scholarly journals First draft genome assembly of an iconic clownfish species (Amphiprion frenatus)

2017 ◽  
Author(s):  
Anna Marcionetti ◽  
Victor Rossier ◽  
Joris A. M. Bertrand ◽  
Glenn Litsios ◽  
Nicolas Salamin
Keyword(s):  
Life History ◽  
Adaptive Radiation ◽  
Life History Traits ◽  
Draft Genome ◽  
Reef Fishes ◽  
Sea Anemones ◽  
Draft Genome Assembly ◽  
Genomic Signatures ◽  
Mutualistic Interaction ◽  
Sequential Hermaphroditism

AbstractClownfishes (or anemonefishes) form an iconic group of coral reef fishes, particularly known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare group to have experienced an adaptive radiation in the marine environment.Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained a total of 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii BUSCOs (Benchmarking Universal Single-Copy Orthologs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies.This resource is valuable for the advancing of studies of the particular life-history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation.

Counting coral reef fishes: Interaction between fish life-history traits and transect design

2010 ◽  
Vol 387 (1-2) ◽  
pp. 15-23 ◽  
Author(s):  
Michel Kulbicki ◽  
Nathaniel Cornuet ◽  
Laurent Vigliola ◽  
Laurent Wantiez ◽  
Gérard Moutham ◽  
...  
Keyword(s):  
Life History ◽  
Coral Reef ◽  
Life History Traits ◽  
Reef Fishes ◽  
Coral Reef Fishes

scholarly journals Seascape and life-history traits do not predict self-recruitment in a coral reef fish

2016 ◽  
Vol 12 (8) ◽  
pp. 20160309 ◽  
Author(s):  
Marcela Herrera ◽  
Gerrit B. Nanninga ◽  
Serge Planes ◽  
Geoffrey P. Jones ◽  
Simon R. Thorrold ◽  
...  
Keyword(s):  
Life History ◽  
Coral Reef ◽  
Spatial Scale ◽  
Papua New Guinea ◽  
Coral Reef Fish ◽  
Microsatellite Dna ◽  
Larval Dispersal ◽  
Life History Traits ◽  
Reef Fishes ◽  
Sibling Pairs

The persistence and resilience of many coral reef species are dependent on rates of connectivity among sub-populations. However, despite increasing research efforts, the spatial scale of larval dispersal remains unpredictable for most marine metapopulations. Here, we assess patterns of larval dispersal in the angelfish Centropyge bicolor in Kimbe Bay, Papua New Guinea, using parentage and sibling reconstruction analyses based on 23 microsatellite DNA loci. We found that, contrary to previous findings in this system, self-recruitment (SR) was virtually absent at both the reef (0.4–0.5% at 0.15 km 2 ) and the lagoon scale (0.6–0.8% at approx. 700 km 2 ). While approximately 25% of the collected juveniles were identified as potential siblings, the majority of sibling pairs were sampled from separate reefs. Integrating our findings with earlier research from the same system suggests that geographical setting and life-history traits alone are not suitable predictors of SR and that high levels of localized recruitment are not universal in coral reef fishes.

scholarly journals Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower

2016 ◽  
Author(s):  
Sean Stankowski ◽  
James M. Sobel ◽  
Matthew A. Streisfeld
Keyword(s):  
Draft Genome ◽  
Flower Color ◽  
Environmental Data ◽  
Ecological Divergence ◽  
Trait Divergence ◽  
Ecotypic Differentiation ◽  
Draft Genome Assembly ◽  
Genomic Signatures ◽  
Genome Wide ◽  
Outlier Loci

A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic, or environmental data that might enhance outlier detection. Geographic cline analysis provides a potential framework for integrating diverse forms of data in a spatially-explicit framework, but it has not been used to study genome-wide patterns of divergence. Aided by a first-draft genome assembly, we combine an FCT scan and geographic cline analysis to characterize patterns of genome-wide divergence between divergent pollination ecotypes of Mimulus aurantiacus. FCT analysis of 58,872 SNPs generated via RADseq revealed little ecotypic differentiation (mean FCT = 0.041), though a small number of loci were moderately to highly diverged. Consistent with our previous results from the gene MaMyb2, which contributes to differences in flower color, 130 loci have cline shapes that recapitulate the spatial pattern of trait divergence, suggesting that they reside in or near the genomic regions that contribute to pollinator isolation. In the narrow hybrid zone between the ecotypes, extensive admixture among individuals and low linkage disequlibrium between markers indicate that outlier loci are scattered throughout the genome, rather than being restricted to one or a few regions. In addition to revealing the genomic consequences of ecological divergence in this system, we discuss how geographic cline analysis is a powerful but under-utilized framework for studying genome-wide patterns of divergence.

scholarly journals Life‐history traits, geographical range, and conservation aspects of reef fishes from the Atlantic and Eastern Pacific

Ecology ◽  
2021 ◽  
Author(s):  
Juan Pablo Quimbayo ◽  
Fernanda Carolina Silva ◽  
Thiago Costa Mendes ◽  
Débora Silva Ferrari ◽  
Samara Leopoldino Danielski ◽  
...  
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Reef Fishes ◽  
Eastern Pacific ◽  
Geographical Range

scholarly journals Higher evolutionary rates in life-history traits in insular than in mainland palms

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Cibele Cássia-Silva ◽  
Cíntia G. Freitas ◽  
Larissa Pereira Lemes ◽  
Gustavo Brant Paterno ◽  
Priscila A. Dias ◽  
...  
Keyword(s):  
Life History ◽  
Adaptive Radiation ◽  
Life History Traits ◽  
Fruit Size ◽  
Habitat Type ◽  
Taxonomic Diversity ◽  
Evolutionary Rates ◽  
Volcanic Island ◽  
Optimal Value ◽  
Volcanic Islands

AbstractIsolated islands, due to the reduced interspecific competition compared to mainland habitats, present ecological opportunities for colonizing lineages. As a consequence, island lineages may be expected to experience higher rates of trait evolution than mainland lineages. However, island effects on key life-history traits of vascular plants remain underexplored at broad spatiotemporal scales, even for emblematic island clades such as palms. Here, we used phylogenetic comparative methods to evaluate potential differences in size and macroevolutionary patterns of height and fruit diameter among mainland, continental, and volcanic island palms. Further, phylogenetic beta-diversity was used to determine if lineage turnover supported an adaptive radiation scenario on volcanic islands. Volcanic island palms were taller than their continental island and mainland counterparts, whereas continental island palms exhibited smaller fruit size. Height and fruit size of palms evolved under evolutionary constraints towards an optimal value. However, scenarios of adaptive radiation and niche conservatism were not supported for the height and fruit size of volcanic and mainland palm clades, respectively, as expected. Instead, continental island palms exhibited higher evolutionary rates for height and fruit size. Insular palm assemblages (continental and volcanic) are composed of unique lineages. Beyond representing evolutionary sources of new palm lineages, our results demonstrate that insular habitats are important in shaping palm trait diversity. Also, the higher phenotypic evolutionary rates of continental island palms suggest disparate selection pressures on this habitat type, which can be an important driver of trait diversification over time. Taken together, these results stress the importance of insular habitats for conservation of functional, phylogenetic, and taxonomic diversity of palms.

Geographic variation in density, demography, and life history traits of a harvested, sex-changing, temperate reef fish

2011 ◽  
Vol 68 (2) ◽  
pp. 288-303 ◽  
Author(s):  
Jennifer E. Caselle ◽  
Scott L. Hamilton ◽  
Donna M. Schroeder ◽  
Milton S. Love ◽  
Julie D. Standish ◽  
...  
Keyword(s):  
Life History ◽  
Geographic Variation ◽  
Life History Traits ◽  
Size Structure ◽  
Spatial Scales ◽  
Reef Fishes ◽  
Kelp Forests ◽  
Underwater Visual Census ◽  
Biogeographic Patterns ◽  
Temperate Reef

Geographic variation in ecological and environmental factors may lead to intraspecific differences among populations. For the California sheephead ( Semicossyphus pulcher ), an important predator in kelp forests and a target of commercial and recreational fisheries, we evaluated the degree to which different populations exhibited variation in density, demography, and life history traits. We assessed biogeographic patterns of abundance through underwater visual census at 39 sites spanning a major portion of the species range (southern California, USA, to Baja California, Mexico) and made collections from seven focal sites to investigate geographic differences in demography and life histories. California sheephead densities were significantly greater in the southern part of their range and at offshore islands than along the mainland coast. At the focal sites, we found significant spatial variation in density, fecundity, size structure, growth rates, annual survivorship, and the timing of maturation and sex change. Density- and temperature-dependent effects helped to explain the intraspecific differences in these parameters. Studies such as this one will allow for demographic plasticity to be incorporated into future stock assessments. Management of temperate reef fishes may best be achieved on smaller spatial scales as we increase our understanding of geographic variation among populations.

scholarly journals Responses of coral reef fishes to past climate changes are related to life-history traits

2017 ◽  
Vol 7 (6) ◽  
pp. 1996-2005 ◽  
Author(s):  
Eduardo Ottimofiore ◽  
Camille Albouy ◽  
Fabien Leprieur ◽  
Patrice Descombes ◽  
Michel Kulbicki ◽  
...  
Keyword(s):  
Life History ◽  
Coral Reef ◽  
Life History Traits ◽  
Climate Changes ◽  
Reef Fishes ◽  
Coral Reef Fishes ◽  
Past Climate
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