Phylogeography on the rocks: The contribution of current and historical factors in shaping the genetic structure of Chthamalus montagui (Crustacea, Cirripedia)

The model marine broadcast-spawner barnacle Chthamalus montagui was investigated to understand its genetic structure and quantify levels of population divergence, and to make inference on historical demography in terms of time of divergence and changes in population size. We collected specimens from rocky shores of the north-east Atlantic Ocean (4 locations), Mediterranean Sea (8) and Black Sea (1). The 312 sequences 537 bp) of the mitochondrial cytochrome c oxidase I allowed to detect 130 haplotypes. High within-location genetic variability was recorded, with haplotype diversity ranging between h = 0.750 and 0.967. Parameters of genetic divergence, haplotype network and Bayesian assignment analysis were consistent in rejecting the hypothesis of panmixia. C. montagui is genetically structured in three geographically discrete populations, which corresponded to north-eastern Atlantic Ocean, western-central Mediterranean Sea, and Aegean Sea-Black Sea. These populations are separated by two main effective barriers to gene flow located at the Almeria-Oran Front and in correspondence of the Cyclades Islands. According to the 'isolation with migration' model, adjacent population pairs diverged during the early to middle Pleistocene transition, a period in which geological events provoked significant changes in the structure and composition of palaeocommunities. Mismatch distributions, neutrality tests and Bayesian skyline plots showed past population expansions, which started approximately in the Mindel-Riss interglacial, in which ecological conditions were favourable for temperate species and calcium-uptaking marine organisms

Genetic compatibility exceeds possible ‘good genes’ effects of sexual selection in lake char

Mating is rarely random in nature, but the effects of mate choice on offspring performance are still poorly understood. We sampled in total 47 wild lake char (Salvelinus umbla) during two breeding seasons and used their gametes to investigate the genetic consequences of different mating scenarios. In a first study, 1,464 embryos that resulted from sperm competition trials were raised singly in either a stress- or non-stress environment. Offspring growth turned out to be strongly reduced with increased genetic relatedness between the parents while male coloration (that reveal aspects of male health) was no significant predictor of offspring performance. In a second experiment one year later, block-wise full-factorial in vitro breeding was used to produce 3,094 embryos that were raised singly after sublethal exposures to a pathogen or water only. Offspring growth was again strongly reduced with increased genetic relatedness between the parents while male coloration was no significant predictor of offspring performance. We conclude that the genetic benefits of mate choice would be strongest if females avoided genetic similarity, while male breeding colors seem more relevant in intra-sexual selection

The influences of maternal effect and inbreeding on phenotypic variation in Alpine whitefish

Phenotypic variation within a population is the result of specific genotype-environment combinations. Maternal effects have thus a major impact on the observed phenotypic variation since changes in maternal phenotypes and genotypes might result in causal changes on offspring phenotypes. The complexity of these dynamics is increased by considering that the maternal genome is itself influenced by other population processes such as inbreeding, a concern for many populations nowadays. In this thesis we tried to understand how maternal effects, inbreeding and their interaction influence population characteristics and offspring performances in whitefish, a salmonid. We estimated the inbreeding coefficient, using next generation sequencing data, to study how inbreeding influences female reproductive traits, including secondary sexual ornamentations, and its intergenerational effect in a species without parental care. We investigated which, among maternal effects, has the greater influence on the offspring phenotypes. We then sought to understand the selective pressures exerted on eggs of different sizes during incubation by exogenous chemical and biological stress factors. We studied the mechanism of sex determination in whitefish to obtain a sex- linked marker that would be essential for aquaculture and conservation purposes. We finally investigated the heritable nature of inbreeding coefficient in a population endemic of a lake that is still recovering from a eutrophication crisis. We found that maternal inbreeding directly influences females reproductive traits and indirectly influences embryos growth, and that inbreeding might have driven the evolution of female sexual ornamentations. We show that maternal age and egg size are the main determinants of offspring size and that larger eggs suffer stronger selective pressures during incubation than smaller eggs. We discovered that the mechanism of sex determination in whitefish relies on the presence of multiple complete copy of the SDY gene in males and in multiple truncated copies in females. We finally found that the inbreeding coefficient can be heritable under specific circumstances. The results of this thesis highlight the importance of maternal effects and inbreeding on population dynamics and phenotypic variability of adults and hatchlings. Not only they have distinct effects, but they interact influencing the characteristics of the next generations. -- La variation phénotypique au sein d'une population est le résultat d’interactions génotype- environnement spécifiques. Les effets maternels ont donc un impact majeur sur la variation phénotypique observée puisque des modifications dans les phénotypes et génotypes maternels peuvent causer des changements importants sur les phénotypes des descendants. La complexité de cette dynamique est encore accrue si l'on considère que le génome maternel est lui-même influencé par divers processus au sein même de la population, tels que la consanguinité, un problème concernant de nombreuses populations de nos jours. Au cours cette thèse, nous avons essayé de comprendre comment les effets maternels, la consanguinité ainsi que leur interaction influencent les caractéristiques de la population et les performances de la descendance chez les Corégones des Alpes, un salmonidé présent dans de nombreux lacs de Suisse. Afin de comprendre comment la consanguinité influence les traits liés à la reproduction et les ornementations sexuelles secondaires chez les femelles, ainsi que son effet intergénérationnel chez cette espèce sans soins parentaux, nous avons utilisé des données de séquençage de nouvelle génération couplées à de nombreuses mesures phénotypiques. Parmi les différents effets maternels, nous avons investigué lequel a la plus forte influence sur les phénotypes de la descendance. Nous avons ensuite étudié l’effet des pressions sélectives exercées par des facteurs de stress chimiques et biologiques exogènes sur des œufs de différentes tailles pendant l'incubation. Par la suite, nous avons caractérisé le mécanisme de détermination du sexe chez les Corégones afin d’identifier un marqueur génétique lié au sexe, ce qui pourrait être avantageux pour l'aquaculture et la conservation. Finalement, nous avons étudié la nature héréditaire du coefficient de consanguinité dans une population endémique d'un lac qui se remet encore actuellement d'une crise d'eutrophisation. Nous avons trouvé, non seulement, que la consanguinité maternelle influence directement les traits reproductifs des femelles et indirectement la croissance des embryons, mais aussi que la consanguinité pourrait avoir conduit à l'évolution des ornementations sexuelles chez les femelles. Nous avons également montré que l'âge de la mère et la taille de l'œuf sont les principaux déterminants de la taille de la progéniture et que les œufs les plus gros subissent des pressions sélectives plus fortes pendant l'incubation par rapport aux œufs plus petits. Nous avons découvert que le mécanisme de détermination du sexe chez les Corégones repose sur la présence de multiples copies complètes du gène SDY chez les mâles et de multiples copies tronquées chez les femelles. Nous avons enfin démontré que le coefficient de consanguinité peut être héritable dans certaines circonstances spécifiques. Les résultats de cette thèse soulignent l'importance des effets maternels et de la consanguinité sur la dynamique des populations et la variabilité phénotypique des adultes et des juvéniles. Ces derniers ont non seulement des effets distincts, mais interagissent aussi entre eux en influençant les caractéristiques des générations suivantes

Struttura genetica di Chthamalus montagui (Crustacea, Cirripedia) dall'intero areale di distribuzione mediante sequenziamento del gene mitocondriale COI

Chthamalus montagui è un crostaceo cirripede con areale di distribuzione geografica ampio, comprendente le coste dell’Atlantico orientale, dal nord della Gran Bretagna alle isole di Capo Verde, e gran parte dei bacini del Mediterraneo e del Mar Nero. Il suo habitat include la zona intertidale delle coste rocciose. Le sue larve, con vita pelagica di 2-4 settimane, gli conferiscono un’elevata capacità di dispersione. Questa tesi ha lo scopo di indagare la struttura genetica della specie tramite l’uso del sequenziamento di 550bp della regione del DNA mitocondriale codificante per la COI (subunità I della citocromo c ossidasi). Inizialmente è stato effettuato uno studio pilota che ha previsto l’analisi di tre campioni di C. montagui geograficamente distanti: Biarritz nell’Oceano Atlantico orientale (N=24), Malta nel Mediterraneo centrale (N=24) e Sozopol nel Mar Nero (N=24). Tutto questo al fine di stabilire l’efficacia del marcatore molecolare scelto per la risoluzione del problema filogeografico da affrontare. I primi risultati hanno mostrato un elevato grado di divergenza genetica tra campioni, indicando come la COI sia un marcatore adatto a questo tipo di indagini. Lo studio sta proseguendo tramite l’analisi di campioni provenienti da altre 10-11 località. L’attività di laboratorio ha previsto la verifica della qualità del DNA, estratto in uno studio precedente, tramite corsa elettroforetica su gel d’agarosio all’1%. Ove necessario si è proceduto all’estrazione di DNA ex novo tramite il metodo del “Salting Out”. Una volta eseguite le opportune diluizioni del DNA estratto, si è proceduto ad amplificare la porzione della COI (circa 550bp) tramite PCR utilizzando i primer universali di Folmer et al. (1994). L’esito dell’amplificazione è stato poi verificato tramite corsa elettroforetica. I prodotti amplificati sono stati quindi purificati tramite precipitazione con etanolo e inviati ad un servizio esterno di sequenziamento. Si è quindi proceduto all’analisi dei cromatogrammi previa revisione delle sequenze. Una volta completate le analisi di laboratorio attualmente in corso saranno effettuate le analisi statistiche per i) stimare la variabilità genetica intra-campione (diversità aplotipica, diversità nucleotidica, numero efficace di aplotipi); ii) stimare la divergenza genetica tra i campioni (F-statistica, stime di flusso genico, albero degli aplotipi, network degli aplotipi, test Bayesiano di assegnazione individuale, test per la valutazione del modello dell'isolamento da distanza); iii) inferire sulla demografia storica (distribuzioni mismatch, Fs di Fu, R2 di Ramos-Onsins & Rozas). I risultati di queste analisi forniranno informazioni nuove sulla genetica di popolazione di C. montagui dall’intero areale di distribuzione. Infine i risultati del presente lavoro saranno confrontati ed integrati con quelli ottenuti in ricerche precedenti che hanno impiegato marcatori microsatellitari sugli stessi individui di C. montagui provenienti dalle stesse località, in modo da comparare l’efficacia dei due marcatori ed indagare più a fondo la struttura genetica della specie

Phylogeography on the rocks: The contribution of current and historical factors in shaping the genetic structure of <i>Chthamalus montagui</i> (Crustacea, Cirripedia) - Fig 2

<p>A. Median-joining network of <i>COI</i> haplotypes obtained in <i>Chthamalus montagui</i> from the 13 sampled locations. Each line in the network represents one mutational step; each small bar on the branches represents an additional mutational step. The area of each circle is proportional to the number of individuals showing that haplotype. B. Bayesian assignment analysis of <i>COI</i> sequences. Each vertical bar represents an individual and its associated probability of belonging to one of the five genetic clusters detected. Asterisks on the bar graph indicate individuals with uncertain assignment (<i>P</i> < 0.05). Pie charts indicate the percentage of genetic clusters contributing to each location. Pie charts were constructed with individual net assignments and after removing individuals with uncertain assignment.</p

Genomic compatibility excels possible ‘good genes’ effects of sexual selection in lake char

Mating is rarely random in nature, but the effects of mate selection on offspring performance are still poorly understood, even in well-established models such as salmonid fish. We sampled wild lake char (Salvelinus umbla) and used their gametes to investigate the genetic consequences of different mating scenarios. In a first study, we used full-factorial breeding to experimentally separate additive genetic from maternal environmental effects. This led to 60 families and in total 1,073 embryos that were raised singly after sublethal exposures to the pathogen Aeromonas salmonicida, the common pollutant ethinylestradiol, or water only. Contrary to predictions of ‘good genes’ sexual selection, offspring of more yellow males were less tolerant to the pathogen than offspring of pale males, while male coloration did not predict offspring tolerance to ethinylestradiol. However, increased kinship between the parents had strong negative effects on embryo development in all treatment groups. In a second experiment, we monitored 1,464 singly-raised embryos that resulted from 70 pair-wise sperm competition trials. These embryos were raised in an environment that supports the growth of symbiotic microbes (sublethal stress) or in a clean environment. Offspring of yellow males were again less stress tolerant than those of pale males, and embryo development was again slowed down with increasing genetic similarity between the parents. We conclude that genetic benefits of mate selection would be strongest if females avoided genetic similarity during mate selection, for example based on MHC-linked signals, while male breeding colors seem more relevant in intra-sexual selection

Persistent high hatchery recruitment despite advanced reoligotrophication and significant natural spawning in a whitefish

Many lakes of the pre-Alpine region suffered from severe eutrophication that affected the natural reproduction of whitefish (Coregonus spp.) and necessitated large-scale supportive breeding programs. With the advanced reoligotrophication, it is now important to evaluate the relevance of continued artificial breeding for population dynamics. We focused on a whitefish population of a lake that has reached phase III of the reoligotrophication, i.e., lake biomass production is declining since 2012 in response to low phosphorus concentrations. We show that most eggs are naturally spawned, the observed oxygen concentrations would again support embryo development at all depths, and ready-to-hatch embryos can indeed be found on spawning grounds. We marked all hatchery-produced eggs of the 2014 cohort with Alizarin red, stocked them as usual (at larval or early juvenile stages), and recaptured them over a period of five years. Fish were aged from yearly growth rings on scales, and otoliths were checked for marks. We found 90.3% of the 2014 cohort to be hatchery-born. This ratio did not decline with fish age. We also determined juvenile growth of the cohorts 2012-2020 (based on the first annual ring on scales) and found that stocking intensity predicted juvenile growth (r2 = 0.67). This strong density dependence of individual growth suggests that stocking has largely determined cohort size over the first nine years of reoligo¬trophication phase III. We conclude that large areas of spawning grounds allow again for successful embryogenesis, that large quantities of eggs are naturally spawned, but that natural recruitment is significantly reduced by ecological or evolutionary factors, e.g., competition with hatchery-born fish, desynchronization of trophic interactions, or long-term effects of fishing- or hatchery-induced evolution

Location of <i>Chthamalus montagui</i> sampling sites.

<p>Location abbreviations are as reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178287#pone.0178287.t001" target="_blank">Table 1</a>.</p