Causes and conditions of formation of the aromorphic organization

Analysis of data concerning the origin of terrestrial vertebrates allows to conclude that the organism undergone the aromorphosis (=arogenesis) not only improves the general degree of organization, but also becomes able to survive in much more complex and diversified environment than its ancestors and, consequently, expands the ancestor's adaptive zone. It was shown that aromorphosis occurs when the ancestral taxon specializes in a narrow adaptive zone having vacant neighboring zone which might be occupied. The aromorphic adaptations are formed very slowly in the course of so-called coherent evolution by accumulation of certain multiply adaptations and by their coordination with each other. In the end, the set of these adaptations overrides the oscillation range of environmental conditions in the ancestral adaptive zone and can be considered as a pre-adaptation to adaptive zone expansion. Some features which are characteristic for the modem 'aromorphic' groups such as Tetrapoda, Avia and Mammalia, appeared independently and asynchronously in many related taxa. However, appearance of a few detached features does not help to widen an ancestral adaptive zone. Taxon becomes really aromorphic only due to the simultaneous formation of all adaptations allowing the expansion of ancestral adaptive zone, i.e. successful exploration and occupation of neighborning adaptive zone.     

Evolution of quassinoids and limonoids in the rutales

The structural types of quassinoids and limonoids can be characterized in terms of complexity according to their skeletal specialization and state of oxidation. The analysis of such dynamic parameters in the quassinoid-limonoid group of families in the Rutales indicates that the Simaroubaceae should form the more primitive taxon, split off from the common ancestral lineage before synthesis of the liminoid precursor. Meliaceae explore limonoid chemistry along several short biosynthetic pathways. One of these pathways is further developed in Rutaceae and another one in Cneoraceae.     

Taxon mapping exemplifies punctuated equilibrium and atavistic saltation

Two or more exemplars of the same taxon forming a nonmonophyletic group on a molecular tree may be viewed as representing surviving populations of a deep shared ancestral taxon, and if different species of the same genus, then theoretically phenotypically static remnants of punctuated equilibrium. That taxon may be mapped on a molecular cladogram and evolutionarily resolved at the taxon level inclusive of all exemplars. The technique for mapping taxa on a molecular tree, termed here caulistics, is much like mapping traits but recovers macroevolutionary information at the taxon level. All lineages arising from the mapped taxon are its direct descendants. Mapped taxa superimposed or overlapping may reveal packaged adaptive traits. When a mapped taxon is well split by another mapped taxon on a molecular tree, atavistic saltation based on triggering an epigenetically retained trait complex is a theoretical explanation. Caulistics combines traditional taxonomy and molecular phylogenetics to reveal previously unknown aspects of the macroevolutionary past.     

Does ecological specialization transcend scale? Habitat partitioning among individuals and species of Anolis lizards

Ecological specialization is common across all levels of biological organization, raising the question of whether the evolution of specialization at one scale in a taxon is linked to specialization at other scales. Anolis lizards have diversified repeatedly along axes of habitat use, but it remains unknown if this diversification into habitat use specialists is underlain by individual specialization. From repeated observations of individuals in a population of Anolis sagrei in Florida, we show that the extent of habitat use specialization among individuals is comparable to the extent of specialization in the same traits among ten sympatric Anolis habitat specialist species in Cuba. However, the adaptive correlations between habitat use and morphology commonly seen across species of Anolis were not observed across individuals in the sampled population. Our results therefore suggest that while patterns of ecological specialization can transcend scale, these parallels are the consequence of distinct ecological processes acting at microevolutionary and macroevolutionary scales.     

Evolution of adaptive phenotypic traits without positive Darwinian selection

Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity-relaxation-mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time.     

Adaptive radiation of Espeletia in the cold andean tropics

The genus Espeletia (Asteraceae) underwent an accelerated adaptive radiation in the new habitats of the high tropical Andes after the retreat of the glaciers. From the ancestral rainforest species, with tree-like forms, the genus diversified at high altitude, developing morphological and physiological adaptations to the peculiar combination of low-temperature, energy and nutrient stresses of the tropical periglacial environments. Espeletia offers an exceptional example of a taxon undergoing a rapid evolutionary process through the colonization of a totally original environment: the cold tropics. Here we review recent research on the ecological, biogeographical, taxonomic, morphological and physiological traits that have led to the adaptive radiation of Espeletia in this extreme habitat.     

The ancestral distance test: what relatedness can reveal about correlated evolution in large lineages with missing character data and incomplete phylogenies

The ancestral distance test is introduced to detect correlated evolution between two binary traits in large phylogenies that may lack resolved subclades, branch lengths, and/or comparative data. We define the ancestral distance as the time separating a randomly sampled taxon from its most recent ancestor (MRA) with extant descendants that have an independent trait. The sampled taxon either has (target sample) or lacks (nontarget sample) a dependent trait. Modeled as a Markov process, we show that the distribution of ancestral distances for the target sample is identical to that of the nontarget sample when characters are uncorrelated, whereas ancestral distances are smaller on average for the target sample when characters are correlated. Simulations suggest that the ancestral distance can be estimated using the time, total branch length, taxonomic rank, or number of speciation events between a sampled taxon and the MRA. These results are shown to be robust to deviations from Markov assumptions. A Monte Carlo technique estimates P-values when fully resolved phylogenies with branch lengths are available, and we evaluate the Monte Carlo approach using a data set with known correlation. Measures of relatedness were found to provide a robust means to test hypotheses of correlated character evolution.     

Reversal versus specialization in floral morphological evolution in Petrocosmea (Gesneriaceae)

A widely held hypothesis in evolution is that adaptive specialization constrains the potential direction of future evolutionary change and thus may be irreversible, also known as Dollo's law. However, this hypothesis has long been subject to debate in evolutionary biology. Floral specialization is intriguing as it is usually linked to reproductive isolation and could affect speciation. Here, following the discovery of four new taxa, we observed some interesting phenomena of reversal versus specialization in morphology in a clade with the most specialized flowers in the genus Petrocosmea. In the phylogenetic tree based on sequences of multiple DNA regions, the morphological reversals, especially the regain of a long corolla tube, are nested within the branches characteristic of normally specialized flowers with a short corolla tube and highly specialized zygomorphy. Our results indicate that the highly specialized floral organ of this clade is still actively evolving in multiple branches toward specialization while reversals to different ancestral states occur in some branches. Great disturbance of ecological environment is likely a crucial factor affecting trait reversibility, such as the rapid uplift of the Himalayan–Tibetan plateau. The four new taxa are treated herein taxonomically. The flowers of this clade represent an interesting model to explore the genetic basis underlying the evolutionary reversal versus specialization and the interplay between genetic factors and environmental variables.     

The evolution of ecomorphological traits within the Abrothrichini (Rodentia: Sigmodontinae): a Bayesian phylogenetics approach

The generally accepted hypothesis regarding the origin of fossorial mammals proposes adaptive convergence from open environments towards the use of subterranean environments. We evaluated this hypothesis for South American mole-mice using conventional and Bayesian frameworks, with independent evidence. By using a molecular approach based on Cytochrome b and IRBP sequences, we evaluated phylogenetic relationships, time of origin, the ancestral trait of fossoriality, and ancestral distributions of species belonging to the Andean Clade (Rodentia: Sigmodontinae). Our results indicate that the Andean Clade is highly sustained; with one clade grouping all fossorial forms and another grouping all cursorial species. We hypothesized that fossoriality originated in the Miocene/Pliocene transition, in the Temperate Forests of southern South America. We conclude that the origin of fossorial ecomorphological traits did not necessarily occur under a general model of open environments, the origin of these traits depends on the ecological-historical relationship of the taxon with the environment.     

ADAPTIVE RADIATION AND ECOLOGICAL DIVERSIFICATION OF SULAWESI'S ANCIENT LAKE SHRIMPS

Ancient lakes are natural laboratories for the study of adaptive radiation. Recently, two lake systems on the Indonesian island Sulawesi have emerged as promising new model systems. A species flock of atyid freshwater shrimps in the Malili lake system comprises 15 colorful endemic taxa. Mitochondrial DNA data suggest two independent colonizations by riverine ancestors. Only one colonization event led to subsequent radiation into 14 species, while the second clade comprises just one species. The vast majority of species (n= 12) are habitat specialists, which are confined to the larger Malili clade and include all taxa with species‐specific color patterns and a restricted distribution within the five connected Malili lakes. Morphological, genetic, and ecological data are consistent with the existence of an adaptive radiation in the Malili lakes, involving the habitat‐specific diversification of trophic morphology. In addition to testing criteria for the recognition of an adaptive radiation, an ancestral state reconstruction reveals an equal probability for either a riverine generalist or a lacustrine specialist as ancestor of the large Malili clade, which is interpreted as indicative of an early stage of habitat specialization within this radiation. Finally, our results suggest that species diversification may have been primarily driven by ecological specialization and allopatric speciation.     

A CLADISTIC TEST OF THE TAXON CYCLE AND TAXON PULSE HYPOTHESES

Abstract— A species' habitat preference is intcrpretablc both as a response to present-day conditions and as a result of evolutionary response to historical conditions. The taxon cycle and taxon pulse have been proposed as hypotheses that allow prediction of patterns of habitat specialization within a lineage. Both are based on common assumptions: (1) habitat specialization is largely irreversible in a lineage, (2) ecological specializations arise in a center of origin, and (3) dispersal events leading to current distributions can be ascertained. Eight taxa of Antillean, Mexican, and Central American Carabidae, for which cladistic hypotheses of relationship have been proposed, are used to test the generality of the taxon cycle and pulse. The patterns of habitat utilization predicted by the taxon cycle and taxon pulse hypotheses are tested by comparing cladistic transformations of habitat preference to randomly generated patterns of data generated under a null hypothesis. Evolutionary changes in habitat are interpreted using Camin-Sokal coding, which assumes irreversible habitat shifts and a predetermined ecological ground state (assumptions of the taxon cycle and taxon pulse). An observed pattern is considered to demonstrate the taxon cycle or pulse when it results in an explanation of the habitat shifts that is more parsimonious than 95 % of the randomly generated patterns. Of the eight carabid groups, only one exhibits a statistically significant pattern supporting the taxon cycle and pulse. The failure of the taxon cycle and pulse as generally predictive hypotheses may be due to historical changes in climate that permit episodes of range expansion for species previously restricted to small ranges, and habitat shifts and specialization that do not progress in a linear transformation series. Habitat shifts are also analyzed using Farris optimization, resulting in the most parsimonious transformation series of habitats, subject to a predefined ordering of habitats, while allowing reversals. Significance of an observed pattern of habitat shifts under Farris optimization implies habitat constancy relative to cladogenesis, and step-wise changes in habitat preference. Two of the eight groups exhibit significant patterns of habitat utilization under Farris optimization, indicating that vicariance of areas of like habitat has been the predominant factor generating species diversity in these groups. The other groups do not exhibit habitat constancy, suggesting rapid changes in habitat preference relative to speciation.     

Historical demographic dynamics underlying local adaptation in the presence of gene flow

The range of a species is the result of the relative contribution of spatial tracking of environmental requirements and adaptation to ecological conditions outside the ancestral niche. The appearance of novel habitats caused by climatic oscillation can promote range expansion and accompanying demographic growth. The demographic dynamics of populations leave a signal in \ patterns. We modeled three competing scenarios pertaining to the circumstance of a range expansion by the Karoo Scrub‐Robin into newly available habitat resulting from the increasing aridification of southern Africa. Genetic variation was contrasted with the theoretical expectations of a spatial range expansion, and compared with data of a putative adaptive trait. We infer that this bird likely colonized the arid zone, as a consequence of adaptive evolution in a small peripheral population, followed by an expansion with recurrent exchange of migrants with the ancestral populations.     

Maximum parsimony on subsets of taxa

In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa.     

A single amino acid polymorphism in a conserved effector of the multihost blast fungus pathogen expands host-target binding spectrum

Accelerated gene evolution is a hallmark of pathogen adaptation and specialization following host-jumps. However, the molecular processes associated with adaptive evolution between host-specific lineages of a multihost plant pathogen remain poorly understood. In the blast fungus Magnaporthe oryzae (Syn. Pyricularia oryzae), host specialization on different grass hosts is generally associated with dynamic patterns of gain and loss of virulence effector genes that tend to define the distinct genetic lineages of this pathogen. Here, we unravelled the biochemical and structural basis of adaptive evolution of APikL2, an exceptionally conserved paralog of the well-studied rice-lineage specific effector AVR-Pik. Whereas AVR-Pik and other members of the six-gene AVR-Pik family show specific patterns of presence/absence polymorphisms between grass-specific lineages of M. oryzae, APikL2 stands out by being ubiquitously present in all blast fungus lineages from 13 different host species. Using biochemical, biophysical and structural biology methods, we show that a single aspartate to asparagine polymorphism expands the binding spectrum of APikL2 to host proteins of the heavy-metal associated (HMA) domain family. This mutation maps to one of the APikL2-HMA binding interfaces and contributes to an altered hydrogen-bonding network. By combining phylogenetic ancestral reconstruction with an analysis of the structural consequences of allelic diversification, we revealed a common mechanism of effector specialization in the AVR-Pik/APikL2 family that involves two major HMA-binding interfaces. Together, our findings provide a detailed molecular evolution and structural biology framework for diversification and adaptation of a fungal pathogen effector family following host-jumps.     

Niche divergence facilitated by fine‐scale ecological partitioning in a recent cichlid fish adaptive radiation

Ecomorphological differentiation is a key feature of adaptive radiations, with a general trend for specialization and niche expansion following divergence. Ecological opportunity afforded by invasion of a new habitat is thought to act as an ecological release, facilitating divergence, and speciation. Here, we investigate trophic adaptive morphology and ecology of an endemic clade of oreochromine cichlid fishes (Alcolapia) that radiated along a herbivorous trophic axis following colonization of an isolated lacustrine environment, and demonstrate phenotype‐environment correlation. Ecological and morphological divergence of the Alcolapia species flock are examined in a phylogenomic context, to infer ecological niche occupation within the radiation. Species divergence is observed in both ecology and morphology, supporting the importance of ecological speciation within the radiation. Comparison with an outgroup taxon reveals large‐scale ecomorphological divergence but shallow genomic differentiation within the Alcolapia adaptive radiation. Ancestral morphological reconstruction suggests lake colonization by a generalist oreochromine phenotype that diverged in Lake Natron to varied herbivorous morphologies akin to specialist herbivores in Lakes Tanganyika and Malawi.     

Colonize,radiate, decline: Unraveling the dynamics of island community assembly with Fijian trap-jaw ants

The study of island community assembly has been fertile ground for developing and testing theoretical ideas in ecology and evolution. The ecoevolutionary trajectory of lineages after colonization has been a particular interest, as this is a key component of understanding community assembly. In this system, existing ideas, such as the taxon cycle, posit that lineages pass through a regular sequence of ecoevolutionary changes after colonization, with lineages shifting toward reduced dispersal ability, increased ecological specialization, and declines in abundance. However, these predictions have historically been difficult to test. Here, we integrate phylogenomics, population genomics, and X-ray microtomography/3D morphometrics, to test hypotheses for whether the ecomorphological diversity of trap-jaw ants (Strumigenys) in the Fijian archipelago is assembled primarily through colonization or postcolonization radiation, and whether species show ecological shifts toward niche specialization, toward upland habitats, and decline in abundance after colonization. We infer that most Fijian endemic Strumigenys evolved in situ from a single colonization and have diversified to fill a large fraction of global morphospace occupied by the genus. Within this adaptive radiation, lineages trend to different degrees toward high elevation, reduced dispersal ability, and demographic decline, and we find no evidence of repeated colonization that displaces the initial radiation. Overall these results are only partially consistent with taxon cycle and associated ideas, while highlighting the potential role of priority effects in assembling island communities.     

Photic niche invasions: phylogenetic history of the dim-light foraging augochlorine bees (Halictidae)

Most bees rely on flowering plants and hence are diurnal foragers. From this ancestral state, dim-light foraging in bees requires significant adaptations to a new photic environment. We used DNA sequences to evaluate the phylogenetic history of the most diverse clade of Apoidea that is adapted to dim-light environments (Augochlorini: Megalopta, Megaloptidia and Megommation). The most speciose lineage, Megalopta, is distal to the remaining dim-light genera, and its closest diurnal relative (Xenochlora) is recovered as a lineage that has secondarily reverted to diurnal foraging. Tests for adaptive protein evolution indicate that long-wavelength opsin shows strong evidence of stabilizing selection, with no more than five codons (2%) under positive selection, depending on analytical procedure. In the branch leading to Megalopta, the amino acid of the single positively selected codon is conserved among ancestral Halictidae examined, and is homologous to codons known to influence molecular structure at the chromophore-binding pocket. Theoretically, such mutations can shift photopigment λ(max) sensitivity and enable visual transduction in alternate photic environments. Results are discussed in light of the available evidence on photopigment structure, morphological specialization and biogeographic distributions over geological time.     

CLADISTIC INFERENCE AND EVOLUTIONARY SCENARIOS: LOCOMOTORY STRUCTURE, FUNCTION, AND PERFORMANCE IN WATER STRIDERS

Abstract — A research methodology that aims to reveal how historical changes in environmental conditions (or selective regimes) have shaped the adaptive evolution of clades is applied to the adaptive evolution of water striders and their allies (Hemiptera-Heteroptera, Gerromorpha), a group of semiaquatic insects which includes species that are conspicuously adapted to life on the surface film of water. Based upon reconstructed phylogenies for the higher gerromorphan taxa, the hypothesis that the hygropetric zone is the ancestral one is confirmed for the Mesoveliidae, Hebridae and the clade comprising the Paraphrynoveliidae, Macroveliidae and Hydrometridae, but not for the Hermatobatidae and Veliidae. There is no support for the hypothesis that the intersection zone was a sort of transitional zone during the ecological evolution of pleustonic bugs. It is shown that the unique morphological and behavioural traits of the most derived members of this group evolved after inferred historical changes in environmental conditions and therefore qualify as adaptations in the sense of Gould and Vrba (1982) , Coddington (1988) and Baum and Larson (1991) . Other predictions about the adaptive evolution of gerromorphan bugs do not pass the cladistic test. The study illustrates that cladistic inference is a valuable tool in clarifying and sharpening retrospective explanations of complex evolutionary scenarios.     

Plant performance and morpho-functional differentiation in response to edaphic variation in Iberian columbines: cues for range distribution?

Aims Experimental studies of the response to environmental variation of closely related taxa are needed to understand the mechanisms underlying phenotypic divergence, habitat segregation and range span within a radiating genus. We explored the magnitude of phenotypic differentiation and adaptive plasticity in relation to edaphic variation and its significance for habitat segregation and range span in Iberian columbines.Methods We performed a common garden experiment varying soil type (calcareous vs. siliceous) and depth (rocky-shallow vs. deep) with two pairs of widespread and narrowly distributed subspecies of Iberian columbines: Aquilegia vulgaris (subspp. vulgaris and nevadensis) and Aquilegia pyrenaica (subspp. pyrenaica and cazorlensis). We compared tolerance to edaphic variation, trait differentiation and adaptive plasticity of 10 morpho-functional traits between species and distribution ranges. Additionally, we obtained estimates of the competitive environment faced by each taxon in two to four populations per taxa.Important findings Results partially support hypotheses of higher competitive ability and tolerance to edaphic variation in widespread than in narrow endemic taxa. At the species level, the widely distributed taxon was the most tolerant to edaphic variation. Within species, no consistent pattern emerged since the population from the most widespread subspecies was the most tolerant in A. vulgaris but not in A. pyrenaica. Columbines were differentiated in many traits at species and range level. However, the pattern of differentiation does not fully support the hypothesis of higher specialization and stress tolerance in narrow endemics. Although plasticity was generally low, the results support the hypothesis of adaptive plasticity in widespread but not in restricted taxa at least at species level. Ecological differences (adaptive plasticity and competitive ability among others) may have contributed to phenotypic divergence and edaphic niche segregation, as well as to differences in range span among columbines.     

Ancestral polymorphism at the major histocompatibility complex (MHCIIbeta) in the Nesospiza bunting species complex and its sister species (Rowettia goughensis)

ABSTRACT: BACKGROUND: The major histocompatibility complex (MHC) is an important component of the vertebrate immune system and is frequently used to characterise adaptive variation in wild populations due to its co-evolution with pathogens. Passerine birds have an exceptionally diverse MHC with multiple gene copies and large numbers of alleles compared to other avian taxa. The Nesospiza bunting species complex (two species on Nightingale Island; one species with three sub-species on Inaccessible Island) represents a rapid adaptive radiation at a small, isolated archipelago, and is thus an excellent model for the study of adaptation and speciation. In this first study of MHC in Nesospiza buntings, we aim to characterize MHCIIbeta variation, determine the strength of selection acting at this gene region and assess the level of shared polymorphism between the Nesospiza species complex and its putative sister taxon, Rowettia goughensis, from Gough Island. RESULTS: In total, 23 unique alleles were found in 14 Nesospiza and 2 R. goughensis individuals encoding at least four presumably functional loci and two pseudogenes. There was no evidence of ongoing selection on the peptide binding region (PBR). Of the 23 alleles, 15 were found on both the islands inhabited by Nesospiza species, and seven in both Nesospiza and Rowettia; indications of shared, ancestral polymorphism. A gene tree of Nesospiza MHCIIbeta alleles with several other passerine birds shows three highly supported Nesospiza-specific groups. All R. goughensis alleles were shared with Nesospiza, and these alleles were found in all three Nesospiza sequence groups in the gene tree, suggesting that most of the observed variation predates their phylogenetic split. CONCLUSIONS: Lack of evidence of selection on the PBR, together with shared polymorphism across the gene tree, suggests that population variation of MHCIIbeta among Nesospiza and Rowettia is due to ancestral polymorphism rather than local selective forces. Weak or no selection pressure could be attributed to low parasite load at these isolated Atlantic islands. The deep divergence between the highly supported Nesospiza-specific sequence Groups 2 and 3, and the clustering of Group 3 close to the distantly related passerines, provide strong support for preserved ancestral polymorphism, and present evidence of one of the rare cases of extensive ancestral polymorphism in birds.