rather shallow divergences detected within N. kaiseri and N. derjugini likely reflect an ongoing speciation process and thus require further investigation. On the contrary, the much deeper genetic divergence found between the two morphologically and geographically differentiated subspecies of N. strauchii leads us to propose that N. s. barani should be considered a distinct species, Neurergus barani Öz, 1994.
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Affiliation(s)
- Loïs Rancilhac
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany.
| | - Forough Goudarzi
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany; Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Marcelo Gehara
- American Museum of Natural History, Department of Herpetology, Central Park West at 79th St, New York, NY 10024, USA
| | - Mahmoud-Reza Hemami
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany
| | - Sebastian Steinfarz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany
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Combining phylogeography and landscape genetics to infer the evolutionary history of a short-range Mediterranean relict, Salamandra salamandra longirostris. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1110-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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35
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Pogoda P, Kupfer A. Flesh and bone: An integrative approach towards sexual size dimorphism of a terrestrial salamander (genus Salamandrina). J Morphol 2018; 279:1468-1479. [PMID: 30184248 DOI: 10.1002/jmor.20883] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 07/10/2018] [Accepted: 07/15/2018] [Indexed: 11/07/2022]
Abstract
Males and females face different selection pressures due to a sexually biased investment into reproduction. This often results in different morphologies. Sexual size dimorphisms (SSD) can give us important hints on the evolution and biology of a species. Salamanders are a perfectly suited system for investigating SSD, including a diversity of reproductive modes and behaviors, and patterns of SSD combined with life history traits in a phylogenetic context help us to understand the evolution of these processes. Because spectacled salamanders (genus Salamandrina) are the phylogenetically most basal taxon of the Salamandridae, they play a key role in reconstructing the evolutionary pattern of SSD. Combining extensive external and skeletal measurements of the cranium, limbs, and the pelvic girdle using high-resolution micro Computer Tomography (μCT) yielded an integrative analysis of expressed SSD of morphology and osteology of Salamandrina perspicillata. Multivariate analysis of external characters showed that males generally had larger cloacae, heads, and limbs relative to body size, while females had larger trunks. Analysis of osteology confirmed this pattern but also revealed new dimorphic characters in the cranium and the pelvic girdle. Dimorphic characters in external morphology and osteology are likely linked to the different reproductive roles of the sexes and support sexual rather than ecological selection as the primary force acting on the phenotype of the phylogenetically basal salamandrids.
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Affiliation(s)
- Peter Pogoda
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany.,Division of Zoology, Comparative Zoology, Institute of Evolution and Ecology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Alexander Kupfer
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany.,Division of Zoology, Institute of Zoology, University of Hohenheim, Stuttgart, Germany
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36
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Maex M, Treer D, De Greve H, Proost P, Van Bocxlaer I, Bossuyt F. Exaptation as a Mechanism for Functional Reinforcement of an Animal Pheromone System. Curr Biol 2018; 28:2955-2960.e5. [DOI: 10.1016/j.cub.2018.06.074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 10/28/2022]
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37
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The complete mitochondrial genome of Myanmar warty newt Tylototriton shanorum (Salamandridae: Tylototriton). CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0813-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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The entire mitochondrial genome of Vietnam Warty Newt Paramesotriton deloustali (Salamandridae: Paramesotriton) with a new distribution record from China. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-017-0804-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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39
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Veith M, Bogaerts S, Pasmans F, Kieren S. The changing views on the evolutionary relationships of extant Salamandridae (Amphibia: Urodela). PLoS One 2018; 13:e0198237. [PMID: 30067741 PMCID: PMC6070172 DOI: 10.1371/journal.pone.0198237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/16/2018] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic relationships among members of the family Salamandridae have been repeatedly investigated over the last 90 years, with changing character and taxon sampling. We review the changing composition and the phylogenetic position of salamandrid genera and species groups and add a new phylogeny based exclusively on sequences of nuclear genes. Salamandrina often changed its position depending on the characters used. It was included several times in a clade together with the primitive newts (Echinotriton, Pleurodeles, Tylototriton) due to their seemingly ancestral morphology. The latter were often inferred as a monophyletic clade. Respective monophyly was almost consistently established in all molecular studies for true salamanders (Chioglossa, Lyciasalamandra, Mertensiella, Salamandra), modern Asian newts (Cynops, Laotriton, Pachytriton, Paramesotriton) and modern New World newts (Notophthalmus, Taricha). Reciprocal non-monophyly has been established through molecular studies for the European mountain newts (Calotriton, Euproctus) and the modern European newts (Ichthyosaura, Lissotriton, Neurergus, Ommatotriton, Triturus) since Calotriton was identified as the sister lineage of Triturus. In pre-molecular studies, their respective monophyly had almost always been assumed, mainly because a complex courtship behaviour shared by their respective members. Our nuclear tree is nearly identical to a mito-genomic tree, with all but one node being highly supported. The major difference concerns the position of Calotriton, which is no longer nested within the modern European newts. This has implications for the evolution of courtship behaviour of European newts. Within modern European newts, Ichthyosaura and Lissotriton changed their position compared to the mito-genomic tree. Previous molecular trees based on seemingly large nuclear data sets, but analysed together with mitochondrial data, did not reveal monophyly of modern European newts since taxon sampling and nuclear gene coverage was too poor to obtain conclusive results. We therefore conclude that mitochondrial and nuclear data should be analysed on their own.
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Affiliation(s)
- Michael Veith
- Department of Biogeography, Trier University, Trier, Germany
- * E-mail:
| | | | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Sarah Kieren
- Department of Biogeography, Trier University, Trier, Germany
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40
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Kieren S, Sparreboom M, Hochkirch A, Veith M. A biogeographic and ecological perspective to the evolution of reproductive behaviour in the family Salamandridae. Mol Phylogenet Evol 2018; 121:98-109. [DOI: 10.1016/j.ympev.2018.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 01/10/2023]
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41
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Wang B, Nishikawa K, Matsui M, Nguyen TQ, Xie F, Li C, Khatiwada JR, Zhang B, Gong D, Mo Y, Wei G, Chen X, Shen Y, Yang D, Xiong R, Jiang J. Phylogenetic surveys on the newt genus Tylototriton sensu lato (Salamandridae, Caudata) reveal cryptic diversity and novel diversification promoted by historical climatic shifts. PeerJ 2018; 6:e4384. [PMID: 29576937 PMCID: PMC5853667 DOI: 10.7717/peerj.4384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
Global climatic transitions and Tibetan Plateau uplifts are hypothesized to have profoundly impacted biodiversity in southeastern Asia. To further test the hypotheses related to the impacts of these incidents, we investigated the diversification patterns of the newt genus Tylototriton sensu lato, distributed across the mountain ranges of southeastern Asia. Gene-tree and species-tree analyses of two mitochondrial genes and two nuclear genes revealed five major clades in the genus, and suggested several cryptic species. Dating estimates suggested that the genus originated in the early-to-middle Miocene. Under different species delimitating scenarios, diversification analyses with birth-death likelihood tests indicated that the genus held a higher diversification rate in the late Miocene-to-Pliocene era than that in the Pleistocene. Ancestral area reconstructions indicated that the genus originated from the northern Indochina Peninsula. Accordingly, we hypothesized that the Miocene Climatic Transition triggered the diversification of the genus, and the reinforcement of East Asian monsoons associated with the stepwise uplifts of the Tibetan Plateau promoted the radiation of the genus in southeastern Asia during the Miocene-to-Pliocene period. Quaternary glacial cycles likely had limited effects on speciation events in the genus, but mainly had contributions on their intraspecific differentiations.
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Affiliation(s)
- Bin Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Truong Quang Nguyen
- Institute of Ecology and Biological Resources, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Feng Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Cheng Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Janak Raj Khatiwada
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Baowei Zhang
- College of Life Science, Anhui University, Hefei, China
| | - Dajie Gong
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Yunming Mo
- Natural History Museum of Guangxi, Nanning, China
| | - Gang Wei
- Biodiversity Conservation Key Laboratory, Guiyang College, Guiyang, China
| | - Xiaohong Chen
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Youhui Shen
- College of Life Science, Hunan Normal University, Changsha, China
| | - Daode Yang
- Institute of Wildlife Conservation, Central South University of Forestry & Technology, Changsha, China
| | - Rongchuan Xiong
- Department of Life Science, Liupanshui Normal University, Liupanshui, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
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42
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Gong Y, Shu G, Huang F, He L, Li C, Xie F. Courtship behaviour and male sexual competition of the Taliang crocodile newt, Liangshantriton taliangensis. AMPHIBIA-REPTILIA 2018. [DOI: 10.1163/15685381-17000136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The Taliang crocodile newt, Liangshantriton taliangensis, which is endemic to south-western China, is a rare salamandrid species with a distinct evolutionary history. Using combined field observations and captive experiments, we studied the courtship behaviour and male sexual interference of this species and composed a complete ethogram of its courtship behaviour. Unlike previous reports on sperm transfer, male L. taliangensis did not deposit spermatophores during ventral amplexus and females did not pick up sperm masses in this courtship phase. Sperm transfer was only performed during arm-hooking pin-wheel circling, which distinguishes L. taliangensis from Tylototriton species and supports the validity of genus Liangshantriton. Whether L. taliangensis shows bimodality in sperm transfer needs to be explored in additional populations. In the presence of sexual competitors, male L. taliangensis adjusted the duration of their behaviour. We found that males with longer snout-vent length, heavier mass, and higher tailfins may have an advantage in intrasexual competition.
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Affiliation(s)
- Yuzhou Gong
- 1Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- 2University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guocheng Shu
- 1Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- 2University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feng Huang
- 3Liziping National Nature Reserve, Yaan, 625400, China
- 4China West Normal University, Nanchong, 637000, China
| | - Liuyang He
- 3Liziping National Nature Reserve, Yaan, 625400, China
- 4China West Normal University, Nanchong, 637000, China
| | - Cheng Li
- 1Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Feng Xie
- 1Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
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43
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Ivanović A, Arntzen JW. Evolution of skull shape in the family Salamandridae (Amphibia: Caudata). J Anat 2017; 232:359-370. [PMID: 29239487 DOI: 10.1111/joa.12759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2017] [Indexed: 11/30/2022] Open
Abstract
We carried out a comparative morphometric analysis of 56 species of salamandrid salamanders, representing 19 out of 21 extant genera, with the aim of uncovering the major patterns of skull shape diversification, and revealing possible trends and directions of evolutionary change. To do this we used micro-computed tomography scanning and three-dimensional geometric morphometrics, along with a well-resolved molecular phylogeny. We found that allometry explains a relatively small amount of shape variation across taxa. Congeneric species of salamandrid salamanders are more similar to each other and cluster together producing distinct groups in morphospace. We detected a strong phylogenetic signal and little homoplasy. The most pronounced changes in the skull shape are related to the changes of the frontosquamosal arch, a unique feature of the cranial skeleton for the family Salamandridae, which is formed by processes arising from the frontal and squamosal bones that arch over the orbits. By mapping character states over the phylogeny, we found that a reduction of the frontosquamosal arch occurs independently in three lineages of the subfamily Pleurodelinae. This reduction can probably be attributed to changes in the development and ossification rates of the frontosquamosal arch. In general, our results are similar to those obtained for caecilian amphibians, with an early expansion into the available morphospace and a complex history characterizing evolution of skull shape in both groups. To evaluate the specificity of the inferred evolutionary trajectories and Caudata-wide trends in the diversity of skull morphology, information from additional groups of tailed amphibians is needed.
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Affiliation(s)
- Ana Ivanović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands
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44
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Wang X, Li J, Zhang L, Li H, Ma K, Han Y. Complete mitochondrial genome of the Southern two-lined salamanders ( Eurycea cirrigera). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:922-923. [PMID: 33474037 PMCID: PMC7800195 DOI: 10.1080/23802359.2017.1413434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete mitochondrial genome of the southern two-lined salamanders (Eurycea cirrigera) was determined in this study. The complete mitogenome sequence of E. cirrigera is 16,759bp in length and contains 37 genes (13 protein coding genes (PGCs), two ribosomal RNA, 22 transfer RNA genes and one control region). This is the first time of the mitochondrial genome sequencing for E. cirrigera.
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Affiliation(s)
- XingRan Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Junkui Li
- Department of Gynecology and Obstetrics, No.254 Hospital of PLA, TianJin, China
| | - LiNa Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - HongQing Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Kai Ma
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
| | - Ying Han
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P.R. China
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45
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Stinson CM, Deban SM. Functional trade-offs in the aquatic feeding performance of salamanders. ZOOLOGY 2017; 125:69-78. [DOI: 10.1016/j.zool.2017.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 10/19/2022]
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46
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Stinson CM, Deban SM. Functional morphology of terrestrial prey capture in salamandrid salamanders. J Exp Biol 2017; 220:3896-3907. [DOI: 10.1242/jeb.164285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/21/2017] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Salamanders use the hyobranchial apparatus and its associated musculature for tongue projection on land and for suction feeding in water. Hyobranchial apparatus composition and morphology vary across species, and different morphologies are better suited for feeding in aquatic versus terrestrial environments. We hypothesize that differences in hyobranchial morphology result in functional trade-offs in feeding performance. We predict that semi-aquatic and aquatic salamandrids with hyobranchial morphology suited for aquatic feeding will have lower performance, in terms of tongue-projection distance, velocity, acceleration and power, compared with terrestrial salamandrids when feeding in a terrestrial environment. We found that semi-aquatic and aquatic newts had lower velocity, acceleration and muscle-mass-specific power of tongue projection when compared with the terrestrial salamanders Chioglossa lusitanica and Salamandra salamandra. The fully aquatic newt, Paramesotriton labiatus, has a robust, heavily mineralized hyobranchial apparatus and was unable to project its tongue during terrestrial feeding, and instead exhibited suction-feeding movements better suited for aquatic feeding. Conversely, terrestrial species have slender, cartilaginous hyobranchial apparatus and enlarged tongue pads that coincided with greater tongue-projection distance, velocity, acceleration and power. Chioglossa lusitanica exhibited extreme tongue-projection performance, similar to that seen in elastically projecting plethodontid salamanders; muscle-mass-specific power of tongue projection exceeded 2200 W kg−1, more than 350 times that of the next highest performer, S. salamandra, which reached 6.3 W kg−1. These findings reveal that two fully terrestrial salamandrids have morphological specializations that yield greater tongue-projection performance compared with species that naturally feed in both aquatic and terrestrial environments.
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Affiliation(s)
- Charlotte M. Stinson
- Department of Biology, California State University, Bakersfield, Bakersfield, CA 93311, USA
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
| | - Stephen M. Deban
- Department of Integrative Biology, University of South Florida, Tampa, FL 33620, USA
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47
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Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches. Mol Phylogenet Evol 2017; 115:16-26. [DOI: 10.1016/j.ympev.2017.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/31/2017] [Accepted: 07/13/2017] [Indexed: 01/31/2023]
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48
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van Riemsdijk I, Arntzen JW, Bogaerts S, Franzen M, Litvinchuk SN, Olgun K, Wielstra B. The Near East as a cradle of biodiversity: A phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation. Mol Phylogenet Evol 2017; 114:73-81. [DOI: 10.1016/j.ympev.2017.05.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 04/04/2017] [Accepted: 05/31/2017] [Indexed: 01/04/2023]
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49
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Liu F, Jiang Y, Wei Z, Zhang M, Wang T, Wang J. The complete mitochondrial genome of Cynops orientalis (Salamandridae: Cynops). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0708-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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50
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Tetrodotoxin in Asian newts (Salamandridae). Toxicon 2017; 134:14-17. [DOI: 10.1016/j.toxicon.2017.05.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/11/2017] [Accepted: 05/15/2017] [Indexed: 11/20/2022]
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