Adaptive Variation Research Articles

Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen.

The rapid adaptive evolution of microbes is driven by strong selection pressure acting on genetic variation. How adaptive genetic variation is generated within species and how such variation influences phenotypic trait expression is often not well understood though. We focused on the recent activity of transposable elements (TEs) using deep population genomics and transcriptomics analyses of a fungal plant pathogen with a highly active content of TEs in the genome. Zymoseptoria tritici causes one of the most damaging diseases on wheat, with recent adaptation to the host and environment being facilitated by TE-associated mutations. We obtained genomic and RNA-sequencing data from 146 isolates collected from a single wheat field. We established a genome-wide map of TE insertion polymorphisms in the population by analyzing recent TE insertions among individuals. We quantified the locus-specific transcription of individual TE copies and found considerable population variation at individual TE loci in the population. About 20% of all TE copies show transcription in the genome suggesting that genomic defenses such as repressive epigenetic marks and repeat-induced polymorphisms are at least partially ineffective at preventing the proliferation of TEs in the genome. A quarter of recent TE insertions are associated with expression variation of neighboring genes providing broad potential to influence trait expression. We indeed found that TE insertions are likely responsible for variation in virulence on the host and potentially diverse components of secondary metabolite production. Our large-scale transcriptomics study emphasizes how TE-derived polymorphisms segregate even in individual microbial populations and can broadly underpin trait variation in pathogens.IMPORTANCEPathogens can rapidly adapt to new hosts, antimicrobials, or changes in the environment. Adaptation arises often from mutations in the genome; however, how such variation is generated remains poorly understood. We investigated the most dynamic regions of the genome of Zymoseptoria tritici, a major fungal pathogen of wheat. We focused on the transcription of transposable elements. A large proportion of the transposable elements not only show signatures of potential activity but are also variable within a single population of the pathogen. We find that this variation in activity is likely influencing many important traits of the pathogen. Hence, our work provides insights into how a microbial species can adapt over the shortest time periods based on the activity of transposable elements.

Adaptive Phase or Variant Formation at the Austenite/Twinned Martensite Interface in Modulated Ni–Mn–Ga Martensite

AbstractThe crystal structure and transformation path from austenite to 10M martensite in Ni–Mn–Ga single crystal are examined employing high‐energy synchrotron radiation, scanning, and transmission electron microscopy. Using temperature gradient, an austenite/twinned martensite interface is stabilized revealing the crystal structure and microstructure of both phases and the transformation sequence across the interface. Depending on the distance from the interface, three distinct types of martensite crystal lattice, namely simple tetragonal and two monoclinic modulated ones, that is, 10M′ and 10M are confirmed. In situ measurements show that lattice mismatch formed at the habit plane is compensated by the formation of micro‐twinned and branched martensite along with an elastic change in lattice parameters. It is shown that the characteristics for periodic shuffling twin boundaries, such as modulation twins or inverted stacking faults, are installed in later stages of transformation. In other words, large microstructure elements that most efficiently accommodate the strain are installed first, and then smaller elements are operable. Overall, the experimental results show that the crystal lattice does not adapt modulated phase at the habit plane and cannot be built up from simple non‐modulated tetragonal blocks but rather a specific sequence of phase transformations using shear/shuffling deformation takes place.

Trophic niche drives the evolution of craniofacial shape in Trinidadian guppies.

Diverse clades of fishes adapted to feeding on the benthos repeatedly converge on steep craniofacial profiles and shorter, wider heads. But in an incipient radiation, to what extent is this morphological evolution measurable and can we distinguish the relative genetic vs. plastic effects? We use the Trinidadian guppy (Poecilia reticulata) to test the repeatability of adaptation and the alignment of genetic and environmental effects shaping poecilid craniofacial morphology. We compare wild-caught and common garden lab-reared fish to quantify the genetic and plastic components of craniofacial morphology across 4 populations from 2 river drainage systems (n = 56 total). We first use micro-computed tomography to capture 3D morphology, then place both landmarks and semilandmarks to perform size-corrected 3D morphometrics and quantify shape space. We find a measurable, significant, and repeatable divergence in craniofacial shape between high-predation invertivore and low-predation detritivore populations. As predicted from previous examples of piscine adaptive trophic divergence, we find increases in head slope and craniofacial compression among the benthic detritivore foragers. Furthermore, the effects of environmental plasticity among benthic detritivores produce exaggerated craniofacial morphological change along a parallel axis to genetic morphological adaptation from invertivore ancestors. Overall, many of the major patterns of benthic-limnetic craniofacial evolution appear convergent among disparate groups of teleost fishes.

Experimental evidence for adaptive divergence in response to a warmed habitat reveals roles for morphology, allometry and parasite resistance.

Ectotherms are expected to be particularly vulnerable to climate change-driven increases in temperature. Understanding how populations adapt to novel thermal environments will be key for informing mitigation plans. We took advantage of threespine stickleback (Gasterosteus aculeatus) populations inhabiting adjacent geothermal (warm) and ambient (cold) habitats to test for adaptive evolutionary divergence using a field reciprocal transplant experiment. We found evidence for adaptive morphological divergence, as growth (length change) in non-native habitats related to head, posterior and total body shape. Higher growth in fish transplanted to a non-native habitat was associated with morphological shape closer to native fish. The consequences of transplantation were asymmetric with cold sourced fish transplanted to the warm habitat suffering from lower survival rates and greater parasite prevalence than warm sourced fish transplanted to the cold habitat. We also found divergent shape allometries that related to growth. Our findings suggest that wild populations can adapt quickly to thermal conditions, but immediate transitions to warmer conditions may be particularly difficult.

Adaptive Evolution of Nearctic Deepwater Fish Vision: Implications for Assessing Functional Variation for Conservation.

Intraspecific functional variation is critical for adaptation to rapidly changing environments. For visual opsins, functional variation can be characterized in vitro and often reflects a species' ecological niche but is rarely considered in the context of intraspecific variation or the impact of recent environmental changes on species of cultural or commercial significance. Investigation of adaptation in postglacial lakes can provide key insight into how rapid environmental changes impact functional evolution. Here, we report evidence for molecular adaptation in vision in 2 lineages of Nearctic fishes that are deep lake specialists: ciscoes and deepwater sculpin. We found depth-related variation in the dim-light visual pigment rhodopsin that evolved convergently in these 2 lineages. In vitro characterization of spectral sensitivity of the convergent deepwater rhodopsin alleles revealed blue-shifts compared with other more widely distributed alleles. These blue-shifted rhodopsin alleles were only observed in deep clear postglacial lakes with underwater visual environments enriched in blue light. This provides evidence of remarkably rapid and convergent visual adaptation and intraspecific functional variation in rhodopsin. Intraspecific functional variation has important implications for conservation, and these fishes are of conservation concern and great cultural, commercial, and nutritional importance to Indigenous communities. We collaborated with the Saugeen Ojibway Nation to develop and test a metabarcoding approach that we show is efficient and accurate in recovering the ecological distribution of functionally relevant variation in rhodopsin. Our approach bridges experimental analyses of protein function and genetics-based tools used in large-scale surveys to better understand the ecological extent of adaptive functional variation.

Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks.

Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.

Morphologic and mechanical adaptive variations in Saiga tatarica calcaneus: A model for interpreting the bone functional adaptation of wild artiodactyl in captivity.

Captivity alters the locomotor behavior of wild artiodactyls and affects the mechanical loading of the calcaneus; however, the resulting adaptive changes in calcaneus morphology have not been sufficiently studied to date. This study aimed to investigate the morphological and mechanical adaptive variations in the calcaneus of Saiga tatarica to understand further the functional adaptation of the calcaneus in wild artiodactyl to captivity. Paired calcanei from autopsy samples of six captive wild artiodactyls (S. tatarica) and six domesticated artiodactyls (Ovis aries) were divided into skeletally immature and mature groups using X-ray evaluation of growth plate closure. High-resolution microcomputed tomography revealed a calcaneal diaphyseal cross-section. The mechanical and nanomorphological characteristics of the trabecular bone were determined by atomic force microscopy. The percent cortical bone area (%CA), cortical thickness ratio (CTR), and Young's modulus (E) differed between species in the immature groups but not in the mature groups. S. tatarica had significantly higher growth rates for %CA, CTR, and E in the mid-shaft than O. aries (p < 0.05). The calcaneus morphology of S. tatarica converges with that of domesticated O. aries during ontogeny. These results indicate that the calcaneus of wild artiodactyls can undergo potentially transitional changes during the short-term adaptation to captivity. The above parameters can be preliminarily identified as morphological signs of functional bone adaptation in artiodactyls.

Intra‐specific variation and climate differentially shape the thermal germination niches of three co‐occurring woodland forbs

AbstractUnderstanding plant responses to temperature is critical for predicting their vulnerability to global warming and for planning management responses. Germination is a key life‐stage, strongly regulated by temperature, that affects the potential for plant populations to persist. Here, we compared the thermal germination niches of three unrelated, declining woodland forb species – Arthropodium fimbriatum (Asparagaceae), Bulbine bulbosa (Asphodelaceae), Microseris walteri (Asteraceae) – across common temperature and precipitation gradients, to characterize the relationships with home‐site climate, and associated implications for ecological restoration in a changing climate. Open‐pollinated seed were sampled from 14–15 populations per species across an aridity gradient in south‐eastern Australia. Germination responses for each population were tested in controlled temperature cabinets under five temperature regimes encompassing contemporary and projected future temperatures. Optimum germination temperature and thermal germination niche were characterized and assessed for associations with home‐site climate and potential germination under projected climate change. The three species showed significant intra‐specific variation in the thermal germination niche. Optimum germination temperature was correlated with home‐site climate, suggesting adaptive variation among populations in germination requirements. However, the pattern of variation in optimum germination across the environmental gradients was not always consistent among the species. Future temperatures projected under climate change tended to be outside the current thermal germination niche for all species, indicating potential benefits of incorporating pre‐adapted populations in ecological restoration. Climate‐related intra‐specific variation in the thermal germination niche provides evidence for local adaptation to climate in all three forb species and suggests potential differences among populations in vulnerability to global warming. These results emphasize the importance of understanding the extent of intra‐specific variation in key life history traits to better manage and conserve populations and restore their ecosystems as climates change.

The geno-geo-climate nexus: contributions of geographic and ecological factors in shaping the genomic divergence of two closely related threatened rainforest species of Fontainea Heckel (Euphorbiaceae)

ContextProcesses that shape genomic and ecological divergence can reveal important evolutionary dynamics to inform the conservation of threatened species. Fontainea is a genus of rainforest shrubs and small trees including critically endangered and threatened species restricted to narrow, but complex geographic and ecological regions. Several species of Fontainea are subject to spatially explicit conditions and experience limited intra-specific gene flow, likely generating genetic differentiation and local adaptation.ObjectivesHere, we explored the genetic and ecological mechanisms underlying patterns of diversification in two, closely related threatened Fontainea species. Our aim was to compare spatial patterns of genetic variation between the vulnerable Fontainea australis (Southern Fontainea) and critically endangered F. oraria (Coastal Fontainea), endemic to the heterogeneous subtropical region of central, eastern Australia, where large-scale clearing has severely reduced rainforest habitat to a fraction (< 1%) of its pre-European settlement extent.MethodsWe used a set of 10,000 reduced-representation markers to infer genetic relationships and the drivers of spatial genetic variation across the two species. In addition, we employed a combination of univariate and multivariate genome-environment association analysis using a set of topo-climatic variables to explore potential patterns of local adaptation as a factor impacting genomic divergence.ResultsOur study revealed that Coastal Fontainea have a close genetic relationship with Southern Fontainea. We showed that isolation by distance has played a key role in their genetic variation, indicating that vicariance can explain the spatial genetic distribution of the two species. Genotype-environment analyses showed a strong association with temperature and topographic features, suggesting adaptation to localised thermal environments. We used a multivariate redundancy analysis to identify a range of putatively adapted loci associated with local environmental conditions.ConclusionsDivergent selection at the local-habitat scale as a result of dispersal limitations and environmental heterogeneity (including physical barriers) are likely contributors to adaptive divergence between the two Fontainea species. Our findings have presented evidence to indicate that Southern and Coastal Fontainea were comprised of distinct genetic groups and ecotypes, that together may form a single species continuum, with further phenotype research suggested to confirm the current species boundaries. Proactive conservation actions, including assisted migration to enhance the resilience of populations lacking stress-tolerant single nucleotide polymorphisms (SNPs) may be required to secure the long-term future of both taxa. This is especially vital for the critically endangered Coastal Fontainea given projections of habitat decline for the species under future climate scenarios.

Joint optimization of sampling point and sensing threshold for spectrum sensing

AbstractWith the continuous evolution and in‐depth integration between wireless communication and emerging technology such as internet of things (IoT), artificial intelligence (AI) etc., wireless terminals are growing exponentially, thus bringing great challenges to available spectrum resources. The contradiction between unlimited frequency needs and limited spectrum resources has become a bottleneck restricting the development of wireless communication technology. As an efficient way to improve spectrum efficiency, cognitive radio (CR) continues to be the focus of wireless communication within decades. To conduct CR, the main procedure is the discovery of available spectral holes by periodically monitoring the target authorized band, namely spectrum sensing (SS). Energy detector (ED) is widely accepted for SS due to its low complexity and high convenience. The essence of traditional ED based SS schemes consist in the adaptive variation of sensing threshold/sampling point with environmental signal‐to‐noise ratio (SNR) at the receiver of CR terminal, namely adaptive sensing threshold/sampling point based SS. However, the performance of both adaptive sensing threshold and adaptive sampling point based SS schemes are always at the expense of computation complexity due to the excessive sampling point. In addition, these two schemes are both about the optimization issue of a single variable under constraints. Actually, both detection probability and false alarm probability of ED are a two‐dimensional function of sensing threshold and sampling point for a given SNR. The optimal solution of sensing performance can not be obtained by optimizing sensing threshold or sampling point alone. Motivated by these, the joint optimization of sampling point and sensing threshold is considered for SS in this paper, where sampling point and sensing threshold are jointly adaptive with the variation of environmental SNR. In addition, Q‐learning is considered in this paper to obtain the sub‐optimal solution due to the non‐convexity of the considered optimization problem. Finally, the simulation experiments are made and the results validate the effectiveness of the proposed scheme.

Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G.

Rainforest hunter-gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S)-fat accumulation localized in the hips (DSWS phenotype). Based on previous evidence in the Andamanese population, we first characterized signatures of adaptive natural selection around the calcium-sensing receptor gene in Southeast Asian rainforest groups presenting the DSWS phenotype and identified the R990G substitution (rs1042636) as a putative adaptive variant for experimental follow-up. Although the calcium-sensing receptor has a critical role in calcium homeostasis by directly regulating the parathyroid hormone secretion, it is expressed in different tissues and has been described to be involved in many biological functions. Previous works have also characterized the R990G substitution as an activating polymorphism of the calcium-sensing receptor associated with hypocalcemia. Therefore, we generated a knock-in mouse for this substitution and investigated organismal phenotypes that could have become adaptive in rainforest hunter-gatherers from Southeast Asia. Interestingly, we found that mouse homozygous for the derived allele show not only lower serum calcium concentration but also greater body weight and fat accumulation, probably because of enhanced preadipocyte differentiation and lipolysis impairment resulting from the calcium-sensing receptor activation mediated by R990G. We speculate that such differential features in humans could have facilitated the survival of hunter-gatherer groups during periods of nutritional stress in the challenging conditions of the Southeast Asian tropical rainforests.

Genomic resources for the Yellowfin tuna Thunnus albacares.

The Yellowfin tuna (Thunnus albacares) is a large tuna exploited by major fisheries in tropical and subtropical waters of all oceans except the Mediterranean Sea. Genomic studies of population structure, adaptive variation or of the genetic basis of phenotypic traits are needed to inform fisheries management but are currently limited by the lack of a reference genome for this species. Here we report a draft genome assembly and a linkage map for use in genomic studies of T. albacares. Illumina and PacBio SMRT sequencing were used in combination to generate a hybrid assembly that comprises 743,073,847 base pairs contained in 2,661 scaffolds. The assembly has a N50 of 351,587 and complete and partial BUSCO scores of 86.47% and 3.63%, respectively.Double-digest restriction associated DNA (ddRAD) was used to genotype the 2 parents and 164 of their F1 offspring resulting from a controlled breeding cross, retaining 19,469 biallelic single nucleotide polymorphism (SNP) loci. The SNP loci were used to construct a linkage map that features 24 linkage groups that represent the 24 chromosomes of yellowfin tuna. The male and female maps span 1,243.8cM and 1,222.9cM, respectively. The map was used to anchor the assembly in 24 super-scaffolds that contain 79% of the yellowfin tuna genome. Gene prediction identified 46,992 putative genes 20,203 of which could be annotated via gene ontology. The draft reference will be valuable to interpret studies of genome wide variation in T. albacares and other Scombroid species.

Responsive Alternative Splicing Events of Opisthopappus Species against Salt Stress.

Salt stress profoundly affects plant growth, prompting intricate molecular responses, such as alternative splicing (AS), for environmental adaptation. However, the response of AS events to salt stress in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear, which is a Taihang Mountain cliff-dwelling species. Using RNA-seq data, differentially expressed genes (DEGs) were identified under time and concentration gradients of salt stress. Two types of AS, skipped exon (SE) and mutually exclusive exons (MXE), were found. Differentially alternative splicing (DAS) genes in both species were significantly enriched in "protein phosphorylation", "starch and sucrose metabolism", and "plant hormone signal transduction" pathways. Meanwhile, distinct GO terms and KEGG pathways of DAS occurred between two species. Only a small subset of DAS genes overlapped with DEGs under salt stress. Although both species likely adopted protein phosphorylation to enhance salt stress tolerance, they exhibited distinct responses. The results indicated that the salt stress mechanisms of both Opisthopappus species exhibited similarities and differences in response to salt stress, which suggested that adaptive divergence might have occurred between them. This study initially provides a comprehensive description of salt responsive AS events in Opisthopappus and conveys some insights into the molecular mechanisms behind species tolerance on the Taihang Mountains.

Genetically Encoded Lizard Color Divergence for Camouflage and Thermoregulation.

Local adaptation is critical in speciation and evolution, yet comprehensive studies on proximate and ultimate causes of local adaptation are generally scarce. Here, we integrated field ecological experiments, genome sequencing, and genetic verification to demonstrate both driving forces and molecular mechanisms governing local adaptation of body coloration in a lizard from the Qinghai-Tibet Plateau. We found dark lizards from the cold meadow population had lower spectrum reflectance but higher melanin contents than light counterparts from the warm dune population. Additionally, the colorations of both dark and light lizards facilitated the camouflage and thermoregulation in their respective microhabitat simultaneously. More importantly, by genome resequencing analysis, we detected a novel mutation in Tyrp1 that underpinned this color adaptation. The allele frequencies at the site of SNP 459# in the gene of Tyrp1 are 22.22% G/C and 77.78% C/C in dark lizards and 100% G/G in light lizards. Model-predicted structure and catalytic activity showed that this mutation increased structure flexibility and catalytic activity in enzyme TYRP1, and thereby facilitated the generation of eumelanin in dark lizards. The function of the mutation in Tyrp1 was further verified by more melanin contents and darker coloration detected in the zebrafish injected with the genotype of Tyrp1 from dark lizards. Therefore, our study demonstrates that a novel mutation of a major melanin-generating gene underpins skin color variation co-selected by camouflage and thermoregulation in a lizard. The resulting strong selection may reinforce adaptive genetic divergence and enable the persistence of adjacent populations with distinct body coloration.

Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur

BackgroundLocal adaptation is a key evolutionary process that enhances the growth of plants in their native habitat compared to non-native habitats, resulting in patterns of adaptive genetic variation across the entire geographic range of the species. The study of population adaptation to local environments and predicting their response to future climate change is important because of climate change.ResultsHere, we explored the genetic diversity of candidate genes associated with bud burst in pedunculate oak individuals sampled from 6 populations in Poland. Single nucleotide polymorphism (SNP) diversity was assessed in 720 candidate genes using the sequence capture technique, yielding 18,799 SNPs. Using landscape genomic approaches, we identified 8 FST outliers and 781 unique SNPs in 389 genes associated with geography, climate, and phenotypic variables (individual/family spring and autumn phenology, family diameter at breast height (DBH), height, and survival) that are potentially involved in local adaptation. Then, using a nonlinear multivariate model, Gradient Forests, we identified vulnerable areas of the pedunculate oak distribution in Poland that are at risk from climate change.ConclusionsThe model revealed that pedunculate oak populations in the eastern part of the analyzed geographical region are the most sensitive to climate change. Our results might offer an initial evaluation of a potential management strategy for preserving the genetic diversity of pedunculate oak.

Designing Compatible Ceramic/Polymer Composite Solid-State Electrolyte for Stable Silicon Nanosheet Anodes.

The commercialization of silicon anode for lithium-ion batteries has been hindered by severe structure fracture and continuous interfacial reaction against liquid electrolytes, which can be mitigated by solid-state electrolytes. However, rigid ceramic electrolyte suffers from large electrolyte/electrode interfacial resistance, and polymer electrolyte undergoes poor ionic conductivity, both of which are worsened by volume expansion of silicon. Herein, by dispersing Li1.3Al0.3Ti1.7(PO4)3 (LATP) into poly(vinylidene fluoride)-hexafluoropropylene (PVDF-HFP) and poly(ethylene oxide) (PEO) matrix, the PVDF-HFP/PEO/LATP (PHP-L) solid-state electrolyte with high ionic conductivity (1.40 × 10-3Scm-1), high tensile strength and flexibility is designed, achieving brilliant compatibility with silicon nanosheets. The chemical interactions between PVDF-HFP and PEO, LATP increase amorphous degree of polymer, accelerating Li+ transfer. Good flexibility of the PHP-L contributes to adaptive structure variation of electrolyte with silicon expansion/shrinkage, ensuring swift interfacial ions transfer. Moreover, the solid membrane with high tensile limits electrode structural degradation and eliminates continuous interfacial growth to form stable 2D solid electrolyte interface (SEI) film, achieving superior cyclic performance to liquid electrolytes. The Si//PHP-L15//LiFePO4 solid-state full-cell exhibits stable lithium storage with 81% capacity retention after 100 cycles. This work demonstrates the effectiveness of composite solid electrolyte in addressing fundamental interfacial and performance challenges of silicon anodes.

Geometric Morphometric Research of the Molars in Tree Shrews (Tupaia belangeri) from Different Regions

Background: Biological traits are mainly determined by genotype and are also influenced by environmental factors, especially in the process of adapting to different environments, corresponding phenotypic variations may occur. Even for the same animal, there may be some morphological differences due to its long-term adaptation to different habitat environments. Molar teeth are the direct contact point between animals and the environment, which are of great significance in the study of animal adaptability to different environments. Methods: To explore the relationship between the morphology of the molars (upper molars and lower molars) of tree shrews (Tupaia belangeri) and environmental variations in different regions, we applied geometric morphometric methods to measure the morphological characteristics of the molars of T. belangeri in 12 different regions of China (Hainan, Daxin, Leye, Xingyi, Xichang, Hekou, Kunming, Mengla, Dali, Tengchong, Pianma, Laboratory bred F1 generation). Result: The results showed that the morphological variations of the lower molars of T. belangeri in 12 different regions were larger, which was more suitable and reference valuable for studying the morphological differences among different geographical populations. The Principal component analysis showed that T. belangeri from 12 regions were clustered into 4 branches: Hainan was clustered into one branch, Daxin was clustered into one branch, Pianma and Tengchong were clustered into one branch and Leye, Xingyi, Hekou, Kunming, Xichang, Mengla, Dali and laboratory bred F1 generation were clustered into one branch. The thin plate spline analysis showed that deformations in the upper molars were mostly concentrated in the alveolar and dental margins. The deformations of the lower molars were mainly concentrated in the alveolar, marginal and occlusal surfaces. Multidimensional scaling showed that there were differences in molars morphology among the 12 locations, with significant variations in Hainan, Daxin, Pianma and Tengchong regions, reflecting the adaptive variation of T. belangeri to different ecological environments. The present results can provide a certain basis for the study of phenotypic adaptation in T. belangeri.

Oryza CLIMtools: A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits

Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To address this issue, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that enable the user to (1) explore the local environments of traditional rice varieties (landraces) in South-East Asia and (2) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We demonstrate the value of these resources by identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1. Prior quantitative trait locus analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing potential evapotranspiration gradient and revealed their regulation of key agronomic traits, including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce climate-resilient crops.

Adaptive divergence of seasonal heart plasticity between Canadian and Spanish pumpkinseed sunfish populations

AbstractLaboratory experiments suggest that reversible changes in the heart ventricle phenotype of fish accompany acclimation to temperature change to maintain cardiac function, but related work in fish living in natural conditions is scant. We investigated seasonal variation in heart ventricular mass and collagen content in pumpkinseed sunfish (Lepomis gibbosus) living in outdoor ponds where they experienced high seasonality conditions. Additionally, we compared populations adapted to high and low seasonality to evaluate potential divergence in seasonal heart plasticity. Heart ventricular mass decreased in the summer compared to colder seasons only in populations adapted to high seasonality. The absence of seasonal variation in ventricular mass in sunfish adapted to low seasonality was not due to changes in foraging activity, suggesting a loss of ventricle size plasticity due to either costs of plasticity or relaxed selection. Seasonal variation in ventricle collagen content also occurred, with the highest collagen content in summer regardless of population adaptation to high or low seasonality. Only the proportion of thick collagen fibres changed across seasons. We conclude that natural seasonal cues induce plastic responses in some functional heart traits and propose that these responses can rapidly diverge among populations under different seasonal regimes.

Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula.

Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure correlating with geographic distance and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modelling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, suggesting the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among populations. Genetic-environment association analyses revealed high levels of adaptive divergence and detected signs of multi-loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.