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Benito JB, Porter ML, Niemiller ML. Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae. BMC Genomics 2024; 25:298. [PMID: 38509489 PMCID: PMC10956265 DOI: 10.1186/s12864-024-10111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 02/09/2024] [Indexed: 03/22/2024] Open
Abstract
Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.
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Affiliation(s)
- Joseph B Benito
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Megan L Porter
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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2
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Powers KE, Thorne ED, Platt LR, Nelson Anderson KM, Van Meter LM, Wozniak CM, Reynolds RJ, Ford WM. Activity Patterns of Allegheny Woodrats (Neotoma magister) and Two Potential Competitors in Virginia. Northeast Nat (Steuben) 2023. [DOI: 10.1656/045.030.0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
| | - Emily D. Thorne
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061
| | - Logan R. Platt
- Biology Department, Radford University, Radford, VA 24142
| | | | | | | | | | - W. Mark Ford
- US Geological Survey, Virginia Cooperative Fish and Wildlife Research Unit and Department of Fisheries and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061
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3
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Lunghi E, Valle B, Guerrieri A, Bonin A, Cianferoni F, Manenti R, Ficetola GF. Environmental DNA of insects and springtails from caves reveals complex processes of eDNA transfer in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154022. [PMID: 35202680 DOI: 10.1016/j.scitotenv.2022.154022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/01/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Subterranean environments host a substantial amount of biodiversity, however assessing the distribution of species living underground is still extremely challenging. Environmental DNA (eDNA) metabarcoding is a powerful tool to estimate biodiversity in poorly known environments and has excellent performance for soil organisms. Here, we tested 1) whether eDNA metabarcoding from cave soils/sediments allows to successfully detect springtails (Hexapoda: Collembola) and insects (Hexapoda: Insecta); 2) whether eDNA mostly represents autochthonous (cave-dwelling) organisms or it also incorporates information from species living in surface environments; 3) whether eDNA detection probability changes across taxa with different ecology. Environmental DNA metabarcoding analyses detected a large number of Molecular Operational Taxonomic Units (MOTUs) for both insects and springtails. For springtails, detection probability was high, with a substantial proportion of hypogean species, suggesting that eDNA provides good information on the distribution of these organisms in caves. Conversely, for insects most of MOTUs represented taxa living outside caves, and the majority of them represented taxa/organisms living in freshwater environments (Ephemeroptera, Plecoptera and Trichoptera). The eDNA of freshwater insects was particularly abundant in deep sectors of caves, far from the entrance. Furthermore, average detection probability of insects was significantly lower than the one of springtails. This suggests that cave soils/sediments act as "conveyer belts of biodiversity information", possibly because percolating water lead to the accumulation of eDNA of organisms living in nearby areas. Cave soils hold a complex mix of autochthonous and allochthonous eDNA. eDNA provided unprecedented information on the understudied subterranean cave organisms; analyses of detection probability and occupancy can help teasing apart local eDNA from the eDNA representing spatially-integrated biodiversity for whole landscape.
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Affiliation(s)
- Enrico Lunghi
- Division of Molecular Biology Ruđer Bošković Institute, Zagreb, Croatia; Natural Oasis, Prato, Italy.
| | - Barbara Valle
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy; Unità di Climatologia ed Ecologia, MUSE-Museo delle Scienze di Trento, Italy
| | - Alessia Guerrieri
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Aurélie Bonin
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Fabio Cianferoni
- Istituto di Ricerca sugli Ecosistemi Terrestri (IRET), Consiglio Nazionale delle Ricerche (CNR), Sesto Fiorentino (Firenze), Italy; Zoologia, La Specola, Museo di Storia Naturale, Università degli Studi di Firenze, Firenze, Italy
| | - Raoul Manenti
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy; Laboratorio di Biologia Sotterranea "Enrico Pezzoli", Parco Regionale del Monte Barro, Galbiate, Italy
| | - Gentile Francesco Ficetola
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Milano, Italy; Laboratoire d'Écologie Alpine (LECA), Université Grenoble Alpes, CNRS, Grenoble, France
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4
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Lunghi E, Bilandžija H. Longevity in Cave Animals. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.874123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An extraordinary longevity has been observed in some cave species, and this raised the hypothesis that a longer lifespan may be considered one of the characteristic traits of these animals. However, only a few cave species have been studied thus far, and a firm conclusion remains to be drawn. Here we review the available knowledge on the longevity of subterranean species, point out the limitations of previous studies, and provide suggestions for future studies to answer important questions regarding the longevity in cave animals, its adaptive value and the related promoting factors. We also argue that studying the longevity in cave animals will contribute to the field of aging, especially to understanding the evolution of this phenomenon.
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Postojna-Planina Cave System in Slovenia, a Hotspot of Subterranean Biodiversity and a Cradle of Speleobiology. DIVERSITY 2021. [DOI: 10.3390/d13060271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Postojna-Planina Cave System (PPCS) in central Slovenia is a globally exceptional site of subterranean biodiversity, comprised of many interconnected caves with cumulative passage length exceeding 34 km. Two rivers sink into the caves of the PPCS, called the Pivka and Rak, and join underground into Unica River, which emerges to the surface. The studies of fauna of PPCS began in the 19th century with the first scientific descriptions of specialized cave animals in the world, making it “the cradle of speleobiology”. Currently, the species list of PPCS contains 116 troglobiotic animal species belonging to eight phyla, confirming its status as the richest in the world. Of these, 47 species have been scientifically described from the PPCS, and more than 10 await formal taxonomic descriptions. We expect that further sampling, detailed analyses of less studied taxa, and the use of molecular methods may reveal more species. To keep the cave animals’ checklist in PPCS up-to-date, we have supplemented the printed checklist with an online interface. As the revised checklist is a necessary first step for further activities, we discuss the importance of PPCS in terms of future research and conservation.
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6
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Abiotic Community Constraints in Extreme Environments: Epikarst Copepods as a Model System. DIVERSITY 2020. [DOI: 10.3390/d12070269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The general hypothesis that the overall presence or absence of one or more species in an extreme habitat is determined by physico-chemical factors was investigated using epikarst copepod communities as a model system, an example of an extreme environment with specialized, often rare species. The relationship between the presence or absence of epikarst copepods from drips in six Slovenian caves and 12 physico-chemical factors (temperature, conductivity, pH, Ca2+, Na+, K+, Mg2+, NH4+, and Cl−, NO2−, NO3−, and SO42−) was explored. Statistical analyses included principal components analysis, logistic mixed models, stepwise logistic multivariate regression, classification trees, and random forests. Parametric statistical analyses demonstrated the overall importance of two variables—temperature and conductivity. The more flexible statistical approaches, namely categorical trees and random forests, indicate that temperature and concentrations of Ca2+ and Mg2+ were important. This may be because they are essential nutrients or, at least in the case of Ca2+, its importance in molting. The correlation of Cl− and NO3− with copepod abundance may be due to unmeasured variables that vary at the scale of individual cave, but in any case, the values have an anthropogenic component. This contrasts with factors important in individual species’ niche separation, which overlap with the community parameters only for NO3−.
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Rolla M, Consuegra S, Garcia de Leaniz C. Trophic Plasticity of the Highly Invasive Topmouth Gudgeon (Pseudorasbora parva) Inferred From Stable Isotope Analysis. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Hart PB, Niemiller ML, Burress ED, Armbruster JW, Ludt WB, Chakrabarty P. Cave-adapted evolution in the North American amblyopsid fishes inferred using phylogenomics and geometric morphometrics. Evolution 2020; 74:936-949. [PMID: 32187649 DOI: 10.1111/evo.13958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 02/23/2020] [Accepted: 02/27/2020] [Indexed: 11/30/2022]
Abstract
Cave adaptation has evolved repeatedly across the Tree of Life, famously leading to pigmentation and eye degeneration and loss, yet its macroevolutionary implications remain poorly understood. We use the North American amblyopsid fishes, a family spanning a wide degree of cave adaptation, to examine the impact of cave specialization on the modes and tempo of evolution. We reconstruct evolutionary relationships using ultraconserved element loci, estimate the ancestral histories of eye-state, and examine the impact of cave adaptation on body shape evolution. Our phylogenomic analyses provide a well-supported hypothesis for amblyopsid evolutionary relationships. The obligate blind cavefishes form a clade and the cave-facultative eyed spring cavefishes are nested within the obligate cavefishes. Using ancestral state reconstruction, we find support for at least two independent subterranean colonization events within the Amblyopsidae. Eyed and blind fishes have different body shapes, but not different rates of body shape evolution. North American amblyopsids highlight the complex nature of cave-adaptive evolution and the necessity to include multiple lines of evidence to uncover the underlying processes involved in the loss of complex traits.
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Affiliation(s)
- Pamela B Hart
- Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama, 35899
| | - Edward D Burress
- Department of Evolution and Ecology, University of California, Davis, California, 95616
| | - Jonathan W Armbruster
- Museum of Natural History and Department of Biological Sciences, Auburn University, Auburn, Alabama, 36830
| | - William B Ludt
- Department of Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, California, 9007
| | - Prosanta Chakrabarty
- Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
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9
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Francois CM, Simon L, Malard F, Lefébure T, Douady CJ, Mermillod‐Blondin F. Trophic selectivity in aquatic isopods increases with the availability of resources. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Clémentine M. Francois
- Univ LyonUniversité Claude Bernard Lyon 1CNRSENTPEUMR5023 LEHNA F-69622Villeurbanne France
| | - Laurent Simon
- Univ LyonUniversité Claude Bernard Lyon 1CNRSENTPEUMR5023 LEHNA F-69622Villeurbanne France
| | - Florian Malard
- Univ LyonUniversité Claude Bernard Lyon 1CNRSENTPEUMR5023 LEHNA F-69622Villeurbanne France
| | - Tristan Lefébure
- Univ LyonUniversité Claude Bernard Lyon 1CNRSENTPEUMR5023 LEHNA F-69622Villeurbanne France
| | - Christophe J. Douady
- Univ LyonUniversité Claude Bernard Lyon 1CNRSENTPEUMR5023 LEHNA F-69622Villeurbanne France
- Institut Universitaire de France Paris France
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10
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Ecophysiological and life-history adaptations of Gammarus balcanicus (Schäferna, 1922) in a sinking-cave stream from Western Carpathians (Romania). ZOOLOGY 2020; 139:125754. [PMID: 32088526 DOI: 10.1016/j.zool.2020.125754] [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: 06/17/2019] [Revised: 12/12/2019] [Accepted: 01/27/2020] [Indexed: 11/21/2022]
Abstract
Freshwater gammarids are known to colonise occasionally sinking-cave streams, providing contrasting morphological, life-history and ecophysiological adaptations compared to their surface conspecifics. In this study, a subterranean and a surface population of the species Gammarus balcanicus was surveyed for one year in a sinking-cave stream from the Western Carpathians (Romania). The results showed that the cave-dwelling population comprised individuals that were significantly larger compared to their surface conspecifics, had larger body-size at sexual maturity and that the females produced fewer, but larger eggs, compared to the population situated outside the cave. The trophic position and the omnivory were significantly higher for the cave-dwelling compared to surface population and the elemental imbalance for C:P molar ratios lower, but similar for C:N. However, the subterranean population did not present troglomorphic characters or longer lifespan as known for other cave-surface paired crustaceans. This, together with the rather extensive hydrological connection of the habitats, suggests active gene-flow between populations and similar response to seasonality for body-size distributions, indicating that the observed ecophysiological and life-history differences are rather the consequence of phenotypic plasticity than the result of genetic adaptation.
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11
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Nair P, Huertas M, Nowlin WH. Metabolic responses to long-term food deprivation in subterranean and surface amphipods. SUBTERRANEAN BIOLOGY 2020. [DOI: 10.3897/subtbiol.33.48483] [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] Open
Abstract
A long-standing hypothesis in subterranean biology posits that organisms living in poor resource subsurface habitats can withstand long periods of bioenergetic shortages due to an innate reduced metabolic rate when compared to their epigean counterparts. However, previous studies have proposed that caves with ample energy resources may not evolve organisms with reduced metabolic rate. The equivocal nature of previous findings suggests that there is a need to compare food deprivation responses of subterranean and surface species in order to elucidate whether there are widespread adaptations to low energy systems in subterranean taxa. The purpose of the study was to examine patterns in basal metabolism and the effects of food deprivation in closely related subterranean- and epigean- amphipods,Stygobromus peckiandSynurellasp. from central and east Texas, USA, respectively. Basal metabolic rates (measured as O2consumption) differed between species, withS. peckihaving substantially lower rates thanSynurella. Individuals of both species were food deprived for a pre-determined time interval and changes in total body protein, lipids, and carbohydrates were measured throughout food deprivation experiments.Stygobromus peckihad larger initial energy stores thanSynurellaand were more conservative in the use of energetic reserves over a prolonged period of food deprivation. Thus, it appears that althoughS. peckiare currently found in shallow phreatic and spring opening environments, they have maintained more efficient metabolic adaptations to deal with prolonged periods of food deprivation.
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12
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Huntsman BM, Venarsky MP, Abadi F, Huryn AD, Kuhajda BR, Cox CL, Benstead JP. Evolutionary history and sex are significant drivers of crayfish demography in resource-limited cave ecosystems. Evol Ecol 2019. [DOI: 10.1007/s10682-019-10029-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Borko Š, Collette M, Brad T, Zakšek V, Flot JF, Vaxevanopoulos M, Sarbu SM, Fišer C. Amphipods in a Greek cave with sulphidic and non-sulphidic water: phylogenetically clustered and ecologically divergent. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1670273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Špela Borko
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI-1000, Slovenia
| | - Martin Collette
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, Brussels, B-1050, Belgium
| | - Traian Brad
- ‘Emil Racoviţă’ Institute of Speleology, Strada Clinicilor 5, Cluj-Napoca, 400006, Romania
| | - Valerija Zakšek
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI-1000, Slovenia
| | - Jean-François Flot
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, Brussels, B-1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels – (IB)2, Brussels, Belgium
| | | | - Serban M. Sarbu
- Department of Biological Sciences, California State University, Chico, Holt Hall 205, Chico, CA, 95929-515, USA
- ‘Emil Racoviţă’ Institute of Speleology, Calea 13 Septembrie 13, Bucharest, 050711, Romania
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana, SI-1000, Slovenia
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Liew JH, Chua KWJ, Arsenault ER, Thorp JH, Suvarnaraksha A, Amirrudin A, Yeo DCJ. Quantifying terrestrial carbon in freshwater food webs using amino acid isotope analysis: Case study with an endemic cavefish. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13230] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jia H. Liew
- Department of Biological Sciences National University of Singapore Republic of Singapore
- School of Biological Science The University of Hong Kong Hong Kong SAR China
| | - Kenny W. J. Chua
- Department of Biological Sciences National University of Singapore Republic of Singapore
| | - Emily R. Arsenault
- Kansas Biological Survey and Department of Ecology & Evolutionary Biology University of Kansas Lawrence Kansas USA
| | - James H. Thorp
- Kansas Biological Survey and Department of Ecology & Evolutionary Biology University of Kansas Lawrence Kansas USA
| | - Apinun Suvarnaraksha
- Faculty of Fisheries Technology and Aquatic Resources Maejo University Chiang Mai Thailand
| | - Ahmad Amirrudin
- School of Marine and Environmental Sciences University Malaysia Terengganu Kuala Terengganu Malaysia
| | - Darren C. J. Yeo
- Department of Biological Sciences National University of Singapore Republic of Singapore
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15
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Fiera C, Habel JC, PuchaŁka R, Ulrich W. Environmental correlates of community structure in springtails (Collembola) from Romanian caves. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Cristina Fiera
- Institute of Biology Bucharest, Romanian Academy, Bucharest, Romania
| | - Jan Christian Habel
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, School of Life Science Weihenstephan, Technische Universität München, Freising, Germany
| | - RadosŁaw PuchaŁka
- Department of Ecology and Biogeography, Nicolaus Copernicus University Toruń, Lwowska, Toruń, Poland
| | - Werner Ulrich
- Department of Ecology and Biogeography, Nicolaus Copernicus University Toruń, Lwowska, Toruń, Poland
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Bradley JG, Eason PK. Predation risk and microhabitat selection by cave salamanders, Eurycea lucifuga (Rafinesque, 1822). BEHAVIOUR 2018. [DOI: 10.1163/1568539x-00003505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Habitat selection is driven by many factors, but no one location is likely to be best for all factors; thus, individuals are subject to trade-offs when selecting habitat. Caves provide a clear example of such trade-offs because these habitats are energy deprived. Cave salamanders (Eurycea lucifuga) commonly inhabit caves at least in part because this habitat is cool and wet. We tested the hypothesis that caves also provide cave salamanders with a reduction in predation risk. We used clay models to test for differences in predation risk in caves vs. forests and at low (e.g., ground) vs. elevated (e.g., cave wall) positions, and recorded locations of cave salamanders to assess vertical (i.e., wall) vs. non-vertical (e.g., ground) substrate selection in a cave. Overall, a mean of 3.2 models in caves were damaged and a mean of 8.2 were damaged in forests. Cave salamanders selected vertical substrate more often than non-vertical substrate (, ), and in caves, low-positioned models were more likely to be damaged than models on walls, although there was no effect of model height in forests. This study suggests that caves provide salamanders a refuge from increased predation pressure, a benefit that likely compensates for the costs of moving between caves and the richer foraging grounds outside them.
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Affiliation(s)
- J. Gavin Bradley
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Perri K. Eason
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
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18
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Halvorson HM, Sperfeld E, Evans‐White MA. Quantity and quality limit detritivore growth: mechanisms revealed by ecological stoichiometry and co‐limitation theory. Ecology 2017; 98:2995-3002. [PMID: 28902394 DOI: 10.1002/ecy.2026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 07/13/2017] [Accepted: 09/01/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Halvor M. Halvorson
- Department of Biological Sciences University of Southern Mississippi 118 College Drive #5018 Hattiesburg Mississippi 39406 USA
| | - Erik Sperfeld
- Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
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Venarsky MP, Benstead JP, Huryn AD, Huntsman BM, Edmonds JW, Findlay RH, Bruce Wallace J. Experimental Detritus Manipulations Unite Surface and Cave Stream Ecosystems Along a Common Energy Gradient. Ecosystems 2017. [DOI: 10.1007/s10021-017-0174-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Lefébure T, Morvan C, Malard F, François C, Konecny-Dupré L, Guéguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Sarkissian CD, Charrier NP, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ. Less effective selection leads to larger genomes. Genome Res 2017; 27:1016-1028. [PMID: 28424354 PMCID: PMC5453316 DOI: 10.1101/gr.212589.116] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/30/2017] [Indexed: 12/18/2022]
Abstract
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical data sets. Here, we tested this hypothesis using 22 de novo transcriptomes and low-coverage genomes of asellid isopods, which represent 11 independent habitat shifts from surface water to resource-poor groundwater. We show that these habitat shifts are associated with higher transcriptome-wide [Formula: see text] After ruling out the role of positive selection and pseudogenization, we show that these transcriptome-wide [Formula: see text] increases are the consequence of a reduction in selection efficacy imposed by the smaller effective population size of subterranean species. This reduction is paralleled by an important increase in genome size (25% increase on average), an increase also confirmed in subterranean decapods and mollusks. We also control for an adaptive impact of genome size on life history traits but find no correlation between body size, or growth rate, and genome size. We show instead that the independent increases in genome size measured in subterranean isopods are the direct consequence of increasing invasion rates by repeat elements, which are less efficiently purged out by purifying selection. Contrary to selection efficacy, polymorphism is not correlated to genome size. We propose that recent demographic fluctuations and the difficulty of observing polymorphism variation in polymorphism-poor species can obfuscate the link between effective population size and genome size when polymorphism data are used alone.
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Affiliation(s)
- Tristan Lefébure
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Claire Morvan
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Florian Malard
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Clémentine François
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Lara Konecny-Dupré
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Laurent Guéguen
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Michèle Weiss-Gayet
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM, Institut NeuroMyoGène, F-69622 Villeurbanne, France
| | - Andaine Seguin-Orlando
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Luca Ermini
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Clio Der Sarkissian
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
| | - N Pierre Charrier
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - David Eme
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Florian Mermillod-Blondin
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Laurent Duret
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.,Institut Universitaire de France, F-75005 Paris, France
| | - Ludovic Orlando
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), CNRS UMR 5288, Laboratoire AMIS, F-31073 Toulouse, France
| | - Christophe Jean Douady
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France.,Institut Universitaire de France, F-75005 Paris, France
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21
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Francois CM, Duret L, Simon L, Mermillod-Blondin F, Malard F, Konecny-Dupré L, Planel R, Penel S, Douady CJ, Lefébure T. No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes. Mol Biol Evol 2016; 33:2605-20. [PMID: 27401232 DOI: 10.1093/molbev/msw131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The field of stoichiogenomics aims at understanding the influence of nutrient limitations on the elemental composition of the genome, transcriptome, and proteome. The 20 amino acids and the 4 nt differ in the number of nutrients they contain, such as nitrogen (N). Thus, N limitation shall theoretically select for changes in the composition of proteins or RNAs through preferential use of N-poor amino acids or nucleotides, which will decrease the N-budget of an organism. While these N-saving mechanisms have been evidenced in microorganisms, they remain controversial in multicellular eukaryotes. In this study, we used 13 surface and subterranean isopod species pairs that face strongly contrasted N limitations, either in terms of quantity or quality. We combined in situ nutrient quantification and transcriptome sequencing to test if N limitation selected for N-savings through changes in the expression and composition of the transcriptome and proteome. No evidence of N-savings was found in the total N-budget of transcriptomes or proteomes or in the average protein N-cost. Nevertheless, subterranean species evolving in N-depleted habitats displayed lower N-usage at their third codon positions. To test if this convergent compositional change was driven by natural selection, we developed a method to detect the strand-asymmetric signature that stoichiogenomic selection should leave in the substitution pattern. No such signature was evidenced, indicating that the observed stoichiogenomic-like patterns were attributable to nonadaptive processes. The absence of stoichiogenomic signal despite strong N limitation within a powerful phylogenetic framework casts doubt on the existence of stoichiogenomic mechanisms in metazoans.
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Affiliation(s)
- Clémentine M Francois
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France
| | - Laurent Duret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Laurent Simon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France
| | - Florian Mermillod-Blondin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France
| | - Florian Malard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France
| | - Lara Konecny-Dupré
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France
| | - Rémi Planel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Simon Penel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France
| | - Christophe J Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France Institut Universitaire de France, Paris, France
| | - Tristan Lefébure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR5023, Villeurbanne, France
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22
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Huntsman BM, Petty JT, Sharma S, Merriam ER. More than a corridor: use of a main stem stream as supplemental foraging habitat by a brook trout metapopulation. Oecologia 2016; 182:463-73. [PMID: 27334869 DOI: 10.1007/s00442-016-3676-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 06/11/2016] [Indexed: 11/30/2022]
Abstract
Coldwater fishes in streams, such as brook trout (Salvelinus fontinalis), typically are headwater specialists that occasionally expand distributions downstream to larger water bodies. It is unclear, however, whether larger streams function simply as dispersal corridors connecting headwater subpopulations, or as critical foraging habitat needed to sustain large mobile brook trout. Stable isotopes (δ(13)C and δ(15)N) and a hierarchical Bayesian mixing model analysis was used to identify brook trout that foraged in main stem versus headwater streams of the Shavers Fork watershed, West Virginia. Headwater subpopulations were composed of headwater and to a lesser extent main stem foraging individuals. However, there was a strong relationship between brook trout size and main stem prey contributions. The average brook trout foraging on headwater prey were limited to 126 mm standard length. This size was identified by mixing models as a point where productivity support switched from headwater to main stem dependency. These results, similar to other studies conducted in this watershed, support the hypothesis that productive main stem habitat maintain large brook trout and potentially facilitates dispersal among headwater subpopulations. Consequently, loss of supplementary main stem foraging habitats may explain loss of large, mobile fish and subsequent isolation of headwater subpopulations in other central Appalachian watersheds.
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Affiliation(s)
- Brock M Huntsman
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, 26506, USA. .,Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, 2980 South Espina Street, 132 Knox Hall, Las Cruces, NM, 88003, USA.
| | - J Todd Petty
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, 26506, USA
| | - Shikha Sharma
- Department of Geology and Geography, West Virginia University, Morgantown, WV, 26506, USA
| | - Eric R Merriam
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, 26506, USA
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23
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Francois CM, Mermillod‐Blondin F, Malard F, Fourel F, Lécuyer C, Douady CJ, Simon L. Trophic ecology of groundwater species reveals specialization in a low‐productivity environment. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12484] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clémentine M. Francois
- Université de Lyon UMR 5023 UMR5023 Écologie des Hydrosystèmes Naturels et Anthropisés Université Lyon 1 ENTPE CNRS 6 rue Raphaël Dubois 69622 Villeurbanne France
| | - Florian Mermillod‐Blondin
- Université de Lyon UMR 5023 UMR5023 Écologie des Hydrosystèmes Naturels et Anthropisés Université Lyon 1 ENTPE CNRS 6 rue Raphaël Dubois 69622 Villeurbanne France
| | - Florian Malard
- Université de Lyon UMR 5023 UMR5023 Écologie des Hydrosystèmes Naturels et Anthropisés Université Lyon 1 ENTPE CNRS 6 rue Raphaël Dubois 69622 Villeurbanne France
| | - Francois Fourel
- Laboratoire de Géologie de Lyon Terre Planétes, Environnement (LGL‐TPE) UMR CNRS 5276 Université Lyon 1 Ecole Normale Supérieure Lyon Campus scientifique de la DOUA 2 rue Dubois69622 Villeurbanne France
| | - Christophe Lécuyer
- Laboratoire de Géologie de Lyon Terre Planétes, Environnement (LGL‐TPE) UMR CNRS 5276 Université Lyon 1 Ecole Normale Supérieure Lyon Campus scientifique de la DOUA 2 rue Dubois69622 Villeurbanne France
- Institut Universitaire de France Paris F‐75005 France
| | - Christophe J. Douady
- Université de Lyon UMR 5023 UMR5023 Écologie des Hydrosystèmes Naturels et Anthropisés Université Lyon 1 ENTPE CNRS 6 rue Raphaël Dubois 69622 Villeurbanne France
- Institut Universitaire de France Paris F‐75005 France
| | - Laurent Simon
- Université de Lyon UMR 5023 UMR5023 Écologie des Hydrosystèmes Naturels et Anthropisés Université Lyon 1 ENTPE CNRS 6 rue Raphaël Dubois 69622 Villeurbanne France
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