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De-Kayne R, Perry BW, McGowan KL, Landers J, Arias-Rodriguez L, Greenway R, Rodríguez Peña CM, Tobler M, Kelley JL. Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes. Genome Biol Evol 2024; 16:evae087. [PMID: 38788745 PMCID: PMC11126329 DOI: 10.1093/gbe/evae087] [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] [Accepted: 04/13/2024] [Indexed: 05/26/2024] Open
Abstract
Adaptation to extreme environments often involves the evolution of dramatic physiological changes. To better understand how organisms evolve these complex phenotypic changes, the repeatability and predictability of evolution, and possible constraints on adapting to an extreme environment, it is important to understand how adaptive variation has evolved. Poeciliid fishes represent a particularly fruitful study system for investigations of adaptation to extreme environments due to their repeated colonization of toxic hydrogen sulfide-rich springs across multiple species within the clade. Previous investigations have highlighted changes in the physiology and gene expression in specific species that are thought to facilitate adaptation to hydrogen sulfide-rich springs. However, the presence of adaptive nucleotide variation in coding and regulatory regions and the degree to which convergent evolution has shaped the genomic regions underpinning sulfide tolerance across taxa are unknown. By sampling across seven independent lineages in which nonsulfidic lineages have colonized and adapted to sulfide springs, we reveal signatures of shared evolutionary rate shifts across the genome. We found evidence of genes, promoters, and putative enhancer regions associated with both increased and decreased convergent evolutionary rate shifts in hydrogen sulfide-adapted lineages. Our analysis highlights convergent evolutionary rate shifts in sulfidic lineages associated with the modulation of endogenous hydrogen sulfide production and hydrogen sulfide detoxification. We also found that regions with shifted evolutionary rates in sulfide spring fishes more often exhibited convergent shifts in either the coding region or the regulatory sequence of a given gene, rather than both.
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Affiliation(s)
- Rishi De-Kayne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Kerry L McGowan
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Jake Landers
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, México
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Carlos M Rodríguez Peña
- Instituto de Investigaciones Botánicas y Zoológicas, Universidad Autónoma de Santo Domingo, Santo Domingo 10105, Dominican Republic
| | - Michael Tobler
- Department of Biology, University of Missouri–St. Louis, St. Louis, MO 63131, USA
- Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, MO 63121, USA
- WildCare Institute, Saint Louis Zoo, St. Louis, MO 63110, USA
| | - Joanna L Kelley
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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2
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Pacher K, Hernández-Román N, Juarez-Lopez A, Jiménez-Jiménez JE, Lukas J, Sevinchan Y, Krause J, Arias-Rodríguez L, Bierbach D. Thermal tolerance in an extremophile fish from Mexico is not affected by environmental hypoxia. Biol Open 2024; 13:bio060223. [PMID: 38314873 PMCID: PMC10868586 DOI: 10.1242/bio.060223] [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: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 02/07/2024] Open
Abstract
The thermal ecology of ectotherm animals has gained considerable attention in the face of human-induced climate change. Particularly in aquatic species, the experimental assessment of critical thermal limits (CTmin and CTmax) may help to predict possible effects of global warming on habitat suitability and ultimately species survival. Here we present data on the thermal limits of two endemic and endangered extremophile fish species, inhabiting a geothermally heated and sulfur-rich spring system in southern Mexico: The sulfur molly (Poecilia sulphuraria) and the widemouth gambusia (Gambusia eurystoma). Besides physiological challenges induced by toxic hydrogen sulfide and related severe hypoxia during the day, water temperatures have been previously reported to exceed those of nearby clearwater streams. We now present temperature data for various locations and years in the sulfur spring complex and conducted laboratory thermal tolerance tests (CTmin and CTmax) both under normoxic and severe hypoxic conditions in both species. Average CTmax limits did not differ between species when dissolved oxygen was present. However, critical temperature (CTmax=43.2°C) in P. sulphuraria did not change when tested under hypoxic conditions, while G. eurystoma on average had a lower CTmax when oxygen was absent. Based on this data we calculated both species' thermal safety margins and used a TDT (thermal death time) model framework to relate our experimental data to observed temperatures in the natural habitat. Our findings suggest that both species live near their thermal limits during the annual dry season and are locally already exposed to temperatures above their critical thermal limits. We discuss these findings in the light of possible physiological adaptions of the sulfur-adapted fish species and the anthropogenic threats for this unique system.
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Affiliation(s)
- Korbinian Pacher
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12487 Berlin, Germany
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University of Berlin, 10115 Berlin, Germany
| | - Natalia Hernández-Román
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma Tabasco, 86150 Villahermosa, Mexico
| | - Alejandro Juarez-Lopez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma Tabasco, 86150 Villahermosa, Mexico
| | | | - Juliane Lukas
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12487 Berlin, Germany
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University of Berlin, 10115 Berlin, Germany
| | - Yunus Sevinchan
- Science of intelligence cluster has the state of a department at TU Berlin, Excellence Cluster Science of Intelligence, Technische Universität Berlin, 10587 Berlin, Germany
| | - Jens Krause
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12487 Berlin, Germany
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University of Berlin, 10115 Berlin, Germany
- Science of intelligence cluster has the state of a department at TU Berlin, Excellence Cluster Science of Intelligence, Technische Universität Berlin, 10587 Berlin, Germany
| | - Lenin Arias-Rodríguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma Tabasco, 86150 Villahermosa, Mexico
| | - David Bierbach
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12487 Berlin, Germany
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, Humboldt University of Berlin, 10115 Berlin, Germany
- Science of intelligence cluster has the state of a department at TU Berlin, Excellence Cluster Science of Intelligence, Technische Universität Berlin, 10587 Berlin, Germany
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3
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DeHaan LM, Burns MD, Egan JP, Bloom DD. Diadromy Drives Elevated Rates of Trait Evolution and Ecomorphological Convergence in Clupeiformes (Herring, Shad, and Anchovies). Am Nat 2023; 202:830-850. [PMID: 38033182 DOI: 10.1086/726894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractMigration can have a profound influence on rates and patterns of phenotypic evolution. Diadromy is the migration between marine and freshwater habitats for feeding and reproduction that can require individuals to travel tens to thousands of kilometers. The high energetic demands of diadromy are predicted to select for ecomorphological traits that maximize swimming and locomotor efficiency. Intraspecific studies have shown repeated instances of divergence among diadromous and nondiadromous populations in locomotor and foraging traits, which suggests that at a macroevolutionary scale diadromous lineages may experience convergent evolution onto one or multiple adaptive optima. We tested for differences in rates and patterns of phenotypic evolution among diadromous and nondiadromous lineages in Clupeiformes, a clade that has evolved diadromy more than 10 times. Our results show that diadromous clupeiforms show convergent evolution for some locomotor traits and faster rates of evolution, which we propose are adaptive responses to the locomotor demands of migration. We also find evidence that diadromous lineages show convergence into multiple regions of multivariate trait space and suggest that these respective trait spaces are associated with differences in migration and trophic ecology. However, not all locomotor traits and no trophic traits show evidence of convergence or elevated rates of evolution associated with diadromy. Our results show that long-distance migration influences the tempo and patterns of phenotypic evolution at macroevolutionary scales, but there is not a single diadromous syndrome.
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Population genetics and independently replicated evolution of predator-associated burst speed ecophenotypy in mosquitofish. Heredity (Edinb) 2022; 128:45-55. [PMID: 34876658 PMCID: PMC8733020 DOI: 10.1038/s41437-021-00487-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023] Open
Abstract
Many species show replicated ecophenotypy due to recurring patterns of natural selection. Based on the presence or absence of pursuit predators, at least 17 species of fish repeatedly differentiated in body shape in a manner that increases burst swimming speed and the likelihood of predator escape. The predator-associated burst speed (PABS) ecophenotype is characterized by a small head and trunk and enlarged caudal region. Mechanisms promoting replicated phenotype-environment association include selection (without evolution), a single instance of adaptive evolution followed by biased habitat occupation, repeated instances of local adaptation, or adaptive phenotypic plasticity. Common garden rearing of mosquitofish, Gambusia affinis, demonstrated a likely heritable basis for PABS phenotypy, but it is unknown whether populations are otherwise genetically distinct or whether replicated ecophenotypy represents a single or replicated instances of adaptation. To genetically characterize the populations and test hypotheses of single or multiple adaptations, we characterized variation in 12 polymorphic DNA microsatellites in the previously studied G. affinis populations. Populations were genetically distinct by multilocus analysis, exhibited high allelic diversity, and were heterozygote deficient, which effects were attributed to G. affinis's shoaling nature and habitat patchiness. Genetic and phenotypic distances among populations were correlated for non-PABS but not PABS morphology. Multilocus analysis demonstrated ecophenotype polyphyly and scattered multivariate genetic structure which support only the replicated-adaptation model. As all of the diverse tests performed demonstrated lack of congruence between patterns of molecular genetic and PABS differentiation, it is likely that divergent natural selection drove multiple instances of adaptive evolution.
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5
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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6
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Owens GL, Veen T, Moxley DR, Arias-Rodriguez L, Tobler M, Rennison DJ. Parallel shifts of visual sensitivity and body coloration in replicate populations of extremophile fish. Mol Ecol 2021; 31:946-958. [PMID: 34784095 DOI: 10.1111/mec.16279] [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: 06/17/2021] [Revised: 11/02/2021] [Accepted: 11/11/2021] [Indexed: 12/20/2022]
Abstract
Visual sensitivity and body pigmentation are often shaped by both natural selection from the environment and sexual selection from mate choice. One way of quantifying the impact of the environment is by measuring how traits have changed after colonization of a novel habitat. To do this, we studied Poecilia mexicana populations that have repeatedly adapted to extreme sulphidic (H2 S-containing) environments. We measured visual sensitivity using opsin gene expression, as well as body pigmentation, for populations in four independent drainages. Both visual sensitivity and body pigmentation showed significant parallel shifts towards greater medium-wavelength sensitivity and reflectance in sulphidic populations. Altogether we found that sulphidic habitats select for differences in visual sensitivity and pigmentation. Shifts between habitats may be due to both differences in the water's spectral properties and correlated ecological changes.
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Affiliation(s)
- Gregory L Owens
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Thor Veen
- Quest University, Squamish, British Columbia, Canada
| | - Dylan R Moxley
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Mexico
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Diana J Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, California, USA
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7
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Friedman ST, Collyer ML, Price SA, Wainwright PC. Divergent processes drive parallel evolution in marine and freshwater fishes. Syst Biol 2021; 71:1319-1330. [PMID: 34605882 DOI: 10.1093/sysbio/syab080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 01/20/2023] Open
Abstract
Evolutionary comparisons between major environmental divides, such as between marine and freshwater systems, can reveal the fundamental processes governing diversification dynamics. Although processes may differ due to the different scales of their biogeographic barriers, freshwater and marine environments nevertheless offer similar opportunities for diversification in benthic, demersal, and pelagic habitats. Here, we compare the evolutionary patterns and processes shaping teleost diversity both in each of these three habitats and between marine and freshwater systems. Using specimens from the National Museum of Natural History, we developed a dataset of linear measurements capturing body shape in 2,266 freshwater and 3,344 marine teleost species. With a novel comparative approach, we contrast the primary axis of morphological diversification in each habitat with the major axis defined by phylogenetic signal. By comparing angles between these axes, we find that fish in corresponding habitats have more similar primary axes of morphological diversity than would be expected by chance, but that different historical processes underlie these parallel patterns in freshwater and marine environments. Marine diversification is more strongly aligned with phylogenetic signal and shows a trend toward lineages occupying separate regions of morphospace. In contrast, ecological signal appears to be a strong driver of diversification in freshwater lineages through repeated morphological evolution in densely packed regions of morphospace. In spite of these divergent histories, our findings reveal that habitat has driven convergent patterns of evolutionary diversification on a global scale.
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Affiliation(s)
- S T Friedman
- Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
| | - M L Collyer
- Department of Science, Chatham University, Pittsburgh, Pennsylvania 15232, USA
| | - S A Price
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - P C Wainwright
- Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
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8
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Epigenetic inheritance of DNA methylation changes in fish living in hydrogen sulfide-rich springs. Proc Natl Acad Sci U S A 2021; 118:2014929118. [PMID: 34185679 PMCID: PMC8255783 DOI: 10.1073/pnas.2014929118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Environmental factors can promote phenotypic variation through alterations in the epigenome and facilitate adaptation of an organism to the environment. Although hydrogen sulfide is toxic to most organisms, the fish Poecilia mexicana has adapted to survive in environments with high levels that exceed toxicity thresholds by orders of magnitude. Epigenetic changes in response to this environmental stressor were examined by assessing DNA methylation alterations in red blood cells, which are nucleated in fish. Males and females were sampled from sulfidic and nonsulfidic natural environments; individuals were also propagated for two generations in a nonsulfidic laboratory environment. We compared epimutations between the sexes as well as field and laboratory populations. For both the wild-caught (F0) and the laboratory-reared (F2) fish, comparing the sulfidic and nonsulfidic populations revealed evidence for significant differential DNA methylation regions (DMRs). More importantly, there was over 80% overlap in DMRs across generations, suggesting that the DMRs have stable generational inheritance in the absence of the sulfidic environment. This is an example of epigenetic generational stability after the removal of an environmental stressor. The DMR-associated genes were related to sulfur toxicity and metabolic processes. These findings suggest that adaptation of P. mexicana to sulfidic environments in southern Mexico may, in part, be promoted through epigenetic DNA methylation alterations that become stable and are inherited by subsequent generations independent of the environment.
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9
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Lukas J, Auer F, Goldhammer T, Krause J, Romanczuk P, Klamser P, Arias-Rodriguez L, Bierbach D. Diurnal Changes in Hypoxia Shape Predator-Prey Interaction in a Bird-Fish System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.619193] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Animals often face changing environments, and behavioral flexibility allows them to rapidly and adaptively respond to abiotic factors that vary more or less regularly. However, abiotic factors that affect prey species do not necessarily affect their predators. Still, the prey’s response might affect the predator indirectly, yet evidence from the wild for such a classical bottom-up effect of abiotic factors shaping several trophic levels remains sparse. In many aquatic environments, daily changes in oxygen concentrations occur frequently. When oxygen levels drop to hypoxic levels, many fishes respond with aquatic surface respiration (ASR), during which they obtain oxygen by skimming the upper, oxygenated surface layer. By increasing time at the surface, fish become more vulnerable to fish-eating birds. We explored these cascading effects in a sulfidic spring system that harbors the endemic sulphur molly (Poecilia sulphuraria) as prey species and several fish-eating bird species. Sulfide-rich springs pose harsh conditions as hydrogen sulfide (H2S) is lethal to most metazoans and reduces dissolved oxygen (DO). Field sampling during three daytimes indicated that water temperatures rose from morning to (after)noon, resulting in the already low DO levels to decrease further, while H2S levels showed no diurnal changes. The drop in DO levels was associated with a decrease in time spent diving in sulphur mollies, which corresponded with an increase in ASR. Interestingly, the laboratory-estimated threshold at which the majority of sulphur mollies initiate ASR (ASR50: <1.7 mg/L DO) was independent of temperature and this value was exceeded daily when hypoxic stress became more severe toward noon. As fish performed ASR, large aggregations built up at the water surface over the course of the day. As a possible consequence of fish spending more time at the surface, we found high activity levels of fish-eating birds at noon and in the afternoon. Our study reveals that daily fluctuations in water’s oxygen levels have the potential to alter predator-prey interactions profoundly and thus highlights the joined actions of abiotic and biotic factors shaping the evolution of a prey species.
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10
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Kelley JL, Desvignes T, McGowan KL, Perez M, Rodriguez LA, Brown AP, Culumber Z, Tobler M. microRNA expression variation as a potential molecular mechanism contributing to adaptation to hydrogen sulphide. J Evol Biol 2020; 34:977-988. [PMID: 33124163 DOI: 10.1111/jeb.13727] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/18/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022]
Abstract
microRNAs (miRNAs) are post-transcriptional regulators of gene expression and can play an important role in modulating organismal development and physiology in response to environmental stress. However, the role of miRNAs in mediating adaptation to diverse environments in natural study systems remains largely unexplored. Here, we characterized miRNAs and their expression in Poecilia mexicana, a species of small fish that inhabits both normal streams and extreme environments in the form of springs rich in toxic hydrogen sulphide (H2 S). We found that P. mexicana has a similar number of miRNA genes as other teleosts. In addition, we identified a large population of mature miRNAs that were differentially expressed between locally adapted populations in contrasting habitats, indicating that miRNAs may contribute to P. mexicana adaptation to sulphidic environments. In silico identification of differentially expressed miRNA-mRNA pairs revealed, in the sulphidic environment, the downregulation of miRNAs predicted to target mRNAs involved in sulphide detoxification and cellular homeostasis, which are pathways essential for life in H2 S-rich springs. In addition, we found that predicted targets of upregulated miRNAs act in the mitochondria (16.6% of predicted annotated targets), which is the main site of H2 S toxicity and detoxification, possibly modulating mitochondrial function. Together, the differential regulation of miRNAs between these natural populations suggests that miRNAs may be involved in H2 S adaptation by promoting functions needed for survival and reducing functions affected by H2 S. This study lays the groundwork for further research to directly demonstrate the role of miRNAs in adaptation to H2 S. Overall, this study provides a critical stepping-stone towards a comprehensive understanding of the regulatory mechanisms underlying the adaptive variation in gene expression in a natural system.
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Affiliation(s)
- Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Kerry L McGowan
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Marcos Perez
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Lenin Arias Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, México
| | - Anthony P Brown
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Zach Culumber
- Biological Sciences Department, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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11
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Martin KE, Currie S. Hydrogen sulphide sensitivity and tolerance in genetically distinct lineages of a selfing mangrove fish (Kryptolebias marmoratus). J Comp Physiol B 2020; 190:761-770. [PMID: 32789701 DOI: 10.1007/s00360-020-01302-4] [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: 04/28/2020] [Revised: 07/16/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
Mangroves are critical marine habitats. High hydrogen sulphide (H2S) is a feature of these important ecosystems and its toxicity creates a challenge for mangrove inhabitants. The mangrove rivulus (Kryptolebias marmoratus) is a selfing, hermaphroditic, amphibious fish that can survive exposure to 1116 μM H2S in the wild. These fish rely on cutaneous respiration for gas and ion exchange when emerged. We hypothesized that the skin surface is fundamentally important in H2S tolerance in these mangrove fish by limiting H2S permeability. To test our hypothesis, we first disrupted the skin surface in one isogenic lineage and measured H2S tolerance and sensitivity. We increased water H2S concentration until emersion as a measure of the ability to sense and react to H2S, which we refer to as sensitivity. We then determined H2S tolerance by preventing emersion and increasing H2S until loss of equilibrium (LOE). The H2S concentration at emersion and LOE were significantly affected by disrupting the skin surface, providing support that the skin is involved in limiting H2S permeability. Capitalizing on their unique reproductive strategy, we used three distinct isogenic lineages to test the hypothesis that there would be genetic differences in H2S sensitivity and tolerance. We found significant differences in emersion concentration only among lineages, suggesting a genetic component to H2S sensitivity but not tolerance. Our study also demonstrated that external skin modifications and avoidance behaviours are two distinct strategies used to tolerate ecologically relevant H2S concentrations and likely facilitate survival in challenging mangrove habitats.
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Affiliation(s)
- Keri E Martin
- Department of Biology, Mount Allison University, Sackville, NB, Canada
| | - Suzanne Currie
- Department of Biology, Acadia University, Wolfville, NS, Canada.
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12
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Greenway R, Barts N, Henpita C, Brown AP, Arias Rodriguez L, Rodríguez Peña CM, Arndt S, Lau GY, Murphy MP, Wu L, Lin D, Tobler M, Kelley JL, Shaw JH. Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments. Proc Natl Acad Sci U S A 2020; 117:16424-16430. [PMID: 32586956 PMCID: PMC7368198 DOI: 10.1073/pnas.2004223117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
Extreme environments test the limits of life; yet, some organisms thrive in harsh conditions. Extremophile lineages inspire questions about how organisms can tolerate physiochemical stressors and whether the repeated colonization of extreme environments is facilitated by predictable and repeatable evolutionary innovations. We identified the mechanistic basis underlying convergent evolution of tolerance to hydrogen sulfide (H2S)-a toxicant that impairs mitochondrial function-across evolutionarily independent lineages of a fish (Poecilia mexicana, Poeciliidae) from H2S-rich springs. Using comparative biochemical and physiological analyses, we found that mitochondrial function is maintained in the presence of H2S in sulfide spring P. mexicana but not ancestral lineages from nonsulfidic habitats due to convergent adaptations in the primary toxicity target and a major detoxification enzyme. Genome-wide local ancestry analyses indicated that convergent evolution of increased H2S tolerance in different populations is likely caused by a combination of selection on standing genetic variation and de novo mutations. On a macroevolutionary scale, H2S tolerance in 10 independent lineages of sulfide spring fishes across multiple genera of Poeciliidae is correlated with the convergent modification and expression changes in genes associated with H2S toxicity and detoxification. Our results demonstrate that the modification of highly conserved physiological pathways associated with essential mitochondrial processes mediates tolerance to physiochemical stress. In addition, the same pathways, genes, and-in some instances-codons are implicated in H2S adaptation in lineages that span 40 million years of evolution.
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Affiliation(s)
- Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506
| | - Nick Barts
- Division of Biology, Kansas State University, Manhattan, KS 66506
| | - Chathurika Henpita
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078
| | - Anthony P Brown
- School of Biological Sciences, Washington State University, Pullman, WA 99163
| | - Lenin Arias Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, 86150, Mexico
| | - Carlos M Rodríguez Peña
- Instituto de Investigaciones Botánicas y Zoológicas, Universidad Autónoma de Santo Domingo, Santo Domingo, 10105, Dominican Republic
| | - Sabine Arndt
- Medical Research Council - Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Gigi Y Lau
- Department of Biosciences, University of Oslo, 0315 Oslo, Norway
| | - Michael P Murphy
- Medical Research Council - Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Lei Wu
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK 74078
| | - Dingbo Lin
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK 74078
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS 66506;
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99163;
| | - Jennifer H Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078;
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13
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St John ME, Holzman R, Martin CH. Rapid adaptive evolution of scale-eating kinematics to a novel ecological niche. J Exp Biol 2020; 223:jeb217570. [PMID: 32029459 PMCID: PMC7097200 DOI: 10.1242/jeb.217570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/29/2020] [Indexed: 01/08/2023]
Abstract
The origins of novel trophic specialization, in which organisms begin to exploit resources for the first time, may be explained by shifts in behavior such as foraging preferences or feeding kinematics. One way to investigate behavioral mechanisms underlying ecological novelty is by comparing prey capture kinematics among species. We investigated the contribution of kinematics to the origins of a novel ecological niche for scale-eating within a microendemic adaptive radiation of pupfishes on San Salvador Island, Bahamas. We compared prey capture kinematics across three species of pupfish while they consumed shrimp and scales in the lab, and found that scale-eating pupfish exhibited peak gape sizes twice as large as in other species, but also attacked prey with a more obtuse angle between their lower jaw and suspensorium. We then investigated how this variation in feeding kinematics could explain scale-biting performance by measuring bite size (surface area removed) from standardized gelatin cubes. We found that a combination of larger peak gape and more obtuse lower jaw and suspensorium angles resulted in approximately 40% more surface area removed per strike, indicating that scale-eaters may reside on a performance optimum for scale biting. To test whether feeding performance could contribute to reproductive isolation between species, we also measured F1 hybrids and found that their kinematics and performance more closely resembled generalists, suggesting that F1 hybrids may have low fitness in the scale-eating niche. Ultimately, our results suggest that the evolution of strike kinematics in this radiation is an adaptation to the novel niche of scale eating.
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Affiliation(s)
- Michelle E St John
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roi Holzman
- School of Zoology, Tel Aviv University, Eilat 6997801, Israel
- Inter-University Institute for Marine Sciences, Eilat 8810302, Israel
| | - Christopher H Martin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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14
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Tobler M, Barts N, Greenway R. Mitochondria and the Origin of Species: Bridging Genetic and Ecological Perspectives on Speciation Processes. Integr Comp Biol 2020; 59:900-911. [PMID: 31004483 DOI: 10.1093/icb/icz025] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondria have been known to be involved in speciation through the generation of Dobzhansky-Muller incompatibilities, where functionally neutral co-evolution between mitochondrial and nuclear genomes can cause dysfunction when alleles are recombined in hybrids. We propose that adaptive mitochondrial divergence between populations can not only produce intrinsic (Dobzhansky-Muller) incompatibilities, but could also contribute to reproductive isolation through natural and sexual selection against migrants, post-mating prezygotic isolation, as well as by causing extrinsic reductions in hybrid fitness. We describe how these reproductive isolating barriers can potentially arise through adaptive divergence of mitochondrial function in the absence of mito-nuclear coevolution, a departure from more established views. While a role for mitochondria in the speciation process appears promising, we also highlight critical gaps of knowledge: (1) many systems with a potential for mitochondrially-mediated reproductive isolation lack crucial evidence directly linking reproductive isolation and mitochondrial function; (2) it often remains to be seen if mitochondrial barriers are a driver or a consequence of reproductive isolation; (3) the presence of substantial gene flow in the presence of mito-nuclear incompatibilities raises questions whether such incompatibilities are strong enough to drive speciation to completion; and (4) it remains to be tested how mitochondrial effects on reproductive isolation compare when multiple mechanisms of reproductive isolation coincide. We hope this perspective and the proposed research plans help to inform future studies of mitochondrial adaptation in a manner that links genotypic changes to phenotypic adaptations, fitness, and reproductive isolation in natural systems, helping to clarify the importance of mitochondria in the formation and maintenance of biological diversity.
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Affiliation(s)
- M Tobler
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - N Barts
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - R Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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15
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Camarillo H, Arias Rodriguez L, Tobler M. Functional consequences of phenotypic variation between locally adapted populations: Swimming performance and ventilation in extremophile fish. J Evol Biol 2020; 33:512-523. [DOI: 10.1111/jeb.13586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 01/06/2020] [Accepted: 01/09/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Henry Camarillo
- Division of Biology Kansas State University Manhattan KS USA
| | - Lenin Arias Rodriguez
- División Académica de Ciencias Biológicas Universidad Juárez Autónoma de Tabasco Villahermosa México
| | - Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
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16
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Styga JM, Pienaar J, Scott PA, Earley RL. Does Body Shape in Fundulus Adapt to Variation in Habitat Salinity? Front Physiol 2019; 10:1400. [PMID: 31803063 PMCID: PMC6872640 DOI: 10.3389/fphys.2019.01400] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 10/30/2019] [Indexed: 01/29/2023] Open
Abstract
Understanding the ecological pressures that generate variation in body shape is important because body shape profoundly affects physiology and overall fitness. Using Fundulus, a genus of fish that exhibits considerable morphological and physiological variation with evidence of repeated transitions between freshwater and saltwater habitats, we tested whether habitat salinity has influenced the macroevolution of body shape at different stages in development. After accounting for phylogenetic inertia, we find that body shape deviates from the optimal streamlined shape in a manner consistent with different osmoregulatory pressures exerted by different salinity niches at every stage of ontogeny that we examined. We attribute variation in body shape to differential selection for osmoregulatory efficiency because: (1) saline intolerant species developed body shapes with relatively low surface areas more conducive to managing osmoregulatory demands and (2) inland species that exhibit high salinity tolerances have body shapes similar to saline tolerant species in marine environments.
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Affiliation(s)
- Joseph M Styga
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, United States.,Biology Program, Centre College, Danville, KY, United States
| | - Jason Pienaar
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, United States
| | - Peter A Scott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, United States.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ryan L Earley
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, United States
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17
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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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18
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Aguilera G, Terán GE, Mirande JM, Alonso F, Rometsch S, Meyer A, Torres-Dowdall J. Molecular and morphological convergence to sulfide-tolerant fishes in a new species of Jenynsia (Cyprinodontiformes: Anablepidae), the first extremophile member of the family. PLoS One 2019; 14:e0218810. [PMID: 31291282 PMCID: PMC6619989 DOI: 10.1371/journal.pone.0218810] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/05/2019] [Indexed: 12/16/2022] Open
Abstract
Freshwater sulfide springs have extreme environmental conditions that only few vertebrate species can tolerate. These species often develop a series of morphological and molecular adaptations to cope with the challenges of life under the toxic and hypoxic conditions of sulfide springs. In this paper, we described a new fish species of the genus Jenynsia, Anablepidae, from a sulfide spring in Northwestern Argentina, the first in the family known from such extreme environment. Jenynsia sulfurica n. sp. is diagnosable by the lack of scales on the pre-pelvic area or the presence of a single row of scales, continuous or not, from the isthmus to the bases of the pelvic fins. Additionally, it presents a series of morphological and molecular characteristics that appear convergent with those seen in other fish species (e.g., Poeciliids) inhabiting sulfide springs. Most notably, J. sulfurica has an enlarged head and postorbital area compared to other fish of the genus and a prognathous lower jaw with a hypertrophied lip, thought to facilitate respiration at the air-water interface. Analyses of cox1 sequence showed that J. sulfurica has two unique mutations resulting in amino acid substitutions convergent to those seen in Poeciliids from sulfide springs and known to provide a physiological mechanism related to living in sulfide environments. A phylogenetic analysis, including molecular and morphological characters, placed J. sulfurica as sister taxa to J. alternimaculata, a species found in nearby, non-sulfide habitats directly connected to the sulfide springs. Thus, it can be inferred that the selection imposed by the presence of H2S has resulted in the divergence between these two species and has potentially served as a barrier to gene flow.
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Affiliation(s)
- Gastón Aguilera
- Fundación Miguel Lillo - Unidad Ejecutora Lillo (CONICET), San Miguel de Tucumán, Tucumán, Argentina
| | - Guillermo Enrique Terán
- Fundación Miguel Lillo - Unidad Ejecutora Lillo (CONICET), San Miguel de Tucumán, Tucumán, Argentina
| | - Juan Marcos Mirande
- Fundación Miguel Lillo - Unidad Ejecutora Lillo (CONICET), San Miguel de Tucumán, Tucumán, Argentina
| | - Felipe Alonso
- Instituto de Bio y Geociencias del NOA (IBIGEO-CONICET), Rosario de Lerma, Salta, Argentina
| | - Sina Rometsch
- Chair of Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
- Hector Fellow Academy, Karlsruhe, Germany
| | - Axel Meyer
- Chair of Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
- Hector Fellow Academy, Karlsruhe, Germany
| | - Julian Torres-Dowdall
- Chair of Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
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19
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Brown AP, McGowan KL, Schwarzkopf EJ, Greenway R, Rodriguez LA, Tobler M, Kelley JL. Local ancestry analysis reveals genomic convergence in extremophile fishes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180240. [PMID: 31154969 DOI: 10.1098/rstb.2018.0240] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The molecular basis of convergent phenotypes is often unknown. However, convergence at a genomic level is predicted when there are large population sizes, gene flow among diverging lineages or strong genetic constraints. We used whole-genome resequencing to investigate genomic convergence in fishes ( Poecilia spp.) that have repeatedly colonized hydrogen sulfide (H2S)-rich environments in Mexico. We identified genomic similarities in both single nucleotide polymorphisms (SNPs) and structural variants (SVs) among independently derived sulfide spring populations, with approximately 1.2% of the genome being shared among sulfidic ecotypes. We compared these convergent genomic regions to candidate genes for H2S adaptation identified from transcriptomic analyses and found that a significant proportion of these candidate genes (8%) were also in regions where sulfidic individuals had similar SNPs, while only 1.7% were in regions where sulfidic individuals had similar SVs. Those candidate genes included genes involved in sulfide detoxification, the electron transport chain (the main toxicity target of H2S) and other processes putatively important for adaptation to sulfidic environments. Regional genomic similarity across independent populations exposed to the same source of selection is consistent with selection on standing variation or introgression of adaptive alleles across divergent lineages. However, combined with previous analyses, our data also support that adaptive changes in mitochondrially encoded subunits arose independently via selection on de novo mutations. Pressing questions remain on what conditions ultimately facilitate the independent rise of adaptive alleles at the same loci in separate populations, and thus, the degree to which evolution is repeatable or predictable. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Anthony P Brown
- 1 School of Biological Sciences, Washington State University , 100 Dairy Road, Pullman, WA 99164 , USA
| | - Kerry L McGowan
- 1 School of Biological Sciences, Washington State University , 100 Dairy Road, Pullman, WA 99164 , USA
| | - Enrique J Schwarzkopf
- 1 School of Biological Sciences, Washington State University , 100 Dairy Road, Pullman, WA 99164 , USA
| | - Ryan Greenway
- 2 Division of Biology, Kansas State University , 116 Ackert Hall, Manhattan, KS 66506 , USA
| | - Lenin Arias Rodriguez
- 3 División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT) , CP 86150 Villahermosa, Tabasco , México
| | - Michael Tobler
- 2 Division of Biology, Kansas State University , 116 Ackert Hall, Manhattan, KS 66506 , USA
| | - Joanna L Kelley
- 1 School of Biological Sciences, Washington State University , 100 Dairy Road, Pullman, WA 99164 , USA
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20
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Lau GY, Barts N, Hartley RC, Tobler M, Richards JG, Murphy MP, Arndt S. Detection of changes in mitochondrial hydrogen sulfide i n vivo in the fish model Poecilia mexicana (Poeciliidae). Biol Open 2019; 8:8/5/bio041467. [PMID: 31072908 PMCID: PMC6550084 DOI: 10.1242/bio.041467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In this paper, we outline the use of a mitochondria-targeted ratiometric mass spectrometry probe, MitoA, to detect in vivo changes in mitochondrial hydrogen sulfide (H2S) in Poecilia mexicana (family Poeciliidae). MitoA is introduced via intraperitoneal injection into the animal and is taken up by mitochondria, where it reacts with H2S to form the product MitoN. The MitoN/MitoA ratio can be used to assess relative changes in the amounts of mitochondrial H2S produced over time. We describe the use of MitoA in the fish species P. mexicana to illustrate the steps for adopting the use of MitoA in a new organism, including extraction and purification of MitoA and MitoN from tissues followed by tandem mass spectrometry. In this proof-of-concept study we exposed H2S tolerant P. mexicana to 59 µM free H2S for 5 h, which resulted in increased MitoN/MitoA in brain and gills, but not in liver or muscle, demonstrating increased mitochondrial H2S levels in select tissues following whole-animal H2S exposure. This is the first time that accumulation of H2S has been observed in vivo during whole-animal exposure to free H2S using MitoA. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Gigi Y. Lau
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada,Authors for correspondence (, )
| | - Nicholas Barts
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Richard C. Hartley
- WestCHEM School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Jeffrey G. Richards
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Michael P. Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Sabine Arndt
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK .,Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, Mainz 55131, Germany
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21
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Hotaling S, Quackenbush CR, Bennett-Ponsford J, New DD, Arias-Rodriguez L, Tobler M, Kelley JL. Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams. MICROBIAL ECOLOGY 2019; 77:559-573. [PMID: 30105506 DOI: 10.1007/s00248-018-1237-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Extreme environments typically require costly adaptations for survival, an attribute that often translates to an elevated influence of habitat conditions on biotic communities. Microbes, primarily bacteria, are successful colonizers of extreme environments worldwide, yet in many instances, the interplay between harsh conditions, dispersal, and microbial biogeography remains unclear. This lack of clarity is particularly true for habitats where extreme temperature is not the overarching stressor, highlighting a need for studies that focus on the role other primary stressors (e.g., toxicants) play in shaping biogeographic patterns. In this study, we leveraged a naturally paired stream system in southern Mexico to explore how elevated hydrogen sulfide (H2S) influences microbial diversity. We sequenced a portion of the 16S rRNA gene using bacterial primers for water sampled from three geographically proximate pairings of streams with high (> 20 μM) or low (~ 0 μM) H2S concentrations. After exploring bacterial diversity within and among sites, we compared our results to a previous study of macroinvertebrates and fish for the same sites. By spanning multiple organismal groups, we were able to illuminate how H2S may differentially affect biodiversity. The presence of elevated H2S had no effect on overall bacterial diversity (p = 0.21), a large effect on community composition (25.8% of variation explained, p < 0.0001), and variable influence depending upon the group-whether fish, macroinvertebrates, or bacteria-being considered. For bacterial diversity, we recovered nine abundant operational taxonomic units (OTUs) that comprised a core H2S-rich stream microbiome in the region. Many H2S-associated OTUs were members of the Epsilonproteobacteria and Gammaproteobacteria, which both have been implicated in endosymbiotic relationships between sulfur-oxidizing bacteria and eukaryotes, suggesting the potential for symbioses that remain to be discovered in these habitats.
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Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | | | - Daniel D New
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, Mexico
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
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22
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Hydrogen sulphide toxicity and the importance of amphibious behaviour in a mangrove fish inhabiting sulphide-rich habitats. J Comp Physiol B 2019; 189:223-235. [PMID: 30719531 DOI: 10.1007/s00360-019-01204-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/16/2019] [Accepted: 01/25/2019] [Indexed: 10/27/2022]
Abstract
We investigated amphibious behaviour, hydrogen sulphide (H2S) tolerance, and the mechanism of H2S toxicity in the amphibious mangrove rivulus (Kryptolebias marmoratus). We found that fish emersed (left water) in response to acutely elevated [H2S] (~ 130-200 µmol l-1). The emersion response to H2S may be influenced by prior acclimation history due to acclimation-induced alterations in gill morphology and/or the density and size of neuroepithelial cells (NECs) on the gills and skin. Thus, we acclimated fish to water (control), H2S-rich water, or air and tested the hypotheses that acclimation history influences H2S sensitivity due to acclimation-induced changes in (i) gill surface area and/or (ii) NEC density and/or size. Air-acclimated fish emersed at significantly lower [H2S] relative to fish acclimated to control or H2S-rich water, but exhibited no change in gill surface area or in NEC density or size in the gills or skin. Despite possessing exceptional H2S tolerance, all fish lost equilibrium when unable to emerse from environments containing extremely elevated [H2S] (2272 ± 46 µmol l-1). Consequently, we tested the hypothesis that impaired blood oxygen transport (i.e., sulphemoglobin formation) causes H2S toxicity in amphibious fishes. In vitro exposure of red blood cells to physiologically relevant [H2S] did not cause a substantial increase in sulphemoglobin formation. We found evidence, however, for an alternative hypothesis that H2S toxicity is caused by impaired oxidative phosphorylation (i.e., cytochrome c oxidase inhibition). Collectively, our results show that amphibious behaviour is critical for the survival of K. marmoratus in H2S-rich environments as fish experience impaired oxidative phosphorylation when unable to emerse.
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23
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Brown AP, Arias-Rodriguez L, Yee MC, Tobler M, Kelley JL. Concordant Changes in Gene Expression and Nucleotides Underlie Independent Adaptation to Hydrogen-Sulfide-Rich Environments. Genome Biol Evol 2018; 10:2867-2881. [PMID: 30215710 PMCID: PMC6225894 DOI: 10.1093/gbe/evy198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2018] [Indexed: 12/23/2022] Open
Abstract
The colonization of novel environments often involves changes in gene expression, protein coding sequence, or both. Studies of how populations adapt to novel conditions, however, often focus on only one of these two processes, potentially missing out on the relative importance of different parts of the evolutionary process. In this study, our objectives were 1) to better understand the qualitative concordance between conclusions drawn from analyses of differential expression and changes in genic sequence and 2) to quantitatively test whether differentially expressed genes were enriched for sites putatively under positive selection within gene regions. To achieve this, we compared populations of fish (Poecilia mexicana) that have independently adapted to hydrogen-sulfide-rich environments in southern Mexico to adjacent populations residing in nonsulfidic waters. Specifically, we used RNA-sequencing data to compare both gene expression and DNA sequence differences between populations. Analyzing these two different data types led to similar conclusions about which biochemical pathways (sulfide detoxification and cellular respiration) were involved in adaptation to sulfidic environments. Additionally, we found a greater overlap between genes putatively under selection and differentially expressed genes than expected by chance. We conclude that considering both differential expression and changes in DNA sequence led to a more comprehensive understanding of how these populations adapted to extreme environmental conditions. Our results imply that changes in both gene expression and DNA sequence-sometimes at the same loci-may be involved in adaptation.
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Affiliation(s)
- Anthony P Brown
- School of Biological Sciences, Washington State University, 100 Dairy Road, Pullman, WA 99164
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150, Villahermosa, Tabasco, México
| | - Muh-Ching Yee
- Stanford Functional Genomics Facility, CCSR 0120, Stanford, CA 94305
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, 100 Dairy Road, Pullman, WA 99164
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24
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Chiozzi G, Stiassny MLJ, de Marchi G, Lamboj A, Fasola M, Fruciano C. A diversified kettle of fish: phenotypic variation in the endemic cichlid genus Danakilia of the Danakil Depression of northeastern Africa. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Giorgio Chiozzi
- Dipartimento di Scienze della Terra e dell’Ambiente, Università degli Studi di Pavia, Pavia, Italy
- Museo di Storia Naturale di Milano, Corso Venezia, Milano, Italy
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY, USA
| | - Giuseppe de Marchi
- Dipartimento di Scienze della Terra e dell’Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Anton Lamboj
- Department of Integrative Zoology, University of Vienna, UZA, Vienna, Austria
| | - Mauro Fasola
- Dipartimento di Scienze della Terra e dell’Ambiente, Università degli Studi di Pavia, Pavia, Italy
| | - Carmelo Fruciano
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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25
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Zimmer C, Riesch R, Jourdan J, Bierbach D, Arias-Rodriguez L, Plath M. Female Choice Undermines the Emergence of Strong Sexual Isolation between Locally Adapted Populations of Atlantic Mollies ( Poecilia mexicana). Genes (Basel) 2018; 9:E232. [PMID: 29724050 PMCID: PMC5977172 DOI: 10.3390/genes9050232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 11/16/2022] Open
Abstract
Divergent selection between ecologically dissimilar habitats promotes local adaptation, which can lead to reproductive isolation (RI). Populations in the Poecilia mexicana species complex have independently adapted to toxic hydrogen sulfide and show varying degrees of RI. Here, we examined the variation in the mate choice component of prezygotic RI. Mate choice tests across drainages (with stimulus males from another drainage) suggest that specific features of the males coupled with a general female preference for yellow color patterns explain the observed variation. Analyses of male body coloration identified the intensity of yellow fin coloration as a strong candidate to explain this pattern, and common-garden rearing suggested heritable population differences. Male sexual ornamentation apparently evolved differently across sulfide-adapted populations, for example because of differences in natural counterselection via predation. The ubiquitous preference for yellow color ornaments in poeciliid females likely undermines the emergence of strong RI, as female discrimination in favor of own males becomes weaker when yellow fin coloration in the respective sulfide ecotype increases. Our study illustrates the complexity of the (partly non-parallel) pathways to divergence among replicated ecological gradients. We suggest that future work should identify the genomic loci involved in the pattern reported here, making use of the increasing genomic and transcriptomic datasets available for our study system.
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Affiliation(s)
- Claudia Zimmer
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, China.
- Department of Ecology and Evolution, Goethe University of Frankfurt, Max-von-Laue-Straße 13, D-60438 Frankfurt am Main, Germany.
| | - Rüdiger Riesch
- Centre for Ecology, Evolution and Behaviour, School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK.
| | - Jonas Jourdan
- Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, D-63571 Gelnhausen, Germany.
| | - David Bierbach
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, D-12587 Berlin, Germany.
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), 86150 Villahermosa, Tabasco, Mexico.
| | - Martin Plath
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling 712100, China.
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26
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Sharpe DMT, Chapman LJ. Contemporary phenotypic change in correlated characters in the African cyprinid, Rastrineobola argentea. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- D M T Sharpe
- Department of Biology, McGill University, Montreal QC, Canada
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27
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Barts N, Greenway R, Passow CN, Arias-Rodriguez L, Kelley JL, Tobler M. Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs. Genome 2018; 61:273-286. [DOI: 10.1139/gen-2017-0051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen sulfide (H2S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H2S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H2S—along with related lineages from non-sulfidic environments—to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H2S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H2S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H2S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H2S-rich environments are not necessarily repeatable across replicated lineages.
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Affiliation(s)
- Nicholas Barts
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Ryan Greenway
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Courtney N. Passow
- Ecology, Evolution and Behavior, University of Minnesota St. Paul, 205 Cargill Building, St. Paul, MN 55108, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150, Villahermosa, Tabasco, México
| | - Joanna L. Kelley
- Department of Biological Sciences, Washington State University, 431 Heald Hall, Pullman, WA 99164, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
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28
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Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Mol Ecol 2018; 27:843-859. [DOI: 10.1111/mec.14497] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA USA
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and Technology Northwest A&F University Yangling Shaanxi China
| | - Rüdiger Riesch
- School of Biological Sciences Centre for Ecology, Evolution and Behaviour Royal Holloway University of London Egham Surrey UK
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29
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Bierbach D, Lukas J, Bergmann A, Elsner K, Höhne L, Weber C, Weimar N, Arias-Rodriguez L, Mönck HJ, Nguyen H, Romanczuk P, Landgraf T, Krause J. Insights into the Social Behavior of Surface and Cave-Dwelling Fish ( Poecilia mexicana) in Light and Darkness through the Use of a Biomimetic Robot. Front Robot AI 2018; 5:3. [PMID: 33500890 PMCID: PMC7805783 DOI: 10.3389/frobt.2018.00003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/15/2018] [Indexed: 11/30/2022] Open
Abstract
Biomimetic robots (BRs) are becoming more common in behavioral research and, if they are accepted as conspecifics, allow for new forms of experimental manipulations of social interactions. Nevertheless, it is often not clear which cues emanating from a BR are actually used as communicative signals and how species or populations with different sensory makeups react to specific types of BRs. We herein present results from experiments using two populations of livebearing fishes that differ in their sensory capabilities. In the South of Mexico, surface-dwelling mollies (Poecilia mexicana) successfully invaded caves and adapted to dark conditions. While almost without pigment, these cave mollies possess smaller but still functional eyes. Although previous studies found cave mollies to show reduced shoaling preferences with conspecifics in light compared to surface mollies, it is assumed that they possess specialized adaptations to maintain some kind of sociality also in their dark habitats. By testing surface- and cave-dwelling mollies with RoboFish, a BR made for use in laboratory experiments with guppies and sticklebacks, we asked to what extent visual and non-visual cues play a role in their social behavior. Both cave- and surface-dwelling mollies followed the BR as well as a live companion when tested in light. However, when tested in darkness, only surface-dwelling fish were attracted by a live conspecific, whereas cave-dwelling fish were not. Neither cave- nor surface-dwelling mollies were attracted to RoboFish in darkness. This is the first study to use BRs for the investigation of social behavior in mollies and to compare responses to BRs both in light and darkness. As our RoboFish is accepted as conspecific by both used populations of the Atlantic molly only under light conditions but not in darkness, we argue that our replica is providing mostly visual cues.
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Affiliation(s)
- David Bierbach
- Humboldt-Universität zu Berlin, bologna.lab, Q-Team Programm, Berlin, Germany.,Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Juliane Lukas
- Humboldt-Universität zu Berlin, bologna.lab, Q-Team Programm, Berlin, Germany.,Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Faculty of Life Sciences, Thaer Institute, Humboldt University of Berlin, Berlin, Germany
| | - Anja Bergmann
- Humboldt-Universität zu Berlin, bologna.lab, Q-Team Programm, Berlin, Germany
| | - Kristiane Elsner
- Humboldt-Universität zu Berlin, bologna.lab, Q-Team Programm, Berlin, Germany
| | - Leander Höhne
- Humboldt-Universität zu Berlin, bologna.lab, Q-Team Programm, Berlin, Germany
| | - Christiane Weber
- Humboldt-Universität zu Berlin, bologna.lab, Q-Team Programm, Berlin, Germany
| | - Nils Weimar
- Humboldt-Universität zu Berlin, bologna.lab, Q-Team Programm, Berlin, Germany
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, Mexico
| | - Hauke J Mönck
- Freie Universität Berlin, FB Mathematik u. Informatik, Berlin, Germany
| | - Hai Nguyen
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Pawel Romanczuk
- Department of Biology, Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Tim Landgraf
- Freie Universität Berlin, FB Mathematik u. Informatik, Berlin, Germany
| | - Jens Krause
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Faculty of Life Sciences, Thaer Institute, Humboldt University of Berlin, Berlin, Germany
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30
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Moody EK, Lozano-Vilano ML. Predation drives morphological convergence in the Gambusia panuco species group among lotic and lentic habitats. J Evol Biol 2017; 31:491-501. [PMID: 29266513 DOI: 10.1111/jeb.13226] [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] [Received: 07/30/2017] [Revised: 12/07/2017] [Accepted: 12/13/2017] [Indexed: 11/28/2022]
Abstract
Fish morphology is often constrained by a trade-off between optimizing steady vs. unsteady swimming performance due to opposing effects of caudal peduncle size. Lotic environments tend to select for steady swimming performance, leading to smaller caudal peduncles, whereas predators tend to select for unsteady swimming performance, leading to larger caudal peduncles. However, it is unclear which aspect of performance should be optimized across heterogeneous flow and predation environments and how this heterogeneity may affect parallel phenotypic evolution. We investigated this question among four Gambusia species in north-eastern Mexico, specifically the riverine G. panuco, the spring endemics G. alvarezi and G. hurtadoi, and a fourth species, G. marshi, found in a variety of habitats with varying predation pressure in the Cuatro Ciénegas Basin and Río Salado de Nadadores. We employed a geometric morphometric analysis to examine how body shapes of both male and female fish differ among species and habitats and with piscivore presence. We found that high-predation and low-predation species diverged morphologically, with G. marshi exhibiting a variable, intermediate body shape. Within G. marshi, body morphology converged in high-predation environments regardless of flow velocity, and fish from high-predation sites had larger relative caudal peduncle areas. However, we found that G. marshi from low-predation environments diverged in morphology between sub-basins of Cuatro Ciénegas, indicating other differences among these basins that merit further study. Our results suggest that a morphological trade-off promotes parallel evolution of body shape in fishes colonizing high-predation environments and that changing predation pressure can strongly impact morphological evolution in these species.
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Affiliation(s)
- E K Moody
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - M L Lozano-Vilano
- Laboratorio de Ictiología, Universidad Autόnoma de Nuevo Leόn, San Nicolás de los Garza, N.L., Mexico
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31
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Bierbach D, Arias-Rodriguez L, Plath M. Intrasexual competition enhances reproductive isolation between locally adapted populations. Curr Zool 2017; 64:125-133. [PMID: 29492045 PMCID: PMC5809038 DOI: 10.1093/cz/zox071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/22/2017] [Indexed: 02/07/2023] Open
Abstract
During adaptation to different habitat types, both morphological and behavioral traits can undergo divergent selection. Males often fight for status in dominance hierarchies and rank positions predict reproductive success. Ecotypes with reduced fighting abilities should have low reproductive success when migrating into habitats that harbor ecotypes with superior fighting abilities. Livebearing fishes in the Poecilia mexicana-species complex inhabit not only regular freshwater environments, but also independently colonized sulfidic (H2S-containing) habitats in three river drainages. In the current study, we found fighting intensities in staged contests to be considerably lower in some but not all sulfidic surface ecotypes and the sulfidic cave ecotype compared with populations from non-sulfidic surface sites. This is perhaps due to selection imposed by H2S, which hampers oxygen uptake and transport, as well as cellular respiration. Furthermore, migrants from sulfidic habitats may lose fights even if they do not show overall reduced aggressiveness, as physiological performance is likely to be challenged in the non-sulfidic environment to which they are not adapted. To test this hypothesis, we simulated migration of H2S-adapted males into H2S-free waters, as well as H2S-adapted cave-dwelling males into sulfidic surface waters. We found that intruders established dominance less often than resident males, independent of whether or not they showed reduced aggressiveness overall. Our study shows that divergent evolution of male aggressive behavior may also contribute to the maintenance of genetic differentiation in this system and we call for more careful evaluation of male fighting abilities in studies on ecological speciation.
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Affiliation(s)
- David Bierbach
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), 86150 Villahermosa, Tabasco, México
| | - Martin Plath
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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32
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Brady SP, Monosson E, Matson CW, Bickham JW. Evolutionary toxicology: Toward a unified understanding of life's response to toxic chemicals. Evol Appl 2017; 10:745-751. [PMID: 29151867 PMCID: PMC5680415 DOI: 10.1111/eva.12519] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Steven P Brady
- Biology Department Southern Connecticut State University New Haven CT USA
| | - Emily Monosson
- The Ronin Institute for Independent Scholars and Department of Environmental Conservation University of Massachusetts Amherst MA USA
| | - Cole W Matson
- Department of Environmental Science and Center for Reservoir and Aquatic Systems Research (CRASR) Baylor University Waco TX USA
| | - John W Bickham
- Department of Wildlife & Fisheries Sciences Texas A&M University College Station College Station TX USA
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33
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Passow CN, Arias-Rodriguez L, Tobler M. Convergent evolution of reduced energy demands in extremophile fish. PLoS One 2017; 12:e0186935. [PMID: 29077740 PMCID: PMC5659789 DOI: 10.1371/journal.pone.0186935] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 10/10/2017] [Indexed: 11/19/2022] Open
Abstract
Convergent evolution in organismal function can arise from nonconvergent changes in traits that contribute to that function. Theory predicts that low resource availability and high maintenance costs in extreme environments select for reductions in organismal energy demands, which could be attained through modifications of body size or metabolic rate. We tested for convergence in energy demands and underlying traits by investigating livebearing fish (genus Poecilia) that have repeatedly colonized toxic, hydrogen sulphide-rich springs. We quantified variation in body size and routine metabolism across replicated sulphidic and non-sulphidic populations in nature, modelled total organismal energy demands, and conducted a common-garden experiment to test whether population differences had a genetic basis. Sulphidic populations generally exhibited smaller body sizes and lower routine metabolic rates compared to non-sulphidic populations, which together caused significant reductions in total organismal energy demands in extremophile populations. Although both mechanisms contributed to variation in organismal energy demands, variance partitioning indicated reductions of body size overall had a greater effect than reductions of routine metabolism. Finally, population differences in routine metabolism documented in natural populations were maintained in common-garden reared individuals, indicating evolved differences. In combination with other studies, these results suggest that reductions in energy demands may represent a common theme in adaptation to physiochemical stressors. Selection for reduced energy demand may particularly affect body size, which has implications for life history evolution in extreme environments.
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Affiliation(s)
- Courtney N. Passow
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
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34
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Passow CN, Henpita C, Shaw JH, Quackenbush CR, Warren WC, Schartl M, Arias-Rodriguez L, Kelley JL, Tobler M. The roles of plasticity and evolutionary change in shaping gene expression variation in natural populations of extremophile fish. Mol Ecol 2017; 26:6384-6399. [PMID: 28926156 DOI: 10.1111/mec.14360] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/22/2022]
Abstract
The notorious plasticity of gene expression responses and the complexity of environmental gradients complicate the identification of adaptive differences in gene regulation among populations. We combined transcriptome analyses in nature with common-garden and exposure experiments to establish cause-effect relationships between the presence of a physiochemical stressor and expression differences, as well as to test how evolutionary change and plasticity interact to shape gene expression variation in natural systems. We studied two evolutionarily independent population pairs of an extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulphide (H2 S)-rich springs and adjacent nontoxic habitats and assessed genomewide expression patterns of wild-caught and common-garden-raised individuals exposed to different concentrations of H2 S. We found that 7.7% of genes that were differentially expressed between sulphidic and nonsulphidic ecotypes remained differentially expressed in the laboratory, indicating that sources of selection other than H2 S-or plastic responses to other environmental factors-contribute substantially to gene expression patterns observed in the wild. Concordantly differentially expressed genes in the wild and the laboratory were primarily associated with H2 S detoxification, sulphur processing and metabolic physiology. While shared, ancestral plasticity played a minor role in shaping gene expression variation observed in nature, we documented evidence for evolved population differences in the constitutive expression as well as the H2 S inducibility of candidate genes. Mechanisms underlying gene expression variation also varied substantially across the two ecotype pairs. These results provide a springboard for studying evolutionary modifications of gene regulatory mechanisms that underlie expression variation in locally adapted populations.
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Affiliation(s)
| | - Chathurika Henpita
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Jennifer H Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Manfred Schartl
- Physiological Chemistry, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.,Hagler Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, TX, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, México
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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35
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Brown AP, Greenway R, Morgan S, Quackenbush CR, Giordani L, Arias-Rodriguez L, Tobler M, Kelley JL. Genome-scale data reveal that endemic Poecilia populations from small sulphidic springs display no evidence of inbreeding. Mol Ecol 2017; 26:4920-4934. [PMID: 28731545 DOI: 10.1111/mec.14249] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/04/2017] [Accepted: 06/21/2017] [Indexed: 12/27/2022]
Abstract
Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulphide-rich springs in southern Mexico, are examples of such populations with inherently small habitats. We used geometric morphometrics and population genetics to quantify phenotypic and genetic variation within and among two populations of P. sulphuraria and one population of P. thermalis. Principal component analyses revealed phenotypic and genetic differences among the populations. Evidence for inbreeding was low compared to populations that have undergone habitat reduction. The genetic data were also used to infer the demographic history of these populations to obtain estimates for effective population sizes and migration rates. Effective population sizes were large given the small habitats of these populations. Our results imply that these three endemic extremophile populations should each be considered separately for conservation purposes. Additionally, this study suggests that populations in naturally small habitats may have lower rates of inbreeding and higher genetic diversity than expected, and therefore may be better equipped to handle environmental perturbations than anticipated. We caution, however, that the inferred lack of inbreeding and the large effective population sizes could potentially be a result of colonization by genetically diverse ancestors.
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Affiliation(s)
- Anthony P Brown
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Samuel Morgan
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | | | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, México
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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36
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Oke KB, Rolshausen G, LeBlond C, Hendry AP. How Parallel Is Parallel Evolution? A Comparative Analysis in Fishes. Am Nat 2017; 190:1-16. [DOI: 10.1086/691989] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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37
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Greenway R, Drexler S, Arias‐Rodriguez L, Tobler M. Adaptive, but not condition‐dependent, body shape differences contribute to assortative mating preferences during ecological speciation. Evolution 2016; 70:2809-2822. [DOI: 10.1111/evo.13087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Ryan Greenway
- Division of Biology Kansas State University Manhattan Kansas 66506
| | - Shannon Drexler
- Department of Biology University of Wisconsin‐Platteville 1 University Plaza Platteville Wisconsin 53818
| | - Lenin Arias‐Rodriguez
- División Académica de Ciencias Biológicas Universidad Juárez Autónoma de Tabasco Villahermosa Tabasco México
| | - Michael Tobler
- Division of Biology Kansas State University Manhattan Kansas 66506
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38
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Tobler M, Passow CN, Greenway R, Kelley JL, Shaw JH. The Evolutionary Ecology of Animals Inhabiting Hydrogen Sulfide–Rich Environments. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032418] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydrogen sulfide (H2S) is a respiratory toxicant that creates extreme environments tolerated by few organisms. H2S is also produced endogenously by metazoans and plays a role in cell signaling. The mechanisms of H2S toxicity and its physiological functions serve as a basis to discuss the multifarious strategies that allow animals to survive in H2S-rich environments. Despite their toxicity, H2S-rich environments also provide ecological opportunities, and complex selective regimes of covarying abiotic and biotic factors drive trait evolution in organisms inhabiting H2S-rich environments. Furthermore, adaptation to H2S-rich environments can drive speciation, giving rise to biodiversity hot spots with high levels of endemism in deep-sea hydrothermal vents, cold seeps, and freshwater sulfide springs. The diversity of H2S-rich environments and their inhabitants provides ideal systems for comparative studies of the effects of a clear-cut source of selection across vast geographic and phylogenetic scales, ultimately informing our understanding of how environmental stressors affect ecological and evolutionary processes.
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Affiliation(s)
- Michael Tobler
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | | | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Jennifer H. Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078
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39
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Weaver PF, Tello O, Krieger J, Marmolejo A, Weaver KF, Garcia JV, Cruz A. Hypersalinity drives physiological and morphological changes in Limia perugiae (Poeciliidae). Biol Open 2016; 5:1093-101. [PMID: 27402966 PMCID: PMC5004605 DOI: 10.1242/bio.017277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/22/2016] [Indexed: 11/20/2022] Open
Abstract
A fundamental question in biology is how an organism's morphology and physiology are shaped by its environment. Here, we evaluate the effects of a hypersaline environment on the morphology and physiology of a population of livebearing fish in the genus Limia (Poeciliidae). We sampled from two populations of Limia perugiae (one freshwater and one hypersaline) in the southwest Dominican Republic. We evaluated relative abundance of osmoregulatory proteins using western blot analyses and used a geometric morphometric approach to evaluate fine-scale changes to size and shape. Our data show that gill tissue isolated from hypersaline fish contained approximately two and a half times higher expression of Na(+)/K(+) ATPase proteins. We also show evidence for mitochondrial changes within the gills, with eight times more complex I and four times higher expression of ATP synthase within the gill tissue from the hypersaline population. The energetic consequences to Limia living in saline and hypersaline environments may be a driver for phenotypic diversity, reducing the overall body size and changing the relative size and shape of the head, as well as impeding the growth of secondary sex features among the males.
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Affiliation(s)
- Pablo F Weaver
- Department of Biology, University of La Verne, 1950 3rd St., La Verne, CA 91750, USA
| | - Oscar Tello
- Department of Biology, University of La Verne, 1950 3rd St., La Verne, CA 91750, USA
| | - Jonathan Krieger
- Herbarium, Library, Art & Archives Directorate, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Arlen Marmolejo
- Instituto de Investigaciones Botánicas y Zoológicas Prof. Rafael M. Moscoso, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - Kathleen F Weaver
- Department of Biology, University of La Verne, 1950 3rd St., La Verne, CA 91750, USA
| | - Jerome V Garcia
- Department of Biology, University of La Verne, 1950 3rd St., La Verne, CA 91750, USA
| | - Alexander Cruz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309-0334, USA
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40
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Palacios M, Voelker G, Arias Rodriguez L, Mateos M, Tobler M. Phylogenetic analyses of the subgenus Mollienesia (Poecilia, Poeciliidae, Teleostei) reveal taxonomic inconsistencies, cryptic biodiversity, and spatio-temporal aspects of diversification in Middle America. Mol Phylogenet Evol 2016; 103:230-244. [PMID: 27472959 DOI: 10.1016/j.ympev.2016.07.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 07/16/2016] [Accepted: 07/22/2016] [Indexed: 01/19/2023]
Abstract
The subgenus Mollienesia is a diverse group of freshwater fishes, including species that have served as important models across multiple biological disciplines. Nonetheless, the taxonomic history of this group has been conflictive and convoluted, in part because the evolutionary relationships have not been rigorously resolved. We conducted a comprehensive molecular phylogenetic analysis of the subgenus Mollienesia to identify taxonomic discrepancies and potentially identify undescribed species, estimate ancestral areas of origin and estimate dates of divergence, as well as explore biogeographical patterns. Our findings confirm the presence of three main clades composed of the P. latipinna, P. sphenops, and P. mexicana species complexes. Unlike previously hypothesized morphology-based analyses, species found on the Caribbean Islands are not part of Mollienesia, but are more closely related to species of the subgenus Limia. Our study also revealed several taxonomic inconsistencies and distinct lineages in the P. mexicana species complex that may represent undescribed species. The diversity in the subgenus Mollienesia is a result of dynamic geologic activity leading to vicariant events, dispersal across geologic blocks, and ecological speciation.
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Affiliation(s)
- Maura Palacios
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 2258 TAMU, College Station, TX 77843, USA.
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 2258 TAMU, College Station, TX 77843, USA
| | - Lenin Arias Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150 Villahermosa, Tabasco, Mexico
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 2258 TAMU, College Station, TX 77843, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
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41
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Sommer-Trembo C, Bierbach D, Arias-Rodriguez L, Verel Y, Jourdan J, Zimmer C, Riesch R, Streit B, Plath M. Does personality affect premating isolation between locally-adapted populations? BMC Evol Biol 2016; 16:138. [PMID: 27338278 PMCID: PMC4918032 DOI: 10.1186/s12862-016-0712-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 06/13/2016] [Indexed: 12/11/2022] Open
Abstract
Background One aspect of premating isolation between diverging, locally-adapted population pairs is female mate choice for resident over alien male phenotypes. Mating preferences often show considerable individual variation, and whether or not certain individuals are more likely to contribute to population interbreeding remains to be studied. In the Poecilia mexicana-species complex different ecotypes have adapted to hydrogen sulfide (H2S)-toxic springs, and females from adjacent non-sulfidic habitats prefer resident over sulfide-adapted males. We asked if consistent individual differences in behavioral tendencies (animal personality) predict the strength and direction of the mate choice component of premating isolation in this system. Results We characterized focal females for their personality and found behavioral measures of ‘novel object exploration’, ‘boldness’ and ‘activity in an unknown area’ to be highly repeatable. Furthermore, the interaction term between our measures of exploration and boldness affected focal females’ strength of preference (SOP) for the resident male phenotype in dichotomous association preference tests. High exploration tendencies were coupled with stronger SOPs for resident over alien mating partners in bold, but not shy, females. Shy and/or little explorative females had an increased likelihood of preferring the non-resident phenotype and thus, are more likely to contribute to rare population hybridization. When we offered large vs. small conspecific stimulus males instead, less explorative females showed stronger preferences for large male body size. However, this effect disappeared when the size difference between the stimulus males was small. Conclusions Our results suggest that personality affects female mate choice in a very nuanced fashion. Hence, population differences in the distribution of personality types could be facilitating or impeding reproductive isolation between diverging populations depending on the study system and the male trait(s) upon which females base their mating decisions, respectively. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0712-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carolin Sommer-Trembo
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, People's Republic of China. .,Department of Ecology and Evolution, J.W. Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany.
| | - David Bierbach
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, CP. 86150, Mexico
| | - Yesim Verel
- Department of Ecology and Evolution, J.W. Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Jonas Jourdan
- Department of Ecology and Evolution, J.W. Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany.,Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Claudia Zimmer
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, People's Republic of China.,Department of Ecology and Evolution, J.W. Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Rüdiger Riesch
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, TW20 0EX, UK
| | - Bruno Streit
- Department of Ecology and Evolution, J.W. Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Martin Plath
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, People's Republic of China
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42
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Riesch R, Tobler M, Lerp H, Jourdan J, Doumas T, Nosil P, Langerhans RB, Plath M. Extremophile Poeciliidae: multivariate insights into the complexity of speciation along replicated ecological gradients. BMC Evol Biol 2016; 16:136. [PMID: 27334284 PMCID: PMC4918007 DOI: 10.1186/s12862-016-0705-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/08/2016] [Indexed: 11/30/2022] Open
Abstract
Background Replicate population pairs that diverge in response to similar selective regimes allow for an investigation of (a) whether phenotypic traits diverge in a similar and predictable fashion, (b) whether there is gradual variation in phenotypic divergence reflecting variation in the strength of natural selection among populations, (c) whether the extent of this divergence is correlated between multiple character suites (i.e., concerted evolution), and (d) whether gradual variation in phenotypic divergence predicts the degree of reproductive isolation, pointing towards a role for adaptation as a driver of (ecological) speciation. Here, we use poeciliid fishes of the genera Gambusia and Poecilia that have repeatedly evolved extremophile lineages able to tolerate high and sustained levels of toxic hydrogen sulfide (H2S) to answer these questions. Results We investigated evolutionary divergence in response to H2S in Gambusia spp. (and to a lesser extent Poecilia spp.) using a multivariate approach considering the interplay of life history, body shape, and population genetics (nuclear miscrosatellites to infer population genetic differentiation as a proxy for reproductive isolation). We uncovered both shared and unique patterns of evolution: most extremophile Gambusia predictably evolved larger heads and offspring size, matching a priori predictions for adaptation to sulfidic waters, while variation in adult life histories was idiosyncratic. When investigating patterns for both genera (Gambusia and Poecilia), we found that divergence in offspring-related life histories and body shape were positively correlated across populations, but evidence for individual-level associations between the two character suites was limited, suggesting that genetic linkage, developmental interdependencies, or pleiotropic effects do not explain patterns of concerted evolution. We further found that phenotypic divergence was positively correlated with both environmental H2S-concentration and neutral genetic differentiation (a proxy for gene flow). Conclusions Our results suggest that higher toxicity exerts stronger selection, and that divergent selection appears to constrain gene flow, supporting a scenario of ecological speciation. Nonetheless, progress toward ecological speciation was variable, partially reflecting variation in the strength of divergent selection, highlighting the complexity of selective regimes even in natural systems that are seemingly governed by a single, strong selective agent. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0705-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rüdiger Riesch
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK. .,Department of Biological Sciences & W. M. Keck Center for Behavioral Biology, North Carolina State University, 127 David Clark Labs, Raleigh, NC, 27695-7617, USA.
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS, 66506, USA
| | - Hannes Lerp
- Natural History Collections, Museum Wiesbaden, Friedrich-Ebert-Allee 2, 65185, Wiesbaden, Germany
| | - Jonas Jourdan
- J. W. Goethe-University Frankfurt/M., Evolutionary Ecology Group, Max-von-Laue Str. 13, 60438, Frankfurt a. M., Germany
| | - Tess Doumas
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd., Houston, TX, 77004, USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - R Brian Langerhans
- Department of Biological Sciences & W. M. Keck Center for Behavioral Biology, North Carolina State University, 127 David Clark Labs, Raleigh, NC, 27695-7617, USA
| | - Martin Plath
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22, Yangling, 712100, People's Republic of China
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Schulz‐Mirbach T, Eifert C, Riesch R, Farnworth MS, Zimmer C, Bierbach D, Klaus S, Tobler M, Streit B, Indy JR, Arias‐Rodriguez L, Plath M. Toxic hydrogen sulphide shapes brain anatomy: a comparative study of sulphide‐adapted ecotypes in the
Poecilia mexicana
complex. J Zool (1987) 2016. [DOI: 10.1111/jzo.12366] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- T. Schulz‐Mirbach
- Department Biology II Ludwig‐Maximilians‐University Munich Planegg‐Martinsried Germany
| | - C. Eifert
- Ecology and Evolution J. W. Goethe University Frankfurt Frankfurt am Main Germany
| | - R. Riesch
- School of Biological Sciences Royal Holloway University of London Egham UK
| | - M. S. Farnworth
- Göttingen Center for Molecular Biosciences Georg‐August‐University Göttingen Göttingen Germany
| | - C. Zimmer
- Ecology and Evolution J. W. Goethe University Frankfurt Frankfurt am Main Germany
| | - D. Bierbach
- Department of Biology and Ecology of Fishes Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - S. Klaus
- Ecology and Evolution J. W. Goethe University Frankfurt Frankfurt am Main Germany
| | - M. Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - B. Streit
- Ecology and Evolution J. W. Goethe University Frankfurt Frankfurt am Main Germany
| | - J. R. Indy
- División Académica de Ciencias Biológicas Universidad Juárez Autónoma de Tabasco (UJAT) Villahermosa Tabasco México
| | - L. Arias‐Rodriguez
- División Académica de Ciencias Biológicas Universidad Juárez Autónoma de Tabasco (UJAT) Villahermosa Tabasco México
| | - M. Plath
- College of Animal Science and Technology Northwest A&F University Yangling China
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Pfenninger M, Patel S, Arias-Rodriguez L, Feldmeyer B, Riesch R, Plath M. Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats of a neotropical fish (Poecilia mexicana). Mol Ecol 2016; 24:5446-59. [PMID: 26405850 DOI: 10.1111/mec.13397] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/05/2015] [Accepted: 09/22/2015] [Indexed: 12/20/2022]
Abstract
Replicated ecological gradients are prime systems to study processes of molecular evolution underlying ecological divergence. Here, we investigated the repeated adaptation of the neotropical fish Poecilia mexicana to habitats containing toxic hydrogen sulphide (H2 S) and compared two population pairs of sulphide-adapted and ancestral fish by sequencing population pools of >200 individuals (Pool-Seq). We inferred the evolutionary processes shaping divergence and tested the hypothesis of increase of parallelism from SNPs to molecular pathways. Coalescence analyses showed that the divergence occurred in the face of substantial bidirectional gene flow. Population divergence involved many short, widely dispersed regions across the genome. Analyses of allele frequency spectra suggest that differentiation at most loci was driven by divergent selection, followed by a selection-mediated reduction of gene flow. Reconstructing allelic state changes suggested that selection acted mainly upon de novo mutations in the sulphide-adapted populations. Using a corrected Jaccard index to quantify parallel evolution, we found a negligible proportion of statistically significant parallel evolution of Jcorr = 0.0032 at the level of SNPs, divergent genome regions (Jcorr = 0.0061) and genes therein (Jcorr = 0.0091). At the level of metabolic pathways, the overlap was Jcorr = 0.2545, indicating increasing parallelism with increasing level of biological integration. The majority of pathways contained positively selected genes in both sulphide populations. Hence, adaptation to sulphidic habitats necessitated adjustments throughout the genome. The largely unique evolutionary trajectories may be explained by a high proportion of de novo mutations driving the divergence. Our findings favour Gould's view that evolution is often the unrepeatable result of stochastic events with highly contingent effects.
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Affiliation(s)
- Markus Pfenninger
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Hessen, Germany
| | - Simit Patel
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Hessen, Germany
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, C.P. 86150 Tabasco, México
| | - Barbara Feldmeyer
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Hessen, Germany
| | - Rüdiger Riesch
- School of Biological Sciences, Centre for Ecology, Evolution and Behaviour, Royal Holloway University of London, Egham Hill, Egham, Surrey TW20 0EX, UK
| | - Martin Plath
- College of Animal Science and Technology, Northwest A&F University, Xinong Road 22, 712100 Yangling, China
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45
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Sex-specific local life-history adaptation in surface- and cave-dwelling Atlantic mollies (Poecilia mexicana). Sci Rep 2016; 6:22968. [PMID: 26960566 PMCID: PMC4785371 DOI: 10.1038/srep22968] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/22/2016] [Indexed: 11/08/2022] Open
Abstract
Cavefishes have long been used as model organisms showcasing adaptive diversification, but does adaptation to caves also facilitate the evolution of reproductive isolation from surface ancestors? We raised offspring of wild-caught surface- and cave-dwelling ecotypes of the neotropical fish Poecilia mexicana to sexual maturity in a 12-month common garden experiment. Fish were raised under one of two food regimes (high vs. low), and this was crossed with differences in lighting conditions (permanent darkness vs. 12:12 h light:dark cycle) in a 2 × 2 factorial design, allowing us to elucidate potential patterns of local adaptation in life histories. Our results reveal a pattern of sex-specific local life-history adaptation: Surface molly females had the highest fitness in the treatment best resembling their habitat of origin (high food and a light:dark cycle), and suffered from almost complete reproductive failure in darkness, while cave molly females were not similarly affected in any treatment. Males of both ecotypes, on the other hand, showed only weak evidence for local adaptation. Nonetheless, local life-history adaptation in females likely contributes to ecological diversification in this system and other cave animals, further supporting the role of local adaptation due to strong divergent selection as a major force in ecological speciation.
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46
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Culumber ZW, Tobler M. Ecological divergence and conservatism: spatiotemporal patterns of niche evolution in a genus of livebearing fishes (Poeciliidae: Xiphophorus). BMC Evol Biol 2016; 16:44. [PMID: 26895994 PMCID: PMC4761163 DOI: 10.1186/s12862-016-0593-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/13/2016] [Indexed: 01/23/2023] Open
Abstract
Background Ecological factors often have a strong impact on spatiotemporal patterns of biodiversity. The integration of spatial ecology and phylogenetics allows for rigorous tests of whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence. We address this question in a genus of livebearing fishes for which the role of sexual selection in speciation has long been studied, but in which the potential role of ecological divergence during speciation has not been tested. Results By combining reconstruction of ancestral climate tolerances and disparity indices, we show that the earliest evolutionary split in Xiphophorus was associated with significant divergence for temperature variables. Niche evolution and present day niches were most closely associated with each species’ geographic distribution relative to a biogeographic barrier, the Trans-Mexican Volcanic Belt. Tests for similarity of the environmental backgrounds of closely related species suggested that the relative importance of niche conservatism and divergence during speciation varied among the primary clades of Xiphophorus. Closely related species in the two swordtail clades exhibited higher levels of niche overlap than expected given environmental background similarity indicative of niche conservatism. In contrast, almost all species of platyfish had significantly divergent niches compared to environmental backgrounds, which is indicative of niche divergence. Conclusion The results suggest that the relative importance of niche conservatism and divergence differed among the clades of Xiphophorus and that traits associated with niche evolution may be more evolutionarily labile in the platyfishes. Our results ultimately suggest that the taxonomic scale of tests for conservatism and divergence could greatly influence inferences of their relative importance in the speciation process. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0593-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zachary W Culumber
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
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47
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Kelley JL, Arias-Rodriguez L, Patacsil Martin D, Yee MC, Bustamante CD, Tobler M. Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments. Mol Biol Evol 2016; 33:1419-34. [PMID: 26861137 PMCID: PMC4868117 DOI: 10.1093/molbev/msw020] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hydrogen sulfide (H2S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H2S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H2S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Variation in the number of differentially expressed genes among population pairs corresponded to differences in divergence times and rates of gene flow, which is consistent with neutral drift driving a substantial portion of gene expression variation among populations. Accordingly, there was little evidence for convergent evolution shaping large-scale gene expression patterns among independent sulfide spring populations. Nonetheless, we identified a small number of genes that was consistently differentially expressed in the same direction in all sulfidic and nonsulfidic population pairs. Functional annotation of shared differentially expressed genes indicated upregulation of genes associated with enzymatic H2S detoxification and transport of oxidized sulfur species, oxidative phosphorylation, energy metabolism, and pathways involved in responses to oxidative stress. Overall, our results suggest that modification of processes associated with H2S detoxification and toxicity likely complement each other to mediate elevated H2S tolerance in sulfide spring fishes. Our analyses allow for the development of novel hypotheses about biochemical and physiological mechanisms of adaptation to extreme environments.
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Affiliation(s)
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | | | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA
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48
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Jansen M, Plath M, Brusquetti F, Ryan MJ. Asymmetric frequency shift in advertisement calls of sympatric frogs. AMPHIBIA-REPTILIA 2016. [DOI: 10.1163/15685381-00003038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Character displacement is commonly observed when species occur in secondary contact zones and traits related to resource competition or reproduction diverge in sympatry. However, few studies have considered the factors determining and delimiting the direction of character evolution in this context. We studied displacement in advertisement calls in two species of hylid frogs from allopatric and sympatric populations, both of which call with similar frequencies but differ substantially in temporal parameters. We found asymmetrical character displacement in sympatry, as only Scinax madeirae (but not S. fuscomarginatus) repeatedly showed displacement. Instead of diverging in already existing differences in temporal characters, S. madeirae showed character displacement for frequency-related characters. We explored possible reasons for this specific pattern concerning the displaced characters and tested if socio-functional constraints in specific call parameters are responsible for the shift of only spectral parameters in that species. Finally, we argue that the simultaneous action of ecological and reproductive character displacement, or alternatively, a short-term behavioral response for the same reason (avoidance of hybridization) could explain the pattern. The present study identifies a set of new hypotheses that will stimulate future research on mechanisms of mate recognition and behavioral responses.
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Affiliation(s)
- Martin Jansen
- Section of Herpetology, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Section of Integrative Biology, University Station C0930, University of Texas, Austin, TX 78712, USA
| | - Martin Plath
- Department of Animal Science, Northwest A & F University, Shaanxi, China
| | - Francisco Brusquetti
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Cx. Postal 199, 13506-906 Rio Claro, São Paulo, Brasil
- Instituto de Investigación Biológica del Paraguay, CP 1429, Asunción, Paraguay
| | - Michael Joseph Ryan
- Section of Integrative Biology, University Station C0930, University of Texas, Austin, TX 78712, USA
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49
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Rolshausen G, Phillip DAT, Beckles DM, Akbari A, Ghoshal S, Hamilton PB, Tyler CR, Scarlett AG, Ramnarine I, Bentzen P, Hendry AP. Do stressful conditions make adaptation difficult? Guppies in the oil-polluted environments of southern Trinidad. Evol Appl 2015; 8:854-70. [PMID: 26495039 PMCID: PMC4610383 DOI: 10.1111/eva.12289] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/26/2015] [Indexed: 12/27/2022] Open
Abstract
The ability of populations to rapidly adapt to new environments will determine their future in an increasingly human-modified world. Although meta-analyses do frequently uncover signatures of local adaptation, they also reveal many exceptions. We suggest that particular constraints on local adaptation might arise when organisms are exposed to novel stressors, such as anthropogenic pollution. To inform this possibility, we studied the extent to which guppies (Poecilia reticulata) show local adaptation to oil pollution in southern Trinidad. Neutral genetic markers revealed that paired populations in oil-polluted versus not-polluted habitats diverged independently in two different watersheds. Morphometrics revealed some divergence (particularly in head shape) between these environments, some of which was parallel between rivers. Reciprocal transplant experiments in nature, however, found little evidence of local adaptation based on survival and growth. Moreover, subsequent laboratory experiments showed that the two populations from oil-polluted sites showed only weak local adaptation even when compared to guppies from oil-free northern Trinidad. We conclude that guppies show little local adaptation to oil pollution, which might result from the challenges associated with adaptation to particularly stressful environments. It might also reflect genetic drift owing to small population sizes and/or high gene flow between environments.
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Affiliation(s)
- Gregor Rolshausen
- Redpath Museum and Department of Biology, McGill University Montreal, QC, Canada
| | - Dawn A T Phillip
- Department of Life Sciences, The University of the West Indies St. Augustine, Trinidad and Tobago
| | - Denise M Beckles
- Department of Chemistry, The University of the West Indies St. Augustine, Trinidad and Tobago
| | - Ali Akbari
- Department of Civil Engineering and Applied Mechanics, McGill University Montreal, QC, Canada
| | - Subhasis Ghoshal
- Department of Civil Engineering and Applied Mechanics, McGill University Montreal, QC, Canada
| | | | | | - Alan G Scarlett
- Biochemistry Research Center, University of Plymouth Drake Circus, Plymouth, UK
| | - Indar Ramnarine
- Department of Life Sciences, The University of the West Indies St. Augustine, Trinidad and Tobago
| | - Paul Bentzen
- Department of Biology, Dalhousie University Halifax, NS, Canada
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University Montreal, QC, Canada
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50
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Fišer C, Luštrik R, Sarbu S, Flot JF, Trontelj P. Morphological evolution of coexisting amphipod species pairs from sulfidic caves suggests competitive interactions and character displacement, but no environmental filtering and convergence. PLoS One 2015; 10:e0123535. [PMID: 25905793 PMCID: PMC4407961 DOI: 10.1371/journal.pone.0123535] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/19/2015] [Indexed: 11/18/2022] Open
Abstract
Phenotypically similar species coexisting in extreme environments like sulfidic water are subject to two opposing eco-evolutionary processes: those favoring similarity of environment-specific traits, and those promoting differences of traits related to resource use. The former group of processes includes ecological filtering and convergent or parallel evolution, the latter competitive exclusion, character displacement and divergent evolution. We used a unique eco-evolutionary study system composed of two independent pairs of coexisting amphipod species (genus Niphargus) from the sulfidic caves Movile in Romania and Frasassi in Italy to study the relative contribution and interaction of both processes. We looked at the shape of the multifunctional ventral channel as a trait ostensibly related to oxygenation and sulfide detoxification, and at body size as a resource-related trait. Phylogenetic analysis suggests that the sulfidic caves were colonized separately by ancestors of each species. Species within pairs were more dissimilar in their morphology than expected according to a null model based on regional species pool. This might indicate competitive interactions shaping the morphology of these amphipod species. Moreover, our results suggest that the shape of the ventral channel is not subject to long-term convergent selection or to the process of environmental filtering, and as such probably does not play a role in sulfide tolerance. Nevertheless, the ancestral conditions reconstructed using the comparative method tended to be more similar than null-model expectations. This shift in patterns may reflect a temporal hierarchy of eco-evolutionary processes, in which initial environmental filtering became later on superseded by character displacement or other competition-driven divergent evolutionary processes.
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Affiliation(s)
- Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- * E-mail:
| | - Roman Luštrik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Serban Sarbu
- Grupul de Explorări Subacvatice şi Speologice, Strada Frumoasă 31, 010986 Bucureşti, Romania
| | - Jean-François Flot
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Peter Trontelj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstrasse 43, Berlin 10115, Germany
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