Contrasting signals from multiple markers illuminate population connectivity in a marine fish

Recent advances in molecular biology and bioinformatics have helped to unveil striking and previously unrecognized patterns of geographic genetic structure in marine populations. Largely driven by the pressing needs of fisheries management and conservation, studies on marine fish populations have played a pivotal role in testing the efficiency of a range of approaches to explore connectivity and dispersal at sea. Here, we employed nuclear and mitochondrial DNA markers and parasitic infestations to examine the nature and patterns of population structure in a warm-temperate coastal marine teleost across major putative biogeographic barriers in the Mediterranean Sea and Eastern Atlantic Ocean. We detected deep genetic divergence between mitochondrial lineages, likely caused by dramatic climatic and geological transformations before and during the Pleistocene. Such long-diverged lineages later came into secondary contact and can now be found in sympatry. More importantly, microsatellite data revealed that these lineages, after millions of years of independent evolution, now interbreed extensively. By combining genetic and parasite data, we were able to identify at least five independent demographic units. While the different genetic and parasite-based methods produce notably contrasting signals and may complicate the reconstruction of connectivity dynamics, we show that by tailoring the correct interpretation to each of the descriptors used, it is possible to achieve a deeper understanding of the micro-evolutionary process and, consequently, resolve population structure

Sex change and effective population size : implications for population genetic studies in marine fish

Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (‘sex-changing’) fish, the sex ratio is typically skewed and biased toward the ‘first’ sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected from two ecologically similar species living along the eastern coast of South Africa: one gonochoristic, the ‘santer’ sea bream Cheimerius nufar, and one protogynous (female-first) sex-changer, the ‘slinger’ sea bream Chrysoblephus puniceus. For both species, no evidence of geneticstructuring, nor significant variation in genetic diversity, were found in the study area. Estimates of contemporary Ne were significantly lower in the protogynous species, but the same pattern was not apparent over historical timescales. Overall, our results show that sequential hermaphroditism may affect Ne differently over varying time frames, and that demographic signatures inferred from genetic markers with different inheritance modes also need to be interpreted cautiously, in relation to sex-changing lifehistories

Ecological and evolutionary consequences of alternative sex-change pathways in fish

Sequentially hermaphroditic fish change sex from male to female (protandry) or vice versa (protogyny), increasing their fitness by becoming highly fecund females or large dominant males, respectively. These life-history strategies present different social organizations and reproductive modes, from near-random mating in protandry, to aggregate- and harem-spawning in protogyny. Using a combination of theoretical and molecular approaches, we compared variance in reproductive success (V k*) and effective population sizes (N e) in several species of sex-changing fish. We observed that, regardless of the direction of sex change, individuals conform to the same overall strategy, producing more offspring and exhibiting greater V k* in the second sex. However, protogynous species show greater V k*, especially pronounced in haremic species, resulting in an overall reduction of N e compared to protandrous species. Collectively and independently, our results demonstrate that the direction of sex change is a pivotal variable in predicting demographic changes and resilience in sex-changing fish, many of which sustain highly valued and vulnerable fisheries worldwide

Evidence for Female-Biased Dispersal in the Protandrous Hermaphroditic Asian Seabass, Lates calcarifer

Movement of individuals influences individual reproductive success, fitness, genetic diversity and relationships among individuals within populations and gene exchange among populations. Competition between males or females for mating opportunities and/or local resources predicts a female bias in taxa with monogamous mating systems and a male-biased dispersal in polygynous species. In birds and mammals, the patterns of dispersal between sexes are well explored, while dispersal patterns in protandrous hermaphroditic fish species have not been studied. We collected 549 adult individuals of Asian seabass (Lates calcarifer) from four locations in the South China Sea. To assess the difference in patterns of dispersal between sexes, we genotyped all individuals with 18 microsatellites. Significant genetic differentiation was detected among and within sampling locations. The parameters of population structure (FST), relatedness (r) and the mean assignment index (mAIC), in combination with data on tagging-recapture, supplied strong evidences for female-biased dispersal in the Asian seabass. This result contradicts our initial hypothesis of no sex difference in dispersal. We suggest that inbreeding avoidance of females, female mate choice under the condition of low mate competition among males, and male resource competition create a female-biased dispersal. The bigger body size of females may be a cause of the female-biased movement. Studies of dispersal using data from DNA markers and tagging-recapture in hermaphroditic fish species could enhance our understanding of patterns of dispersal in fish

Genetic variability in the tolerance of natural populations of Simocephalus vetulus (Müller, 1776) to lethal levels of sodium chloride

Using several clonal lineages of Simocephalus vetulus (Cladocera, Daphniidae) as a random sample, we investigated the genetic component of the halotolerance of one brackish and two freshwater populations of this littoral filter feeder. We hypothesized that genotypes from the brackish population were more tolerant than freshwater ones, via adaptation to local environmental conditions. Clonal identity was established by a cost-effective molecular fingerprinting technique (microsatellite-primed polymerase chain reaction (MSP-PCR)). Two distinct methodologies were used to assess cladoceran sensitivity to syntheticgrade sodium chloride (NaCl): (i) standard 48-h acute assays and (ii) 12-h survival time (ST) trials. No correlation was found between acute EC50 and ST values. The sensitivity of brackish and freshwater clones was comparable in terms of acute EC50 (varied from 2.28 to 3.83 g.Lx1). On the contrary, genetically determined differential tolerance to NaCl among populations was found for ST: all brackish genotypes, except one, were more resilient (ST>120 min) than freshwater clones (ST<120 min). Bearing in mind that these results were obtained with isolates from the extant population, it is surprising that the range of acute sensitivity of the freshwater and brackish genotypes was similar, and that the only difference between them was the ability of brackish clones to survive longer under high salinity stress (6 g.Lx1, in ST trials). We must conclude that the effect of salinity (original environment context) on the selection of genotypes was weaker than we had expected and than other authors have shown for other stressors.publishe

Establishment of a coastal fish in the Azores : recent colonisation or suddenexpansion of an ancient relict population?

The processes and time scales associated with ocean-wide changes in the distribution of marinespecies have intrigued biologists since Darwin’s earliest insights into biogeography. The Azores, amid-Atlantic volcanic archipelago located more than 1000 km off the European continental shelf,offers ideal opportunities to investigate phylogeographic colonization scenarios. The benthopelagicsparid fish known as the common two-banded seabream (Diplodus vulgaris) is now relativelycommon along the coastline of the Azores archipelago, but was virtually absent prior to the 1990s.We employed a multiple genetic marker approach to test whether the successful establishment of theAzorean population derives from a recent colonization from western continental/island populationsor from the demographic explosion of an ancient relict population.Results from nuclear and mtDNA sequences show that all Atlantic and Mediterranean populationsbelong to the same phylogroup, though microsatellite data indicate significant genetic divergencebetween the Azorean sample and all other locations, as well as among Macaronesian, westernIberian and Mediterranean regions. The results from Approximate Bayesian Computation indicatethat D. vulgaris has likely inhabited the Azores for approximately 40 (95% C.I.: 5.5─83.6) to 52(95% C.I.; 6.32─89.0) generations, corresponding to roughly 80-150 years, which suggests nearcontemporary colonisation, followed by a more recent demographic expansion which could havebeen facilitated by changing climate conditions. Moreover, the lack of previous records of thisspecies over the past century, together with the absence of lineage separation and the presence ofrelatively few private alleles, do not exclude the possibility of an even more recent colonisationevent

Sex change and the genetic structure of marine fish populations

The interaction between environmental forces and dispersal characteristics is largely responsible for the patterns of population structure in marine fish. Yet, crucial gaps in knowledge on life-histories and the relative contributions of numerous environmental factors still hinder a thorough understanding of marine population connectivity. One life-history trait so far overlooked by most fish population geneticists is sequential hermaphroditism, whereby individuals first mature as one sex and later in life reverse into the other sex. Population genetic theory predicts that sex-changing fish will present a higher potential for more spatially structured populations than gonochoristic species, as a result of their naturally skewed sex ratio, which is expected to reduce effective population size and hence increase genetic drift. We gathered published data on genetic population structure in marine fish, as summarized by the popular FST index, and – after controlling for several potentially confounding factors – we tested the hypothesis that sex-changing species are more genetically structured than gonochoristic ones. Although we found no evidence to support the theoretical expectations, our results suggest new working hypotheses that can stimulate new research avenues at the intersection between physiology, genetics and fisheries science

Variations clonales de la croissance et adaptations locales du métabolisme chez des populations de daphnies originaires d'environnements thermiques différents

La température influence directement l'ensemble des activités biologiques des ectothermes. Elle limite la répartition spatiale et temporelle des espèces et détermine les performances et les capacités compétitives des organismes. L'objectif de cette étude est de mesurer les effets directs de la température sur la croissance, le métabolisme et la fitness de Daphnia magna et d'évaluer si des clones originaires de trois populations (Churchill, Nebraska, et Israël), subissant des régimes thermiques différents, présentent des adaptations à la température. L'hypothèse de la variation à contre-gradient établit que les ectothermes originaires des hautes latitudes possèdent de meilleures capacités de croissance pour pouvoir compléter leur cycle de vie malgré les températures froides et les courtes saisons estivales. De plus, d'autres études ont montré que des ectothermes de hautes latitudes possèdaient de meilleures capacités métaboliques. Pour tester ces hypothèses, différents clones des trois populations ont été placés en environnement commun à 15°C et 25°C et les tailles à la naissance, à la première et troisième reproduction ont été mesurées. La consommation d'oxygène a été mesurée lorsque les organismes étaient nourris puis à jeun afin de pouvoir déterminer le registre aérobie de chaque daphnie. Les résultats montrent que les daphnies ont un taux de croissance deux fois plus élevé à 25°C qu'à 15°C et que leur taille asymptotique est supérieure à 15°C. Aucune différence significative de croissance n'a été mesurée entre les populations démontrant que les daphnies de cette espèce sont capables d'optimiser leur croissance en fonction des conditions environnementales ou encore que la croIssance est contrainte par la température. Les variations importantes du taux de croissance entre les clones d'une même population suggèrent que la diversité génétique et phénotypique d'une population pourrait résulter de l' adaptation aux variations saisonnières de la température. Les résultats de consommation d' oxygène montrent que le métabolisme des différentes populations de D. magna semble être adapté à leurs environnements thermiques spécifiques. Le métabolisme des daphnies de Churchill est plus élevé à 15°C, celui des daphnies du Nebraska est plus élevé à 25°C et celui des daphnies d' Israël ne varie pas significativement avec la température. La présence de populations de D. magna dans différents environnements thermiques pourrait être lié à un potentiel adaptatif élevé de cette espèce qui serait associé à une forte variabilité interclonale à l' interieur de chacune des populations

Calculating Ne and Ne/N in age-structured populations: a hybrid Felsenstein-Hill approach

The concept of effective population size (Ne) was developed under a discrete generation model, but most species have overlapping generations. In the early 1970s, J. Felsenstein and W. G. Hill independently developed methods for calculating Ne in age structured populations; the two approaches produce the same answer under certain conditions and have contrasting advantages and disadvantages. Here, we describe a hybrid approach that combines useful features of both. Like Felsenstein’s model, the new method is based on age specific survival and fertility rates and therefore can be directly applied to any species for which life table data are available. Like Hill, we relax the restrictive assumption in Felsenstein’s model regarding random variance in reproductive success, which allows more general application. The basic principle underlying the new method is that age structure stratifies a population into winners and losers in the game of life: individuals that live longer have more opportunities to reproduce and therefore have a higher mean lifetime reproductive success. This creates different classes of individuals within the population, and grouping individuals by age at death provides a simple means of calculating lifetime variance in reproductive success of a newborn cohort. The new method has the following features: (1) it can accommodate unequal sex ratio and sex-specific vital rates and over dispersed variance in reproductive success; (2) it can calculate effective size in species that change sex during their lifetime; (3) it can calculate Ne and the ratio Ne /N based on various ways of defining N; (4) it allows one to explore the relationship between Ne and the effective number of breeders per year (Nb), which is a quantity that genetic estimators of contemporary Ne commonly provide information about; and (5) it is implemented in freely available software (AgeNe)

Geographic patterns of genetic variation in four Neotropical rodents: Conservation implications for small game mammals in French Guiana

The Neotropics contributes significantly to global biodiversity yet little is known about its mammalian fauna. Given our limited knowledge, concerns are that extinctions at the local level may cause a decline in genetic diversity through the loss of unique alleles. Here we report the geographical population structure of four rodent species from French Guiana: Dasyprocta leporina, Agouti paca, Proechimys cayennensis and P. cuvieri. Two of them (Dasyprocta and Agouti) are commonly harvested throughout the country for subsistence and/or game hunting. Cytochrome b and control region sequences revealed the presence of a number of maternal lineages occurring in sympatry throughout French Guiana. We applied two cytochrome b rodent clock calibrations (7.5% and 12% per million years) to our data, and placed the divergence of the maternal lineages to between 160 000 and 260 000 years ago for the more diverse D. leporina and P. cuvieri, and between 66 000 and 46 000 years ago for the more recent A paca and P. cayennensis. The clades appear to be widespread throughout South America as indicated by specimens sampled in Brazil, Peru, and Venezuela. At the population level, AMOVA revealed little or no geographical structure within French Guiana. However, this conclusion is based on a single genetic marker and relatively few specimens. © 2004 The Linnean Society of London.Articl