Positive phenotypic selection inferred from phylogenies

Rates of phenotypic evolution vary widely in nature and these rates may often reflect the intensity of natural selection. Here we outline an approach for detecting exceptional shifts in the rate of phenotypic evolution across phylogenies. We introduce a simple new branch-specific metric ∆V/∆B that divides observed phenotypic change along a branch into two components: (1) that attributable to the background rate (∆B), and (2) that attributable to departures from the background rate (∆V). Where the amount of expected change derived from variation in the rate of morphological evolution doubles that explained by to the background rate (∆V/∆B > 2), we identify this as positive phenotypic selection. We apply our approach to six datasets, finding multiple instances of positive selection in each. Our results support the growing appreciation that the traditional gradual view of phenotypic evolution is rarely upheld, with a more episodic view taking its place. This moves focus away from viewing phenotypic evolution as a simple homogeneous process and facilitates reconciliation with macroevolutionary interpretations from a genetic perspective, paving the way to novel insights into the link between genotype and phenotype. The ability to detect positive selection when genetic data are unavailable or unobtainable represents an attractive prospect for extant species, but when applied to fossil data it can reveal patterns of natural selection in deep time that would otherwise be impossible.

The stationary distribution of a continuously varying strategy in a class-structured population under mutation-selection-drift balance.

Many traits and/or strategies expressed by organisms are quantitative phenotypes. Because populations are of finite size and genomes are subject to mutations, these continuously varying phenotypes are under the joint pressure of mutation, natural selection and random genetic drift. This article derives the stationary distribution for such a phenotype under a mutation-selection-drift balance in a class-structured population allowing for demographically varying class sizes and/or changing environmental conditions. The salient feature of the stationary distribution is that it can be entirely characterized in terms of the average size of the gene pool and Hamilton's inclusive fitness effect. The exploration of the phenotypic space varies exponentially with the cumulative inclusive fitness effect over state space, which determines an adaptive landscape. The peaks of the landscapes are those phenotypes that are candidate evolutionary stable strategies and can be determined by standard phenotypic selection gradient methods (e.g. evolutionary game theory, kin selection theory, adaptive dynamics). The curvature of the stationary distribution provides a measure of the stability by convergence of candidate evolutionary stable strategies, and it is evaluated explicitly for two biological scenarios: first, a coordination game, which illustrates that, for a multipeaked adaptive landscape, stochastically stable strategies can be singled out by letting the size of the gene pool grow large; second, a sex-allocation game for diploids and haplo-diploids, which suggests that the equilibrium sex ratio follows a Beta distribution with parameters depending on the features of the genetic system.

The contribution of a pollinating seed predator to selection on Silene latifolia females.

Interactions, antagonistic or mutualistic, can exert selection on plant traits. We explored the role of Hadena bicruris, a pollinating seed predator, as a selective agent on its host, the dioecious plant Silene latifolia. We exposed females from artificial-selection lines (many, small flowers (SF) vs. few, large flowers (LF)) to this moth. Infestation did not differ significantly between lines, but the odds of attacked fruits aborting were higher in SF females. We partitioned selection between that caused by moth attack and that resulting from all other factors. In both lines, selection via moth attack for fewer, smaller flowers contrasted with selection via other factors for more flowers. In LF females, selection via the two components was strongest and selection via moth attack also favoured increased fruit abortion. This suggests that the moths act as more of a selective force on flower size and number via their predating than their pollinating role.

Selection strategies for dairy buffaloes: economic and genetic consequences

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models

Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document micro-evolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have causal effects on fitness, but few valid tests of this exist. Here we show, using a quantitative genetic framework and six decades of life-history data on two free-living populations of great tits Parus major, that selection estimates for egg-laying date and clutch size are relatively unbiased. Predicted responses to selection based on the Robertson-Price Identity were similar to those based on the multivariate breeder’s equation, indicating that unmeasured covarying traits were not missing from the analysis. Changing patterns of phenotypic selection on these traits (for laying date, linked to climate change) therefore reflect changing selection on breeding values, and genetic constraints appear not to limit their independent evolution. Quantitative genetic analysis of correlational data from pedigreed populations can be a valuable complement to experimental approaches to help identify whether apparent associations between traits and fitness are biased by missing traits, and to parse the roles of direct versus indirect selection across a range of environments.

Selection and Floral Evolution in Platanthera bifolia and P. chlorantha (Orchidaceae)

Natural selection mediated by pollinators has influenced the evolution of floral diversity of the flowering plants (angiosperms). The scope of this thesis was to study: 1) phenotypic selection, 2) mating systems, and 3) floral shifts involved in plant speciation. Model plant species were Platanthera bifolia and P. chlorantha (Orchidaceae). These orchids are moth-pollinated, strictly co-sexual (bisexual flowers), and produce a spike that displays 10-20 white flowers. I explored the influence of characters on plant fitness by using multiple linear regressions. Pollen removal (male fitness) and fruit set (female fitness) increased with more flowers per plant in three P. bifolia populations. There was selection towards longer spurs in a dry year when average spur length was shorter than in normal-wet years. Female function was sensitive to drought, which enabled an application of the male function hypothesis of floral evolution (Bateman's principle). The results show that selection may vary between populations, years, and sex-functions. I examined inbreeding by estimating levels of geitonogamy (self-pollination between flowers of an individual) with an emasculation method in two P. bifolia populations. Geitonogamy did not vary with inflorescence size. Levels of geitonogamy was 20-40% in the smaller, but non-significant in the larger population. This may relate to lower number of possible mates and pollinator activity in the smaller population. Platanthera bifolia exhibits the ancestral character state of tongue-attachment of pollinia on the pollinator. Its close relative P. chlorantha attaches its pollinia onto the pollinator's eyes. To explore the mechanism of a floral shift, pollination efficiency and speed was compared between the two species. The results showed no differences in pollination efficiency, but P. chlorantha had faster pollen export and import. Efficiency of pollination in terms of speed may cause floral shifts, and thus speciation.

Lucerne biology and genetic improvement - an analysis of past activities and future goals in Australia

Breeding methodologies for cultivated lucerne (Medicago sativa L.), an autotetraploid, have changed little over the last 50 years, with reliance on polycross methods and recurrent phenotypic selection. There has been, however, an increase in our understanding of lucerne biology, in particular the genetic relationships between members of the M. sativa complex, as deduced by DNA analysis. Also, the differences in breeding behaviour and vigour of diploids versus autotetraploids, and the underlying genetic causes, are discussed in relation to lucerne improvement. Medicago falcata, a member of the M. sativa complex, has contributed substantially to lucerne improvement in North America, and its diverse genetics would appear to have been under-utilised in Australian programs over the last two decades, despite the reduced need for tolerance to freezing injury in Australian environments. Breeding of lucerne in Australia only commenced on a large scale in 1977, driven by an urgent need to introgress aphid resistance into adapted backgrounds. The release in the early 1980s of lucernes with multiple pest and disease resistance (aphids, Phytophthora, Colletotrichum) had a significant effect on increasing lucerne productivity and persistence in eastern Australia, with yield increases under high disease pressure of up to 300% being recorded over the predominant Australian cultivar, up to 1977, Hunter River. Since that period, irrigated lucerne yields have plateaued, highlighting the need to identify breeding objectives, technologies, and the germplasm that will create new opportunities for increasing performance. This review discusses major goals for lucerne improvement programs in Australia, and provides indications of the germplasm sources and technologies that are likely to deliver the desired outcomes.

Estimativa de parâmetros genéticos, correlações fenotípicas e ambientais no girassol do cerrado do Distrito Federal.

RESUMO: O propósito deste trabalho foi avaliar a estima - tiva de parâmetros genéticos, correlações fe - notipicas e ambientais no girassol do Cerrado do Distrito Federal. Os caracteres analisados foram: rendimento de grãos, tamanho do ca - pítulo, peso de mil aquênios, altura de plantas e dias para floração inicial. Foram constatadas diferenças altamente significativas entre os ge - nótipos para todas as características morfoa - gronômicas avaliadas. Para o coeficiente CVr a maioria dos valores foram superior a 1 nos dois anos considerados, indicando que para a maioria dos caracteres aferidos há a possibi - lidade de êxito na seleção fenotípica uma vez que a variância genética superou a ambiental. Na herdabilidade, a maior estimativa verifica - da foi para o caráter PMA (98,76%) em 2013 e para DFI (99,68%) em 2014. Foram cons - tatadas diferenças altamente significativas en - tre os genótipos para todas as características morfoagronômicas avaliadas. O alto coeficiente de variação genético destaca a possibilidade de obter ganhos genéticos para todas as caracte - rísticas analisadas salvo em tamanho de capi - tulo. Materiais genéticos com potencial para as características agronômicas pesquisadas foram identificados no trabalho, podem ser indicadas ao sistema de produção irrigado no Cerrado. abstract: The purpose of this study was to estimate ge - netic parameters, phenotypic and environmen - tal correlations in sunflower of Brazilian savan - nah. The characters analyzed were: grain yield, chapter length, weight of a thousand achenes, plant height and days to start flowering. Hi - ghly significant differences were observed among genotypes for all morphoagronomic cha - racteristics evaluated. For the most CVr coe - fficient values were higher than 1 in the two years under consideration, indicating that for the majority of measured characters there is the possibility of successful phenotypic selection once the genetic variance exceeded the envi - ronmental. The heritability estimate was the hi - ghest for the PMA character (98,76%) in 2013 and DFI (99,68%) in 2014. Highly significant differences were observed among genotypes for all morphoagronomic characteristics evalu - ated. The high coefficient of genetic variation show the possibility of obtaining genetic gain for all examined characteristics except in chap - ter length. Genetic material with potential for the researched agronomic characteristics were identified in the work, can be indicated to the irrigated production system in the Brazilian sa - vannah.

Environment-dependent microevolution in a Mediterranean pine (Pinus pinaster Aiton).

BACKGROUND: A central question for understanding the evolutionary responses of plant species to rapidly changing environments is the assessment of their potential for short-term (in one or a few generations) genetic change. In our study, we consider the case of Pinus pinaster Aiton (maritime pine), a widespread Mediterranean tree, and (i) test, under different experimental conditions (growth chamber and semi-natural), whether higher recruitment in the wild from the most successful mothers is due to better performance of their offspring; and (ii) evaluate genetic change in quantitative traits across generations at two different life stages (mature trees and seedlings) that are known to be under strong selection pressure in forest trees. RESULTS: Genetic control was high for most traits (h2 = 0.137-0.876) under the milder conditions of the growth chamber, but only for ontogenetic change (0.276), total height (0.415) and survival (0.719) under the more stressful semi-natural conditions. Significant phenotypic selection gradients were found in mature trees for traits related to seed quality (germination rate and number of empty seeds). Moreover, female relative reproductive success was significantly correlated with offspring performance for specific leaf area (SLA) in the growth chamber experiment, and stem mass fraction (SMF) in the experiment under semi-natural conditions, two adaptive traits related to abiotic stress-response in pines. Selection gradients based on genetic covariance of seedling traits and responses to selection at this stage involved traits related to biomass allocation (SMF) and growth (as decomposed by a Gompertz model) or delayed ontogenetic change, depending also on the testing environment. CONCLUSIONS: Despite the evidence of microevolutionary change in adaptive traits in maritime pine, directional or disruptive changes are difficult to predict due to variable selection at different life stages and environments. At mature-tree stages, higher female effective reproductive success can be explained by differences in their production of offspring (due to seed quality) and, to a lesser extent, by seemingly better adapted seedlings. Selection gradients and responses to selection for seedlings also differed across experimental conditions. The distinct processes involved at the two life stages (mature trees or seedlings) together with environment-specific responses advice caution when predicting likely evolutionary responses to environmental change in Mediterranean forest trees.

The genetical theory of social behaviour.

We survey the population genetic basis of social evolution, using a logically consistent set of arguments to cover a wide range of biological scenarios. We start by reconsidering Hamilton's (Hamilton 1964 J. Theoret. Biol. 7, 1-16 (doi:10.1016/0022-5193(64)90038-4)) results for selection on a social trait under the assumptions of additive gene action, weak selection and constant environment and demography. This yields a prediction for the direction of allele frequency change in terms of phenotypic costs and benefits and genealogical concepts of relatedness, which holds for any frequency of the trait in the population, and provides the foundation for further developments and extensions. We then allow for any type of gene interaction within and between individuals, strong selection and fluctuating environments and demography, which may depend on the evolving trait itself. We reach three conclusions pertaining to selection on social behaviours under broad conditions. (i) Selection can be understood by focusing on a one-generation change in mean allele frequency, a computation which underpins the utility of reproductive value weights; (ii) in large populations under the assumptions of additive gene action and weak selection, this change is of constant sign for any allele frequency and is predicted by a phenotypic selection gradient; (iii) under the assumptions of trait substitution sequences, such phenotypic selection gradients suffice to characterize long-term multi-dimensional stochastic evolution, with almost no knowledge about the genetic details underlying the coevolving traits. Having such simple results about the effect of selection regardless of population structure and type of social interactions can help to delineate the common features of distinct biological processes. Finally, we clarify some persistent divergences within social evolution theory, with respect to exactness, synergies, maximization, dynamic sufficiency and the role of genetic arguments.

Correlated genetic effects on reproduction define a domestication syndrome in a forest tree.

Compared to natural selection, domestication implies a dramatic change in traits linked to fitness. A number of traits conferring fitness in the wild might be detrimental under domestication, and domesticated species typically differ from their ancestors in a set of traits known as the domestication syndrome. Specifically, trade-offs between growth and reproduction are well established across the tree of life. According to allocation theory, selection for growth rate is expected to indirectly alter life-history reproductive traits, diverting resources from reproduction to growth. Here we tested this hypothesis by examining the genetic change and correlated responses of reproductive traits as a result of selection for timber yield in the tree Pinus pinaster. Phenotypic selection was carried out in a natural population, and progenies from selected trees were compared with those of control trees in a common garden experiment. According to expectations, we detected a genetic change in important life-history traits due to selection. Specifically, threshold sizes for reproduction were much higher and reproductive investment relative to size significantly lower in the selected progenies just after a single artificial selection event. Our study helps to define the domestication syndrome in exploited forest trees and shows that changes affecting developmental pathways are relevant in domestication processes of long-lived plants.

Mapping of QTLs related with wood quality and developmental characteristics in hybrids (Eucalyptus grandis x Eucalyptus urophylla)

The present work aimed to characterize and identify QTLs for wood quality and growth traits in E. grandis x E. urophylla hybrids. For this purpose a RAPD linkage map was developed for the hybrids (LOD=3 and r=0.40) containing 52 markers and 12 linkage groups. Traits related to wood quality and growth were evaluated in the QTL analyses. QTL analyses were performed using chi-square tests, single-marker, interval mapping and composite interval mapping analyses. All approaches led to the identification of similar QTLs associated with wood density, cellulose pulp yield and percentage of extractives, which were detected and confirmed by both the interval mapping and composite interval mapping methodologies. Some QTLs regions were confirmed only by the composite interval mapping methodology: percentage of soluble lignin, percentage of insoluble lignin, CBH and total height. Overlapping QTLs regions were detected, and these, can be the result of major genes involved in the regulation and control of the growth traits by epistatic interactions. In order to evaluate the effect of early selection using RAPD molecular data, molecular markers adjacent to QTLs were used genotype selection. The analysis of selection differential values suggests that for all the traits the phenotypic selection at seven years should generate larger genetic gains than early selection assisted by molecular markers and the combination of the strategies should elevate the selection efficiency.