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Ship pipe route design (SPRD) aims to generate pipe layouts while considering various objectives and constraints in a confined 3D space, leading to extremely high complexity. To solve the problem of SPRD, traditional methods often adopt weighted summation of sub-objectives, introduce penalty functions to convert it to a single-objective optimization problem. However, these methods tend to yield a single optimal pipe route design pattern, and some existing multi-objective pipe routing algorithms do not have high search performance or sufficient treatment of constraints. Based on the grid-space decomposition model, this paper establishes a multi-objective pipe routing optimization model with several sub-objectives including path length, bends number, path energy, number of air-pockets, and number of violated bending distance, which also considers pipe routing for different diameters and interface direction requirements. A ship pipe route design framework based on the NSGA-III (Non-dominated Sorting Genetic algorithm III) is proposed, and its embedded pathfinding algorithm can explore pipe route using heuristic information and failure retry strategy, which greatly reduces the algorithm complexity compared to the classical algorithms such as A* and LEE and also facilitates parallel implementation. By employing OpenMP technology to achieve parallel evolution of multiple populations, more Pareto optimal solutions can be obtained in approximately the same timeframe as single population evolution. Finally, through comparative experiments using simulated cases, the feasibility and advancement of the proposed method are verified. • The NSGA-III for SPRD excels in multi-objective optimization, and the embedded pathfinding algorithm runs faster. • The parallel evolutionary framework NSGA-III_OMP exploits processor capabilities to find more Pareto solutions. • The proposed algorithm considers more objectives and constraints, making it more practical and user-friendly. [ABSTRACT FROM AUTHOR]

A new genus and species, Latidorsum carinbifarium Wang, Tang & Yao gen. et sp. nov., is assigned to Phatnomatini (Tinginae), which is described from the mid-Cretaceous Burmese amber. A parsimonious analysis based on 50 morphological characters with 26 terminals clarifies the phylogenetic status of the new fossils and examined relationships among the presently analysed genera of the family Tingidae. The resulting cladogram supporting Tingidae are reconfirmed as monophyletic and divided into four main clades, with relationships as follows: (Vianaidinae + ((Burmacader multivenosus + Burmavianaida anomalocapitata) + (Sinaldocader rasnitsyni + (Gyaclavator kohlsi + Tinginae + Cantacaderinae)))). Anterior length of bucculae distinctly projecting in front of head, sometimes in contact is not a synapomorphic character for Cantacaderinae, which evolves in parallel in Tinginae and Cantacaderinae.

Abstract Analysis of spatial and temporal genetic heterogeneity in human cancers has revealed that somatic cancer evolution in most cancers is not a simple linear process composed of a few sequential steps of mutation acquisitions and clonal expansions. Parallel evolution has been observed in many early human cancers resulting in genetic heterogeneity as well as multilineage progression. Moreover, aneuploidy as well as structural chromosomal aberrations seems to be acquired in a non-linear, punctuated mode where most aberrations occur at early stages of somatic cancer evolution. At later stages, the cancer genomes seem to get stabilized and acquire only few additional rearrangements. While parallel evolution suggests positive selection of driver mutations at early stages of somatic cancer evolution, stabilization of structural aberrations at later stages suggests that negative selection takes effect when cancer cells progressively lose their tolerance towards additional mutation acquisition. Mixing of genetically heterogeneous subclones in cancer samples reduces sensitivity of mutation detection. Moreover, driver mutations present only in a fraction of cancer cells are more likely to be mistaken for passenger mutations. Therefore, genetic heterogeneity may be considered a limitation negatively affecting detection sensitivity of driver mutations. On the other hand, identification of subclones and subclone lineages in human cancers may lead to a more profound understanding of the selective forces which shape somatic cancer evolution in human cancers. Identification of parallel evolution by analyzing spatial heterogeneity may hint to driver mutations which might represent additional therapeutic targets besides driver mutations present in a monoclonal state. Likewise, stabilization of cancer genomes which can be identified by analyzing temporal genetic heterogeneity might hint to genes and pathways which have become essential for survival of cancer cell lineages at later stages of cancer evolution. These genes and pathways might also constitute patient specific therapeutic targets.

Amphisbaenians are one of the most derived fossorial groups among Squamata. Studies of their evolution were hampered by their specialized limbless morphology and unrecognized early fossil record. This study presents a detailed description of the postcranial anatomy of the oldest known stem-amphisbaenian Slavoia darevskii. The skeleton shows an incipient adaptation to the fossorial mode of life, expressed in the early stages of limb reduction and elongation of the trunk, typical aspects of modern worm lizards. The forelimbs show a hyperphalangy of the first digit. They were probably strengthened this way to support the head in burrowing. Such an anatomy of the most ancient amphisbaenians implies that the forelimbs were lost multiple times in the amphisbaenians to be retained only in the Bipedidae. The hindlimb reduction was initiated early (before the split into modern families) but may have been completed independently. Despite these changes, S. darevskii still had the plesiomorphic 26 presacral vertebrae but the neck region was shorter, as shown by the ribs morphology and position.

Understanding patterns of population diversity and structuring among marine populations is of great importance for evolutionary biology, and can also directly inform fisheries management and conservation. In this study, genotyping-by-sequencing was used to assess population genetic diversity and connectivity of Sebastiscus marmoratus. Based on 130 individuals sampled from 10 locations in the northwestern Pacific Ocean, we identified and genotyped 17 653 single-nucleotide polymorphisms. The patterns of genetic diversity and population differentiation suggested that the Okinawa Trough might be the ancestral centre of S. marmoratus after the Last Glacial Maximum. A shallow genetic structure was observed among sampled populations based on the implemented structuring approaches. Surprisingly, we detected genetic homogeneity in two population pairs (i.e. Xiamen–Niigata and Zhuhai–Iki Island), in which populations have large geographical and latitudinal intervals. Population structure and allele frequency distribution based on outlier loci also mirrored the observed genetic homogeneity in the above-mentioned population pairs. Integrated with biological, environmental and genomic data, our results provide possible genetic evidence for parallel evolution. Our study also provides new perspectives on the population structure of S. marmoratus, which could have important implications for sound management and conservation of this fishery species.

Regulation of gene expression is thought to play a major role in adaptation, but the relative importance of cis- and trans- regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater ecotype pairs and their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates gene expression divergence. Genes showing parallel marine-freshwater expression divergence are found near to adaptive genomic regions, show signatures of natural selection around their transcription start sites and are enriched for cis-regulatory control. For genes with parallel increased expression among freshwater fish, the quantitative degree of cis- and trans-regulation is also highly correlated across populations, suggesting a shared genetic basis. Compared to other forms of regulation, cis-regulation tends to show greater additivity and stability across different genetic and environmental contexts, making it a fertile substrate for the early stages of adaptive evolution.

Vertical gradients in microclimate, resource availability, and interspecific interactions are thought to underly stratification patterns in tropical insect communities. However, only a few studies have explored the adaptive significance of vertical space use during the early stages of reproductive isolation. We analysed flight-height variation across speciation events in Heliconius butterflies, representing parallel colonizations of high-altitude forest. We measured flight-height in wild H. erato venus and H. chestertonii, parapatric lowland and mountain specialists, respectively, and found that H. chestertonii consistently flies at a lower height. By comparing our data to previously published results for the ecologically equivalent H. e. cyrbia (lowland) and H. himera (high altitude), we found that the species flying closest to the ground are those that recently colonized high-altitude forests. We show that these repeated trends largely result from shared patterns of ecological selection producing parallel trait-shifts in H. himera and H. chestertonii. Although our results imply a signature of local adaptation, we did not find an association between resource distribution and flight-height in H. e. venus and H. chestertonii. We discuss how this pattern may be explained by variations in forest structure and microclimate. Overall, our findings underscore the importance of behavioural adjustments during early divergence mediated by altitude-shifts., (© The Author(s) 2023. Published by Oxford University Press on behalf of the European Society of Evolutionary Biology.)

Importance: What are the roles of determinism and contingency in evolution? The paleontologist and evolutionary biologist Stephen J. Gould raised this question in his famous thought experiment of "replaying life's tape." Settings where independent lineages have repeatedly adapted to similar ecological niches (i.e., parallel evolution) are well suited to address this question. Here, we quantified whether repeated ecological shifts across 53 mammalian and 50 avian host species are associated with parallel gut microbiota changes. Our results indicate that parallel shifts in host diet are associated with greater gut microbiota parallelism (i.e., more deterministic). While further research will be necessary to obtain a comprehensive picture of the circumstances under which deterministic gut microbiota changes might be expected, our study can be instrumental in motivating the use of more quantitative methods in microbiota research. This, in turn, can help us better understand microbiota dynamics during adaptive evolution of their hosts., Competing Interests: The authors declare no conflict of interest.

The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from the repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we use three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host–microbe interactions might play an important role in host adaptation and diversification. [ABSTRACT FROM AUTHOR]

A new nemacheilid loach, Lefua tokaiensis sp. nov., is described from the small mountain streams in the Tokai region, central Honshu, Japan. Lefua tokaiensis is distinguished from all other species of Lefua by the following combination of characters: eyes located dorsally on the head, presence of a narrow conspicuous longitudinal mark between the base of the outer rostral barbel and the eye, absence of a rhomboid or triangular dark blotches on the middle of the caudal fin base, absence of a black longitudinal stripe on both body sides in mature males, absence of dusky cross bars on the dorsal area of the body, absence of a dusky bar beside the dorsal fin base, typical presence of small dark spots on the dorsal and caudal fins, presence of the obscure dark band in skin of the caudal fin base, caudal fin slightly squared off at the apex, and modally four hypurals. [ABSTRACT FROM AUTHOR]

One of the most intriguing puzzles in biology is the degree to which evolution is repeatable. The repeatability of evolution, or parallel evolution, has been studied in a variety of model systems, but has rarely been investigated with clinically relevant viruses. To investigate parallel evolution of HIV-1, we passaged two replicate HIV-1 populations for almost 1 year in each of two human T-cell lines. For each of the four evolution lines, we determined the genetic composition of the viral population at nine time points by deep sequencing the entire genome. Mutations that were carried by the majority of the viral population accumulated continuously over 1 year in each evolution line. Many majority mutations appeared in more than one evolution line, that is, our experiments showed an extreme degree of parallel evolution. In one of the evolution lines, 62% of the majority mutations also occur in another line. The parallelism impairs our ability to reconstruct the evolutionary history by phylogenetic methods. We show that one can infer the correct phylogenetic topology by including minority mutations in our analysis. We also find that mutation diversity at the beginning of the experiment is predictive of the frequency of majority mutations at the end of the experiment. [ABSTRACT FROM AUTHOR]

The selection pressure exerted by herbicides has led to the repeated evolution of herbicide resistance in weeds. The evolution of herbicide resistance on contemporary timescales in turn provides an outstanding opportunity to investigate key questions about the genetics of adaptation, in particular the relative importance of adaptation from new mutations, standing genetic variation, or geographic spread of adaptive alleles through gene flow. Glyphosate-resistant Amaranthus tuberculatus poses one of the most significant threats to crop yields in the Midwestern United States, with both agricultural populations and herbicide resistance only recently emerging in Canada. To understand the evolutionary mechanisms driving the spread of resistance, we sequenced and assembled the A. tuberculatus genome and investigated the origins and population genomics of 163 resequenced glyphosate-resistant and susceptible individuals from Canada and the United States. In Canada, we discovered multiple modes of convergent evolution: in one locality, resistance appears to have evolved through introductions of preadapted US genotypes, while in another, there is evidence for the independent evolution of resistance on genomic backgrounds that are historically nonagricultural. Moreover, resistance on these local, nonagricultural backgrounds appears to have occurred predominantly through the partial sweep of a single haplotype. In contrast, resistant haplotypes arising from the Midwestern United States show multiple amplification haplotypes segregating both between and within populations. Therefore, while the remarkable species-wide diversity of A. tuberculatus has facilitated geographic parallel adaptation of glyphosate resistance, more recently established agricultural populations are limited to adaptation in a more mutation-limited framework. [ABSTRACT FROM AUTHOR]

When the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favoured over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricket Laupala. We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and whether the likelihood of QTL sharing is related to QTL effect size. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more frequently than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory. [ABSTRACT FROM AUTHOR]

Summary: A crucial step in the transition from outcrossing to self‐fertilization is the loss of genetic self‐incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self‐incompatibility locus (S‐locus). Theory predicts that S‐linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species.Here, we investigate the genetic basis of loss of SI in the self‐fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long‐read sequencing of complete S‐haplotypes, gene expression analyses and controlled crosses.We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S‐locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S‐linked small RNA that is predicted to cause dominance of self‐compatibility.Our results agree with predictions on the contribution of dominant S‐linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions. [ABSTRACT FROM AUTHOR]

Studies of parallel evolution are seldom able to disentangle the influence of cryptic environmental variation from that of evolutionary history; whereas the unique life history of pink salmon (Oncorhynchus gorbuscha) presents an opportunity to do so. All pink salmon mature at age two and die after breeding. Hence, pink salmon bred in even years are completely reproductively isolated from those bred in odd years, even if the two lineages bred in same location. We used time series (mean = 7 years, maximum = 74 years) of paired even‐ and odd‐year populations from 36 rivers spanning over 2000 km to explore parallelism in migration timing, a trait with a strong genetic basis. Migration timing was highly parallel, being determined almost entirely by local environmental differences among rivers. Interestingly, interannual changes in migration timing different somewhat between lineages. Overall, our findings indicate very strong determinism, with only a minor contribution of contingency. [ABSTRACT FROM AUTHOR]

Summary: Artificial selection has produced varieties of domesticated maize that thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and subtropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full‐length reference transcriptome for Tripsacum dactyloides generated using long‐read Iso‐Seq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation in other cold‐adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes that were targets of artificial selection during the adaptation of maize to temperate climates and those that were targets of natural selection in temperate‐adapted T. dactyloides. Genes related to growth, development, response to stimulus, signaling, and organelles were enriched in the set of genes identified as both targets of natural and artificial selection. Significance Statement: Corn was domesticated in Central America and is sensitive to cold temperatures, while its close relative, Eastern gamagrass, can survive the winter. We compared rates of protein sequence evolution across orthologous genes in seven grass species to identify genes involved in adapting gamagrass to life in the United States Corn Belt and found that the same genes were targets of artificial selection when new varieties of corn were developed to grow in temperate North America. [ABSTRACT FROM AUTHOR]

Gene expression changes contribute to complex trait variations in both individuals and populations. However, the evolution of gene expression underlying complex traits over macroevolutionary timescales remains poorly understood. Snake venoms are proteinaceous cocktails where the expression of each toxin can be quantified and mapped to a distinct genomic locus and traced for millions of years. Using a phylogenetic generalized linear mixed model, we analyzed expression data of toxin genes from 52 snake species spanning the 3 venomous snake families and estimated phylogenetic covariance, which acts as a measure of evolutionary constraint. We find that evolution of toxin combinations is not constrained. However, although all combinations are in principle possible, the actual dimensionality of phylomorphic space is low, with envenomation strategies focused around only four major toxin families: metalloproteases, three-finger toxins, serine proteases, and phospholipases A2. Although most extant snakes prioritize either a single or a combination of major toxin families, they are repeatedly recruited and lost. We find that over macroevolutionary timescales, the venom phenotypes were not shaped by phylogenetic constraints, which include important microevolutionary constraints such as epistasis and pleiotropy, but more likely by ecological filtering that permits a small number of optimal solutions. As a result, phenotypic optima were repeatedly attained by distantly related species. These results indicate that venoms evolve by selection on biochemistry of prey envenomation, which permit diversity through parallelism, and impose strong limits, since only a few of the theoretically possible strategies seem to work well and are observed in extant snakes. [ABSTRACT FROM AUTHOR]

Localadaptationtoclimateallowsplantstocopewithtemporallyandspatiallyheterogeneousenvironments,andparallelphenotypic clines provide a natural experiment to uncover the genomic architecture of adaptation. Though extensive effort has been made to investigate the genomic basis of local adaptation to climate across the latitudinal range of tree species, less is known for altitudinal clines. We used exome capture to genotype 451 Populus trichocarpa genotypes across altitudinal and latitudinal gradients spanning the natural species range, and phenotyped these trees for a variety of adaptive traits in two common gardens. We observed clinal variation in phenotypic traits across the two transects, which indicates climate-driven selection, and coupled gene-based genotype- phenotype and genotype-environment association scans to identify imprints of climatic adaptation on the genome. Although many ofthephenotype-andclimate-associatedgeneswereuniquetoonetransect,wefoundevidenceofparallelismbetweenlatitudeand altitude,aswellassignificantconvergencewhenwecomparedouroutliergeneswiththoseputativelyinvolvedinclimaticadaptation in two gymnosperm species. These results suggest that not only genomic constraint during adaptation to similar environmental gradients in poplar but also different environmental contexts, spatial scale, and perhaps redundant function among potentially adaptive genes and polymorphisms lead to divergent adaptive architectures. [ABSTRACT FROM AUTHOR]

The repeated evolutionary specialization of distantly related insects to cardenolide-containing host plants provides a stunning example of parallel adaptation. Hundreds of herbivorous insect species have independently evolved insensitivity to cardenolides, which are potent inhibitors of the alpha-subunit of Na+,K+-ATPase (ATPa). Previous studies investigating ATPa-mediated cardenolide insensitivity in five insect orders have revealed remarkably high levels of parallelism in the evolution of this trait, including the frequent occurrence of parallel amino acid substitutions at two sites and recurrent episodes of duplication followed by neo-functionalization. Here we add data for a sixth insect order, Orthoptera, which includes an ancient group of highly aposematic cardenolide-sequestering grasshoppers in the family Pyrgomorphidae. We find that Orthopterans exhibit largely predictable patterns of evolution of insensitivity established by sampling other insect orders. Taken together the data lend further support to the proposal that negative pleiotropic constraints are a key determinant in the evolution of cardenolide insensitivity in insects. Furthermore, analysis of our expanded taxonomic survey implicates positive selection acting on site 111 of cardenolide-sequestering species with a single-copy of ATPa, and sites 115, 118 and 122 in lineages with neo-functionalized duplicate copies, all of which are sites of frequent parallel amino acid substitution. [ABSTRACT FROM AUTHOR]

The repeated evolution of similar phenotypes in independent populations (i.e. parallel or convergent evolution) provides an opportunity to identify genetic and ecological factors that influence the process of adaptation. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model for such studies, as they have repeatedly adapted to divergent habitats across the Northern hemisphere. Here, we use genomic, ecological and morphological data from 16 independent pairs of stickleback populations adapted to divergent lake and stream habitats. We combine a population genomic approach to identify regions of the genome that are likely under selection in these divergent habitats with an association mapping approach to identify regions of the genome that underlie variation in ecological factors and morphological traits. Over 37% of genomic windows are repeatedly differentiated across lake-stream pairs. Similarly, many genomic windows are associated with variation in abiotic factors, diet items and morphological phenotypes. Both the highly differentiated windows and candidate trait windows are non-randomly distributed across the genome and show some overlap. However, the overlap is not significant on a genome-wide scale. Together, our data suggest that adaptation to divergent food resources and predation regimes are drivers of differentiation in lake-stream stickleback, but that additional ecological factors are also important. [ABSTRACT FROM AUTHOR]

Eukaryotic genomes contain thousands of genes organized into complex and interconnected genetic interaction networks. Most of our understanding of how genetic variation affects these networks comes from quantitative-trait loci mapping and from the systematic analysis of double-deletion (or knockdown) mutants, primarily in the yeast Saccharomyces cerevisiae. Evolve and re-sequence experiments are an alternative approach for identifying novel functional variants and genetic interactions, particularly between non-lossof-function mutations. These experiments leverage natural selection to obtain genotypes with functionally important variants and positive genetic interactions. However, no systematic methods for detecting genetic interactions in these data are yet available. Here, we introduce a computational method based on the idea that variants in genes that interact will co-occur in evolved genotypes more often than expected by chance. We apply this method to a previously published yeast experimental evolution dataset. We find that genetic targets of selection are distributed non-uniformly among evolved genotypes, indicating that genetic interactions had a significant effect on evolutionary trajectories. We identify individual gene pairs with a statistically significant genetic interaction score. The strongest interaction is between genes TRK1 and PHO84, genes that have not been reported to interact in previous systematic studies. Our work demonstrates that leveraging parallelism in experimental evolution is useful for identifying genetic interactions that have escaped detection by other methods. [ABSTRACT FROM AUTHOR]

Summary: Root system architecture (RSA) is a critical aspect of plant growth and competitive ability. Here we used two independently evolved strains of weedy rice, a de‐domesticated form of rice, to study the evolution of weed‐associated RSA traits and the extent to which they evolve through shared or different genetic mechanisms.We characterised 98 two‐dimensional and three‐dimensional RSA traits in 671 plants representing parents and descendants of two recombinant inbred line populations derived from two weed × crop crosses. A random forest machine learning model was used to assess the degree to which root traits can predict genotype and the most diagnostic traits for doing so. We used quantitative trait locus (QTL) mapping to compare genetic architecture between the weed strains.The two weeds were distinguishable from the crop in similar and predictable ways, suggesting independent evolution of a 'weedy' RSA phenotype. Notably, comparative QTL mapping revealed little evidence for shared underlying genetic mechanisms.Our findings suggest that despite the double bottlenecks of domestication and de‐domestication, weedy rice nonetheless shows genetic flexibility in the repeated evolution of weedy RSA traits. Whereas the root growth of cultivated rice may facilitate interactions among neighbouring plants, the weedy rice phenotype may minimise below‐ground contact as a competitive strategy. [ABSTRACT FROM AUTHOR]

Elucidation of the diversification process of organisms is one of the important tasks of biology. From the viewpoint of species diversity, insects are the most successful group among the diverse organisms on earth and evolutionary adaptation is one of the important factors driving this pattern. Evolutionary adaptation is one of the important factors in the diversification of insects. One of the representative examples of environmental adaptation in insects is the shortening and loss of wings in subalpine and alpine zones. In this study, we focused on the Japanese scorpionfly, Panorpodes paradoxus. In this species, individuals that inhabit mountainous regions and subalpine zones have long wings (the "general type"), and individuals that inhabit higher altitudinal ranges have short wings (the "alpine type"). We collected samples of all Japanese Panorpodes species and one Korean Panorpodes species, and conducted molecular phylogenetic analyses of the mtDNA COI (610 bp), COII (688 bp), and 16S rRNA (888 bp) and nuDNA EF1‐α (658 bp) and 28S rRNA (524 bp) regions in order to reveal the evolutionary history of the alpine type of P. paradoxus. As a result of molecular phylogenetic analyses, it was revealed that the alpine type of P. paradoxus was polyphyletic, and had evolved to become the alpine type at least twice independently at separate mountain locations. In addition, the result of divergence time estimation suggested that the alpine type is an "ecomorph", having recently adapted to low temperature habitats following mountain uplift within the Japanese Archipelago and subsequent glacial‐interglacial cycles. see also the Perspective by Emerson et al. [ABSTRACT FROM AUTHOR]

Summary: The evolution of herbicide resistance in crop weeds presents one of the greatest challenges to agriculture and the production of food. Herbicide resistance has been studied for more than 60 yr, in the large part by researchers seeking to design effective weed control programs. As an outcome of this work, various unique questions in plant adaptation have been addressed. Here, I collate recent research on the herbicide‐resistant problem in light of key questions and themes in evolution and ecology. I highlight discoveries made on herbicide‐resistant weeds in three broad areas – the genetic basis of adaptation, evolutionary constraints, experimental evolution – and similarly discuss questions left to be answered. I then develop how one would use herbicide‐resistance evolution as a model for studying eco‐evolutionary dynamics within a community context. My overall goals are to highlight important findings in the weed science literature that are relevant to themes in plant adaptation and to stimulate the use of herbicide‐resistant plants as models for addressing key questions within ecology and evolution. [ABSTRACT FROM AUTHOR]

Premise: Ring species have long fascinated evolutionary biologists for their potential insights into lineage divergence and speciation across space. Few studies have investigated the potential for convergent or parallel evolution along the diverging fronts of ring species. We investigated a potential case of parallel floral variation in the Caribbean spurge Euphorbia tithymaloides, the only plant system with molecular support as a ring species. The terminal populations of each front, despite being the most divergent, exhibit such similar floral traits that they were originally considered each other's closest relative. Methods: We evaluated convergence in floral and leaf traits in relation to geography across 95 populations spanning the distribution of E. tithymaloides. We also reanalyzed available genetic data (from previous phylogenetic analyses) in an explicitly spatial framework. Results: Floral morphology appears to have shifted in a convergent fashion along both geographic fronts of E. tithymaloides, resulting in shorter and more compact inflorescences in Antillean populations compared to the typical elongate "slipper‐like" cyathia characteristic of the area of origin. Patterns of spatial genetic variation were more consistent with a two‐fronted invasion of the Caribbean than with a simpler model of isolation‐by‐distance. Conclusions: Floral divergence in E. tithymaloides is consistent with convergent evolution along the two fronts of a ring species. We outline several (not mutually exclusive) mechanisms that could be driving patterns in morphology, including shifts toward generalized pollination with reduced reliance on hummingbirds, shifts in floral structure closely matching available hummingbird bill traits, and shifts toward increased selfing. [ABSTRACT FROM AUTHOR]

Cell segmentation in microscopy is a challenging problem, since cells are often asymmetric and densely packed. Successful cell segmentation algorithms rely identifying seed points, and are highly sensitive to variablility in cell size. In this paper, we present an efficient and highly parallel formulation for symmetric three-dimensional contour evolution that extends previous work on fast two-dimensional snakes. We provide a formulation for optimization on 3D images, as well as a strategy for accelerating computation on consumer graphics hardware. The proposed software takes advantage of Monte-Carlo sampling schemes in order to speed up convergence and reduce thread divergence. Experimental results show that this method provides superior performance for large 2D and 3D cell localization tasks when compared to existing methods on large 3D brain images. [ABSTRACT FROM AUTHOR]

The mass application of whole mitogenome (MG) sequencing has great potential for resolving complex phylogeographic patterns that cannot be resolved by partial mitogenomic sequences or nuclear markers. North American periodical cicadas (Magicicada) are well known for their periodical mass emergence at 17- and 13-year intervals in the north and south, respectively. Magicicada comprises three species groups, each containing one 17-year species and one or two 13-year species. Within each life cycle, single-aged cohorts, called broods, of periodical cicadas emerge in different years, and most broods contain members of all three species groups. There are 12 and three extant broods of 17- and 13-year cicadas, respectively. The phylogeographic relationships among the populations and broods within the species groups have not been clearly resolved. We analyzed 125 whole MG sequences from all broods and seven species within three species groups to ascertain the divergence history of the geographic and allochronic populations and their life cycles. Our mitogenomic phylogeny analysis clearly revealed that each of the three species groups had largely similar phylogeographic subdivisions (east, middle, and west) and demographic histories (rapid population expansion after the last glacial period). The mitogenomic phylogeny also partly resolved the brood diversification process, which could be explained by hypothetical temporary life cycle shifts, and showed that none of the 13- and 17-year species within the species groups was monophyletic, possibly due to gene flow between them. Our findings clearly reveal phylogeographic structures in the three Magicicada species groups, demonstrating the advantage of whole MG sequence data in phylogeographic studies. [ABSTRACT FROM AUTHOR]

Rapid adaptation can prevent extinction when populations are exposed to extremely marginal or stressful environments. Factors that affect the likelihood of evolutionary rescue from extinction have been identified, but much less is known about the evolutionary dynamics (e.g., rates and patterns of allele frequency change) and genomic basis of successful rescue, particularly in multicellular organisms. We conducted an evolve‐and‐resequence experiment to investigate the dynamics of evolutionary rescue at the genetic level in the cowpea seed beetle, Callosobruchus maculatus, when it is experimentally shifted to a stressful host plant, lentil. Low survival (~1%) at the onset of the experiment caused population decline. But adaptive evolution quickly rescued the population, with survival rates climbing to 69% by the F5 generation and 90% by the F10 generation. Population genomic data showed that rescue likely was caused by rapid evolutionary change at multiple loci, with many alleles fixing or nearly fixing within five generations of selection on lentil. Selection on these loci was only moderately consistent in time, but parallel evolutionary changes were evident in sublines formed after the lentil line had passed through a bottleneck. By comparing estimates of selection and genomic change on lentil across five independent C. maculatus lines (the new lentil‐adapted line, three long‐established lines and one case of failed evolutionary rescue), we found that adaptation on lentil occurred via somewhat idiosyncratic evolutionary changes. Overall, our results suggest that evolutionary rescue in this system can be caused by very strong selection on multiple loci driving rapid and pronounced genomic change. [ABSTRACT FROM AUTHOR]

Understanding the number of times a trait has evolved is a necessary foundation for comprehending its potential relationships with selective regimes, developmental constraints and evolutionary diversification. Rodents make up over 40% of extant mammalian species, and their ecological and evolutionary success has been partially attributed to the increase in biting efficiency that resulted from a forward shift of one or two portions of the masseter muscle from the zygomatic arch onto the rostrum. This forward shift has occurred in three discrete ways, but the number of times it has occurred has never been explicitly quantified. We estimated an ultrametric phylogeny, the first to include all rodent families, using thousands of ultraconserved elements. We examined support for evolutionary relationships among the five rodent suborders and then incorporated relevant fossils, fitted models of character evolution, and used stochastic character mapping to determine that a portion of the masseter muscle has moved forward onto the rostrum at least seven times (with one reversal) during the approximately 70 Myr history of rodents. Combined, the repeated evolution of this key innovation, its increasing prevalence through time, and the species diversity of clades with this character underscores the adaptive value of improved biting efficiency and the relative ease with which some advantageous traits arise. [ABSTRACT FROM AUTHOR]

Diverging semi‐isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both reduce gene flow between groups. Rarely are these two patterns of spatial distribution reported in the same study system. Here, we report that the long‐snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones. Along the European Atlantic coasts, a northern and a southern lineage meet in the southwest of France where they coexist in sympatry—i.e., in the same geographical zone—with little hybridization. In the Mediterranean Sea, two lineages have a mosaic distribution, associated with lagoon‐like and marine habitats. A fifth lineage was identified in the Black Sea. Genetic homogeneity over large spatial scales contrasts with isolation maintained in sympatry or close parapatry at a fine scale. A high variation in locus‐specific introgression rates provides additional evidence that partial reproductive isolation must be maintaining the divergence. We find that fixed differences between lagoon and marine populations in the Mediterranean Sea belong to the most differentiated SNPs between the two Atlantic lineages, against the genome‐wide pattern of structure that mostly follow geography. These parallel outlier SNPs cluster on a single chromosome‐wide island of differentiation. Since Atlantic lineages do not map to lagoon‐sea habitat variation, genetic parallelism at the genomic island suggests a shared genetic barrier contributes to reproductive isolation in contrasting contexts–i.e., spatial versus ecological. We discuss how a genomic hotspot of parallel differentiation could have evolved and become associated both with space and with a patchy environment in a single study system. [ABSTRACT FROM AUTHOR]

Evidence that organisms evolve rapidly enough to alter ecological dynamics necessitates investigation of the reciprocal links between ecology and evolution. Data that link genotype to phenotype to ecology are needed to understand both the process and ecological consequences of rapid evolution. Here, we quantified the suite of elements in individuals (i.e., ionome) and differences in the fluxes of key nutrients across populations of threespine stickleback. We find that allelic variation associated with freshwater adaptation that controls bony plating is associated with changes in the ionome and nutrient recycling. More broadly, we find that adaptation of marine stickleback to freshwater conditions shifts the ionomes of natural populations and populations raised in common gardens. In both cases ionomic divergence between populations was primarily driven by differences in trace elements rather than elements typically associated with bone. These findings demonstrate the utility of ecological stoichiometry and the importance of ionome‐wide data in understanding eco‐evolutionary dynamics. [ABSTRACT FROM AUTHOR]

The Crenicichla mandelburgeri species complex from the Middle Paraná basin is a diverse group of cichlid species and contains all known ecomorphs found within the entire genus Crenicichla. Here, we study the phylogenetic relationships within the C. mandelburgeri species complex using ddRAD sequencing with focus on its two candidate species flocks endemic to the Iguazú and Urugua-í Rivers, and on two putative sympatric species in the Piray Guazú River. These species flocks include four and three syntopic species, respectively, which are strongly adapted to different trophic niches and include derived ecomorphs of Crenicichla (molluscivores, a periphyton grazer, and a crevice-feeding thick-lipped invertivore). Our phylogenomic analyses strongly support monophyly and rapid diversification of the Iguazú species flock, but reveal more complex evolutionary histories in the Urugua-í and Piray Guazú tributaries. Most species in the Middle Paraná, including one species in the Urugua-í and both species in the Piray Guazú show cytonuclear discordance, and in both of these tributaries, we also found hybridization in one of the resident species. Population-level analyses reveal complete isolation of the Iguazú species and coupled with their dramatic ecological diversity, this radiation exemplifies characteristics of a species flock that arose via ecological speciation. [ABSTRACT FROM AUTHOR]

Adaptation often proceeds from standing variation, and natural selection acting on pairs of populations is a quantitative continuum ranging from parallel to divergent. Yet, it is unclear how the extent of parallel genetic evolution during adaptation from standing variation is affected by the difference in the direction of selection between populations. Nor is it clear whether the availability of standing variation for adaptation affects progress toward speciation in a manner that depends on the difference in the direction of selection. We conducted a theoretical study investigating these questions and have two primary findings. First, the extent of parallel genetic evolution between two populations rapidly declines as selection changes from fully parallel toward divergent, and this decline is steeper in organisms with more traits (i.e., greater dimensionality). This rapid decline happens because small differences in the direction of selection greatly reduce the fraction of alleles that are beneficial in both populations. For example, populations adapting to optima separated by an angle of 33° might have only 50% of potentially beneficial alleles in common. Second, relative to when adaptation is from only new mutation, adaptation from standing variation improves hybrid fitness under parallel selection and reduces hybrid fitness under divergent selection. Under parallel selection, genetic parallelism from standing variation reduces the phenotypic segregation variance in hybrids, thereby increasing mean fitness in the parental environment. Under divergent selection, larger pleiotropic effects of alleles fixed from standing variation cause maladaptive transgressive phenotypes when combined in hybrids. Adaptation from standing genetic variation therefore slows progress toward speciation under parallel selection and facilitates progress toward speciation under divergent selection. [ABSTRACT FROM AUTHOR]

Studies of parallel or convergent evolution (the repeated, independent evolution of similar traits in similar habitats) rarely explicitly quantify the extent of parallelism (i.e. variation in the direction and/or magnitude of divergence) between the sexes; instead, they often investigate both sexes together or exclude one sex. However, differences in male and female patterns of divergence could contribute to overall variation in the extent of parallelism among ecotype pairs, especially in sexually dimorphic traits. Failing to properly attribute such variation could lead to underestimates of the importance of environmental variation in shaping phenotypes. We investigate the extent of parallelism in the body shape of male and female beach and creek spawning sockeye salmon (Oncorhynchus nerka) from two lake systems in western Alaska that were colonized independently after the last ice age. Although both sexes showed some degree of parallelism, patterns of beach‐creek body shape divergence vary between the sexes and between lake systems. Phenotypic change vector analyses revealed highly parallel aspects of divergence between males from different lake systems (males from beaches had deeper bodies than males from creeks) but weaker parallelism in females and high parallelism between the sexes in one lake system but not the other. Body shape also had population‐specific components, which were mostly, but not entirely, explained by environmental variation in the form of creek depth. Our results highlight the importance of explicitly considering the extent of parallelism between the sexes and environmental variation among sites within habitat types. [ABSTRACT FROM AUTHOR]

To reveal phenotypic and functional genomic patterns of mitonuclear adaptation, a laboratory adaptation study with Caenorhabditis elegans nematodes was conducted in which independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain (ETC) mutant, gas-1. Following 60 generations of evolution in large population sizes with competition for food resources, two distinct classes of lines representing different degrees of adaptive response emerged: a low-fitness class that exhibited minimal or no improvement compared to the gas-1 mutant ancestor, and a high-fitness class containing lines that exhibited partial recovery of wild-type fitness. Many lines that achieved higher reproductive and competitive fitness levels were also noted to evolve high frequencies of males during the experiment, consistent with adaptation in these lines having been facilitated by outcrossing. Whole-genome sequencing and analysis revealed an enrichment of mutations in loci that occur in a gas-1-centric region of the C. elegans interactome and could be classified into a small number of functional genomic categories. A highly nonrandom pattern of mitochondrial DNA mutation was observed within high-fitness gas-1 lines, with parallel fixations of nonsynonymous base substitutions within genes encoding NADH dehydrogenase subunits I and VI. These mitochondrial gene products reside within ETC complex I alongside the nuclear-encoded GAS-1 protein, suggesting that rapid adaptation of select gas-1 recovery lines was driven by fixation of compensatory mitochondrial mutations. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • An integrative taxonomy approach was used to delimit species in the U. cornuta aggr. • STACEY is a powerful tool for species delimitation in this difficult group. • A high genetic diversity (14 lineages) was evidenced within the U. cornuta aggr. • Most of the nine supported lineages (over 14) are characterized by a single chemotype. • Some lineages display intercontinental geographic ranges across Americas and Europe. Abstract Biological processes such as hybridization, incomplete lineage sorting and gene flow can obscure the recognition of distinct evolutionary lineages, particularly in groups of organisms that have recently diverged. Therefore, compiling pieces of evidence from diverse data sources is critical to accurately assess species boundaries in such groups. The increasing availability of DNA sequence data allows for a much deeper understanding of diversification and speciation processes and their consequences on biodiversity. In this study, we applied an integrative approach based on DNA sequence, chemical, geographic and morphological data to attempt to define species boundaries in the lichen-forming genus Usnea (Parmeliaceae), particularly the U. cornuta aggregate, a cosmopolitan species group. We provide the first species delimitation for this group in the neotropics based on the multispecies coalescent (MSC) model. Using ITS rDNA and two protein-coding genes, Mcm7 and RPB1 , we estimated the species tree under the MSC model in a Bayesian framework using STACEY. Our results indicate that at least nine strongly supported distinct lineages coexist in the U. cornuta aggregate, which are well chemically characterized. Additionally, we found evidence for the polyphyly of three morphospecies, Usnea brasiliensis , U. cornuta and U. dasaea. [ABSTRACT FROM AUTHOR]

Genomic studies of parallel (or convergent) evolution often compare multiple populations diverged into two ecologically different habitats to search for loci repeatedly involved in adaptation. Because the shared ancestor of these populations is generally unavailable, the source of the alleles at adaptation loci, and the direction in which their frequencies were shifted during evolution, remain elusive. To shed light on these issues, we here use multiple populations of threespine stickleback fish adapted to two different types of derived freshwater habitats—basic and acidic lakes on the island of North Uist, Outer Hebrides, Scotland—and the present‐day proxy of their marine ancestor. In a first step, we combine genome‐wide pooled sequencing and targeted individual‐level sequencing to demonstrate that ecological and phenotypic parallelism in basic‐acidic divergence is reflected by genomic parallelism in dozens of genome regions. Exploiting data from the ancestor, we next show that the acidic populations, residing in ecologically more extreme derived habitats, have adapted by accumulating alleles rare in the ancestor, whereas the basic populations have retained alleles common in the ancestor. Genomic responses to selection are thus predictable from the ecological difference of each derived habitat type from the ancestral one. This asymmetric sorting of standing genetic variation at loci important to basic‐acidic divergence has further resulted in more numerous selective sweeps in the acidic populations. Finally, our data suggest that the maintenance in marine fish of standing variation important to adaptive basic‐acidic differentiation does not require extensive hybridization between the marine and freshwater populations. Overall, our study reveals striking genome‐wide determinism in both the loci involved in parallel divergence, and in the direction in which alleles at these loci have been selected. [ABSTRACT FROM AUTHOR]

The Trinidadian guppy is emblematic of parallel and convergent evolution, with repeated demonstrations that predation regime is a driver of adaptive trait evolution. A classic and foundational experiment in this system was conducted by John Endler 40 years ago, where male guppies placed into low‐predation environments in the laboratory evolved increased color in a few generations. However, Endler's experiment did not employ the now typical design for a parallel/convergent evolution study, which would employ replicates of different ancestral lineages. We therefore implemented an experiment that seeded replicate mesocosms with small founding populations of guppies originating from high‐predation populations of two very different lineages. The different mesocosms were maintained identically, and male guppy color was quantified every four months. After one year, we tested whether male color had increased, whether replicates within a lineage had parallel phenotypic trajectories, and whether the different lineages converged on a common phenotype. Results showed that male guppy color generally increased through time, primarily due to changes in melanic color, whereas the other colors showed inconsistent and highly variable trajectories. Most of the nonparallelism in phenotypic trajectories was among mesocosms containing different lineages. In addition to this mixture of parallelism and nonparallelism, convergence was not evident in that the variance in color among the mesocosms actually increased through time. We suggest that our results reflect the potential importance of high variation in female preference and stochastic processes such as drift and founder effects, both of which could be important in nature. The Trinidadian guppy is emblematic of parallel and convergent evolution, with repeated demonstrations that predation regime is a driver of adaptive trait evolution. We implemented an experiment that seeded replicate mesocosms with small founding populations of guppies originating from high‐predation populations of two different lineages. Results showed that male guppy color generally increased through time, but individual color groups showed inconsistent and highly variable trajectories. Most of the nonparallelism in phenotypic trajectories was among mesocosms containing different lineages. [ABSTRACT FROM AUTHOR]

Community coalescence, the mixing of multiple communities, is ubiquitous in natural microbial communities. During coalescence, theory suggests the success of a population will be enhanced by the presence of species it has coevolved with (relative to foreign species), because coevolution will result in greater resource specialization to minimize competition. Thus, more coevolved communities should dominate over less coevolved communities during coalescence events. We test these hypotheses using the bacterium Pseudomonas fluorescens which diversifies into coexisting niche‐specialist morphotypes. We first evolved replicate populations for ~40 generations and then isolated evolved genotypes. In a series of competition trials, we determined if using coevolved versus random genotypes affected the relative performance of "communities" of single and multiple genotypes. We found no effect of coevolutionary history on either genotype fitness or community performance, which suggests parallel (co)evolution between communities. However, fitness was enhanced by the presence of other genotypes of the same strain type (wild‐type or an isogenic strain with a LacZ marker; the inclusion of the latter necessary to distinguish genotypes during competition), indicative of local adaptation with respect to genetic background. Our results are the first to investigate the effect of (co)evolution on the outcome of coalescence and suggest that when input populations are functionally similar and added at equal mixing ratios, the outcome community may not be asymmetrically dominated by either input population. [ABSTRACT FROM AUTHOR]