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Li W, Kuzoff R, Wong CK, Tucker A, Lynch M. Characterization of newly gained introns in Daphnia populations. Genome Biol Evol 2014; 6:2218-34. [PMID: 25123113 PMCID: PMC4202315 DOI: 10.1093/gbe/evu174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
As one of the few known species in an active phase of intron proliferation, the microcrustacean Daphnia pulex is an especially attractive system for interrogating the gain and loss of introns in natural populations. In this study, we used a comparative population-genomic approach to identify and characterize 90 recently gained introns in this species. Molecular clock analyses indicate that these introns arose between 3.9 × 10(5) and 1.45 × 10(4) years ago, with a spike in intron proliferation approximately 5.2 × 10(4) to 1.22 × 10(5) years ago. Parallel gains at homologous positions contribute to 47.8% (43/90) of discovered new introns. A disproportionally large number of new introns were found in historically isolated populations in Oregon. Nonetheless, derived, intron-bearing alleles were also identified in a wide range of geographic locations, suggesting intron gain and, to a lesser degree, intron loss are important sources of genetic variation in natural populations of Daphnia. A majority (55/90 or 61.1%) of the identified neointrons have associated internal direct repeats with lengths and compositions that are unlikely to occur by chance, suggesting repeated bouts of staggered double-strand breaks (DSBs) during their evolution. Accordingly, internal, staggered DSBs may contribute to a passive trend toward increased length and sequence diversity in nascent introns.
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Affiliation(s)
- Wenli Li
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin
| | - Robert Kuzoff
- Department of Biology, University of Wisconsin-Whitewater
| | - Chen Khuan Wong
- Genetics and Genomics Program, Department of Medicine, Boston University
| | | | - Michael Lynch
- Department of Biology, Indiana University, Bloomington
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Bellati A, Tiberti R, Cocca W, Galimberti A, Casiraghi M, Bogliani G, Galeotti P. A dark shell hiding great variability: a molecular insight into the evolution and conservation of melanicDaphniapopulations in the Alps. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12151] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Adriana Bellati
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Rocco Tiberti
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
- Alpine Wildlife Research Centre; Gran Paradiso National Park; Degioz 11 11010 Valsavarenche Aosta Italy
| | - Walter Cocca
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Andrea Galimberti
- ZooPlantLab; Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Maurizio Casiraghi
- ZooPlantLab; Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Giuseppe Bogliani
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
| | - Paolo Galeotti
- Department of Earth and Environmental Sciences; University of Pavia; Via Ferrata 9 27100 Pavia Italy
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Abstract
Determining the distribution of population extinction times is a fundamental problem in theoretical population biology. In particular, the tail properties, patterns in the probability of long-term persistence, have not been studied. Further, until now there have been no experimental or observational data sets with which to empirically test the "rare event" predictions of the standard stochastic theory of extinction, which holds that extinction times should be exponentially distributed. I performed an experimental study of extinction in a large number of replicate (n = 1076) laboratory populations of the waterflea Daphnia pulicaria. Observed extinction time ranged from 1 to 1239 days. Statistical models supported the hypothesis of a power-law distribution over the exponential distribution and other alternatives. This pattern contradicts the notion that population extinction time has an exponential tail, questioning its ubiquitous use in theoretical ecology. It is also a rare instance of a data set that exhibits power-law scaling under appropriate statistical criteria.
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Jeong H, Kotov AA, Lee W. Checklist of the freshwater Cladocera (Crustacea: Branchiopoda) of South Korea. P BIOL SOC WASH 2014. [DOI: 10.2988/0006-324x-127.1.216] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Lindholm M. Morphologically Conservative but Physiologically Diverse: The Mode of Stasis in Anostraca (Crustacea: Branchiopoda). Evol Biol 2014; 41:503-507. [PMID: 25152547 PMCID: PMC4129224 DOI: 10.1007/s11692-014-9283-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 05/12/2014] [Indexed: 11/18/2022]
Abstract
The essay discusses whether biotic and abiotic environments differ in their ability to speed up or slow down morphological change and the generation of new lineages. Examples from the class Branchiopoda show that morphological conservatism is associated with enemy free space in species-poor habitats dominated by abiotic factors, while Red Queen mechanisms are predominant in larger systems with complex biotic interactions. Splitting of Branchiopod main lineages is associated with increased fish predation during the Devonian. The order Cladocera adapted and remained in larger aquatic systems, and subsequently generated a variety of new families, genera and species. The order Anostraca, on the other hand, maintained its ancestral morphology and survived only as "living fossils" in isolated ponds of harsh habitats. Despite their archaic morphology, however, they possess highly sophisticated adaptations to local physicochemical properties of their extreme environment. Hence, although morphologically conservative and possessing traits typical for "living fossils", anostracan physiological abilities are closely adapted to the challenging and variable physicochemical conditions of ponds and ephemeral pools.
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Affiliation(s)
- Markus Lindholm
- Norwegian Institute for Water Research/NIVA, Gaustadalleen 23, 0349 Oslo, Norway
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56
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A checklist of epibiotic ciliates (Peritrichia and Suctoria) on the cladoceran crustaceans. Biologia (Bratisl) 2013. [DOI: 10.2478/s11756-013-0180-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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57
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Kirdyasheva AG, Kotov AA. Morphology and age variability of Daphnia galeata Sars (Cladocera: Daphniidae) in two adjacent water bodies of the Kola Peninsula. BIOL BULL+ 2013. [DOI: 10.1134/s106235901301009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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58
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HAMROVÁ EVA, KRAJICEK MARTIN, KARANOVIC TOMISLAV, ČERNÝ MARTIN, PETRUSEK ADAM. Congruent patterns of lineage diversity in two species complexes of planktonic crustaceans,Daphnia longispina(Cladocera) andEucyclops serrulatus(Copepoda), in East European mountain lakes. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00864.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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59
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Orsini L, Mergeay J, Vanoverbeke J, De Meester L. The role of selection in driving landscape genomic structure of the waterflea Daphnia magna. Mol Ecol 2012; 22:583-601. [PMID: 23174029 DOI: 10.1111/mec.12117] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 10/08/2012] [Accepted: 10/11/2012] [Indexed: 01/08/2023]
Abstract
The combined analysis of neutral and adaptive genetic variation is crucial to reconstruct the processes driving population genetic structure in the wild. However, such combined analysis is challenging because of the complex interaction among neutral and selective processes in the landscape. Overcoming this level of complexity requires an unbiased search for the evidence of selection in the genomes of populations sampled from their natural habitats and the identification of demographic processes that lead to present-day populations' genetic structure. Ecological model species with a suite of genomic tools and well-understood ecologies are best suited to resolve this complexity and elucidate the role of selective and demographic processes in the landscape genomic structure of natural populations. Here we investigate the water flea Daphnia magna, an emerging model system in genomics and a renowned ecological model system. We infer past and recent demographic processes by contrasting patterns of local and regional neutral genetic diversity at markers with different mutation rates. We assess the role of the environment in driving genetic variation in our study system by identifying correlates between biotic and abiotic variables naturally occurring in the landscape and patterns of neutral and adaptive genetic variation. Our results indicate that selection plays a major role in determining the population genomic structure of D. magna. First, environmental selection directly impacts genetic variation at loci hitchhiking with genes under selection. Second, priority effects enhanced by local genetic adaptation (cf. monopolization) affect neutral genetic variation by reducing gene flow among populations and genetic diversity within populations.
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Affiliation(s)
- Luisa Orsini
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Leuven, Belgium.
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60
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Schwentner M, Clavier S, Fritsch M, Olesen J, Padhye S, Timms BV, Richter S. Cyclestheria hislopi (Crustacea: Branchiopoda): a group of morphologically cryptic species with origins in the Cretaceous. Mol Phylogenet Evol 2012. [PMID: 23178560 DOI: 10.1016/j.ympev.2012.11.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hislopi represents a single circumtropic species. South American (French Guiana), Asian (India, Indonesia, Singapore) and several Australian populations were included in our investigation. Phylogenetic and genetic distance analyses revealed remarkable intercontinental genetic differentiation (uncorrected p-distances COI>13%, EF1α>3% and 28S>4%). Each continent was found to have at least one distinct Cyclestheria species, with Australia boasting four distinct main lineages which may be attributed to two to three species. The divergence of these species (constituting crown group Cyclestherida) was, on the basis of phylogenetic analyses of COI and EF1α combined with molecular clock estimates using several fossil branchiopod calibration points or a COI substitution rate of 1.4% per million years, dated to the Cretaceous. This was when the South American lineage split from the Asian-Australian lineage, with the latter diverging further in the Paleogene. Today's circumtropic distribution of Cyclestheria may be best explained by a combination of Gondwana vicariance and later dispersal across Asia and Australia when the tectonic plates of the two continents drew closer in the early Miocene. The lack of morphological differentiation that has taken place in this taxon over such a long evolutionary period contrasts with the high level of differentiation and diversification observed in its sister taxon the Cladocera. Further insights into the evolution of Cyclestheria may help us to understand the evolutionary success of the Cladocera.
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Affiliation(s)
- Martin Schwentner
- Universität Rostock, Allgemeine und Spezielle Zoologie, Institut für Biowissenschaften, Universitätsplatz 2, 18055 Rostock, Germany.
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61
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Crease TJ, Omilian AR, Costanzo KS, Taylor DJ. Transcontinental phylogeography of the Daphnia pulex species complex. PLoS One 2012; 7:e46620. [PMID: 23056371 PMCID: PMC3463573 DOI: 10.1371/journal.pone.0046620] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 09/03/2012] [Indexed: 11/22/2022] Open
Abstract
Daphnia pulex is quickly becoming an attractive model species in the field of ecological genomics due to the recent release of its complete genome sequence, a wide variety of new genomic resources, and a rich history of ecological data. Sequences of the mitochondrial NADH dehydrogenase subunit 5 and cytochrome c oxidase subunit 1 genes were used to assess the global phylogeography of this species, and to further elucidate its phylogenetic relationship to other members of the Daphnia pulex species complex. Using both newly acquired and previously published data, we analyzed 398 individuals from collections spanning five continents. Eleven strongly supported lineages were found within the D. pulex complex, and one lineage in particular, panarctic D. pulex, has very little phylogeographical structure and a near worldwide distribution. Mismatch distribution, haplotype network, and population genetic analyses are compatible with a North American origin for this lineage and subsequent spatial expansion in the Late Pleistocene. In addition, our analyses suggest that dispersal between North and South America of this and other species in the D. pulex complex has occurred multiple times, and is predominantly from north to south. Our results provide additional support for the evolutionary relationships of the eleven main mitochondrial lineages of the D. pulex complex. We found that the well-studied panarctic D. pulex is present on every continent except Australia and Antarctica. Despite being geographically very widespread, there is a lack of strong regionalism in the mitochondrial genomes of panarctic D. pulex--a pattern that differs from that of most studied cladocerans. Moreover, our analyses suggest recent expansion of the panarctic D. pulex lineage, with some continents sharing haplotypes. The hypothesis that hybrid asexuality has contributed to the recent and unusual geographic success of the panarctic D. pulex lineage warrants further study.
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Affiliation(s)
- Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
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62
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Phylogeographic Diversity of the Lower Central American Cichlid Andinoacara coeruleopunctatus (Cichlidae). INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:780169. [PMID: 23008800 PMCID: PMC3447354 DOI: 10.1155/2012/780169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/29/2012] [Indexed: 11/17/2022]
Abstract
It is well appreciated that historical and ecological processes are important determinates of freshwater biogeographic assemblages. Phylogeography can potentially lend important insights into the relative contribution of historical processes in biogeography. However, the extent that phylogeography reflects historical patterns of drainage connection may depend in large part on the dispersal capability of the species. Here, we test the hypothesis that due to their relatively greater dispersal capabilities, the neotropical cichlid species Andinoacara coeruleopunctatus will display a phylogeographic pattern that differs from previously described biogeographic assemblages in this important region. Based on an analysis of 318 individuals using mtDNA ATPase 6/8 sequence and restriction fragment length polymorphism data, we found eight distinct clades that are closely associated with biogeographic patterns. The branching patterns among the clades and a Bayesian clock analysis suggest a relatively rapid colonization and diversification among drainages in the emergent Isthmus of Panama followed by the coalescing of some drainages due to historical connections. We also present evidence for extensive cross-cordillera sharing of clades in central Panama and the Canal region. Our results suggest that contemporary phylogeographic patterns and diversification in Lower Central American fishes reflect an interaction of historical drainage connections, dispersal, and demographic processes.
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63
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Cryptic species of the Eucypris virens species complex (Ostracoda, Crustacea) from Europe have invaded Western Australia. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0224-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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64
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Vanschoenwinkel B, Pinceel T, Vanhove MPM, Denis C, Jocque M, Timms BV, Brendonck L. Toward a global phylogeny of the "living fossil" crustacean order of the Notostraca. PLoS One 2012; 7:e34998. [PMID: 22529967 PMCID: PMC3329532 DOI: 10.1371/journal.pone.0034998] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 03/08/2012] [Indexed: 11/23/2022] Open
Abstract
Tadpole shrimp (Crustacea, Notostraca) are iconic inhabitants of temporary aquatic habitats worldwide. Often cited as prime examples of evolutionary stasis, surviving representatives closely resemble fossils older than 200 mya, suggestive of an ancient origin. Despite significant interest in the group as 'living fossils' the taxonomy of surviving taxa is still under debate and both the phylogenetic relationships among different lineages and the timing of diversification remain unclear. We constructed a molecular phylogeny of the Notostraca using model based phylogenetic methods. Our analyses supported the monophyly of the two genera Triops and Lepidurus, although for Triops support was weak. Results also revealed high levels of cryptic diversity as well as a peculiar biogeographic link between Australia and North America presumably mediated by historic long distance dispersal. We concluded that, although some present day tadpole shrimp species closely resemble fossil specimens as old as 250 mya, no molecular support was found for an ancient (pre) Mesozoic radiation. Instead, living tadpole shrimp are most likely the result of a relatively recent radiation in the Cenozoic era and close resemblances between recent and fossil taxa are probably the result of the highly conserved general morphology in this group and of homoplasy.
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Affiliation(s)
- Bram Vanschoenwinkel
- Laboratory of Aquatic Ecology and Evolutionary Biology, KU Leuven, Leuven, Belgium.
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65
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Miner BE, De Meester L, Pfrender ME, Lampert W, Hairston NG. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model. Proc Biol Sci 2012; 279:1873-82. [PMID: 22298849 DOI: 10.1098/rspb.2011.2404] [Citation(s) in RCA: 192] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances.
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Affiliation(s)
- Brooks E Miner
- Department of Biology, University of Washington, PO Box 351800, Seattle, WA 98195, USA.
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66
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Cristescu ME, Constantin A, Bock DG, Cáceres CE, Crease TJ. Speciation with gene flow and the genetics of habitat transitions. Mol Ecol 2012; 21:1411-22. [PMID: 22269101 DOI: 10.1111/j.1365-294x.2011.05465.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Whether speciation can advance to completion in the face of initially high levels of gene flow is a very controversial topic in evolutionary biology. Extensive gene exchange is generally considered to homogenize populations and counteract divergence. Moreover, the role of introgressive hybridization in evolution remains largely unexplored in animals, particularly in freshwater zooplankton in which allopatric speciation is considered to be the norm. Our work investigates the genetic structure of two young ecological species: the pond species, Daphnia pulex and the lake species, Daphnia pulicaria. Phylogenetic and population genetics analyses were conducted on mitochondrial NADH dehydrogenase 5 (ND5) gene, the nuclear Lactate dehydrogenase (Ldh) gene and 21 nuclear microsatellite markers in 416 individuals from habitats with various degrees of permanence. The strong and consistent phylogenetic discordance between nuclear and mitochondrial markers suggests a complex evolutionary history of multiple independent habitat transition events that involved hybridization and introgression between lake and pond Daphnia. On the other hand, the low level of contemporary gene flow between adjacent populations indicates the presence of effective habitat isolating barriers. The Daphnia system provides strong evidence for a divergence-with-gene flow speciation model that involves multiple habitat transition events.
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Affiliation(s)
- Melania E Cristescu
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.
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67
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68
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Latta LC, Frederick S, Pfrender ME. Diet restriction and life history trade-offs in short- and long-lived species of Daphnia. ACTA ACUST UNITED AC 2011; 315:610-7. [PMID: 21953827 DOI: 10.1002/jez.710] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 08/01/2011] [Accepted: 08/24/2011] [Indexed: 11/10/2022]
Abstract
The life-extending effects of diet restriction are well documented. One evolutionary model that accounts for this widespread conservation is the resource allocation model, where the selected individuals are those that can delay reproduction during periods of resource limitation. In this study, we use closely related species of a model organism, Daphnia, with widely divergent lifespans to address the relationship between diet restriction and longevity and assess whether the relationships are owing to trade-offs between reproductive and somatic investment. Specifically, we conducted a common garden experiment and constructed reaction norms for lifespan, fecundity, and body size as a function of food concentration. Our study provides evidence that the short-lived species in our study, D. pulex, shows the classically observed relationship of enhanced lifespan in response to reduced diet intake, but does not divert resources to somatic maintenance at the expense of reproduction during chronic diet restriction. In contrast, we find no evidence that the long-lived species in our study, D. pulicaria, gains any life-extending effects through diet restriction. Combined, our results provide evidence that the resource allocation model is not sufficient to explain the evolution of diet-mediated lifespan plasticity.
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Affiliation(s)
- Leigh Clark Latta
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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69
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Simon JC, Pfrender ME, Tollrian R, Tagu D, Colbourne JK. Genomics of environmentally induced phenotypes in 2 extremely plastic arthropods. J Hered 2011; 102:512-25. [PMID: 21525179 PMCID: PMC3156564 DOI: 10.1093/jhered/esr020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 02/27/2011] [Accepted: 03/02/2011] [Indexed: 11/14/2022] Open
Abstract
Understanding how genes and the environment interact to shape phenotypes is of fundamental importance for resolving important issues in adaptive evolution. Yet, for most model species with mature genetics and accessible genomic resources, we know little about the natural environmental factors that shape their evolution. By contrast, animal species with deeply understood ecologies and well characterized responses to environmental cues are rarely subjects of genomic investigations. Here, we preview advances in genomics in aphids and waterfleas that may help transform research on the regulatory mechanisms of phenotypic plasticity. This insect and crustacean duo has the capacity to produce extremely divergent phenotypes in response to environmental stimuli. Sexual fate and reproductive mode are condition-dependent in both groups, which are also capable of altering morphology, physiology and behavior in response to biotic and abiotic cues. Recently, the genome sequences for the pea aphid Acyrthosiphon pisum and the waterflea Daphnia pulex were described by their respective research communities. We propose that an integrative study of genome biology focused on the condition-dependent transcriptional basis of their shared plastic traits and specialized mode of reproduction will provide broad insight into adaptive plasticity and genome by environment interactions. We highlight recent advances in understanding the genome regulation of alternative phenotypes and environmental cue processing, and we propose future research avenues to discover gene networks and epigenetic mechanisms underlying phenotypic plasticity.
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Affiliation(s)
- Jean-Christophe Simon
- INRA, UMR BiO3P, Biologie des Organismes et des Populations appliquée à la Protection des Plantes, Le Rheu cedex, France.
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70
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Kotov AA, Taylor DJ. Mesozoic fossils (>145 Mya) suggest the antiquity of the subgenera of Daphnia and their coevolution with chaoborid predators. BMC Evol Biol 2011; 11:129. [PMID: 21595889 PMCID: PMC3123605 DOI: 10.1186/1471-2148-11-129] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 05/19/2011] [Indexed: 12/04/2022] Open
Abstract
Background The timescale of the origins of Daphnia O. F. Mueller (Crustacea: Cladocera) remains controversial. The origin of the two main subgenera has been associated with the breakup of the supercontinent Pangaea. This vicariance hypothesis is supported by reciprocal monophyly, present day associations with the former Gondwanaland and Laurasia regions, and mitochondrial DNA divergence estimates. However, previous multilocus nuclear DNA sequence divergence estimates at < 10 Million years are inconsistent with the breakup of Pangaea. We examined new and existing cladoceran fossils from a Mesozoic Mongolian site, in hopes of gaining insights into the timescale of the evolution of Daphnia. Results We describe new fossils of ephippia from the Khotont site in Mongolia associated with the Jurassic-Cretaceous boundary (about 145 MYA) that are morphologically similar to several modern genera of the family Daphniidae, including the two major subgenera of Daphnia, i.e., Daphnia s. str. and Ctenodaphnia. The daphniid fossils co-occurred with fossils of the predaceous phantom midge (Chaoboridae). Conclusions Our findings indicate that the main subgenera of Daphnia are likely much older than previously known from fossils (at least 100 MY older) or from nuclear DNA estimates of divergence. The results showing co-occurrence of the main subgenera far from the presumed Laurasia/Gondwanaland dispersal barrier shortly after formation suggests that vicariance from the breakup of Pangaea is an unlikely explanation for the origin of the main subgenera. The fossil impressions also reveal that the coevolution of a dipteran predator (Chaoboridae) with the subgenus Daphnia is much older than previously known -- since the Mesozoic.
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Affiliation(s)
- Alexey A Kotov
- AN Severtsov Institute of Ecology and Evolution, Leninsky Prospect, Moscow, Russia.
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71
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Jeffery NW, Elías-Gutiérrez M, Adamowicz SJ. Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada. PLoS One 2011; 6:e18364. [PMID: 21610864 PMCID: PMC3096620 DOI: 10.1371/journal.pone.0018364] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 03/05/2011] [Indexed: 11/19/2022] Open
Abstract
The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has completed a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems using molecular markers. We have employed DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation. The standard animal barcode marker (COI) was sequenced for 327 specimens, and a 3% divergence threshold was used to delineate potential species. We found 42 provisional and valid branchiopod species from this survey alone, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works. Using published sequence data, we explored the phylogeographic affinities of Churchill's branchiopods, finding that the Churchill fauna apparently originated from all directions from multiple glacial refugia (including southern, Beringian, and high arctic regions). Overall, these microcrustaceans are very diverse in Churchill and contain multiple species complexes. The present study introduces among the first sequences for some understudied genera, for which further work is required to delineate species boundaries and develop a more complete understanding of branchiopod diversity over a larger spatial scale.
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Affiliation(s)
- Nicholas W Jeffery
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada.
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Abstract
Physical isolation has long been the null hypothesis of speciation, with exceptional evidence required to suggest speciation with gene flow. Following recent persuasive theoretical support and strong empirical examples of nonallopatric speciation, one might expect a changed view. However, a review of 73 recent empirical studies shows that when allopatric speciation is suggested, a nonallopatric alternative is rarely considered, whereas the opposite is true in studies suggesting sympatric speciation, indicating a biased treatment of different speciation models. Although increasing support for ecological speciation suggests natural selection as the most critical component of speciation, gene flow remains an issue. Methods for unbiased hypothesis testing are available, and the genetic and phylogeographic data required for appropriate tests can be generated. Focus on phylogenies and functions of individual genes have revealed strong idiosyncratic elements of speciation, such as single genes with possible allopatric origin that make significant contributions during nonallopatric phases of speciation. Hence a more complex picture of speciation is now emerging that will benefit from unbiased evaluation of both allopatric and sympatric mechanisms of speciation.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Ecology, Tjärnö, Strömstad, University of Gothenburg, Sweden.
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Costanzo KS, Taylor DJ. Rapid ecological isolation and intermediate genetic divergence in lacustrine cyclic parthenogens. BMC Evol Biol 2010; 10:166. [PMID: 20525388 PMCID: PMC2895610 DOI: 10.1186/1471-2148-10-166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 06/05/2010] [Indexed: 11/18/2022] Open
Abstract
Background Ecological shifts can promote rapid divergence and speciation. However, the role of ecological speciation in animals that reproduce predominantly asexually with periodic sex and strong dispersal, such as lacustrine cladocerans, is poorly understood. These life history traits may slow or prevent ecological lineage formation among populations. Proponents of the postglacial ecological isolation hypothesis for Daphnia suggest that some species have formed postglacially in adjacent, but ecologically different habitats. We tested this hypothesis with ecological, morphological, and multilocus coalescence analyses in the putative lacustrine sister species, Daphnia parvula and Daphnia retrocurva. Results Daphnia parvula and D. retrocurva showed strong habitat separation with rare co-occurrence. Lakes inhabited by D. parvula were smaller in size and contained lower densities of invertebrate predators compared to lakes containing D. retrocurva. In the laboratory, D. retrocurva was less vulnerable to invertebrate predation, whereas D. parvula was less vulnerable to vertebrate predation and was smaller and more transparent than D. retrocurva. The species are significantly differentiated at mitochondrial and nuclear loci and form an intermediate genetic divergence pattern between panmixia and reciprocal monophyly. Coalescence and population genetic modelling indicate a Late or Post Glacial time of divergence with a demographic expansion. Conclusions Despite their young age and mixed breeding system, D. parvula and D. retrocurva exhibit significant ecological and genetic divergence that is coincident with the formation of deep temperate glacial lakes. We propose that predation may have facilitated the rapid divergence between D. parvula and D. retrocurva and that intermediate divergence of aquatic cyclic parthenogens is likely more common than previously thought.
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Affiliation(s)
- Katie S Costanzo
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY 14260, USA.
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Sharp phylogeographic breaks and patterns of genealogical concordance in the brine shrimp Artemia franciscana. Int J Mol Sci 2009; 10:5455-5470. [PMID: 20054480 PMCID: PMC2802004 DOI: 10.3390/ijms10125455] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 12/16/2009] [Accepted: 12/17/2009] [Indexed: 11/29/2022] Open
Abstract
Genealogical concordance is a critical overlay of all phylogenetic analyses, irrespective of taxonomic level. To assess such patterns of congruence we have compiled and derived sequence data for two mitochondrial (16S rRNA, COI) and two nuclear (ITS1, p26) markers in 14 American populations of the hypersaline branchiopod Artemia franciscana. Cladistic analysis revealed three reciprocally monophyletic mitochondrial clades. For nuclear DNA, incomplete lineage sorting was evident presumably as a result of slower coalescence or male-mediated dispersal. Our findings capture the genealogical interval between gene splitting and population divergence. In this sense, strong indications are provided in favour of a superspecies status and ongoing speciation in A. franciscana.
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XU S, HEBERT PDN, KOTOV AA, CRISTESCU ME. The noncosmopolitanism paradigm of freshwater zooplankton: insights from the global phylogeography of the predatory cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda). Mol Ecol 2009; 18:5161-79. [DOI: 10.1111/j.1365-294x.2009.04422.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gießler S, Englbrecht CC. Dynamic reticulate evolution in aDaphniamultispecies complex. ACTA ACUST UNITED AC 2009; 311:530-48. [DOI: 10.1002/jez.550] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kappas I, Baxevanis AD, Maniatsi S, Abatzopoulos TJ. Porous genomes and species integrity in the branchiopod Artemia. Mol Phylogenet Evol 2009; 52:192-204. [PMID: 19306934 DOI: 10.1016/j.ympev.2009.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 03/13/2009] [Accepted: 03/14/2009] [Indexed: 11/25/2022]
Abstract
Over the years, studies on interspecific hybridization have highlighted cases where gene exchange between taxa continues for a significant amount of time after speciation. The reasons for this lag of reproductive isolation relative to genetic isolation are largely unclear, and the question still remains whether the resulting hybrids represent novel biological (and taxonomic) diversity or merely an evolutionary liability. We provide strong indications in the branchiopod Artemia that hybrids between distantly related species may not be evolutionary inconsequential. Based on a global sampling of published and newly derived nuclear (ITS1) and mitochondrial (16S rRNA) sequence data from all representatives of the genus, we have identified natural hybrids between Artemia species (A. persimilisxA. franciscana, A. salinaxA. franciscana) separated by evolutionary interludes of tens of millions of years. Our combined analytical framework of cladistic and network methods provides evidence that hybridizations are the result of recent secondary contact following pronounced allopatric differentiation. The detection of mitochondrial introgression from A. persimilis to A. franciscana attests F(1) hybrid fertility. The reasons for this apparent unidirectionality of introgression are currently unknown but a likely explanation is provided based on morphometric divergence. We discuss the evolutionary implications of our results within the broader context of continental zooplankters.
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Affiliation(s)
- Ilias Kappas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
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A "crown of thorns" is an inducible defense that protects Daphnia against an ancient predator. Proc Natl Acad Sci U S A 2009; 106:2248-52. [PMID: 19144929 DOI: 10.1073/pnas.0808075106] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic data has become an essential part of ecological studies, because the analyses of diversity within and among natural populations may grant access to previously overlooked ecological and evolutionary causalities, especially among cryptic species. Here, we present an example of how phylogenetic analysis of molecular data obtained within a DNA barcoding study, in combination with morphological and ecological data from the field and laboratory experiments, unraveled a striking predator-prey interaction between aquatic organisms. The "crown of thorns," a conspicuous morphological feature among water fleas of the Daphnia atkinsoni species complex (Crustacea: Cladocera), is considered to represent a species-specific trait. However, our study, initiated by the analysis of sequence variation in 2 mitochondrial genes, shows that this feature is phenotypically plastic and is induced by chemical cues released by Triops cancriformis, the tadpole shrimp (Notostraca). The trait acts as an effective antipredator defense, and is found in several Daphnia lineages coexisting with notostracans. These facts suggest that the "crown of thorns" evolved in coexistence with this ancient predator group.
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