Are shoals of minnow Phoxinus phoxinus formed by close kin?

A molecular analysis examining the level of relatedness in shoaling minnows Phoxinus phoxinus was conducted. The results revealed that individuals from within the same shoal were not more closely related to each other than to individuals from other shoals. This led to the conclusion that Schreckstoff may be less likely to have evolved in the context of kin selection.     

Genetic diversity shaped by historical and recent factors in the live‐bearing twoline skiffia Neotoca bilineata

The endangered twoline skiffia Neotoca bilineata, a viviparous fish of the subfamily Goodeinae, endemic to central Mexico (inhabiting two basins, Cuitzeo and Lerma‐Santiago) was evaluated using genetic and habitat information. The genetic variation of all remaining populations of the species was analysed using both mitochondrial and microsatellite markers and their habitat conditions were assessed using a water quality index (I_WQ). An 80% local extinction was found across the distribution of N. bilineata. The species was found in three of the 16 historical localities plus one previously unreported site. Most areas inhabited by the remaining populations had I_WQ scores unsuitable for the conservation of freshwater biodiversity. Populations showed low but significant genetic differentiation with both markers (mtDNA φ_ST = 0·076, P < 0·001; microsatellite F_ST = 0·314, P < 0·001). Borbollon, in the Cuitzeo Basin, showed the highest level of differentiation and was identified as a single genetic unit by Bayesian assignment methods. Rio Grande de Morelia and Salamanca populations showed the highest genetic diversity and also a high migration rate facilitated by an artificial channel that connected the two basins. Overall, high genetic diversity values were observed compared with other freshwater fishes (average N_a = 16 alleles and loci and mean ±s.d . H_o = 0·63 ± 0·10 and nucleotide diversity π = 0·006). This suggests that the observed genetic diversity has not diminished as rapidly as the species' habitat destruction. No evidence of correlation between habitat conditions and genetic diversity was found. The current pattern of genetic diversity may be the result of both historical factors and recent modifications of the hydrological system. The main threat to the species may be the rapid habitat deterioration and associated demographic stochasticity rather than genetic factors.     

The QTN program and the alleles that matter for evolution: all that's gold does not glitter

The search for the alleles that matter, the quantitative trait nucleotides (QTNs) that underlie heritable variation within populations and divergence among them, is a popular pursuit. But what is the question to which QTNs are the answer? Although their pursuit is often invoked as a means of addressing the molecular basis of phenotypic evolution or of estimating the roles of evolutionary forces, the QTNs that are accessible to experimentalists, QTNs of relatively large effect, may be uninformative about these issues if large‐effect variants are unrepresentative of the alleles that matter. Although 20th century evolutionary biology generally viewed large‐effect variants as atypical, the field has recently undergone a quiet realignment toward a view of readily discoverable large‐effect alleles as the primary molecular substrates for evolution. I argue that neither theory nor data justify this realignment. Models and experimental findings covering broad swaths of evolutionary phenomena suggest that evolution often acts via large numbers of small‐effect polygenes, individually undetectable. Moreover, these small‐effect variants are different in kind, at the molecular level, from the large‐effect alleles accessible to experimentalists. Although discoverable QTNs address some fundamental evolutionary questions, they are essentially misleading about many others.     

Assessing adaptive phenotypic plasticity by means of conditional strategies from empirical data: the latent environmental threshold model

Conditional strategies are the most common form of discrete phenotypic plasticity. In a conditional strategy, the phenotype expressed by an organism is determined by the difference between an environmental cue and a threshold, both of which may vary among individuals. The environmental threshold model (ETM) has been proposed as a mean to understand the evolution of conditional strategies, but has been surprisingly seldom applied to empirical studies. A hindrance for the application of the ETM is that often, the proximate cue triggering the phenotypic expression and the individual threshold are not measurable, and can only be assessed using a related observable cue. We describe a new statistical model that can be applied in this common situation. The Latent ETM (LETM) allows for a measurement error in the phenotypic expression of the individual environmental cue and a purely genetically determined threshold. We show that coupling our model with quantitative genetic methods allows an evolutionary approach including an estimation of the heritability of conditional strategies. We evaluate the performance of the LETM with a simulation study and illustrate its utility by applying it to empirical data on the size-dependent smolting process for stream-dwelling Atlantic salmon juveniles.     

The genetic basis of behavioral isolation between Drosophila mauritiana and D. sechellia

Understanding how species form is a fundamental question in evolutionary biology. Identifying the genetic bases of barriers that prevent gene flow between species provides insight into how speciation occurs. Here, I analyze a poorly understood reproductive isolating barrier, prezygotic reproductive isolation. I perform a genetic analysis of prezygotic isolation between two closely related species of Drosophila, D. mauritiana and D. sechellia. I first confirm the existence of strong behavioral isolation between D. mauritiana females and D. sechellia males. Next, I examine the genetic basis of behavioral isolation by (1) scanning an existing set of introgression lines for chromosomal regions that have a large effect on isolation; and (2) mapping quantitative trait loci (QTL) that underlie behavioral isolation via backcross analysis. In particular, I map QTL that determine whether a hybrid backcross female and a D. sechellia male will mate. I identify a single significant QTL, on the X chromosome, suggesting that few major-effect loci contribute to behavioral isolation between these species. In further work, I refine the map position of the QTL to a small region of the X chromosome.     

Genetic divergence is decoupled from ecological diversification in the hawaiian nesosydne planthoppers

Adaptive radiation involves ecological shifts coupled with isolation of gene pools. However, we know little about what drives the initial stages of divergence. We study a system in which ecological diversification is found within a chronologically well-defined geological matrix to provide insight into this enigmatic phase of radiation. We tested the hypothesis that a period of geographic isolation precedes ecological specialization in an adaptive radiation of host-specialized Hawaiian planthoppers. We examined population structure and history using mitochondrial and multiple independent microsatellite loci in a species whose geographic distribution on the island of Hawaii enabled us to observe the chronology of divergence in its very earliest stages. We found that genetic divergence is associated with geographic features but not different plant hosts and that divergence times are very recent and on the same timescales as the dynamic geology of the island. Our results suggest an important role for geography in the dynamics of the early stages of divergence.     

Independent axes of genetic variation and parallel evolutionary divergence of opercle bone shape in threespine stickleback

Evolution of similar phenotypes in independent populations is often taken as evidence of adaptation to the same fitness optimum. However, the genetic architecture of traits might cause evolution to proceed more often toward particular phenotypes, and less often toward others, independently of the adaptive value of the traits. Freshwater populations of Alaskan threespine stickleback have repeatedly evolved the same distinctive opercle shape after divergence from an oceanic ancestor. Here we demonstrate that this pattern of parallel evolution is widespread, distinguishing oceanic and freshwater populations across the Pacific Coast of North America and Iceland. We test whether this parallel evolution reflects genetic bias by estimating the additive genetic variance-covariance matrix (G) of opercle shape in an Alaskan oceanic (putative ancestral) population. We find significant additive genetic variance for opercle shape and that G has the potential to be biasing, because of the existence of regions of phenotypic space with low additive genetic variation. However, evolution did not occur along major eigenvectors of G, rather it occurred repeatedly in the same directions of high evolvability. We conclude that the parallel opercle evolution is most likely due to selection during adaptation to freshwater habitats, rather than due to biasing effects of opercle genetic architecture.     

PATERNAL CARE: DIRECT AND INDIRECT GENETIC EFFECTS OF FATHERS ON OFFSPRING PERFORMANCE

Knowledge of how genetic effects arising from parental care influence the evolution of offspring traits comes almost exclusively from studies of maternal care. However, males provide care in some taxa, and often this care differs from females in quality or quantity. If variation in paternal care is genetically based then, like maternal care and maternal effects, paternal effects may have important consequences for the evolution of offspring traits via indirect genetic effects (IGEs). IGEs and direct–indirect genetic covariances associated with parental care can contribute substantially to total heritability and influence predictions about how traits respond to selection. It is unknown, however, if the magnitude and sign of parental effects arising from fathers are the same as those arising from mothers. We used a reciprocal cross‐fostering experiment to quantify environmental and genetic effects of paternal care on offspring performance in the burying beetle, Nicrophorus vespilloides. We found that IGEs were substantial and direct–indirect genetic covariances were negative. Combined, these patterns led to low total heritabilities for offspring performance traits. Thus, under paternal care, offspring performance traits are unlikely to evolve in response to selection, and variation in these traits will be maintained in the population despite potentially strong selection on these traits. These patterns are similar to those generated by maternal care, indicating that the genetic effects of care on offspring performance are independent of the caregiver's sex.     

Genetic architecture and adaptive significance of the selfing syndrome in Capsella

The transition from outcrossing to predominant self-fertilization is one of the most common evolutionary transitions in flowering plants. This shift is often accompanied by a suite of changes in floral and reproductive characters termed the selfing syndrome. Here, we characterize the genetic architecture and evolutionary forces underlying evolution of the selfing syndrome in Capsella rubella following its recent divergence from the outcrossing ancestor C. grandiflora. We conduct genotyping by multiplexed shotgun sequencing and map floral and reproductive traits in a large (N= 550) F2 population. Our results suggest that in contrast to previous studies of the selfing syndrome, changes at a few loci, some with major effects, have shaped the evolution of the selfing syndrome in Capsella. The directionality of QTL effects, as well as population genetic patterns of polymorphism and divergence at 318 loci, is consistent with a history of directional selection on the selfing syndrome. Our study is an important step toward characterizing the genetic basis and evolutionary forces underlying the evolution of the selfing syndrome in a genetically accessible model system.