Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management

Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.

The Evolution of Modularity in the Mammalian Skull II: Evolutionary Consequences

Changes in patterns and magnitudes of integration may influence the ability of a species to respond to selection. Consequently, modularity has often been linked to the concept of evolvability, but their relationship has rarely been tested empirically. One possible explanation is the lack of analytical tools to compare patterns and magnitudes of integration among diverse groups that explicitly relate these aspects to the quantitative genetics framework. We apply such framework here using the multivariate response to selection equation to simulate the evolutionary behavior of several mammalian orders in terms of their flexibility, evolvability and constraints in the skull. We interpreted these simulation results in light of the integration patterns and magnitudes of the same mammalian groups, described in a companion paper. We found that larger magnitudes of integration were associated with a blur of the modules in the skull and to larger portions of the total variation explained by size variation, which in turn can exert a strong evolutionary constraint, thus decreasing the evolutionary flexibility. Conversely, lower overall magnitudes of integration were associated with distinct modules in the skull, to smaller fraction of the total variation associated with size and, consequently, to weaker constraints and more evolutionary flexibility. Flexibility and constraints are, therefore, two sides of the same coin and we found them to be quite variable among mammals. Neither the overall magnitude of morphological integration, the modularity itself, nor its consequences in terms of constraints and flexibility, were associated with absolute size of the organisms, but were strongly associated with the proportion of the total variation in skull morphology captured by size. Therefore, the history of the mammalian skull is marked by a trade-off between modularity and evolvability. Our data provide evidence that, despite the stasis in integration patterns, the plasticity in the magnitude of integration in the skull had important consequences in terms of evolutionary flexibility of the mammalian lineages.

Ecological and evolutionary consequences of living in a defaunated world

Defaunation, the loss or population decline of medium and large native vertebrates represents a significant threat to the biodiversity of tropical ecosystems. Here we review the anthropogenic drivers of defaunation, provide a brief historical account of the development of this field, and analyze the types of biological consequences of this impact on the structure and functioning of tropical ecosystems. We identify how defaunation, operating at a variety of scales, from the plot to the global level, affects biological systems along a gradient of processes ranging from plant physiology (vegetative and reproductive performance) and animal behavior (movement, foraging and dietary patterns) in the immediate term; to plant population and community dynamics and structure leading to disruptions of ecosystem functioning (and thus degrading environmental services) in the short to medium term; to evolutionary changes (phenotypic changes and population genetic structure) in the long-term. We present such a synthesis as a preamble to a series of papers that provide a compilation of our current understanding of the impact and consequences of tropical defaunation. We close by identifying some of the most urgent needs and perspectives that warrant further study to improve our understanding of this field, as we confront the challenges of living in a defaunated world. © 2013 Elsevier Ltd.

DNA polymerase active site is highly mutable: Evolutionary consequences

DNA polymerases contain active sites that are structurally superimposable and highly conserved in sequence. To assess the significance of this preservation and to determine the mutational burden that active sites can tolerate, we randomly mutated a stretch of 13 amino acids within the polymerase catalytic site (motif A) of Thermus aquaticus DNA polymerase I. After selection, by using genetic complementation, we obtained a library of approximately 8,000 active mutant DNA polymerases, of which 350 were sequenced and analyzed. This is the largest collection of physiologically active polymerase mutants. We find that all residues of motif A, except one (Asp-610), are mutable while preserving wild-type activity. A wide variety of amino acid substitutions were obtained at sites that are evolutionarily maintained, and conservative substitutions predominate at regions that stabilize tertiary structures. Several mutants exhibit unique properties, including DNA polymerase activity higher than the wild-type enzyme or the ability to incorporate ribonucleotide analogs. Bacteria dependent on these mutated polymerases for survival are fit to replicate repetitively. The high mutability of the polymerase active site in vivo and the ability to evolve altered enzymes may be required for survival in environments that demand increased mutagenesis. The inherent substitutability of the polymerase active site must be addressed relative to the constancy of nucleotide sequence found in nature.

Evolutionary consequences of food chain length in kelp forest communities.

Kelp forests are strongly influenced by macroinvertebrate grazing on fleshy macroalgae. In the North Pacific Ocean, sea otter predation on macroinvertebrates substantially reduces the intensity of herbivory on macroalgae. Temperate Australasia, in contrast, has no known predator of comparable influence. These ecological and biogeographic patterns led us to predict that (i) the intensity of herbivory should be greater in temperate Australasia than in the North Pacific Ocean; thus (ii) Australasian seaweeds have been under stronger selection to evolve chemical defenses and (iii) Australasian herbivores have been more strongly selected to tolerate these compounds. We tested these predictions first by measuring rates of algal tissue loss to herbivory at several locations in Australasian and North Pacific kelp forests. There were significant differences in grazing rates among sea otter-dominated locations in the North Pacific (0-2% day-1), Australasia (5-7% day-1), and a North Pacific location lacking sea otters (80% day-1). The expectations that chronically high rates of herbivory in Australasia have selected for high concentrations of defensive secondary metabolites (phlorotannins) in brown algae and increased tolerance of these defenses in the herbivores also were supported. Phlorotannin concentrations in kelps and fucoids from Australasia were, on average, 5-6 times higher than those in a comparable suite of North Pacific algae, confirming earlier findings. Furthermore, feeding rates of Australasian herbivores were largely unaffected by phlorotannins, regardless of the compounds' regional source. North Pacific herbivores, in contrast, were consistently deterred by phlorotannins from both Australasia and the North Pacific. These findings suggest that top-level consumers, acting through food chains of various lengths, can strongly influence the ecology and evolution of plantherbivore interactions.

Unlocking ecological history using fish remains: Eco-evolutionary consequences of exploitation in the Atlantic bluefin tuna

During recent decades, the health of ocean ecosystems and fish populations has been threatened by overexploitation, pollution, and anthropogenic-driven climate change. Due to a lack of long-term data, we have a poor understanding of when intensive exploitation began and what impact anthropogenic activities have had on the ecology and evolution of fishes. Such information is crucial to recover degraded and depleted marine ecosystems and fish populations, maximise their productivity in-line with historical levels, and predict their future dynamics. In this thesis, I evaluate anthropogenic impacts on the iconic Atlantic bluefin tuna (Thunnus thynnus; BFT), one of the longest and recently most intensely exploited marine fishes, with a tremendous cultural and economic importance. Using a long-time series of archaeological and archived faunal remains (bones) dating back to approximately two millennia ago, I apply morphological, isotopic, and genomic techniques to perform the first studies on long-term BFT size and growth, diet and habitat use, and demography and adaptation, and produce the first genome-wide data on this species. My findings suggest that exploitation had impacted BFT foraging behaviour by the ~16th century when coastal ecosystem degradation induced a pelagic shift in diet and habitat use. I reveal that BFT biomass began to decline much earlier than hitherto documented, by the 19th century, consistent with intensive tuna trap catches during this period and catch-at-size increasing. I find that BFT juvenile growth had increased by the early 1900s (and more dramatically by the 21st century) which may reflect an evolutionary response to size selective harvest–which I find putative genomic signatures of. Further, I observed that BFT foraging behaviours have been modified following overexploitation during the 20th century, which previously included a isotopically distinct, Black Sea niche. Finally, I show that despite biomass declining from centuries ago, BFT has retained genomic diversity.

Patterns of evolutionary constraints on genes in humans

Background: Different regions in a genome evolve at different rates depending on structural and functional constraints. Some genomic regions are highly conserved during metazoan evolution, while other regions may evolve rapidly, either in all species or in a lineage-specific manner. A strong or even moderate change in constraints in functional regions, for example in coding regions, can have significant evolutionary consequences. Results: Here we discuss a novel framework, 'BaseDiver', to classify groups of genes in humans based on the patterns of evolutionary constraints on polymorphic positions in their coding regions. Comparing the nucleotide-level divergence among mammals with the extent of deviation from the ancestral base in the human lineage, we identify patterns of evolutionary pressure on nonsynonymous base-positions in groups of genes belonging to the same functional category. Focussing on groups of genes in functional categories, we find that transcription factors contain a significant excess of nonsynonymous base-positions that are conserved in other mammals but changed in human, while immunity related genes harbour mutations at base-positions that evolve rapidly in all mammals including humans due to strong preference for advantageous alleles. Genes involved in olfaction also evolve rapidly in all mammals, and in humans this appears to be due to weak negative selection. Conclusion: While recent studies have identified genes under positive selection in humans, our approach identifies evolutionary constraints on Gene Ontology groups identifying changes in humans relative to some of the other mammals.

Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes.

Trait decoupling, wherein evolutionary release of constraints permits specialization of formerly integrated structures, represents a major conceptual framework for interpreting patterns of organismal diversity. However, few empirical tests of this hypothesis exist. A central prediction, that the tempo of morphological evolution and ecological diversification should increase following decoupling events, remains inadequately tested. In damselfishes (Pomacentridae), a ceratomandibular ligament links the hyoid bar and lower jaws, coupling two main morphofunctional units directly involved in both feeding and sound production. Here, we test the decoupling hypothesis by examining the evolutionary consequences of the loss of the ceratomandibular ligament in multiple damselfish lineages. As predicted, we find that rates of morphological evolution of trophic structures increased following the loss of the ligament. However, this increase in evolutionary rate is not associated with an increase in trophic breadth, but rather with morphofunctional specialization for the capture of zooplanktonic prey. Lineages lacking the ceratomandibular ligament also shows different acoustic signals (i.e. higher variation of pulse periods) from others, resulting in an increase of the acoustic diversity across the family. Our results support the idea that trait decoupling can increase morphological and behavioural diversity through increased specialization rather than the generation of novel ecotypes.

Evolutionary perspective on the interplay between family life, and parent and offspring personality

Consistent inter-individual variation in behaviour over time and across contexts has been reported for a wide variety of animals, a phenomenon commonly referred to as personality. As behavioural patterns develop inside families, rearing conditions could have lasting effects on the expression of adult personality. In species with parental care, conflicts among family members impose selection on parental and offspring behaviour through co-adaptation. Here, we argue that the interplay between the evolution of personality traits (i.e. boldness, exploration, activity, aggressiveness and sociability) expressed outside the family context and the specialized behaviours expressed inside families (i.e. offspring begging behaviour and parental response to offspring solicitations) can have important evolutionary consequences. Personality differences among parents may relate to the typically observed variation in the way they respond to offspring demand, and dependent offspring may already express personality differences which may relate to the way they communicate with their parents and siblings. However, there has been little research on how personality relates to parental and offspring behaviours. Future research should thus focus on how and why personality may be related to the specialized parent and offspring behaviour that evolved as adaptations to family life.

The evolutionary impact of invasive species

Since the Age of Exploration began, there has been a drastic breaching of biogeographic barriers that previously had isolated the continental biotas for millions of years. We explore the nature of these recent biotic exchanges and their consequences on evolutionary processes. The direct evidence of evolutionary consequences of the biotic rearrangements is of variable quality, but the results of trajectories are becoming clear as the number of studies increases. There are examples of invasive species altering the evolutionary pathway of native species by competitive exclusion, niche displacement, hybridization, introgression, predation, and ultimately extinction. Invaders themselves evolve in response to their interactions with natives, as well as in response to the new abiotic environment. Flexibility in behavior, and mutualistic interactions, can aid in the success of invaders in their new environment.

The early sperm gets the good egg: mating order effects in free spawners

Mating order can have important consequences for the fertilization success of males whose ejaculates compete to fertilize a clutch of eggs. Despite an excellent body of literature on mating-order effects in many animals, they have rarely been considered in marine free-spawning invertebrates, where both sexes release gametes into the water column. In this study, we show that in such organisms, mating order can have profound repercussions for male reproductive success. Using in vitro fertilization for two species of sea urchin we found that the 'fertilization history' of a clutch of eggs strongly influenced the size distribution of unfertilized eggs, and consequently the likelihood that they will be fertilized. Males that had first access to a batch of eggs enjoyed elevated fertilization success because they had privileged access to the largest and therefore most readily fertilizable eggs within a clutch. By contrast, when a male's sperm were exposed to a batch of unfertilized eggs left over from a previous mating event, fertilization rates were reduced, owing to smaller eggs remaining in egg clutches previously exposed to sperm. Because of this size-dependent fertilization, the fertilization history of eggs also strongly influenced the size distribution of offspring, with first-spawning males producing larger, and therefore fitter, offspring. These findings suggest that when there is variation in egg size, mating order will influence not only the quantity but also the quality of offspring sired by competing males.

Estrategias reproductivas de lagartos del género tupinambis en distintos contextos ecológicos de la Provincia de Córdoba. Reproductive strategies of lizards of genus tupinambis in different ecological contexts of the Cordoba province.

Los caracteres de historia de vida son sensibles a la variación histórica o actual de los factores ambientales. Estudiar dicha variabilidad mediante la realización de estudios comparativos permite obtener evidencias sobre las causas de la evolución de ciertos caracteres. Los lagartos son excelentes modelos para el estudio de selección sexual y evolución del comportamiento social y reproductivo debido a que su relativa baja dispersión podría tener consecuencias evolutivas profundas en el desarrollo de distintas estrategias, ya que las poblaciones, al encontrarse más aisladas, podrían verse influenciadas por las fuerzas selectivas locales, mostrando una alta heterogeneidad espacial y temporal. Por eso nos propusimos realizar este trabajo para evaluar si existen diferentes estrategias reproductivas en los lagartos del género Tupinambis en distintos contextos ecológicos de la provincia de Córdoba. Para ello analizaremos distintas características de la historia de vida en poblaciones de estas especies tales como estructura de tamaño, sexo operativo, frecuencia reproductiva, tamaño de camada, condición corporal reproductiva, tamaño de madurez sexual, características espermáticas, elección de sitios de nidificación, etc. Además analizaremos la estructura genética de las poblaciones para inferir procesos demográficos históricos y patrones actuales de flujo génico y conectividad. The life history traits are sensitive to historical or current variation of environmental factors. Studying this variability by performing comparative studies allows obtaining evidence on the causes of the evolution of certain characters. Lizards are excellent models for studying sexual selection and evolution of social and reproductive behavior because their relatively low dispersal capabilities could have profound evolutionary consequences in the development of different strategies, since isolated populations may be stronger influenced by local selective forces, showing a high spatial and temporal heterogeneity. We decided to perform this study to assess whether there are different reproductive strategies in lizards of the genus Tupinambis in different ecological contexts of the Cordoba province. We will analyze different life history traits in populations of these species such as size structure, operational sex ratio, reproductive frequency, litter size, body condition, size at sexual maturity, sperm characteristics, choice of nesting sites, etc.. We also analyzed the genetic structure of populations to infer historical demographic processes and current patterns of gene flow and connectivity.

Genetic diversity and differentiation processes in the ploidy series of Olea europaea L.: a multiscale approach from subspecies to insular populations.

Geographical isolation and polyploidization are central concepts in plant evolution. The hierarchical organization of archipelagos in this study provides a framework for testing the evolutionary consequences for polyploid taxa and populations occurring in isolation. Using amplified fragment length polymorphism and simple sequence repeat markers, we determined the genetic diversity and differentiation patterns at three levels of geographical isolation in Olea europaea: mainland-archipelagos, islands within an archipelago, and populations within an island. At the subspecies scale, the hexaploid ssp. maroccana (southwest Morocco) exhibited higher genetic diversity than the insular counterparts. In contrast, the tetraploid ssp. cerasiformis (Madeira) displayed values similar to those obtained for the diploid ssp. guanchica (Canary Islands). Geographical isolation was associated with a high genetic differentiation at this scale. In the Canarian archipelago, the stepping-stone model of differentiation suggested in a previous study was partially supported. Within the western lineage, an east-to-west differentiation pattern was confirmed. Conversely, the easternmost populations were more related to the mainland ssp. europaea than to the western guanchica lineage. Genetic diversity across the Canarian archipelago was significantly correlated with the date of the last volcanic activity in the area/island where each population occurs. At the island scale, this pattern was not confirmed in older islands (Tenerife and Madeira), where populations were genetically homogeneous. In contrast, founder effects resulted in low genetic diversity and marked genetic differentiation among populations of the youngest island, La Palma.

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In so-called unisexual teleost fishes, a broad spectrum of evolutionaty stages with varying amounts of sexual elements has evolved. These range from pure sperm-dependent parthenogenesis (gynogenesis) without or with different amounts of paternal leakage to hybridogenesis with hemiclonal diploid gametogenesis or genome elimination folowed by meiosis (meiotic hybridogenesis). All of these phenomena are hybrid origin. Many of these fish form complexes which involve the coexistence of one or more sexually reproducing species with derived all-female forms that have various ploidy levels and reproductive modes, including gynogenesis, (meiotic) hybridogenesis nnd sexual reproduction. In teleosts, parthenogenetic reproduction is strictly dependent on sperm to initate embryonic development. As opposed to true parthenogenesis, sperm-dependent parthenogenetic teleost lineages must primarily coexist with their "sperm donor", usually males from a parental sexual lineage or from a related sexual species. In some systems, gynogens were able to escape from their initial sperm donors ("host switch") and therefore, to enlarge their ranges and ecological niches. Sperm donors normally do not contribue genetically to the next generation. However, paternal leakage is observed in many systems contributing differing amounts of genetic material (from microchromosomes to entire chromosome sets) allowing interaction between genomes of different origin. Hybridogenesis is similar to gynogenesis in depending upon coexisence with sexual species but incorporates recombined genetic material by true fertilizazion. While hybridogens usually form clonal gametes, some triploids are capable of genome elimination followed by a normal diploid meiosis. Sperm-dependent parthenogenesis and hybridogenesis combine disadvantages and advantages from both sexuality and asexuality. Here, we give an overview of sperm-dependent breeding complexes in fishes, discuss the evolutionary consequences of paternal leakage, and speculate about the evolutionary significance of intergenomic (re)combination.

Local adaptation and life history traits evolution in heterogeneous environment : an empirical example in the freshwater snail, Galba truncatula

Abstract: To understand the processes of evolution, biologists are interested in the ability of a population to respond to natural or artificial selection. The amount of genetic variation is often viewed as the main factor allowing a species to answer to selection. Many theories have thus focused on the maintenance of genetic variability. Ecologists and population geneticists have long-suspected that the structure of the environment is connected to the maintenance of diversity. Theorists have shown that diversity can be permanently and stably maintained in temporal and spatial varying environment in certain conditions. Moreover, varying environments have been also theoretically demonstrated to cause the evolution of divergent life history strategies in the different niches constituting the environment. Although there is a huge number of theoretical studies selection and on life history evolution in heterogeneous environments, there is a clear lack of empirical studies. The purpose of this thesis was to. empirically study the evolutionary consequences of a heterogeneous environment in a freshwater snail Galba truncatula. Indeed, G. truncatula lives in two habitat types according the water availability. First, it can be found in streams or ponds which never completely dry out: a permanent habitat. Second, G. truncatula can be found in pools that freeze during winter and dry during summer: a temporary habitat. Using a common garden approach, we empirically demonstrated local adaptation of G. truncatula to temporary and permanent habitats. We used at first a comparison of molecular (FST) vs. quantitative (QST) genetic differentiation between temporary and permanent habitats. To confirm the pattern QST> FST between habitats suggesting local adaptation, we then tested the desiccation resistance of individuals from temporary and permanent habitats. This study confirmed that drought resistance seemed to be the main factor selected between habitats, and life history traits linked to the desiccation resistance were thus found divergent between habitats. However, despite this evidence of selection acting on mean values of traits between habitats, drift was suggested to be the main factor responsible of variation in variances-covariances between populations. At last, we found life history traits variation of individuals in a heterogeneous environment varying in parasite prevalence. This thesis empirically demonstrated the importance of heterogeneous environments in local adaptation and life history evolution and suggested that more experimental studies are needed to investigate this topic. Résumé: Les biologistes se sont depuis toujours intéressés en l'aptitude d'une population à répondre à la sélection naturelle. Cette réponse dépend de la quantité de variabilité génétique présente dans cette population. Plus particulièrement, les théoriciens se sont penchés sur la question du maintient de la variabilité génétique au sein d'environnements hétérogènes. Ils ont alors démontré que, sous certaines conditions, la diversité génétique peut se maintenir de manière stable et permanente dans des environnements variant au niveau spatial et temporel. De plus, ces environments variables ont été démontrés comme responsable de divergence de traits d'histoire de vie au sein des différentes niches constituant l'environnement. Cependant, malgré ce nombre important d'études théoriques portant sur la sélection et l'évolution des traits d'histoire de vie en environnement hétérogène, les études empiriques sont plus rares. Le but de cette thèse était donc d'étudier les conséquences évolutives d'un environnement hétérogène chez un esgarcot d'eau douce Galba truncatula. En effet, G. truncatula est trouvé dans deux types d'habitats qui diffèrent par leur niveau d'eau. Le premier, l'habitat temporaire, est constitué de flaques d'eau qui peuvent s'assécher pendant l'été et geler pendant l'hiver. Le second, l'habitat permanent, correspond à des marres ou à des ruisseaux qui ont un niveau d'eau constant durant toute l'année. Utilisant une approche expérimentale de type "jardin commun", nous avons démontré l'adaptation locale des individus à leur type d'habitat, permanent ou temporaire. Nous avons utilisé l'approche Fsr/QsT qui compare la différentiation génétique moléculaire avec la différentiation génétique quantitative entre les 2 habitats. Le phénomène d'adapation locale démontré par QsT > FsT, a été testé experimentalement en mesurant la résistance à la dessiccation d'individus d'habitat temporaire et permanent. Cette étude confirma que la résistance à la sécheresse a été sélectionné entre habitats et que les traits responsables de cette resistance sont différents entre habitats. Cependant si la sélection agit sur la valeur moyenne des traits entre habitats, la dérive génétique semble être le responsable majeur de la différence de variances-covariances entre populations. Pour finir, une variation de traits d'histoire de vie a été trouvée au sein d'un environnement hétérogène constitué de populations variants au niveau de leur taux de parasitisme. Pour conclure, cette thèse a donc démontré l'importance d'un environnement hétérogène sur l'adaptation locale et l'évolution des traits d'histoire de vie et suggère que plus d'études empiriques sur le sujet sont nécessaires.