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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 DOI: 10.1093/gbe/evae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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3
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Lukas J, Krause J, Träger AS, Piotrowski JM, Romanczuk P, Sprekeler H, Arias-Rodriguez L, Krause S, Schutz C, Bierbach D. Multispecies collective waving behaviour in fish. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220069. [PMID: 36802783 PMCID: PMC9939262 DOI: 10.1098/rstb.2022.0069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/20/2022] [Indexed: 02/21/2023] Open
Abstract
Collective behaviour is widely accepted to provide a variety of antipredator benefits. Acting collectively requires not only strong coordination among group members, but also the integration of among-individual phenotypic variation. Therefore, groups composed of more than one species offer a unique opportunity to look into the evolution of both mechanistic and functional aspects of collective behaviour. Here, we present data on mixed-species fish shoals that perform collective dives. These repeated dives produce water waves capable of delaying and/or reducing the success of piscivorous bird attacks. The large majority of the fish in these shoals consist of the sulphur molly, Poecilia sulphuraria, but we regularly also found a second species, the widemouth gambusia, Gambusia eurystoma, making these shoals mixed-species aggregations. In a set of laboratory experiments, we found that gambusia were much less inclined to dive after an attack as compared with mollies, which almost always dive, though mollies dived less deep when paired with gambusia that did not dive. By contrast, the behaviour of gambusia was not influenced by the presence of diving mollies. The dampening effect of less responsive gambusia on molly diving behaviour can have strong evolutionary consequences on the overall collective waving behaviour as we expect shoals with a high proportion of unresponsive gambusia to be less effective at producing repeated waves. This article is part of a discussion meeting issue 'Collective behaviour through time'.
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Affiliation(s)
- Juliane Lukas
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
| | - Jens Krause
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
- Cluster of Excellence ‘Science of Intelligence’, Technical University of Berlin, Marchstrasse 23, 10587 Berlin, Germany
| | - Arabella Sophie Träger
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Jonas Marc Piotrowski
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Cluster of Excellence ‘Science of Intelligence’, Technical University of Berlin, Marchstrasse 23, 10587 Berlin, Germany
| | - Pawel Romanczuk
- Cluster of Excellence ‘Science of Intelligence’, Technical University of Berlin, Marchstrasse 23, 10587 Berlin, Germany
- Department of Biology, Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Philippstrasse 13, 10115 Berlin, Germany
| | - Henning Sprekeler
- Cluster of Excellence ‘Science of Intelligence’, Technical University of Berlin, Marchstrasse 23, 10587 Berlin, Germany
- Institute of Software Engineering and Theoretical Computer Science, Berlin Institute of Technology, 10587 Berlin, Germany
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma Tabasco, 86150 Villahermosa, Mexico
| | - Stefan Krause
- Department of Electrical Engineering and Computer Science, Lübeck University of Applied Sciences, 23562 Lübeck, Germany
| | - Christopher Schutz
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Cluster of Excellence ‘Science of Intelligence’, Technical University of Berlin, Marchstrasse 23, 10587 Berlin, Germany
| | - David Bierbach
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
- Cluster of Excellence ‘Science of Intelligence’, Technical University of Berlin, Marchstrasse 23, 10587 Berlin, Germany
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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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] [What about the content of this article? (0)] [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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Bierbach D, Krause S, Romanczuk P, Lukas J, Arias-Rodriguez L, Krause J. An interaction mechanism for the maintenance of fission-fusion dynamics under different individual densities. PeerJ 2020; 8:e8974. [PMID: 32461823 PMCID: PMC7231501 DOI: 10.7717/peerj.8974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/24/2020] [Indexed: 11/20/2022] Open
Abstract
Animals often show high consistency in their social organisation despite facing changing environmental conditions. Especially in shoaling fish, fission-fusion dynamics that describe for which periods individuals are solitary or social have been found to remain unaltered even when density changed. This compensatory ability is assumed to be an adaptation towards constant predation pressure, but the mechanism through which individuals can actively compensate for density changes is yet unknown. The aim of the current study is to identify behavioural patterns that enable this active compensation. We compared the fission-fusion dynamics of two populations of the live-bearing Atlantic molly (Poecilia mexicana) that live in adjacent habitats with very different predator regimes: cave mollies that inhabit a low-predation environment inside a sulfidic cave with a low density of predatory water bugs (Belostoma sp.), and mollies that live directly outside the cave (henceforth called "surface" mollies) in a high-predation environment. We analysed their fission-fusion dynamics under two different fish densities of 12 and 6 fish per 0.36 m2. As expected, surface mollies spent more time being social than cave mollies, and this difference in social time was a result of surface mollies being less likely to discontinue social contact (once they had a social partner) and being more likely to resume social contact (once alone) than cave mollies. Interestingly, surface mollies were also less likely to switch among social partners than cave mollies. A random walk simulation predicted each population to show reduced social encounters in the low density treatment. While cave mollies largely followed this prediction, surface mollies maintained their interaction probabilities even at low density. Surface mollies achieved this by a reduction in the size of a convex polygon formed by the group as density decreased. This may allow them to largely maintain their fission-fusion dynamics while still being able to visit large parts of the available area as a group. A slight reduction (21%) in the area visited at low densities was also observed but insufficient to explain how the fish maintained their fission-fusion dynamics. Finally, we discuss potential movement rules that could account for the reduction of polygon size and test their performance.
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Affiliation(s)
- David Bierbach
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Faculty of Life Sciences, Thaer Institute, Humboldt Universität Berlin, Berlin, Germany
| | - Stefan Krause
- Department of Electrical Engineering and Computer Science, Lübeck University of Applied Sciences, Lübeck, Germany
| | - Pawel Romanczuk
- Department of Biology, Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany
- Bernstein Center for Computational Neuroscience, Humboldt Universität Berlin, Berlin, Germany
| | - Juliane Lukas
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Faculty of Life Sciences, Thaer Institute, Humboldt Universität Berlin, Berlin, Germany
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Mexico
| | - 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 Universität Berlin, Berlin, Germany
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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8
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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. Microb Ecol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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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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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Passow CN, Brown AP, Arias-Rodriguez L, Yee MC, Sockell A, Schartl M, Warren WC, Bustamante C, Kelley JL, Tobler M. Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). Mol Ecol 2017; 26:4211-4225. [PMID: 28598519 DOI: 10.1111/mec.14198] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/18/2017] [Accepted: 05/24/2017] [Indexed: 12/31/2022]
Abstract
Variation in gene expression can provide insights into organismal responses to environmental stress and physiological mechanisms mediating adaptation to habitats with contrasting environmental conditions. We performed an RNA-sequencing experiment to quantify gene expression patterns in fish adapted to habitats with different combinations of environmental stressors, including the presence of toxic hydrogen sulphide (H2 S) and the absence of light in caves. We specifically asked how gene expression varies among populations living in different habitats, whether population differences were consistent among organs, and whether there is evidence for shared expression responses in populations exposed to the same stressors. We analysed organ-specific transcriptome-wide data from four ecotypes of Poecilia mexicana (nonsulphidic surface, sulphidic surface, nonsulphidic cave and sulphidic cave). The majority of variation in gene expression was correlated with organ type, and the presence of specific environmental stressors elicited unique expression differences among organs. Shared patterns of gene expression between populations exposed to the same environmental stressors increased with levels of organismal organization (from transcript to gene to physiological pathway). In addition, shared patterns of gene expression were more common between populations from sulphidic than populations from cave habitats, potentially indicating that physiochemical stressors with clear biochemical consequences can constrain the diversity of adaptive solutions that mitigate their adverse effects. Overall, our analyses provided insights into transcriptional variation in a unique system, in which adaptation to H2 S and darkness coincide. Functional annotations of differentially expressed genes provide a springboard for investigating physiological mechanisms putatively underlying adaptation to extreme environments.
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Affiliation(s)
| | - Anthony P Brown
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | - Muh-Ching Yee
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.,Texas A&M Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Joanna L Kelley
- Department of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
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18
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Cribbin KM, Quackenbush CR, Taylor K, Arias-Rodriguez L, Kelley JL. Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar. BMC Genomics 2017; 18:283. [PMID: 28388875 PMCID: PMC5383948 DOI: 10.1186/s12864-017-3652-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/22/2017] [Indexed: 02/06/2023] Open
Abstract
Background The tropical gar (Atractosteus tropicus) is the southernmost species of the seven extant species of gar fishes in the world. In Mexico and Central America, the species is an important food source due to its nutritional quality and low price. Despite its regional importance and increasing concerns about overexploitation and habitat degradation, basic genetic information on the tropical gar is lacking. Determining genetic information on the tropical gar is important for the sustainable management of wild populations, implementation of best practices in aquaculture settings, evolutionary studies of ancient lineages, and an understanding of sex-specific gene expression. In this study, the transcriptome of the tropical gar was sequenced and assembled de novo using tissues from three males and three females using Illumina sequencing technology. Sex-specific and highly differentially expressed transcripts in brain and muscle tissues between adult males and females were subsequently identified. Results The transcriptome was assembled de novo resulting in 80,611 transcripts with a contig N50 of 3,355 base pairs and over 168 kilobases in total length. Male muscle, brain, and gonad as well as female muscle and brain were included in the assembly. The assembled transcriptome was annotated to identify the putative function of expressed transcripts using Trinotate and SwissProt, a database of well-annotated proteins. The brain and muscle datasets were then aligned to the assembled transcriptome to identify transcripts that were differentially expressed between males and females. The contrast between male and female brain identified 109 transcripts from 106 genes that were significantly differentially expressed. In the muscle comparison, 82 transcripts from 80 genes were identified with evidence for significant differential expression. Almost all genes identified as differentially expressed were sex-specific. The differentially expressed transcripts were enriched for genes involved in cellular functioning, signaling, immune response, and tissue-specific functions. Conclusions This study identified differentially expressed transcripts between male and female gar in muscle and brain tissue. The majority of differentially expressed transcripts had sex-specific expression. Expanding on these findings to other developmental stages, populations, and species may lead to the identification of genetic factors contributing to the skewed sex ratio seen in the tropical gar and of sex-specific differences in expression in other species. Finally, the transcriptome assembly will open future research avenues on tropical gar development, cell function, environmental resistance, and evolution in the context of other early vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3652-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kayla M Cribbin
- 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
| | - Kyle Taylor
- 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), C.P. 86150, Villahermosa, Tabasco, Mexico
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.
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19
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Majtánová Z, Symonová R, Arias-Rodriguez L, Sallan L, Ráb P. "Holostei versus Halecostomi" Problem: Insight from Cytogenetics of Ancient Nonteleost Actinopterygian Fish, Bowfin Amia calva. J Exp Zool B Mol Dev Evol 2017; 328:620-628. [PMID: 28074622 DOI: 10.1002/jez.b.22720] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/12/2016] [Accepted: 11/22/2016] [Indexed: 12/17/2022]
Abstract
Bowfin belongs to an ancient lineage of nonteleost ray-finned fishes (actinopterygians) and is the only extant survivor of a once diverged group, the Halecomorphi or Amiiformes. Owing to the scarcity of extant nonteleost ray-finned lineages, also referred as "living fossils," their phylogenetic interrelationships have been the target of multiple hypotheses concerning their sister group relationships. Molecular and morphological data sets have produced controversial results; bowfin is considered as either the sister group to genome-duplicated teleosts (together forming the group of Halecostomi) or to gars (Lepisosteiformes; together forming the group of Holostei). However, any detailed cytogenetic analysis of bowfin chromosomes has never been performed to address this issue. Here we examined bowfin chromosomes by conventional (Giemsa-staining, C-banding, base-specific fluorescence and silver staining) and molecular (FISH with rDNA probes) cytogenetic protocols. We identified diploid chromosome number 2n = 46 with a middle-sized submetacentric chromosome pair as the major ribosomal DNA-bearing (45S rDNA), GC-positive and silver-positive element. The minor rDNA (5S rDNA) sites were localized in the pericentromeric region of one middle-sized acrocentric chromosome pair. Comparison with available cytogenetic data of other nonteleost actinopterygians (bichirs, sturgeons, gars) and teleost species including representative of basally branching lineages showed bowfin chromosomal characteristics more similar to the teleost type than to any other nonteleosts. Particularly striking differences were identified between bowfin and gars, the latter of which were found to mimic mammalian AT/GC genomic organisation. Such conclusion however contradicts the most recent phylogenomic results and raises the question what states are ancestral and what are derived.
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Affiliation(s)
- Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic.,Department of Zoology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Radka Symonová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic.,Research Institute for Limnology, University of Innsbruck, Mondsee, Austria
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, México
| | - Lauren Sallan
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
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20
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Symonová R, Majtánová Z, Arias-Rodriguez L, Mořkovský L, Kořínková T, Cavin L, Pokorná MJ, Doležálková M, Flajšhans M, Normandeau E, Ráb P, Meyer A, Bernatchez L. Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray-Finned Fish. J Exp Zool (Mol Dev Evol ) 2016; 328:607-619. [DOI: 10.1002/jez.b.22719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 11/13/2016] [Accepted: 11/22/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Radka Symonová
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague 2 Czech Republic
- Research Institute for Limnology; University of Innsbruck; Mondsee Austria
| | - Zuzana Majtánová
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague 2 Czech Republic
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas; Universidad Juárez Autónoma de Tabasco (UJAT); Villahermosa Tabasco México
| | - Libor Mořkovský
- Department of Zoology; Faculty of Science; Charles University; Prague 2 Czech Republic
| | - Tereza Kořínková
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
| | - Lionel Cavin
- Muséum d'Histoire Naturelle; Geneva 6 Switzerland
| | - Martina Johnson Pokorná
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
- Department of Ecology; Faculty of Science; Charles University; Prague 2 Czech Republic
| | - Marie Doležálková
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague 2 Czech Republic
| | - Martin Flajšhans
- Faculty of Fisheries and Protection of Waters; South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses; University of South Bohemia in České Budějovice; Vodňany Czech Republic
| | - Eric Normandeau
- IBIS, Department of Biology, University Laval, Pavillon Charles-Eugène-Marchand; Avenue de la Médecine Quebec City; Canada
| | - Petr Ráb
- Laboratory of Fish Genetics; Institute of Animal Physiology and Genetics; The Czech Academy of Sciences; Liběchov Czech Republic
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Konstanz Germany
| | - Louis Bernatchez
- IBIS, Department of Biology, University Laval, Pavillon Charles-Eugène-Marchand; Avenue de la Médecine Quebec City; Canada
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Passow CN, Greenway R, Arias-Rodriguez L, Jeyasingh PD, Tobler M. Reduction of Energetic Demands through Modification of Body Size and Routine Metabolic Rates in Extremophile Fish. Physiol Biochem Zool 2015; 88:371-83. [PMID: 26052634 DOI: 10.1086/681053] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Variation in energy availability or maintenance costs in extreme environments can exert selection for efficient energy use, and reductions in organismal energy demand can be achieved in two ways: reducing body mass or metabolic suppression. Whether long-term exposure to extreme environmental conditions drives adaptive shifts in body mass or metabolic rates remains an open question. We studied body size variation and variation in routine metabolic rates in locally adapted populations of extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulfide-rich springs and caves. We quantified size distributions and routine metabolic rates in wild-caught individuals from four habitat types. Compared with ancestral populations in nonsulfidic surface habitats, extremophile populations were characterized by significant reductions in body size. Despite elevated metabolic rates in cave fish, the body size reduction precipitated in significantly reduced energy demands in all extremophile populations. Laboratory experiments on common garden-raised fish indicated that elevated routine metabolic rates in cave fish likely have a genetic basis. The results of this study indicate that adaptation to extreme environments directly impacts energy metabolism, with fish living in cave and sulfide spring environments expending less energy overall during routine metabolism.
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Affiliation(s)
- Courtney N Passow
- Department of Zoology, Oklahoma State University, 501 Life Sciences West, Stillwater, Oklahoma 74078; 2División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, Mexico
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25
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Eifert C, Farnworth M, Schulz-Mirbach T, Riesch R, Bierbach D, Klaus S, Wurster A, Tobler M, Streit B, Indy JR, Arias-Rodriguez L, Plath M. Brain size variation in extremophile fish: local adaptation versus phenotypic plasticity. J Zool (1987) 2014. [DOI: 10.1111/jzo.12190] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- C. Eifert
- Department of Ecology and Evolution; J.W. Goethe University Frankfurt; Frankfurt am Main Germany
| | - M. Farnworth
- Department of Ecology and Evolution; J.W. Goethe University Frankfurt; Frankfurt am Main Germany
| | - T. Schulz-Mirbach
- Department Biology II; Ludwig-Maximilians-University; Planegg Germany
| | - R. Riesch
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- School of Biological Sciences; Centre for Ecology, Evolution and Behaviour; Royal Holloway University of London; Egham Surrey UK
| | - D. Bierbach
- Department of Ecology and Evolution; J.W. Goethe University Frankfurt; Frankfurt am Main Germany
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Berlin Germany
| | - S. Klaus
- Department of Ecology and Evolution; J.W. Goethe University Frankfurt; Frankfurt am Main Germany
| | - A. Wurster
- Department of Ecology and Evolution; J.W. Goethe University Frankfurt; Frankfurt am Main Germany
| | - M. Tobler
- Department of Zoology; Oklahoma State University; Stillwater OK USA
| | - B. Streit
- Department of 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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26
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Culumber ZW, Bautista-Hernández CE, Monks S, Arias-Rodriguez L, Tobler M. Variation in Melanism and Female Preference in Proximate but Ecologically Distinct Environments. Ethology 2014. [DOI: 10.1111/eth.12282] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Zachary W. Culumber
- Centro de Investigaciones Cientificas de las Huastecas “Aguazarca”; Calnali Hidalgo Mexico
- Centro de Investigaciones Biologicas; Universidad Autónoma del Estado de Hidalgo; Pachuca Hidalgo Mexico
| | - Christian E. Bautista-Hernández
- Centro de Investigaciones Cientificas de las Huastecas “Aguazarca”; Calnali Hidalgo Mexico
- Centro de Investigaciones Biologicas; Universidad Autónoma del Estado de Hidalgo; Pachuca Hidalgo Mexico
| | - Scott Monks
- Centro de Investigaciones Biologicas; Universidad Autónoma del Estado de Hidalgo; Pachuca Hidalgo Mexico
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas; Universidad Juárez Autónoma de Tabasco (UJAT); Villahermosa Tabasco Mexico
| | - Michael Tobler
- Department of Zoology; Oklahoma State University; Stillwater OK USA
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27
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Hernández-Guzmán J, Indy JR, Yasui GS, Arias-Rodriguez L. [Tropical turtles chromosomes: Kinosternon leucostomum, Trachemys scripta and Staurotypus triporcatus (Testudines: Kinosternidae/Emydidae)]. REV BIOL TROP 2014; 62:671-88. [PMID: 25102649 DOI: 10.15517/rbt.v62i2.10843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Mexico is a biodiverse country in several taxa as reptiles, that include several species of freshwater and marine turtles. Eventhough most of this group species are under protection, Tabasco State has nine native freshwater turtles, like Kinosternon leucostomum, Trachemys scripta and Staurotypus triporcatus that are very important in traditional dishes. This has resulted in a critical level of their populations, together with little biological knowledge for their conservation. Therefore, this study was dedicated to turtle cytogenetics. The study was conducted using the conventional methods for cytogenetics. The results showed the modal diploid and haploid number for K. leucostomum of 2n = 56 (2n = 56+3 microchromosomes "B") and 1n = 28 chromosomes in mitosis and meiosis, respectively. In T. scripta 2n = 50 chromosomes (2n = 50+2 microchromosomes "B") and 1n = 25 chromosomes were also characterized. Whereas in S. triporcatus we only report the 2 = 54 chromosomes (2n = 54+2 microchromosomes "B"). The karyological formula for K. leucostomum was integrated by 12 metacentric-submetacentric chromosomes "msm"/"A"+22 subtelocentric-telocentric chromosomes "stt"/"B"+22 telocentric chromosomes "T"/"C" with fundamental number (FN) of 90 chromosome arms. While T. scripta karyotype was integrated by 32 "msm/"A"+10 "stt"/"B"+8"T/"C" chromosomes, with FN of 92 arms. S. triporcatus karyotype formula was built up by 20 chromosomes "msm"/"A"+34 chromosomes "T"/"C" with FN of 74. The variation in chromosome classification, the fundamental number and the presence of supernumerary microchromosomes "B" in the studied species, were evidence of a particular chromosome cytotypes in Tabasco. We considered that the presence of microchromosomes "B" probably has different origins, and they may be very important as a pattern for the formation or separation of new species. This study also showed the absence of heterologous chromosomes between the females and males karyotypes from the studied species.
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Jourdan J, Bierbach D, Riesch R, Schießl A, Wigh A, Arias-Rodriguez L, Indy JR, Klaus S, Zimmer C, Plath M. Microhabitat use, population densities, and size distributions of sulfur cave-dwelling Poecilia mexicana. PeerJ 2014; 2:e490. [PMID: 25083351 PMCID: PMC4106196 DOI: 10.7717/peerj.490] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/28/2014] [Indexed: 11/20/2022] Open
Abstract
The Cueva del Azufre in Tabasco, Mexico, is a nutrient-rich cave and its inhabitants need to cope with high levels of dissolved hydrogen sulfide and extreme hypoxia. One of the successful colonizers of this cave is the poeciliid fish Poecilia mexicana, which has received considerable attention as a model organism to examine evolutionary adaptations to extreme environmental conditions. Nonetheless, basic ecological data on the endemic cave molly population are still missing; here we aim to provide data on population densities, size class compositions and use of different microhabitats. We found high overall densities in the cave and highest densities at the middle part of the cave with more than 200 individuals per square meter. These sites have lower H2S concentrations compared to the inner parts where most large sulfide sources are located, but they are annually exposed to a religious harvesting ceremony of local Zoque people called La Pesca. We found a marked shift in size/age compositions towards an overabundance of smaller, juvenile fish at those sites. We discuss these findings in relation to several environmental gradients within the cave (i.e., differences in toxicity and lighting conditions), but we also tentatively argue that the annual fish harvest during a religious ceremony (La Pesca) locally diminishes competition (and possibly, cannibalism by large adults), which is followed by a phase of overcompensation of fish densities.
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Affiliation(s)
- Jonas Jourdan
- Evolutionary Ecology Group, Goethe University of Frankfurt , Frankfurt am Main , Germany ; Biodiversity and Climate Research Centre (BiKF) , Frankfurt am Main , Germany
| | - David Bierbach
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries , Berlin , Germany
| | - Rüdiger Riesch
- Department of Animal and Plant Sciences, University of Sheffield , Sheffield , UK
| | - Angela Schießl
- Evolutionary Ecology Group, Goethe University of Frankfurt , Frankfurt am Main , Germany
| | - Adriana Wigh
- Evolutionary Ecology Group, Goethe University of Frankfurt , Frankfurt am Main , Germany
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT) , Villahermosa, Tabasco , México
| | - Jeane Rimber Indy
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT) , Villahermosa, Tabasco , México
| | - Sebastian Klaus
- Evolutionary Ecology Group, Goethe University of Frankfurt , Frankfurt am Main , Germany
| | - Claudia Zimmer
- Evolutionary Ecology Group, Goethe University of Frankfurt , Frankfurt am Main , Germany
| | - Martin Plath
- Evolutionary Ecology Group, Goethe University of Frankfurt , Frankfurt am Main , Germany
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Del Río-Portilla MA, Vargas-Peralta CE, Lafarga-De La Cruz F, Arias-Rodriguez L, Delgado-Vega R, Galván-Tirado C, García-de-León FJ. The complete mitochondrial DNA of the tropical gar (Atractosteus tropicus). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:557-8. [PMID: 24708123 DOI: 10.3109/19401736.2014.905856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitogenome of the tropical gar, Atractosteus tropicus, (GeneBank accession number KJ531198) has a total length of 16,280 bp, and the arrangement consist of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA similar to other Lepisosteidae family mitogenomes.
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Affiliation(s)
- Miguel A Del Río-Portilla
- a Departamento de Acuicultura , Centro de Investigación Científica y de Educación Superior de Ensenada , Ensenada , B. C. México
| | - Carmen E Vargas-Peralta
- a Departamento de Acuicultura , Centro de Investigación Científica y de Educación Superior de Ensenada , Ensenada , B. C. México
| | - Fabiola Lafarga-De La Cruz
- a Departamento de Acuicultura , Centro de Investigación Científica y de Educación Superior de Ensenada , Ensenada , B. C. México
| | - Lenin Arias-Rodriguez
- b División Académica de Ciencias Biológicas , Universidad Juárez Autónoma de Tabasco (UJAT) , Tabasco , México , and
| | - Rigoberto Delgado-Vega
- a Departamento de Acuicultura , Centro de Investigación Científica y de Educación Superior de Ensenada , Ensenada , B. C. México
| | - Carolina Galván-Tirado
- c Laboratorio de Genética para la Conservación , Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Instituto Politécnico Nacional , Baja California Sur , México
| | - Francisco J García-de-León
- c Laboratorio de Genética para la Conservación , Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Instituto Politécnico Nacional , Baja California Sur , México
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30
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Arias-Rodriguez L, Páramo-Delgadillo S, Durán-González ADLL. Caraterización citogenética del pez tropical de agua dulce Parachromis managuensis (Pisces: Cichlidae). REV BIOL TROP 2014. [DOI: 10.15517/rbt.v54i1.13986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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31
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Palacios M, Arias-Rodriguez L, Plath M, Eifert C, Lerp H, Lamboj A, Voelker G, Tobler M. The rediscovery of a long described species reveals additional complexity in speciation patterns of poeciliid fishes in sulfide springs. PLoS One 2013; 8:e71069. [PMID: 23976979 PMCID: PMC3745397 DOI: 10.1371/journal.pone.0071069] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 07/01/2013] [Indexed: 12/02/2022] Open
Abstract
The process of ecological speciation drives the evolution of locally adapted and reproductively isolated populations in response to divergent natural selection. In Southern Mexico, several lineages of the freshwater fish species of the genus Poecilia have independently colonized toxic, hydrogen sulfide-rich springs. Even though ecological speciation processes are increasingly well understood in this system, aligning the taxonomy of these fish with evolutionary processes has lagged behind. While some sulfide spring populations are classified as ecotypes of Poecilia mexicana, others, like P. sulphuraria, have been described as highly endemic species. Our study particularly focused on elucidating the taxonomy of the long described sulfide spring endemic, Poecilia thermalis Steindachner 1863, and investigates if similar evolutionary patterns of phenotypic trait divergence and reproductive isolation are present as observed in other sulfidic species of Poecilia. We applied a geometric morphometric approach to assess body shape similarity to other sulfidic and non-sulfidic fish of the genus Poecilia. We also conducted phylogenetic and population genetic analyses to establish the phylogenetic relationships of P. thermalis and used a population genetic approach to determine levels of gene flow among Poecilia from sulfidic and non-sulfidic sites. Our results indicate that P. thermalis' body shape has evolved in convergence with other sulfide spring populations in the genus. Phylogenetic analyses placed P. thermalis as most closely related to one population of P. sulphuraria, and population genetic analyses demonstrated that P. thermalis is genetically isolated from both P. mexicana ecotypes and P. sulphuraria. Based on these findings, we make taxonomic recommendations for P. thermalis. Overall, our study verifies the role of hydrogen sulfide as a main factor shaping convergent, phenotypic evolution and the emergence of reproductive isolation between Poecilia populations residing in adjacent sulfidic and non-sulfidic environments.
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Affiliation(s)
- Maura Palacios
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | - Martin Plath
- Evolutionary Ecology Group, J. W. Goethe University Frankfurt am Main, Frankfurt, Hessen, Germany
| | - Constanze Eifert
- Evolutionary Ecology Group, J. W. Goethe University Frankfurt am Main, Frankfurt, Hessen, Germany
| | - Hannes Lerp
- Evolutionary Ecology Group, J. W. Goethe University Frankfurt am Main, Frankfurt, Hessen, Germany
| | - Anton Lamboj
- Department for Integrative Zoology, University of Vienna, Vienna, Austria
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Michael Tobler
- Department of Zoology, Oklahoma State University, Stillwater, Oklahoma, United States of America
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Plath M, Pfenninger M, Lerp H, Riesch R, Eschenbrenner C, Slattery PA, Bierbach D, Herrmann N, Schulte M, Arias-Rodriguez L, Rimber Indy J, Passow C, Tobler M. Genetic differentiation and selection against migrants in evolutionarily replicated extreme environments. Evolution 2013; 67:2647-61. [PMID: 24033173 DOI: 10.1111/evo.12133] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 04/02/2013] [Indexed: 01/18/2023]
Abstract
We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RI(s)) was negatively correlated with the strength of natural selection (RI(m)), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage.
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Affiliation(s)
- Martin Plath
- J. W. Goethe-University Frankfurt/M., Evolutionary Ecology Group, Max-von-Laue Str. 13, 60438, Frankfurt, a. M., Germany.
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Bierbach D, Schulte M, Herrmann N, Zimmer C, Arias-Rodriguez L, Indy JR, Riesch R, Plath M. Predator avoidance in extremophile fish. Life (Basel) 2013; 3:161-80. [PMID: 25371337 PMCID: PMC4187198 DOI: 10.3390/life3010161] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/28/2013] [Accepted: 01/28/2013] [Indexed: 11/16/2022] Open
Abstract
Extreme habitats are often characterized by reduced predation pressures, thus representing refuges for the inhabiting species. The present study was designed to investigate predator avoidance of extremophile populations of Poecilia mexicana and P. sulphuraria that either live in hydrogen sulfide-rich (sulfidic) springs or cave habitats, both of which are known to have impoverished piscine predator regimes. Focal fishes that inhabited sulfidic springs showed slightly weaker avoidance reactions when presented with several naturally occurring predatory cichlids, but strongest differences to populations from non-sulfidic habitats were found in a decreased shoaling tendency with non-predatory swordtail (Xiphophorus hellerii) females. When comparing avoidance reactions between P. mexicana from a sulfidic cave (Cueva del Azufre) and the adjacent sulfidic surface creek (El Azufre), we found only slight differences in predator avoidance, but surface fish reacted much more strongly to the non-predatory cichlid Vieja bifasciata. Our third experiment was designed to disentangle learned from innate effects of predator recognition. We compared laboratory-reared (i.e., predator-naïve) and wild-caught (i.e., predator-experienced) individuals of P. mexicana from a non-sulfidic river and found no differences in their reaction towards the presented predators. Overall, our results indicate (1) that predator avoidance is still functional in extremophile Poecilia spp. and (2) that predator recognition and avoidance reactions have a strong genetic basis.
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Affiliation(s)
- David Bierbach
- Department of Ecology & Evolution, J.W. Goethe University Frankfurt, Max-von-Laue-Straße 13, Frankfurt am Main, D-60438, Germany; E-Mails: (C.Z.); (M.P.)
| | - Matthias Schulte
- Institute of Biochemistry & Biology, Unit of Animal Ecology, University of Potsdam, Maulbeerallee 1, Potsdam, 14469, Germany; E-Mails: (M.S.); (N.H.)
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, CP 86150, México; E-Mails: (L.A.-R); (J.R.I.)
| | - Nina Herrmann
- Institute of Biochemistry & Biology, Unit of Animal Ecology, University of Potsdam, Maulbeerallee 1, Potsdam, 14469, Germany; E-Mails: (M.S.); (N.H.)
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, CP 86150, México; E-Mails: (L.A.-R); (J.R.I.)
| | - Claudia Zimmer
- Department of Ecology & Evolution, J.W. Goethe University Frankfurt, Max-von-Laue-Straße 13, Frankfurt am Main, D-60438, Germany; E-Mails: (C.Z.); (M.P.)
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, CP 86150, México; E-Mails: (L.A.-R); (J.R.I.)
| | - Jeane Rimber Indy
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, CP 86150, México; E-Mails: (L.A.-R); (J.R.I.)
| | - Rüdiger Riesch
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK; E-Mail:
| | - Martin Plath
- Department of Ecology & Evolution, J.W. Goethe University Frankfurt, Max-von-Laue-Straße 13, Frankfurt am Main, D-60438, Germany; E-Mails: (C.Z.); (M.P.)
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Bierbach D, Schulte M, Herrmann N, Tobler M, Stadler S, Jung CT, Kunkel B, Riesch R, Klaus S, Ziege M, Indy JR, Arias-Rodriguez L, Plath M. Predator-induced changes of female mating preferences: innate and experiential effects. BMC Evol Biol 2011; 11:190. [PMID: 21726456 PMCID: PMC3141438 DOI: 10.1186/1471-2148-11-190] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 07/04/2011] [Indexed: 11/27/2022] Open
Abstract
Background In many species males face a higher predation risk than females because males display elaborate traits that evolved under sexual selection, which may attract not only females but also predators. Females are, therefore, predicted to avoid such conspicuous males under predation risk. The present study was designed to investigate predator-induced changes of female mating preferences in Atlantic mollies (Poecilia mexicana). Males of this species show a pronounced polymorphism in body size and coloration, and females prefer large, colorful males in the absence of predators. Results In dichotomous choice tests predator-naïve (lab-reared) females altered their initial preference for larger males in the presence of the cichlid Cichlasoma salvini, a natural predator of P. mexicana, and preferred small males instead. This effect was considerably weaker when females were confronted visually with the non-piscivorous cichlid Vieja bifasciata or the introduced non-piscivorous Nile tilapia (Oreochromis niloticus). In contrast, predator experienced (wild-caught) females did not respond to the same extent to the presence of a predator, most likely due to a learned ability to evaluate their predators' motivation to prey. Conclusions Our study highlights that (a) predatory fish can have a profound influence on the expression of mating preferences of their prey (thus potentially affecting the strength of sexual selection), and females may alter their mate choice behavior strategically to reduce their own exposure to predators. (b) Prey species can evolve visual predator recognition mechanisms and alter their mate choice only when a natural predator is present. (c) Finally, experiential effects can play an important role, and prey species may learn to evaluate the motivational state of their predators.
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Affiliation(s)
- David Bierbach
- Department of Ecology & Evolution, JW Goethe University Frankfurt, Siesmayerstrasse 70-72, D-60054 Frankfurt am Main, Germany.
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Arias-Rodriguez L, Indy JR, Ahumada-Hernández RI, Barragán-Cupido H, Avalos-Lázaro AA, Páramo-Delgadillo S. [Karyotypic characterization in mitosis and meiosis of the common snook Centropomus undecimalls (Pisces: Centropomidae)]. REV BIOL TROP 2011; 59:683-692. [PMID: 21721233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
The common snook Centropomus undecimalis inhabits marine, brackish and freshwater habitats in the Western Central Atlantic Ocean, including the Gulf of Mexico. Common snook is an economically important fish in many localities, nevertheless the number of studies on its biology and genetics are still few. The present study attempts to establish the cytogenetic profiles of the specimens collected in Paraiso Municipality Tabasco, Mexico. Tissue of five females and eight male organisms were processed by conventional cytological techniques to obtain chromosome slides of high quality in order to assemble the karyotype. The results from the kidney tissue analysis showed that 85.1% of 288 mitosis had a 2n = 48 chromosomes, and 52.8% of 104 meiosis exhibited the haploid number 1n = 24. The diploid karyotype showed 48 monoarmed chromosomes of the telocentric (T) type. There was no chromosome heteromorphism between females and males. The diploid karyotype was very similar to that observed in the majority of marine fishes.
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Affiliation(s)
- Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150, Villahermosa, Tabasco, México.
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Tobler M, Palacios M, Chapman LJ, Mitrofanov I, Bierbach D, Plath M, Arias-Rodriguez L, de León FJG, Mateos M. Evolution in extreme environments: replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs. Evolution 2011; 65:2213-28. [PMID: 21790570 DOI: 10.1111/j.1558-5646.2011.01298.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated replicated ecological speciation in the livebearing fish Poecilia mexicana and P. sulphuraria (Poeciliidae), which inhabit freshwater habitats and have also colonized multiple sulfidic springs in southern Mexico. These springs exhibit extreme hypoxia and high concentrations of hydrogen sulfide, which is lethal to most metazoans. We used phylogenetic analyses to test whether springs were independently colonized, performed phenotypic assessments of body and gill morphology variation to identify convergent patterns of trait differentiation, and conducted an eco-toxicological experiment to detect differences in sulfide tolerances among ecotypes. Our results indicate that sulfidic springs were colonized by three different lineages, two within P. mexicana and one representing P. sulphuraria. Colonization occurred earlier in P. sulphuraria, whereas invasion of sulfidic springs in P. mexicana was more recent, such that each population is more closely related to neighboring populations from adjacent nonsulfidic habitats. Sulfide spring fish also show divergence from nonsulfidic phenotypes and a phenotypic convergence toward larger heads, larger gills, and increased tolerance to H(2) S. Together with previous studies that indicated significant reproductive isolation between fish from sulfidic and nonsulfidic habitats, this study provides evidence for repeated ecological speciation in the independent sulfide spring populations of P. mexicana and P. sulphuraria.
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Affiliation(s)
- Michael Tobler
- Department of Zoology, Oklahoma State University, 501 Life Sciences West, Stillwater, Oklahoma 74078, USA.
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Köhler A, Hildenbrand P, Schleucher E, Riesch R, Arias-Rodriguez L, Streit B, Plath M. Effects of male sexual harassment on female time budgets, feeding behavior, and metabolic rates in a tropical livebearing fish (Poecilia mexicana). Behav Ecol Sociobiol 2011. [DOI: 10.1007/s00265-011-1161-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Hernández-Guzmán J, Arias-Rodriguez L, Indy JR. [Meiotic chromosomes of the tree frog Smilisca baudinii (Anura: Hylidae)]. REV BIOL TROP 2011; 59:355-362. [PMID: 21516655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
The Mexican tree frog Smilisca baudinii, is a very common frog in Central America. In spite their importance to keep the ecological equilibrium of the rainforest, its biology and genetics are poorly known. In order to contribute with its biological knowledge, we described the typical meiotic karyotype based in standard cytogenetic protocols to specimens collected in Tabasco, Mexico. The study was centered in the analysis of 131 chromosome spreads at meiotic stage from two adults of the species (one female and one male). The metaphase analysis allowed the establishment of the modal haploid number of 1n = 12 bivalent chromosomes. The chromosomic formulae from the haploid bivalent karyotype was integrated by 12 biarmed chromosomes characterized by twelve pairs of metacentric-submetacentric (msm) chromosomes. The meiotic counting gives the idea that diploid chromosome number is integrated by a complement of 2n = 24 biarmed chromosomes. The presence of sex chromosomes from female and male meiotic spreads was not observed. Current results suggest that S. baudinii chromosome structure is well shared among Hylidae family and "B" chromosomes are particular structures that have very important evolutionary consequences in species diversification.
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Indy JR, Arias-Rodriguez L, Páramo-Delgadillo S, Hernández-Vidal U, Alvarez-González CA, Contreras-Sánchez WM. Mitotic karyotype of the tropical freshwater crayfish Procambarus (Austrocambarus) llamasi (Decapoda: Cambaridae). REV BIOL TROP 2010; 58:655-62. [PMID: 20527466 DOI: 10.15517/rbt.v58i2.5236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In Mexico, the biology of Procambarus has been more studied than the biology of other Cambarids because of its diversity and potential use in aquaculture. We determined the karyotype of the Mexican tropical freshwater crayfish Procambarus (Austrocambarus) llamasi from 189 metaphase spreads from gill tissues of 17 adults. They had 98-120 chromosomes (mode 2n=120 chromosomes). There are 60 pairs of monoarm, telocentric chromosomes. Sex chromosomes were not detected and we propose that the P. llamasi karyotype can be used to distinguish this species from other Mexican crayfish. Additionally, we suggest using karyological data in aquaculture and conservation biology.
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Affiliation(s)
- Jeane R Indy
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, México, C.P. 86150.
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Hernández-Guzmán J, Arias-Rodriguez L, Rimber Indy J. Los cromosomas meióticos de la rana arborícola Smilisca baudinii (Anura: Hylidae). REV BIOL TROP 2010. [DOI: 10.15517/rbt.v59i1.3204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Arias-Rodriguez L, R. Indy J, I. Ahumada-Hernández R, Barragán- Cupido H, A. Ávalos-Lázaro A, Páramo-Delgadillo S. Caracterización cariotípica en mitosis y meiosis del robalo blanco Centropomus undecimalis (Pisces: Centropomidae). REV BIOL TROP 2010. [DOI: 10.15517/rbt.v0i0.3132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Yasui GS, Arias-Rodriguez L, Fujimoto T, Arai K. Simple and inexpensive method for cryopreservation of fish sperm combining straw and powdered dry ice. Cryo Letters 2008; 29:383-390. [PMID: 18946552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Here, we propose a simple and inexpensive method for fish sperm cryopreservation. Sperm samples of the loach Misgurnus anguillicaudatus (Teleostei: Cobitidae) were diluted 7-fold by an extender containing 63.5 mM NaCl, 114 mM KCl, 20 mM Tris and 10% methanol. The cryogenic straws were placed in three kinds of self-made tubes which diameter was changed by commercially available materials and then immersed into powdered dry ice for 2 min and plunged into liquid nitrogen. This procedure resulted in a cooling rate at -421.4 +/- 119.84 (control), -55.8 +/- 4.32 (tube 1), -40.2 +/- 3.43 (tube 2) and -33.3 +/- 2.09 C/min (tube 3). In the slowest cooling rate by the tube 3, total motility (72 +/- 3 %), duration (146 +/- 12 s) and hatching rates (29 +/- 04 %) were higher than those by other rates. Progressive motility (83 +/- 5 %) did not differ significantly from fresh samples.
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Affiliation(s)
- George Shigueki Yasui
- Graduate School of Fisheries Science, Division of Marine Life Sciences, Laboratory of Aquaculture Genetics and Genomics, Hokkaido University, Hokkaido, Japan.
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Arias-Rodriguez L, Ibarra-Castro L. [The mitotic and meiotic chromosomes of the tropical fish Petenia splendida (Cichlidae)]. REV BIOL TROP 2008; 56:895-907. [PMID: 19256452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
The karyotype of bay snook, Petenia splendida, is described based on mitotic and meiotic stages of sixty larvae and twelve juveniles from Tabasco, Mexico. Standard cytological procedures with minor modifications were followed to obtain mitotic and meiotic chromosome spreads. One hundred chromosome slides were analyzed and 290 chromosome spreads were counted. High-quality spreads in mitosis and meiosis were used for karyotype analysis. Mitotic chromosome spreads showed 76.7% of such cells with 2n=48 chromosomes, while meiotic spreads revealed 55.2% with 24 chromosomes in haploid stage. Photographic documentation of eight high-quality pictures showed that the karyotype consists of three pairs of bi-armed metacentric-submetacentric chromosomes (msm) and 21 pairs with uni-armed subtelocentric-acrocentric chromosomes (sta), with a fundamental number (FN) of 54 arms. Karyotype chromosomes were verified by analysis of haploid and diploid metaphases at meiotic stage I. Abundant chromosome spreads were observed more frequently on slides from larvae. No evidence ofheteromorphism to discriminate sexual chromosomes was detected. There were "dot-like" chromatic bodies in both sexes and they were classified as "B" chromosomes. The karyotype of P. splendida is type "A", i.e., primitive in the Cichlid family, similar to other species of Cichlasoma. The occurrence of supernumerary chromosomes is still unknown: studies on the effects of pollution and hybridization might be important to understand that phenomenon.
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Arias-Rodriguez L, González-Hermoso JP, Fletes-Regalado H, Rodriguez-Ibarra LE, Del Valle Pignataro G. [Karyotypes of the purple snails Plicopurpura pansa and Plicopurpura columellaris (Gastropoda: Muricidae)]. REV BIOL TROP 2007; 55:853-866. [PMID: 19086390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
The karyotypes of the purple snails Plicopurpura pansa (Gould, 1853) and P. columellaris (Lamarck, 1816) were established from 17 and 13 adults, respectively; and from eight capsules with embryos of P. pansa. In P. pansa were counted 59 mitotic fields in the adults and 127 in embryos; and 118 fields in P columellaris. Chromosome numbers from 30 to 42 were observed in both species. Such a variation was notorious in each sample and there was no evidence of any relationship with tissue (gill, muscle and stomach). Both species has a typical modal number of 2n=36 chromosomes. Five good quality chromosome spreads were selected from adults of each species to assemble the karyotype. Classic cytogenetics statistics like relative lengths, arm ratio, centromeric index and the difference between long and short arms are presented. There were three pairs ofmetacentric and fifteen pairs oftelocentric chromosomes in both species. This classification was not strong enough, so the chromosome complement by species was divided in four groups ("a", "b", "c" and "d") on the basis of relative lengths (p+q). A comparison of p+q in each chromosome pair was estimated within and between species by two ways analysis of variance and Tukey tests (P < 0.05). Significant differences were identified among chromosome groups in each species; the differences between species were given by the first three pairs of chromosomes (group "a" biarmed) and the last two pairs (group "d" uniarmed). Deviations in chromosome number and relative lengths probably are given by chromosome rearrangements, related with chromosome polymorphism and presence of the atypical microchromosome "B". The fundamental number in both species was characterized by 42 chromosome arms. No sex chromosomes were identified.
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Affiliation(s)
- Lenin Arias-Rodriguez
- Centro de Investigación en Alimentación y Desarrollo, A.C. Unidad, Mazatlán, Sábalo-Cerritos S/N Estero del Yugo, A.P. 711, Mazatlán, Sinaloa, México.
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