Search

Goldfish (Carassius auratus auratus) are important ornamental fish that have experienced extreme anthropogenic selection and exhibit diverse phenotypes. Loss of the dorsal fin is a key characteristic that distinguishes the Egg-goldfish from the Wen-goldfish. However, the mechanisms underlying the divergence in dorsal fin development are still unknown between the Egg-goldfish and the Wen-goldfish. In this study, we sought to unravel the postembryonic developmental processes of two goldfish strains, Red Cap Oranda, a representative of the Wen-goldfish, and Ranchu, a representative of the Egg-goldfish. We examined the developmental morphology of the dorsal fin in five-month-old goldfish larvae using both Alcian blue-alizarin red staining and X-ray photography. We showed that the developmental processes of the dorsal fin fold were different in Ranchu compared to Red Cap Oranda, despite similarity in their general developmental processes. We categorized the postembryonic development of Ranchu larvae into four types based on the number of the initial residual dorsal fin fold appearing at protruding-mouth stage. The number, size and position of the initial residual dorsal fin fold appeared at hatching affected and eventually determined the phenotypic variations in dorsal fin defects in Ranchu. In addition, we genotyped the eomesa gene to determine whether it would be a candidate gene responsible for the loss of the dorsal fin in Ranchu. The eomesa CDS sequence exhibited no nonsense mutation in Ranchu. In summary, the absence of the dorsal fin fold during postembryonic development eventually resulted in the loss of the dorsal fin in Ranchu. Further investigation is required to determine whether other genes and developmental pathways play important roles in the loss of the dorsal fin in Ranchu.

Aim Understanding the phylogeography of a species complex can provide important insights into its evolutionary history. However, phylogeographic inference often faces the dilemma of regionally inadequate sampling. Pungitius sticklebacks are a case in point: although the highest species diversity is found in Northeast Asia, their phylogeography in this region is still poorly understood. Location Northeast Asia. Methods With the aid of whole-genome resequencing data, we investigated the phylogeography of Northeast Asian Pungitius sticklebacks, with newly sampled 83 worldwide Pungitius individuals from 11 locations including eight Chinese locations reported to host only P. sinensis. Results We discovered that three of the eight Chinese locations hosted populations of P. kaibarae and P. bussei, species new to the fauna of China. Phylogeographic analyses further clarified the sequence and timing of colonization of Northeast Asia by different Pungitius species, shedding new light on their origins and current distribution ranges. Colonization of inland Northeast Asia by Pungitius sticklebacks occurred in multiple waves, and the widespread P. sinensis expanded its range relatively late in the Pleistocene. Main conclusions This study complements our understanding of the phylogeography of Pungitius sticklebacks by extending sampling to cover an area that comprises nearly half of the known distribution area of this genus in Northeast Asia. The discovery of three Pungitus species from China is of particular interest, as translocations to support locally declining populations have occurred under the assumption that all sticklebacks in China-except the endangered P. stenurus-are P. sinensis, raising conservation concerns associated with unintentional translocations and possible admixture.

Understanding the origins of phenotypic diversity among closely related species remains an important largely unsolved question in evolutionary biology. With over 800 species, Lake Malawi haplochromine cichlid fishes are a prominent example of extremely fast evolution of diversity including variation in coloration. Previously, a single major effect gene, agrp2 (asip2b), has been linked to evolutionary losses and gains of horizontal stripe patterns in cichlids, but it remains unknown what causes more fine-scale variation in the number and continuity of the stripes. Also, the genetic basis of the most common color pattern in African cichlids, vertical bars, and potential interactions between the two color patterns remain unknown. Based on a hybrid cross of the horizontally striped Lake Malawi cichlid Pseudotropheus cyaneorhabdos and the vertically barred species Chindongo demasoni we investigated the genetic basis of both color patterns. The distribution of phenotypes in the F2 generation of the cross indicates that horizontal stripes and vertical bars are independently inherited patterns that are caused by two sets of genetic modules. While horizontal stripes are largely controlled by few major effect loci, vertical bars are a highly polygenic trait. Horizontal stripes show substantial variation in the F2 generation that, interestingly, resemble naturally occurring phenotypes found in other Lake Malawi cichlid species. Quantitative trait loci (QTL) mapping of this cross reveals known (agrp2) and unknown loci underlying horizontal stripe patterns. These findings provide novel insights into the incremental fine-tuning of an adaptive trait that diversified through the evolution of additional modifier loci.

Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species.

The resolution of cryptic diversity is essential for understanding the evolutionary diversification of lineages and establishing conservation priorities. We examine relationships in Eriogoneae (Polygonaceae), a diverse lineage in western North America. We ask whether Eriogonum umbellatum, a morphologically and ecologically diverse species, is monophyletic and whether its varieties represent evolutionary lineages. We use genotyping-by-sequencing to assemble a SNP dataset for 51 species in the genera Chorizanthe, Eriogonum and Sidotheca. We report a hierarchical phylogenetic analysis using maximum likelihood to estimate the evolutionary history of Eriogoneae. We illustrate admixture components for 21 populations of E. umbellatum, representing four varieties, and test for lineage structure using TreeMix. We identify strongly supported clades within Eriogoneae. Many relationships in the Eucycla + Oregonium and Latifolia clades are supported, while most relationships within the Eriogonum subg. Oligogonum clade and a clade with most Chorizanthe remain unresolved. Eriogonum congdonii resolves within the main E. umbellatum clade, while populations of three varieties of E. umbellatum are closely related to E. ursinum and are associated with serpentine soils. ADmixture and TreeMix analyses suggest E. umbellatum varieties represent evolutionary lineages. These results from SNP data are largely consistent with previous phylogenetic studies of Eriogoneae based on sequence variation. Structure within Oligogonum suggests consistent environmental association and radiation after initial colonization of serpentine. Morphology is unreliable for the infraspecific taxonomy of E. umbellatum. Additional molecular studies are needed to resolve the evolutionary relationships and ecological diversification within this species, in Oligogonum, and in Eriogoneae. We thank SGIker research support services at the University of the Basque Country, Leioa, Spain for DNA extraction and quality control, and acknowledge Centro Nacional de d-Analisi Genomica in Barcelona, Spain for GBS sequencing. We thank J. Andre, N.J. Jensen and J. Steele for contributing samples and D. Marino for collaboration in nucleic acid extractions. We acknowledge the contributions of O. Lao Grueso to the ADmixture and TreeMix analyses. We thank U.S. Forest Service employees D. Austin, J. Fedorchuk, M. Friend, J. Haas, D. Ikeda, L. Janeway, J. Nelson, D. Netz, A. Sanger, and S. Weis among others for facilitating permitting and collecting. This work was supported by funds from the Basque Government in support of the Terrestrial Plant Diversity group of the Department of Plant Biology and Ecology, University of the Basque Country, and an ERC Advanced Grant, FP7-IDEAS-ERC, `ADAPT', project 339941 awarded to T. Brown.

The slow-worm lizards of the genus Anguis show significant morphological, behavioural and ecological uniformity owing to their limbless, elongated bodies and semifossorial lifestyle. This makes the delimitation of species challenging. Five monophyletic, deeply divergent and mostly parapatric mitochondrial lineages are currently recognized, although hybridization occurs along contact zones. In the southern edge of the range of the genus, two endemic Balkan Anguis (Anguis graeca and Anguis cephallonica) share a broad area of co-distribution and intermediate morphological characteristics. Expecting to retrieve hybrids within the overlap in their distributions, we used genome-wide single nucleotide polymorphisms but did not recover any evidence of interspecific gene flow. Within each species, genomic data revealed shallow population structuring influenced by spatial isolation, with the exception of the southernmost population of A. cephallonica from the Mani Peninsula. Species distribution modelling showed a lack of strong niche overlap and specific environmental preferences; both species showed a precipitation dependence, but A. cephallonica was better acclimatized to high temperatures. Finally, geometric morphometrics of the head shape suggested morphological divergence, mostly seen in the elongation of the head of A. cephallonica. All the evidence supports a long and complete reproductive isolation between the two southern slow worms and raises questions about how ecomorphological divergence might have acted to promote their speciation.

By shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage disequilibrium prespeciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and Drosophila persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between D. pseudoobscura and D. persimilis over three distinct timescales: (1) segregation of ancestral polymorphism early in the speciation process, (2) gene flow after the split of D. pseudoobscura and D. persimilis, but prior to the split of D. pseudoobscura subspecies, and (3) recent gene flow between sympatric D. pseudoobscura and D. persimilis, after the split of D. pseudoobscura subspecies. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in other systems.

Introduction: Extreme patterns of vertical facial divergence are of great importance to clinicians because of their association with dental malocclusion and functional problems of the orofacial complex. Understanding the growth patterns associated with vertical facial divergence is critical for clinicians to provide optimal treatment. This study evaluates and compares growth patterns from childhood to adulthood among 3 classifications of vertical facial divergence using longitudinal, lateral cephalograms from the Craniofacial Growth Consortium Study. Methods: Participants (183 females, 188 males) were classified into 1 of 3 facial types on the basis of their adult mandibular plane angle (MPA): hyperdivergent (MPA >39°; n = 40), normodivergent (28° ≤ MPA ≤ 39°; n = 216), and hypodivergent (MPA

Summary ・Phytochromes play a central role in mediating adaptive responses to light and temperature throughout plant life cycles. Despite evidence for adaptive importance of natural variation in phytochromes, little information is known about molecular mechanisms that modulate physiological responses of phytochromes in nature. ・We show evolutionary divergence in physiological responses relevant to thermal stability of a physiologically active form of phytochrome (Pfr) between two sister species of Brassicaceae growing at different latitudes. The higher latitude species (Cardamine bellidifolia; Cb) responded more strongly to light‐limited conditions compared with its lower latitude sister (C. nipponica; Cn). Moreover, CbPHYB conferred stronger responses to both light‐limited and warm conditions in the phyB‐deficient mutant of Arabidopsis thaliana than CnPHYB: that is Pfr CbphyB was more stable in nuclei than CnphyB. ・Our findings suggest that fine tuning Pfr stability is a fundamental mechanism for plants to optimise phytochrome‐related traits in their evolution and adapt to spatially varying environments, and open a new avenue to understand molecular mechanisms that fine tune phytochrome responses in nature.

OBJECTIVE: To further develop methods to assess corticospinal divergence and muscle coupling using transcranial magnetic stimulation (TMS). METHODS: Ten healthy right-handed adults participated (7 females, age 34.0 ± 12.9 years). Monophasic single pulses were delivered to 14 sites over the right primary motor cortex at 40, 60, 80 and 100% of maximum stimulator output (MSO), using MRI-based neuronavigation. Motor evoked potentials (MEPs) were recorded simultaneously from 9 muscles of the contralateral hand, wrist and arm. For each intensity, corticospinal divergence was quantified by the average number of muscles that responded to TMS per cortical site, coactivation across muscle pairs as reflected by overlap of cortical representations, and correlation of MEP amplitudes across muscle pairs. RESULTS: TMS to each muscle’s most responsive site elicited submaximal MEPs in most other muscles. The number of responsive muscles per cortical site and the extent of coactivation increased with increasing intensity (ANOVA, p < 0.001). In contrast, correlations of MEP amplitudes did not differ across the 60, 80 and 100% MSO intensities (ANOVA, p = 0.34), but did differ across muscle pairs (ANOVA, p < 0.001). Post hoc analysis identified 4 sets of muscle pairs (Tukey homogenous subsets, p < 0.05). Correlations were highest for pairs involving two hand muscles and lowest for pairs that included an upper arm muscle. CONCLUSIONS: Correlation of MEP amplitudes may quantify varying levels of muscle coupling. In future studies, this approach may be a biomarker to reveal altered coupling induced by neural injury, neural repair and/or motor learning.

Many plant families lack substantive fossil records, limiting our understanding of their origin and evolution. The abundance and preservation potential of pollen through geological time have helped to overcome such limitations and have provided reliable fossils for reconstructing biogeographical history and character evolution in many angiosperm families. Here, using scanning electron microscopy, we identified six Ebenaceae-type fossil pollen grains from early Palaeogene sediments of western India. Phenetic and phylogenetic analyses using pollen characters of fossil and extant taxa reavealed affinities of these fossils to three genera of Ebenaceae (Euclea, Royena and Diospyros). Furthermore, our divergence dating analysis using these fossils as priors suggested a Gondwanan origin for the family during the mid-Cretaceous [c. 107 Mya, 95% highest posterior density (HPD): 100–112 Mya] and supports the boreotropical and ‘out of India’ dispersal hypotheses as the most probable explanations for the present global distribution of the family. The study also supports the dispersal of the family into India, from Africa, through the Kohistan–Ladakh Arc during the Palaeocene. Finally, comparative phylogenetic analyses suggest significant synapomorphic and phylogenetic signals for a few selected pollen characters in Ebenaceae. Our findings have important implications for understanding the biogeography and evolution of the highly diverse and ecologically and economically important family Ebenaceae.

The spiral arrangement (phyllotaxis) of leaves is a shared morphology in land plants, and exhibits diversity constrained to the Fibonacci sequence. Phyllotaxis in vascular plants is produced at a multicellular meristem, whereas bryophyte phyllotaxis emerges from a single apical stem cell (AC) that is embedded in a growing tip of the gametophyte. An AC is asymmetrically divided into itself and a single ‘merophyte’, producing a future leaf and a portion of the stem. Although it has been suggested that the arrangement of merophytes is regulated by a rotation of the division plane of an AC, the quantitative description of the merophyte arrangement and its regulatory mechanism remain unclear. To clarify them, we examined three moss species, Tetraphis pellucida, Physcomitrium patens, and Niphotrichum japonicum, which exhibit 1/3, 2/5, and 3/8 spiral phyllotaxis, respectively. We measured the angle between the centroids of adjacent merophytes relative to the AC centroid on cross-transverse sections. At the outer merophytes, this divergence angle converged to nearly 120 $$^\circ$$ in T. pellucida, 136 $$^\circ$$ in N. japonicum, and 141 $$^\circ$$ in P. patens, which was nearly consistent with phyllotaxis, whereas the divergence angle deviated from the converged angle at the inner merophytes near an AC. A mathematical model, which assumes scaling growth of AC and merophytes and a constant angle of division plane rotation, quantitatively reproduced the sequence of the divergence angles. This model showed that successive relocations of the centroid position of an AC upon its division inevitably result in the transient deviation of the divergence angle. As a result, the converged divergence angle was equal to the rotation angle, predicting that the latter is a major regulator of the spiral phyllotaxis diversity in mosses.

Cuscuta gronovii Willd. ex Roem. & Schult. is a parasitic plant and widely distributed in Europe and North America. Here, we compared the plastome sequences of a C. gronovii plant collected from China and other 16 Cuscuta plastomes, including one C. gronovii plastome from North America. The plastome was 86,727 bp in size with a pair of inverted repeats (IRs) of 14,354 bp, a large single-copy (LSC) region of 50,956 bp, and a small single-copy (SSC) region of 7,063 bp. We predicted 97 genes in the plastome, including 61 protein-coding genes, eight ribosomal RNA genes, and 28 transfer RNA genes. We detected a total of 21 microsatellite, 16 tandem, and ten interspersed repeats in the genome. Gene contents analysis of 17 Cuscuta plastomes showed the loss of the entire ndh gene family. The phylogenomic analysis using 22 shared protein sequences shows that the two C. gronovii formed a cluster. Thirteen of Cuscuta plastomes showed no rearrangement. The other three showed smaller inversions and smaller numbers of gene deletion. Next, we identified the two INDELs, one SNP site between the two C. gronovii plastomes. And we identified two putative RNA editing sites. Lastly, to distinguish between C. gronovii and two medicinal Cuscuta species, C. chinensis and C. australis, we identified ten molecular markers based on the genome sequences. The overall large-scale gene loss, conserved gene order, low intraspecific divergence are consistent with the adaptation of C. gronovii to a parasitic lifestyle.

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microbiota in dioecious plants remains largely unexplored. Here, the diversity and composition of female and male Populus cathayana phyllosphere bacterial and fungal communities were investigated using 16S rRNA/ITS1 gene–based MiSeq sequencing. The divergences of bacterial and fungal community compositions occurred between females and males. Both females and males had their unique phyllosphere bacterial and fungal microbiota, such as bacterial Gemmata spp. (5.41%) and fungal Pringsheimia spp. (0.03%) in females and bacterial Chitinophaga spp. (0.009%) and fungal Phaeococcomyces spp. (0.02%) in males. Significant differences in the relative abundance of phyla Proteobacteria and Planctomycetes bacteria and phyla Ascomycota and Basidiomycota fungi (P < 0.05) were also found between females and males. Some bacterial species of genera Spirosoma and Amnibacterium and fungal genera Venturia, Suillus, and Elmerina spp. were significantly enriched in males (P < 0.05). In contrast, levels of fungal genera Phoma and Aureobasidium spp. were significantly higher in females than in males (P < 0.05). The mineral, inorganic, and organic nutrients content contributed differently to the divergence of female and male phyllosphere microbial communities, with 87.08 and 45.17% of the variations being explained for bacterial and fungal communities, respectively. These results highlight the sexual discrimination of phyllosphere microbes on the dioecious plants and provide hints on the potential host-associated species in phyllosphere environments. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Life-history variation plays a central role in evolutionary and ecological processes and might be especially pertinent to divergence in closely related species. We investigated differences in life history in a pair of parapatric species of ambush bugs (Phymata) and a putative hybrid population. Despite the evidence of gene flow among these species, we found clear divergence between these parapatric populations for a suite of juvenile and adult life-history traits, including components of fitness. The higher latitude species was also less active, suggestive of potential divergence in dispersal. Increased melanism was correlated with longevity in one species, although it was unclear whether this relationship was causal. Observed differences in the life history between species were consistent with expectations of high-latitude species putting a premium on early or rapid development and increased reproductive rates. However, these results were not consistent with ‘pace-of-life syndromes’ at the species level. Individuals from the putative hybrid zone exhibited intermediate values for most traits, although they had slower development and reduced mobility, consistent with some previous work suggesting natural selection via hybrid breakdown.

The genus Pygopleurus includes some of the most important beetle pollinators of the Eastern Mediterranean islands, showing a particular affinity to red-guild flowers. Focussing on the Aegean Archip...

Photosynthetic capacity per unit irradiance is greater, and the marginal carbon revenue of water (∂A/∂E) is smaller, in shaded leaves than sunlit leaves, apparently contradicting optimization theory. I tested the hypothesis that these patterns arise from optimal carbon partitioning subject to biophysical constraints on leaf water potential. In a whole plant model with two canopy modules, I adjusted carbon partitioning, nitrogen partitioning and leaf water potential to maximize carbon profit or canopy photosynthesis, and recorded how gas exchange parameters compared between shaded and sunlit modules in the optimum. The model predicted that photosynthetic capacity per unit irradiance should be larger, and ∂A/∂E smaller, in shaded modules compared to sunlit modules. This was attributable partly to radiation-driven differences in evaporative demand, and partly to differences in hydraulic conductance arising from the need to balance marginal returns on stem carbon investment between modules. The model verified, however, that invariance in the marginal carbon revenue of N (∂A/∂N) is in fact optimal. The Cowan-Farquhar optimality solution (invariance of ∂A/∂E) does not apply to spatial variation within a canopy. The resulting variation in carbon-water economy explains differences in capacity per unit irradiance, reconciling optimization theory with observations.

Methicillin-resistant Staphylococcus aureus (MRSA) of the ST1-SCCmecIV lineage has been associated with community-acquired (CA) infections in North America and Australia. In Brazil, multi-drug resistant ST1-SCCmecIV MRSA has emerged in hospital-associated (HA) diseases in Rio de Janeiro. To understand these epidemiological differences, genomic and phylogenetic analyses were performed. In addition, virulence assays were done for representative CA – and HA-MRSA strains. Despite the conservation of the virulence repertoire, some genes were missing in Brazilian ST1-SCCmecIV including lukSF-PV, fnbB, and several superantigen-encoded genes. Additionally, CA-MRSA lost the splDE while HA-MRSA strains conserved the complete operon. Most of these variable genes were located in mobile genetic elements (MGE). However, conservation and maintenance of MGEs were often observed despite the absence of their associated virulence markers. A Bayesian phylogenetic tree revealed the occurrence of more than one entrance of ST1 strains in Rio de Janeiro. The tree shape and chronology allowed us to infer that the hospital-associated ST1-SCCmecIV from Brazil and the community-acquired USA400 from North America are not closely related and that they might have originated from different MSSA strains that independently acquired SCCmecIV cassettes. As expected, representatives of ST1 strains from Brazil showed lower cytotoxicity and a greater ability to survive inside human host cells. We suggest that Brazilian ST1-SCCmecIV strains have adapted to the hospital setting by reducing virulence and gaining the ability to persist and survive inside host cells. Possibly, these evolutionary strategies may balance the biologic cost of retaining multiple antibiotic resistance genes.

Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char (Salvelinus sp.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length‐frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus was likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present‐day char populations. Although some lakes exhibit bimodal size distributions, using model‐based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genomic analyses using 15,934 SNPs obtained from genotyping by sequencing demonstrated differences among lake groups related to historical biogeography, but within lake groups and within individual lakes, genetic differentiation was not related to total body length. We used PERMANOVA to identify environmental and biological factors related to observed char size structure. Significant predictors included water transparency (i.e., a primary productivity proxy), char density (fish·ha‐1), and lake group. Larger char occurred in lakes with greater primary production and lower char densities, suggesting less intraspecific competition and resource limitation. Thus, char populations in more productive and connected lakes may prove more stable to environmental changes, relative to food‐limited and closed lakes, if lake productivity increases concomitantly. Our findings provide some of the first descriptions of genomic characteristics of char populations in arctic Alaska, and offer important consideration for the persistence of these populations for subsistence and conservation., In this study, we described the morphological and genetic diversity of seven populations of arctic char with varying length‐frequency distributions across two distinct groups of lakes in northern Alaska. Although some lakes exhibit multimodal size distributions, using model‐based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genetic analyses demonstrated differences among lake groups, but within lake groups and within individual lakes, genetic differentiation was not related to total body length.

In their comprehensive review of sex differences in the brain, Eliot et al. (2021) conclude that (1) men and women significantly differ in global brain size, but this "mostly parallels the divergence of male/female body size during development" and that (2) "once we account for individual differences in brain size, there is almost no difference in the volume of specific cortical or subcortical structures between men and women". In sum, almost all brain differences would directly or indirectly follow from differences in body size. In a recent study that does not have the same limitations as most studies reviewed by Eliot et al., we find that sex differences in total brain volume are not accounted for by sex differences in height and weight, and that once global brain size is taken into account, there remain numerous regional sex differences in both directions (Williams et al., 2021).

Buccinum undatum is a subtidal gastropod that exhibits clear spatial variation in several phenotypic shell traits (color, shape, and thickness) across its North Atlantic distribution. Studies of spatial phenotypic variation exist for the species; however, population genetic studies have thus far relied on a limited set of mitochondrial and microsatellite markers. Here, we greatly expand on previous work by characterizing population genetic structure in B. undatum across the North Atlantic from SNP variation obtained by RAD sequencing. There was a high degree of genetic differentiation between Canadian and European populations (Iceland, Faroe Islands, and England) consistent with the divergence of populations in allopatry (FST > 0.57 for all pairwise comparisons). In addition, B. undatum populations within Iceland, the Faroe Islands, and England are typified by weak but significant genetic structuring following an isolation‐by‐distance model. Finally, we established a significant correlation between genetic structuring in Iceland and two phenotypic traits: shell shape and color frequency. The works detailed here enhance our understanding of genetic structuring in B. undatum and establish the species as an intriguing model for future genome‐wide association studies.

By perturbing co-evolved interactions, biological invasions provide an opportunity to study the evolution of interactions between hosts and their parasites on ecological timescales. We studied the interaction between the cane toad (Rhinella marina) and its direct-lifecycle lungworm (Rhabdias pseudosphaerocephala) that was brought from South America to Australia with the toads in 1935. Compared with infective parasite larvae from long-established (range-core) toad populations, parasite larvae from toads near the invasion front were larger, lived longer and were better able to resist exposure to toxin from the parotoid glands of toads. Experimentally, we infected the common-garden-reared progeny of toads from range-core and invasion-front populations within Australia with lungworms from both populations. Infective larvae from invasion-front (vs. range-core) populations of the parasite were more successful at entering toads (by skin penetration) and establishing infections in the lungs. Toads from invasion-front populations were less prone to infection by either type of larvae. Thus, within 84 years, parasites at an invasion front have increased infectivity, whereas hosts have increased resistance to parasite infection compared with range-core populations. Rapid evolution of traits might affect host–parasite interactions during biological invasions, generating unpredictable effects both on the invaders and on native ecosystems.

Habitats can select for specialized phenotypic characteristics in animals. However, the consistency of evolutionary responses to particular environmental conditions remains difficult to predict. One trait of great ecological importance is brain form, which is expected to vary between habitats that differ in their cognitive requirements. Here, we compared divergence in brain form and oral jaw size across a common littoral-pelagic ecological axis in two sunfishes at both the intraspecific and interspecific levels. Brain form differed between habitats at every level of comparison; however, divergence was inconsistent, despite consistent differences in oral jaw size. Pumpkinseed and bluegill species differed in cerebellum, optic tectum and olfactory bulb size. These differences are consistent with a historical ecological divergence because they did not manifest between littoral and pelagic ecotypes within either species, suggesting constraints on changes to these regions over short evolutionary time scales. There were also differences in brain form between conspecific ecotypes, but they were inconsistent between species. Littoral pumpkinseed had larger brains than their pelagic counterpart, and littoral bluegill had smaller telencephalons than their pelagic counterpart. Inconsistent brain form divergence between conspecific ecotypes of pumpkinseed and bluegill sharing a common littoral-pelagic habitat axis suggests that contemporary ecological conditions and historic evolutionary context interact to influence evolutionary changes in brain form in fishes.

In East Asia, genetic divergence is usually considered to be correlated to different floristic regions, however, subtropical-tropical divergence is largely ignored, compared to widely explored temperate-subtropical divergence. Lindera aggregata (Lauraceae), a dominant species in South-East China was selected to address this issue. Fifteen low-copy nuclear genes (LCGs) and four chloroplast DNA (cpDNA) fragments were used to detect its evolutionary history. In LCGs, STRUCTURE and dated Bayesian phylogeny analyses detect distinct subtropical-tropical divergence since late Pleistocene. Approximate Bayesian calculation (ABC) further supports the distinct subtropical-tropical divergence, and close related Taiwan and South China populations are diverged at the last interglacial. Isolation by distance, isolation by environment and isolation by resistance analyses suggest the current climatic difference rather than geographical distance contributes to the genetic differentiation. Principle component analysis shows populations of tropical cluster occur in warmer area with higher precipitation. Ancestral area reconstruction based on Bayesian phylogeny indicates that ancestral L. aggregata populations are distributed in tropical region. In cpDNA, although unique haplotypes are found in tropical region, distinct subtropical-tropical divergence is absent. In conclusion, distinct late Pleistocene subtropical-tropical divergence of L. aggregata is triggered by climate. It is likely that L. aggregata is originated in Southwest-South China and experienced hierarchical dispersal from south to north. The South China Sea land bridge has dual role in connecting or isolating Taiwan and mainland populations since the last glaciation.

Adaptive diversification is a product of both phylogenetic constraint and ecological opportunity. The species-rich parrotfish genera Scarus and Chlorurus display considerable variation in trophic cranial morphology, but these parrotfishes are often described as generalist herbivores. Recent work has suggested that parrotfish partition trophic resources at very fine spatial scales, raising the question of whether interspecific differences in cranial morphology reflect trophic partitioning. We tested this hypothesis by comparing targeted feeding substrata with a previously published dataset of nine cranial morphological traits. We sampled feeding substrata of 15 parrotfish species at Lizard Island, Great Barrier Reef, Australia, by following individuals until focused biting was observed, then extracting a bite core 22 mm in diameter. Three indices were parameterized for each bite core: substratum taphonomy, maximum turf height and cover of crustose coralline algae. Parrotfish species were spread along a single axis of variation in feeding substrata: successional status of the substratum taphonomy and epilithic and endolithic biota. This axis of trophic variation was significantly correlated with cranial morphology, indicating that morphological disparity within this clade is associated with interspecific partitioning of feeding substrata. Phylogenetic signal and phylomorphospace analyses revealed that the evolution of this clade involved a hitherto-unrecognized level of trophic diversification.

The biodiversity of the tropical Americas is a consequence of the interplay between geological and climatic events, with the Andean uplift being a major driver of speciation. Multiple studies have shown that species diversification promoted by the Andes can occur in the presence or absence of gene flow. However, to date, the majority of research addressing this aspect has been conducted in vertebrates, whereas other highly diverse tropical organisms such as arthropods remain uninvestigated. We used a combination of phylogenetics, population genetic analyses and species distribution models to explore whether the northern Andes played a role in the diversification of Ancylometes bogotensis. We detected two major lineages that are separated by the Eastern Cordillera of the Colombian Andes, and they share the same climatic niche. These groups diverged at ~3.85 Mya and exhibit no signatures of gene flow, which can be a consequence of the Andean highlands being poorly suited habitats for this species, thus preventing their genetic connectivity. Our study reveals that the genetic structure of an arachnid species that has limited dispersal capacity and is highly dependent on water bodies is shaped by the Andean orogeny. The generality of this observation remains to be assessed in other invertebrates.

Background DNA methylation is a significant epigenetic modification that is evolutionarily conserved in various species and often serves as a repressive mark for transcription. DNA methylation levels and patterns are regulated by a balance of opposing enzyme functions, DNA methyltransferases, DNMT1/3A/3B and methylcytosine dioxygenases, TET1/2/3. In mice, the TET enzyme converts DNA cytosine methylation (5mC) to 5-hydroxymethylcytosine (5hmC) at the beginning of fertilisation and gastrulation and initiates a global loss of 5mC, while the 5mC level is increased on the onset of cell differentiation during early embryonic development. Objective Global loss and gain of DNA methylation may be differently regulated in diverged species. Methods Chicken B-cell lymphoma DT40 cells were used as an avian model to compare differences in the overall regulation of DNA modification with mammals. Results We found that DNA methylation is maintained at high levels in DT40 cells through compact chromatin formation, which inhibits TET-mediated demethylation. Human and mouse chromosomes introduced into DT40 cells by cell fusion lost the majority of 5mC, except for human subtelomeric repeats. Conclusion Our attempt to elucidate the differences in the epigenetic regulatory mechanisms between birds and mammals explored the evidence that they share a common chromatin-based regulation of TET–DNA access, while chicken DNMT1 is involved in different target sequence recognition systems, suggesting that factors inducing DNMT–DNA association have already diverged.

The paper gives the results of the first studies on the molecular divergence between native and non-native populations of Speonomus normandi hydrophilus (Jeannel, 1907). This species is endemic to Massif Arize in the Central Pyrenees (France), and represents highly specialised organisms that live underground. In 1982, one hundred specimens of S. normandi hydrophilus had been experimentally introduced into the Dzwonnica Cave (Poland). Since then, a numerous population has developed in the Towarna-Dzwonnica cave system, and the neighbouring Cabanowa Cave. After almost 40 years of isolation between native and non-native populations, the genetic variations were examined using the COI and 28S rDNA genes. Analyses of the haplotypes of 28S showed one common haplogroup, which confirms the origin of the Polish group. The differentiation of haplotypes for the COI marker was high for both the French and Polish populations. Altogether 18 haplotypes of this marker have been detected, 12 in the French population and 9 in the Polish. However, only a portion of the haplotypes is shared between the native and introduced population.

The distribution pattern and genetic structure of plant species have been profoundly influenced by climate oscillations. Phylogeographic analyses have been numerously conducted in biodiversity hotspot regions and some general conclusions have been documented. However, other regions have received less attentions and these places may serve as potential glacial refugia for plant species to survive the Quaternary glaciation. Here, we used six nuclear and three cpDNA markers to estimate the phylogeographic pattern of

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times. Los pennatuláceos son un componente importante de las comunidades bentónicas marinas generalmente relacio- nados con fondos blandos. A pesar de su importante papel ecológico, la información sobre su origen y tiempo de divergencia es aún escasa. Los primeros intentos de establecer relaciones filogenéticas entre géneros datan de principios del siglo XX, cuando sólo estaban disponibles caracteres morfológicos. En la última década, los análisis filogenéticos basados en secuen- cias de ADN mitocondrial procedentes de un limitado número de especies han propuesto un ancestro hipotético diferente para este grupo, pero sus relaciones intergenéricas permanecen oscuras. La presente investigación está basada en una combinación de marcadores mitocondriales y nuclear (mtMutS, Cox1 y ADNr 28S), aportando nueva información molecular sobre las relaciones filogenéticas entre los géneros de pennatuláceos, incluyendo 38 nuevas secuencias pertenecientes a 13 especies. Algunas de las relaciones filogenéticas inferidas en el presente estudio cuestionan la actual clasificación de las plumas de mar basada en la morfología (a diferentes niveles taxonómicos), indicando claramente que los dos grupos principales Sessiliflorae y Subselliflorae, algunas de sus principales familias (por ejemplo Pennatulidae, Umbellulidae, Virgulariidae) y algunos gé- neros (por ejemplo Umbellula, Veretillum) son no-monofiléticos. Asimismo, los veretílidos, tradicionalmente considerados los pennatuláceos más primitivos, no se muestran como el taxón divergente más antiguo. Además, un análisis del tiempo de divergencia realizado en este trabajo sugirió que el origen de los pennatuláceos data del Cretácico Inferior (Berriasiano, ~ 144 Ma), de acuerdo con su escasamente conocido registro fósil, mientras que la divergencia inicial de la mayoría de los géneros existentes ocurrió en tiempos del Oligoceno y Mioceno. LAMPOS, ANT XIX/5-REN2001-4929-E/ANT CLIMANT, ANT XXIII/8-POL2006-06399/CGL INDEMARES Cap de Creus, INDEMARES Alborán e INDEMARES Chica-LIFE07/NAT/E/000732 LIFE+ INDEMARES Comisión Nacional de Investigación Científica y Tecnológica de Chile. (CONICYT)-PCHA/Doctorado Nacional/2017–21170438 Ministerio de Economia, Industria y Competitividad de España. (MINECO)- CTM2017-83920-P (DIVERSICORAL)

BackgroundThe vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored.ResultsHere, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group.ConclusionsWe provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

The mechanisms underlying the evolutionary adaptation of animals that transcend the ecological barrier separating the intertidal and supratidal zones of rocky shores are poorly understood. Different wetting frequencies in these zones in tropical regions (daily vs. seasonally, respectively) impose different physical stressors, which should drive phenotypic variation and ultimately speciation in the animals that inhabit them. We studied morphological, physiological and genetic variation in a tropical high-shore gastropod that transcends these zones [Echinolittorina malaccana (Philippi, 1847)]. Variation in melanization, shell features and evaporative water loss was linked to regular seawater wetting, frequent activity and feeding, and solar exposure in intertidal snails, and to inactivity and prolonged aestivation in the shade during continuous air exposure in supratidal snails. Despite selective pressure for phenotypic divergence, and reproductive isolation of the populations in either zone, their mitochondrial COI gene sequences confirmed that they represent a single species. Speciation in our study case is probably constrained by the limitation on activity, mating and reproduction of supratidal snails, such that their populations can only be sustained through intertidal pelagic larval recruitment. Comparisons with other studies suggest that supratidal speciation and specialization for life in this zone probably require moderation of the abiotic (desiccative) conditions, to facilitate greater activity and interaction of animals during air exposure.

The distributions of many sister species in the sea overlap geographically but are partitioned along depth gradients. The genetic changes leading to depth segregation may evolve in geographic isolation as a prerequisite to coexistence or may emerge during primary divergence leading to new species. These alternatives can now be distinguished via the power endowed by the thousands of scorable loci provided by second‐generation sequence data. Here, we revisit the case of two depth‐segregated, genetically isolated ecotypes of the nominal Caribbean candelabrum coral Eunicea flexuosa. Previous analyses based on a handful of markers could not distinguish between models of genetic exchange after a period of isolation (consistent with secondary contact) and divergence with gene flow (consistent with primary divergence). Analyses of the history of isolation, genetic exchange and population size based on 15,640 new SNP markers derived from RNAseq data best support models where divergence began 800K BP and include epochs of divergence with gene flow, but with an intermediate period of transient isolation. Results also supported the previous conclusion that recent exchange between the ecotypes occurs asymmetrically from the Shallow lineage to the Deep. Parallel analyses of data from two other corals with depth‐segregated populations (Agaricia fragilis and Pocillopora damicornis) suggest divergence leading to depth‐segregated populations may begin with a period of symmetric exchange, but that an epoch of population isolation precedes more complete isolation marked by asymmetric introgression. Thus, while divergence‐with‐gene flow may account for much of the differentiation that separates closely related, depth‐segregated species, it remains to be seen whether any critical steps in the speciation process only occur when populations are isolated., Two depth‐segregated, genetically isolated ecotypes of the sea fan Eunicea flexuosa co‐occur across the Caribbean, with high levels of gene flow among populations. Demographic analyses based on SNPs derived from RNA‐seq data suggest a long history of genetic exchange during this pairs' divergence, but also 100K years of transient isolation that may have played a key role in finalizing speciation.

Heterotachy-the change in sequence evolutionary rate over time-is a common feature of protein molecular evolution. Decades of studies have shed light on the conditions under which heterotachy occurs, and there is evidence that site-specific evolutionary rate shifts are correlated with changes in protein function. Here, we present a large-scale, computational analysis using thousands of protein sequence alignments from animal and plant proteomes, representing genes related either by orthology (speciation events) or paralogy (gene duplication), to compare sequence divergence patterns in orthologous vs. paralogous sequence alignments. We use sequence-based phylogenetic analyses to infer overall sequence divergence (tree length/number of sequences) and to fit site-specific rates to a discrete gamma distribution with a shape parameter α. This inference method is applied to real protein sequence alignments, as well as alignments simulated under various models of protein sequence evolution. Our simulations indicate that sequence divergence and the α parameter are positively correlated when sequences evolve with heterotachy, meaning that inferred site rate distributions appear more uniform as sequences diverge. Divergence and α are also positively correlated in both orthologous and paralogous genes, but the average increase in α (as a function of divergence) is significantly higher in paralogous protein alignments than in orthologous alignments. This result is consistent with the widely held view that recently duplicated proteins initially evolve under relaxed selective pressure, promoting functional divergence by accumulation of amino acid replacements, and hence experience more evolutionary rate fluctuations than orthologous proteins. We discuss these findings in the context of the ortholog conjecture, a long-standing assumption in molecular evolution, which posits that protein sequences related by orthology tend to be more functionally conserved than paralogous proteins.

Insects that feed on plants are widely used for studies of host-plant-associated speciation due to their diversity and tractability. The value of these studies necessarily depends upon an accurate understanding of the diet of the focal insects. In North America, the 12 Phytomyza Fallén (Diptera: Agromyzidae) leafmining fly species feeding on hollies (Ilex spp. (Aquifoliaceae: Ilex)) initially appeared to be primarily a host-plant-associated radiation of largely monophagous species. However, our increased collecting efforts found that a majority of the morphospecies are oligophagous, feeding on multiple Ilex species. Patterns of host-associations suggest that colonization of new hosts followed by host-associated speciation may be an important feature of diversification. Analyses of mitochondrial COI data in three oligophagous species found evidence of host-associated genetic structure consistent with processes of host-associated divergence. However, in one of these species, evidence of geographic divergence as well as host-associated divergence was detected, illustrating complexity in factors relating to speciation and host-use evolution in this radiation of leafmining flies.

In studies of ontogenetic allometry, ontogenetic scaling has often been invoked to explain cranial morphological differences between smaller and larger forms of closely related taxa. These scaled variants in shape have been hypothesized to be the result of the extension or truncation of common growth allometries. In this scenario, change in size is the determining factor, perhaps under direct selection, and changes in cranial shapes are byproducts, not under direct selection themselves. However, many of these conclusions are based on studies that used bivariate generalizations of shape. Even among multivariate analyses of growth allometries, there are discrepancies as to the prevalence of ontogenetic scaling among primates, how shared the trajectories need to be, and which taxa evince properties of scaled variants. In this investigation, we use a large, comparative ontogenetic sample, geometric morphometric methods, and multivariate statistical tests to examine ontogenetic allometry and evaluate if differences in cranial shape among closely related catarrhines of varying sizes are primarily driven by size divergence, that is, ontogenetic scaling. We then evaluate the hypothesis of size as a line of least evolutionary resistance in catarrhine cranial evolution. We found that patterns of ontogenetic allometry vary among taxa, indicating that ontogenetic scaling sensu stricto does not often account for most morphological differences and that large and small taxa within clades are generally not scaled variants. The presence of a variety of ontogenetic pathways for the evolution of cranial shapes provides indirect evidence for selection acting directly on the cranial shape, rather than on size alone.

Habitat-associated morphological divergence of the three-spined stickleback, Gasterosteus aculeatus populations was investigated in the southern Caspian Sea basin using landmark-based geometric morphometric method to understand the population structure of this invasive species. A total of 127 specimens were collected from three stations, including the Babol River estuary (center), Gomishan Wetland (east) and the Gisum Coast (west). The left side of each specimen was photographed and 23 landmarks-points were selected to extract body shape data. After generalized procrustes, the data analysis was analyzed using principal components analysis, multivariate analysis of variance/canonical variate analysis and cluster analysis. The results showed a significant difference in body shape between three studied populations (P

Isolation-by-distance is a widespread pattern in nature that describes the reduction of genetic correlation between subpopulations with increased geographic distance. In the population ancestral to modern sister species, this pattern may hypothetically inflate population divergence time estimation due to allele frequency differences in subpopulations at the ends of the ancestral population. In this study, we analyze the relationship between the time to the most recent common ancestor and the population divergence time when the ancestral population model is a linear stepping-stone. Using coalescent simulations, we compare the coalescent time to the population divergence time for various ratios of the divergence time over the population size. Next, we simulate whole genomes to obtain single nucleotide polymorphisms (SNPs), and use the Bayesian coalescent program SNAPP to estimate divergence times. We find that as the rate of migration between neighboring demes decreases, the coalescent time becomes significantly greater than the population divergence time when sampled from end demes. Divergence-time overestimation in SNAPP becomes severe when the divergence-to-population size ratio < 10 and migration is low. Finally, we demonstrate the impact of ancestral isolation-by-distance on divergence-time estimation using an empirical dataset of squamates (Tropidurus) endemic to Brazil. We conclude that studies estimating divergence times should be cognizant of the potential ancestral population structure in an explicitly spatial context or risk dramatically overestimating the timing of population splits.

Polyomaviruses (PyVs) are small, circular dsDNA viruses carried by diverse vertebrates, including bats. Although previous studies have reported several horseshoe bat PyVs collected in Zambia and China, it is still unclear how PyVs evolved in this group of widely dispersed mammals. Horseshoe bats (genus Rhinolophus) are distributed across the Old World and are natural reservoirs of numerous pathogenic viruses. Herein, non-invasive bat samples from European horseshoe bat species were collected in Hungary for PyV identification and novel PyVs with complete genomes were successfully recovered from two different European horseshoe bat species. Genomic and phylogenetic analysis of the Hungarian horseshoe bat PyVs supported their classification into the genera Alphapolyomavirus and Betapolyomavirus. Notably, despite the significant geographical distances between the corresponding sampling locations, Hungarian PyVs exhibited high genetic relatedness with previously described Zambian and Chinese horseshoe bat PyVs, and phylogenetically clustered with these viruses in each PyV genus. Correlation and virus–host relationship analysis suggested that these PyVs co-diverged with their European, African and Asian horseshoe bat hosts distributed on different continents during their evolutionary history. Additionally, assessment of selective pressures over the major capsid protein (VP1) of horseshoe bat PyVs showed sites under positive selection located in motifs exposed to the exterior of the capsid. In summary, our findings revealed a pattern of stable intrahost divergence of horseshoe bat PyVs with their mammalian hosts on the African and Eurasian continents over evolutionary time.

Karyological and molecular genetic study of the sculpins of the genus Myoxocephalus is conducted. Molecular genetic analysis demonstrates that the genus is heterogeneous in the contemporary composition and is divided into Pacific and Arctic-Atlantic groups. In the Pacific group, a close phylogenetic relationship is found between the species M. stelleri, M. polyacanthocephalus, and M. jaok. The representative of the Arctic-Atlantic group, M. quadricornis, is monotypic and sister to Megalocottus platycephalus. Close relations of M. scorpius and the sculpins of the Pacific group are revealed on the basis of the molecular genetic and karyological data. Analysis of M. brandtii, M. ochotensis, and M. jaok from different parts of their habitats shows the absence of karyological variability. The degree and direction of the divergence of the karyotypes in Pacific species M. brandtii, M. ochotensis, M. jaok, M. polyacanthocephalus, M. stelleri, and M. scorpius are established.

Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans-Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds, and passerines) at population, subspecies, and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split-migration model (divergence with gene flow), three best fit a secondary-contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (FST ), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed SNPs, and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.

This study was designed to assess morphological changes between cultured and wild tilapia, Oreochromis niloticus (L.). Wild fish samples were obtained from fishermen operating in the waters of the vicinity of the province Parakou, Benin in November 2014, while the cultured samples were obtained from a fish farm in the municipality of Sô-Ava in the Atlantic region of the southern part of the Republic of Benin. Significant differences were observed in all nine morphometric traits measured. Discriminant analysis of morphometric parameters showed high divergence between the populations. The meristic count, however, overlapped broadly showing no divergence between the populations. The morphometric differences between the cultured and wild tilapia, O. niloticus, could have been linked to genetic differences or environmental factors or a combination of these.

OCBIL theory provides a basis for understanding of the evolution and ecology of biota on old, climatically buffered, infertile landscapes (OCBILs) worldwide. Here, we test a genetic hypothesis presented in OCBIL theory that predicts highly differentiated intraspecific population systems on OCBILs vs. more limited differentiation on young, often disturbed, fertile landscapes (YODFELs). We examined patterns of genomic and morphological divergence in Banksia seminuda across OCBILs and YODFELs in south-western Australia. We also used these data to determine whether these OCBIL and YODFEL populations represent distinct subspecific lineages, a point of previous contention among taxonomists. As hypothesized, genomic analyses based on 3466 SNP loci revealed strong structuring within B. seminuda, with high differentiation across narrow geographic scales among OCBIL populations vs. lower differentiation across much larger geographic scales among YODFEL populations. In addition, genomic and morphological divergence was found between OCBIL and YODFEL populations, providing comprehensive quantitative evidence for two subspecies. These findings have taxonomic implications for the species and provide support for OCBIL theory and its insights into the evolution, ecology and conservation of biota on ancient landscapes.

Many eusocial insects, including ants, show complex colony structures, distributions, and reproductive strategies. In the ant Vollenhovia emeryi Wheeler (Hymenoptera: Myrmicinae), queens and males are produced clonally, while sterile workers arise sexually, unlike other ant species and Hymenopteran insects in general. Furthermore, there is a wing length polymorphism in the queen caste. Despite its evolutionary remarkable traits, little is known about the population structure of this ant species, which may provide insight into its unique reproductive mode and polymorphic traits. We performed in‐depth analyses of ant populations from Korea, Japan, and North America using three mitochondrial genes (COI, COII, and Cytb). The long‐winged (L) morph is predominant in Korean populations, and the short‐winged (S) morph is very rare. Interestingly, all L morphs were infected with Wolbachia, while all Korean S morphs lacked Wolbachia, demonstrating a association between a symbiont and a phenotypic trait. A phylogenetic analysis revealed that the S morph is derived from the L morph. We propose that the S morph is associated with potential resistance to Wolbachia infection and that Wolbachia infection does not influence clonal reproduction (as is the case in other ant species).

The current study focused on characterization of the underlying genetic divergence in inbred lines developed from local landraces of North Eastern Hill Region of India – a designated Asiatic maize diversity centre – following six generations of inbreeding. Substantial genetic differentiation was indicated based on very high to moderateFstvalues for 22 of the 38 simple sequence repeat markers studied. STRUCTURE analysis partitioned the subset into two distinct and one admixture subgroup (Populations I, II and III respectively) accompanied by a significant reduction in heterozygosity. Population II was further subdivided into subpopulations Pop-M9 and Pop-T9. Nei's pairwise genetic distance and populationFstvalues indicated that Populations I and II were more divergent with neighbour joining clustering analysis clearly defining landraces originating from the states of Tripura (Population II) and Sikkim (Population I) as most divergent. Principal coordinates analysis could explain 31.26% of the variation present in the subgroups wherein Population I was more variable. Analysis of molecular variance andFstcoefficients (P< 0.001) indicated 17% population structuring with 55% variation detected for individuals within populations. These results combined with the presence of phenotypic variability in the subgroups for yield traits supported by results of a preliminary partial diallel analysis strongly suggest the existence of distinct heterotic groups. Divergence studies are crucial for exploiting heterosis, and the current study would go a long way to help establish a germplasm base for developing varieties with improved agronomic performance and surer commercial prospects no reports of which are available thus far.

Gossypium hirsutum L. (Upland cotton) has an evolutionary history involving inter-genomic hybridization, polyploidization, and subsequent domestication. We analyzed the developmental dynamics of the cotton fiber transcriptome accompanying domestication using gene coexpression networks for both joint and homoeologous networks. Remarkably, most genes exhibited expression for at least one homoeolog, confirming previous reports of widespread gene usage in cotton fibers. Most coexpression modules comprising the joint network are preserved in each subgenomic network and are enriched for similar biological processes, showing a general preservation of network modular structure for the two co-resident genomes in the polyploid. Interestingly, only one fifth of homoeologs co-occur in the same module when separated, despite similar modular structures between the joint and homoeologous networks. These results suggest that the genome-wide divergence between homoeologous genes is sufficient to separate their co-expression profiles at the intermodular level, despite conservation of intramodular relationships within each subgenome. Most modules exhibit D-homoeolog expression bias, although specific modules do exhibit A-homoeolog bias. Comparisons between wild and domesticated coexpression networks revealed a much tighter and denser network structure in domesticated fiber, as evidenced by its fewer modules, 13-fold increase in the number of development-related module member genes, and the poor preservation of the wild network topology. These results demonstrate the amazing complexity that underlies the domestication of cotton fiber.

The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.

Population divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide datasets allows discrimination between alternative scenarios for these processes even in non-model taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum (bSFS), the second on the Pairwise Sequentially Markovian Coalescent (PSMC)) to infer the divergence history of a fig wasp,Pleistodontes nigriventris. Pleistodontes nigriventrisand its fig tree mutualistFicus watkinsianaare restricted to rain forest patches along the eastern coast of Australia, and are separated into northern and southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations ofP. nigriventris,and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of post divergence gene flow.Pleistodontes nigriventrishas low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations divergedca. 196kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture eventca.57kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, non-model organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.

DNA barcoding is a rapid, precise, and effective way of species identification. A short and standard target gene marker is used to create sequence profile of identified species. Specific tag or marker is used, which is derived from mitochondrial COI for identification. Effectiveness of this method axes the degree of divergence among species. Identification is necessary for their representation. In the present work, Catla catla was used to study by using Cytochrome C Oxidase 1.The genetic distances were computed, and Neighbor Joining tree was constructed based on the Kimura 2 Parameter method. GenBank and BOLD revealed definitive identity matches. Conspecific and congeneric K2P nucleotide divergence was estimated. Evolutionary tree was analyzed clearly by relating their species to phylogenetic tree, as same as species were bunched under same tree node, while species were differently clustered under distinct nodes. These findings conclude that the gene sequence may serve as a milestone for identification and phylogenetic history of related species at molecular level.