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1,133 results for “Copepod”
Data from: Reverse genetics in the tidepool: knockdown of target gene expression via RNA interference in the copepod Tigriopus californicus
Reverse genetic tools are essential for characterizing phenotypes of novel genes and testing functional hypotheses generated from next-generation sequencing studies. RNA interference (RNAi) has been a widely used technique for describing or quantifying physiological, developmental or behavioural roles of target genes by suppressing their expression. The marine intertidal copepod Tigriopus californicus has become an emerging model for evolutionary and physiological studies, but this species is not amenable to most genetic manipulation approaches. As crustaceans are susceptible to RNAi-mediated gene knock-down, we developed a simple method for delivery of gene-specific double-stranded RNA that results in significant suppression of target gene transcription levels. The protocol was examined on five genes of interest, and for each, at least 50% knock-down in expression was achieved. While knock-down levels did not reach 100% in any trial, a well-controlled experiment with one heat-shock gene showed unambiguously that such partial gene suppression may cause dramatic changes in phenotype. Copepods with suppressed expression of heat-shock protein beta 1 (hspb1) exhibited dramatically decreased tolerance to high temperatures, validating the importance of this gene during thermal stress, as proposed by a previous study. The application of this RNAi protocol in T. californicus will be invaluable for examining the role of genes putatively involved in reproductive isolation, mitochondrial function and local adaptation.
Data from: Fitness and morphological outcomes of many generations of hybridization in the copepod Tigriopus californicus
Hybridization between genetically divergent populations is an important evolutionary process, with an outcome that is difficult to predict. We used controlled crosses and freely mating hybrid swarms, followed for up to 30 generations, to examine the morphological and fitness consequences of interpopulation hybridization in the copepod Tigriopus californicus. Patterns of fitness in two generations of controlled crosses were partly predictive of long-term trajectories in hybrid swarms. For one pair of populations, controlled crosses revealed neutral or beneficial effects of hybridization, and hybrid swarm fitness always equalled or exceeded that of the midparent. For a second pair, controlled crosses showed F2 hybrid breakdown, but elevated fitness in backcrosses, and hybrid swarm fitness deviated both above and below that of the parentals. Nevertheless, individual swarm replicates exhibited divergent fitness trajectories over time that were not related in a simple manner to their hybrid genetic composition, and fixation of fitter hybrid phenotypes was not observed. Hybridization did not generally increase overall morphological variation, and underlying genetic changes may have been masked by phenotypic plasticity. Nevertheless, one type of hybrid swarm exhibited a repeatable pattern of transgressively large eggsacs, suggesting a positive effect of hybridization on individual fecundity. Additionally both parental and hybrid swarms exhibited common phenotypic trends over time, indicating common selective pressures in the laboratory environment. Our results suggest that, in a system where much work has focused on F2 hybrid breakdown, the long-term fitness consequences of interpopulation hybridization are surprisingly benign.
Data from: Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod
Organisms may respond to changing environments through phenotypic plasticity or adaptive evolution. These two processes are not mutually exclusive and may either dampen or strengthen each other's effects, depending on the genetic correlation between trait values and the slopes of their norms of reaction. To examine the effect of adaptation to heat stress on the plasticity of heat tolerance, we hybridized populations of the crustacean Tigriopus californicus that show divergent phenotypes for heat tolerance. We then selected for increased heat tolerance in hybrids and measured heat tolerance and the phenotypic plasticity of heat tolerance in both selected lines and unselected controls. To test whether the changes in phenotypic plasticity were associated with changes in the plasticity of gene expression, we also sequenced transcriptomes of selected and unselected lines, both under heat shock and at ambient temperatures. We observed increased heat tolerance in selected lines, but also lower phenotypic and transcriptional plasticity in response to heat stress. The plastic response to heat stress was highly enriched for hydrolytic and catalytic activities, suggesting a prominent role for degradation of misfolded proteins. Our findings have important implications for biological responses to climate change: if adaptation to environmental stress reduces plasticity, then plasticity and adaptive evolution will make overlapping, rather than additive contributions to buffering populations from environmental change.
Data from: A metagenetic approach for revealing community structure of marine planktonic copepods
Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We determined an appropriate similarity threshold for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) using an artificial community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads of each MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. Further, MOTUs were successfully classified into taxonomic groups at the family level at 97% similarity; similar patterns of species richness and biomass were revealed within families with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.
Data from: Gene conversion yields novel gene combinations in paralogs of GOT1 in the copepod Tigriopus californicus
Background: Gene conversion of duplicated genes can slow the divergence of paralogous copies over time but can also result in other interesting evolutionary patterns. Islands of genetic divergence that persist in the face of gene conversion can point to gene regions undergoing selection for new functions. Novel combinations of genetic variation that differ greatly from the original sequence can result from the transfer of genetic variation between paralogous genes by rare gene conversion events. Genetically divergent populations of the copepod Tigriopus californicus provide an excellent model to look at the patterns of divergence among paralogs across multiple independent evolutionary lineages. Results: In this study the evolution of a set of paralogous genes encoding putative aspartate transaminase proteins (called GOT1 here) are examined in populations of the copepod T. californicus. One pair of duplicated genes, GOT1p1 and GOT1p2, has regions of high divergence between the copies in the face of apparent on-going gene conversion. The GOT1p2 gene also has unique haplotypes in two populations that appear to have resulted from a transfer of genetic variation via inter-paralog gene conversion. A second pair of duplicated genes GOT1Sr and GOT1Sd also shows evidence of gene conversion, but this gene conversion does not appear to have maintained each as a functional copy in all populations. Conclusions: The patterns of conservation and sequence divergence across this set of paralogous genes among populations of T. californicus suggest that some interesting evolutionary patterns are occurring at these loci. The results for the GOT1p1/GOT1p2 paralogs illustrate how gene conversion can factor in the creation of a mosaic pattern of regions of high divergence and low divergence. When coupled with rare gene conversion events of divergent regions, this pattern can result in the formation of novel proteins differing substantially from either original protein. The evolutionary patterns across these paralogs show how gene conversion can both constrain and facilitate diversification of genetic sequences.
FIGURE 3 in A new family of poecilostomatoid copepods (Strepidae fam. nov.) associated with the sun coral, Tubastraea coccinea Lesson, 1829 in Taiwan
FIGURE 3. Maximum likelihood tree of 75 species of Copepoda based on 18S rDNA sequences. Numbers below nodes represent support based on 1,000 bootstraps; only boot strap values higher than 70 are indicated on the nodes.
FIGURE 3 in Copepods associated with scleractinian corals: a worldwide checklist and a case study of their impact on the reef-building coral Pocillopora damicornis (Linnaeus, 1758) (Pocilloporidae)
FIGURE 3. Multidimensional scaling (MDS) plot of 75% similarity in species composition and abundance of symbiotic copepods amongst various sampling periods.
FIGURES 16–27 in Parasitic copepods infesting the olfactory sacs of skates from the southwestern Atlantic with the description of a new species of Kroeyerina Wilson, 1932
FIGURES 16–27. Kroeyerina sudamericana sp. nov. (adult male). 16, general habitus, dorsal; 17, general habitus, ventral; 18, posterior portion of abdomen and caudal rami; 19, fifth leg; 20, sixth leg; 21, antennule; 22, rostral area; 23, antenna; 24, mandible; 25, maxillule; 26, maxilla; 27, maxilliped. Scale bars: 16–17 = 200 µm; 18, 21–27 = 50 µm; 19–20 = 25 µm; 22 = 20 µm.
FIGURES 28–31 in Parasitic copepods infesting the olfactory sacs of skates from the southwestern Atlantic with the description of a new species of Kroeyerina Wilson, 1932
FIGURES 28–31. Kroeyerina sudamericana sp. nov. (adult male). 28, first leg; 29, second leg; 30, third leg; 31, fourth leg. Scale bars: 100 µm.
FIGURES 12–15 in Parasitic copepods infesting the olfactory sacs of skates from the southwestern Atlantic with the description of a new species of Kroeyerina Wilson, 1932
FIGURES 12–15. Kroeyerina sudamericana sp. nov. (adult female). 12, first leg; 13, second leg; 14, third leg; 15, fourth leg. Scale bars: 100 µm.
FIGURES 1–11 in Parasitic copepods infesting the olfactory sacs of skates from the southwestern Atlantic with the description of a new species of Kroeyerina Wilson, 1932
FIGURES 1–11. Kroeyerina sudamericana sp. nov. (adult female). 1, general habitus, dorsal; 2, general habitus, ventral; 3, caudal ramus; 4, fifth leg; 5, antennule; 6, rostral area; 7, antenna; 8, mandible; 9, maxillule; 10, maxilla; 11, maxilliped. Scale bars: 1–2 = 200 µm; 3–4, 7–11 = 50 µm; 5 = 100 µm; 6 = 20 µm.
FIGURE 2 in A new family of poecilostomatoid copepods (Strepidae fam. nov.) associated with the sun coral, Tubastraea coccinea Lesson, 1829 in Taiwan
FIGURE 2. Strepus elongatus gen. et sp. nov. (female, A–B; male, C–E). A, maxilla; B, maxilliped; C, habitus, lateral; D, leg 1; E, leg 2. Scale bars: A–B, D–E = 0.02 mm; C = 0.5 mm.
FIGURE 4 in Copepods associated with scleractinian corals: a worldwide checklist and a case study of their impact on the reef-building coral Pocillopora damicornis (Linnaeus, 1758) (Pocilloporidae)
FIGURE 4. Principal component analysis (PCA) of square root-transformed data from five functional categories of copepods (see text for descriptions.) defined based on behaviour (endo-/ectoparasitic or benthic) and the structure of the feeding appendages (mandibles vs. siphon) at various sampling periods. PC1 accounted for 77.2% of the variability, and PC2 accounted for 13.7%.
FIGURE 1 in A new family of poecilostomatoid copepods (Strepidae fam. nov.) associated with the sun coral, Tubastraea coccinea Lesson, 1829 in Taiwan
FIGURE 1. Strepus elongatus gen. et sp. nov. (female). A, habitus, dorsal; B, habitus, lateral; C, urosome; D, caudal ramus; E, cephalosome, ventral; F, cephalosome, lateral; G, rostrum and antennule (dot indicating position of aesthetasc in male); H, antenna; I, mandible; J, maxillule. A1 = antennule, A2 = antenna, MD = mandible, MX1 = maxillule, MX2 = maxilla, MXPD = maxilliped. Scale bars: A–B = 0.5 mm; C = 0.2 mm; D–E = 0.04 mm; F = 0.1 mm; G–J = 0.02 mm.
FIGURE 2 in Copepods associated with scleractinian corals: a worldwide checklist and a case study of their impact on the reef-building coral Pocillopora damicornis (Linnaeus, 1758) (Pocilloporidae)
FIGURE 2. Relationships between copepod infection and the amount of resources (Symbiodinium densities and surface areas) provided by host corals. A–E: Mean densities of symbiotic copepods (A: Siphonostomatoida, B: Cyclopoida, C: Harpacticoida, D: all copepods) among 480 Pocillopora damicornis colonies with varying Symbiodinium densities. E–H: Relationship between mean densities of symbiotic copepods (E: Siphonostomatoida, F: Cyclopoida, G: Harpacticoida, H: all copepods) and surface areas of host corals.
FIGURE 1 in Copepods associated with scleractinian corals: a worldwide checklist and a case study of their impact on the reef-building coral Pocillopora damicornis (Linnaeus, 1758) (Pocilloporidae)
FIGURE 1. Variation in seawater temperature and Symbiodinium density (mean ± SE) observed in Pocillopora damicornis colonies of Nanwan Bay, Southern Taiwan between July 2007 and November 2008. Lowercase and uppercase letters (a, b, c, and d) refer to the results of Tukey's post-hoc comparisons of monthly temperature and Symbiodinium density means, respectively, as a significant effect of time was detected in the overall ANOVA models (p <0.05 for both parameters).
FIGURE 8. Stygiopontius lomonosovi n in Copepods of the family Dirivultidae (Siphonostomatoida) from deepsea hydrothermal vent fields on the MidAtlantic Ridge at 14 ºN and 5 ºS
FIGURE 8. Stygiopontius lomonosovi n. sp., allotype ɗ: A, antennule; B, antennule, outgrowth of segment 3; C, modified seta of segment 5; D, 6 distalmost segments of antennule, modified setae arrowed; E, maxilliped, anterior; F, maxilliped, posterior.
FIGURE 9. Stygiopontius lomonosovi n in Copepods of the family Dirivultidae (Siphonostomatoida) from deepsea hydrothermal vent fields on the MidAtlantic Ridge at 14 ºN and 5 ºS
FIGURE 9. Stygiopontius lomonosovi n. sp., allotype ɗ: A, distal endopodal segment of leg 1, posterior; B, endopod, inner margin of coxa and basis, intercoxal sclerite of leg 2, anterior; C, distal exopodal segment of leg 3, anterior; D, leg 5, ventral.
FIGURE 7. Stygiopontius lomonosovi n in Copepods of the family Dirivultidae (Siphonostomatoida) from deepsea hydrothermal vent fields on the MidAtlantic Ridge at 14 ºN and 5 ºS
FIGURE 7. Stygiopontius lomonosovi n. sp., allotype ɗ: A, habitus, dorsal; B, ventral view of cephalothorax, position of cephalic appendages marked by dashed circles; C, urosome, dorsal, arrow indicates missing seta; D, urosome, ventral; E, urosome, lateral.
FIGURE 3. Stygiopontius lomonosovi n in Copepods of the family Dirivultidae (Siphonostomatoida) from deepsea hydrothermal vent fields on the MidAtlantic Ridge at 14 ºN and 5 ºS
FIGURE 3. Stygiopontius lomonosovi n. sp., holotype Ψ: A, habitus, dorsal; B, urosome, dorsal; C, right genital field, seta of right leg 6; D, ventrolateral outgrowth near posterior edge of genital doublesomite; E, anal somite and caudal rami, dorsal; F, anal somite and left caudal ramus, lateral. Arrows indicate missing setae.
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