101
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Ladds MA, Sibanda N, Arnold R, Dunn MR. Creating functional groups of marine fish from categorical traits. PeerJ 2018; 6:e5795. [PMID: 30370185 PMCID: PMC6202955 DOI: 10.7717/peerj.5795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/20/2018] [Indexed: 11/20/2022] Open
Abstract
Background Functional groups serve two important functions in ecology: they allow for simplification of ecosystem models and can aid in understanding diversity. Despite their important applications, there has not been a universally accepted method of how to define them. A common approach is to cluster species on a set of traits, validated through visual confirmation of resulting groups based primarily on expert opinion. The goal of this research is to determine a suitable procedure for creating and evaluating functional groups that arise from clustering nominal traits. Methods To do so, we produced a species by trait matrix of 22 traits from 116 fish species from Tasman Bay and Golden Bay, New Zealand. Data collected from photographs and published literature were predominantly nominal, and a small number of continuous traits were discretized. Some data were missing, so the benefit of imputing data was assessed using four approaches on data with known missing values. Hierarchical clustering is utilised to search for underlying data structure in the data that may represent functional groups. Within this clustering paradigm there are a number of distance matrices and linkage methods available, several combinations of which we test. The resulting clusters are evaluated using internal metrics developed specifically for nominal clustering. This revealed the choice of number of clusters, distance matrix and linkage method greatly affected the overall within- and between- cluster variability. We visualise the clustering in two dimensions and the stability of clusters is assessed through bootstrapping. Results Missing data imputation showed up to 90% accuracy using polytomous imputation, so was used to impute the real missing data. A division of the species information into three functional groups was the most separated, compact and stable result. Increasing the number of clusters increased the inconsistency of group membership, and selection of the appropriate distance matrix and linkage method improved the fit. Discussion We show that the commonly used methodologies used for the creation of functional groups are fraught with subjectivity, ultimately causing significant variation in the composition of resulting groups. Depending on the research goal dictates the appropriate strategy for selecting number of groups, distance matrix and clustering algorithm combination.
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Affiliation(s)
- Monique A Ladds
- School of Mathematics and Statistics, Victoria University of Wellington, Kelburn, Wellington, New Zealand
| | - Nokuthaba Sibanda
- School of Mathematics and Statistics, Victoria University of Wellington, Kelburn, Wellington, New Zealand
| | - Richard Arnold
- School of Mathematics and Statistics, Victoria University of Wellington, Kelburn, Wellington, New Zealand
| | - Matthew R Dunn
- Population Modelling Group, National Institute of Water and Atmospheric Research, Wellington, New Zealand
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Neubauer P, Thorson JT, Melnychuk MC, Methot R, Blackhart K. Drivers and rates of stock assessments in the United States. PLoS One 2018; 13:e0196483. [PMID: 29750789 PMCID: PMC5947900 DOI: 10.1371/journal.pone.0196483] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/13/2018] [Indexed: 11/18/2022] Open
Abstract
Fisheries management is most effective when based on scientific estimates of sustainable fishing rates. While some simple approaches allow estimation of harvest limits, more data-intensive stock assessments are generally required to evaluate the stock's biomass and fishing rates relative to sustainable levels. Here we evaluate how stock characteristics relate to the rate of new assessments in the United States. Using a statistical model based on time-to-event analysis and 569 coastal marine fish and invertebrate stocks landed in commercial fisheries, we quantify the impact of region, habitat, life-history, and economic factors on the annual probability of being assessed. Although the majority of landings come from assessed stocks in all regions, less than half of the regionally-landed species currently have been assessed. As expected, our time-to-event model identified landed tonnage and ex-vessel price as the dominant factors determining increased rates of new assessments. However, we also found that after controlling for landings and price, there has been a consistent bias towards assessing larger-bodied species. A number of vulnerable groups such as rockfishes (Scorpaeniformes) and groundsharks (Carcharhiniformes) have a relatively high annual probability of being assessed after controlling for their relatively small tonnage and low price. Due to relatively low landed tonnage and price of species that are currently unassessed, our model suggests that the number of assessed stocks will increase more slowly in future decades.
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Affiliation(s)
| | - James T. Thorson
- NOAA Northwest Fisheries Science Center, Seattle, WA, United States of America
| | - Michael C. Melnychuk
- School of Aquatic and Fisheries Science, University of Washington, Seattle, WA, United States of America
| | - Richard Methot
- NOAA Northwest Fisheries Science Center, Seattle, WA, United States of America
| | - Kristan Blackhart
- ECS Federal, INC., Fairfax, VA, United States of America, on behalf of NOAA Fisheries, Office of Science and Technology
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103
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Abstract
The diversity of forms found among animals on Earth is striking. Despite decades of study, it has been difficult to reconcile the patterns of diversity seen between closely related species with those observed when studying single species on ecological timescales. We propose a set of models, called Lévy processes, to attempt to reconcile rapid evolution between species with the relatively stable distributions of phenotypes seen within species. These models, which have been successfully used to model stock market data, allow for long periods of stasis followed by bursts of rapid change. We find that many vertebrate groups are well fitted by Lévy models compared with models for which traits evolve toward a stationary optimum or evolve in an incremental and wandering manner. The relative importance of different modes of evolution in shaping phenotypic diversity remains a hotly debated question. Fossil data suggest that stasis may be a common mode of evolution, while modern data suggest some lineages experience very fast rates of evolution. One way to reconcile these observations is to imagine that evolution proceeds in pulses, rather than in increments, on geological timescales. To test this hypothesis, we developed a maximum-likelihood framework for fitting Lévy processes to comparative morphological data. This class of stochastic processes includes both an incremental and a pulsed component. We found that a plurality of modern vertebrate clades examined are best fitted by pulsed processes over models of incremental change, stationarity, and adaptive radiation. When we compare our results to theoretical expectations of the rate and speed of regime shifts for models that detail fitness landscape dynamics, we find that our quantitative results are broadly compatible with both microevolutionary models and observations from the fossil record.
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104
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A global database on freshwater fish species occurrence in drainage basins. Sci Data 2017; 4:170141. [PMID: 28972575 PMCID: PMC5625552 DOI: 10.1038/sdata.2017.141] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/01/2017] [Indexed: 11/08/2022] Open
Abstract
A growing interest is devoted to global-scale approaches in ecology and evolution that examine patterns and determinants of species diversity and the threats resulting from global change. These analyses obviously require global datasets of species distribution. Freshwater systems house a disproportionately high fraction of the global fish diversity considering the small proportion of the earth's surface that they occupy, and are one of the most threatened habitats on Earth. Here we provide complete species lists for 3119 drainage basins covering more than 80% of the Earth surface using 14953 fish species inhabiting permanently or occasionally freshwater systems. The database results from an extensive survey of native and non-native freshwater fish species distribution based on 1436 published papers, books, grey literature and web-based sources. Alone or in combination with further datasets on species biological and ecological characteristics and their evolutionary history, this database represents a highly valuable source of information for further studies on freshwater macroecology, macroevolution, biogeography and conservation.
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105
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Improving understanding of the functional diversity of fisheries by exploring the influence of global catch reconstruction. Sci Rep 2017; 7:10746. [PMID: 28878250 PMCID: PMC5587757 DOI: 10.1038/s41598-017-10723-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/14/2017] [Indexed: 11/08/2022] Open
Abstract
Functional diversity is thought to enhance ecosystem resilience, driving research focused on trends in the functional composition of fisheries, most recently with new reconstructions of global catch data. However, there is currently little understanding of how accounting for unreported catches (e.g. small-scale and illegal fisheries, bycatch and discards) influences functional diversity trends in global fisheries. We explored how diversity estimates varied among reported and unreported components of catch in 2010, and found these components had distinct functional fingerprints. Incorporating unreported catches had little impact on global-scale functional diversity patterns. However, at smaller, management-relevant scales, the effects of incorporating unreported catches were large (changes in functional diversity of up to 46%). Our results suggest there is greater uncertainty about the risks to ecosystem integrity and resilience from current fishing patterns than previously recognized. We provide recommendations and suggest a research agenda to improve future assessments of functional diversity of global fisheries.
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106
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McCurry MR, Fitzgerald EMG, Evans AR, Adams JW, McHenry CR. Skull shape reflects prey size niche in toothed whales. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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107
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Martin BT, Heintz R, Danner EM, Nisbet RM. Integrating lipid storage into general representations of fish energetics. J Anim Ecol 2017; 86:812-825. [PMID: 28326538 DOI: 10.1111/1365-2656.12667] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 03/01/2017] [Indexed: 11/26/2022]
Abstract
Fish, even of the same species, can exhibit substantial variation in energy density (energy per unit wet weight). Most of this variation is due to differences in the amount of storage lipids. In addition to their importance as energy reserves for reproduction and for survival during unfavourable conditions, the accumulation of lipids represents a large energetic flux for many species, so figuring out how this energy flux is integrated with other major energy fluxes (growth, reproduction) is critical for any general theory of organismal energetics. Here, we synthesize data from a wide range of fish species and identify patterns of intraspecific variation in energy storage, and use these patterns to formulate a general model of energy allocation between growth, lipid storage and reproduction in fishes. From the compiled data we identified two patterns: (1) energy density increases with body size during the juvenile period, but is invariant with body size within the adult size range for most species, and (2) energy density changes across seasons, with depletion over winter, but increases fastest in periods of transition between favourable and unfavourable conditions for growth (i.e. fall). Based on these patterns we propose DEBlipid, a simple, general model of energy allocation that is closely related to a simplified version of Dynamic Energy Budget theory, DEBkiss. The crux of the model is that assimilated energy is partitioned, with κ fraction of energy allocated to pay maintenance costs first, and the surplus allocated to growth, and 1 - κ fraction of assimilated energy is allocated to accumulating storage lipids during the juvenile phase, and later to reproduction as adults. This mechanism, in addition to capturing the two patterns that motivated the model, was able to predict lipid dynamics in a novel context, the migration of anadromous fish from low-food freshwater to high-food marine environments. Furthermore, the model was used to explain intra and interspecific variation in reproductive output based on patterns of lipid accumulation as juveniles. Our results suggest that many seemingly complex, adaptive energy allocation strategies in response to ontogeny, seasonality and habitat quality can emerge from a simple physiological heuristic.
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Affiliation(s)
- Benjamin T Martin
- Cooperative Institute for Marine Ecosystems and Climate (CIMEC), University of California, 1156 High St, Santa Cruz, CA, 95064, USA.,Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, 110 Shaffer Road, Santa Cruz, CA, 95060, USA
| | - Ron Heintz
- Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, 7600 Sand Point Way N.E., Building 4, Seattle, WA, 98115, USA
| | - Eric M Danner
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, 110 Shaffer Road, Santa Cruz, CA, 95060, USA
| | - Roger M Nisbet
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106-9610, USA
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108
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Michonneau F, Brown JW, Winter DJ. rotl: an R package to interact with the Open Tree of Life data. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12593] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- François Michonneau
- Whitney Laboratory for Marine Sciences University of Florida St. Augustine FL 32080 USA
- Florida Museum of Natural History University of Florida Gainesville FL 32611‐7800 USA
| | - Joseph W. Brown
- Department of Ecology & Evolutionary Biology University of Michigan Ann Arbor MI 48109 USA
| | - David J. Winter
- Virginia G. Piper Centre for Personalized Diagnostics The Biodesign Institute, Arizona State University Tempe AZ 85287‐5001 USA
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109
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Bastos WR, Dórea JG, Bernardi JVE, Manzatto AG, Mussy MH, Lauthartte LC, Lacerda LD, Malm O. Sex-related mercury bioaccumulation in fish from the Madeira River, Amazon. ENVIRONMENTAL RESEARCH 2016; 144:73-80. [PMID: 26580025 DOI: 10.1016/j.envres.2015.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 11/01/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
UNLABELLED Sex plays an important role in the kinetics and dynamics of methylmercury in some animals. Although fish is the main source of mercury exposure to consumers, the role of sex in fish-Hg bioaccumulation is less known. We studied total Hg (THg) concentrations in 2538 samples (males=1052, females=1486) of fish from different trophic levels (herbivorous, planctivorous, detritivorous, omnivorous, carnivorous, piscivorous); for each species we made a post hoc estimation of the minimum number of samples required to detect variance-based differences between sexes. Only five of the 41 studied species showed significant difference between sexes; but, no consistent dominant pattern of THg concentrations favored either sex. When grouped by trophic levels, overall mean difference in THg concentrations between males and females were not statistically significant. Correlation analysis showed sex-dependent THg bio-accumulation as a function of condition factor was statistically significant and negative for all trophic levels (detritivorous, herviborous, omnivorous, planctivorous, carnivorous, and piscivorous). CONCLUSIONS Sex is not the main driver of Hg bioaccumulation in most Amazonian fish species; however, studies have to consider the minimum number of samples required to ascertain sex effects on THg bioaccumulation. Therefore, neither the surveillance of environmental pollution nor the current food advisories based on muscle THg need to change because of fish sex.
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Affiliation(s)
- Wanderley R Bastos
- Laboratório de Biogeoquímica Ambiental, Universidade Federal de Rondônia, Brazil.
| | - José G Dórea
- Faculdade de Ciências da Saúde, Universidade de Brasília, Brazil
| | | | - Angelo G Manzatto
- Laboratório de Biogeoquímica Ambiental, Universidade Federal de Rondônia, Brazil
| | - Marilia H Mussy
- Laboratório de Biogeoquímica Ambiental, Universidade Federal de Rondônia, Brazil; Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
| | | | - Luiz D Lacerda
- Laboratório de Biogeoquímica Costeira, Instituto de Ciências do Mar, Universidade Federal do Ceará, Brazil
| | - Olaf Malm
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
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110
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McGee MD, Borstein SR, Neches RY, Buescher HH, Seehausen O, Wainwright PC. A pharyngeal jaw evolutionary innovation facilitated extinction in Lake Victoria cichlids. Science 2015; 350:1077-9. [PMID: 26612951 DOI: 10.1126/science.aab0800] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Evolutionary innovations, traits that give species access to previously unoccupied niches, may promote speciation and adaptive radiation. Here, we show that such innovations can also result in competitive inferiority and extinction. We present evidence that the modified pharyngeal jaws of cichlid fishes and several marine fish lineages, a classic example of evolutionary innovation, are not universally beneficial. A large-scale analysis of dietary evolution across marine fish lineages reveals that the innovation compromises access to energy-rich predator niches. We show that this competitive inferiority shaped the adaptive radiation of cichlids in Lake Tanganyika and played a pivotal and previously unrecognized role in the mass extinction of cichlid fishes in Lake Victoria after Nile perch invasion.
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Affiliation(s)
- Matthew D McGee
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA. Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland. Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland.
| | - Samuel R Borstein
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Russell Y Neches
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Heinz H Buescher
- Zoological Institute, University of Basel, CH-4051 Basel, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland. Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
| | - Peter C Wainwright
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA
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111
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Co-extinction in a host-parasite network: identifying key hosts for network stability. Sci Rep 2015; 5:13185. [PMID: 26278333 PMCID: PMC4538395 DOI: 10.1038/srep13185] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 07/21/2015] [Indexed: 01/05/2023] Open
Abstract
Parasites comprise a substantial portion of total biodiversity. Ultimately, this means that host extinction could result in many secondary extinctions of obligate parasites and potentially alter host-parasite network structure. Here, we examined a highly resolved fish-parasite network to determine key hosts responsible for maintaining parasite diversity and network structure (quantified here as nestedness and modularity). We evaluated four possible host extinction orders and compared the resulting co-extinction dynamics to random extinction simulations; including host removal based on estimated extinction risk, parasite species richness and host level contributions to nestedness and modularity. We found that all extinction orders, except the one based on realistic extinction risk, resulted in faster declines in parasite diversity and network structure relative to random biodiversity loss. Further, we determined species-level contributions to network structure were best predicted by parasite species richness and host family. Taken together, we demonstrate that a small proportion of hosts contribute substantially to network structure and that removal of these hosts results in rapid declines in parasite diversity and network structure. As network stability can potentially be inferred through measures of network structure, our findings may provide insight into species traits that confer stability.
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112
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Bastos WR, Dórea JG, Bernardi JVE, Lauthartte LC, Mussy MH, Lacerda LD, Malm O. Mercury in fish of the Madeira river (temporal and spatial assessment), Brazilian Amazon. ENVIRONMENTAL RESEARCH 2015; 140:191-197. [PMID: 25863592 DOI: 10.1016/j.envres.2015.03.029] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 03/27/2015] [Accepted: 03/29/2015] [Indexed: 06/04/2023]
Abstract
The Madeira River is the largest tributary of the Amazon River Basin and one of the most impacted by artisanal gold-mining activities, deforestation for agricultural projects, and recent hydroelectric reservoirs. Total Hg (and methylmercury-MeHg) concentrations was determined in 3182 fish samples of 84 species from different trophic levels as a function of standard size. Species at the top of the trophic level (Piscivorous, Carnivorous) showed the highest mean total Hg concentrations (51-1242 µg/kg), Planctivorous and Omnivorous species showed intermediate total Hg concentrations (26-494 µg/kg), while Detritivorous and Herbivorous species showed the lowest range of mean total Hg concentrations (9-275 µg/kg). Significant correlations between fish size (standard length) and total Hg concentrations were seen for Planctivorous (r=0.474, p=0.0001), Piscivorous (r=0.459, p=0.0001), Detritivorous (r=0.227, p=0.0001), Carnivorous (r=0.212, p=0.0001), and Herbivorous (r=0.156, p=0.01), but not for the Omnivorous species (r=-0.064, p=0.0685). Moreover, fish trophic levels influenced the ratio of MeHg to total Hg (ranged from 70% to 92%). When adjusted for standard body length, significant increases in Hg concentrations in the last 10 years were species specific. Spatial differences, albeit significant for some species, were not consistent with time trends for environmental contamination from past alluvial gold mining activities. Fish-Hg bioaccumulation is species specific but fish feeding strategies are the predominant influence in the fish-Hg bioaccumulation pattern.
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Affiliation(s)
- Wanderley R Bastos
- Laboratório de Biogeoquímica Ambiental, Universidade Federal de Rondônia, Brazil.
| | - José G Dórea
- Faculdade de Ciências da Saúde, Universidade de Brasília, Brazil
| | | | | | - Marilia H Mussy
- Laboratório de Biogeoquímica Ambiental, Universidade Federal de Rondônia, Brazil; Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
| | - Luiz D Lacerda
- Laboratório de Biogeoquímica Costeira, Instituto de Ciências do Mar, Universidade Federal do Ceará, Ceará, Brazil
| | - Olaf Malm
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
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113
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Collins RA, Britz R, Rüber L. Phylogenetic systematics of leaffishes (Teleostei: Polycentridae, Nandidae). J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rupert A. Collins
- Laboratório de Evolução e Genética Animal; Departamento de Biologia; Universidade Federal do Amazonas; Manaus Amazonas Brasil
| | - Ralf Britz
- Vertebrates Division; Department of Life Sciences; Natural History Museum; London UK
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern; Bern Switzerland
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114
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Collins RA, Duarte Ribeiro E, Nogueira Machado V, Hrbek T, Farias IP. A preliminary inventory of the catfishes of the lower Rio Nhamundá, Brazil (Ostariophysi, Siluriformes). Biodivers Data J 2015; 3:e4162. [PMID: 25977611 PMCID: PMC4426332 DOI: 10.3897/bdj.3.e4162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 04/25/2015] [Indexed: 12/03/2022] Open
Abstract
The Rio Nhamundá is a poorly-known clearwater river draining the southern Guiana Shield of Brazil. In this study we report the findings of a preliminary ichthyological survey, focusing on catfishes (Siluriformes). We identify a total of 36 species (31 genera, seven families) from the Nhamundá, including 11 species already recorded from the river. Overall, our survey results show that even rapid surveys can provide important information on Amazon fish biodiversity, suggesting potential new species, providing range extensions for nominal species, and additionally highlighting taxa in need of taxonomic revision and genetic study. As well as the traditional forms of data collected on biodiversity surveys (i.e. preserved specimen vouchers), our study also provides "new" types of data in the form of DNA barcodes and images of fishes exhibiting colouration in life, information that will be invaluable in future work addressing difficult groups. O Rio Nhamundá é um rio de água clara, pouco conhecido, que drena parte do Escudo das Guianas em território brasileiro. Nesse estudo, nós reportamos os resultados de um levantamento ictiofaunístico preliminar dessa área, tendo como foco os bagres (Siluriformes). Nós identificamos um total de 36 espécies (31 gêneros, sete famílias) provenientes de nossa coleta, e adicionamos 11 espécies já conhecidas para o rio. De maneira geral, os resultados de nossa pesquisa mostram que mesmo levantamentos rápidos podem gerar informações importantes sobre a biodiversidade de peixes amazônicos, sugerindo potenciais espécies novas, ampliando a área de distribuição de espécies, além de apontar a necessidade de revisões taxonômicas e estudos genéticos para alguns taxa. Para além das formas tradicionais de dados coletados em pesquisas de biodiversidade (i.e. espécimes preservados), nosso estudo fornece "novas" formas de dados, como DNA barcodes e imagens com o padrão de coloração dos espécimes vivos, informações essas que serão de valor inestimável para futuros estudos que abordem grupos taxonômicos difíceis.
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Affiliation(s)
- Rupert A. Collins
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, Brazil
| | - Emanuell Duarte Ribeiro
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, Brazil
- Programa de Pós-Graduação em Genética Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Valéria Nogueira Machado
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, Brazil
| | - Izeni Pires Farias
- Laboratório de Evolução e Genética Animal, Departamento de Biologia, Universidade Federal do Amazonas, Manaus, Brazil
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115
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Boeger WA, Marteleto FM, Zagonel L, Braga MP. Tracking the history of an invasion: the freshwater croakers (Teleostei: Sciaenidae) in South America. ZOOL SCR 2014. [DOI: 10.1111/zsc.12098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Walter A. Boeger
- Laboratório de Ecologia Molecular e Parasitologia Evolutiva; Department de Zoologia; Universidade Federal do Paraná; Caixa Postal 19073 Curitiba PR 81531-9890 Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico; Curitiba Brazil
| | - Flávio M. Marteleto
- Laboratório de Ecologia Molecular e Parasitologia Evolutiva; Department de Zoologia; Universidade Federal do Paraná; Caixa Postal 19073 Curitiba PR 81531-9890 Brazil
- Curso de Pós Graduação em Ecologia e Conservação; Universidade Federal do Paraná; Curitiba PR 81531-9890 Brazil
| | - Letícia Zagonel
- Laboratório de Ecologia Molecular e Parasitologia Evolutiva; Department de Zoologia; Universidade Federal do Paraná; Caixa Postal 19073 Curitiba PR 81531-9890 Brazil
| | - Mariana P. Braga
- Laboratório de Ecologia Molecular e Parasitologia Evolutiva; Department de Zoologia; Universidade Federal do Paraná; Caixa Postal 19073 Curitiba PR 81531-9890 Brazil
- Curso de Pós Graduação em Ecologia e Conservação; Universidade Federal do Paraná; Curitiba PR 81531-9890 Brazil
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Price SA, Schmitz L, Oufiero CE, Eytan RI, Dornburg A, Smith WL, Friedman M, Near TJ, Wainwright PC. Two waves of colonization straddling the K-Pg boundary formed the modern reef fish fauna. Proc Biol Sci 2014; 281:20140321. [PMID: 24695431 PMCID: PMC3996619 DOI: 10.1098/rspb.2014.0321] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Living reef fishes are one of the most diverse vertebrate assemblages on Earth. Despite its prominence and ecological importance, the origins and assembly of the reef fish fauna is poorly described. A patchy fossil record suggests that the major colonization of reef habitats must have occurred in the Late Cretaceous and early Palaeogene, with the earliest known modern fossil coral reef fish assemblage dated to 50 Ma. Using a phylogenetic approach, we analysed the early evolutionary dynamics of modern reef fishes. We find that reef lineages successively colonized reef habitats throughout the Late Cretaceous and early Palaeogene. Two waves of invasion were accompanied by increasing morphological convergence: one in the Late Cretaceous from 90 to 72 Ma and the other immediately following the end-Cretaceous mass extinction. The surge in reef invasions after the Cretaceous–Palaeogene boundary continued for 10 Myr, after which the pace of transitions to reef habitats slowed. Combined, these patterns match a classic niche-filling scenario: early transitions to reefs were made rapidly by morphologically distinct lineages and were followed by a decrease in the rate of invasions and eventual saturation of morphospace. Major alterations in reef composition, distribution and abundance, along with shifts in climate and oceanic currents, occurred during the Late Cretaceous and early Palaeogene interval. A causal mechanism between these changes and concurrent episodes of reef invasion remains obscure, but what is clear is that the broad framework of the modern reef fish fauna was in place within 10 Myr of the end-Cretaceous extinction.
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Affiliation(s)
- S A Price
- Department of Evolution and Ecology, University of California, , Davis, CA 95618, USA, W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, , 925 North Mills Avenue, Claremont, CA 91711, USA, Department of Biological Science, Towson University, , Towson, MD 21252, USA, Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, , New Haven, CT, USA, Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, , Lawrence, KS 66045, USA, Department of Earth Sciences, University of Oxford, , Oxford OX1 3AN, UK
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117
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Visual acuity in pelagic fishes and mollusks. Vision Res 2013; 92:1-9. [DOI: 10.1016/j.visres.2013.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/13/2013] [Accepted: 08/16/2013] [Indexed: 11/20/2022]
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118
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Miya M, Friedman M, Satoh TP, Takeshima H, Sado T, Iwasaki W, Yamanoue Y, Nakatani M, Mabuchi K, Inoue JG, Poulsen JY, Fukunaga T, Sato Y, Nishida M. Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families. PLoS One 2013; 8:e73535. [PMID: 24023883 PMCID: PMC3762723 DOI: 10.1371/journal.pone.0073535] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/22/2013] [Indexed: 11/25/2022] Open
Abstract
Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae “Pelagia” in reference to the common habitat preference that links the 15 families.
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Affiliation(s)
- Masaki Miya
- Natural History Museum and Institute, Chiba, Chiba, Japan
- * E-mail:
| | - Matt Friedman
- Department of Earth Sciences, University of Oxford, Oxford, United Kingdom
| | - Takashi P. Satoh
- National Museum of Nature and Science, Tsukuba-shi, Ibaraki, Japan
| | - Hirohiko Takeshima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Tetsuya Sado
- Natural History Museum and Institute, Chiba, Chiba, Japan
| | - Wataru Iwasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Yusuke Yamanoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Masanori Nakatani
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Kohji Mabuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Jun G. Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Jan Yde Poulsen
- Natural History Collections, Bergen Museum, University of Bergen, Bergen, Norway
| | - Tsukasa Fukunaga
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Yukuto Sato
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Mutsumi Nishida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, Japan
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119
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Boettiger C, Temple Lang D. Treebase: an R package for discovery, access and manipulation of online phylogenies. Methods Ecol Evol 2012. [DOI: 10.1111/j.2041-210x.2012.00247.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Carl Boettiger
- Center for Population Biology; University of California; Davis CA 95616 USA
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