Evolutionary history predicts high‐impact invasions by herbivorous insects

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The impact of rate heterogeneity on inference of phylogenetic models of trait evolution

Rates of trait evolution are known to vary across phylogenies; however, standard evolutionary models assume a homogeneous process of trait change. These simple methods are widely applied in small‐scale phylogenetic studies, whereas models of rate heterogeneity are not, so the prevalence and patterns of potential rate variation in groups up to hundreds of species remain unclear. The extent to which trait evolution is modelled accurately on a given phylogeny is also largely unknown because studies typically lack absolute model fit tests. We investigated these issues by applying both rate‐static and variable‐rates methods on (i) body mass data for 88 avian clades of 10–318 species, and (ii) data simulated under a range of rate‐heterogeneity scenarios. Our results show that rate heterogeneity is present across small‐scaled avian clades, and consequently applying only standard single‐process models prompts inaccurate inferences about the generating evolutionary process. Specifically, these approaches underestimate rate variation, and systematically mislabel temporal trends in trait evolution. Conversely, variable‐rates approaches have superior relative fit (they are the best model) and absolute fit (they describe the data well). We show that rate changes such as single internal branch variations, rate decreases and early bursts are hard to detect, even by variable‐rates models. We also use recently developed absolute adequacy tests to highlight misleading conclusions based on relative fit alone (e.g. a consistent preference for constrained evolution when isolated terminal branch rate increases are present). This work highlights the potential for robust inferences about trait evolution when fitting flexible models in conjunction with tests for absolute model fit.     

Parallelism in adaptive radiations of experimental Escherichia coli populations

Adaptive radiations are major contributors to species diversity. Although the underlying mechanisms of adaptive radiations, specialization and trade‐offs, are relatively well understood, the tempo and repeatability of adaptive radiations remain elusive. Ecological specialization can occur through the expansion into novel niches or through partitioning of an existing niche. To test how the mode of resource specialization affects the tempo and repeatability of adaptive radiations, we selected replicate bacterial populations in environments that promoted the evolution of diversity either through niche expansion or through niche partitioning, and in a third low‐quality single‐resource environment, in which diversity was not expected to evolve. Colony size diversity evolved equally fast in environments that provided ecological opportunities regardless of the mode of resource specialization. In the low‐quality environments, diversity did not consistently evolve. We observed the largest fitness improvement in the low‐quality environment and the smallest the glucose‐limited environment. We did not observe a change in the rate of evolutionary change in either trait or environment, suggesting that the pool of beneficial mutations was not exhausted. Overall, the mode of resource specialization did not affect the tempo or repeatability of adaptive radiations. These results demonstrate the limitations of eco‐evolutionary feedbacks to affect evolutionary outcomes.     

Diversification and functional evolution of reef fish feeding guilds

A core eco‐evolutionary aim is to better understand the factors driving the diversification of functions in ecosystems. Using phylogenetic, trophic, and functional information, we tested whether trophic habits (i.e. feeding guilds) affect lineage and functional diversification in two major radiations of reef fishes. Our results from wrasses (Labridae) and damselfishes (Pomacentridae) do not fully support the ‘dead‐end’ hypothesis that specialisation leads to reduce speciation rates because the tempo of lineage diversification did not substantially vary among guilds in both fish families. Our findings also demonstrate a tight relationship between trophic habits and functional roles held by fish in reef ecosystems, which is not associated with a variation in the tempo of functional diversification among guilds. By illustrating the pivotal importance of the generalist feeding strategy during the evolutionary history of reef fishes, our study emphasises the role of this feeding guild as a reservoir for future diversity.     

Convergence and functional evolution of longirostry in crocodylomorphs

During the Mesozoic, Crocodylomorpha had a much higher taxonomic and morphological diversity than today. Members of one particularly successful clade, Thalattosuchia, are well‐known for being longirostrine: having long, slender snouts. It has generally been assumed that Thalattosuchia owed their success in part to the evolution of longirostry, leading to a feeding ecology similar to that of the living Indian gharial, Gavialis. Here, we compare form and function of the skulls of the thalattosuchian Pelagosaurus and Gavialis using digital reconstructions of the skull musculoskeletal anatomy and finite element models to show that they had different jaw muscle arrangements and biomechanical behaviour. Additionally, the relevance of feeding‐related mandibular traits linked to longirostry in the radiation of crocodylomorph clades was investigated by conducting an evolutionary rates analysis under the variable rates model. We find that, even though Pelagosaurus and Gavialis share similar patterns of stress distribution in their skulls, the former had lower mechanical resistance. This suggests that compared to Gavialis, Pelagosaurus was unable to process large, mechanically less tractable prey, instead operating as a specialized piscivore that fed on softer and smaller prey. Secondly, innovation of feeding strategies was achieved by rate acceleration of functional characters of the mandible, a key mechanism for the diversification of certain clades like thalattosuchians and eusuchians. Different rates of functional evolution suggest divergent diversification dynamics between teleosaurids and metriorhynchids in the Jurassic.     

Joint evolution of differential seed dispersal and self‐fertilization

Differential seed dispersal, in which selfed and outcrossed seeds possess different dispersal propensities, represents a potentially important individual‐level association. A variety of traits can mediate differential seed dispersal, including inflorescence and seed size variation. However, how natural selection shapes such associations is poorly known. Here, we developed theoretical models for the evolution of mating system and differential seed dispersal in metapopulations, incorporating heterogeneous pollination, dispersal cost, cost of outcrossing and environment‐dependent inbreeding depression. We considered three models. In the ‘fixed dispersal model’, only selfing rate is allowed to evolve. In the ‘fixed selfing model’, in which selfing is fixed but differential seed dispersal can evolve, we showed that natural selection favours a higher, equal or lower dispersal rate for selfed seeds to that for outcrossed seeds. However, in the ‘joint evolution model’, in which selfing and dispersal can evolve together, evolution necessarily leads to higher or equal dispersal rate for selfed seeds compared to that for outcrossed. Further comparison revealed that outcrossed seed dispersal is selected against by the evolution of mixed mating or selfing, whereas the evolution of selfed seed dispersal undergoes independent processes. We discuss the adaptive significance and constraints for mating system/dispersal association.     

Subspecies delineation amid phenotypic,geographic and genetic discordance in a songbird

Understanding the processes that drive divergence within and among species is a long‐standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra‐ and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and salt marsh (Ammodramus caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies of A. nelsoni and A. caudacutus using a reduced‐representation sequencing approach to generate a panel of 1929 SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh and coastal brackish–water marsh habitats. These patterns support the current species‐level recognition but do not match the subspecies‐level taxonomy within each species—a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.     

Beyond the phenotypic gambit: molecular behavioural ecology and the evolution of genetic architecture

Most studies of behaviour examine traits whose proximate causes include sensory input and neural decision-making, but conflict and collaboration in biological systems began long before brains or sensory systems evolved. Many behaviours result from non-neural mechanisms such as direct physical contact between recognition proteins or modifications of development that coincide with altered behaviour. These simple molecular mechanisms form the basis of important biological functions and can enact organismal interactions that are as subtle, strategic and interesting as any. The genetic changes that underlie divergent molecular behaviours are often targets of selection, indicating that their functional variation has important fitness consequences. These behaviours evolve by discrete units of quantifiable phenotypic effect (amino acid and regulatory mutations, often by successive mutations of the same gene), so the role of selection in shaping evolutionary change can be evaluated on the scale at which heritable phenotypic variation originates. We describe experimental strategies for finding genes that underlie biochemical and developmental alterations of behaviour, survey the existing literature highlighting cases where the simplicity of molecular behaviours has allowed insight to the evolutionary process and discuss the utility of a genetic knowledge of the sources and spectrum of phenotypic variation for a deeper understanding of how genetic and phenotypic architectures evolve.     

Intraclass Evolution and Classification of the Colpodea (Ciliophora)

ABSTRACT. Using nine new taxa and statistical inferences based on morphological and molecular data, we analyze the evolution within the class Colpodea. The molecular and cladistic analyses show four well‐supported clades: platyophryids, bursariomorphids, cyrtolophosidids, and colpodids. There is a widespread occurrence of homoplasies, affecting even conspicuous morphological characteristics, e.g. the inclusion of the micronucleus in the perinuclear space of the macronucleus. The most distinct changes in the morphological classification are the lack of a basal divergence into two subclasses and the split of the cyrtolophosidids into two main clades, differing mainly by the presence vs. absence of an oral cavity. The most complex clade is that of the colpodids. We partially reconcile the morphological and molecular data using evolutionary systematics, providing a scenario in which the colpodids evolved from a Bardeliella‐like ancestor and the genus Colpoda performed an intense adaptive radiation, giving rise to three main clades: Colpodina n. subord., Grossglockneriina, and Bryophryina. Three new taxa are established: Colpodina n. subord., Tillinidae n. fam., and Ottowphryidae n. fam. Colpodean evolution and classification are far from being understood because sequences are lacking for most species and half of their diversity is possibly undescribed.     

Evolutionary trend of Zoophycos morphotypes from the Upper Cretaceous–Lower Miocene in the type pelagic sections of Gubbio,Italy

About 200 Zoophycos specimens, including 90 specimens studied in detail, have been analysed in the continuous Upper Cretaceous–Lower Miocene pelagic sedimentary type sections of the Gubbio area (the Contessa Highway, Contessa Quarry and Bottaccione sections, Northern Apennines). The sediments are reddish to grey limestones and marls of the Scaglia Group and marls with volcaniclastic deposits of the Bisciaro Formation. The aim was to examine the evolutionary trend of what is probably the most debated trace fossil of all time, from the Upper Cretaceous to Lower Miocene. Despite having been found in beds ranging from the Cambrian to the present, no consensus has been reached regarding mode of construction, tracemaker or ethological explanation for Zoophycos. Four Zoophycos morphotypes are recognized at Gubbio showing variations of major and minor lamellae, apex, lobes and whorls: the Cretaceous–Eocene cone‐shaped type 1, the Upper Eocene–Middle Oligocene helicoidal type 2, the Oligocene lobate type 3 and the Upper Oligocene–Lower Miocene flat type 4. The very high ichnodensity in some beds (hundreds of specimens in discrete levels of the Bisciaro Formation, now destroyed by quarrying) seems to find explanation in abnormal concentrations of phytodetritus and organic matter on the seafloor in some periods. This very high abundance in discrete levels reflects a change in sedimentation and seafloor conditions at pre‐flysch deposition. Due to such high ichnodensity, many adjacent specimens display deformed outer margins. Taphonomic analysis shows a variation of whorls, laminae and U‐shaped lobes, reflecting ontogenetic development of the tracemaker(s) (?sipunculid worms).