Evolutionary Physiology of Closely Related Taxa: Analyses of Enzyme Expression

Comparative biochemistry and physiology offer the advantageof specifically defining the functional parameters or traitsthat affect an organism's performance (e.g., amino acids thataffect K_m, enzymes that affect metabolism). By combining thesefunctional determinations with both intraspecific and phylogeneticallyappropriate analyses, comparative biologists can indicate thata trait is biologically important by demonstrating that it isevolving by natural selection. An evolutionary approach maybenefit from the analysis of variation within and among closelyrelated species. The advantages of analyzing closely relatedspecies are that they allow one to identify more definitivelythe derived conditions and suggest why differences arose. Importantly,there is substantial variation in physiological and biochemicaltraits within and among closely related species. For example,among species within a single genus of teleost, Fundulus, thevariation in enzyme expression is similar to the variation seenamong most superorders of teleost. However, most of the variationwithin the genus Fundulus is most readily explained by evolutionarydistance, and thus there is no compelling reason for furtheradaptive hypotheses. Extending this observation, the greaterthe phylogenetic distance between taxa in a comparative study,the more likely there will be a statistically significant differencethat may only represent evolutionary time. The molecular mechanismsaffecting adaptive variation in enzyme expression appear tobe readily altered and may vary within a species or betweenacclimation conditions. Thus, studies among closely relatedorganisms are more likely to identify the specific molecularor biochemical changes responsible for adaptive variation.     

Pattern and process in the evolution of insect-plant associations: Yponomeuta as an example

Phylogenetic studies are increasing our understanding of the evolution of associations between phytophagous insects and their host plants. Sequential evolution, i.e. the shift of insect herbivores onto pre-existing plant species, appears to be much more common than coevolution, where reciprocal selection between interacting insects and plants is thought to induce chemical diversification and resistance in plants and food specialization in insects.Extreme host specificity is common in phytophagous insects and future studies are likely to reveal even more specialization. Hypotheses that assume that food specialists have selective advantages over generalists do not seem to provide a general explanation for the ubiquity of specialist insect herbivores. Specialists are probably committed to remain so, because they have little evolutionary opportunity to reverse the process due to genetically determined constraints on the evolution of their physiology or nervous system. The same constraints might result in phylogenetic conservatism, i.e. the frequent association of related insect herbivores with related plants. Current phylogenetic evidence, however, indicates that there is no intrinsic direction to the evolution of specialization.Historical aspects of insect-host plant associations will be illustrated with the small ermine moth genus Yponomeuta. Small ermine moths show an ancestral host association with the family Celastraceae. The genus seems to be committed to specialization per se rather than to a particular group of plants. Whatever host shift they have made in their evolutionary past (onto Rosaceae, Crassulaceae, and Salicaceae), they remain monophagous. The oligophagous Y. padellus is the only exception. This species might comprise a mosaic of genetically divergent host-associated populations.     

Phylogeny of the avian genus Pitohui and the evolution of toxicity in birds

Bird species in the avian genus Pitohui contain potent neurotoxic alkaloids that may be used for defense. The genus comprises multiple species that are endemic to New Guinea and were presumed to belong to the family Pachycephalidae or Colluricinclidae, within the core corvoidea, an ancient Australasian radiation of crow-like birds. In order to understand the evolution of toxicity within the genus Pitohui, we sequenced three mitochondrial and two nuclear gene segments and reconstructed a phylogeny of the genus Pitohui and its putative relatives. We show that the genus Pitohui is polyphyletic, and consists of five different lineages. Using Bayesian ancestral state reconstruction, we estimate that toxicity likely evolved multiple times within this group. Furthermore, because the morphological and behavioral similarity among these poisonous birds appears to have evolved convergently, we hypothesize that this may be a possible example of Müllerian mimicry in birds. The Morningbird of Palau, Micronesia, that has often been included in the genus Pitohui, actually belongs in the genus Pachycephala and offers an intriguing case of pronounced evolution on a remote oceanic island.     

ADAPTATION AND CONSTRAINT IN THE EVOLUTION OF SPECIALIZATION OF BAHAMIAN ANOLIS LIZARDS

Interspecific interactions affect habitat use and subsequent morphological adaptation in Anolis lizards. We examined populations of two species of Anolis lizards that evolved in the species-rich communities of Cuba and are now widespread in the Bahamas. Because the species occupy islands in the Bahamas that vary in the number of lizard species present and other characteristics, we predicted that directional selection should have led to morphological differentiation. In particular, we expected that populations on one-species islands should have evolved toward a generalist morphology because of the lack of competitors. Divergence in both species has been adaptive; populations that use wider perches have longer legs. Nonetheless, these differences are relatively minor, and none of the populations appears to have differentiated from its ancestral “ecomorph” type toward a more generalized morphology. This stasis mirrors a trend observed in the radiation of Caribbean anoles, which exhibits repeated instances of evolutionary specialization, but few or no cases of reversion to a more generalized condition. The explanation for this directionality of evolution is not obvious but probably involves the tendency of specialized species to continue using and further adapting the niches for which they are specialized even as conditions change.     

Differences in strategies to combat osmotic stress in Burkholderia cenocepacia elucidated by NMR-based metabolic profiling

Aims: To investigate mechanisms of osmotic tolerance in Burkholderia cenocepacia, a member of the B. cepacia complex (Bcc) of closely related strains, which is of clinical as well as environmental importance. Methods and Results: We employed NMR‐based metabolic profiling (metabolomics) to elucidate the metabolic consequences of high osmotic stress for five isolates of B. cenocepacia. The strains differed significantly in their levels of osmotic stress tolerance, and we identified three different sets of metabolic responses with the strains least impacted by osmotic stress exhibiting higher levels of the osmo‐protective metabolites glycine‐betaine and/or trehalose. Strains either increased concentrations or had constitutively high levels of these metabolites. Conclusions: Even within the small set of B. cenocepacia isolates, there was a surprising degree of variability in the metabolic responses to osmotic stress. Significance and impact of the study: The metabolic responses, and hence osmotic stress tolerance, vary between different B. cenocepacia isolates. This study provides a first look into the potentially highly diverse physiology of closely related strains of one species of the Bcc and illustrates that physiological or clinically relevant phenotypes are unlikely to be inferable from genetic relatedness within this species group.     

Evolution of Thermotolerance in Hot Spring Cyanobacteria of the Genus Synechococcus

The extension of ecological tolerance limits may be an important mechanism by which microorganisms adapt to novel environments, but it may come at the evolutionary cost of reduced performance under ancestral conditions. We combined a comparative physiological approach with phylogenetic analyses to study the evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Among the 20 laboratory clones of Synechococcus isolated from collections made along an Oregon hot spring thermal gradient, four different 16S rRNA gene sequences were identified. Phylogenies constructed by using the sequence data indicated that the clones were polyphyletic but that three of the four sequence groups formed a clade. Differences in thermotolerance were observed for clones with different 16S rRNA gene sequences, and comparison of these physiological differences within a phylogenetic framework provided evidence that more thermotolerant lineages of Synechococcus evolved from less thermotolerant ancestors. The extension of the thermal limit in these bacteria was correlated with a reduction in the breadth of the temperature range for growth, which provides evidence that enhanced thermotolerance has come at the evolutionary cost of increased thermal specialization. This study illustrates the utility of using phylogenetic comparative methods to investigate how evolutionary processes have shaped historical patterns of ecological diversification in microorganisms.     

The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles

Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e., the ability to osmoregulate in hyperosmotic media) and habitat transitions in the water beetle genus Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced desiccation resistance evolved before increases in hyporegulation ability or vice versa, or whether the two mechanisms evolved in parallel. The most recent ancestor of Lumetus was inferred to have high desiccation resistance and moderate hyporegulation ability. There were repeated shifts between habitats with differing levels of salinity in the radiation of the group, those to the most saline habitats generally occurring more rapidly than those to less saline ones. Significant and accelerated changes in hyporegulation ability evolved in parallel with smaller and more progressive increases in desiccation resistance across the phylogeny, associated with the colonization of meso‐ and hypersaline waters during global aridification events. All species with high hyporegulation ability were also desiccation‐resistant, but not vice versa. Overall, results are consistent with the hypothesis that desiccation resistance mechanisms evolved first and provided the physiological basis for the development of hyporegulation ability, allowing these insects to colonize and diversify across meso‐ and hypersaline habitats.     

Evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus

The extension of ecological tolerance limits may be an important mechanism by which microorganisms adapt to novel environments, but it may come at the evolutionary cost of reduced performance under ancestral conditions. We combined a comparative physiological approach with phylogenetic analyses to study the evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Among the 20 laboratory clones of Synechococcus isolated from collections made along an Oregon hot spring thermal gradient, four different 16S rRNA gene sequences were identified. Phylogenies constructed by using the sequence data indicated that the clones were polyphyletic but that three of the four sequence groups formed a clade. Differences in thermotolerance were observed for clones with different 16S rRNA gene sequences, and comparison of these physiological differences within a phylogenetic framework provided evidence that more thermotolerant lineages of Synechococcus evolved from less thermotolerant ancestors. The extension of the thermal limit in these bacteria was correlated with a reduction in the breadth of the temperature range for growth, which provides evidence that enhanced thermotolerance has come at the evolutionary cost of increased thermal specialization. This study illustrates the utility of using phylogenetic comparative methods to investigate how evolutionary processes have shaped historical patterns of ecological diversification in microorganisms.     

Freeze tolerance evolution among anurans: Frequency and timing of appearance

Despite numerous mechanistic studies on physiological responses supporting freeze tolerance in anurans, few have addressed the evolutionary significance of this trait. We thus investigated the phylogenetic relationships among anuran species whose freeze tolerance has been assessed and in combination with new data on freezing tolerance of two closely related species of the European brown frogs (Rana temporaria and Rana dalmatina). The species we studied exhibited short survival times in frozen state (around 8 h for both species). Phylogenetic analysis suggests that freeze tolerance evolved at least two times among Ranidae and one or two times among Hylidae and never in Bufonidae. Furthermore, in order to assess the timing of divergence of this character we used a relaxed molecular clock created, and found that the most recent separation between a freeze tolerant species and a freeze intolerant species dates from 15.9 ± 7.6 Myr (Rana arvalis and R. temporaria). The comparison between these two species thus represents the best current model to understand freeze tolerance evolution. Addressing the evolution of this trait with such large-scale approaches will not only improve our understanding of cold hardiness strategies, but might also create a framework guiding future comparative studies.     

Competition and Coexistence Among Four Estuarine Species of Fundulus

Four sympatric species of Fundulus (F. heteroclitus, F. majalis,F. diaphanus, and F. luciae) are distributed along tidal heightand salinity gradients such that F. heteroclitus co-occurs witheach species, while the remaining species rarely occur together.Feeding habitats of all the species are similar, and food hasbeen shown to limit population size of F. heteroclitus. Thispaper examines whether competition is an important structuringforce within this guild by addressing two questions: 1) is thespatial separation exhibited by three of the species due tophysiological barriers or due to competitive exlusion? and 2)when F. heteroclitus occurs with other Fundulus species doescompetition for resources take place? Laboratory studies indicate that all four species are tolerantof a wide range of environmental conditions; available evidencesuggests that physiological barriers are an unlikely explanationfor spatial segregation among some members of this guild. Competitiveexclusion seems a likely alternate explanation, but is supportedonly by studies of diet overlap. Similarly, only inference fromdiet overlap is available to answer the second question. A fieldexperiment is presented here in which F. heteroclitus and F.majalis were placed in enclosures separately and together. Competitionbetween these species appears to be important, and similar fieldexperiments are recommended to investigate competitive interactionsamong other species pairs within the genus     

Genetic basis for rapidly evolved tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species

Atlantic killifish (Fundulus heteroclitus) residing in some urban and industrialized estuaries of the US eastern seaboard demonstrate recently evolved and extreme tolerance to toxic aryl hydrocarbon pollutants, characterized as dioxin‐like compounds (DLCs). Here, we provide an unusually comprehensive accounting (69%) through quantitative trait locus (QTL) analysis of the genetic basis for DLC tolerance in killifish inhabiting an urban estuary contaminated with PCB congeners, the most toxic of which are DLCs. Consistent with mechanistic knowledge of DLC toxicity in fish and other vertebrates, the aryl hydrocarbon receptor (ahr2) region accounts for 17% of trait variation; however, QTL on independent linkage groups and their interactions have even greater explanatory power (44%). QTL interpreted within the context of recently available Fundulus genomic resources and shared synteny among fish species suggest adaptation via interacting components of a complex stress response network. Some QTL were also enriched in other killifish populations characterized as DLC‐tolerant and residing in distant urban estuaries contaminated with unique mixtures of pollutants. Together, our results suggest that DLC tolerance in killifish represents an emerging example of parallel contemporary evolution that has been driven by intense human‐mediated selection on natural populations.     

Laboratory maintenance does not alter ecological and physiological patterns among species: a Drosophila case study

Large comparative studies in animal ecology, physiology and evolution often use animals reared in the laboratory for many generations; however, the relevance of these studies hinges on the assumption that laboratory populations are still representative for their wild living conspecifics. In this study, we investigate whether laboratory‐maintained and freshly collected animal populations are fundamentally different and whether data from laboratory‐maintained animals are valid to use in large comparative investigations of ecological and physiological patterns. Here, we obtained nine species of Drosophila with paired populations of laboratory‐maintained and freshly collected flies. These species, representing a range of ecotypes, were assayed for four stress‐tolerance, two body‐size traits and six life‐history traits. For all of these traits, we observed small differences in species‐specific comparisons between field and laboratory populations; however, these differences were unsystematic and laboratory maintenance did not eclipse fundamental species characteristics. To investigate whether laboratory maintenance influence the general patterns in comparative studies, we correlated stress tolerance and life‐history traits with environmental traits for the laboratory‐maintained and freshly collected populations. Based on this analysis, we found that the comparative physiological and ecological trait correlations are similar irrespective of provenience. This finding is important for comparative biology in general because it validates comparative meta‐analyses based on laboratory‐maintained populations.     

Phylogenetic species recognition reveals host-specific lineages among poplar rust fungi

Fungal species belonging to the genus Melampsora (Basidiomycota, Pucciniales) comprise rust pathogens that alternate between Salicaceae and other plant hosts. Species delineation and identification are difficult within this group due to the paucity of observable morphological features. Several Melampsora rusts are highly host-specific and this feature has been used for identification at the species level. However, this criterion is not always reliable since different Melampsora rust species can overlap on one host but specialize on a different one. To date, two different species recognition methods are used to recognize and define species within the Melampsora genus: (i) morphological species recognition, which is based solely on morphological criteria; and (ii) ecological species recognition, which combines morphological criteria with host range to recognize and define species. In order to clarify species recognition within the Melampsora genus, we applied phylogenetic species recognition to Melampsora poplar rusts by conducting molecular phylogenetic analyses on 15 Melampsora taxa using six nuclear and mitochondrial loci. By assessing the genealogical concordance between phylogenies, we identified 12 lineages that evolved independently, corresponding to distinct phylogenetic species. All 12 lineages were concordant with host specialization, but only three belonged to strictly defined morphological species. The estimation of the species tree obtained with Bayesian concordance analysis highlighted a potential co-evolutionary history between Melampsora species and their reciprocal aecial host plants. Within the Melampsora speciation process, aecial host may have had a strong effect on ancestral evolution, whereas telial host specificity seems to have evolved more recently. The morphological characters initially used to define species boundaries in the Melampsora genus are not reflective of the evolutionary and genetic relationships among poplar rusts. In order to construct a more meaningful taxonomy, host specificity must be considered an important criterion for delineating and describing species within the genus Melampsora as previously suggested by ecological species recognition.     

Phylogenetic evidence for the evolution of ecological specialization in Timema walking‐sticks

We used phylogenetic and ecological information to study the evolution of host‐plant specialization and colour polymorphism in the genus Timema, which comprises 14 species of walking‐sticks that are subject to strong selection for cryptic coloration on their host‐plants. Phylogenetic analysis indicated that this genus consists of three main lineages. Two of the lineages include highly generalized basal species and relatively specialized distal species, and one of the lineages comprises four specialized species. We tested for phylogenetic conservatism in the traits studied via randomizing host‐plant use, and the four basic Timema colour patterns, across the tips of the phylogeny, and determining if the observed number of inferred changes was significantly low compared to the distribution of numbers of inferred changes expected under the null model. This analysis showed that (1) host‐plant use has evolved nonrandomly, such that more closely related species tend to use similar sets of hosts and (2) colour pattern evolution exhibits considerable lability. Inference of ancestral states using maximum parsimony, under four models for the relative ease of gain and loss of plant hosts or colour morphs, showed that (1) for all models with gains of host‐plants even marginally more difficult than losses, and for most optimizations with gains and losses equally difficult, the ancestral Timema were generalized, feeding on the chaparral plants Ceanothus and Adenostoma and possibly other taxa, and (2) for all models with gains of colour morphs more difficult than losses, the ancestral Timema were polymorphic for colour pattern. Generation of null distributions of inferred ancestral states showed that the maximum‐parsimony inference of host‐plant generalization was most robust for the most speciose of the three main Timema lineages. Ancestral states were also inferred using maximum likelihood, after recoding host‐plant use and colour polymorphism as dichotomous characters. Likelihood analyses provided some support for inference of generalization in host‐plant use at ancestral nodes of the two lineages exhibiting mixtures of generalists and specialists, although levels of uncertainty were high. By contrast, likelihood analysis did not estimate ancestral colour morph patterns with any confidence, due to inferred rates of change that were high with respect to speciation rates. Information from biogeography, floristic history and the timing of diversification of the genus are compatible with patterns of inferred ancestral host‐plant use. Diversification in the genus Timema appears to engender three main processes: (1) increased specialization via loss of host‐plants, (2) retention of the same, single, host‐plant and (3) shifts to novel hosts to which lineages were ‘preadapted’ in colour pattern. Our evidence suggests that the radiation of this genus has involved multiple evolutionary transitions from individual‐level specialization (multiple‐niche polymorphism) to population‐level and species‐level specialization. Ecological studies of Timema suggest that such transitions are driven by diversifying selection for crypsis. This paper provides the first phylogeny‐based evidence for the macroevolutionary importance of predation by generalist natural enemies in the evolution of specialization.     

The conquest of fresh water by the palaemonid shrimps: an evolutionary history scripted in the osmoregulatory epithelia of the gills and antennal glands

Extant Palaemonidae occupy aquatic environments that have generated physiological diversity during their evolutionary history. We analyze ultrastructural traits in gills and antennal glands of palaemonid species from distinct osmotic niches, and employ phylogenetic comparative methods to ascertain whether transformations in their osmoregulatory epithelia have evolved in tandem, driven by salinity. Gill pillar cells exhibit apical evaginations whose surface density (S_v, μm² plasma membrane area/μm³ cytoplasmic volume) ranges from 6.3–7.1 in Palaemon, and 0.7–38.4 in Macrobrachium. In the septal cells, S_v varies from 8.9–10.0 in Palaemon, and 3.3–21.6 in Macrobrachium; mitochondrial volumes (V_mit) range from 43.3–46.8% in Palaemon and 34.9–53.4% in Macrobrachium. In the renal proximal tubule cells, apical microvilli S_v varies from 27.0–34.3 in Palaemon, and 38.3–47.8 in Macrobrachium; basal invagination S_v ranges from 18.7–20.0 in Palaemon and 30.8–40.8 in Macrobrachium. Septal cell S_v shows phylogenetic signal; evagination height/density, apical S_v, and V_mit vary independently of species relatedness. Salt transport capability by the gill and renal epithelia has increased during palaemonid evolution, reflecting amplified membrane availability for ion transporter insertion. These traits underpin the increased osmotic gradients maintained against the external media. Gill ultrastructure and osmotic gradient have evolved in tandem, driven by salinity at the genus level. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 673–688.     

Genetic diversity promotes homeostasis in insect colonies

Although most insect colonies are headed by a singly mated queen, some ant, wasp and bee taxa have evolved high levels of multiple mating or 'polyandry'. We argue here that a contributing factor towards the evolution of polyandry is that the resulting genetic diversity within colonies provides them with a system of genetically based task specialization, enabling them to respond resiliently to environmental perturbation. An alternate view is that genetic contributions to task specialization are a side effect of multiple mating, which evolved through other causes, and that genetically based task specialization now makes little or no contribution to colony fitness.     

Feast and famine in plant genomes

Plant genomes vary over several orders of magnitude in size, even among closely related species, yet the origin, genesis and significance of this variation are not clear. Because DNA content varies over a sevenfold range among diploid species in the cotton genus (Gossypium) and its allies, this group offers opportunities for exploring patterns and mechanisms of genome size evolution. For example, the question has been raised whether plant genomes have a one-way ticket to genomic obesity, as a consequence of retroelement accumulation. Few empirical studies directly address this possibility, although it is consistent with recent insights gleaned from evolutionary genomic investigations. We used a phylogenetic approach to evaluate the directionality of genome size evolution among Gossypium species and their relatives in the cotton tribe (Gossypieae, Malvaceae). Our results suggest that both DNA content increase and decrease have occurred repeatedly during evolution. In contrast to a model of unidirectional genome size change, the frequency of inferred genome size contraction exceeded that of expansion. In conjunction with other evidence, this finding highlights the dynamic nature of plant genome size evolution, and suggests that poorly understood genomic contraction mechanisms operate on a more extensive scale that previously recognized. Moreover, the research sets the stage for fine-scale analysis of the evolutionary dynamics and directionality of change for the full spectrum of genomic constituents.