Natural hybridization in tropical spikerushes of Eleocharis subgenus Limnochloa (Cyperaceae): Evidence from morphology and DNA markers

? Premise of the study: Natural hybridization represents an important force driving plant evolution and affecting community structure and functioning. Hybridization may be overlooked, however, among morphologically highly uniform congeners. An excellent example of such a group is Eleocharis subgenus Limnochloa, which has no reliably proven hybrids. Does this reflect biological barriers to interspecific crosses or difficulties in detecting the hybrids? We tested the hypothesis that hybridization occurs among sympatric Eleocharis cellulosa, E. interstincta, and E. mutata in northern Belize, Central America. ? Methods: Morphometric study (407 plants) was followed by examination of inter-simple sequence repeat (ISSR) polymorphisms (44 plants) and ITS sequence variation (33 plants). ? Key results: Two putatively hybrid morphotypes were discerned-E. cellulosa-resembling and E. interstincta-resembling. DNA markers of E. cellulosa and E. interstincta displayed additive constitution in plants from one E. cellulosa-resembling population only. The other putatively hybrid populations contained ISSR and ITS markers of the species they resembled morphologically, several unique ISSR markers, and ITS sequences of an undescribed South American Limnochloa entity. DNA markers of E. mutata were absent in the putative hybrids. ? Conclusions: Simultaneous use of various types of molecular markers can overcome many pitfalls of investigations concerning hybridization among closely related and morphologically similar species. Northern Belize represents a hybrid zone of E. cellulosa and E. interstincta. A third participant in the hybridization events occurring in this zone is an unknown Limnochloa lineage but is not E. mutata. Interspecific hybridization may play a significant role in the diversification of Eleocharis.     

Environmental correlates of phenotypic evolution in ecologically diverse Liolaemus lizards

Evolutionary correlations between phenotypic and environmental traits characterize adaptive radiations. However, the lizard genus Liolaemus, one of the most ecologically diverse terrestrial vertebrate radiations on earth, has so far shown limited or mixed evidence of adaptive diversification in phenotype. Restricted use of comprehensive environmental data, incomplete taxonomic representation and not considering phylogenetic uncertainty may have led to contradictory evidence. We compiled a 26‐taxon dataset for the Liolaemus gracilis species group, representing much of the ecological diversity represented within Liolaemus and used environmental data to characterize how environments occupied by species'' relate to phenotypic evolution. Our analyses, explicitly accounting for phylogenetic uncertainty, suggest diversification in phenotypic traits toward the present, with body shape evolution rapidly evolving in this group. Body shape evolution correlates with the occupation of different structural habitats indicated by vegetation axes suggesting species have adapted for maximal locomotory performance in these habitats. Our results also imply that the effects of phylogenetic uncertainty and model misspecification may be more extensive on univariate, relative to multivariate analyses of evolutionary correlations, which is an important consideration in analyzing data from rapidly radiating adaptive radiations.     

Trends in the sand: Directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae)

Directional evolution is one of the most compelling evolutionary patterns observed in macroevolution. Yet, despite its importance, detecting such trends in multivariate data remains a challenge. In this study, we evaluate multivariate evolution of shell shape in 93 bivalved scallop species, combining geometric morphometrics and phylogenetic comparative methods. Phylomorphospace visualization described the history of morphological diversification in the group; revealing that taxa with a recessing life habit were the most distinctive in shell shape, and appeared to display a directional trend. To evaluate this hypothesis empirically, we extended existing methods by characterizing the mean directional evolution in phylomorphospace for recessing scallops. We then compared this pattern to what was expected under several alternative evolutionary scenarios using phylogenetic simulations. The observed pattern did not fall within the distribution obtained under multivariate Brownian motion, enabling us to reject this evolutionary scenario. By contrast, the observed pattern was more similar to, and fell within, the distribution obtained from simulations using Brownian motion combined with a directional trend. Thus, the observed data are consistent with a pattern of directional evolution for this lineage of recessing scallops. We discuss this putative directional evolutionary trend in terms of its potential adaptive role in exploiting novel habitats.     

A new phylogenetic test for comparing multiple high‐dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae)

The interplay between evolutionary rates and modularity influences the evolution of organismal body plans by both promoting and constraining the magnitude and direction of trait response to ecological conditions. However, few studies have examined whether the best‐fit hypothesis of modularity is the same as the shape subset with the greatest difference in evolutionary rate. Here, we develop a new phylogenetic comparative method for comparing evolutionary rates among high‐dimensional traits, and apply this method to analyze body shape evolution in bioluminescent lanternfishes. We frame the study of evolutionary rates and modularity through analysis of three hypotheses derived from the literature on fish development, biomechanics, and bioluminescent communication. We show that a development‐informed partitioning of shape exhibits the greatest evolutionary rate differences among modules, but that a hydrodynamically informed partitioning is the best‐fit modularity hypothesis. Furthermore, we show that bioluminescent lateral photophores evolve at a similar rate as, and are strongly integrated with, body shape in lanternfishes. These results suggest that overlapping life‐history constraints on development and movement define axes of body shape evolution in lanternfishes, and that the positions of their lateral photophore complexes are likely a passive outcome of the interaction of these ecological pressures.     

Towards a historization of aposematism

Aposematism is one of the oldest phenomena in evolutionary biology and still a major puzzle to biologists. Despite its evolutionary nature, most attempts to understand aposematism are devoid of phylogenetic components. In addition, most studies that do take phylogeny into account need to bring the analysis even further. We argue that in order to fully understand aposematism we must have a clear picture of the evolutionary history behind present behaviours. In this paper we frame aposematism in a phylogenetic context and argue that most studies still are wanting in terms of demonstrating aposematism. Aposematism is not an end product but rather evolutionary scenarios including character transformations as well as prey–predator interactions. Finally, we suggest that, regardless how we restrict the concept of aposematism, knowing the directions of events facilitate all kinds of comparisons with a promise of uniting functional and evolutionary aspects into a historization of aposematism.     

Heterochronic detection through a function for the ontogenetic variation of bone shape

Heterochrony, evolutionary modifications in the rates and/or the timing of development, is widely recognized as an important agent of evolutionary change. In this paper, we are concerned with the detection of this evolutionary mechanism through the analysis of long bone growth. For this, we provide a function sigma (t) for the ontogenetic variation of bone shape by taking the ratio of two Gompertz curves explaining, respectively, the relative contribution to long bone growth of (a) endochondral ossification and (b) periosteal ossification. The significance of the fitting of this function to empirical data was tested in Anas platyrhynchos (Anseriformes). In this function sigma (t), the time t(m) at which periosteal growth rate first equalizes endochondral growth rate was taken as the timing parameter to be compared between taxa. On the other hand, the maximum rate of ontogenetic change in bone shape (maximum slope, beta) from hatching to t(m) was taken as the rate parameter to be compared. Comparisons of these parameters between the plesiomorphic condition and the derived character state would provide evidence for hypomorphosis (earlier occurrence of t(m)), hyper-morphosis (delayed occurrence of t(m)), deceleration (smaller beta) or acceleration (higher beta).Regarding the phylogenetic context, the ancestral condition for the character of interest should be estimated to polarize the direction of the heterochronic change. We have quantified the influence of the phylogenetic history on the variation of adult bone shape in a sample of 13 species of Anseriformes and 17 species from other neornithine orders of birds by using permutational phylogenetic regressions. Phylogenetic effects are significant, and this fact allows the optimization of bone shape onto a phylogenetic tree of Anseriformes to estimate the ancestral condition for Anas platyrhynchos.     

Key Innovations: Further Remarks on the Importance of Morphology in Elucidating Systematic Relationships and Adaptive Radiations

The present paper is an argument in support of the continued importance of morphological systematics and a plea for improving molecular phylogenetic analyses by addressing explicit character transformations. We use here the inference of key innovations and adaptive radiations to demonstrate why morphological systematics is still relevant and necessary. After establishing that theories of phylogenetic relationship offer robust explanatory bases for discussing evolutionary diversification, the following topics are addressed: (1) the inference of key innovations grounded in phylogenetic analyses; (2) the epistemic distinction between character ‘mapping’ and relevant evidence in systematic and evolutionary studies; and (3) key innovations in molecular phylogenetics. We emphasize that the discovery of key innovations, in fossil or extant taxa, further strengthens the importance of morphology in systematic and evolutionary inferences, as they reveal scenarios of character transformation that have led to asymmetrical sister-group diversification. Our main conclusion is that understanding characters in and of themselves, when properly contextualized systematically, is what evolutionary biologists should be concerned with, whereas the analysis of tree topology alone, in which statistical nodal support measures are the sole indicators of phylogenetic affinity, does not lead to a fuller understanding of key innovations.     

Strong character incongruence and character choice in phylogeny of sea stars of the Asterinidae

Abstract. Historically, characters from early animal development have been a potentially rich source of phylogenetic information, but many traits associated with the gametes and larval stages of animals with complex life cycles are widely suspected to have evolved frequent convergent similarities. Such convergences will confound true phylogenetic relationships. We compared phylogenetic inferences based on early life history traits with those from mitochondrial DNA sequences for sea stars in the genera Asterina, Cryptasterina , and Patiriella (Valvatida: Asterinidae). Analysis of these two character sets produced phylogenies that shared few clades. We quantified the degree of homoplasy in each character set when mapped onto the phylogeny inferred from the alternative characters. The incongruence between early life history and nucleotide characters implies more homoplasy in the life history character set. We suggest that the early life history traits in this case are most likely to be misleading as phylogenetic characters because simple adaptive models predict convergence in early life histories. We show that adding early life history characters may slightly improve a phylogeny based on nucleotide sequences, but adding nucleotide characters may be critically important to improving inferences from phylogenies based on early life history characters.     

The origins of molluscs

The interrelationships and evolutionary history of molluscs have seen great advances in the last decade. Recent phylogenetic studies have allowed alternative morphology‐based evolutionary scenarios to be tested and, most significantly, shown that the aplacophorans are sister group to polyplacophorans (chitons), corroborating palaeontological and embryological evolutionary scenarios in which aplacophorans are secondarily simplified from a chiton‐like ancestor. Aplacophoran morphology therefore does not represent the plesiomorphic condition for molluscs as a whole. The mollusc crown group radiated in the Early Cambrian, and rapidly thereafter, stem lineages to the major molluscan classes emerged: cephalopods, gastropods, bivalves (= pelecypods), monoplacophorans, rostroconchs (inferred stem scaphopods) and aculiferans. This attests to the fast, adaptive radiation of the crown group during the Cambrian explosion. Kimberella from the latest Ediacaran exhibits several molluscan traits, which justifies its position as a molluscan stem‐group member, rather than as a more basal Lophotrochozoan. The interrelationships among the conchiferan molluscs are still a matter of contention and require further palaeontological and molecular phylogenetic scrutiny.     

Evidence of constrained phenotypic evolution in a cryptic species complex of agamid lizards

Lineages that exhibit little morphological change over time provide a unique opportunity to explore whether nonadaptive or adaptive processes explain the conservation of morphology over evolutionary time scales. We provide the most comprehensive evaluation to date of the evolutionary processes leading to morphological similarity among species in a cryptic species complex, incorporating two agamid lizard species (Diporiphora magna and D. bilineata). Phylogenetic analysis of mitochondrial (ND2) and nuclear (RAG-1) gene regions revealed the existence of eight deeply divergent clades. Analysis of morphological data confirmed the presence of cryptic species among these clades. Alternative evolutionary hypotheses for the morphological similarity of species were tested using a combination of phylogenetic, morphological, and ecological data. Likelihood model testing of morphological data suggested a history of constrained phenotypic evolution where lineages have a tendency to return to their medial state, whereas ecological data showed support for both Brownian motion and constrained evolution. Thus, there was an overriding signature of constrained evolution influencing morphological divergence between clades. Our study illustrates the utility of using a combination of phylogenetic, morphological, and ecological data to investigate evolutionary mechanisms maintaining cryptic species.     

Anatomical variation in Cactaceae and relatives: Trait lability and evolutionary innovation

The cacti have undergone extensive specialization in their evolutionary history, providing an excellent system in which to address large-scale questions of morphological and physiological adaptation. Recent molecular phylogenetic studies suggest that (1) Pereskia, the leafy genus long interpreted as the sister group of all other cacti, is likely paraphyletic, and (2) Cactaceae are nested within a paraphyletic Portulacaceae as a member of the "ACPT" clade (Anacampseroteae, Cactaceae, Portulaca, and Talinum). We collected new data on the vegetative anatomy of the ACPT clade and relatives to evaluate whether patterns in the distributions of traits may provide insight into early events in the evolutionary transition to the cactus life form. Many traits had high levels of homoplasy and were mostly equivocal with regard to infraclade relationships of ACPT, although several characters do lend further support to a paraphyletic Pereskia. These include a thick stem cuticle, prominent stem mucilage cells, and hypodermal calcium oxalate druses, all of which are likely to be important traits for stem water storage and photosynthesis. We hypothesize that high lability of many putative "precursor" traits may have been critical in generating the organismal context necessary for the evolution of an efficient and integrated photosynthetic stem.     

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)

Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study, we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using micro‐computed tomographic (µCT) scanning and geometric morphometrics, we quantified body shape, size, and vertebral counts of 31 belonid species. We then examined the pattern and tempo of body shape and size evolution using phylogenetic comparative methods. Our results show that transitions from marine to freshwater habitats have altered the adaptive landscape for needlefishes and expanded morphospace relative to marine taxa. We provide further evidence that freshwater taxa attain reduced sizes either through dwarfism (as inferred from axial skeletal reduction) or through developmental truncation (as inferred from axial skeletal loss). We propose that transitions to freshwater habitats produce morphological novelty in response to novel prey resources and changes in locomotor demands. We find that repeated invasions of different habitats have prompted predictable changes in morphology.     

Correlates of rate heterogeneity in avian ecomorphological traits

Heterogeneity in rates of trait evolution is widespread, but it remains unclear which processes drive fast and slow character divergence across global radiations. Here, we test multiple hypotheses for explaining rate variation in an ecomorphological trait (beak shape) across a globally distributed group (birds). We find low support that variation in evolutionary rates of species is correlated with life history, environmental mutagenic factors, range size, number of competitors, or living on islands. Indeed, after controlling for the negative effect of species' age, 80% of variation in species‐specific evolutionary rates remains unexplained. At the clade level, high evolutionary rates are associated with unusual phenotypes or high species richness. Taken together, these results imply that macroevolutionary rates of ecomorphological traits are governed by both ecological opportunity in distinct adaptive zones and niche differentiation among closely related species.     

Bayesian inference of character evolution

Much recent progress in evolutionary biology is based on the inference of ancestral states and past transformations in important traits on phylogenetic trees. These exercises often assume that the tree is known without error and that ancestral states and character change can be mapped onto it exactly. In reality, there is often considerable uncertainty about both the tree and the character mapping. Recently introduced Bayesian statistical methods enable the study of character evolution while simultaneously accounting for both phylogenetic and mapping uncertainty, adding much needed credibility to the reconstruction of evolutionary history.     

Integration of conflict into integrative taxonomy: fitting hybridization in species delimitation of Mesocarabus (Coleoptera: Carabidae)

In species differentiation, characters may not diverge synchronously, and there are also processes that shuffle character states in lineages descendant from a common ancestor. Species are thus expected to show some degree of incongruence among characters; therefore, taxonomic delimitation can benefit from integrative approaches and objective strategies that account for character conflict. We illustrate the potential of exploiting conflict for species delimitation in a study case of ground beetles of the subgenus Carabus (Mesocarabus), where traditional taxonomy does not accurately delimit species. The molecular phylogenies of four mitochondrial and three nuclear genes, cladistic analysis of the aedeagus, ecological niche divergence and morphometry of pronotal shape in more than 500 specimens of Mesocarabus show that these characters are not fully congruent. For these data, a three‐step operational strategy is proposed for species delimitation by (i) delineating candidate species based on the integration of incongruence among conclusive lines of evidence, (ii) corroborating candidate species with inconclusive lines of evidence and (iii) refining a final species proposal based on an integrated characterization of candidate species based on the evolutionary analysis of incongruence. This procedure provided a general understanding of the reticulate process of hybridization and introgression acting on Mesocarabus and generated the hypothesis of seven Mesocarabus species, including two putative hybrid lineages. Our work emphasizes the importance of incorporating critical analyses of character and phylogenetic conflict to infer both the evolutionary history and species boundaries through an integrative taxonomic approach.     

How phenotypic convergence arises in experimental evolution

Evolutionary convergence is a core issue in the study of adaptive evolution, as well as a highly debated topic at present. Few studies have analyzed this issue using a “real‐time” or evolutionary trajectory approach. Do populations that are initially differentiated converge to a similar adaptive state when experiencing a common novel environment? Drosophila subobscura populations founded from different locations and years showed initial differences and variation in evolutionary rates in several traits during short‐term (～20 generations) laboratory adaptation. Here, we extend that analysis to 40 more generations to analyze (1) how differences in evolutionary dynamics among populations change between shorter and longer time spans, and (2) whether evolutionary convergence occurs after 60 generations of evolution in a common environment. We found substantial variation in longer term evolutionary trajectories and differences between short‐ and longer term evolutionary dynamics. Although we observed pervasive patterns of convergence toward the character values of long‐established populations, populations still remain differentiated for several traits at the final generations analyzed. This pattern might involve transient divergence, as we report in some cases, indicating that more generations should lead to final convergence. These findings highlight the importance of longer term studies for understanding convergent evolution.     

The roles of ecological fitting, phylogeny and physiological equivalence in understanding realized and fundamental host ranges in endoparasitoid wasps

Co-evolutionary theory underpins our understanding of interactions in nature involving plant-herbivore and host-parasite interactions. However, many studies that are published in the empirical literature that have explored life history and development strategies between endoparasitoid wasps and their hosts are based on species that have no evolutionary history with one another. Here, we investigated novel associations involving two closely related solitary endoparasitoids that originate from Europe and North America and several of their natural and factitious hosts from both continents. The natural hosts of both species are also closely related, all being members of the same family. We compared development and survival of both parasitoids on the four host species and predicted that parasitoid performance is better on their own natural hosts. In contrast with this expectation, survival, adult size and development time of both parasitoids were similar on all (with one exception) hosts, irrespective as to their geographic origin. Our results show that phylogenetic affinity among the natural and factitious hosts plays an important role in their nutritional suitability for related parasitoids. Evolved traits in parasitoids, such as immune suppression and development, thus enable them to successfully develop in novel host species with which they have no evolutionary history. Our results show that host suitability for specialized organisms like endoparasitoids is closely linked with phylogenetic history and macro-evolution as well as local adaptation and micro-evolution. We argue that the importance of novel interactions and 'ecological fitting' based on phylogeny is a greatly underappreciated concept in many resource-consumer studies.     

On the evolution of structure in aminoacyl-tRNA synthetases.

The aminoacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the correct amino acid. The evolution of the tRNA synthetases is of fundamental importance with respect to the nature of the biological cell and the transition from an RNA world to the modern world dominated by protein-enzymes. We present a structure-based phylogeny of the aminoacyl-tRNA synthetases. By using structural alignments of all of the aminoacyl-tRNA synthetases of known structure in combination with a new measure of structural homology, we have reconstructed the evolutionary history of these proteins. In order to derive unbiased statistics from the structural alignments, we introduce a multidimensional QR factorization which produces a nonredundant set of structures. Since protein structure is more highly conserved than protein sequence, this study has allowed us to glimpse the evolution of protein structure that predates the root of the universal phylogenetic tree. The extensive sequence-based phylogenetic analysis of the tRNA synthetases (Woese et al., Microbiol. Mol. Biol. Rev. 64:202-236, 2000) has further enabled us to reconstruct the complete evolutionary profile of these proteins and to make connections between major evolutionary events and the resulting changes in protein shape. We also discuss the effect of functional specificity on protein shape over the complex evolutionary course of the tRNA synthetases.     

Review Canalized pathways of change and constraints in the evolution of reproductive modes of microarthropods

This study investigates how the course of evolutionary change of an organismal pattern is canalized by organismal properties. As an example we use the mechanisms of indirect sperm transfer of some microarthropod groups. Miniaturized droplet spermatophores, characterized by a rather similar pattern of structural and functional components, are shown to have evolved independently in the Acari–Actinotrichida and the Pseudoscorpiones within the Arachnida and in the Entognatha (Collembola and Diplura–Campodeoidea), Symphyla, Pauropoda and Pselaphognatha within the Antennata. At least in the phylogenetic lineages leading to the various antennatan groups, evolution of miniaturized spermatophores took place in a similar sequence of transformation steps. It is likely that – originally – large sac spermatophores with a rigid sheath were deposited on the ground. The subsequent sequence of evolution involved carrying structures, a viscous sheath of the spermatophore-droplets, a stable water balance of the spermatophore under habitat conditions and miniaturized spermatophore droplets with immobilized sperm cells. Finally, mate dissociation became a common mode of behaviour in all groups mentioned. Each of the transformation steps was not only an adaptation to a particular selective condition, but additionally a precondition for further adaptive innovation. In this way the sequence of evolutionary change was rigidly determined. Moreover, integration of subsequently evolved components of the spermatophores into a complex network of interacting components obviously caused constraints of interaction, which in turn have caused a remarkable evolutionary stability of the character patterns. Using water mites as an example, it is shown how in a changed environment few behavioural changes have initiated an evolutionary sequence which has finally led convergently in several lineages to semi-direct or direct sperm transfer and to a massive repatterning of the original reproduction pattern. © Rapid Science Ltd. 1998     

Evolution of reproductive traits in the mahagony family (Meliaceae)

Meliaceae are a mostly pantropical family in the Sapindales, bearing flowers typically provided with a staminal tube, formed by filaments that are fused partially or totally. Nevertheless, several genera of subfamily Cedreloideae have free stamens, which may be adnate to an androgynophore in some taxa. The fact that the family exhibits a wide diversity of floral and fruit features, as well as of sexual systems and pollination syndromes, presents interesting questions on the evolutionary processes that might have taken place during its history. In this study, we analyzed the distribution of 20 reproductive morphological traits of Meliaceae, upon an available molecular phylogenetic framework, using 31 terminals from the family's two main clades (Cedreloideae and Melioideae), plus six Simaroubaceae taxa as outgroup. We aimed to identify and/or confirm synapomorphies for clades within the family and to develop hypotheses on floral evolution and sexual systems in the group. Our reconstruction suggests that the ancestor of Meliaceae was possibly provided with united stamens and unisexual flowers in dioecious individuals, with a subsequent change to free stamens and monoecy in the ancestor of Cedreloideae. Most characters studied show some degree of homoplasy, but some are unique synapomorphies of clades, such as the haplostemonous androecium. An androgynophore defines the Cedrela‐Toona clade. The comparative approach of our study and the evolutionary hypotheses generated herein reveal several aspects demanding further structural investigation, and possible evolutionary pathways of the reproductive structures along with the lineages' diversification, mostly related to the specialization of sexual systems, floral biology, and dispersal strategies.