1
|
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.
Collapse
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
| |
Collapse
|
2
|
Ryan K, Greenway R, Landers J, Arias-Rodriguez L, Tobler M, Kelley JL. Selection on standing genetic variation mediates convergent evolution in extremophile fish. Mol Ecol 2023; 32:5042-5054. [PMID: 37548336 DOI: 10.1111/mec.17081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.
Collapse
Affiliation(s)
- Kara Ryan
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Ryan Greenway
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Constance, Germany
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Jake Landers
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Mexico
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA
| |
Collapse
|
3
|
Cobo-Simón I, Maloof JN, Li R, Amini H, Méndez-Cea B, García-García I, Gómez-Garrido J, Esteve-Codina A, Dabad M, Alioto T, Wegrzyn JL, Seco JI, Linares JC, Gallego FJ. Contrasting transcriptomic patterns reveal a genomic basis for drought resilience in the relict fir Abies pinsapo Boiss. TREE PHYSIOLOGY 2023; 43:315-334. [PMID: 36210755 DOI: 10.1093/treephys/tpac115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Climate change challenges the adaptive capacity of several forest tree species in the face of increasing drought and rising temperatures. Therefore, understanding the mechanistic connections between genetic diversity and drought resilience is highly valuable for conserving drought-sensitive forests. Nonetheless, the post-drought recovery in trees from a transcriptomic perspective has not yet been studied by comparing contrasting phenotypes. Here, experimental drought treatments, gas-exchange dynamics and transcriptomic analysis (RNA-seq) were performed in the relict and drought-sensitive fir Abies pinsapo Boiss. to identify gene expression differences over immediate (24 h) and extended drought (20 days). Post-drought responses were investigated to define resilient and sensitive phenotypes. Single nucleotide polymorphisms (SNPs) were also studied to characterize the genomic basis of A. pinsapo drought resilience. Weighted gene co-expression network analysis showed an activation of stomatal closing and an inhibition of plant growth-related genes during the immediate drought, consistent with an isohydric dynamic. During the extended drought, transcription factors, as well as cellular damage and homeostasis protection-related genes prevailed. Resilient individuals activate photosynthesis-related genes and inhibit aerial growth-related genes, suggesting a shifting shoot/root biomass allocation to improve water uptake and whole-plant carbon balance. About, 152 fixed SNPs were found between resilient and sensitive seedlings, which were mostly located in RNA-activity-related genes, including epigenetic regulation. Contrasting gene expression and SNPs were found between different post-drought resilience phenotypes for the first time in a forest tree, suggesting a transcriptomic and genomic basis for drought resilience. The obtained drought-related transcriptomic profile and drought-resilience candidate genes may guide conservation programs for this threatened tree species.
Collapse
Affiliation(s)
- Irene Cobo-Simón
- Dpto Sistemas Físicos, Químicos y Naturales, Univ. Pablo de Olavide, 41013 Sevilla, Spain
- Dpto Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid 28040, Spain
| | - Julin N Maloof
- University of California at Davis, Department of Plant Biology, Davis, CA 95616, USA
| | - Ruijuan Li
- University of California at Davis, Department of Plant Biology, Davis, CA 95616, USA
| | - Hajar Amini
- University of California at Davis, Department of Plant Biology, Davis, CA 95616, USA
| | - Belén Méndez-Cea
- Dpto Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid 28040, Spain
| | - Isabel García-García
- Dpto Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid 28040, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - José Ignacio Seco
- Dpto Sistemas Físicos, Químicos y Naturales, Univ. Pablo de Olavide, 41013 Sevilla, Spain
| | - Juan Carlos Linares
- Dpto Sistemas Físicos, Químicos y Naturales, Univ. Pablo de Olavide, 41013 Sevilla, Spain
| | - Francisco Javier Gallego
- Dpto Genética, Fisiología y Microbiología, Unidad de Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid 28040, Spain
| |
Collapse
|
4
|
Sun Y, Wang M, Zhong Z, Chen H, Wang H, Zhou L, Cao L, Fu L, Zhang H, Lian C, Sun S, Li C. Adaption to hydrogen sulfide-rich environments: Strategies for active detoxification in deep-sea symbiotic mussels, Gigantidas platifrons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150054. [PMID: 34509839 DOI: 10.1016/j.scitotenv.2021.150054] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 05/27/2023]
Abstract
The deep-sea mussel Gigantidas platifrons is a representative species that relies on nutrition provided by chemoautotrophic endosymbiotic bacteria to survive in both hydrothermal vent and methane seep environments. However, vent and seep habitats have distinct geochemical features, with vents being more harsh than seeps because of abundant toxic chemical substances, particularly hydrogen sulfide (H2S). Until now, the adaptive strategies of G. platifrons in a heterogeneous environment and their sulfide detoxification mechanisms are still unclear. Herein, we conducted 16S rDNA sequencing and metatranscriptome sequencing of G. platifrons collected from a methane seep at Formosa Ridge in the South China Sea and a hydrothermal vent at Iheya North Knoll in the Mid-Okinawa Trough to provide a model for understanding environmental adaption and sulfide detoxification mechanisms, and a three-day laboratory controlled Na2S stress experiment to test the transcriptomic responses under sulfide stress. The results revealed the active detoxification of sulfide in G. platifrons gills. First, epibiotic Campylobacterota bacteria were more abundant in vent mussels and contributed to environmental adaptation by active oxidation of extracellular H2S. Notably, a key sulfide-oxidizing gene, sulfide:quinone oxidoreductase (sqr), derived from the methanotrophic endosymbiont, was significantly upregulated in vent mussels, indicating the oxidization of intracellular sulfide by the endosymbiont. In addition, transcriptomic comparison further suggested that genes involved in oxidative phosphorylation and mitochondrial sulfide oxidization pathway played important roles in the sulfide tolerance of the host mussels. Moreover, transcriptomic analysis of Na2S stressed mussels confirmed the upregulation of oxidative phosphorylation and sulfide oxidization genes in response to sulfide exposure. Overall, this study provided a systematic transcriptional analysis of both the active bacterial community members and the host mussels, suggesting that the epibionts, endosymbionts, and mussel host collaborated on sulfide detoxification from extracellular to intracellular space to adapt to harsh H2S-rich environments.
Collapse
Affiliation(s)
- Yan Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Minxiao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhaoshan Zhong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hao Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lei Cao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lulu Fu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Huan Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chao Lian
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Song Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 10049, China.
| | - Chaolun Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 10049, China.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus. Genes (Basel) 2019; 11:genes11010042. [PMID: 31905778 PMCID: PMC7016750 DOI: 10.3390/genes11010042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 12/18/2022] Open
Abstract
Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.
Collapse
|
7
|
Mead A, Peñaloza Ramirez J, Bartlett MK, Wright JW, Sack L, Sork VL. Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations. Mol Ecol 2019; 28:5248-5264. [PMID: 31652373 DOI: 10.1111/mec.15289] [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: 06/23/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/16/2022]
Abstract
Drought is a major stress for plants, creating a strong selection pressure for traits that enable plant growth and survival in dry environments. Many drought responses are conserved species-wide responses, while others vary among populations distributed across heterogeneous environments. We tested how six populations of the widely distributed California valley oak (Quercus lobata) sampled from contrasting climates would differ in their response to soil drying relative to well-watered controls in a common environment by measuring ecophysiological traits in 93 individuals and gene expression (RNA-seq) in 42 individuals. Populations did not differ in their adjustment of turgor loss point during soil drying, suggesting a generalized species-wide response. Differential expression analysis identified 689 genes with a common response to treatment across populations and 470 genes with population-specific responses. Weighted gene co-expression network analysis (WGCNA) identified groups of genes with similar expression patterns that may be regulated together (gene modules). Several gene modules responded differently to water stress among populations, suggesting regional differences in gene network regulation. Populations from sites with a high mean annual temperature responded to the imposed water stress with significantly greater changes in gene module expression, indicating that these populations may be locally adapted to respond to drought. We propose that this variation among valley oak populations provides a mechanism for differential tolerance to the increasingly frequent and severe droughts in California.
Collapse
Affiliation(s)
- Alayna Mead
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Juan Peñaloza Ramirez
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Megan K Bartlett
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jessica W Wright
- USDA Forest Service, Pacific Southwest Research Station, Davis, CA, USA
| | - Lawren Sack
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA.,Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA.,Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
8
|
McGowan KL, Passow CN, Arias-Rodriguez L, Tobler M, Kelley JL. Expression analyses of cave mollies ( Poecilia mexicana) reveal key genes involved in the early evolution of eye regression. Biol Lett 2019; 15:20190554. [PMID: 31640527 DOI: 10.1098/rsbl.2019.0554] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Eye regression occurs across cave-dwelling populations of many species and is often coupled with a decrease or loss in eye function. Teleost fishes are among the few vertebrates to undergo widespread colonization of caves and often exhibit eye regression with blindness. Cave populations of the poeciliid fish Poecilia mexicana (cave molly) exhibit reduced-albeit functional-eyes, offering the opportunity to investigate partial eye regression. We sequenced eye transcriptomes of cave and surface populations of P. mexicana to identify differentially expressed genes that potentially underlie eye regression in cave mollies. We identified 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signaling. Twenty-six of these genes were downregulated in cave compared to surface populations. Functional enrichment analysis revealed eye-related gene ontologies that were under-represented in cave mollies. In addition, a set of co-expressed genes related to vision and circadian rhythm was correlated with habitat type (cave versus surface). Our study suggests that differential gene expression plays a key role in the beginning evolutionary stages of eye regression in P. mexicana, shedding further light on regressive evolution in cavefish.
Collapse
Affiliation(s)
- Kerry L McGowan
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Courtney N Passow
- Department of Ecology, Evolution and Behavior, University of Minnesota-Twin Cities, St. Paul, MN 55108, USA.,Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco 86150, Mexico
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| |
Collapse
|
9
|
Lou F, Han Z, Gao T. Transcriptomic Responses of Two Ecologically Divergent Populations of Japanese Mantis Shrimp ( Oratosquilla oratoria) under Thermal Stress. Animals (Basel) 2019; 9:ani9070399. [PMID: 31262058 PMCID: PMC6680513 DOI: 10.3390/ani9070399] [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: 03/04/2019] [Accepted: 06/28/2019] [Indexed: 01/12/2023] Open
Abstract
Simple Summary Rising ocean temperature would change the seawater chemistry and affect the external and internal physiology of crustaceans due to their lack of certain efficient temperature regulators. In addition, the infraspecific populations of crustaceans might also have different response strategies to the rising of temperature. Therefore, we identified the transcriptomic variations to the same thermal stress between ecologically divergent populations of Oratosquilla oratoria. The aim of this study was to investigate the population-specific function genes and relevant pathways in response to thermal stress in O. oratoria. The results showed that gene-expressed variation was in a population-specific pattern, which indicated that the local environment could lead to the evolvement of changes in gene regulation, ultimately leading to adaptive divergences. Additionally, we found several genes with large pleiotropic effects in the Zhoushan population, which might indicate that the regulation mechanisms of the Zhoushan population were more efficient than those of the Qingdao population under same thermal stress. The results provided some novel insights into the local adaptive differences of the infraspecific populations of O. oratoria and other crustaceans. Abstract Crustaceans are generally considered more sensitive to ocean warming due to their lack of certain efficient regulators. However, the alterations in the physiology and behavior of crustaceans in response to thermal stress differ vastly even among the infraspecific populations of heterogeneous landscapes. Consequently, understanding the impact of temperature fluctuation on crustacean infraspecific populations might be essential for maintaining a sustainable persistence of populations at existing locations. In the present study, we chose the Japanese mantis shrimp (Oratosquilla oratoria) as the representative crustacean population, and conducted transcriptome analyses in two divergent O. oratoria populations (the Zhoushan and Qingdao populations) under same thermal stress (20–28 °C) to identify the population-specific expression response to thermal stress. The results showed significant differences in gene expressions, GO terms and metabolic pathways between the two populations. We hypothesized that intraspecific mutations in the same or different genes might lead to thermal adaptive divergences. Temperature increases from 20–28 °C produced significant enrichment in GO terms and altered the metabolic pathways in the Zhoushan population despite the lack of differentially expressed unigenes. Therefore, several functional genes with large pleiotropic effects may underlie the response to thermal stress in the Zhoushan population. Furthermore, the most significantly enriched biological processes of the Qingdao population were associated with the state or activity of cells and its significant enriched pathways with genetic information processing as well as immune and environmental information processing. In contrast, the differentially regulated unigenes of the Zhoushan population were primarily involved in the regulatory cellular and transcription processes and the most significant pathways found were metabolic and digestive. Consequently, the regulatory mechanisms of the Zhoushan population are probably more efficient than those of the Qingdao population under the same thermal stress.
Collapse
Affiliation(s)
- Fangrui Lou
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China
- Fishery College, Ocean University of China, Qingdao 266003, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan 316022, China.
| |
Collapse
|
10
|
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'.
Collapse
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
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|