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Fig. 4. Mismatch distribution for mitochondrial haplotypes for 92 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction
Fig. 4. Mismatch distribution for mitochondrial haplotypes for 92 individuals of Brycon nattereri from the Laranjinha River.
Fig. 2 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction
Fig. 2. Bayesian analysis results (Structure). a. Values of K obtained based on ΔK. b. Values of K obtained based on mean likelihood Ln (K). c. Graphic representation of K = 2. Each column represents a different individual and the colors denote the probable ancestry coefficient of the individual and each genetic cluster.
Fig. 1 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction
Fig. 1. Brycon nattereri sampling sites along the Laranjinha River (A, B, C and D). Also shown are the sampling sites used in a previous study (D, E, F, G, H, I and J) and the number of individuals of B. nattereri collected at each site (in parentheses). On the South America map, numbers and arrows indicate the Paraná, Tocantins, and São Francisco basins and the asterisks indicate the areas with records of Brycon nattereri (Rosa, Lima, 2008; Viana et al., 2013; Frota et al., 2016).
Data from: Dispersal capacity predicts both population genetic structure and species richness in reef fishes
Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.
Data from: Low inter-basin connectivity in a facultatively diadromous fish: evidence from genetics and otolith chemistry
Southern smelts (Retropinna spp.) in coastal rivers of Australia are facultatively diadromous, with populations potentially containing individuals with diadromous or wholly freshwater life-histories. The presence of diadromous individuals is expected to reduce genetic structuring between river basins due to larval dispersal via the sea. We use otolith chemistry to distinguish between diadromous and non-diadromous life-histories and population genetics to examine inter-basin connectivity resulting from diadromy. Otolith strontium isotope (87Sr:86Sr) transects identified three main life history patterns: amphidromy, freshwater residency and estuarine/marine residency. Despite the potential for inter-basin connectivity via larval mixing in the marine environment, we found unprecedented levels of genetic structure for an amphidromous species. Strong hierarchical structure along putative taxonomic boundaries was detected, along with highly structured populations within groups using microsatellites (FST = 0.046 – 0.181), and mtDNA (ΦST = 0.498 – 0.816). The presence of strong genetic subdivision, despite the fact that many individuals reside in saline water during their early life-history, appears incongruous. However, analysis of multi-elemental signatures in the otolith cores of diadromous fish revealed strong discrimination between river basins, suggesting that diadromous fish spend their early lives within chemically distinct estuaries rather than the more homogenous marine environment, thus avoiding dispersal and maintaining genetic structure.
Data from: Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish
How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (VA) and trait differentiation (QST) from small to large population size. Alternatively, small populations might exhibit larger variation in VA and QST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating VA and QST using nine fragmented populations of brook trout varying 50-fold in census size N (179-8416) and 10-fold in effective number of breeders, Nb (18-135). Across 15 traits, no evidence was found for consistent differences in VA and QST with population size and almost no evidence for increased variability of VA or QST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made.
Data from: Enriched rearing environment and wild genetic background can enhance survival and disease resistance of salmonid fishes during parasite epidemics
The importance and volume of aquaculture is increasing world-wide. Rearing practices play a key role in determining growth rate, survival and disease resistance in aquaculture fishes. Recent evidence suggests that in comparison with a standard stimulus-poor rearing environment, an enriched or variable rearing environment has significant positive effects on several traits underlying growth and well-being of fish. However, the effect of enriched rearing on one of the most important threats for aquaculture development, occurrence of parasitic infections, remains unknown. We used surveillance data of experimental salmonid populations of wild and hatchery origin under semi-natural parasite exposure to explore effects of enriched rearing on outbreaks of important aquaculture pathogens and associated fish mortalities in production-scale fish densities. We also conducted controlled parasite exposures to investigate if enriched rearing reduces susceptibility of fish to infection in comparison with standard rearing conditions. We found evidence of enriched rearing influencing survival and disease resistance of aquaculture fish during parasite epidemics. Essentially, populations from enriched rearing had a higher survival rate, lower parasite occurrence and greater resistance to most infections compared to fish held in standard rearing conditions. Similarly, fish of wild genetic background had lower mortality during some of the epidemics compared to fish of hatchery origin. However, we also demonstrate significant variation in these patterns and in some cases a tendency for opposite effects of enriched rearing and genetic background depending on the fish species and nature of the epidemic. Synthesis and applications. Our results suggest that parasitic infections and epidemics can be managed through enriched rearing conditions. This may have important implications for economically and ecologically sustainable parasite and disease prevention strategies in aquaculture.
Data from: A population genetic assessment of taxonomic species: the case of Lake Malawi cichlid fishes
Organisms sampled for population level research are typically assigned to species by morphological criteria. But if those criteria are limited to one sex or life stage, or the organisms come from a complex of closely related forms, the species assignments may misdirect analyses. The impact of such sampling can be assessed from the correspondence of genetic clusters, identified only from patterns of genetic variation, to the species identified using only phenotypic criteria. We undertook this protocol with the rock-dwelling mbuna cichlids of Lake Malawi, for which species within genera are usually identified by investigators using adult male coloration patterns. Given high local endemism of male color patterns, and considerable allele sharing among species, there persists considerable taxonomic uncertainty in these fishes. Over 700 individuals from a single transect were photographed, genotyped, and separately assigned: (1) to morphospecies using photographs; and (2) to genetic clusters using five widely used methods. Overall, the correspondence between clustering methods was strong for larger clusters, but methods varied widely in estimated number of clusters. The correspondence between morphospecies and genetic clusters was also strong for larger clusters, as well as some smaller clusters for some methods. These analyses generally affirm (1) adult male-limited sampling and (2) the taxonomic status of Lake Malawi mbuna, as the species in our study largely appear to be well-demarcated genetic entities. More generally, our analyses highlight the challenges for clustering methods when the number of populations is unknown, especially in cases of highly uneven sample sizes.
Data from: Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity
Adaptive differences across species' ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of drift from those of selection, and identifying subtle signatures of polygenic adaptation. We used paired-end restriction-site associated-DNA sequencing data (6605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene-association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature- and precipitation-related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomics studies.
Data from: Inbred and furious: negative association between aggression and genetic diversity in highly inbred fish
Aggressive behaviour plays an important role in securing resources, defending against predators and shaping social interactions. Although aggression can have positive effects on growth and reproductive success, it is also energetically costly and may increase injury and compromise survival. Individual genetic diversity has been positively associated with aggression, but the cause for such an association is not clear, and it might be related to the ability to recognize kin. To disentangle the relationships between genetic diversity, kinship and aggression, we quantified aggressive behaviour in a wild, self-fertilizing fish (Kryptolebias marmoratus) with naturally variable degrees of genetic diversity, relatedness and familiarity. We found that in contrast to captive fish, levels of aggression among wild K. marmoratus are positively associated with individual homozygosity, but not with relatedness or familiarity. We suggest that the higher aggression shown by homozygous fish could be related to better kin discrimination and may be facilitated by hermaphrodite competition for scarce males, given the fitness advantages provided by outcrossing in terms of parasite resistance. It seems likely that the relationship between aggression and genetic diversity is largely influenced by both the environment and population history.
Data from: Novel adverse outcome pathways revealed by chemical genetics in a developing marine fish
Crude oil spills are a worldwide ocean conservation threat. Fish are particularly vulnerable to the oiling of spawning habitats, and crude oil causes severe abnormalities in embryos and larvae. However, the underlying mechanisms for these developmental defects are not well understood. Here, we explore the transcriptional basis for four discrete crude oil injury phenotypes in the early life stages of the commercially important Atlantic haddock (Melanogrammus aeglefinus). These include defects in (1) cardiac form and function, (2) craniofacial development, (3) ionoregulation and fluid balance, and (4) cholesterol synthesis and homeostasis. Our findings suggest a key role for intracellular calcium cycling and excitation-transcription coupling in the dysregulation of heart and jaw morphogenesis. Moreover, the disruption of ionoregulatory pathways sheds new light on buoyancy control in marine fish embryos. Overall, our chemical-genetic approach identifies initiating events for distinct adverse outcome pathways and novel roles for individual genes in fundamental developmental processes.
Data from: Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon
<p>Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population histories and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism (SNP) genotypic data from archival scale samples, and demonstrate its application to a study of kokanee salmon (<i>Oncorhynchus nerka</i>) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (>90% average genotyping across all individuals) and low genotyping error (<0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrate GT-seq as a valuable tool for genome-wide data collection from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.</p>
FIGURE 2 in Genetic differentiation through dispersal and isolation in two freshwater fish species from coastal basins of Northeastern Brazil
FIGURE 2 | Distribution and haplotype structure of Schizodon dissimilis. A. Paleodrainage reconstruction of coastal basins from northeastern Brazil and geographic distribution of groups defined by SAMOVA. B. Estimate of the probable groups of populations produced by the BAPS. C. Haplotypes network of cytochrome oxidase I (coI). All analysis recovered a total of three groups in this area. The colors used to highlight areas in the network correspond to populations in map.
FIGURE 1 in Genetic differentiation through dispersal and isolation in two freshwater fish species from coastal basins of Northeastern Brazil
FIGURE 1 | Species used in this study, Schizodon dissimilis (above) and Prochilodus lacustris (below).
FIGURE 2 in Genetic evidence supports polygamous mating system in a wild population of Prochilodus lineatus (Characiformes: Prochilodontidae), a Neotropical shoal spawner fish
FIGURE 2 | Alternative schematic representations of spawning in Prochilodus lineatus. A. Schematic drawing of spawning moment of Prochilodus lineatus (=Prochilodus scrofa), according to Godoy (1975), whom described that males, positioned in the center of the river channel, performed distinctive sounds, possibly attracting females (figure drawn by Josiane Ribolli and Dennis Fernando Moreno, inspired from the original by Godoy, M. P, 1975, fig. 153, p.684); B. Hypothetical schematic representation of reproduction and spawning of P. lineatus in the wild according to direct observations made by Evoy Zaniboni-Filho (personal communication). The exhausted mature female is marked with an asterisk. Figure drawn by Josiane Ribolli and Dennis Fernando Moreno.
FIGURE 1 in Genetic evidence supports polygamous mating system in a wild population of Prochilodus lineatus (Characiformes: Prochilodontidae), a Neotropical shoal spawner fish
FIGURE 1 | Inferred parentage and mating patterns derived from analysis of 87 Prochilodus lineatus larvae sampled at the Middle Uruguay River in Brazil. A. Number of adults identified as parents of the sampled larvae; B. Number of different mates inferred for males and females.
Data from: The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes
The evolution of convergent phenotypes is one of the most interesting outcomes of replicate adaptive radiations. Remarkable cases of convergence involve the thick-lipped phenotype found across cichlid species flocks in the East African Great Lakes. Unlike most other convergent forms in cichlids, which are restricted to East Africa, the thick-lipped phenotype also occurs elsewhere, e.g. in the Central American Midas Cichlid assemblage. Here we use an ecological genomic approach to study the function, the evolution and the genetic basis of this phenotype in two independent cichlid adaptive radiations on two continents. We applied phylogenetic, demographic, geometric morphometric and stomach-content analyses to an African (Lobochilotes labiatus) and a Central American (Amphilophus labiatus) thick-lipped species. We found that similar morphological adaptations occur in both thick-lipped species and that the 'fleshy' lips are associated with hard-shelled prey in the form of mollusks and invertebrates. We then used comparative Illumina RNA sequencing of thick versus normal lip tissue in East African cichlids and identified a set of 141 candidate genes that appear to be involved in the morphogenesis of this trait. A more detailed analysis of six of these genes led to three strong candidates: Actb, Cldn7 and Copb. The function of these genes can be linked to the loose connective tissue constituting the fleshy lips. Similar trends in gene expression between African and Central American thick-lipped species appear to indicate that an overlapping set of genes was independently recruited to build this particular phenotype in both lineages.
Fish and Marine Fatty Acids, Genetic Signatures of Diet Adaptation, and Long-term Weight Changes
ClinicalTrials.gov study NCT03348566. IPD Sharing: NO. Countries: 0. Publications: 2.
Data from: A critical assessment of estimating census population size from genetic population size (or vice versa) in three fishes
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Data from: A population genetic assessment of taxonomic species: the case of Lake Malawi cichlid fishes
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