Consequences Of Evolutionary Changes Research Articles

Acquisition of new function through gene duplication in the metallocarboxypeptidase family

Gene duplication is a key first step in the process of expanding the functionality of a multigene family. In order to better understand the process of gene duplication and its role in the formation of new enzymes, we investigated recent duplication events in the M14 family of proteolytic enzymes. Within vertebrates, four of 23 M14 genes were frequently found in duplicate form. While AEBP1, CPXM1, and CPZ genes were duplicated once through a large-scale, likely whole-genome duplication event, the CPO gene underwent many duplication events within fish and Xenopus lineages. Bioinformatic analyses of enzyme specificity and conservation suggested a greater amount of neofunctionalization and purifying selection in CPO paralogs compared with other CPA/B enzymes. To examine the functional consequences of evolutionary changes on CPO paralogs, the four CPO paralogs from Xenopus tropicalis were expressed in Sf9 and HEK293T cells. Immunocytochemistry showed subcellular distribution of Xenopus CPO paralogs to be similar to that of human CPO. Upon activation with trypsin, the enzymes demonstrated differential activity against three substrates, suggesting an acquisition of new function following duplication and subsequent mutagenesis. Characteristics such as gene size and enzyme activation mechanisms are possible contributors to the evolutionary capacity of the CPO gene.

Meiotic, genomic and evolutionary properties of crossover distribution in Drosophila yakuba.

The number and location of crossovers across genomes are highly regulated during meiosis, yet the key components controlling them are fast evolving, hindering our understanding of the mechanistic causes and evolutionary consequences of changes in crossover rates. Drosophila melanogaster has been a model species to study meiosis for more than a century, with an available high-resolution crossover map that is, nonetheless, missing for closely related species, thus preventing evolutionary context. Here, we applied a novel and highly efficient approach to generate whole-genome high-resolution crossover maps in D. yakuba to tackle multiple questions that benefit from being addressed collectively within an appropriate phylogenetic framework, in our case the D. melanogaster species subgroup. The genotyping of more than 1,600 individual meiotic events allowed us to identify several key distinct properties relative to D. melanogaster. We show that D. yakuba, in addition to higher crossover rates than D. melanogaster, has a stronger centromere effect and crossover assurance than any Drosophila species analyzed to date. We also report the presence of an active crossover-associated meiotic drive mechanism for the X chromosome that results in the preferential inclusion in oocytes of chromatids with crossovers. Our evolutionary and genomic analyses suggest that the genome-wide landscape of crossover rates in D. yakuba has been fairly stable and captures a significant signal of the ancestral crossover landscape for the whole D. melanogaster subgroup, even informative for the D. melanogaster lineage. Contemporary crossover rates in D. melanogaster, on the other hand, do not recapitulate ancestral crossovers landscapes. As a result, the temporal stability of crossover landscapes observed in D. yakuba makes this species an ideal system for applying population genetic models of selection and linkage, given that these models assume temporal constancy in linkage effects. Our studies emphasize the importance of generating multiple high-resolution crossover rate maps within a coherent phylogenetic context to broaden our understanding of crossover control during meiosis and to improve studies on the evolutionary consequences of variable crossover rates across genomes and time.

Personality-dependent breeding dispersal in rural but not urban burrowing owls

Dispersal propensity has been correlated with personality traits, conspecific density and predation risk in a variety of species. Thus, changes in the relative frequency of behavioural phenotypes or in the ecological pressures faced by individuals in contrasting habitats can have unexpected effects on their dispersal strategies. Here, using the burrowing owl Athene cunicularia as a study model, we test whether changes in the behavioural profile of individuals and changes in conspecific density and predation pressure associated with urban life influence their breeding dispersal decisions compared to rural conspecifics. Our results show that breeding dispersal behaviour differs between rural and urban individuals. Site fidelity was lower among rural than among urban birds, and primarily related to an individual’s behaviours (fear of humans), which has been reported to reflect individual personality. In contrast, the main determinant of site fidelity among urban owls was conspecific density. After taking the decision of dispersing, urban owls moved shorter distances than rural ones, with females dispersing farther than males. Our results support a personality-dependent dispersal pattern that might vary with predation risk. However, as multiple individuals of two populations (one urban, one rural) were used for this research, differences can thus also be caused by other factors differing between the two populations. Further research is needed to properly understand the ecological and evolutionary consequences of changes in dispersal behaviours, especially in terms of population structuring and gene flow between urban and rural populations.

Neurocomputational Consequences of Evolutionary Connectivity Changes in Perisylvian Language Cortex.

The human brain sets itself apart from that of its primate relatives by specific neuroanatomical features, especially the strong linkage of left perisylvian language areas (frontal and temporal cortex) by way of the arcuate fasciculus (AF). AF connectivity has been shown to correlate with verbal working memory—a specifically human trait providing the foundation for language abilities—but a mechanistic explanation of any related causal link between anatomical structure and cognitive function is still missing. Here, we provide a possible explanation and link, by using neurocomputational simulations in neuroanatomically structured models of the perisylvian language cortex. We compare networks mimicking key features of cortical connectivity in monkeys and humans, specifically the presence of relatively stronger higher-order “jumping links” between nonadjacent perisylvian cortical areas in the latter, and demonstrate that the emergence of working memory for syllables and word forms is a functional consequence of this structural evolutionary change. We also show that a mere increase of learning time is not sufficient, but that this specific structural feature, which entails higher connectivity degree of relevant areas and shorter sensorimotor path length, is crucial. These results offer a better understanding of specifically human anatomical features underlying the language faculty and their evolutionary selection advantage.SIGNIFICANCE STATEMENT Why do humans have superior language abilities compared to primates? Recently, a uniquely human neuroanatomical feature has been demonstrated in the strength of the arcuate fasciculus (AF), a fiber pathway interlinking the left-hemispheric language areas. Although AF anatomy has been related to linguistic skills, an explanation of how this fiber bundle may support language abilities is still missing. We use neuroanatomically structured computational models to investigate the consequences of evolutionary changes in language area connectivity and demonstrate that the human-specific higher connectivity degree and comparatively shorter sensorimotor path length implicated by the AF entail emergence of verbal working memory, a prerequisite for language learning. These results offer a better understanding of specifically human anatomical features for language and their evolutionary selection advantage.

Identification of two lineages of host-associated eriophyoid mites predisposed to different levels of host diversification

Herbivorous arthropods can diversify as a consequence of evolutionary changes in response to their plant hosts. Current patterns of host association of herbivores are likely to reflect a long evolutionary history of herbivore-plant co-evolution. Here, we used molecular phylogenetics to track the evolutionary history of host shifts and diversification of 66 eriophyoid mites (Acari, Eriophyoidea), and linked past patterns of evolutionary diversification to more recent patterns of divergence by tracking population genetic variation in 13 of the eriophyoid mite species feeding on different gymnosperm hosts. This allowed us to explore the relationship between a past history of diversification and the current potential of mites to undergo host range shifts. We found that population-level diversity across gymnosperm hosts as measured by 28S rRNA markers was greater in species from the mite clade that had radiated across evolutionary time to utilize a variety of hosts including angiosperms, compared to species from the clade that has remained restricted to ancestral gymnosperm hosts. Species from the radiated clade exhibited higher variation in host use. Lineages of mites that have in the past been able to radiate and adapt to diverse plants may therefore be predisposed to continue their expansion on new hosts, although additional clades need to be tested.

Evolutionary consequence of a change in life cycle complexity: A link between precocious development and evolution toward female-biased sex allocation in a hermaphroditic parasite.

The evolutionary consequences of changes in the complex life cycles of parasites are not limited to the traits that directly affect transmission. For instance, mating systems that are altered due to precocious sexual maturation in what is typically regarded as an intermediate host may impact opportunities for outcrossing. In turn, reproductive traits may evolve to optimize sex allocation. Here, we test the hypothesis that sex allocation evolved toward a more female-biased function in populations of the hermaphroditic digenean trematode Alloglossidium progeneticum that can precociously reproduce in their second hosts. In these precocious populations, parasites are forced to self-fertilize as they remain encysted in their second hosts. In contrast, parasites in obligate three-host populations have more opportunities to outcross in their third host. We found strong support that in populations with precocious development, allocation to male resources was greatly reduced. We also identified a potential phenotypically plastic response in a body size sex allocation relationship that may be driven by the competition for mates. These results emphasize how changes in life cycle patterns that alter mating systems can impact the evolution of reproductive traits in parasites.

Invited perspective: bryophytes as models for understanding the evolution of sexual systems

One of the first life history characters that students of bryology learn is the bryophyte life cycle. Roughly half of the bryophytes have separate sexes (dioicous) and half are hermaphroditic (monoicous). This variation is important for taxonomic purposes but also has major consequences for nearly every aspect of bryophyte biology. For example, dioicous species generally reproduce less frequently than monoicous species (Longton & Schuster 1983) but harbor more genetic variation than monoicous species (Eppley et al. 2006). More broadly, however, the maintenance of both sexual systems at nearly equal frequencies in the bryophytes is quite unusual among the eukaryotes. This situation makes bryophytes an important model system for studying the evolutionary consequences of changes in sexual system. Bryophytes have a long history as model systems in cytology and genetics. Sex chromosomes in plants were first discovered in the liverwort Sphaerocarpus donnellii (Allen 1917), and the term ‘‘heterochromatin’’ was coined for the dark staining heteromorphic pair of chromosomes in many bryophytes (Heitz 1932). Bryophytes have long served as model genetic systems because the dominant part of the life cycle (i.e., the gametophyte) is haploid, and the phenotype of the plant directly reflects its genotype without the masking of dominance (Allen 1919; Ashton & Cove 1977; Engel 1968; von Wettstein 1924). More recently, efficient gene targeting via homologous recombination was discovered in Physcomitrella patens (Kammerer & Cove 1996; Schaefer & Zryd 1997; Strepp et al. 1998) and Ceratodon purpureus (Brucker et al. 2005; Mittmann et al. 2009; Trouiller et al. 2007). With this tool researchers can construct powerful tests for associations between genes and traits. In addition, the genome of P. patens has now been completely sequenced (Rensing et al. 2008), and sequencing projects for C. purpureus (http://www.jgi.doe.gov/ sequencing/why/ceratodon.html), Phaeoceros laevis (http://ldl.genomics.org.cn/page/searchplant. jsp?speciesname5phaeoceros), and Marchantia polymorpha (http://www.jgi.doe.gov/sequencing/ why/99191.html) are now underway. Together the natural variation in sexual system and the potential for laboratory study make bryophytes ideal for studying the causes and consequences of changes in sexual system. The purpose of this perspective is to highlight areas where interdisciplinary research can provide new insights into the evolution of bryophyte sexual systems. We have structured the perspective around three major evolutionary transitions: 1) the evolution of dioicy; 2) the evolution of sex chromosomes; and 3) the evolution of monoicy. We first provide a brief outline of the evolutionary theory underlying each of these phenomena. Since much of this theory was developed for angiosperms, we suggest how it can be applied to bryophytes. Second, we indicate how 3 Corresponding author’s e-mail: stuartmcdaniel@ufl.edu DOI: 10.1639/0007-2745-115.1.1

Evolutionary changes in plant reproductive traits following habitat fragmentation and their consequences for population fitness

Summary1. The effects of habitat fragmentation on plant population genetic structure and diversity are relatively well studied. Yet, most of these studies used molecular tools focusing on neutral genetic markers, and much less is known about the potential evolutionary consequences of habitat fragmentation on ecologically relevant plant traits.2. It can be expected that the altered biotic and abiotic conditions and limited gene flow following habitat fragmentation may impose strong selection pressures on traits important for plant fitness. Responses to these selection pressures may, however, be hampered by reduced genetic diversity through genetic drift. Conversely, evolutionary changes in flower or dispersal traits may itself impact the strength of inbreeding and genetic drift.3. In this review, we highlight different reproductive plant traits that may be under selection following habitat fragmentation, and we examine studies that have shown indications for rapid evolutionary responses.4. There are still relatively few studies that have convincingly shown that habitat fragmentation generates rapid evolutionary responses. Separating genetic from plastic trait responses and quantifying the long‐term fitness consequences of evolutionary changes in plant traits also remain major challenges.5. Synthesis. Many plant traits may be subject to selection following habitat fragmentation, but, until now, studies that quantified evolutionary responses to habitat fragmentation are limited. To study the consequences of changing plant traits for population fitness, we advocate applying population models that link demographic vital rates, the responding plant traits and their heritability.

Toward an integration of evolutionary biology and ecosystem science

At present, the disciplines of evolutionary biology and ecosystem science are weakly integrated. As a result, we have a poor understanding of how the ecological and evolutionary processes that create, maintain, and change biological diversity affect the flux of energy and materials in global biogeochemical cycles. The goal of this article was to review several research fields at the interfaces between ecosystem science, community ecology and evolutionary biology, and suggest new ways to integrate evolutionary biology and ecosystem science. In particular, we focus on how phenotypic evolution by natural selection can influence ecosystem functions by affecting processes at the environmental, population and community scale of ecosystem organization. We develop an eco-evolutionary model to illustrate linkages between evolutionary change (e.g. phenotypic evolution of producer), ecological interactions (e.g. consumer grazing) and ecosystem processes (e.g. nutrient cycling). We conclude by proposing experiments to test the ecosystem consequences of evolutionary changes.

Communication in troubled waters: responses of fish communication systems to changing environments

Fish populations are increasingly being subjected to anthropogenic changes to their sensory environments. The impact of these changes on inter- and intra-specific communication, and its evolutionary consequences, has only recently started to receive research attention. A disruption of the sensory environment is likely to impact communication, especially with respect to reproductive interactions that help to maintain species boundaries. Aquatic ecosystems around the world are being threatened by a variety of environmental stressors, causing dramatic losses of biodiversity and bringing urgency to the need to understand how fish respond to rapid environmental changes. Here, we discuss current research on different communication systems (visual, chemical, acoustic, electric) and explore the state of our knowledge of how complex systems respond to environmental stressors using fish as a model. By far the bulk of our understanding comes from research on visual communication in the context of mate selection and competition for mates, while work on other communication systems is accumulating. In particular, it is increasingly acknowledged that environmental effects on one mode of communication may trigger compensation through other modalities. The strength and direction of selection on communication traits may vary if such compensation occurs. However, we find a dearth of studies that have taken a multimodal approach to investigating the evolutionary impact of environmental change on communication in fish. Future research should focus on the interaction between different modes of communication, especially under changing environmental conditions. Further, we see an urgent need for a better understanding of the evolutionary consequences of changes in communication systems on fish diversity.

It's About Time: Divergence, Demography, and the Evolution of Developmental Modes in Marine Invertebrates

Differences in larval developmental mode are predicted to affect ecological and evolutionary processes ranging from gene flow and population bottlenecks to rates of population recovery from anthropogenic disturbance and capacity for local adaptation. The most powerful tests of these predictions use comparisons among species to ask how phylogeographic patterns are correlated with the evolution and loss of prolonged planktonic larval development. An important and largely untested assumption of these studies is that interspecific differences in population genetic structure are mainly caused by differences in dispersal and gene flow (rather than by differences in divergence times among populations or changes in effective population sizes), and that species with similar patterns of spatial genetic variation have similar underlying temporal demographic histories. Teasing apart these temporal and spatial patterns is important for understanding the causes and consequences of evolutionary changes in larval developmental mode. New analytical methods that use the coalescent history of allelic diversity can reveal these temporal patterns, test the strength of traditional population-genetic explanations for variation in spatial structure based on differences in dispersal, and identify strongly supported alternative explanations for spatial structure based on demographic history rather than on gene flow alone. We briefly review some of these recent analytical developments, and show their potential for refining ideas about the correspondence between the evolution of larval developmental mode, population demographic history, and spatial genetic variation.

When Two Is Better Than One

Gene duplication and divergence has long been considered an important route to adaptation and phenotypic evolution. Reporting in Nature, Hittinger and Carroll (2007) provide the first clear example of adaptations in both regulatory regions and protein-coding regions after gene duplication. This combination of evolutionary changes appears to have resolved an adaptive conflict, leading to increased organismal fitness.

Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation.

Evolutionary changes in transcriptional regulation undoubtedly play an important role in creating morphological diversity. However, there is little information about the evolutionary dynamics of cis-regulatory sequences. This study examines the functional consequence of evolutionary changes in the Endo16 promoter of sea urchins. The Endo16 gene encodes a large extracellular protein that is expressed in the endoderm and may play a role in cell adhesion. Its promoter has been characterized in exceptional detail in the purple sea urchin, Strongylocentrotus purpuratus. We have characterized the structure and function of the Endo16 promoter from a second sea urchin species, Lytechinus variegatus. The Endo16 promoter sequences have evolved in a strongly mosaic manner since these species diverged approximately 35 million years ago: the most proximal region (module A) is conserved, but the remaining modules (B-G) are unalignable. Despite extensive divergence in promoter sequences, the pattern of Endo16 transcription is largely conserved during embryonic and larval development. Transient expression assays demonstrate that 2.2 kb of upstream sequence in either species is sufficient to drive GFP reporter expression that correctly mimics this pattern of Endo16 transcription. Reciprocal cross-species transient expression assays imply that changes have also evolved in the set of transcription factors that interact with the Endo16 promoter. Taken together, these results suggest that stabilizing selection on the transcriptional output may have operated to maintain a similar pattern of Endo16 expression in S. purpuratus and L. variegatus, despite dramatic divergence in promoter sequence and mechanisms of transcriptional regulation.

Relationship between song characters and morphology in New World pigeons

We studied the pattern of variation in song characters among 16 New World pigeon species belonging to different taxonomic groups defined by morphological characters. Structural, temporal and frequency characters of the song were analysed. Principal components analyses showed that species belonging to the same taxonomic group were also grouped together by their song characters. In addition, individuals were correctly assigned into taxonomic groups by discriminant function analyses in more than 87.8% of cases. These analyses also showed that more than 87.5% of the individuals could be correctly classified by species when all song characters were included. Correct classification of individuals by species and taxonomic groups dropped when character types were analysed separately, thus showing that structural, as well as temporal and frequency characters are fundamental to define species- and group-specific identities of New World pigeon's songs. Correspondence between patterns of vocal and morphological variation found in this study can be a consequence of evolutionary changes in morphology affecting song production, as for example body size changes that constrain the syrinx to produce certain acoustic frequencies.

Relationship between song characters and morphology in New World pigeons

We studied the pattern of variation in song characters among 16 New World pigeon species belonging to different taxonomic groups defined by morphological characters. Structural, temporal and frequency characters of the song were analysed. Principal components analyses showed that species belonging to the same taxonomic group were also grouped together by their song characters. In addition, individuals were correctly assigned into taxonomic groups by discriminant function analyses in more than 87.8% of cases. These analyses also showed that more than 87.5% of the individuals could be correctly classified by species when all song characters were included. Correct classification of individuals by species and taxonomic groups dropped when character types were analysed separately, thus showing that structural, as well as temporal and frequency characters are fundamental to define species- and group-specific identities of New World pigeon's songs. Correspondence between patterns of vocal and morphological variation found in this study can be a consequence of evolutionary changes in morphology affecting song production, as for example body size changes that constrain the syrinx to produce certain acoustic frequencies.

Evolutionary consequences of changes in species' geographical distributions driven by Milankovitch climate oscillations.

We suggest Milankovitch climate oscillations as a common cause for geographical patterns in species diversity, species' range sizes, polyploidy, and the degree of specialization and dispersability of organisms. Periodical changes in the orbit of the Earth cause climatic changes termed Milankovitch oscillations, leading to large changes in the size and location of species' geographical distributions. We name these recurrent changes "orbitally forced species' range dynamics" (ORD). The magnitude of ORD varies in space and time. ORD decreases gradual speciation (attained by gradual changes over many generations), increases range sizes and the proportions of species formed by polyploidy and other "abrupt" mechanisms, selects against specialization, and favor dispersability. Large ORD produces species prone neither to extinction nor gradual speciation. ORD increases with latitude. This produces latitudinal patterns, among them the gradient in species diversity and species' range sizes (Rapoport's rule). Differential ORD and its evolutionary consequences call for new conservation strategies on the regional to global scale.

Landscape dynamics and evolution of colonizer syndromes: interactions between reproductive effortand dispersal in a metapopulation

The evolutionary consequences of changes in landscape dynamics for the evolution of life history syndromes are studied using a metapopulation model. We consider in turn the long-term effects of a change in the local disturbance rate, in the maximal local population persistence, in habitat productivity, and in habitat fragmentation. We examine the consequences of selective interactions between dispersal and reproductive effort by comparing the outcome of joint evolution to a situation where the species has lost the potential to evolve either its reproductive effort or its dispersal rate. We relax the classical assumption that any occupied site in the metapopulation reaches its carrying capacity immediately after recolonization. Our main conclusions are the following: (1) genetic diversity modifies the range of landscape parameters for which the metapopulation is viable, but it alters very little the qualitative evolutionary trends observed for each trait within this range. Although they are both part of a competition/colonization axis, reproductive effort and dispersal are not substitutable traits: their evolution reflects more directly the change in the landscape dynamics, than a selective interaction among them. (2) no general syndrome of covariation between reproductive effort and dispersal can be predicted: the pattern of association between the two traits depends on the type of change in landscape dynamics and on the saturation level. We review empirical evidence on colonizer syndromes and suggest lines for further empirical work.

Evolution and the Consequences of Species Introductions and Deletions

The addition or deletion of a species from a community is likely to have effects on the trait values of other species and on their population densities. This article argues that current theory is insufficiently developed to provide guidance in predicting what might happen to either traits or population densities. In addition, there has been relatively little empirical work to examine many of the phenomena that have been predicted by the limited available theory. The example of character displacement of competitors is reviewed to reveal some of the gaps in our knowledge about the evolutionary consequences of additions or deletions. The example of evolution of traits related to predation in food webs is used to reveal gaps in our knowledge of the population—level consequences of evolutionary changes initiated by a species addition or deletion. Several approaches to studying combined evolutionary and ecological processes in multispecies communities are discussed. Some previous multispecies models have been too abstract to be easily related to more mechanistic two—species models, but recent methods derived from quantitative genetics may result in significant advances in understanding multispecies systems and their relationship to communities with fewer species.

Anomalous distribution of nuclear and mitochondrial DNA markers in periodical cicadas

Ecological genetics theory identifies the age at first reproduction and life-cycle length as important components of life-history strategies, and predicts that variation in these traits can have significant evolutionary consequences1. Changes in the timing of reproduction can affect the fitness of an organism2, disrupt gene flow3 and lead to speciation4. The existence of two life-cycle lengths differing by four years in periodical cicadas of the genus Magicicada provides an excellent opportunity to investigate both the control and evolutionary consequences of changes in the timing of reproduction. In Magicicada, life-cycle length has been assumed to be a genetically fixed species-specific trait5. Alternatively, however, periodical cicadas could switch between the two life-cycle lengths in response to either genetic6 or environmental7 factors possibly providing a mechanism for the generation of the extant year classes of cicadas8, called broods9. Here we describe a survey of populations of 13- and 17-year periodical cicadas which suggests that 13-year cicadas in a large region of central North America are descendents of 17-year cicadas that switched their life-cycle length to 13 years, providing the first strong genetic evidence that life-cycle length is a plastic trait. The change in maturation time and the resultant anomalous distribution of cytoplasmic and nuclear gene markers implies that these cicadas became temporally isolated from the parent brood, joined an already existing brood, and thus brought together two independently evolving gene pools.