Evolutionary patterns in early tetrapods. II. Differing constraints on available character space among clades

Radiations of large clades often accompany rapid morphological diversification. Evolutionary biologists debate the impact of external restrictions imposed by ecology, and intrinsic constraints imposed by development and genetics, on the rate at which morphological innovations are gained. These issues are particularly interesting for groups such as tetrapods, which evolved novel body plans relative to their piscine ancestors and which also invaded new ecosystems following terrestrialization. Prior studies have addressed these issues by looking at either ranges of morphological variation or rates of character change. Here, we address a related but distinct issue: the numbers of characters that freely vary within a clade. We modify techniques similar to those used by ecologists to infer species richnesses to estimate the number of potentially varying characters given the distributions of changes implied by a model phylogeny. Our results suggest both increasing constraints/restrictions and episodes of 'character release' (i.e. increasing the number of potentially varying characters). In particular, we show that stem lissamphibians had a restricted character space relative to that of stem amniotes, and that stem amniotes both had restrictions on some parts of character space but also invaded new character space that had been unavailable to stem tetrapods.     

Evolutionary patterns of diversification in the Andean hummingbird genus Adelomyia

The patterns of genetic diversity and morphological variation are of central importance in understanding the evolutionary process that drive diversification. We use molecular, morphological, and ecological data to explore the influence of geography and ecology in promoting speciation in the widespread Andean hummingbird genus Adelomyia. Six monophyletic clades were recovered which show distributional limits at well-defined geographic barriers. Percentage sequence divergence ranged between 5.8% and 8.2% between phylogroups separated by large (>4000 km) and small (<50 km) distances respectively, suggesting that geographic isolation may be influential at very different scales. We show that morphological traits in independent phylogroups are more related to environmental heterogeneity than to geographic barriers. We provide a molecular reconstruction of relationships within Adelomyia and recommend its use in future comparative studies of historical biogeography and diversification in the Andes.     

Global variation in diversification rates of flowering plants: energy vs. climate change

We used the largest DNA-based phylogeny of flowering plants to date to evaluate the importance of energy vs. past climate change in predicting global patterns in diversification. Relative diversification rates increased towards the equator, suggesting that differences in per-lineage net diversification may be an important component of the latitudinal diversity gradient. The amplitude of Quaternary climate oscillations experienced by families explained variation in diversification equally well compared to contemporary energy measures, and energy and climate change measures were intercorrelated, making it difficult to reject either as a causal mechanism. Many putative mechanisms linking diversification to energy availability do not apply to plants, whereas the climate change mechanism has more support. We also present the first global map of angiosperm diversification, showing that, after correcting for family range-size, tropical diversification rates were fastest for clades currently in regions with high endemic species richness outside the main lowland rainforest areas.     

Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.     

A supertree of temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods

As the most diverse group of early tetrapods, temnospondyls provide a unique opportunity to investigate cladogenetic patterns among basal limbed vertebrates. We present five species-level supertrees for temnospondyls, built using a variety of methods. The standard MRP majority rule consensus including minority components shows slightly greater resolution than other supertrees, and its shape matches well several currently accepted hypotheses of higher-level phylogeny for temnospondyls as a whole. Also, its node support is higher than those of other supertrees (except the combined standard plus Purvis MRP supertree). We explore the distribution of significant as well as informative changes (shifts) in branch splitting employing the standard MRP supertree as a reference, and discuss the temporal distribution of changes in time-sliced, pruned trees derived from this supertree. Also, we analyse those shifts that are most relevant to the end-Permian mass extinction. For the Palaeozoic, shifts occur almost invariably along branches that connect major Palaeozoic groups. By contrast, shifts in the Mesozoic occur predominantly within major groups. Numerous shifts bracket narrowly the end-Permian extinction, indicating not only rapid recovery and extensive diversification of temnospondyls over a short time period after the extinction event (possibly less than half a million years), but also the role of intense cladogenesis in the late part of the Permian (although this was counteracted by numerous 'background' extinctions).     

Increased early growth rates decrease longevities of conifers in subalpine forests

For trees, fast growth rates and large size seem to be a fitness benefit because of increased competitiveness, attainment of reproductive size earlier, reduction of generation times, and increased short‐term survival chances. However, fast growth rates and large size entail reduced investment in defenses, lower wood density and mechanical strength, increased hydraulic resistance as well as problems with down‐regulation of growth during periods of stress, all of which may decrease tree longevity. In this study, we investigated the relationship between longevity and growth rates of trees and quantified effects of spatial environmental variation (elevation, slope steepness, aspect, soil depth) on tree longevity. Radial growth rates and longevities were determined from tree‐ring samples of 161 dead trees from three conifer species in subalpine forests of the Colorado Rocky Mountains (Abies lasiocarpa, Picea engelmannii) and the Swiss Alps (Picea abies). For all three species, we found an apparent tradeoff between growth rate to the age of 50 years and longevity (i.e. fast early growth is associated with decreased longevity). This association was particularly pronounced for larger P. engelmannii and P. abies, which attained canopy size, however, there were also significant effects for smaller P. engelmannii and P. abies. For the more shade‐tolerant A. lasiocarpa, tree size did not have any effect. Among the abiotic variables tested only northerly aspect significantly favored longevity of A. lasiocarpa and P. engelmannii. Trees growing on south‐facing aspects probably experience greater water deficits leading to premature tree death, and/or shorter life spans may reflect shorter fire intervals on these more xeric aspects. Empirical evidence from other studies has shown that global warming affects growth rates of trees over large spatial and temporal scales. For moist‐cool subalpine forests, we hypothesize that the higher growth rates associated with global warming may in turn result in reduced tree longevity and more rapid turnover rates.     

Temporal patterns in rates of community change during succession

While ecological dogma holds that rates of community change decrease over the course of succession, this idea has yet to be tested systematically across a wide variety of successional sequences. Here, I review and define several measures of community change rates for species presence-absence data and test for temporal patterns therein using data acquired from 16 studies comprising 62 successional sequences. Community types include plant secondary and primary succession as well as succession of arthropods on defaunated mangrove islands and carcasses. Rates of species gain generally decline through time, whereas rates of species loss display no systematic temporal trends. As a result, percent community turnover generally declines while species richness increases--both in a decelerating manner. Although communities with relatively minor abiotic and dispersal limitations (e.g., plant secondary successional communities) exhibit rapidly declining rates of change, limitations arising from harsh abiotic conditions or spatial isolation of the community appear to substantially alter temporal patterns in rates of successional change.     

Evolutionary potential of Chamaecrista fasciculata in relation to climate change. I. Clinal patterns of selection along an environmental gradient in the great plains

Climate change will alter natural selection on native plant populations. Little information is available to predict how selection will change in the future and how populations will respond. Insight can be obtained by comparing selection regimes in current environments to selection regimes in environments similar to those predicted for the future. To mimic predicted temporal change in climate, three natural populations of the annual legume Chamaecrista fasciculata were sampled from a climate gradient in the Great Plains and progeny of formal crosses were reciprocally planted back into common gardens across this climate gradient. In each garden, native populations produced significantly more seed than the other populations, providing strong evidence of local adaptation. Phenotypic selection analysis conducted by site showed that plants with slower reproductive development, more leaves, and thicker leaves were favored in the most southern garden. Evidence of clinal variation in selection regimes was also found; selection coefficients were ordered according to the latitude of the common gardens. The adaptive value of native traits was indicated by selection toward the mean of local populations. Repeated clinal patterns in linear and nonlinear selection coefficients among populations and within and between sites were found. To the extent that temporal change in climate into the future will parallel the differences in selection across this spatial gradient, this study suggests that selection regimes will be displaced northward and different trait values will be favored in natural populations.     

Rapid change in nest size of a bird related to change in a secondary sexual character

Among bird species in which males contribute to nest building,sexual selection has favored larger nests. I investigated determinantsof nest size in the barn swallow Hirundo rustica and how nestsize changed during the period 1977–2003, when tail length(a male secondary sexual character) increased by more than 1.2standard deviations. Males with short tails contributed moreto nest building than long-tailed males, signaling their futureinvestment in food provisioning of offspring. Pairs of barnswallows were consistent in nest size when build ing new neststhe same or different years, and level of phenotypic plasticityin nest size was small and could not account for temporal patternsin nest size. Offspring resembled their parents with respectto nest size, indicating a significant heritability of nestsize, independent of whether offspring were reared by theirparents or by foster parents, and there was a significant negativegenetic correlation between male tail length and outer nestvolume and amount of nest material. The temporal increase inmale tail length was associated with a decrease in nest size,with the amount of nest material in 2003 on average being lessthan a third of the amount used in 1977. Temporal change innest size could be accounted for by indirect selection on taillength causing change in nest size to match that predicted fromchange in tail length and the genetic correlation between maletail length and nest size.     

Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus

Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein‐coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein‐coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH‐psbA, trnK_UUU‐rps16, trnfM_CAU‐rps14, trnS_GCU‐trnG_GCC, and atpF‐atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear.     

Rapid evolution in response to introduced predators I: rates and patterns of morphological and life-history trait divergence

Background  

Introduced species can have profound effects on native species, communities, and ecosystems, and have caused extinctions or declines in native species globally. We examined the evolutionary response of native zooplankton populations to the introduction of non-native salmonids in alpine lakes in the Sierra Nevada of California, USA. We compared morphological and life-history traits in populations of Daphnia with a known history of introduced salmonids and populations that have no history of salmonid introductions.     

Development and evolution of lateral line placodes in amphibians. - II. Evolutionary diversification

The amphibian lateral line system develops from a series of lateral line placodes. The different phases of development from early induction, to pattern formation, differentiation, morphogenesis, and metamorphic fate were summarized in the first part of this review (Schlosser, 2002a). Here, a survey of the diversity of lateral line systems in amphibians is presented indicating that most phases of lateral line development have been subject to evolutionary changes. Several trends suggest important roles for both adaptive changes and internal constraints in amphibian lateral line evolution. Many of these trends involved the coordinated modification of different derivatives of lateral line placodes suggesting that these placodes are not only autonomous developmental modules, but also units of evolutionary variation that tend to be modified in a coherent and largely context-independent fashion.     

Evolutionary change in the functional specificity of genes.

Species throughout the animal kingdom share not only housekeeping but also many key regulatory genes. Nonetheless, species differ from one another developmentally and thus, also morphologically. One of the general aims of comparative developmental genetics is to understand how similar molecules can generate the known diversity of biological form. Here, we argue that gene function can change in different ways during the evolution of developmental processes. Genes can be recruited to serve completely new functions in a new regulatory linkage (co-option), they can change their molecular specificity while remaining in the original (homologous) developmental program and can, at the same time, retain other functions. We describe evidence for such evolutionary patterns based on the comparison of loss-of-function mutations of homologous genes of the two free-living nematodes Caenorhabditis elegans and Pristionchus pacificus. Ultimately, it is the interplay of conservation and change of the specificity of genes and genetic networks that generates developmental novelty over evolutionary time.     

Evolutionary patterns of shape and functional diversification in the skull and jaw musculature of triggerfishes (Teleostei: Balistidae)

The robust skull and highly subdivided adductor mandibulae muscles of triggerfishes provide an excellent system within which to analyze the evolutionary processes underlying phenotypic diversification. We surveyed the anatomical diversity of balistid jaws using Procrustes‐based geometric morphometric analyses and a phylomorphospace approach to quantifying morphological transformation through evolution. We hypothesized that metrics of interspecific cranial shape would reveal patterns of phylogenetic diversification that are congruent with functional and ecological transformation. Morphological landmarks outlining skull and adductor mandibulae muscle shape were collected from 27 triggerfish species. Procrustes‐transformed skull shape configurations revealed significant phylogenetic and size‐influenced structure. Phylomorphospace plots of cranial shape diversity reveal groupings of shape between different species of triggerfish that are mostly consistent with phylogenetic relatedness. Repeated instances of convergence upon similar cranial shape by genetically disparate taxa are likely due to the functional demands of shared specialized dietary habits. This study shows that the diversification of triggerfish skulls occurs via modifications of cranial silhouette and the positioning of subdivided jaw adductor muscles. Using the morphometric data collected here as input to a biomechanical model of triggerfish jaw function, we find that subdivided jaw adductors, in conjunction with a unique cranial skeleton, have direct biomechanical consequences that are not always congruent with phylomorphospace patterns in the triggerfish lineage. The integration of geometric morphometrics with biomechanical modeling in a phylogenetic context provides novel insight into the evolutionary patterns and ecological role of muscle subdivisions in triggerfishes. J. Morphol. 277:737–752, 2016. © 2016 Wiley Periodicals, Inc.     

Macroevolutionary patterns in the diversification of parrots: effects of climate change,geological events and key innovations

Aim Parrots are thought to have originated on Gondwana during the Cretaceous. The initial split within crown group parrots separated the New Zealand taxa from the remaining extant species and was considered to coincide with the separation of New Zealand from Gondwana 82–85 Ma, assuming that the diversification of parrots was mainly shaped by vicariance. However, the distribution patterns of several extant parrot groups cannot be explained without invoking transoceanic dispersal, challenging this assumption. Here, we present a temporal and spatial framework for the diversification of parrots using external avian fossils as calibration points in order to evaluate the relative importance of the influences of past climate change, plate tectonics and ecological opportunity. Location Australasian, African, Indo‐Malayan and Neotropical regions. Methods Phylogenetic relationships were investigated using partial sequences of the nuclear genes c‐mos, RAG‐1 and Zenk of 75 parrot and 21 other avian taxa. Divergence dates and confidence intervals were estimated using a Bayesian relaxed molecular clock approach. Biogeographic patterns were evaluated taking temporal connectivity between areas into account. We tested whether diversification remained constant over time and if some parrot groups were more species‐rich than expected given their age. Results Crown group diversification of parrots started only about 58 Ma, in the Palaeogene, significantly later than previously thought. The Australasian lories and possibly also the Neotropical Arini were found to be unexpectedly species‐rich. Diversification rates probably increased around the Eocene/Oligocene boundary and in the middle Miocene, during two periods of major global climatic aberrations characterized by global cooling. Main conclusions The diversification of parrots was shaped by climatic and geological events as well as by key innovations. Initial vicariance events caused by continental break‐up were followed by transoceanic dispersal and local radiations. Habitat shifts caused by climate change and mountain orogenesis may have acted as a catalyst to the diversification by providing new ecological opportunities and challenges as well as by causing isolation as a result of habitat fragmentation. The lories constitute the only highly nectarivorous parrot clade, and their diet shift, associated with morphological innovation, may have acted as an evolutionary key innovation, allowing them to explore underutilized niches and promoting their diversification.     

Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in Caribbean and mainland Anolis lizards

Many of the classic examples of adaptive radiation, including Caribbean Anolis lizards, are found on islands. However, Anolis also exhibits substantial species richness and ecomorphological disparity on mainland Central and South America. We compared patterns and rates of morphological evolution to investigate whether, in fact, island Anolis are exceptionally diverse relative to their mainland counterparts. Quite the contrary, we found that rates and extent of diversification were comparable--Anolis adaptive radiation is not an island phenomenon. However, mainland and Caribbean anoles occupy different parts of morphological space; in independent colonizations of both island and mainland habitats, island anoles have evolved shorter limbs and better-developed toe pads. These patterns suggest that the two areas are on different evolutionary trajectories. The ecological causes of these differences are unknown, but may relate to differences in predation or competition among mainland and island communities.