Phylogenetic perspective on ecological niche evolution in american blackbirds (Family Icteridae)

Analysis of ecological characters on phylogenetic frameworks has only recently appeared in the literature, with several studies addressing patterns of niche evolution, generally over relatively recent time frames. In the present study, we examined patterns of niche evolution for a broad radiation of American blackbird species (Family Icteridae), exploring more deeply into phylogenetic history. Within each of three major blackbird lineages, overlap of ecological niches in principal components analysis transformed environmental space varied from high to none. Comparative phylogenetic analyses of ecological niche characteristics showed a general pattern of niche conservatism over evolutionary time, with differing degrees of innovation among lineages. Although blackbird niches were evolutionarily plastic over differing periods of time, they diverged within a limited set of ecological possibilities, resulting in examples of niche convergence among extant blackbird species. Hence, an understanding of the patterns of ecological niche evolution on broad phylogenetic scales sets the stage for framing questions of evolutionary causation, historical biogeography, and ancestral ecological characteristics more appropriately.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 869–878.     

Climate niche conservatism does not explain restricted distribution patterns in Tynanthus (Bignonieae,Bignoniaceae)

Studies on niche evolution allow us to establish how species niches have changed over time and to identify how long‐term evolutionary processes have led to present‐day species distributions. Here, we investigate the patterns of climatic niche evolution in Tynanthus (Bignonieae, Bignoniaceae), a genus of narrowly distributed species. We test the hypothesis that niche conservatism has played an important role in the history of this group of Neotropical lianas. We perform univariate and multivariate comparisons between climatic niches of species and associated environmental data with information on phylogenetic relationships. We encountered considerable divergence in niches among species, indicating that niche conservatism in climatic variables does not seem to have played a key role in the history of the genus. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 95–109.     

Differing evolutionary patterns underlie convergence on elongate morphology in endemic fishes of Lake Waccamaw, North Carolina

An extensive body of research has recently demonstrated patterns of parallel and/or convergent evolution that arise from divergent natural selection pressures exerted across environmental gradients. These studies, although providing some of our best empirical evidence for natural selection, have focused on rather narrow phylogenetic scopes, more often than not comparing patterns of morphological change among closely‐related taxa within a single genus. Organisms in replicated populations in these studies are often assumed to have accomplished convergence via similar underlying processes. However, such assumptions cannot be made when looking at evolution across broader phylogenetic and ecological spectra. In the present study, we assessed morphological change across a much broader scale to test whether similar evolutionary and developmental patterns underlie convergence. Specifically, we studied morphological change that has occurred in a novel lake environment (Lake Waccamaw, North Carolina, USA) where three phylogenetically‐disparate fishes representing different orders have speciated and independently evolved streamlined morphologies relative to their deeper‐bodied progenitors occupying nearby streams and coastal regions. Geometric morphometric analyses revealed that, although the bulk of shape change between environments is similar across taxa, significant species‐specific responses, concordant with differing expectations based on the ecologies of these taxa, were also found. Moreover, allometry analyses indicated that the developmental patterns underlying this change also differ across taxa. The present study provides evidence that, within a common environment, convergence can be achieved by different evolutionary and developmental patterns in phylogenetically‐ and ecologically‐disparate taxa. Finally, these results contradict the commonly‐held hypothesis that fishes should be more streamlined in streams than lakes and emphasize the need to also consider other environmental characteristics, such as water clarity and physical complexity, in studies of divergence. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 636–645.     

Biodiversity inhibits species' evolutionary responses to changing environments

Despite growing interplay between ecological and evolutionary studies, the question of how biodiversity influences evolutionary dynamics within species remains understudied. Here, using a classical model of phenotypic evolution in species occupying a patchy environment, but introducing global change affecting patch conditions, we show that biodiversity can inhibit species' evolution during global change. The presence of several species increases the chance that one or more species are pre-adapted to new conditions, which restricts the ecological opportunity for evolutionary responses in all the species. Consequently, environmental change tends to select for changes in species abundances rather than for changing phenotypes within each species. The buffering effects of species diversity that we describe might be one important but neglected explanation for widely observed niche conservatism in natural systems. Furthermore, the results show that attempts to understand biotic responses to environmental change need to consider both ecological and evolutionary processes in a realistically diverse setting.     

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.     

Climatic Niche Dynamics and Its Role in the Insular Endemism of <Emphasis Type="Italic">Anolis</Emphasis> Lizards

Insular systems are usually characterized by have a high species diversity, endemism, and evolutionary uniqueness. Although ecological and evolutionary factors shaping insular diversity and endemism are relatively well established, there is a little understanding about climatic niche dynamics for many insular adaptive radiations. Here, we evaluate the tempo and mode of climatic niche evolution in an iconic insular radiation of lizards. By using an extensive dataset of phylogenetic and coarse-grain climatic niches, we evaluated phylogenetic niche divergence and niche conservatism across temporal and spatial scales in the Caribbean Anolis lizard radiation. We found several instances of niche shifts during the anole radiation across islands. Many of these niche shifts converged to similar climatic regimes between different islands. Furthermore, we find evidence that single-island endemic species are more limited by low suitability of climatic conditions outside its native islands than oceanic barriers due to the high climatic heterogeneity observed at least between Greater Antillean islands. These results suggest that within-lineage climatic niche conservatism has been prevalent in short time scales and likely played a role driving the exceptional insular endemism observed today.     

Latitudinal gradients in climatic‐niche evolution accelerate trait evolution at high latitudes

Despite the importance of divergent selection to the speed of evolution, it remains poorly understood if divergent selection is more prevalent in the tropics (where species richness is highest), or at high latitudes (where paleoclimate change has been most intense). We tested whether the rate of climatic‐niche evolution – one proxy for divergent selection – varies with latitude for 111 pairs of bird species. Using Brownian motion and Ornsetin–Ulhenbeck models, we show that evolutionary rates along two important axes of the climatic‐niche – temperature and seasonality – have been faster at higher latitudes. We then tested whether divergence of the climatic‐niche was associated with evolution in traits important in ecological differentiation (body mass) and reproductive isolation (song), and found that climatic divergence is associated with faster rates in both measures. These results highlight the importance of climate‐mediated divergent selection pressures in driving evolutionary divergence and reproductive isolation at high latitudes.     

Tempo and mode of climatic niche evolution in Primates

Climatic niches have increasingly become a nexus in our understanding of a variety of ecological and evolutionary phenomena, from species distributions to latitudinal diversity gradients. Despite the increasing availability of comprehensive datasets on species ranges, phylogenetic histories, and georeferenced environmental conditions, studies on the evolution of climate niches have only begun to understand how niches evolve over evolutionary timescales. Here, using primates as a model system, we integrate recently developed phylogenetic comparative methods, species distribution patterns, and climatic data to explore primate climatic niche evolution, both among clades and over time. In general, we found that simple, constant‐rate models provide a poor representation of how climatic niches evolve. For instance, there have been shifts in the rate of climatic niche evolution in several independent clades, particularly in response to the increasingly cooler climates of the past 10 My. Interestingly, rate accelerations greatly outnumbered rate decelerations. These results highlight the importance of considering more realistic evolutionary models that allow for the detection of heterogeneity in the tempo and mode of climatic niche evolution, as well as to infer possible constraining factors for species distributions in geographical space.     

Using ecological niche modelling to evaluate niche stability in deep time

Aim To investigate relative niche stability in species responses to various types of environmental pressure (biotic and abiotic) on geological time‐scales using the fossil record. Location The case study focuses on Late Ordovician articulate brachiopods of the Cincinnati Arch in eastern North America. Methods Species niches were modelled for a suite of fossil brachiopod species based on five environmental variables inferred from sedimentary parameters using GARP and Maxent . Niche stability was assessed by comparison of (1) the degree of overlap of species distribution models developed for a time‐slice and those generated by projecting niche models of the previous time‐slice onto environmental layers of a second time‐slice using GARP and Maxent , (2) Schoener’s D statistic, and (3) the similarity of the contribution of each environmental parameter within Maxent niche models between adjacent time‐slices. Results Late Ordovician brachiopod species conserved their niches with high fidelity during intervals of gradual environmental change but responded to inter‐basinal species invasions through niche evolution. Both native and invasive species exhibited similar levels of niche evolution in the invasion and post‐invasion intervals. Niche evolution was related mostly to decreased variance within the former ecological niche parameters rather than to shifts to new ecospace. Main conclusions Although the species examined exhibited morphological stasis during the study interval, high levels of niche conservatism were observed only during intervals of gradual environmental change. Rapid environmental change, notably inter‐basinal species invasions, resulted in high levels of niche evolution among the focal taxa. Both native and invasive species responded with similar levels of niche evolution during the invasion interval and subsequent environmental reorganization. The assumption of complete niche conservatism frequently employed in ecological niche modelling (ENM) analyses to forecast or hindcast species geographical distributions is more likely to be accurate for climate change studies than for invasive species analyses over geological time‐scales.     

Evolution of skull and body shape in Triturus newts reconstructed from three‐dimensional morphometric data and phylogeny

To explore the relationship between morphological change and species diversification, we reconstructed the evolutionary changes in skull size, skull shape, and body elongation in a monophyletic group of eight species that make up salamander genus Triturus. Their well‐studied phylogenetic relationships and the marked difference in ecological preferences among five species groups makes this genus an excellent model system for the study of morphological evolution. The study involved three‐dimensional imagery of the skull and the number of trunk vertebrae, in material that represents the morphological, spatial, and molecular diversity of the genus. Morphological change largely followed the pattern of descent. The reconstruction of ancestral skull shape indicated that morphological change was mostly confined to two episodes, corresponding to the ancestral lineage that all crested newts have in common and the Triturus dobrogicus lineage. When corrected for common descent, evolution of skull shape was correlated to change in skull size. Also, skull size and shape, as well as body shape, as inferred from the number of trunk vertebrae, were correlated, indicating a marked impact of species' ecological preferences on morphological evolution, accompanied by a series of niche shifts, with the most pronounced one in the T. dobrogicus lineage. The presence of phylogenetic signal and correlated evolutionary changes in skull and body shape suggested complex interplay of niche shifts, natural selection, and constraints by a common developmental system. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 243–255.     

Contrasting global‐scale evolutionary radiations: phylogeny,diversification, and morphological evolution in the major clades of iguanian lizards

Parallel evolutionary radiations in adjacent locations have been documented in many systems, but typically at limited geographical scales. Here, we compare patterns of evolutionary radiation at the global scale in iguanian lizards, the dominant clade of lizards. We generated a new time‐calibrated phylogeny including 153 iguanian species (based on mitochondrial and nuclear data) and obtained data on morphology and microhabitats. We then compared patterns of species diversification, morphological disparity, and ecomorphological relationships in the predominantly Old World and New World clades (Acrodonta and Pleurodonta, respectively), focusing on the early portions of these radiations. Acrodonts show relatively constant rates of species diversification and disparity over time. In contrast, pleurodonts show an early burst of species diversification and less‐than‐expected morphological disparity early in their history, and slowing diversification and increasing disparity more recently. Analyses including all species (with MEDUSA) suggest accelerated diversification rates in certain clades within both Acrodonta and Pleurodonta, which strongly influences present‐day diversity patterns. We also find substantial differences in ecomorphological relationships between these clades. Our results demonstrate that sister clades in different global regions can undergo very different patterns of evolutionary radiation over similar time frames. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●● , ●●–●●.     

Scaling between macro- to microscale climatic data reveals strong phylogenetic inertia in niche evolution in plethodontid salamanders

Macroclimatic niches are indirect and potentially inadequate predictors of the realized environmental conditions that many species experience. Consequently, analyses of niche evolution based on macroclimatic data alone may incompletely represent the evolutionary dynamics of species niches. Yet, understanding how an organisms’ climatic (Grinnellian) niche responds to changing macroclimatic conditions is of vital importance for predicting their potential response to global change. In this study, we integrate microclimatic and macroclimatic data across 26 species of plethodontid salamanders to portray the relationship between microclimatic niche evolution in response to changing macroclimate. We demonstrate stronger phylogenetic signal in microclimatic niche variables than at the macroclimatic scale. Even so, we find that the microclimatic niche tracks climatic changes at the macroscale, but with a phylogenetic lag at million-year timescales. We hypothesize that behavioral tracking of the microclimatic niche over space and phenology generates the lag: salamanders preferentially select microclimates similar to their ancestral conditions rather than adapting with changes in physiology. We demonstrate that macroclimatic variables are weak predictors of niche evolution and that incorporating spatial scale into analyses of niche evolution is critical for predicting responses to climate change.     

What big lips are good for: on the adaptive function of repeatedly evolved hypertrophied lips of cichlid fishes

Linking phenotypic traits to an adaptive ecological function is a major goal of evolutionary biology. However, this task is challenging and has been accomplished in only a handful of species and ecological model systems. The repeatedly evolved adaptive radiations of cichlid fishes are composed of an enormously diverse set of species that differ in trophic morphology, body shape, coloration, and behaviour. Ecological guilds of species with conspicuously hypertrophied lips have evolved in parallel in all major cichlid radiations and are characterized by large lips and pointed and narrow heads. In the present study, we experimentally tested the adaptive significance of this set of conspicuous traits by comparing the success of hypertrophied‐lipped and closely‐related thin‐lipped endemic Lake Victoria cichlids in a novel foraging assay. The hypertrophied‐lipped species (Haplochromis chilotes) was clearly more successful in exploiting food resources from narrow crevices and the observed difference in foraging success increased more at narrower angles. Furthermore, pronounced differences in exploratory behaviour between the species suggest that the evolution of hypertrophied‐lipped species involved the co‐evolution of a suite of traits that include foraging behaviour. The repeated evolution of hypertrophied‐lip morphology in conjunction with a narrow and pointed head shape in cichlids represents an evolutionary innovation that facilitates foraging in rocky crevices, thus allowing access to a novel niche. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 448–455.     

Early vertebrate evolution

Debate over the origin and evolution of vertebrates has occupied biologists and palaeontologists alike for centuries. This debate has been refined by molecular phylogenetics, which has resolved the place of vertebrates among their invertebrate chordate relatives, and that of chordates among their deuterostome relatives. The origin of vertebrates is characterized by wide‐ranging genomic, embryologic and phenotypic evolutionary change. Analyses based on living lineages suggest dramatic shifts in the tempo of evolutionary change at the origin of vertebrates and gnathostomes, coincident with whole‐genome duplication events. However, the enriched perspective provided by the fossil record demonstrates that these apparent bursts of anatomical evolution and taxic richness are an artefact of the extinction of phylogenetic intermediates whose fossil remains evidence the gradual assembly of crown gnathostome characters in particular. A more refined understanding of the timing, tempo and mode of early vertebrate evolution rests with: (1) better genome assemblies for living cyclostomes; (2) a better understanding of the anatomical characteristics of key fossil groups, especially the anaspids, thelodonts, galeaspids and pituriaspids; (3) tests of the monophyly of traditional groups; and (4) the application of divergence time methods that integrate not just molecular data from living species, but also morphological data and extinct species. The resulting framework will provide for rigorous tests of rates of character evolution and diversification, and of hypotheses of long‐term trends in ecological evolution that themselves suffer for lack of quantitative functional tests. The fossil record has been silent on the nature of the transition from jawless vertebrates to the jawed vertebrates that have dominated communities since the middle Palaeozoic. Elucidation of this most formative of episodes likely rests with the overhaul of early vertebrate systematics that we propose, but perhaps more fundamentally with fossil grades that await discovery.     

Evolution of the climatic niche in scaly tree ferns (Cyatheaceae,Polypodiopsida)

Although climatic niche conservatism has been assumed by a large number of studies focused on climatic niche evolution, there are examples of climatic niche diversification and adaptation to changing climates. In this article, we reconstruct a climatic niche of scaly tree ferns (Cyatheaceae) using a rigorous analytical procedure which combines climatic niche modelling with reconstruction of continuous characters given a phylogenetic hypothesis. To estimate the limits to climatic niches of species, we used climate envelope modelling and ordination. Ancestral climatic niches of species were reconstructed by maximum likelihood and least‐squares analyses. We observed a trend towards niche conservatism with occasional events of niche transformations in scaly tree ferns. We discuss the implications of our study with respect to the potential and limitations for applications of niche modelling to evolutionary studies. We suggest that future studies of evolution of climatic niches could be considerably improved by employing approaches enabling reconstruction of continuous response to climatic gradients. Further progress may also be achieved by exploring models of character evolution other than the Brownian motion model. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 1–19.     

Is There Any Evidence for Rapid,Genetically-Based,Climatic Niche Expansion in the Invasive Common Ragweed?

Climatic niche shifts have been documented in a number of invasive species by comparing the native and adventive climatic ranges in which they occur. However, these shifts likely represent changes in the realized climatic niches of invasive species, and may not necessarily be driven by genetic changes in climatic affinities. Until now the role of rapid niche evolution in the spread of invasive species remains a challenging issue with conflicting results. Here, we document a likely genetically-based climatic niche expansion of an annual plant invader, the common ragweed (Ambrosia artemisiifolia L.), a highly allergenic invasive species causing substantial public health issues. To do so, we looked for recent evolutionary change at the upward migration front of its adventive range in the French Alps. Based on species climatic niche models estimated at both global and regional scales we stratified our sampling design to adequately capture the species niche, and localized populations suspected of niche expansion. Using a combination of species niche modeling, landscape genetics models and common garden measurements, we then related the species genetic structure and its phenotypic architecture across the climatic niche. Our results strongly suggest that the common ragweed is rapidly adapting to local climatic conditions at its invasion front and that it currently expands its niche toward colder and formerly unsuitable climates in the French Alps (i.e. in sites where niche models would not predict its occurrence). Such results, showing that species climatic niches can evolve on very short time scales, have important implications for predictive models of biological invasions that do not account for evolutionary processes.     

Cultural niche construction and human evolution

Organisms frequently choose, regulate, construct and destroy important components of their environments, in the process changing the selection pressures to which they and other organisms are exposed. We refer to these processes as niche construction. In humans, culture has greatly amplified our capacity for niche construction and our ability to modify selection pressures. We use gene‐culture coevolutionary models to explore the evolutionary consequences of culturally generated niche construction through human evolution. Our analysis suggests that where cultural traits are transmitted in an unbiased fashion from parent to offspring, cultural niche construction will have a similar effect to gene‐based niche construction. However, cultural transmission biases favouring particular cultural traits may either increase or reduce the range of parameter space over which niche construction has an impact, which means that niche construction with biased transmission will either have a much smaller or a much bigger effect than gene‐based niche construction. The analysis also reveals circumstances under which cultural transmission can overwhelm natural selection, accelerate the rate at which a favoured gene spreads, initiate novel evolutionary events and trigger hominid speciation. Because cultural processes typically operate faster than natural selection, cultural niche construction probably has more profound consequences than gene‐based niche construction, and is likely to have played an important role in human evolution.     

Morphological convergence of shell shape in distantly related scallop species (Mollusca: Pectinidae)

Morphological convergence is a central concept in evolutionary biology, but convergent patterns remain under‐studied in nonvertebrate organisms. Some scallop species exhibit long‐distance swimming, a behaviour whose biomechanical requirements probably generate similar selective regimes. We tested the hypothesis that shell shape similarity in long‐distance swimming species is a result of convergent evolution. Using landmark‐based geometric morphometrics, we quantified shell shape in seven species representing major behavioural habits. All species displayed distinct shell shapes, with the exception of the two long‐distance swimmers, whose shells were indistinguishable. These species also displayed reduced morphological variance relative to other taxa. Finally, a phylogenetic simulation revealed that these species were more similar in their shell shape than was expected under Brownian motion, the model of character evolution that best described changes in shell shape. Together, these findings reveal that convergent evolution of shell shape occurs in scallops, and suggest that selection for shell shape and behaviour may be important in the diversification of the group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 571–584.     

Regeneration niche of three epiphytic species of Gesneriaceae from Chilean rainforests: implications for the evolution of growth habits in Coronanthereae

Ecological and evolutionary studies of the epiphytic growth habit in angiosperms are limited. In this article, we assess the relationship between growth habit and regeneration niche in Coronanthereae (Gesneriaceae) and discuss its implications for the evolution of epiphytism in this lineage. In the temperate rainforest of southern Chile, we quantified the vertical distribution and experimentally examined the regeneration niche of three endemic species of Coronanthereae. One species was a holoepiphyte, which was more frequent in the upper canopy, and two species were secondary hemiepiphytes, which decreased in abundance with tree height. Seed germination of the holoepiphyte was higher on tree bark substrates and under open canopy than on forest soil and in the shade. In contrast, seed germination of both secondary hemiepiphytes did not differ between substrates (bark vs. soil) or light conditions (light vs. shade). Seedling survival percentage of secondary hemiepiphytes was higher on forest soil and under a closed canopy, thus behaving as shade‐tolerant species. In turn, the holoepiphyte behaved as a shade‐intolerant species. The reconstruction of the ancestral growth habits and regeneration niches on the inferred phylogenetic tree of Coronanthereae revealed that the specialized regeneration niche of Sarmienta repens, characterized by requirements of shade intolerance and germination on tree bark, was coupled with the evolution of the holoepiphytic growth habit. We conclude that differentiation in the regeneration niche is a key process in the evolution of epiphytic growth habits in Coronanthereae. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 79–92.     

Snake diets and the deep history hypothesis

The structure of animal communities has long been of interest to ecologists. Two different hypotheses have been proposed to explain origins of ecological differences among species within present‐day communities. The competition–predation hypothesis states that species interactions drive the evolution of divergence in resource use and niche characteristics. This hypothesis predicts that ecological traits of coexisting species are independent of phylogeny and result from relatively recent species interactions. The deep history hypothesis suggests that divergences deep in the evolutionary history of organisms resulted in niche preferences that are maintained, for the most part, in species represented in present‐day assemblages. Consequently, ecological traits of coexisting species can be predicted based on phylogeny regardless of the community in which individual species presently reside. In the present study, we test the deep history hypothesis along one niche axis, diet, using snakes as our model clade of organisms. Almost 70% of the variation in snake diets is associated with seven major divergences in snake evolutionary history. We discuss these results in the light of relevant morphological, behavioural, and ecological correlates of dietary shifts in snakes. We also discuss the implications of our results with respect to the deep history hypothesis. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 476–486.