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Metamodels play a crucial role in any model-based application. They underpin the definition of models and tools, and the development of model management operations, including model transformations and analysis. Like any software artifacts, metamodels are subject to evolution to improve their quality or implement unforeseen requirements. Metamodels can be defined in terms of existing ones to increase the separation of concerns and foster reuse. However, the induced coupling can give additional evolution complexity, and dedicated support is needed to avoid breaking metamodels defined in terms of those being changed. This paper presents a tool-supported approach that can automatically analyze the available metamodels and alert modelers in case of change operations that can give place to invalid situations like dangling references. The approach has been implemented in the Edelta development environment and successfully applied to metamodels retrieved from a publicly available Ecore models dataset.

Mammals have evolved different tooth phenotypes that are hypothesized to be associated with feeding habits. However, the genetic basis for the linkage has not been well explored. In this study, we investigated 13 tooth-related genes, including seven enamel-related genes (AMELX, AMBN, ENAM, AMTN, ODAM, KLK4 and MMP20) and six dentin-related genes (DSPP, COL1A1, DMP1, IBSP, MEPE and SPP1), from 63 mammals to determine their evolutionary history. Our results showed that different evolutionary histories have evolved among divergent feeding habits in mammals. There was stronger positive selection for eight genes (ENAM, AMTN, ODAM, KLK4, DSPP, DMP1, COL1A1, MEPE) in herbivore lineages. In addition, AMELX, AMBN, ENAM, AMTN, MMP20 and COL1A1 underwent accelerated evolution in herbivores. While relatively strong positive selection was detected in IBSP, SPP1, and DSPP, accelerated evolution was only detected for MEPE and SPP1 genes among the carnivorous lineages. We found positive selection on AMBN and ENAM genes for omnivorous primates in the catarrhini clade. Interestingly, a significantly positive association between the evolutionary rate of ENAM, ODAM, KLK4, MMP20 and the average enamel thickness was found in primates. Additionally, we found molecular convergence in some amino acid sites of tooth-related genes among the lineages whose feeding habit are similar. The positive selection of related genes might promote the formation and bio-mineralization of tooth enamel and dentin, which would make the tooth structure stronger. Our results revealed that mammalian tooth-related genes have experienced variable evolutionary histories, which provide some new insights into the molecular basis of dietary adaptation in mammals.

The three-spined stickleback (Gasterosteus aculeatus) is an important model system for the study of parallel evolution in the wild, having repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes but these had typically limited geographic sampling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global samples of the three-spined stickleback marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Most signatures of parallel evolution were unique to the Eastern Pacific and trans-oceanic marine-freshwater differentiation was restricted to a limited number of shared genomic regions, including three chromosomal inversions. On the basis of simulations and empirical data, we demonstrate that this could result from the stochastic loss of freshwater-adapted alleles during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which can reduce standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the elevated linkage disequilibrium associated with marine-freshwater differentiation in the Eastern Pacific is consistent with secondary contact between marine and freshwater populations that evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies from the Eastern Pacific region have led us to believe, parallel marine-freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range. Population genomic data from a global dataset of three-spined sticklebacks show that parallel signatures of marine to freshwater differentiation are less common than previously thought.

It has been hypothesized that the Neolithic transition towards an agricultural and pastoralist economy facilitated the emergence of human adapted pathogens. Here, we recovered eight Salmonella enterica subsp. enterica genomes from human skeletons of transitional foragers, pastoralists, and agro-pastoralists in western Eurasia that were up to 6,500 years old. Despite the high genetic diversity of S. enterica all ancient bacterial genomes clustered in a single previously uncharacterized branch that contains S. enterica adapted to multiple mammalian species. All ancient bacterial genomes from prehistoric (agro-)pastoralists fall within a part of this branch that also includes the human-specific S. enterica Paratyphi C, illustrating the evolution of a human pathogen over a period of five thousand years. Bacterial genomic comparisons suggest that the earlier ancient strains were not host specific, differed in pathogenic potential, and experienced convergent pseudogenization that accompanied their downstream host adaptation. These observations support the concept that the emergence of human adapted S. enterica is linked to human cultural transformations.

BackgroundCotton stem trichomes and seed fibers are each single celled structures formed by protrusions of epidermal cells, and were found sharing the overlapping molecular mechanism. Compared with fibers, cotton stem trichomes are more easily observed, but the molecular mechanisms underlying their development are still poorly understood.ResultsIn this study,Gossypium hirsutum(Gh) andG. barbadense(Gb)were found to differ greatly in percentages of varieties/accessions with glabrous stems and in trichome density, length, and number per trichopore.Ghvarieties normally had long singular and clustered trichomes, whileGbvarieties had short clustered trichomes. Genetic mapping using five F2populations from crosses between glabrous varieties and those with different types of stem trichomes revealed that much variation among stem trichome phenotypes could be accounted for by different combinations of genes/alleles on Chr. 06 and Chr. 24. The twenty- six F1generations from crosses between varieties with different types of trichomes had varied phenotypes, further suggesting that the trichomes of tetraploid cotton were controlled by different genes/alleles. Compared to modern varieties, a greater proportion ofGhwild accessions were glabrous or had shorter and denser trichomes; whereas a smaller proportion ofGbprimitive accessions had glabrous stems. A close correlation between fuzz fiber number and stem trichome density was observed in bothGhandGbprimitive accessions and modern varieties.ConclusionBased on these findings, we hypothesize that stem trichomes evolved in parallel with seed fibers during the domestication of cultivated tetraploid cotton. In addition, the current results illustrated that stem trichome can be used as a morphological index of fiber quality in cotton conventional breeding.

Annual fishes of the genus Nothobranchius inhabit ephemeral habitats in Eastern and Southeastern Africa. Their life cycle is characterized by very rapid maturation, a posthatch lifespan of a few weeks to months and embryonic diapause to survive the dry season. The speciesN. furzeriholds the record of the fastest-maturing vertebrate and of the vertebrate with the shortest captive lifespan and is emerging as model organism in biomedical research, evolutionary biology, and developmental biology. Extensive characterization of age-related phenotypes in the laboratory and of ecology, distribution, and demography in the wild are available. Species/populations from habitats differing in precipitation intensity show parallel evolution of lifespan and age-related traits that conform to the classical theories on aging. Genome sequencing and the establishment of CRISPR/Cas9 techniques made this species particularly attractive to investigate the effects genetic and non-genetic intervention on lifespan and aging-related phenotypes. At the same time, annual fishes are a very interesting subject for comparative approaches, including genomics, transcriptomics, and proteomics. TheN. furzericommunity is highly diverse and rapidly expanding and organizes a biannual meeting.

BackgroundTo date, evidence for the relative prevalence or rarity of molecular convergent and parallel evolution is conflicting, and understanding of how these processes contribute to adaptation is limited. We compared four high-elevation anuran species (Bufo tibetanus,Nanorana parkeri,Rana kukunorisandScutiger boulengeri) from the Tibetan region, and examined convergent and parallel amino acid substitutions between them and how they may have contributed to high-elevation adaptation.ResultsGenomic data of the four high-elevation species and eight of their low-elevation close relatives were gathered. A total of 1098 orthologs shared by all species were identified. We first conducted pairwise comparisons using Zhang and Kumar’s test. Then, theRconvindex was calculated and convergence/divergence correlation plotting was conducted. Furthermore, genes under positive selection and with elevated evolutionary rate were examined. We detected a large number of amino acid sites with convergent or parallel substitutions. Several pairs of high-elevation species, in particular,R. kukunorisvsN. parkeriandB. tibetanusvsS. boulengeri, had excessive amounts of convergent substitutions compared to neutral expectation. Nevertheless, these sites were mostly concentrated in a small number of genes (3–32), and no genome-wide convergence was detected. Furthermore, the majority of these convergent genes were neither under detectable positive selection nor had elevated evolutionary rates, although functional prediction analysis suggested some of the convergent genes could potentially contribute to high-elevation adaptation.ConclusionsThere is a substantial amount of convergent evolution at the amino-acid level among high-elevation amphibians, although these sites are concentrated in a few genes, not widespread across the genomes. This may attribute to the fact that all the target species are from the same environment. The relative prevalence of convergent substitutions among high-elevation amphibians provides an excellent opportunity for further study of molecular convergent evolution.

Background The three-spined stickleback (Gasterosteus aculeatus) is a remarkable system to study the genetic mechanisms underlying parallel evolution during the transition from marine to freshwater habitats. Although the majority of previous studies on the parallel evolution of sticklebacks have mainly focused on postglacial freshwater populations in the Pacific Northwest of North America and northern Europe, we recently use Japanese stickleback populations for investigating shared and unique features of adaptation and speciation between geographically distant populations. However, we currently lack a comprehensive phylogeny of the Japanese three-spined sticklebacks, despite the fact that a good phylogeny is essential for any evolutionary and ecological studies. Here, we conducted a phylogenomic analysis of the three-spined stickleback in the Japanese Archipelago. Results We found that freshwater colonization occurred in multiple waves, each of which may reflect different interglacial isolations. Some of the oldest freshwater populations from the central regions of the mainland of Japan (hariyo populations) were estimated to colonize freshwater approximately 170,000 years ago. The next wave of colonization likely occurred approximately 100,000 years ago. The inferred origins of several human-introduced populations showed that introduction occurred mainly from nearby habitats. We also found a new habitat of the three-spined stickleback sympatric with the Japan Sea stickleback (Gasterosteus nipponicus). Conclusions These Japanese stickleback systems differ from those in the Pacific Northwest of North America and northern Europe in terms of divergence time and history. Stickleback populations in the Japanese Archipelago offer valuable opportunities to study diverse evolutionary processes in historical and contemporary timescales.

Studying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.

The presence of osteoderms in the skin of some extinct sloths and in cingulates (armadillos, pampatheres, and glyptodonts) has often been considered a pleisomorphic character of the Xenarthra. While osteoderms are known from the earliest cingulates, they are absent in most sloths including the two extant taxa and only appear late in their fossil record. Osteoderms are currently only reported from five genera of mylodonts and two megatheres, out of the over 100 currently recognized genera of sloths. Consequently, rather than a plesiomorphic character of the Xenarthra, which has been secondarily lost in sloths, it is more likely that osteoderms in sloths are the result of parallel evolution to the cingulates that independently evolved in one, possibly two different sloth clades.

The repeated phenotypic patterns that characterize populations undergoing parallel evolution provide support for a deterministic role of adaptation by natural selection. Determining the level of parallelism also at the genetic level is thus central to our understanding of how natural selection works. Many studies have looked for repeated genomic patterns in natural populations, but work on gene expression is less common. The studies that have examined gene expression have found some support for parallelism, but those studies almost always used samples collected from the wild that potentially confounds the effects of plasticity with heritable differences. Here we use two independent pairs of lake and stream threespine stickleback (Gasterosteus aculeatus) raised in common garden conditions to assess both parallel and antiparallel (that is, similar versus different directions of lake-stream expression divergence in the two watersheds) heritable gene expression differences as measured by total RNA sequencing. We find that more genes than expected by chance show either parallel (22 genes, 0.18% of expressed genes) or antiparallel (24 genes, 0.20% of expressed genes) lake-stream expression differences. These results correspond well with previous genomic studies in stickleback ecotype pairs that found similar levels of parallelism. We suggest that parallelism might be similarly constrained at the genomic and transcriptomic levels.

We report a strong pattern of molecular-level convergent/parallel evolution of the MYBPC2 gene. Three high-elevation amphibian species, Bufo gargarizans minshanicus, Nanorana pleskei, Rana kukunoris, revealed remarkable numbers of convergent and parallel amino acid substitutions. On the MYBPC2 gene tree of eleven anurans, the three distantly related species formed a strongly supported clade that was away from their respective relatives. Furthermore, we generated both model-based and empirical data-based null distributions for neutral convergent evolution. All three pairwise comparisons among the three species showed significantly more convergent and parallel substitutions than the null distributions. This study adds to the very small roster of clear cases of non-neutral molecular convergent evolution (e.g. prestin, rhodopsin). Molecular convergent evolution has significant implications in biology and detailed case studies will likely provide more insight into its genetic mechanisms.

Interspecific morph variations in trophic morphology related to skull-bones and head traits is associated to ecological segregation of Arctic charr morphs (genus Salvelinus) in two sub-arctic lakes (Fjellfrosvatn and Skogsfjordvatn, Norway). The replicated morph pair, the profundal spawning benthivorous PB-morph and the littoral spawning omnivorous LO-morph of Arctic charr, diverge along the shallow-deep-water resource axis. In Skogsfjordvatn there is also a profundal spawning piscivorous PP-morph. The PB-morphs from both lakes have similar skull-bone traits and head morphology such as elongated jaw-bones, small opercular bones and relatively longer heads. The PP-morph also has an elongated head, relatively small opercular bones as well as larger jaw-bones. In contrast, the LO-morphs in both lakes have shorter jaw-bones, larger opercular bones in addition to relatively small heads. However, some small non-parallel differences exist among the morphs from the two lakes. Overall, all profundal morphs (PB and PP) have relatively similar skull-bone structures, suggesting adaptations to the deep-water environment but also to their separated dietary niches. There is strong evidence for parallel evolution with some local adaptations in skull-bones and head morphology of the PB-morph and the LO-morph from separate lakes.

BackgroundEnvironmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geographic area in Japan and additionally identified putative environmental drivers and their effect on co-existing multiple stonefly species. Double-digest restriction-associated DNA (ddRAD) libraries were independently sequenced for 219 individuals from 23 sites across four geographical regions along a nationwide latitudinal gradient in Japan.ResultsA total of 4,251 candidate single nucleotide polymorphisms (SNPs) strongly associated with local adaptation were discovered using Latent mixed models; of these, 294 SNPs showed strong correlation with environmental variables, specifically precipitation and altitude, using distance-based redundancy analysis. Genome–genome comparison among the seven species revealed a high sequence similarity of candidate SNPs within a geographical region, suggesting the occurrence of a parallel evolution process.ConclusionsOur results revealed genomic signatures of local adaptation and their influence on multiple, co-occurring species. These results can be potentially applied for future studies on river management and climatic stressor impacts.

A biometric study of Chattian–Early Aquitanian taxa from shallow marine transgressive carbonate deposits in the Oligo-Miocene sedimentary basin of Kirkuk, Iraq, provides new insight into their taxonomy, stratigraphy, and palaeobiogeography. Their evolution is based on a distinct change in general nepiont morphology, which agrees with the principle of nepionic acceleration. Each Miogypsinoides group is represented by more than one lineage. We demonstrate for the first time the parallel evolution of Miogypsina and Miogypsinoides in the late Chattian of north-eastern Iraq. We assign specimens into two lineage groups: Miogypsinoides formosensis of the Late Chattian, with smaller embryon and longer post-embryonic spirals, which evolved into Miogypsinoides bantamensis of the Early Aquitanian; and Miogypsinoides sivasensis, with shorter spirals and larger embryon, originally found in late Chattian to Early Aquitanian deposits. This group evolved into large embryon and longer post-embryonic spiral specimens of the upper Azkand Formation, assigned to Miogypsinoides dehaartii and associated with Miogypsina gunteri-basraensis and M. gunteri due to their peculiar morphological features. Miogypsina specimens are related to Miogypsina basraensis, which have much smaller embryon dimensions. This part of the sequence corresponds to Ms. formosensis and is overlain by a Miogypsina ex. interc. gunteri-basraensis succession, a composite species that evolved to Miogypsina gunteri, the most common Miogypsinids taxon in the carbonate upper Azkand Formation, thereby acting as a reference for the evolution of this taxon and its transition to M. ex. interc. tani-gunteri. Miogypsinoides evolution in the Iraqi sedimentary basin is similar to Western Tethys evolution yet differs from Indo-Pacific evolution.

Parallel adaptive divergence of migratory and reproductive behavior can occur in multiple populations when similar selection is acting on these traits. Timing of migration, sexual maturity, and reproduction can have major impacts on the dynamics and viability of a population. Life-history variation in steelhead, Oncorhynchus mykiss, including variation in anadromous run timing, reproductive maturity, and spawn timing, represents an important aspect of their biology and adaptation to local habitats. Here we present a genetic analysis of naturally spawning steelhead to evaluate the genetic relationships and ancestry of summer- and winter-run reproductive ecotypes from multiple river basins in Oregon and Northern California. We infer the phylogeographic relationships among populations of both summer- and winter-run steelhead ecotypes using 12 microsatellite loci and 90 single nucleotide polymorphisms. Phylogenetic trees and analysis of molecular genetic variance revealed that pairs of phenotypically and genetically distinct reproductive ecotypes within rivers were each other’s closest relatives. Isolation by distance was also observed, confirming that genetic relatedness was strongly associated with geographic distance, and indicating limited gene flow among river basins. These patterns support the hypothesis that the summer-run steelhead ecotype has repeatedly evolved through parallel evolution in multiple river basins. Our results, together with further investigations of the underlying molecular basis for the divergence of winter- and summer-run steelhead life-history traits, inform management efforts for these ecotypes and improve our understanding of the role of adaptive genetic variation in conservation.

We report a fossil specimen referable to Sinomastodontinae gen. et sp. indet. from the Neogene strata at Yanghecun locality, Xihe County, Gansu Province, China. The specimen is characterized by a brevirostrine mandible, complete pretrite trefoils, and relatively simple posttrite half lophids, showing typical features of Sinomastodon. It differs from the other known species of Sinomastodon by the following features: relatively short and wide m3 due to fewer lophid numbers, less inflated pretrite accessory central conules, poorly developed secondary trefoils and cementum, and relatively strong cingulid. All of these features indicate a bias towards pleisiomorphies of Sinomastodon, implying that this specimen is more ancestral than any known species of Sinomastodon. The symphysis of the new specimen is relatively long, which differs from the typical brevirostrine Sinomastodon, and thus we consider it a gen. et sp. indet. in the Subfamily Sinomastodontinae. In addition, the horizon in which the present specimen was found probably represents the Upper Miocene because it is lower than Pliocene strata yielding Hipparion (Proboscidipparon) pater. Generally, Sinomastodon is considered to have migrated from North America at about the time of the Miocene/Pliocene boundary, and to have been derived from a certain clade of American gomphotheres. However, the discovery of the Yanghecun specimen verifies that Sinomastodon lived in East Asia during the Late Miocene, and probably derived from Old World gomphotheres (e.g., G. wimani). The similarity between the members of the Subfamilies Sinomastodontinae and those of Cuvieroniinae is suggested to have been the result of parallel evolution.

Body size during larval development is one of the most important attributes of aquatic animals. The optimal size for changing form or habitat may vary according to ecological traits of species, while phylogenetic constraints also play a significant role. The major goal of this study is to reveal the patterns in the settlement size of planktotrophic larvae in an archaic gastropod superorder Neritimorpha. We take advantage of the fact that size at various ontogenetic stages of neritimorphs can be rigorously estimated by measuring features of the adult opercula. This unique feature of neritimorphs has allowed us to generate the largest data set so far on larval settlement sizes within a group of marine invertebrates that recruit into very different post-metamorphic habitats. Eighty-eight species that represent most extant genera from rocky shores, seagrass beds, mangroves, estuaries, streams, submarine caves, deep-sea vents or seeps showed negligible intraspecific variation and considerable interspecific differences in settlement size, particularly between genera or families. Settlement size is determined primarily by phylogenetic constraints, while parallel evolution toward smaller sizes was shown to occur exclusively in four independent clades (two living and two extinct) of amphidromous snails with a marine larval period followed by a limnic adult phase. The smaller settlement size may possibly reduce the risk of being wafted away from the estuaries of their natal streams through less time achieving metamorphic competence, while ability to make occasional long-distance trips is retained by the presence of a sufficiently long delay period. This delay period also seems to obscure the possible correlation between settlement size and geographic distribution range of neritimorph species, both fully marine and amphidromous.

Pollen grains from 20 spruce species were examined using scanning electron microscopy, to study the phylogeny of pollen morphology in spruce. Morphological characteristics of the pollen were examined among different species based on statistical data and photographic observation. The mean pollen size of 20 spruce species ranged from 84.327 to 118.793.18 μm. Based on morphological photography, two zygomorphic bladders were distributed on the underside of the corpus and were found at the edge of the cap near the corpus surface. The bladder’s surface texture was smooth and had no distinct variations among species. Germinal furrows formed clear striates between the two bladders. According to clustering analysis, 20 spruce species were classified into three sections, namely, Castict, Schrenkiana and Picea, and the Picea section was classified into two subsections, Jezonensis and Picea. Corpus veins experienced notable differentiation among sections, and their evolutionary trend progressed through sections Castict, Schrenkiana and Picea. Within subsection Picea, parallel evolution occurred between the two subsections.

The degree of concordance between patterns of divergence in genetic and morphological characters provides insight into the process of evolutionary diversification. We analyzed species-wide morphological variation in a broadly distributed species of small mammal, the bushy-tailed woodrat (Neotoma cinerea), for comparison against a recently developed mitochondrial phylogeny. We focused our analyses on patterns of qualitative and quantitative craniodental morphological variation throughout the distribution of this taxon. We found strong concordance between the morphology of one prominent craniodental feature (sphenopalatine vacuity) and the major mitochondrial lineages, but only minimal differentiation in overall morphometric variation between these clades. Further, in contrast to the largely east–west subdivision of mitochondrial and sphenopalatine vacuity variation, cluster analyses of morphometric variation revealed a north–south morphological subdivision irrespective of mitochondrial clade. Our combined character sets are best explained by a deep history of evolutionary divergence within this taxon accompanied or followed by broad-scale convergent or parallel evolution.

We present a molecular phylogenetic study of the lichen genus Sticta focusing on Colombia, using the ITS fungal barcoding gene for a total of 370 ingroup OTUs, with 322 newly generated sequences. The topology resulting from a maximum likelihood approach does not support current species concepts in Sticta, which use a morphological concept, but in contrast shows that similar morphodemes evolved multiple times independently within the genus. As a consequence, currently applied names such as S. fuliginosa and S. weigelii comprise numerous (up to more than 20) unrelated species-level lineages, which can be distinguished also phenotypically using previously unrecognized characters such as lobe configuration, lobe surface structure, tomentum type, and anatomy of the basal membrane of the cyphellae. We conclude that the genus Sticta contains about four to five times the number of species currently recognized. In Colombia alone, approximately 150 species of Sticta are present.

The adoption of agriculture was one of the most momentous transformations in human history. It set into motion forces that changed our species from living in small numbers within the confines of local ecosystems into one that is now changing the biophysical characteristics of the entire planet. We argue that this transformation can be understood as a leap to ultrasociality—a type of social organization rare in nature but wildly successful when it occurs. Several species of ants and termites made a similar leap in social organization and the broad characteristics of their societies are remarkably similar to post hunter-gatherer human societies. Ultrasocial species dominate the ecosystems they occupy in terms of sheer numbers and the scale of ecosystem exploitation. We argue that the drivers for the ultrasocial transition to agriculture are economic. These societies operate as superorganisms exhibiting an unparalleled degree of division of labor and an economic organization centered around surplus production. We suggest that the origin of human and insect agriculture is an example of parallel evolution driven by similar forces of multi-level selection. Only with the evolution of expansionist agriculturalist societies did humans join ants and termites in the social domination of Earth. Viewing agriculture as an ultrasocial transition offers insights not only about the origins of agriculture and its consequences, but also about the forces shaping the current demographic transition and the modern global socio-economic system.

Background The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. Results We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms. Conclusions Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0299-5) contains supplementary material, which is available to authorized users.

Many ecologically important traits exhibit latitudinal variation. Body size clines have been described repeatedly in insects across multiple continents, suggesting that similar selective forces are shaping these geographical gradients. It is unknown whether these parallel clinal patterns are controlled by the same or different genetic mechanism(s). We present here, quantitative trait loci (QTL) analysis of wing size variation in Drosophila simulans. Our results show that much of the wing size variation is controlled by a QTL on Chr 3L with relatively minor contribution from other chromosome arms. Comparative analysis of the genomic positions of the QTL indicates that the major QTL on Chr 3 are distinct in D. simulans and D. melanogaster, whereas the QTL on Chr 2R might overlap between species. Our results suggest that parallel evolution of wing size clines could be driven by non-identical genetic mechanisms but in both cases involve a major QTL as well as smaller effects of other genomic regions.

The shift from outcrossing to selfing is one of the most common evolutionary trends in plants, and there is intense interest in why this is so. The genus Leavenworthia has been the focus of research on this question for half of a century, with particular attention paid to the evolution of self-compatibility from self-incompatibility. In this review, we discuss the last 50 years of research concerning this evolutionary transition in Leavenworthia. Selfing appears to have evolved independently at minimum three times within this genus of eight species. Work on the ecological basis of mating system evolution in Leavenworthia has clarified that selection among individuals is likely a major force behind the recurrent evolution of selfing. Although inadequate pollination is appreciated as a factor favoring selfing, definitive ecological mechanisms that act to favor selfing are still not known and future work on the efficacy of pollinating bees and the effects of climate change is needed. Recent research has likely identified the SRK ortholog at the S-locus controlling self-incompatibility in Leavenworthia alabamica. Analyses of S-locus variation have revealed substantial S-allele diversity in outcrossing populations, with the recurrent fixation of mutations at the S-locus permitting the parallel evolution of selfing in this species. Although we appreciate some of the factors that may explain the evolution of selfing in this group, there is less known about the mechanisms underlying the widespread maintenance of outcrossing at the population and species levels. Studies in Leavenworthia have revealed that genetic diversity is lost over the long-term within selfing populations and leads to elevated population subdivision, but work is needed to determine why these genetic consequences of selfing cause lineages to become evolutionary dead ends.

A number of authors have pointed to “convergent evolution” as evidence for the central role of natural selection in shaping predictable trajectories of macroevolution. However, there are numerous conceptual and empirical difficulties that arise in broadly appealing to the frequency of homoplasy as evidence for a non-contingently constrained adaptational design space. Most important is the need to distinguish between convergent (externally constrained) and parallel (internally constrained) evolution, and to consider how the respective frequencies of these significantly different sources of homoplasy affect a strong adaptationist view of life. In this paper, I critically evaluate Simon Conway Morris’s use of the homoplasy literature to support his argument for a non-contingent, counterfactually stable account of macroevolutionary pattern. In so doing, I offer a conception of parallelism which avoids the charge that it differs from convergence merely in degree and not in kind. I argue that although organisms sharing a homoplastic trait will also share varying degrees of homology, it is the underlying developmental homology with respect to the generators directly causally responsible for the homoplastic event that defines parallel evolution and non-arbitrarily distinguishes it from convergence. The notion of “screening-off” is used to distinguish the proximal generators of a homoplastic trait from its more distal genetic causes (such as a master control gene).

The acquisition of physiological strategies to tolerate novel thermal conditions allows organisms to exploit new environments. As a result, thermal tolerance is a key determinant of the global distribution of biodiversity, yet the constraints on its evolution are not well understood. Here we investigate parallel evolution of cold tolerance in New Zealand stick insects, an endemic radiation containing three montane-occurring species. Using a phylogeny constructed from 274 orthologous genes, we show that stick insects have independently colonized montane environments at least twice. We compare supercooling point and survival of internal ice formation among ten species from eight genera, and identify both freeze tolerance and freeze avoidance in separate montane lineages. Freeze tolerance is also verified in both lowland and montane populations of a single, geographically widespread, species. Transcriptome sequencing following cold shock identifies a set of structural cuticular genes that are both differentially regulated and under positive sequence selection in each species. However, while cuticular proteins in general are associated with cold shock across the phylogeny, the specific genes at play differ among species. Thus, while processes related to cuticular structure are consistently associated with adaptation for cold, this may not be the consequence of shared ancestral genetic constraints., Scientific Reports, 5, ISSN:2045-2322

Background PsbO, the manganese-stabilising protein, is an indispensable extrinsic subunit of photosystem II. It plays a crucial role in the stabilisation of the water-splitting Mn4CaO5 cluster, which catalyses the oxidation of water to molecular oxygen by using light energy. PsbO was also demonstrated to have a weak GTPase activity that could be involved in regulation of D1 protein turnover. Our analysis of psbO sequences showed that many angiosperm species express two psbO paralogs, but the pairs of isoforms in one species were not orthologous to pairs of isoforms in distant species. Results Phylogenetic analysis of 91 psbO sequences from 49 land plant species revealed that psbO duplication occurred many times independently, generally at the roots of modern angiosperm families. In spite of this, the level of isoform divergence was similar in different species. Moreover, mapping of the differences on the protein tertiary structure showed that the isoforms in individual species differ from each other on similar positions, mostly on the luminally exposed end of the β-barrel structure. Comparison of these differences with the location of differences between PsbOs from diverse angiosperm families indicated various selection pressures in PsbO evolution and potential interaction surfaces on the PsbO structure. Conclusions The analyses suggest that similar subfunctionalisation of PsbO isoforms occurred parallelly in various lineages. We speculate that the presence of two PsbO isoforms helps the plants to finely adjust the photosynthetic apparatus in response to variable conditions. This might be mediated by diverse GTPase activity, since the isoform differences predominate near the predicted GTP-binding site. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0523-4) contains supplementary material, which is available to authorized users.

The origin of brain mechanisms that support human language-whether these originated de novo in humans or evolved from a neural substrate that existed in a common ancestor-remains a controversial issue. Although the answer is not provided by the fossil record, it is possible to make inferences by studying living species of nonhuman primates. Here we identified neural systems associated with perceiving species-specific vocalizations in rhesus macaques using H(2)(15)O positron emission tomography (PET). These vocalizations evoke distinct patterns of brain activity in homologs of the human perisylvian language areas. Rather than resulting from differences in elementary acoustic properties, this activity seems to reflect higher order auditory processing. Although parallel evolution within independent primate species is feasible, this finding suggests the possibility that the last common ancestor of macaques and humans, which lived 25-30 million years ago, possessed key neural mechanisms that were plausible candidates for exaptation during the evolution of language.

Iceland is unique in terms of geologically young freshwater systems and rapid adaptations of fresh water fishes to diverse habitats, e.g. lava with ground water flow. Iceland has six species of freshwater fishes, including Arctic charr, Salvelinus alpinus. Previous research has shown great diversity within this species. Four different morphs of Arctic charr are found in one lake, Thingvallavatn, including a small benthivorous charr. Similar populations of small benthic charr are known from several other Icelandic freshwater locations, including Nautavakir in Grimsnes. Our comparison of the small benthic charr morphs in Thingvallavatn and in Grimsnes showed that they are similar in morphology but distinguishable in several characteristics. Small benthic charr in Grimsnes and Thingvallavatn demonstrate similar adaptations and are an example of parallel evolution. However, subtle morphological differences between them indicate further specialized adaptations at each location.

Cochlearia macrorrhiza is one of the most highly endangered species in Central Europe and less than five individuals survived at its natural stand in a lowland area between the Eastern Alps and the Carpathians. Amplified fragment length polymorphisms (AFLPs) confirmed the status of C. macrorrhiza as a distinct taxon. Lowland C. macrorrhiza does not bridge the distribution of montainous and alpine Cochlearia species from the Eastern Alps and the Carpathians genetically, and C. macrorrhiza represents a separate lineage which evolved from diploid Cochlearia as C. excelsa in East Austrian high alpine regions did. Another species considered in this study, the Romanian C. borzaeana is more closely related to C. tatrae from the High Tatra mountains than to C. pyrenaica from Slovakia or Austria and the AFLP results suggest a single origin of alpine 2n=42 taxa. Genetic differentiation within and between populations is highly structured geographically, and the AFLP data favour a former widespread distribution of C. pyrenaica in mountainous regions and a parallel evolution of high alpine taxa in the Eastern Alps and the Carpathians, respectively.

Internal transcribed spacer (ITS) region sequences of nuclear ribosomal DNA (nrDNA) were used in the phylogenetic reconstruction of Pedicularis, a genus with strong adaptive radiation. Forty-two species representing 12 greges of the genus were all, except P. resupinata, sampled from the Hengduan Mountain region, China. A high level of ITS sequence variation was found among the species distributed in such a small geographical area, which had been rarely reported in other groups. The great ITS divergence in Pedicularis could be explained by a relatively ancient origin and diversification of the genus followed by migration of different floristic components into the Hengduan Mountains, or accelerated rates of molecular evolution in parasitic lineages of Orobanchaceae. In the present ITS phylogeny, almost all the main clades are not consistent with the high hierarchical taxa within Pedicularis, which implies that significant parallel evolution occurred in floral morphology of the genus, and that undue attention has been paid to corolla characters in the intragenus classifications.

Sympatrically occurring steelhead and rainbowtrout (n = 100) were collected from fiveriver systems in British Columbia, Canada, and1300 bp from the mitochondrial genome and 270bp of the nuclear growth hormone 2 gene weresequenced to determine if the two forms aregenetically differentiated. ND3 and D-loopsequence differences produced nine haplotypeswhile two length variants of the GH2 intron Dwere present. In one river system, steelheadand rainbow were genetically divergent based onmtDNA data but overall, no consistent geneticdifference between life history types wasfound. Rather, genetic differences wereassociated with geography, suggesting thatsteelhead and rainbow trout are polyphyleticand the result of parallel evolution ratherthan members of two distinct lineages.

Parallel evolution of similar traits in independent populations that inhabit ecologically similar environments strongly implicates natural selection as the cause of evolution1. Parallel speciation is a special form of parallel evolution where traits that determine reproductive isolation evolve repeatedly, in closely related populations, as by-products of adaptation to ecological conditions1,2. The outcome of such parallel evolution is that ecologically divergent pairs of populations exhibit greater levels of reproductive isolation than ecologically similar pairs of populations of a similar or younger age2,3,4. The parallel evolution of reproductive isolation provides strong evidence for natural selection in the process of speciation1, but only one conclusive example from nature is known2. Populations of the walking-stick insect Timema cristinae that use different host-plant species have diverged in body size and shape, host preference, behaviour and the relative frequency of two highly cryptic colour-pattern morphs5,6. Here we report that divergent selection for host adaptation, and not genetic drift, has promoted the parallel evolution of sexual isolation in this species. Our findings represent a clear demonstration that host-plant adaptation can play a crucial and repeatable role in the early stages of speciation.

Our analysis indicates that much of the lower part of the tetrapodomorph stem lineage consisted of ‘osteolepiform’ fishes. The character attributes of this part of the stem lineage can be reconstructed with precision. Parallel evolution towards the morphology of a large predator, with reduced median fins and elaborate anterior dentition, occurred at about the same time in rhizodonts, tristichopterids, and elpistostegids+tetrapods (Fig. 4). The evolution of two latter clades, having extra synapomorphies, also paralleled each other more closely. The Tetrapoda thus arose out of one of several similar evolutionary ‘experiments’ with a large aquatic predator role. Closer study of these parallel radiations should cast much new light on the ecological background to the origin of tetrapods.

The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup. Trees estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated or summing up log-likelihood scores for each gene). Although the overall evidence strongly suggests ((primates, ferungulates), rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates). To clarify whether this contradiction is due to (1) a stochastic (sampling) error; (2) minor model-based errors (e.g., ignoring site rate variability), or (3) convergent and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + monotremes) were sequenced. The phylogenetic analyses were extensive and aimed to eliminate the following artifacts as possible causes of the aberrant result: base composition biases, unequal site substitution rates, or the cumulative effects of both. Neither more sophisticated evolutionary analyses nor the addition of species changed the previous conclusion. That is, the statistical support for grouping rodents and primates to the exclusion of all other taxa fluctuates upward or downward in quite a tight range centered near 95% confidence. These results and a site-by-site examination of the sequences clearly suggest that convergent or parallel evolution has occurred in ND1 between primates and rodents and/or between ferungulates and the outgroup. While the primate/rodent grouping is strange, ND1 also throws some interesting light on the relationships of some eutherian orders, marsupials, and montremes. In these parts of the tree, ND1 shows no apparent tendency for unexplained convergences.

The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution.

Molecular phylogenetic analyses using mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequences representing all 15 species and the majority of subspecies or races of the Ohomopterus ground beetles from all over the Japanese archipelago have uncovered a remarkable evolutionary history. Clustering of the species in the molecular phylogenetic tree is linked to their geographic distribution and does not correlate with morphological characters. Taxonomically the "same" species or the members belonging to the same species-group fall out in more than two different places on the ND5 tree. Evidence has been presented against a possible participation of ancestral polymorphism and random lineage sorting or of hybrid individuals for the observed distribution of mitochondrial DNA haplotypes. The most plausible explanation of our results is that parallel evolution took place in different lineages. Most notably, O. dehaanii, O. yaconinus, and O. japonicus in a lineage reveal almost identical morphology with those of the "same" species (or subspecies) but belonging to the phylogenetically remote lineages.

Background Cetaceans (whales, dolphins and porpoises) are a group of adapted marine mammals with an enigmatic history of transition from terrestrial to full aquatic habitat and rapid radiation in waters around the world. Throughout this evolution, the pathogen stress-response proteins must have faced challenges from the dramatic change of environmental pathogens in the completely different ecological niches cetaceans occupied. For this reason, cetaceans could be one of the most ideal candidate taxa for studying evolutionary process and associated driving mechanism of vertebrate innate immune systems such as Toll-like receptors (TLRs), which are located at the direct interface between the host and the microbial environment, act at the first line in recognizing specific conserved components of microorganisms, and translate them rapidly into a defense reaction. Results We used TLR4 as an example to test whether this traditionally regarded pattern recognition receptor molecule was driven by positive selection across cetacean evolutionary history. Overall, the lineage-specific selection test showed that the dN/dS (ω) values along most (30 out of 33) examined cetartiodactylan lineages were less than 1, suggesting a common effect of functional constraint. However, some specific codons made radical changes, fell adjacent to the residues interacting with lipopolysaccharides (LPS), and showed parallel evolution between independent lineages, suggesting that TLR4 was under positive selection. Especially, strong signatures of adaptive evolution on TLR4 were identified in two periods, one corresponding to the early evolutionary transition of the terrestrial ancestors of cetaceans from land to semi-aquatic (represented by the branch leading to whale + hippo) and from semi-aquatic to full aquatic (represented by the ancestral branch leading to cetaceans) habitat, and the other to the rapid diversification and radiation of oceanic dolphins. Conclusions This is the first study thus far to characterize the TLR gene in cetaceans. Our data present evidences that cetacean TLR4 has undergone adaptive evolution against the background of purifying selection in response to the secondary aquatic adaptation and rapid diversification in the sea. It is suggested that microbial pathogens in different environments are important factors that promote adaptive changes at cetacean TLR4 and new functions of some amino acid sites specialized for recognizing pathogens in dramatically contrasted environments to enhance the fitness for the adaptation and survival of cetaceans.

Aspects of the regulatory interactions among genes are probably as old as most genes are themselves. Correspondingly, similar predispositions to changes in such interactions must have existed for long evolutionary periods. Features of the structure and the evolution of the system of gene regulation furnish the background necessary for a molecular understanding of parallel evolution. Patently “unrelated” organs, such as the fat body of a fly and the liver of a mammal, can exhibit fractional homology, a fraction expected to become subject to quantitation. This also seems to hold for different organs in the same organism, such as wings and legs of a fly. In informational macromolecules, on the other hand, homology is indeed all or none. In the quite different case of organs, analogy is expected usually to represent attenuated homology. Many instances of putative convergence are likely to turn out to be predominantly parallel evolution, presumably including the case of the vertebrate and cephalopod eyes. Homology in morphological features reflects a similarity in networks of active genes. Similar nexuses of active genes can be established in cells of different embryological origins. Thus, parallel development can be considered a counter part to parallel evolution. Specific macromolecular interactions leading to the regulation of the c -fos gene are given as an example of a “controller node” defined as a regulatory unit. Quantitative changes in gene control are distinguished from relational changes, and frequent parallelism in quantitative changes is noted in Drosophila enzymes. Evolutionary reversions in quantitative gene expression are also expected. The evolution of relational patterns is attributed to several distinct mechanisms, notably the shuffling of protein domains. The growth of such patterns may in part be brought about by a particular process of compensation for “controller gene diseases,” a process that would spontaneously tend to lead to increased regulatory and organismal complexity. Despite the inferred increase in gene interaction complexity, whose course over evolutionary time is unknown, the number of homology groups for the functional and structural protein units designated as domains has probably remained rather constant, even as, in some of its branches, evolution moved toward “higher” organisms. In connection with this process, the question is raised of parallel evolution within the purview of activating and repressing master switches and in regard to the number of levels into which the hierarchies of genic master switches will eventually be resolved.

Populations of the land snail Albinaria hippolyti from Crete were sampled across two hybrid zones separating A. h. aphrodite from A. h. holtzi and A. h. harmonia and studied by means of starch gel electrophoresis. At both sites, frequencies of an otherwise rare allele of sAat reached 0.70 and 0.18, respectively, in the centres of the hybrid zones. It is argued that the allele is deleterious and that it is maintained in the zones by a balance between elevated mutation rates (at least 1.4 × 10−4 and 3.2 × 10−4, respectively) and selection (at least 2 × 10−4 and 1.8 × 10−3, respectively). The observed parallellism may be the result of constraints on the numbers of metabolically active sAat variants possible.

The classical concept that all complex life evolved from a simple bacterium-like life form has been questioned by comparative genomics and proteomics. Several discoveries, including the occurrence of entirely new genes in unexpected life forms without any precursors, and the random mosaic distribution of genes across organisms in higher taxa undermine the principal assertions of this theory. We present a new model of the pre-biotic parallel evolution of eukaryotic genomes starting with the structurally complex split genes, which are far more probable of supporting biological information and of occurring in random DNA sequences than contiguous genes. By comparing the mosaic patterns of simulated genomes and extant genomes, we show that genomes arising from simulated assembly of random split genes form the same gene distribution patterns observed in extant eukaryotes. This parallel genome origin model eliminates the post-genomic and classical conundrums faced by the linear branching evolution model.

Research on human evolution and sexual dimorphism motivates an interesting test problem. In studying hominid phylogeny it is of interest to test whether parallel evolution plays a role. With regard to sexual dimorphism it is of interest to know whether the directions of sexual dimorphism in the populations being compared are the same. We show that testing these two problems gives rise to the same type of hypothesis testing, viz. the problem of testing the hypothesis that the means of independent, normally distributed random vectors with unit covariance matrices are situated on a straight line through the origin. A test is proposed and applied to study the sexual dimorphism of 20 recent skull populations. In this example the hypothesis of equal directions of sexual dimorphism is rejected. The classical theory of constructing multiple discriminant functions (canonical variates) is adapted to the problem of comparing sexual dimorphisms.

The genus Veronica s. lat. comprises about 450 species (including about 180 species from the southern hemisphere Hebe-complex), many of which grow in the Mediterranean area. Their extreme variability in morphology, life form and habitats has led to many suggestions regarding evolution and biogeography. Difficulties arise from parallel syndromes, widespread among alpine spe- cies and lowland perennials, and particularly among annual species of the genus. We have used sequences of the plastid trnL-F region and nuclear ribosomal ITS sequences to differentiate between different clades of Veronica and reveal cases of parallel evolution. Based on this data, cases of parallel evolution have been found in biogeograph- ical patterns among the alpine species of Veroni- ceae, in which species from European mountains have affinities to those in the Central Asian/ Himalayan region whereas alpine species from Turkey are probably more recently derived from lowland southwestern Asian taxa. Different sub- species of Veronica bombycina gained their charac- teristic morphology independently and parallel in adaptation to their alpine environment. Pinnatifid leaves have been gained parallel in perennial grassland species of Veronica. Finally, parallel evolutionary trends in many characters, not only morphological but also molecular characters, are common among annual species of Veronica.

Whole-genome sequences from a marine fish that has adjusted to life in fresh water give hints about general genetic mechanisms that drive the evolution of adaptations to new environmental niches. See Article p.55 Threespine sticklebacks have become a powerful model for studying the molecular basis of adaptive evolution. This paper presents a high-quality reference genome sequence, along with genomes of 20 further individuals from a global set of marine and freshwater populations. Genomic analysis reveals that reuse of globally shared standing genetic variation plays an important part in repeated evolution of distinct stickleback populations, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. The data are consistent with an important role for regulatory changes during parallel evolution of marine and freshwater sticklebacks.

Background Understanding the genetic basis of adaptive evolution is one of the major goals in evolutionary biology. Recently, it has been revealed that gene copy number variations (GCNVs) constitute significant proportions of genomic diversities within natural populations. However, it has been unclear whether GCNVs are under positive selection and contribute to adaptive evolution. Parallel evolution refers to adaptive evolution of the same trait in related but independent lineages, and three-spined stickleback (Gasterosteus aculeatus) is a well-known model organism. Through identification of genetic variations under parallel selection, i.e., variations shared among related but independent lineages, evidence of positive selection is obtained. In this study, we investigated whole-genome resequencing data from the marine and freshwater groups of three-spined sticklebacks from diverse areas along the Pacific and Atlantic Ocean coastlines, and searched for GCNVs under parallel selection. Results We identified 24 GCNVs that showed significant differences in the numbers of mapped reads between the two groups, and this number was significantly larger than that expected by chance. The derived group, i.e., freshwater group, was typically characterized by larger gene-copy numbers, which implied that gene duplications or multiplications helped with adaptation to the freshwater environment. Some of the identified GCNVs were those of multigenic family genes, which is consistent with the theory that fatal effects due to copy-number changes of multigenic family genes tend to be less than those of single-copy genes. Conclusion The identification of GCNVs that were likely under parallel selection suggests that contribution of GCNVs should be considered in studies on adaptive evolution. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-735) contains supplementary material, which is available to authorized users.

How predictable is evolution at the molecular level? An example of repeated evolution in rice and Brassica illustrates how selection might preferentially target certain genes and mutations.

A newly described 334-million-year-old fossil of an amphibian will give students of vertebrate evolution much to think about, for it has characters that were previously ascribed to three different types of early four-legged creature. Together with other examples, the fossil shows that during evolution new features seem to have been 'cut and pasted' on different groups at different times. Understanding such parallel evolution will require understanding the molecular and developmental basis by which such features arise.