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Siepielski AM, DiBattista JD, Carlson SM. It’s about time: the temporal dynamics of phenotypic selection in the wild. Ecol Lett 2009; 12:1261-76. [DOI: 10.1111/j.1461-0248.2009.01381.x] [Citation(s) in RCA: 471] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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471 |
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Siepielski AM, Morrissey MB, Buoro M, Carlson SM, Caruso CM, Clegg SM, Coulson T, DiBattista J, Gotanda KM, Francis CD, Hereford J, Kingsolver JG, Augustine KE, Kruuk LEB, Martin RA, Sheldon BC, Sletvold N, Svensson EI, Wade MJ, MacColl ADC. Precipitation drives global variation in natural selection. Science 2017; 355:959-962. [PMID: 28254943 DOI: 10.1126/science.aag2773] [Citation(s) in RCA: 204] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 06/27/2016] [Accepted: 02/02/2017] [Indexed: 12/31/2022]
Abstract
Climate change has the potential to affect the ecology and evolution of every species on Earth. Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation-natural selection-are largely unknown. We report that aspects of precipitation and potential evapotranspiration, along with the North Atlantic Oscillation, predicted variation in selection across plant and animal populations throughout many terrestrial biomes, whereas temperature explained little variation. By showing that selection was influenced by climate variation, our results indicate that climate change may cause widespread alterations in selection regimes, potentially shifting evolutionary trajectories at a global scale.
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Research Support, Non-U.S. Gov't |
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204 |
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Siepielski AM, Gotanda KM, Morrissey MB, Diamond SE, DiBattista JD, Carlson SM. The spatial patterns of directional phenotypic selection. Ecol Lett 2013; 16:1382-92. [DOI: 10.1111/ele.12174] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/20/2013] [Accepted: 08/07/2013] [Indexed: 11/26/2022]
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169 |
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Martel-Pelletier J, McCollum R, DiBattista J, Faure MP, Chin JA, Fournier S, Sarfati M, Pelletier JP. The interleukin-1 receptor in normal and osteoarthritic human articular chondrocytes. Identification as the type I receptor and analysis of binding kinetics and biologic function. ARTHRITIS AND RHEUMATISM 1992; 35:530-40. [PMID: 1533521 DOI: 10.1002/art.1780350507] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To identify and investigate the kinetic binding properties of interleukin-1 receptors (IL-1R), and examine the abilities of the 2 IL-1 isoforms to stimulate metalloprotease synthesis, in normal and osteoarthritic (OA) chondrocytes. METHODS Receptor affinity and density were determined using radioligand binding experiments and flow cytometry. Immunocytochemical analysis and affinity cross-linking studies were performed for characterization of IL-1R. RESULTS While no difference in receptor affinity between normal and OA chondrocytes was noted in binding studies (Kd approximately 30 pM), a 2-fold increase in receptor density was found in OA chondrocytes as compared with normal chondrocytes (mean 4,069 sites/cell versus 2,315 sites/cell). Flow cytometry experiments also showed a significant increase in receptor density in OA cells, as well as an enhancement in the percentage of positive cells in diseased cartilage compared with normal. Binding data for both IL-1 isoforms revealed a single class of binding sites and receptor specificity. Factors such as IL-2, interferon-gamma, tumor necrosis factor alpha, and bovine insulin did not compete with IL-1 beta. By covalent ligand cross-linking and electrophoretic analysis, only type I IL-1R, a protein of 80 kd, was detected on chondrocytes. By immunocytochemical analysis, IL-1R was identified at the cell membrane level, in both normal and OA chondrocytes. The presence of nuclear staining was also observed, but only in OA chondrocytes. Recombinant human IL-1 (alpha and beta) induced the secretion of stromelysin and collagenase in a dose-dependent manner. The IL-1 concentration required for half-maximal metalloprotease stimulation was 3-4 times lower in OA chondrocytes than in normal cells. CONCLUSION These results indicate that OA chondrocytes have a higher sensitivity to the stimulation of metalloprotease synthesis by IL-1 than do normal cells. This could be related to the increased levels of IL-1R expressed in the OA cells. The implications of these findings with regard to the possible roles of IL-1 and IL-1R in the pathogenesis of OA are discussed.
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Feldheim KA, Gruber SH, DiBattista JD, Babcock EA, Kessel ST, Hendry AP, Pikitch EK, Ashley MV, Chapman DD. Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks. Mol Ecol 2013; 23:110-7. [DOI: 10.1111/mec.12583] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/25/2013] [Accepted: 10/25/2013] [Indexed: 11/29/2022]
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116 |
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DiBattista JD, Anisman H, Whitehead M, Gilmour KM. The effects of cortisol administration on social status and brain monoaminergic activity in rainbow troutOncorhynchus mykiss. J Exp Biol 2005; 208:2707-18. [PMID: 16000540 DOI: 10.1242/jeb.01690] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARYThe hypothesis that circulating cortisol levels influence the outcome of social interactions in rainbow trout was tested. Juvenile rainbow trout Oncorhynchus mykiss were given a single intraperitoneal (i.p.)implant containing either cortisol (110 mg kg–1 fish), or cortisol plus the glucocorticoid receptor antagonist RU486 (mifepristone; 1100 mg kg–1 fish), and sampled after 5 days of social interactions with either a similar sized (<1.5% difference in fork length)or smaller conspecific (>5% difference). Within size-matched pairs of fish,cortisol treatment significantly increased the probability that the treated fish within each pair became subordinate, an effect that was abolished by simultaneous administration of RU486. Cortisol treatment also reduced the usual success of the larger fish within a pair to preferentially become dominant from 86% to 40% of pairs. To investigate one potential mechanism underlying the apparent effect of cortisol in predisposing trout to low social status, fish were treated with cortisol or cortisol+RU486 for 5 days, after which brain monoamines [5-hydroxytryptamine (5-HT); dopamine (DA)] and their major metabolites [5-hydroxyindolacetic acid (5-HIAA);3,4-dihydroxy-phenylacetic acid (DOPAC)] were measured. Significant increases of serotonergic activity ([5-HIAA]/[5-HT] ratio) were detected in the telencephalon with cortisol treatment, an effect that was eliminated by simultaneous administration of RU486. Also, cortisol treatment significantly decreased dopaminergic activity in the telencephalon. Somewhat surprisingly,the effects of cortisol treatment on monoaminergic activity in the hypothalamus were opposite to those in the telencephalon. Moreover, in no case did administration of RU486 abolish these effects. These results suggest that the effects of cortisol on social status in rainbow trout may be mediated via the modulation of central signaling systems and subsequent changes in behaviour and/or competitive ability, although the exact site of action in the brain remains uncertain.
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Siepielski AM, DiBattista JD, Evans JA, Carlson SM. Differences in the temporal dynamics of phenotypic selection among fitness components in the wild. Proc Biol Sci 2010; 278:1572-80. [PMID: 21047862 DOI: 10.1098/rspb.2010.1973] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The balance of selection acting through different fitness components (e.g. fecundity, mating success, survival) determines the potential tempo and trajectory of adaptive evolution. Yet the extent to which the temporal dynamics of phenotypic selection may vary among fitness components is poorly understood. Here, we compiled a database of 3978 linear selection coefficients from temporally replicated studies of selection in wild populations to address this question. Across studies, we find that multi-year selection through mating success and fecundity is stronger than selection through survival, but varies less in direction. We also report that selection through mating success varies more in long-term average strength than selection through either survival or fecundity. The consistency in direction and stronger long-term average strength of selection through mating success and fecundity suggests that selection through these fitness components should cause more persistent directional evolution relative to selection through survival. Similar patterns were apparent for the subset of studies that evaluated the temporal dynamics of selection on traits simultaneously using several different fitness components, but few such studies exist. Taken together, these results reveal key differences in the temporal dynamics of selection acting through different fitness components, but they also reveal important limitations in our understanding of how selection drives adaptive evolution.
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Research Support, U.S. Gov't, Non-P.H.S. |
15 |
94 |
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Koziol A, Stat M, Simpson T, Jarman S, DiBattista JD, Harvey ES, Marnane M, McDonald J, Bunce M. Environmental DNA metabarcoding studies are critically affected by substrate selection. Mol Ecol Resour 2018; 19:366-376. [DOI: 10.1111/1755-0998.12971] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/08/2018] [Accepted: 11/14/2018] [Indexed: 01/24/2023]
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DiBattista JD, Feldheim KA, Gruber SH, Hendry AP. Are indirect genetic benefits associated with polyandry? Testing predictions in a natural population of lemon sharks. Mol Ecol 2008; 17:783-95. [PMID: 18194167 DOI: 10.1111/j.1365-294x.2007.03623.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multiple mating has clear fitness benefits for males, but uncertain benefits and costs for females. We tested for indirect genetic benefits of polyandry in a natural population, by using data from a long-term genetic and demographic study of lemon sharks (Negaprion brevirostris) at Bimini, Bahamas. To do so, we followed the fates of individuals from six cohorts (450 age-0 and 254 age-1 fish) in relation to their individual level of genetic variation, and whether they were from polyandrous or monoandrous litters. We find that offspring from polyandrous litters did not have a greater genetic diversity or greater survival than did the offspring of monoandrous litters. We also find no evidence of positive associations between individual offspring genetic diversity metrics and our surrogate measure of fitness (i.e. survival). In fact, age-1 individuals with fewer heterozygous microsatellite loci and more genetically similar parents were more likely to survive to age-2. Thus, polyandry in female lemon sharks does not appear to be adaptive from the perspective of indirect genetic benefits to offspring. It may instead be the result of convenience polyandry, whereby females mate multiply to avoid harassment by males. Our inability to find indirect genetic benefits of polyandry despite detailed pedigree and survival information suggests the need for similar assessments in other natural populations.
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Research Support, U.S. Gov't, Non-P.H.S. |
17 |
65 |
10
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West KM, Stat M, Harvey ES, Skepper CL, DiBattista JD, Richards ZT, Travers MJ, Newman SJ, Bunce M. eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem. Mol Ecol 2020; 29:1069-1086. [PMID: 32045076 DOI: 10.1111/mec.15382] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 01/30/2020] [Accepted: 02/06/2020] [Indexed: 01/10/2023]
Abstract
Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.
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Research Support, Non-U.S. Gov't |
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63 |
11
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DiBattista JD, Rocha LA, Craig MT, Feldheim KA, Bowen BW. Phylogeography of two closely related Indo-Pacific butterflyfishes reveals divergent evolutionary histories and discordant results from mtDNA and microsatellites. ACTA ACUST UNITED AC 2012; 103:617-29. [PMID: 22888133 DOI: 10.1093/jhered/ess056] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Marine biogeographic barriers can have unpredictable consequences, even among closely related species. To resolve phylogeographic patterns for Indo-Pacific reef fauna, we conducted range-wide surveys of sister species, the scrawled butterflyfish (Chaetodon meyeri; N = 134) and the ornate butterflyfish (Chaetodon ornatissimus; N = 296), using mitochondrial DNA cytochrome b sequences and 10 microsatellite loci. The former is distributed primarily in the Indian Ocean but also extends to the Line Islands in the Central Pacific, whereas the latter is distributed primarily in the Central-West Pacific (including Hawaii and French Polynesia) but extends to the eastern margin of the Indian Ocean. Analyses of molecular variance and Bayesian STRUCTURE results revealed 1 range-wide group for C. meyeri and 3 groups for C. ornatissimus: 1) eastern Indian Ocean and western Pacific, 2) Central Pacific, and 3) Hawaii. Estimates of the last population expansion were much more recent for C. meyeri (61 500 to 95 000 years) versus C. ornatissimus (184 700 to 286 300 years). Despite similarities in ecology, morphology, life history, and a broadly overlapping distribution, these sister species have divergent patterns of dispersal and corresponding evolutionary history. The mtDNA and microsatellite markers did not provide concordant results within 1 of our study species (C. meyeri), or in 7 out of 12 other cases of marine fishes in the published literature. This discordance renews caution in relying on one or a few markers for reconstructing historical demography.
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Research Support, U.S. Gov't, Non-P.H.S. |
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Stat M, John J, DiBattista JD, Newman SJ, Bunce M, Harvey ES. Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2019; 33:196-205. [PMID: 30004598 PMCID: PMC7379492 DOI: 10.1111/cobi.13183] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/11/2018] [Accepted: 06/30/2018] [Indexed: 05/19/2023]
Abstract
Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty-two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs' spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (∼35 km2 ). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems.
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DiBattista JD, Levesque HM, Moon TW, Gilmour KM. Growth Depression in Socially Subordinate Rainbow TroutOncorhynchus mykiss: More than a Fasting Effect. Physiol Biochem Zool 2006; 79:675-87. [PMID: 16826494 DOI: 10.1086/504612] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2005] [Indexed: 11/03/2022]
Abstract
To assess the effects of subordinate social status on digestive function, metabolism, and enzyme activity in salmonid fish, juvenile rainbow trout Oncorhynchus mykiss were paired with size-matched conspecifics (<1.5% difference in fork length) for 5 d. Fish that were fasted for 5 d and fish sampled directly from the holding tank were used as control groups. Both subordinate and fasted fish experienced significant decreases in intestine mass (P = 0.043), and the gall bladder showed marked and significant changes in both size (P = 0.004) and appearance. These findings suggest that the negative effect of social subordination on digestive function reflects in large part a lack of feeding. Hepatic phosphoenolpyruvate carboxykinase activity was significantly higher in subordinate fish relative to dominants, whereas subordinate hepatic pyruvate kinase activity was significantly lower; activities of both enzymes were significantly correlated with plasma cortisol concentrations and behavior scores. Dominant-subordinate differences in the activities of these enzymes were eliminated by administration of the glucocorticoid receptor antagonist RU486, underlining a role for circulating cortisol in eliciting the differences. Significant increases relative to control fish were also detected in red and white muscles from subordinate fish in the activities of protein catabolic enzymes (aspartate aminotransferase, alanine aminotransferase, glutamate dehydrogenase). These differences occurred in the absence of any change in plasma free amino acid or ammonia concentrations, supporting an enhanced turnover of amino acids in muscle in subordinate fish. The results support the hypothesis that changes in metabolism, beyond those elicited by low food consumption, may be responsible at least in part for the low growth rates typical of subordinate fish and that these changes may be related specifically to circulating cortisol levels in subordinate fish.
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DiBattista JD, Feldheim KA, Thibert-Plante X, Gruber SH, Hendry AP. A genetic assessment of polyandry and breeding-site fidelity in lemon sharks. Mol Ecol 2008; 17:3337-51. [PMID: 18564083 DOI: 10.1111/j.1365-294x.2008.03833.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We here employ 11 microsatellite markers and recently developed litter reconstruction methods to infer mating system parameters (i.e. polyandry and breeding-site fidelity) at a lemon shark nursery site in Marquesas Key, Florida. Four hundred and eight juvenile or subadult sharks were genotyped over eight complete breeding seasons. Using this information, we were able to infer family structure, as well as fully or partially reconstruct genotypes of 46 mothers and 163 fathers. Multiple litter reconstruction methods were used, and novel simulations helped define apparent bias and precision of at least some mating system parameters. For Marquesas Key, we find that adult female lemon sharks display high levels of polyandry (81% of all litters sampled) and stronger fidelity to the nursery site than do males. Indeed, few male sharks sired offspring from more than one litter during the course of the study. These findings were quite similar to previous results from another lemon shark nursery site (Bimini, Bahamas), suggesting conserved mating system parameters despite significant variation in early life-history traits (i.e. body size and growth) among sites. The finding of at least some site fidelity in females also supports the need for careful conservation of each nursery.
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Research Support, U.S. Gov't, Non-P.H.S. |
17 |
39 |
15
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Jones J, DiBattista JD, Stat M, Bunce M, Boyce MC, Fairclough DV, Travers MJ, Huggett MJ. The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish. Front Microbiol 2018; 9:2000. [PMID: 30210475 PMCID: PMC6121097 DOI: 10.3389/fmicb.2018.02000] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/08/2018] [Indexed: 01/01/2023] Open
Abstract
Globally, marine species’ distributions are being modified due to rising ocean temperatures. Increasing evidence suggests a circum-global pattern of poleward extensions in the distributions of many tropical herbivorous species, including the ecologically important rabbitfish Siganus fuscescens. Adaptability of a species to such new environments may be heavily influenced by the composition of their gastrointestinal microbe fauna, which is fundamentally important to animal health. Siganus fuscescens thus provides an opportunity to assess the stability of gastrointestinal microbes under varying environmental conditions. The gastrointestinal microbial communities of S. fuscescens were characterized over 2,000 km of Australia’s western coast, from tropical to temperate waters, including near its current southern distributional limit. Sequencing of the 16S rRNA gene demonstrated that each population had a distinct hindgut microbial community, and yet, 20 OTUs occurred consistently in all samples. These OTUs were considered the ‘core microbiome’ and were highly abundant, composing between 31 and 54% of each population. Furthermore, levels of short chain fatty acids, an indicator of microbial fermentation activity, were similar among tropical and temperate locations. These data suggest that flexibility in the hindgut microbiome may play a role in enabling such herbivores to colonize new environments beyond their existing range.
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Journal Article |
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38 |
16
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DiBattista JD, Travers MJ, Moore GI, Evans RD, Newman SJ, Feng M, Moyle SD, Gorton RJ, Saunders T, Berry O. Seascape genomics reveals fine-scale patterns of dispersal for a reef fish along the ecologically divergent coast of Northwestern Australia. Mol Ecol 2017; 26:6206-6223. [DOI: 10.1111/mec.14352] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 01/04/2023]
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DiBattista JD, Reimer JD, Stat M, Masucci GD, Biondi P, De Brauwer M, Wilkinson SP, Chariton AA, Bunce M. Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems. Sci Rep 2020; 10:8365. [PMID: 32433472 PMCID: PMC7239923 DOI: 10.1038/s41598-020-64858-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/23/2020] [Indexed: 01/29/2023] Open
Abstract
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities.
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Research Support, Non-U.S. Gov't |
5 |
36 |
18
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Malvezzi AJ, Murray CS, Feldheim KA, DiBattista JD, Garant D, Gobler CJ, Chapman DD, Baumann H. A quantitative genetic approach to assess the evolutionary potential of a coastal marine fish to ocean acidification. Evol Appl 2015; 8:352-62. [PMID: 25926880 PMCID: PMC4408146 DOI: 10.1111/eva.12248] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/15/2015] [Indexed: 12/24/2022] Open
Abstract
Assessing the potential of marine organisms to adapt genetically to increasing oceanic CO2 levels requires proxies such as heritability of fitness-related traits under ocean acidification (OA). We applied a quantitative genetic method to derive the first heritability estimate of survival under elevated CO2 conditions in a metazoan. Specifically, we reared offspring, selected from a wild coastal fish population (Atlantic silverside, Menidia menidia), at high CO2 conditions (∼2300 μatm) from fertilization to 15 days posthatch, which significantly reduced survival compared to controls. Perished and surviving offspring were quantitatively sampled and genotyped along with their parents, using eight polymorphic microsatellite loci, to reconstruct a parent–offspring pedigree and estimate variance components. Genetically related individuals were phenotypically more similar (i.e., survived similarly long at elevated CO2 conditions) than unrelated individuals, which translated into a significantly nonzero heritability (0.20 ± 0.07). The contribution of maternal effects was surprisingly small (0.05 ± 0.04) and nonsignificant. Survival among replicates was positively correlated with genetic diversity, particularly with observed heterozygosity. We conclude that early life survival of M. menidia under high CO2 levels has a significant additive genetic component that could elicit an evolutionary response to OA, depending on the strength and direction of future selection.
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Journal Article |
10 |
35 |
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Pelletier JP, McCollum R, DiBattista J, Loose LD, Cloutier JM, Martel-Pelletier J. Regulation of human normal and osteoarthritic chondrocyte interleukin-1 receptor by antirheumatic drugs. ARTHRITIS AND RHEUMATISM 1993; 36:1517-27. [PMID: 8240429 DOI: 10.1002/art.1780361106] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
OBJECTIVE To determine the effect of antirheumatic drugs and corticosteroids on interleukin-1 receptor (IL-1R) levels in, and IL-1-stimulated metalloprotease synthesis and expression by, normal and osteoarthritic (OA) human articular chondrocytes. METHODS IL-1R affinity and density of human chondrocytes were determined using radioligand binding experiments. Collagenase and stromelysin synthesis activities were analyzed by 14C-labeled type I collagen and Azocoll assays, respectively. Their messenger RNA (mRNA) levels were determined by Northern blot analysis. IL-1 alpha, IL-1 beta, IL-1 receptor antagonist, and beta 2-microglobulin were measured using enzyme-linked immunosorbent assays. Protein synthesis was determined by 3H-leucine incorporation. RESULTS Antirheumatic drugs reduced the IL-1R level in normal and OA chondrocytes in a dose-dependent manner. In normal chondrocytes, tenidap reduced the IL-1R level by 44% at 5 micrograms/ml to 88% at 100 micrograms/ml (50% inhibition constant [IC50] 10.1 micrograms/ml), indomethacin reduced IL-1R by 6% at 1.5 micrograms/ml to 43% at 60 micrograms/ml, and naproxen reduced IL-1R by 10% at 10 micrograms/ml to 41% at 300 micrograms/ml; the effects observed with indomethacin and naproxen occurred only when the drugs were used at levels above their therapeutic concentrations. In OA chondrocytes, the effect of indomethacin and naproxen on the IL-1R level was greatly reduced, whereas tenidap still had a marked effect (IC50 22.5 micrograms/ml). Dexamethasone and hydrocortisone had no consistent effect on the IL-1R level. At a therapeutic concentration (20 micrograms/ml), tenidap was found to reduce the IL-1R level in a time-dependent manner, with maximum inhibition (98%) by 48 hours. Tenidap was also found to markedly reduce collagenase and stromelysin synthesis and mRNA levels in IL-1-stimulated chondrocytes. CONCLUSION The suppressive effects of tenidap on IL-1-stimulated metalloprotease synthesis and expression in OA and normal chondrocytes are likely related to a decrease in IL-1R levels. At therapeutic concentrations, tenidap has a greater effect on the IL-1R level than is seen with indomethacin or naproxen, and glucocorticoids have no effect on IL-1R.
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DiBattista JD, Feldheim KA, Garant D, Gruber SH, Hendry AP. EVOLUTIONARY POTENTIAL OF A LARGE MARINE VERTEBRATE: QUANTITATIVE GENETIC PARAMETERS IN A WILD POPULATION. Evolution 2009; 63:1051-67. [DOI: 10.1111/j.1558-5646.2008.00605.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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West K, Travers MJ, Stat M, Harvey ES, Richards ZT, DiBattista JD, Newman SJ, Harry A, Skepper CL, Heydenrych M, Bunce M. Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13228] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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DiBattista JD, Whitney J, Craig MT, Hobbs JPA, Rocha LA, Feldheim KA, Berumen ML, Bowen BW. Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes. Mol Phylogenet Evol 2016; 101:203-215. [DOI: 10.1016/j.ympev.2016.04.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/12/2016] [Accepted: 04/29/2016] [Indexed: 11/27/2022]
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Coleman RR, Eble JA, DiBattista JD, Rocha LA, Randall JE, Berumen ML, Bowen BW. Regal phylogeography: Range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean. Mol Phylogenet Evol 2016; 100:243-253. [PMID: 27068838 DOI: 10.1016/j.ympev.2016.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 11/27/2022]
Abstract
The regal angelfish (Pygoplites diacanthus; family Pomacanthidae) occurs on reefs from the Red Sea to the central Pacific, with an Indian Ocean/Rea Sea color morph distinct from a Pacific Ocean morph. To assess population differentiation and evaluate the possibility of cryptic evolutionary partitions in this monotypic genus, we surveyed mtDNA cytochrome b and two nuclear introns (S7 and RAG2) in 547 individuals from 15 locations. Phylogeographic analyses revealed four mtDNA lineages (d=0.006-0.015) corresponding to the Pacific Ocean, the Red Sea, and two admixed lineages in the Indian Ocean, a pattern consistent with known biogeographic barriers. Christmas Island in the eastern Indian Ocean had both Indian and Pacific lineages. Both S7 and RAG2 showed strong population-level differentiation between the Red Sea, Indian Ocean, and Pacific Ocean (ΦST=0.066-0.512). The only consistent population sub-structure within these three regions was at the Society Islands (French Polynesia), where surrounding oceanographic conditions may reinforce isolation. Coalescence analyses indicate the Pacific (1.7Ma) as the oldest extant lineage followed by the Red Sea lineage (1.4Ma). Results from a median-joining network suggest radiations of two lineages from the Red Sea that currently occupy the Indian Ocean (0.7-0.9Ma). Persistence of a Red Sea lineage through Pleistocene glacial cycles suggests a long-term refuge in this region. The affiliation of Pacific and Red Sea populations, apparent in cytochrome b and S7 (but equivocal in RAG2) raises the hypothesis that the Indian Ocean was recolonized from the Red Sea, possibly more than once. Assessing the genetic architecture of this widespread monotypic genus reveals cryptic evolutionary diversity that merits subspecific recognition. We recommend P.d. diacanthus and P.d. flavescens for the Pacific and Indian Ocean/Red Sea forms.
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DiBattista JD, Reimer JD, Stat M, Masucci GD, Biondi P, De Brauwer M, Bunce M. Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient. PeerJ 2019; 7:e6379. [PMID: 30755831 PMCID: PMC6368839 DOI: 10.7717/peerj.6379] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/24/2018] [Indexed: 11/20/2022] Open
Abstract
Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.
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DiBattista JD, Feldheim KA, Garant D, Gruber SH, Hendry AP. Anthropogenic disturbance and evolutionary parameters: a lemon shark population experiencing habitat loss. Evol Appl 2010; 4:1-17. [PMID: 25567949 PMCID: PMC3352521 DOI: 10.1111/j.1752-4571.2010.00125.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 02/19/2010] [Indexed: 11/26/2022] Open
Abstract
The level of genetic variation in natural populations influences evolutionary potential, and may therefore influence responses to selection in the face of future environmental changes. By combining long-term monitoring of marked individuals with genetic pedigree reconstruction, we assessed whether habitat loss influenced genetic variation in a lemon shark (Negaprion brevirostris) population at an isolated nursery lagoon (Bimini, Bahamas). We also tracked changes in the strength and direction of natural selection. Contrary to initial expectations, we found that after the habitat loss neutral genetic variation increased, as did additive genetic variance for juvenile morphological traits (body length and mass). We hypothesize that these effects might result from philopatric behavior in females coupled with a possible influx of male genotypes from other nursery sites. We also found changes in the strength of selection on morphological traits, which weakened considerably after the disturbance; habitat loss therefore changed the phenotypes favored by natural selection. Because such human-induced shifts in the adaptive landscape may be common, we suggest that conservation biologists should not simply focus on neutral genetic variation per se, but also on assessing and preserving evolutionary parameters, such as additive genetic variation and selection.
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