Darwin's finches - an adaptive radiation constructed from ancestral genetic modules

Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is the relative importance of new mutations, ancestral variants, and introgressive hybridization for phenotypic evolution and speciation. Here we address this issue using Darwin's finches, which vary in size from an 8g warbler finch with a pointed beak to a 40g large ground finch with a massive blunt beak. We present a highly contiguous genome assembly for one of the species and investigate the genomic architecture underlying phenotypic diversity in the entire radiation. Admixture mapping for beak and body size in the small, medium and large ground finches revealed 28 loci showing strong genetic differentiation. These loci represent ancestral haplotype blocks with origins as old as the Darwin's finch phylogeny (1-2 million years). Genes expressed in the developing beak are overrepresented in these genomic regions. Frequencies of allelic variants at the 28 loci covary with phenotypic similarities in body and beak size across the Darwin's finch phylogeny. These ancestral haplotypes constitute genetic modules for selection, and act as key determinants of the exceptional phenotypic diversity of Darwin's finches. Such ancestral haplotype blocks can be critical for how species adapt to environmental variability and change.

Testing the influence of crushing-surface variation on seed cracking performance between beak morphs of the African seedcracker Pyrenestes ostrinus

Extreme phenotypic polymorphism is an oft-cited example of evolutionary theory in practise. Although these morphological variations are assumed to be adaptive, few studies have biomechanically tested such hypotheses. Pyrenestes ostrinus (the African seedcracker finch) shows an intraspecific polymorphism in beak size and shape that is entirely diet driven and allelically determined. Three distinct morphs feed upon soft sedge seeds during times of abundance, but switch to specializing on three different species of sedge seeds that differ significantly in hardness during lean times. Here we test the hypothesis that beak morphology is directly related to consuming seeds of different hardness. We used a novel experimental analysis to test how beak morphology affects the efficiency of cracking sedge seeds of variable hardness. We found that neither mandibular ramus width nor crushing surface morphology had significant effects on the ability to crack different seed types. It is likely that feeding performance is correlated with other aspects of beak size and shape such as beak depth and strength, muscle force, or gape. Our results highlight how even seemingly straightforward examples of adaptive selection in nature can be complex in practice.

The latitudinal gradient in rates of evolution for bird beaks, a species interaction trait

Where is evolution fastest? The biotic interactions hypothesis proposes that greater species richness creates more ecological opportunity, driving faster evolution at low latitudes, whereas the “empty niches” hypothesis proposes that ecological opportunity is greater where diversity is low, spurring faster evolution at high latitudes. Here we tested these contrasting predictions by analyzing rates of bird beak evolution for a global dataset of 1141 sister pairs of birds. Beak size evolves at similar rates across latitudes, while beak shape evolves faster in the temperate zone, consistent with the empty niches hypothesis. We show in a meta-analysis that trait evolution and recent speciation rates are faster in the temperate zone, while rates of molecular evolution are slightly faster in the tropics. Our results suggest that drivers of evolutionary diversification are more potent at higher latitudes, thus calling into question multiple hypotheses invoking faster tropical evolution to explain the latitudinal diversity gradient.

Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions

Biotic interactions are hypothesized to be one of the main processes shaping trait and biogeographic evolution during lineage diversification. Theoretical and empirical evidence suggests that species with similar ecological requirements either spatially exclude each other, by preventing the colonization of competitors or by driving coexisting populations to extinction, or show niche divergence when in sympatry. However, the extent and generality of the effect of interspecific competition in trait and biogeographic evolution has been limited by a dearth of appropriate process-generating models to directly test the effect of biotic interactions. Here, we formulate a phylogenetic parametric model that allows interdependence between trait and biogeographic evolution, thus enabling a direct test of central hypotheses on how biotic interactions shape these evolutionary processes. We adopt a Bayesian data augmentation approach to estimate the joint posterior distribution of trait histories, range histories, and coevolutionary process parameters under this analytically intractable model. Through simulations, we show that our model is capable of distinguishing alternative scenarios of biotic interactions. We apply our model to the radiation of Darwin’s finches—a classic example of adaptive divergence—and find limited support for in situ trait divergence in beak size, but stronger evidence for convergence in traits such as beak shape and tarsus length and for competitive exclusion throughout their evolutionary history. These findings are more consistent with presympatric, rather than postsympatric, niche divergence. Our modeling framework opens new possibilities for testing more complex hypotheses about the processes underlying lineage diversification. More generally, it provides a robust probabilistic methodology to model correlated evolution of continuous and discrete characters. [Bayesian; biotic interactions; competition; data augmentation; historical biogeography; trait evolution.]

Young Broiler Feeding Kinematic Analysis as A Function of the Feed Type

Past publications describe the various impact of feeding behavior of broilers on productivity and physiology. However, very few publications have considered the impact of biomechanics associated with the feeding process in birds. The present study aims at comparing the kinematic variables of young broiler chicks (3–4 days old; 19 specimens) while feeding them with three different feed types, such as fine mash (F1), coarse mash (F2), and crumbled feed (F3). The feeding behavior of the birds was recorded using a high-speed camera. Frames sequences of each mandibulation were selected manually and classified according to the temporal order that occurred (first, second, third, or fourth, and further). The head displacement and the maximum beak gape were automatically calculated by image analysis. The results did not indicate strong correlations between birds’ weight, beak size (length and width), and the kinematic variables of feeding. The differences between the tested feed were found mostly in the first and second mandibulations, probably explained by the higher incidence of “catch-and-throw” movements in F3 (33%) and F1 (26%) than F2 (20%). The “catch-and-throw” movements in F1 (the smallest feed particle) mostly occurred in the first mandibulation, as in F3 (the largest feed particle) also occurred in the latest mandibulations. It might be suggested that the adoption of “catch-and-throw” in the latest mandibulations increases with larger particles. The kinematic variables in the latest mandibulations (from the third one on) seem to be similar for all feed types, which represent the swallowing phase. It might be inferred that the temporal sequence of the mandibulations should be essential to describe the kinematics of a feeding scene of broiler chickens, and the first and second mandibulations are potentially the key factors for the differences accounted by the diverse feed particle sizes.

Temporally varying disruptive selection in the medium ground finch ( Geospiza fortis )

Disruptive natural selection within populations exploiting different resources is considered to be a major driver of adaptive radiation and the production of biodiversity. Fitness functions, which describe the relationships between trait variation and fitness, can help to illuminate how this disruptive selection leads to population differentiation. However, a single fitness function represents only a particular selection regime over a single specified time period (often a single season or a year), and therefore might not capture longer-term dynamics. Here, we build a series of annual fitness functions that quantify the relationships between phenotype and apparent survival. These functions are based on a 9-year mark–recapture dataset of over 600 medium ground finches ( Geospiza fortis ) within a population bimodal for beak size. We then relate changes in the shape of these functions to climate variables. We find that disruptive selection between small and large beak morphotypes, as reported previously for 2 years, is present throughout the study period, but that the intensity of this selection varies in association with the harshness of environment. In particular, we find that disruptive selection was strongest when precipitation was high during the dry season of the previous year. Our results shed light on climatic factors associated with disruptive selection in Darwin's finches, and highlight the role of temporally varying fitness functions in modulating the extent of population differentiation.

Genetics of Inheritance and Interrelationship of Various Agronomic Traits of F2 Population in Cotton (Gossypium hirsutum L.)

Background: Cotton (Gossypium hirsutum L.) is grown in more than sixty countries worldwide. It is an important fiber crop in the world. It plays a vital role in our national economy being the source of earning of foreign exchange, therefore, it is considered to be the backbone of the economy of Pakistan. In Pakistan, millions of families are associated with cotton and textile industry for their livelihood. Results: In this experiment F2 population of the cross L. A. Frego Bract x CIM-600 and their parents was sown in randomized complete block design with three replications during normal growing season of the year 2014 to sort out best performing genotypes for yield related traits. Analysis of variance (ANOVA) revealed that parental and their F2 population showed significant differences for all the observed agronomic traits (plant height, number of monopodia branches, number of sympodial branches, number of bolls per plant, boll weight, ginning out turn, bract type, boll shape, beak size, seed cotton yield, staple length, fiber strength and fiber fineness). Estimation of correlation revealed that seed cotton yield was found positively correlated sympodial branches, fiber fineness and boll weight while ginning out turn, bract type, beak size, staple length and fiber strength were negatively associated with seed cotton yield. Epistasis was not found to be involved in any of the traits. Conclusion: The correlation and genetics study of various yield related traits provides us useful information for effective selection and sustainable breeding programs. Estimation of broad sense heritability ( ) in F2 populations for different traits vary as following order; ginning out turn>plant height>seed cotton yield>sympodia branches>fiber length>fiber strength>bolls per plant>monopodia branches>boll weight>fiber fineness with heritability 0.90, 0.79, 0.78, 0.75, 0.73, 0.71 0.67, 0.64, 0.63 and 0.50 respectively. Results suggested form heritability and correlation that these traits can be improved either through appropriate selection method or hybrid breeding programme.

Contrasting female mate preferences for red coloration in a fish

Understanding how animals select their mates requires knowing the factors that shape mate preferences. Recent theoretical and empirical considerations suggest that female mating status can influence the degree to which a female engages in mate choice, with virgin females predicted to be less choosy than mated females. In this study, we investigated mate choice in both virgin and mated females in the pygmy halfbeak Dermogenys collettei. Halfbeaks are small, live-bearing, internally fertilizing freshwater fish that live in mixed-sex groups where females have ample opportunity to engage in mate choice. Using a dichotomous choice assay, we quantified and contrasted in virgin and mated females mate preferences for differences in male body size, beak size, and area of yellow and red coloration. We also examined how mating status influenced the amount of time a female associated with the first male encountered and the relative amount of time a female associated with each male. We demonstrate that mate preferences of female halfbeaks are driven primarily by the size of red coloration present on males. Females showed contrasting preferences based on mating status, with virgin females preferentially associating with drab males whereas mated females preferentially associate with males possessing large areas of red. Contrary to expectations, female mating status did not influence how females associate with the first males encountered or how females biased their association time among males. Although the precise drivers of these effects need further studying, our finding highlights a possible explanation for how variation in male ornamentation can be maintained.

Interdependent Phenotypic and Biogeographic Evolution Driven by Biotic Interactions

Biotic interactions are hypothesized to be one of the main processes shaping trait and biogeographic evolution during lineage diversification. Theoretical and empirical evidence suggests that species with similar ecological requirements either spatially exclude each other, by preventing the colonization of competitors or by driving coexisting populations to extinction, or show niche divergence when in sympatry. However, the extent and generality of the effect of interspecific competition in trait and biogeographic evolution has been limited by a dearth of appropriate process-generating models to directly test the effect of biotic interactions. Here, we formulate a phylogenetic parametric model that allows interdependence between trait and biogeographic evolution, thus enabling a direct test of central hypotheses on how biotic interactions shape these evolutionary processes. We adopt a Bayesian data augmentation approach to estimate the joint posterior distribution of trait histories, range histories, and co-evolutionary process parameters under this analytically intractable model. Through simulations, we show that our model is capable of distinguishing alternative scenarios of biotic interactions. We apply our model to the radiation of Darwin’s finches—a classic example of adaptive divergence—and find support for in situ trait divergence in beak size, convergence in traits such as beak shape and tarsus length, and strong competitive exclusion throughout their evolutionary history. Our modeling framework opens new possibilities for testing more complex hypotheses about the processes underlying lineage diversification. More generally, it provides a robust probabilistic methodology to model correlated evolution of continuous and discrete characters.