The present investigation focuses on population genetic structure analysis of the endangered giant clam species Tridacna maxima across part of the Red Sea,with the main aim of assessing the influence of postulated pot...The present investigation focuses on population genetic structure analysis of the endangered giant clam species Tridacna maxima across part of the Red Sea,with the main aim of assessing the influence of postulated potential barriers to gene flow(i.e.,particular oceanographic features and marked environmental heterogeneity)on genetic connectivity among populations of this poorly dispersive bivalve species.For this purpose,a total of 44 specimens of T.maxima were collected from five sampling locations along the Saudi Arabian coast and examined for genetic variability at the considerably variable mitochondrial gene cytochrome c oxidase I(COI).Our results revealed lack of population subdivision and phylogeographic structure across the surveyed geographic spectrum,suggesting that neither the short pelagic larval dispersal nor the various postulated barriers to gene flow in the Red Sea can trigger the onset of marked genetic differentiation in T.maxima.Furthermore,the discerned shallow COI haplotype genealogy(exhibiting high haplotype diversity and low nucleotide diversity),associated with recent demographic and spatial expansion events,can be considered as residual effect of a recent evolutionary history of the species in the Red Sea.展开更多
The present study reports on population structure analysis of the marbled crab Pachygrapsus marmoratus （Fabricius, 1787） from the Tunisian coast, an appropriate location to study biogeographical processes because of...The present study reports on population structure analysis of the marbled crab Pachygrapsus marmoratus （Fabricius, 1787） from the Tunisian coast, an appropriate location to study biogeographical processes because of the presence of a well-known discontinuous biogeographic area （the Siculo-Tunisian Strait）. Patterns of morphological and genetic variation of this highly dispersive and continuously distributed decapod species were assessed among its geographically close populations which cover almost the entire Tunisian coastline. A total of 386 specimens from nine sites were collected and examined for morphometric variability at 14 morphometric traits. The results of multivariate analyses of linear morphometric traits showed the existence of sexual dimorphism in this species by PERMANOVA （Permutational multivariate analysis of variance）. In addition, both CDA （Canonical discriminant analysis） and NPMANOVA （Non parametric MANOVA test） analyses revealed statistically significant differences among the studied locations for both sexes. Overall, the outcome of CDA analysis showed that over 87% of individuals could be assigned correctly to three regional groups in both sexes （North, Center and South）. Specifically, SIMPER （Similarity Percentages） analysis showed that carapace length, carapace width and merus length were major contributors to the morphometric separation between populations. The pattern of phenotypic variation suggested by morphometric analyses was found to be highly discordant with that suggested by the analysis of a mitochondrial marker （cytochrome oxidase I, COI）. Indeed, the results inferred from restriction fragment analysis of the COI in 180 crabs, suggested high genetic homogeneity. Very low levels of haplotype diversity （h） were found in almost all the studied populations, associated with non significant genetic distances for nearly all population comparisons. Explanations to these morphometric and mtDNA patterns as well as the discrepancy between them are discus展开更多
The prevalence of sexual reproduction has long been an outstanding problem of evolutionary biology. Different explanations have been offered to explain the prevalence of sexual reproduction. These explanations mainly ...The prevalence of sexual reproduction has long been an outstanding problem of evolutionary biology. Different explanations have been offered to explain the prevalence of sexual reproduction. These explanations mainly focus on the benefits of sexual reproduction’s ability to shuffle and recombine genes. In this paper, we propose an alternative and comprehensive point of view to this important problem. We first hypothesize that sexual reproduction leads to genetic homogeneity and maintains adaptational advantages of organisms. In stable conditions with strong selective pressures, the maintenance of desired adaptational advantages is one benefit of sexual reproduction. We further hypothesize that sexual reproduction provides a mechanism by which entire populations of similar genomes can interact and collaborate with one another in order to improve the population’s average genomic fitness, a phenomena we call coerced collaborative group evolution. We show that groups of individuals will improve as a whole, even though each individual is still operating under their own best interests. We also argue that the so-called ‘two-fold cost of males’ is misguided if we take limited resources in any environment into consideration. Finally, we propose an intuitive and visualized view to connect different theories on sexual reproduction to establish a comprehensive theory to explain sexual reproduction’s prevalence.展开更多
Family-based tests of association between a genetic marker and a disease constitute a common design to dissect the genetic architecture of complex traits. The FBAT software is one of the most popular tools to perform ...Family-based tests of association between a genetic marker and a disease constitute a common design to dissect the genetic architecture of complex traits. The FBAT software is one of the most popular tools to perform such studies. However, researchers are also often interested in the genetic contribution to a more specific manifestation of the phenotype (e.g. severe vs. non-severe form) known as a secondary outcome. Here, what we demonstrate is the limited power of the classical formulation of the FBAT statistic to detect the effect of genetic variants that influence a secondary outcome, in particular when these variants also impact on the onset of the disease, the primary outcome. We prove that this loss of power is driven by an implicit hypothesis, and we propose a derivation of the original FBAT statistic, free from this implicit hypothesis. Finally, we demonstrate analytically that our new statistic is robust and more powerful than FBAT for the detection of association between a genetic variant and a secondary outcome.展开更多
文摘The present investigation focuses on population genetic structure analysis of the endangered giant clam species Tridacna maxima across part of the Red Sea,with the main aim of assessing the influence of postulated potential barriers to gene flow(i.e.,particular oceanographic features and marked environmental heterogeneity)on genetic connectivity among populations of this poorly dispersive bivalve species.For this purpose,a total of 44 specimens of T.maxima were collected from five sampling locations along the Saudi Arabian coast and examined for genetic variability at the considerably variable mitochondrial gene cytochrome c oxidase I(COI).Our results revealed lack of population subdivision and phylogeographic structure across the surveyed geographic spectrum,suggesting that neither the short pelagic larval dispersal nor the various postulated barriers to gene flow in the Red Sea can trigger the onset of marked genetic differentiation in T.maxima.Furthermore,the discerned shallow COI haplotype genealogy(exhibiting high haplotype diversity and low nucleotide diversity),associated with recent demographic and spatial expansion events,can be considered as residual effect of a recent evolutionary history of the species in the Red Sea.
文摘The present study reports on population structure analysis of the marbled crab Pachygrapsus marmoratus （Fabricius, 1787） from the Tunisian coast, an appropriate location to study biogeographical processes because of the presence of a well-known discontinuous biogeographic area （the Siculo-Tunisian Strait）. Patterns of morphological and genetic variation of this highly dispersive and continuously distributed decapod species were assessed among its geographically close populations which cover almost the entire Tunisian coastline. A total of 386 specimens from nine sites were collected and examined for morphometric variability at 14 morphometric traits. The results of multivariate analyses of linear morphometric traits showed the existence of sexual dimorphism in this species by PERMANOVA （Permutational multivariate analysis of variance）. In addition, both CDA （Canonical discriminant analysis） and NPMANOVA （Non parametric MANOVA test） analyses revealed statistically significant differences among the studied locations for both sexes. Overall, the outcome of CDA analysis showed that over 87% of individuals could be assigned correctly to three regional groups in both sexes （North, Center and South）. Specifically, SIMPER （Similarity Percentages） analysis showed that carapace length, carapace width and merus length were major contributors to the morphometric separation between populations. The pattern of phenotypic variation suggested by morphometric analyses was found to be highly discordant with that suggested by the analysis of a mitochondrial marker （cytochrome oxidase I, COI）. Indeed, the results inferred from restriction fragment analysis of the COI in 180 crabs, suggested high genetic homogeneity. Very low levels of haplotype diversity （h） were found in almost all the studied populations, associated with non significant genetic distances for nearly all population comparisons. Explanations to these morphometric and mtDNA patterns as well as the discrepancy between them are discus
文摘The prevalence of sexual reproduction has long been an outstanding problem of evolutionary biology. Different explanations have been offered to explain the prevalence of sexual reproduction. These explanations mainly focus on the benefits of sexual reproduction’s ability to shuffle and recombine genes. In this paper, we propose an alternative and comprehensive point of view to this important problem. We first hypothesize that sexual reproduction leads to genetic homogeneity and maintains adaptational advantages of organisms. In stable conditions with strong selective pressures, the maintenance of desired adaptational advantages is one benefit of sexual reproduction. We further hypothesize that sexual reproduction provides a mechanism by which entire populations of similar genomes can interact and collaborate with one another in order to improve the population’s average genomic fitness, a phenomena we call coerced collaborative group evolution. We show that groups of individuals will improve as a whole, even though each individual is still operating under their own best interests. We also argue that the so-called ‘two-fold cost of males’ is misguided if we take limited resources in any environment into consideration. Finally, we propose an intuitive and visualized view to connect different theories on sexual reproduction to establish a comprehensive theory to explain sexual reproduction’s prevalence.
基金supported by the Programme Blanc de l’Agence National de la Recherche.
文摘Family-based tests of association between a genetic marker and a disease constitute a common design to dissect the genetic architecture of complex traits. The FBAT software is one of the most popular tools to perform such studies. However, researchers are also often interested in the genetic contribution to a more specific manifestation of the phenotype (e.g. severe vs. non-severe form) known as a secondary outcome. Here, what we demonstrate is the limited power of the classical formulation of the FBAT statistic to detect the effect of genetic variants that influence a secondary outcome, in particular when these variants also impact on the onset of the disease, the primary outcome. We prove that this loss of power is driven by an implicit hypothesis, and we propose a derivation of the original FBAT statistic, free from this implicit hypothesis. Finally, we demonstrate analytically that our new statistic is robust and more powerful than FBAT for the detection of association between a genetic variant and a secondary outcome.
