Advantages of nonlinear mixed models for fitting avian growth curves

Our understanding of avian growth rates can benefit from the use of two statistical approaches that explicitly model the sources of intraspecific variation. First, random effects can evaluate whether there are consistent differences between individuals and groups of siblings within a population, and also account for any lack of statistical independence among data points. Second, nonlinear fixed‐effect functions can be extended to test specific biological hypotheses of interest, such as for differences between groups or populations. We illustrate the advantages of these methods by using nonlinear mixed models to study variation in the growth trajectories of nestling orange‐crowned warblers Oreothylpis celata. Specifically, we quantify the sources of variation within populations, analyze the effects of asynchronous hatching, and test for a difference in the growth rates of populations in Alaska and California, which are at the northern and southern limits of the species’ breeding distribution. We found that growth rates did not consistently vary between nests and individuals within populations and were not affected by asynchronous hatching, but were higher in Alaska than in California. Our extensions of traditional methods allowed us to accurately quantify this difference between populations, which is consistent with life history theory but has rarely been demonstrated in previous comparisons of intraspecific passerine populations. The methods we present can be applied to any taxonomic group and adjusted to fit any nonlinear function, and we provide code and implementation advice to facilitate the use of this analytical framework in future studies.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Biosynthesis of a P1-2-acetamido-2-deoxy-D-glucosyl P2-polyisoprenyl pyrophosphate by calf pancreas microsomes

Incubation of UDP-[¹⁴C]-$\text{N}$-acetylglucosamine with calf pancreas microsomes in the presence of Mn⁺⁺ and potassium thiocyanate gave a labeled glycolipid, tentatively identified as $\text{P}$¹-2-acetamido-2-deoxy-$\text{D}$-glucosyl $\text{P}$²-dolichyl pyrophosphate on the basis of cochromatography with synthetic $\text{P}$¹-2-acetamido-2-deoxy-α-$\text{D}$-glucopyranosyl $\text{P}$²-dolichyl pyrophosphate, similar chemical and enzymic hydrolyses of the biosynthetic and synthetic compounds, and stimulation of the biosynthesis by addition to the incubation mixture o dolichyl phosphate or a crude lipid fraction extracted from microsomes.     

Islands within an island: Repeated adaptive divergence in a single population

Physical barriers to gene flow were once viewed as prerequisites for adaptive evolutionary divergence. However, a growing body of theoretical and empirical work suggests that divergence can proceed within a single population. Here we document genetic structure and spatially replicated patterns of phenotypic divergence within a bird species endemic to 250 km² Santa Cruz Island, California, USA. Island scrub‐jays (Aphelocoma insularis) in three separate stands of pine habitat had longer, shallower bills than jays in oak habitat, a pattern that mirrors adaptive differences between allopatric populations of the species’ mainland congener. Variation in both bill measurements was heritable, and island scrub‐jays mated nonrandomly with respect to bill morphology. The population was not panmictic; instead, we found a continuous pattern of isolation by distance across the east–west axis of the island, as well as a subtle genetic discontinuity across the boundary between the largest pine stand and adjacent oak habitat. The ecological factors that appear to have facilitated adaptive differentiation at such a fine scale—environmental heterogeneity and localized dispersal—are ubiquitous in nature. These findings support recent arguments that microgeographic patterns of adaptive divergence may be more common than currently appreciated, even in mobile taxonomic groups like birds.     

Constraints on adaptive evolution: the functional trade-off between reproduction and fast-start swimming performance in the Trinidadian guppy (Poecilia reticulata)

The empirical study of natural selection reveals that adaptations often involve trade-offs between competing functions. Because natural selection acts on whole organisms rather than isolated traits, adaptive evolution may be constrained by the interaction between traits that are functionally integrated. Yet, few attempts have been made to characterize how and when such constraints are manifested or whether they limit the adaptive divergence of populations. Here we examine the consequences of adaptive life-history evolution on locomotor performance in the live-bearing guppy. In response to increased predation from piscivorous fish, Trinidadian guppies evolve an increased allocation of resources toward reproduction. These populations are also under strong selection for rapid fast-start swimming performance to evade predators. Because embryo development increases a female's wet mass as she approaches parturition, an increased investment in reproductive allocation should impede fast-start performance. We find evidence for adaptive but constrained evolution of fast-start swimming performance in laboratory trials conducted on second-generation lab-reared fish. Female guppies from high-predation localities attain a faster acceleration and velocity and travel a greater distance during fast-start swimming trials. However, velocity and distance traveled decline more rapidly over the course of pregnancy in these same females, thus reducing the magnitude of divergence in swimming performance between high- and low-predation populations. This functional trade-off between reproduction and swimming performance reveals how different aspects of the phenotype are integrated and highlights the complexity of adaptation at the whole-organism level.     

Experimental studies of evolution in guppies: a model for understanding the evolutionary consequences of predator removal in natural communities

Guppies (Poecilia reticulata) in Trinidadian streams are found with a diversity of predators in the lower reaches of streams, but few predators in the headwaters. These differences have caused the adaptive evolution of guppy behaviour, morphology, male colouration and life history. Waterfalls often serve as barriers to the upstream distribution of predators and/or guppies. Such discontinuities make it possible to treat streams like giant test tubes by introducing guppies or predators to small segments of streams from which they were previously excluded. Such experiments enable us to document how fast evolution can occur and the fine spatial scales over which adaptation is possible. They also demonstrate that the role predators play in structuring this ecosystem resembles many others studied from a more purely ecological perspective; in these streams, as elsewhere, predators depress the numbers of individuals in prey species which in turn reduces the effects of the prey species on other trophic levels and hence the structure of the ecosystem. A focus on predators is important in conservation biology because predators are often the organisms that are most susceptible to local extinction. Their selective loss occurs because large predators have been deliberately exterminated and/or are more susceptible to environmental disturbances. Furthermore, we will argue that predator re-introductions might be destabilizing if, in the absence of predators, their prey have evolved in a fashion that makes them highly susceptible to predation, even after time intervals as short as 50-100 years. A better understanding of the evolutionary impacts of top predators will be critical goal for the policy and practice of large carnivore restoration in the future.     

LOCAL ADAPTATION AND THE EVOLUTION OF PHENOTYPIC PLASTICITY IN TRINIDADIAN GUPPIES (POECILIA RETICULATA)

Divergent selection pressures across environments can result in phenotypic differentiation that is due to local adaptation, phenotypic plasticity, or both. Trinidadian guppies exhibit local adaptation to the presence or absence of predators, but the degree to which predator‐induced plasticity contributes to population differentiation is less clear. We conducted common garden experiments on guppies obtained from two drainages containing populations adapted to high‐ and low‐predation environments. We reared full‐siblings from all populations in treatments simulating the presumed ancestral (predator cues present) and derived (predator cues absent) conditions and measured water column use, head morphology, and size at maturity. When reared in presence of predator cues, all populations had phenotypes that were typical of a high‐predation ecotype. However, when reared in the absence of predator cues, guppies from high‐ and low‐predation regimes differed in head morphology and size at maturity; the qualitative nature of these differences corresponded to those that characterize adaptive phenotypes in high‐ versus low‐predation environments. Thus, divergence in plasticity is due to phenotypic differences between high‐ and low‐predation populations when reared in the absence of predator cues. These results suggest that plasticity might initially play an important role during colonization of novel environments, and then evolve as a by‐product of adaptation to the derived environment.     

Ecological correlates of the distribution limits of two poeciliid species along a salinity gradient

Identifying the environmental factors responsible for the formation of a species' distribution limit is challenging because organisms interact in complex ways with their environments. However, the use of statistical niche models in combination with the analysis of phenotypic variation along environmental gradients can help to reduce such complexity and identify a subset of candidate factors. In the present study, we used such approaches to describe and identify factors responsible for the parapatric distribution of two closely‐related livebearer fish species along a salinity gradient in the lowlands of Trinidad, West Indies. The downstream distribution limits of Poecilia reticulata were strongly correlated with the brackish–freshwater interface. We did not observe significant phenotypic variation in life‐history traits for this species when comparing marginal with more central populations, suggesting that abrupt changes in conditions at the brackish–freshwater interface limit its distribution. By contrast, Poecilia picta was present across a wide range of salinities, although it gradually disappeared from upstream freshwater localities. In addition, P. picta populations exhibited an increase in offspring size in localities where they coexist with P. reticulata, suggesting a role for interspecific competition. The parapatric distribution of these two species, suggests that P. reticulata distributions are limited by an abiotic factor (salinity), whereas P. picta is limited by a biotic factor (interspecific competition). Similar parapatric patterns have been previously described in other systems, suggesting they might be a common pattern in nature. © 2013 The Linnean Society of London