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Žagar A, Dajčman U, Megía-Palma R, Simčič T, Barroso FM, Baškiera S, Carretero MA. Analysis of subcellular energy metabolism in five Lacertidae lizards across varied environmental conditions. Comp Biochem Physiol A Mol Integr Physiol 2024; 297:111729. [PMID: 39181180 DOI: 10.1016/j.cbpa.2024.111729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024]
Abstract
Aerobic respiration is the main energy source for most eukaryotes, and efficient mitochondrial energy transfer greatly influences organismal fitness. To survive environmental changes, cells have evolved to adjust their biochemistry. Thus, measuring energy metabolism at the subcellular level can enhance our understanding of individual performance, population dynamics, and species distribution ranges. We investigated three important metabolic traits at the subcellular level in five lacertid lizard species sampled from different elevations, from sea level up to 2000 m. We examined hemoglobin concentration, two markers of oxidative stress (catalase activity and carbonyl concentration) and maximum rate of metabolic respiration at the subcellular level (potential metabolic activity at the electron transport system). The traits were analysed in laboratory acclimated adult male lizards to investigate the adaptive metabolic responses to the variable environmental conditions at the local sampling sites. Potential metabolic activity at the cellular level was measured at four temperatures - 28 °C, 30 °C, 32 °C and 34 °C - covering the range of preferred body temperatures of the species studied. Hemoglobin content, carbonyl concentration and potential metabolic activity did not differ significantly among species. Interspecific differences were found in the catalase activity, Potential metabolic activity increased with temperature in parallel in all five species. The highest response of the metabolic rate with temperature (Q10) and Arrhenius activation energy (Ea) was recorded in the high-mountain species Iberolacerta monticola.
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Affiliation(s)
- Anamarija Žagar
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia; CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 7. 4485-661 Vairão, Vila do Conde, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
| | - Urban Dajčman
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia; Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ulica 101, Ljubljana, Slovenia
| | - Rodrigo Megía-Palma
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 7. 4485-661 Vairão, Vila do Conde, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Universidad de Alcalá (UAH), Department of Biomedicine and Biotechnology, School of Pharmacy, E-28805, Alcalá de Henares, Madrid, Spain
| | - Tatjana Simčič
- National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Frederico M Barroso
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 7. 4485-661 Vairão, Vila do Conde, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Senka Baškiera
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Miguel A Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 7. 4485-661 Vairão, Vila do Conde, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
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2
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Santos BS, Marques MP, Ceríaco LMP. Lack of country-wide systematic herpetology collections in Portugal jeopardizes future research and conservation. AN ACAD BRAS CIENC 2024; 96:e20230622. [PMID: 38451598 DOI: 10.1590/0001-3765202420230622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/27/2023] [Indexed: 03/08/2024] Open
Abstract
Natural History Collections (NHCs) represent the world's largest repositories of long-term biodiversity datasets. Specimen collection and voucher deposition has been the backbone of NHCs since their inception, but recent decades have seen a drastic decline in rates of growth via active collecting. Amphibians and reptiles are amongst the most threatened zoological groups on the planet and are historically underrepresented in most worldwide NHCs. As part of an ongoing project to review the Portuguese zoological collections in the country's NHCs, herpetological data from its three major museums and smaller collections was gathered and used to examine the coverage and representation of the different taxa extant in Portugal. These collections are not taxonomically, geographically, or temporally complete. Approximately 90% of the Portuguese herpetological taxa are represented in the country's NHCs, and around half of the taxa are represented by less than 50 specimens. Geographically, the collections cover less than 30% of the country's territory and almost all of the occurring taxa have less than 10% of their known distribution represented in the collections. A discussion on the implications for science of such incomplete collections and a review of the current status of Portuguese NHCs is presented.
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Affiliation(s)
- Bruna S Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- Universidade do Porto, Departamento de Biologia, Faculdade de Ciências, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Mariana P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- Universidade do Porto, Departamento de Biologia, Faculdade de Ciências, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA 15213, U.S.A
| | - Luis M P Ceríaco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Carnegie Museum of Natural History, 4400 Forbes Avenue, Pittsburgh, PA 15213, U.S.A
- Universidade Federal do Rio de Janeiro, Departamento de Vertebrados, Museu Nacional, Quinta da Boavista, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
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3
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Caeiro-Dias G, Brelsford A, Meneses-Ribeiro M, Crochet PA, Pinho C. Hybridization in late stages of speciation: Strong but incomplete genome-wide reproductive isolation and 'large Z-effect' in a moving hybrid zone. Mol Ecol 2023. [PMID: 37316984 DOI: 10.1111/mec.17035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023]
Abstract
In organisms reproducing sexually, speciation occurs when increasing divergence results in pre- or post-zygotic reproductive isolation between lineages. Studies focusing on reproductive isolation origin in early stages of speciation are common and many rely on genomic scans to infer introgression providing limited information on the genomic architecture of reproductive isolation long-term maintenance. This study analyses a natural hybrid zone between two species in a late stage of speciation. We used ddRADseq genotyping in the contact between Podarcis bocagei and P. carbonelli to examine admixture extent, analyse hybrid zone stability and assess genome-wide variation in selection against introgression. We confirmed strong but incomplete reproductive isolation in a bimodal hybrid zone. New findings revealed population genetic structure within P. carbonelli in the contact zone; geographical and genomic clines analysis suggested strong selection against gene flow, but a relatively small proportion of the loci can introgress, mostly within the narrow contact zone. However, geographical clines revealed that a few introgressed loci show signs of potential positive selection, particularly into P. bocagei. Geographical clines also detected a signal of hybrid zone movement towards P. bocagei distribution. Genomic cline analysis revealed heterogeneous patterns of introgression among loci within the syntopy zone, but the majority maintain a strong association with the genomic background of origin. However, incongruences between both cline approaches were found, potentially driven by confounding effects on genomic clines. Last, an important role of the Z chromosome in reproductive isolation is suggested. Importantly, overall patterns of restricted introgression seem to result from numerous strong intrinsic barriers across the genome.
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Affiliation(s)
- Guilherme Caeiro-Dias
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Biology Department, University of California Riverside, Riverside, California, USA
| | - Mariana Meneses-Ribeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pierre-André Crochet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Catarina Pinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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Pinho C, Kaliontzopoulou A, Ferreira CA, Gama J. Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Automated image classification is a thriving field of machine learning, and various successful applications dealing with biological images have recently emerged. In this work, we address the ability of these methods to identify species that are difficult to tell apart by humans due to their morphological similarity. We focus on distinguishing species of wall lizards, namely those belonging to the Podarcis hispanicus species complex, which constitutes a well-known example of cryptic morphological variation. We address two classification experiments: (1) assignment of images of the morphologically relatively distinct P. bocagei and P. lusitanicus; and (2) distinction between the overall more cryptic nine taxa that compose this complex. We used four datasets (two image perspectives and individuals of the two sexes) and three deep-learning models to address each problem. Our results suggest a high ability of the models to identify the correct species, especially when combining predictions from different perspectives and models (accuracy of 95.9% and 97.1% for females and males, respectively, in the two-class case; and of 91.2% to 93.5% for females and males, respectively, in the nine-class case). Overall, these results establish deep-learning models as an important tool for field identification and monitoring of cryptic species complexes, alleviating the burden of expert or genetic identification.
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Affiliation(s)
- Catarina Pinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto , 4485-661 Vairão , Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO , Campus de Vairão, 4485-661 Vairão , Portugal
| | - Antigoni Kaliontzopoulou
- Department of Evolutionary Biology, Ecology and Environmental Sciences, and Biodiversity Research Institute (IRBio), Universitat de Barcelona , E-08028 Barcelona, Catalonia , Spain
| | | | - João Gama
- INESC TEC , Rua Dr. Roberto Frias, 4200-465 Porto , Portugal
- FEP - University of Porto , Rua Dr. Roberto Frias, 4200-464 Porto , Portugal
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5
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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6
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Caeiro-Dias G, Rocha S, Couto A, Pereira C, Brelsford A, Crochet PA, Pinho C. Nuclear phylogenies and genomics of a contact zone establish the species rank of Podarcis lusitanicus (Squamata, Lacertidae). Mol Phylogenet Evol 2021; 164:107270. [PMID: 34352374 DOI: 10.1016/j.ympev.2021.107270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 05/19/2021] [Accepted: 07/26/2021] [Indexed: 11/27/2022]
Abstract
Unravelling when divergent lineages constitute distinct species can be challenging, particularly in complex scenarios combining cryptic diversity and phylogenetic discordances between different types of molecular markers. Combining a phylogenetic approach with the study of contact zones can help to overcome such difficulties. The Podarcis hispanicus species complex has proven to be prosperous in independent evolutionary units, sometimes associated with cryptic diversity. Previous studies have revealed that one of the species of this complex, P. guadarramae, comprises two deeply divergent yet morphologically indistinguishable evolutionary units, currently regarded as subspecies (P. g. guadarramae and P. g. lusitanicus). In this study we used molecular data to address the systematics of the two lineages of Podarcis guadarramae and the closely related P. bocagei. Firstly, we reconstructed the species tree of these three and two additional taxa based on 30 nuclear loci using the multispecies coalescent with and without gene flow. Secondly, we used SNPs obtained from RADseq data to analyze the population structure across the distribution limits P. g. lusitanicus and P. g. guadarramae, and for comparison, a contact zone between P. bocagei and P. g. lusitanicus. Nuclear phylogenetic relationships between these three taxa are clearly difficult to determine due to the influence of gene flow, but our results give little support to the monophyly of P. guadarramae, potentially due to a nearly simultaneous divergence between them. Genetic structure and geographic cline analysis revealed that the two lineages of P. guadarramae replace each other abruptly across the sampled region and that gene flow is geographically restricted, implying the existence of strong reproductive isolation. Podarcis bocagei and P. g. lusitanicus show a similar degree of genetic differentiation and reproductive isolation, with very low levels of admixture in syntopy. These results support that all three forms are equally differentiated and reproductively isolated. In consequence, we conclude that the two former subspecies of Podarcis guadarramae constitute valid, yet cryptic species, that should be referred to as P. lusitanicus and P. guadarramae.
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Affiliation(s)
- Guilherme Caeiro-Dias
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBio, Vairão, Portugal.
| | - Sara Rocha
- CINBIO, Universidade de Vigo, 36310 Vigo, España; Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
| | - Alvarina Couto
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBio, Vairão, Portugal
| | - Carolina Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBio, Vairão, Portugal
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland; Biology Department, University of California Riverside, CA, USA
| | | | - Catarina Pinho
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBio, Vairão, Portugal
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7
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Caeiro-Dias G, Brelsford A, Kaliontzopoulou A, Meneses-Ribeiro M, Crochet PA, Pinho C. Variable levels of introgression between the endangered Podarcis carbonelli and highly divergent congeneric species. Heredity (Edinb) 2021; 126:463-476. [PMID: 33199832 PMCID: PMC8027454 DOI: 10.1038/s41437-020-00386-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Recent empirical studies have demonstrated that speciation with gene flow is more common than previously thought. From a conservation perspective, the potential negative effects of hybridization raise concerns on the genetic integrity of endangered species. However, introgressive hybridization has also been growingly recognized as a source of diversity and new advantageous alleles. Carbonell's wall lizard (Podarcis carbonelli) is an endangered species whose distribution overlaps with four other congeneric species. Our goal here was to determine whether P. carbonelli is completely reproductively isolated from its congeners and to evaluate the relevance of hybridization and interspecific gene flow for developing a conservation plan. We used restriction site associated DNA (RAD) sequencing to discover SNPs in samples from four contact zones between P. carbonelli and four other species. Principal component analysis, multilocus genotype assignment and interspecific heterozygosity suggest incomplete reproductive isolation and ongoing gene flow between species. However, hybridization dynamics vary across all pairs, suggesting complex interactions between multiple intrinsic and extrinsic barriers. Despite seemingly ubiquitous interspecific gene flow, we found evidence of strong reproductive isolation across most contact zones. Instead, indirect effects of hybridization like waste of reproductive effort in small isolated populations may be more problematic. Our results highlight the need to further evaluate the consequences of introgression for P. carbonelli, both on a geographic and genomic level and included in a comprehensive and urgently needed conservation plan. Besides, those findings will add important insights on the potential effects of hybridization and introgression for endangered species.
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Affiliation(s)
- Guilherme Caeiro-Dias
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, Université Paul Valéry Montpellier 3, Montpellier, France.
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Biology Department, University of California Riverside, Riverside, CA, USA
| | - Antigoni Kaliontzopoulou
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal
| | - Mariana Meneses-Ribeiro
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal
| | - Pierre-André Crochet
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, Université Paul Valéry Montpellier 3, Montpellier, France
| | - Catarina Pinho
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBIO, Universidade do Porto, Vairão, Portugal
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8
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S'khifa A, Koziel G, Vences M, Carretero MA, Slimani T. Ecophysiology of a lacertid community in the high Moroccan mountains suggests conservation guidelines. J Therm Biol 2020; 94:102743. [PMID: 33292984 DOI: 10.1016/j.jtherbio.2020.102743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 10/23/2022]
Abstract
Lizard species may differ in their ecophysiology due to adaptation, plasticity and/or phylogeny. In restrictive environments, ecophysiological differences of species living in sympatry are expected to reveal long-term evolutionary responses to the abiotic environment while competitive interactions should be limited. These influences can be disentangled by combining field monitoring with experimental tests. Here, three lacertid lizard species, Atlantolacerta andreanskyi, Scelarcis perspicillata and Podarcis vaucheri sharing high mountain habitats in Oukaimeden (High Atlas, Morocco), were studied. In the field, spatiotemporal variation of the thermal and hydric environment used by the lizards was monitored using data-loggers. In the lab, thermal and hydric ecophysiology was estimated through assessments of preferred temperatures (Tp) and water loss (WL) rates. Species differed in microhabitat use and, hence, in their exposure to variations in temperature and humidity. However, they only differed in their WL (A. andreanskyi > S. perspicillata > P. vaucheri) while their Tp were similar. Such partial differences of species in in the fundamental niche, likely derived from their long-term independent phylogenetic trajectories, can be used to predict their responses to climate and habitat shifts in this and other parts of their respective ranges. Results also confirm previous suggestions that, together with thermal physiology, hydric physiology plays a prominent role in the organisation of lizard communities in the temperate region.
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Affiliation(s)
- Abderrahim S'khifa
- Faculty of Sciences Semlalia, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, PO Box: 2390, Marrakech 40 000, Morocco
| | - Giannina Koziel
- Zoological Institute. Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Miguel Vences
- Zoological Institute. Braunschweig University of Technology, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Miguel A Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas No. 7. 4485-661 Vairão, Vila do Conde, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Tahar Slimani
- Faculty of Sciences Semlalia, Biodiversity and Ecosystem Dynamics Laboratory, Cadi Ayyad University, PO Box: 2390, Marrakech 40 000, Morocco.
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Zhao T, Zhang W, Zhou J, Zhao C, Liu X, Liu Z, Shu G, Wang S, Li C, Xie F, Chen Y, Jiang J. Niche divergence of evolutionarily significant units with implications for repopulation programs of the world's largest amphibians. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:140269. [PMID: 32806366 DOI: 10.1016/j.scitotenv.2020.140269] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/21/2020] [Accepted: 06/14/2020] [Indexed: 06/11/2023]
Abstract
The niche divergence and potential climate change-induced loss of evolutionarily significant units (ESUs) of flagship amphibian species in China, the Chinese giant salamander clade, were investigated. We tested niche-related ecological hypotheses and identified suitable habitats that are essential for the conservation of ESUs in response to future climate change according to ecological niche models (ENMs). We predicted the localized habitat loss crisis of ESUs induced by global climate heating using the predicted climate derived from two representative concentration pathway (RCP) scenarios 2.6 and 8.5, respectively. In our study, a niche conservatism pattern was found between the two distinctive northern and southern ESUs with sufficient distributional records, but their niches were not equivalent. Furthermore, there was neither abrupt environmental change in nor remarkable biogeographic barriers between the suitable habitats of the species, as indicated by random linear, blob and ribbon range-breaking tests. Under the low-emission scenario RCP2.6, the northern ESU had a moderate loss of suitable range, while the southern ESU had range expansion in the 2070s. The climatic velocities were low in the ranges of both ESUs. However, under the high-emission scenario RCP8.5, the climatic velocities were found to become larger in the suitable ranges of both ESUs. Moreover, the northern ESU had severe habitat loss, bringing it to the edge of extinction, while the southern ESU also had intensified range loss. Considering this, climatic velocity can be an effective indicator of range loss. We argued conclusively that conservation prioritization of ESUs should effectively take into account the underlying geographic and ecological mechanisms driving the speciation process. The conservation of ESUs should consider the conservation of both evolutionary potential and ecological adaptation capacity of each lineage. The present study provided practical guidelines for repopulation programs for endangered species and the conservation of evolutionary diversity.
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Affiliation(s)
- Tian Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Wenyan Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Zhou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Chunlin Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xiaoke Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhidong Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guocheng Shu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Sishuo Wang
- Chinese University of Hong Kong, Hong Kong, China
| | - Cheng Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Feng Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Youhua Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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10
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Bassitta M, Buades JM, Pérez‐Cembranos A, Pérez‐Mellado V, Terrasa B, Brown RP, Navarro P, Lluch J, Ortega J, Castro JA, Picornell A, Ramon C. Multilocus and morphological analysis of south‐eastern Iberian Wall lizards (Squamata,
Podarcis
). ZOOL SCR 2020. [DOI: 10.1111/zsc.12450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marta Bassitta
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Joana M. Buades
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | | | | | - Barbara Terrasa
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Richard P. Brown
- School of Biological & Environmental Sciences Liverpool John Moores University Liverpool United Kingdom
| | - Pilar Navarro
- Departamento de Zoología Facultad de Ciencias Biológicas Universitat de València Valencia Spain
| | - Javier Lluch
- Departamento de Zoología Facultad de Ciencias Biológicas Universitat de València Valencia Spain
| | - Jesús Ortega
- Evolutionary Ecology Unit Department of Biology Lund University Lund Sweden
| | - Jose A. Castro
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Antònia Picornell
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Cori Ramon
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
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11
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Niche models at inter- and intraspecific levels reveal hierarchical niche differentiation in midwife toads. Sci Rep 2020; 10:10942. [PMID: 32616878 PMCID: PMC7331615 DOI: 10.1038/s41598-020-67992-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/15/2020] [Indexed: 11/09/2022] Open
Abstract
Variation and population structure play key roles in the speciation process, but adaptive intraspecific genetic variation is commonly ignored when forecasting species niches. Amphibians serve as excellent models for testing how climate and local adaptations shape species distributions due to physiological and dispersal constraints and long generational times. In this study, we analysed the climatic factors driving the evolution of the genus Alytes at inter- and intraspecific levels that may limit realized niches. We tested for both differences among the five recognized species and among intraspecific clades for three of the species (Alytes obstetricans, A. cisternasii, and A. dickhilleni). We employed ecological niche models with an ordination approach to perform niche overlap analyses and test hypotheses of niche conservatism or divergence. Our results showed strong differences in the environmental variables affecting species climatic requirements. At the interspecific level, tests of equivalence and similarity revealed that sister species were non-identical in their environmental niches, although they neither were entirely dissimilar. This pattern was also consistent at the intraspecific level, with the exception of A. cisternasii, whose clades appeared to have experienced a lower degree of niche divergence than clades of the other species. In conclusion, our results support that Alytes toads, examined at both the intra- and interspecific levels, tend to occupy similar, if not identical, climatic environments.
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12
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Carvalho SB, Torres J, Tarroso P, Velo-Antón G. Genes on the edge: A framework to detect genetic diversity imperiled by climate change. GLOBAL CHANGE BIOLOGY 2019; 25:4034-4047. [PMID: 31230387 DOI: 10.1111/gcb.14740] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 05/10/2019] [Accepted: 06/13/2019] [Indexed: 06/09/2023]
Abstract
Ongoing global warming is disrupting several ecological and evolutionary processes, spanning different levels of biological organization. Species are expected to shift their ranges as a response to climate change, with relevant implications to peripheral populations at the trailing and leading edges. Several studies have analyzed the exposure of species to climate change but few have explored exposure at the intraspecific level. We introduce a framework to forecast exposure to climate change at the intraspecific level. We build on existing methods by combining correlative species distribution models, a model of species range dynamics, and a model of phylogeographic interpolation. We demonstrate the framework by applying it to 20 Iberian amphibian and reptile species. Our aims were to: (a) identify which species and intraspecific lineages will be most exposed to future climate change; (b) test if nucleotide diversity at the edges of species ranges are significantly higher or lower than on the overall range; and (c) analyze if areas of higher species gain, loss, and turnover coincide with those predicted for lineages richness and nucleotide diversity. We found that about 80% of the studied species are predicted to contract their range. Within each species, some lineages were predicted to contract their range, while others were predicted to maintain or expand it. Therefore, estimating the impacts of climate change at the species level only can underestimate losses at the intraspecific level. Some species had significant high amount of nucleotide at the trailing or leading edge, or both, but we did not find a consistent pattern across species. Spatial patterns of species richness, gain, loss, and turnover were fairly concurrent with lineages richness and nucleotide diversity. Our results support the need for increased attention to intraspecific diversity regarding monitoring and conservation strategies under climate change.
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Affiliation(s)
- Sílvia Benoliel Carvalho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
| | - João Torres
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
| | - Pedro Tarroso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Vairão, Portugal
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13
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Increase of genetic diversity indicates ecological opportunities in recurrent-fire landscapes for wall lizards. Sci Rep 2019; 9:5383. [PMID: 30926838 PMCID: PMC6441018 DOI: 10.1038/s41598-019-41729-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 03/15/2019] [Indexed: 12/02/2022] Open
Abstract
Socioeconomic and climatic factors are modifying fire regimes with an increase of fire frequency and extension. Unfortunately, the effects of recurrent fires on biological processes that ultimately affect the genetic diversity of animal populations are mostly unknown. We examined genetic patterns of diversity in the wall lizard Podarcis guadarramae in northern Portugal, one of the European regions with the highest percentage of burnt land. This species is a small saxicolous lizard as it inhabits natural outcrops and artificial stone walls, likely in recurrent-fire landscapes. We genotyped nine microsatellites from ten populations selected according to a gradient in fire recurrence, and compared genetic diversity indexes and demographic patterns among them. At the population level, we hypothesize that a high level of mortality and population bottlenecks are expected to reduce genetic heterozygosity in sampled localities affected by recurrent fires. Alternatively, genetic signatures are expected to be absent whether fire did not cause high mortality. Regardless of levels of mortality, we expect a gain in genetic diversity whether recurrent fires facilitate lizard dispersal and migration due to the increased quality of the habitat for wall lizards. At the regional level, we examine whether a recurrent fire regime may disrupt the spatial structure of populations. Our results showed an increase in genetic diversity in recurrently burnt populations, and a decline in longer-unburnt populations. We did not detect bottleneck effects in repeatedly-burnt populations. High genetic diversity in recurrent fire populations suggests a high dispersion rate between adjacent metapopulations and perhaps immigration from outside the fire boundary. At the regional level, lizard populations show low differentiation and weak genetic structure, suggesting no effects of fire. This study confirms field-based censuses showing that recurrent-fire regimes give ecological opportunities to wall lizards that benefit from habitat openness.
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Zhong H, Shang S, Zhang H, Chen J, Wu X, Zhang H. Characterization and phylogeny of bitter taste receptor genes (Tas2r) in Squamata. Genetica 2019; 147:131-139. [PMID: 30840187 DOI: 10.1007/s10709-019-00056-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/02/2019] [Indexed: 01/22/2023]
Abstract
The perception of bitter taste is linked to the detection of toxins. Therefore, it facilitates avoiding the consumption of potential toxins in the diet. At the molecular level, bitter taste is mediated by taste 2 receptors (Tas2rs). Studies on Tas2r have made major advances in recent years. However, little is known about Tas2rs in Squamata, the second largest order of extant vertebrates. To explore the repertoire and phylogenetic relationships among Tas2r genes in Squamata, we identified and characterized Tas2rs from genome assemblies of 15 Squamata species. We observed considerable Tas2r contraction and expansion in the suborders Serpentes and Lacertilia, respectively. Phylogenetic and reconciliation analysis suggested that lineage-specific gene gains and losses could have led to the Tas2r contraction and expansion in Squamata. Different Tas2r repertoires in Serpents and Lacertilia also reflect their oral anatomical features and taste behaviors. Our findings offer novel perspectives into the study of taste and dietary protection in Squamata species.
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Affiliation(s)
- Huaming Zhong
- College of Life Science, Qufu Normal University, Qufu, Shandong, China
| | - Shuai Shang
- College of Marine Life, Ocean University of China, Qingdao, Shandong, China.,Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou, Shandong, China.,College of Biological and Environmental Engineering, Binzhou University, Binzhou, Shandong, China
| | - Huanxin Zhang
- College of Marine Life, Ocean University of China, Qingdao, Shandong, China
| | - Jun Chen
- College of Marine Life, Ocean University of China, Qingdao, Shandong, China
| | - Xiaoyang Wu
- College of Life Science, Qufu Normal University, Qufu, Shandong, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, Shandong, China.
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