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Extreme environmental adaptations in hydrothermal vent invertebrates are driven by distinct genetic mechanisms. Many genes have been confirmed to be involved in these adaptations. Thermal adaptations in hydrothermal vent invertebrates is driven by unique adaptations strategy, such as protein stability enhancements and specialized amino acid compositions. Genetic adaptations to hypoxia in hydrothermal vent organisms include the expansion of oxygen-binding proteins and the evolution of mitochondrial genes to enhance energy metabolism. Multiomics analyses highlight the role of sensory perception and circadian rhythm genes in adaptations to low light and chemically active environments. Vent invertebrates can mitigate cellular damage caused by high metal ion concentrations through metal-tolerant proteins to maintain homeostasis and activate antioxidant pathways. Hydrothermal vents are unique habitats like an oases of life compared with typical deep-sea, soft-sediment environments. Most animals that live in these habitats are invertebrates, and they have adapted to extreme vent environments that include high temperatures, hypoxia, high sulfide, high metal concentration, and darkness. The advent of next-generation sequencing technology, especially the coming of the new era of omics, allowed more studies to focus on the molecular adaptation of these invertebrates to vent habitats. Many genes linked to hydrothermal adaptation have been studied. We summarize the findings related to these genetic adaptations and discuss which new techniques can facilitate studies in the future. [ABSTRACT FROM AUTHOR]

Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31 generations ago. Using whole‐genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72—a 2040‐fold decrease. As expected with a severe founder event, we show reductions in genome‐wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species‐specific agent‐based model to rule out genetic drift and conclude our results support a strong response to selection occurring in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation. [ABSTRACT FROM AUTHOR]

Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China. Here, 3 highly differentiated subpopulations were discovered using high‐quality single‐nucleotide polymorphism and structural variant datasets across China, corresponding to northern, southern China regions, and the Yunnan‐Guizhou Plateau, with significant patterns of isolation by geographic and environmental distances. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations. Selective sweep analyses estimated strong selection at insect cuticle glycine‐rich cuticular protein genes which are associated with enhanced desiccation adaptability in the northern group, and at the histone‐lysine‐N‐methyltransferase gene associated with range expansion and local adaptation in the Shandong population. Our findings have significant implications for the development of effective strategies to control this pest. [ABSTRACT FROM AUTHOR]

Genetic adaptation of soybean phenological stages to high‐latitude long‐day environments is the major pre‐requisite for enhancing regional plant‐based protein production. Both E‐genes controlling flowering and growing environment determine timing of flowering and maturity, and E‐gene composition might differ between Chinese and European soybeans bearing the potential for improving adaptability. Therefore, 140 early maturity elite soybean cultivars of either Chinese or European origin were genotyped for the E1 to E4 flowering loci, and genotypes were tested across 17 European environments spanning a latitude range from 45 to 52°N in order to determine effects of various E‐allele combinations. Differences in E‐allele composition between Chinese and European cultivars were largest for the loci E1 and E3. Wild‐type alleles significantly delayed flowering, and effects of particular E‐alleles were depending on geographic latitude. Consequently, photoperiod‐insensitive E‐haplotypes carrying several non‐functional alleles proved to be suitable for cultivation in higher latitudes, whereas photoperiod‐sensitive late‐maturity E‐haplotypes are adapted to lower latitudes only. Thus, breeding for new E‐haplotypes through combining Chinese and European alleles could enhance the potential for further soybean adaptation to northern growing regions. [ABSTRACT FROM AUTHOR]

Genetic adaptation is the change of a population toward a phenotype that best fits the present ecological conditions of the environment it inhabits. As environmental conditions change, allele frequencies shift, resulting in different populations of the same species possessing genetic variation and divergent phenotypes. Cooperatively breeding common mole-rats (Cryptomys hottentotus hottentotus) inhabit environments along an aridity gradient in South Africa, which provides an opportunity for local genetic adaptations to occur. Using one mitochondrial gene (cytochrome b) and 3,540 SNP loci across the whole genome, we determined the phylogenetic relationship, population structure and genetic diversity of five populations of C. h. hottentotus located along an aridity gradient. Mitochondrial data identified population-specific clades that were less distinct in the two mesic populations, potentially indicating historical or recent gene flow, or the retention of ancestral haplotypes. Arid and semi-arid populations formed a distinct cluster from the non-arid populations. Genetic diversity and gene flow were higher in arid-dwelling individuals, suggesting greater connectivity and interactions between colonies in arid regions in comparison to mesic ones. Using an Aridity Index, we determined that isolation by environment, rather than isolation by geographical distance, best explains the genetic distance between the populations. Further analyses using target loci may determine if there are differing underlying genetic adaptations among populations of C. h. hottentotus. These analyses could help unravel population differences in response to environmental factors within a subspecies of bathyergid mole-rat and determine the adaptive capacity of this small nonmigratory subterranean rodent species in response to aridification in the face of climate change. [ABSTRACT FROM AUTHOR]

The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA , which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB , a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors. [ABSTRACT FROM AUTHOR]

ABSTRACT: The wide distribution and diverse varieties of chickens make them important models for studying genetic adaptation. The aim of this study was to identify genes that alter heat adaptation in commercial chicken breeds by comparing genetic differences between tropical and cold-resistant chickens. We analyzed whole-genome resequencing data of 186 chickens across various regions in Asia, including the following breeds: Bian chickens (B), Dagu chickens (DG), Beijing-You chickens (BY), and Gallus gallus jabouillei from China; Gallus gallus murghi from India; Vietnam native chickens (VN); Thailand native chickens (TN) and Gallus gallus spadiceus from Thailand; and Indonesia native chickens (IN), Gallus gallus gallus, and Gallus gallus bankiva from Indonesia. In total, 5,454,765 SNPs were identified for further analyses. Population genetic structure analysis revealed that each local chicken breed had undergone independent evolution. Additionally, when K = 5, B, BY, and DG chickens shared a common ancestor and exhibited high levels of inbreeding, suggesting that northern cold-resistant chickens are likely the result of artificial selection. In contrast, the runs of homozygosity (ROH) and the ROH-based genomic inbreeding coefficient (FROH) results for IN, TN, and VN chickens showed low levels of inbreeding. Low population differentiation index values indicated low differentiation levels, suggesting low genetic diversity in tropical chickens, implying increased vulnerability to environmental changes, decreased adaptability, and disease resistance. Whole-genome selection sweep analysis revealed 69 candidate genes, including LGR4, G6PC, and NBR1, between tropical and cold-resistant chickens. The genes were further subjected to GO and KEGG enrichment analyses, revealing that most of the genes were primarily enriched in biological synthesis processes, metabolic processes, central nervous system development, ion transmembrane transport, and the Wnt signaling pathway. Our study identified heat adaptation genes and their functions in chickens that primarily affect chickens in high-temperature environments through metabolic pathways. These heat-resistance genes provide a theoretical basis for improving the heat-adaptation capacity of commercial chicken breeds.

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. [ABSTRACT FROM AUTHOR]

Many high-altitude mammals, including humans, display signatures of selection on genes of the Hypoxia Inducible Factor (HIF) pathway, particularly HIF2A and PHD2. HIF2A , encoding the transcription factor HIF-2α, is a recurrent target of selection. Mechanisms of convergent evolution include impaired heterodimerization, defective coactivator recruitment, and possibly decreased transcription of the HIF2A gene. It has been observed that high altitude-associated amino acid changes in PHD2 and HIF-2α occur in nonconserved, unstructured regions of these proteins, and these changes can selectively alter interactions with other proteins, producing partial as opposed to complete loss of function. In Tibetans, pairing of a partial loss-of-function PHD2 allele with a partial loss-of-function HIF2A allele could produce a panel of adaptive phenotypes that neither allele alone could produce, raising the possibility that this could be mimicked pharmacologically. Humans and other mammals inhabit hypoxic high-altitude locales. In many of these species, genes under positive selection include ones in the Hypoxia Inducible Factor (HIF) pathway. One is PHD2 (EGLN1), which encodes for a key oxygen sensor. Another is HIF2A (EPAS1), which encodes for a PHD2-regulated transcription factor. Recent studies have provided insights into mechanisms for these high-altitude alleles. These studies have (i) shown that selection can occur on nonconserved, unstructured regions of proteins, (ii) revealed that high altitude-associated amino acid substitutions can have differential effects on protein–protein interactions, (iii) provided evidence for convergent evolution by different molecular mechanisms, and (iv) suggested that mutations in different genes can complement one another to produce a set of adaptive phenotypes. [ABSTRACT FROM AUTHOR]

Compared with lowlander migrants, native Tibetans have a higher reproductive success at high altitude though the underlying mechanism remains unclear. Here, we compared the transcriptome and histology of full-term placentas between native Tibetans and Han migrants. We found that the placental trophoblast shows the largest expression divergence between Tibetans and Han, and Tibetans show decreased immune response and endoplasmic reticulum stress. Remarkably, we detected a sex-biased expression divergence, where the male-infant placentas show a greater between-population difference than the female-infant placentas. The umbilical cord plays a key role in the sex-biased expression divergence, which is associated with the higher birth weight of the male newborns of Tibetans. We also identified adaptive histological changes in the male-infant placentas of Tibetans, including larger umbilical artery wall and umbilical artery intima and media, and fewer syncytial knots. These findings provide valuable insights into the sex-biased adaptation of human populations, with significant implications for medical and genetic studies of human reproduction.

Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba , showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change. [ABSTRACT FROM AUTHOR]

Hypertension is one of the primary risk factors associated with cardiovascular diseases (CVDs). It is a condition that affects people worldwide, and its prevalence is increasing due to several factors, such as lack of physical activity, population aging, and unhealthy diets. Notably, this increase has primarily occurred in low and middle-income countries (LMICs). In Latin America, approximately 40% of adults have been diagnosed with hypertension. Moreover, reports have shown that the Latin American genetic composition is highly diverse, and this genetic background can influence various biological processes, including disease predisposition and treatment effectiveness. Research has shown that Western dietary patterns, which include increased consumption of red meat, refined grains, sugar, and ultra-processed food, have spread across the globe, including Latin America, due to globalization processes. Furthermore, a higher than recommended sodium consumption, which has been associated with hypertension, has been identified across different regions, including Asia, Europe, America, Oceania, and Africa. In conclusion, hypertension is a multifactorial disease involving environmental and genetic factors. In Latin America, hypertension prevalence is increasing due to various factors, including age, the adoption of a “Westernized” diet, and potential genetic predisposition factors involving the ACE gene. Furthermore, identifying the genetic and molecular mechanisms of the disease, its association with diet, and how they interact is essential for the development of personalized treatments to increase its efficacy and reduce side effects.

This article, titled "Editorial: Genetics, genomics and climatic adaptation in tropical conditions," discusses the impact of climate change on livestock breeds in tropical regions. The authors highlight the importance of genetic diversity assessment, strengthening local breeds, genetic selection, crossbreeding, and spatial genetic patterns in mitigating the effects of climate change. The article also explores the genetic basis of breed formation and the potential for genetic selection to improve heat stress tolerance in livestock populations. Additionally, the authors discuss the regulation of milk production in dairy cattle in response to amino acids and heat stress. [Extracted from the article]

The wide distribution and diverse varieties of chickens make them important models for studying genetic adaptation. The aim of this study was to identify genes that alter heat adaptation in commercial chicken breeds by comparing genetic differences between tropical and cold-resistant chickens. We analyzed whole-genome resequencing data of 186 chickens across various regions in Asia, including the following breeds: Bian chickens (B), Dagu chickens (DG), Beijing-You chickens (BY), and Gallus gallus jabouillei from China; Gallus gallus murghi from India; Vietnam native chickens (VN); Thailand native chickens (TN) and Gallus gallus spadiceus from Thailand; and Indonesia native chickens (IN), Gallus gallus gallus , and Gallus gallus bankiva from Indonesia. In total, 5,454,765 SNPs were identified for further analyses. Population genetic structure analysis revealed that each local chicken breed had undergone independent evolution. Additionally, when K = 5, B, BY, and DG chickens shared a common ancestor and exhibited high levels of inbreeding, suggesting that northern cold-resistant chickens are likely the result of artificial selection. In contrast, the runs of homozygosity (ROH) and the ROH-based genomic inbreeding coefficient (FROH) results for IN, TN, and VN chickens showed low levels of inbreeding. Low population differentiation index values indicated low differentiation levels, suggesting low genetic diversity in tropical chickens, implying increased vulnerability to environmental changes, decreased adaptability, and disease resistance. Whole-genome selection sweep analysis revealed 69 candidate genes, including LGR4, G6PC , and NBR1 , between tropical and cold-resistant chickens. The genes were further subjected to GO and KEGG enrichment analyses, revealing that most of the genes were primarily enriched in biological synthesis processes, metabolic processes, central nervous system development, ion transmembrane transport, and the Wnt signaling pathway. Our study identified heat adaptation genes and their functions in chickens that primarily affect chickens in high-temperature environments through metabolic pathways. These heat-resistance genes provide a theoretical basis for improving the heat-adaptation capacity of commercial chicken breeds. [ABSTRACT FROM AUTHOR]

The Atlantic herring and Atlantic cod are two marine fish species that have successfully adapted to the brackish Baltic Sea, and the former is able to spawn in near-freshwater conditions in the inner Gulf of Bothnia. Here, we review the state of current knowledge concerning ecological adaptation in the two species and make an attempt to predict how they will be able to cope with future climate change. Previous whole genome sequencing studies in Atlantic herring have revealed hundreds of genetic loci underlying ecological adaptation, including several loci that show very strong associations to variation in salinity and temperature. These results suggest the existence of standing genetic variation available for adaptation to a changing environment. However, although Atlantic herring probably has the genetic potential to adapt, its future status also depends on how climate change will affect plankton production and competing species, such as sprat and three-spined stickleback. In cod, the situation is challenging, as there is only one true Baltic population, spawning east of Bornholm and then dispersing towards the east and north. This Baltic cod population is threatened by overfishing, low oxygen levels in benthic waters and generally bad physiological condition of individual fish, in addition to being completely isolated from gene flow from nearby cod populations at the entrance of the Baltic Sea.

Climate change may force organisms to adapt genetically or plastically to new environmental conditions. Invasive species show remarkable potential for rapid adaptation. The ovoviviparous New Zealand mud snail (NZMS), Potamopyrgus antipodarum, has successfully established across Europe with two clonally reproducing mitochondrial lineages since its arrival in the first half of the 19th century. Its remarkable variation in shell morphology was shown to be fitness relevant. We investigated the effects of temperature on shell morphology across 11 populations from Germany and the Iberian Peninsula in a common garden across three temperatures. We analyzed size and shape using geometric morphometrics. For both, we compared reaction norms and estimated heritabilities. For size, the interaction of temperature and haplotype explained about 50% of the total variance. We also observed more genotype by environment interactions indicating a higher degree of population differentiation than in shape. Across the three temperatures, size followed the expectations of the temperature‐size rule, with individuals growing larger in cold environments. Changes in shape may have compensated for changes in size affecting space for brooding embryos. Heritability estimates were relatively high. As indicated by the very low coefficients of variation for clonal repeatability (CVA), they can probably not be compared in absolute terms. However, they showed some sensitivity to temperature, in haplotype t more so than in z, which was only found in Portugal. The low CVA values indicate that genetic variation among European populations is still restricted with a low potential to react to selection. A considerable fraction of the genetic variation was due to differences between the clonal lineages. The NZMS has apparently not been long enough in Europe to accumulate significant genetic variation relevant for morphological adaptation. As temperature is obviously not the sole factor influencing shell morphology, their interaction will probably not be a factor limiting population persistence under a warming climate in Europe. [ABSTRACT FROM AUTHOR]

Abstract Climate change may force organisms to adapt genetically or plastically to new environmental conditions. Invasive species show remarkable potential for rapid adaptation. The ovoviviparous New Zealand mud snail (NZMS), Potamopyrgus antipodarum, has successfully established across Europe with two clonally reproducing mitochondrial lineages since its arrival in the first half of the 19th century. Its remarkable variation in shell morphology was shown to be fitness relevant. We investigated the effects of temperature on shell morphology across 11 populations from Germany and the Iberian Peninsula in a common garden across three temperatures. We analyzed size and shape using geometric morphometrics. For both, we compared reaction norms and estimated heritabilities. For size, the interaction of temperature and haplotype explained about 50% of the total variance. We also observed more genotype by environment interactions indicating a higher degree of population differentiation than in shape. Across the three temperatures, size followed the expectations of the temperature‐size rule, with individuals growing larger in cold environments. Changes in shape may have compensated for changes in size affecting space for brooding embryos. Heritability estimates were relatively high. As indicated by the very low coefficients of variation for clonal repeatability (CVA), they can probably not be compared in absolute terms. However, they showed some sensitivity to temperature, in haplotype t more so than in z, which was only found in Portugal. The low CVA values indicate that genetic variation among European populations is still restricted with a low potential to react to selection. A considerable fraction of the genetic variation was due to differences between the clonal lineages. The NZMS has apparently not been long enough in Europe to accumulate significant genetic variation relevant for morphological adaptation. As temperature is obviously not the sole factor influencing shell morphology, their interaction will probably not be a factor limiting population persistence under a warming climate in Europe.

The neritid snail Theodoxus fluviatilis has formed regional subgroups in northern Europe, where it appears in both freshwater (FW) and brackish water (BW) in coastal areas of the Baltic Sea. These ecotypes show clear differences in osmotolerance and in the modes of accumulating organic osmolytes under hyperosmotic stress. We reasoned that the expression patterns of soluble proteins in the two ecotypes may differ as well. BW snails have to deal with a higher salinity (up to 20‰) than FW snails (0.5‰) and also cope with frequent fluctuations in environmental salinity that occur after heavy rains or evaporation caused by extended periods of intense sunshine. Therefore, the protein expression patterns of specimens collected at five different FW and BW sites were analyzed using 2D SDS‐PAGE, mass spectrometry, and sequence comparisons based on a transcriptome database for Theodoxus fluviatilis. We identified 89 differentially expressed proteins. The differences in the expression between FW and BW snails may be due to phenotypic plasticity, but may also be determined by local genetic adaptations. Among the differentially expressed proteins, 19 proteins seem to be of special interest as they may be involved in mediating the higher tolerance of BW animals towards environmental change compared with FW animals. [ABSTRACT FROM AUTHOR]

Background. Sherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, which may be achieved by mechanisms promoting microcirculatory blood flow and capillary density at high altitudes for restoring oxygen supply to tissues. Vascular endothelial growth factors (VEGFs) are important signaling proteins involved in vasculogenesis and angiogenesis which are stimulated by hypoxia. We hypothesize that the VEGF-A, the major member of the VEGF family, and the gene encoding VEGF-A (VEGFA) play a part in the adaptation to high-altitude hypoxia in Sherpa highlanders. Methods. Fifty-one Sherpa highlanders in Namche Bazaar village at a high altitude of 3,440 meters (m) above sea level and 76 non-Sherpa lowlanders in Kathmandu city at 1,300 m in Nepal were recruited for the study. Venous blood was sampled to obtain plasma and extract DNA from each subject. The plasma VEGF-A concentrations were measured and five single-nucleotide polymorphisms (SNPs, rs699947, rs833061, rs1570360, rs2010963, and rs3025039) in the VEGFA were genotyped. The VEGF-A levels and allelic frequencies of the SNPs were compared between the two populations. Results. A significant difference in oxygen saturation (SpO2) was observed between the two ethnic groups locating at different elevations (93.7±0.2% in Sherpas at 3,440mvs. 96.7 ± 0.2% in non-Sherpas at 1,300 m, P <0:05). The plasma VEGF-A concentration in the Sherpas at high altitude was on the same level as that in the non-Sherpas at low altitude (262.8 ± 17.9 pg/ml vs. 266.8 ± 21.8 pg/ml, P D0:88). This result suggested that the plasma VEGF-A concentration in Sherpa highlanders was stable despite a high-altitude hypoxic stimulus and that therefore the Sherpas exhibited a phenotype of blunted response to hypoxic stress. Moreover, the allele frequencies of the SNPs rs699947, rs833061, and rs2010963 in the promoter region of the VEGFA were different between the Sherpa highlanders and non-Sherpa lowlanders (corrected P values D 3.30 x10X5, 4.95 x10-4, and 1.19 x10-7, respectively). Conclusions. Sherpa highlanders exhibited a blunted VEGF-A response to hypoxia at high altitudes, which was speculated to be associated with the distinctive genetic variations of the SNPs and haplotype in the promoter region of VEGFA in Sherpa highlanders. [ABSTRACT FROM AUTHOR]

While adaptation is commonly thought to result from selection on DNA sequence‐based variation, recent studies have highlighted an analogous epigenetic component as well. However, the relative roles of these mechanisms in facilitating population persistence under environmental heterogeneity remain unclear. To address the underlying genetic and epigenetic mechanisms and their relationship during environmental adaptation, we screened the genomes and epigenomes of nine global populations of a predominately sessile marine invasive tunicate, Botryllus schlosseri. We detected clear population differentiation at the genetic and epigenetic levels. Patterns of genetic and epigenetic structure were significantly influenced by local environmental variables. Among these variables, minimum annual sea surface temperature was identified as the top explanatory variable for both genetic and epigenetic variation. However, patterns of population structure driven by genetic and epigenetic variation were somewhat distinct, suggesting possible autonomy of epigenetic variation. We found both shared and specific genes and biological pathways among genetic and epigenetic loci associated with environmental factors, consistent with complementary and independent contributions of genetic and epigenetic variation to environmental adaptation in this system. Collectively, these mechanisms may facilitate population persistence under environmental change and sustain successful invasions across novel environments. [ABSTRACT FROM AUTHOR]

Infectious diseases are recognized as one of the greatest global threats to biodiversity and ecosystem functioning. Consequently, there is a growing urgency to understand the speed at which adaptive phenotypes can evolve and spread in natural populations to inform future management. Here we provide evidence of rapid genomic changes in wild Australian blacklip abalone (Haliotis rubra) following a major population crash associated with an infectious disease. Genome scans on H. rubra were performed using pooled whole genome resequencing data from commercial fishing stocks varying in historical exposure to haliotid herpesvirus‐1 (HaHV‐1). Approximately 25,000 single nucleotide polymorphism loci associated with virus exposure were identified, many of which mapped to genes known to contribute to HaHV‐1 immunity in the New Zealand pāua (Haliotis iris) and herpesvirus response pathways in haliotids and other animal systems. These findings indicate genetic changes across a single generation in H. rubra fishing stocks decimated by HaHV‐1, with stock recovery potentially determined by rapid evolutionary changes leading to virus resistance. This is a novel example of apparently rapid adaptation in natural populations of a nonmodel marine organism, highlighting the pace at which selection can potentially act to counter disease in wildlife communities. [ABSTRACT FROM AUTHOR]

It is unclear whether recurrent sputum culture with Pseudomonas aeruginosa from patients with chronic obstructive pulmonary disease (COPD) is caused by intermittent airway carriage by different P. aeruginosa lineages or persistent carriage by the same lineage, and whether lineages genetically adapt during carriage. Whole-genome sequencing was performed for P. aeruginosa isolates sampled longitudinally from sputum cultures in patients with COPD who were enrolled in an ongoing randomized controlled trial (clinicaltrials.gov: NCT03262142). A total of 153 P. aeruginosa isolates were sequenced for 23 patients during 365 days of follow-up. Recurrent presence of P. aeruginosa was seen in 19 patients (83%) and was caused by persistence of the same clonal lineage in all but one patient. We identified 38 genes mutated in parallel in two or more lineages, suggesting positive selection for adaptive mutations. Mutational enrichment analysis revealed genes important in antibiotic resistance and chronic infections to be more frequently mutated. Recurrent P. aeruginosa was common and carried for a prolonged time after initial detection in the airways of patients with COPD. Recurrence was caused by persistence of the same clonal lineage and was associated with genetic adaptation. Trial data on possible clinical benefits of attempting antibiotic eradication of P. aeruginosa in COPD are warranted. [ABSTRACT FROM AUTHOR]

Striped catfish (Pangasianodon hypophthalmus), a freshwater species cultured mainly in the Mekong Delta region in Southern Vietnam, is facing a significant challenge due to salinity intrusion as a result of climatic changes. Given these evolving environmental conditions, selecting new strains with a higher salinity tolerance could make production of striped catfish economically feasible in brackish environments. In this study, we carried out a selection program aimed at developing a striped catfish strain able to survive and grow fast in a saline environment. To implement the selection program, we first collected males and females from different provinces in the Mekong delta. We next performed a factorial cross of these breeders to produce half- and full-sib families. When fish reached fry stage (47 dph), we put them in a saline environment (10 ppt) and subsequently kept 50 % of the fastest-growing fish after 143 days post hatching (dph). We repeated this mass selection procedure after 237 dph and 340 dph. We maintained in parallel a randomly selected group in saline conditions and a group of fish reared in freshwater to serve as controls. After crossing the selected individuals, we performed several tests on the next generation of fish to evaluate the effectiveness of selection after one generation in saline conditions. Average direct responses to selection were 18.0 % for growth and 11.4 % for survival rate after one generation of selection. We estimated a moderate realized heritability (0.29) for body weight. The genetic gains obtained in our study for body weight and survival rate after one generation of selection under saline conditions suggest that selection can be effective to improve ability of striped catfish to cope with saline stress. We conclude that our selection program has succeeded in developing a productive strain of striped catfish with better tolerance to salinity.

Environmental stressors have, over generations, influenced the morphology, anatomy, behaviour, physiology, and genetic structure of small ruminants. The widespread dispersal of small ruminants over vast geographical areas occurred along with human migration, thereby promoting the adaptative process to different environmental conditions mainly through natural selection. Ongoing global warming prompted scientific efforts to deepen the knowledge and understanding of adaptation traits in small ruminants. Compared to other ruminants, sheep and goats seem to have a better adaptation ability to environmental stressors, as evident by their presence across different geographic areas on a global level. Adaptation to a specific environment leads to variations in precise genomic regions, allowing for the identification and selection of animals with a high capacity of adaptation to environmental stressors. Rapid development in sequencing technologies, together with bioinformatics tools, make it possible to analyse the genomic regions related to environmental adaptation. Hence, the aims of this review were (i) to outline the main steps of the evolution process in sheep and goat species, (ii) to summarise candidate genes related to environmental adaptation, and (iii) to evaluate both selection and conservation possibilities of these genes in native small ruminant breeds for future challenges to better face the global warming. [ABSTRACT FROM AUTHOR]

Context. Few studies have been conducted with the Brazilian Embrapa 051 hens to improve the feed conversion rate and control skeletal health in this breed. Aims. To determine how different feeding volumes affect the laying rate and bone quality of the Embrapa 051 (E051) strain in comparison with Lohmann Brown (LB). Methods. In total, 600 E051 and 200 LB hens were subjected to the following treatments: (1) control (LB fed 100% of their dietary requirements), (2) E051 fed 93% of the control diet, (3) E051 fed 100% of the control diet, and (4) E051 fed 107% of the control diet. Key results. Throughout the 37-72 weeks of age, LB hens presented a higher egg production rate than E051 hens (P < 0.05). The bodyweight and egg production rate were lower in E051 when hens received 93% of the E051 control diet. The E051 hens achieved higher values for tibia weight and length and Seedor index than did LB hens (P < 0.05). At Week 40, the E051 hens fed 93% of the control diet presented a greater tibia weight (12.6 vs 11.5 g), length (124.5 vs 118.9 mm) and strength (21.9 vs 15.5 kgf), Seedor index (101.7 vs 96.13), and ash (33.0 vs 29.6%), calcium (11.1 vs 9.8%) and phosphorus (4.9 vs 4.5%) concentrations than did LB hens. However, at 73 weeks of age, the only differences observed in favour of E051 hens fed 93% of the control diet were for tibia weight, tibia length and tibia strength in comparison with LB hens (P < 0.05). Conclusions. LB hens showed a higher performance, but lower bone quality than did E051 hens. E051 receiving 7% less feed showed a reduced laying rate but, in contrast, better bone quality. This study showed that the best feeding strategy for Embrapa 051 hens was to use the same feeding volume as recommended for Lohmann Brown hens. Implications. Despite E051 hens showing a lower laying rate than that of LB hens, especially when receiving a restricted amount of feed, E051 is an accessible alternative breed with excellent bone quality for free-range systems in Brazil. [ABSTRACT FROM AUTHOR]

Admixture has been a pervasive phenomenon in human history, extensively shaping the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as "adaptive admixture." However, the role of adaptive admixture in human evolution and the power to detect it remain poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, assuming multiple admixture scenarios. We show that statistics based on admixture proportions, F adm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas other statistics, including iHS and F ST , falsely detect neutral mutations that have been selected in the source populations only. By combining F adm and LAD into a single, powerful statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africans and in Malagasy, North Africans, and South Asians, respectively. Our approach also uncovers other cases of adaptive admixture, including APOL1 in Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides evidence that adaptive admixture has occurred in human populations whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow. [ABSTRACT FROM AUTHOR]

Abstract The resistance of pest species to chemical controls has vast ecological, economic, and societal costs. In most cases, resistance is only detected after spreading throughout an entire population. Detecting resistance in its incipient stages, by comparison, provides time to implement preventative strategies. Incipient resistance can be detected by coupling standard toxicology assays with large‐scale gene expression experiments. We apply this approach to a system where an invasive parasite, sea lamprey (Petromyzon marinus), has been treated with the highly effective pesticide 3‐trifluoromethyl‐4‐nitrophenol (TFM) for 60 years. Toxicological experiments revealed that lamprey from treated populations did not have higher survival to TFM exposure than lamprey from untreated populations, demonstrating that full‐fledged resistance has not yet evolved. In contrast, we find hundreds of genes differentially expressed in response to TFM in the population with the longest history of exposure, many of which relate to TFM’s primary mode of action, the uncoupling of oxidative phosphorylation, and subsequent depletion of ATP. Three genes critical to oxidative phosphorylation, ATP5PB, PLCB1, and NDUFA9, were nearly fixed for alternative alleles in comparisons of SNPs between treated and untreated populations (FST > 5 SD from the mean). ATP5PB encodes subunit b of ATP synthase and an additional subunit, ATP5F1B, was canalized for high expression in treated populations, but remained plastic in response to TFM treatment in individuals from the untreated population. These combined genomic and transcriptomic results demonstrate that an adaptive, genetic response to TFM is likely driving incipient resistance in a damaging pest species.

Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices, yet the evolutionary mechanisms that allow pests to rapidly adapt to control tactics remains unclear. Here, we examine how a global super-pest, the Colorado potato beetle (CPB), Leptinotarsa decemlineata , rapidly evolves resistance to insecticides. Using whole-genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, nonmutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit similar levels of nucleotide diversity, relative to nonpest populations, and show evidence of recent expansion. Genome scans provide clear signatures of repeated adaptation across CPB populations, with especially strong evidence of selection on insecticide resistance genes in different populations. Analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. CPB evolves insecticide resistance repeatedly across agricultural regions, leveraging similar genetic pathways but different genes, demonstrating a polygenic trait architecture for insecticide resistance that can evolve from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. These results suggest that integrated pest management practices must mitigate the evolution of polygenic resistance phenotypes among local pest populations, in order to maintain the efficacy and sustainability of novel control techniques. [ABSTRACT FROM AUTHOR]

Global change confronts organisms with multiple stressors causing nonadditive effects. Persistent stress, however, leads to adaptation and related trade-offs. The question arises: How can the resulting effects of these contradictory processes be predicted? Here we show that Gammarus pulex from agricultural streams were more tolerant to clothianidin (mean EC 50 148 μg/L) than populations from reference streams (mean EC 50 67 μg/L). We assume that this increased tolerance results from a combination of physiological acclimation, epigenetic effects, and genetic evolution, termed as adaptation. Further, joint exposure to pesticide mixture and temperature stress led to synergistic interactions of all three stressors. However, these combined effects were significantly stronger in adapted populations as shown by the model deviation ratio (MDR) of 4, compared to reference populations (MDR = 2.7). The pesticide adaptation reduced the General-Stress capacity of adapted individuals, and the related trade-off process increased vulnerability to combined stress. Overall, synergistic interactions were stronger with increasing total stress and could be well predicted by the stress addition model (SAM). In contrast, traditional models such as concentration addition (CA) and effect addition (EA) substantially underestimated the combined effects. We conclude that several, even very disparate stress factors, including population adaptations to stress, can act synergistically. The strong synergistic potential underscores the critical importance of correctly predicting multiple stresses for risk assessment.

The evolution of light-skin pigmentation among Eurasians is considered as an adaptation to the high-latitude environments. East Asians are ideal populations for studying skin color evolution because of the complex environment of East Asia. Here, we report a strong selection signal for the pigmentation gene phenylalanine hydroxylase (PAH) in light-skinned Han Chinese individuals. The intron mutation rs10778203 in PAH is enriched in East Asians and is significantly associated with skin color of the back of the hand in Han Chinese males (P < 0.05). In vitro luciferase and transcription factor binding assays show that the ancestral allele of rs10778203 could bind to SMAD2 and has a significant enhancer activity for PAH. However, the derived T allele (the major allele in East Asians) of rs10778203 decreases the binding activity of transcription factors and enhancer activity. Meanwhile, the derived T allele of rs10778203 shows a weaker ultraviolet radiation response in A375 cells and zebrafish embryos. Furthermore, rs10778203 decreases melanin production in transgenic zebrafish embryos after ultraviolet B (UVB) treatment. Collectively, PAH is a potential pigmentation gene that regulates skin tanning ability. Natural selection has enriched the adaptive allele, resulting in weakened tanning ability in East Asians, suggesting a unique genetic mechanism for evolutionary skin lightening in East Asians., Competing Interests: Conflict of interest The authors declare no conflicts of interest., (Copyright © 2024 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.)

Adaptive evolution to cellular stress is a process implicated in a wide range of biological and clinical phenomena. Two major routes of adaptation have been identified: non-genetic changes, which allow expression of different phenotypes in novel environments, and genetic variation achieved by selection of fitter phenotypes. While these processes are broadly accepted, their temporal and epistatic features in the context of cellular evolution and emerging drug resistance are contentious. In this manuscript, we generated hypomorphic alleles of the essential nuclear pore complex (NPC) gene NUP58. By dissecting early and long-term mechanisms of adaptation in independent clones, we observed that early physiological adaptation correlated with transcriptome rewiring and upregulation of genes known to interact with the NPC; long-term adaptation and fitness recovery instead occurred via focal amplification of NUP58 and restoration of mutant protein expression. These data support the concept that early phenotypic plasticity allows later acquisition of genetic adaptations to a specific impairment. We propose this approach as a genetic model to mimic targeted drug therapy in human cells and to dissect mechanisms of adaptation. [ABSTRACT FROM AUTHOR]

Following domestication in the lower Yangtze River valley 9400 years ago, rice farming spread throughout China and changed lifestyle patterns among Neolithic populations. Here, we report evidence that the advent of rice domestication and cultivation may have shaped humans not only culturally but also genetically. Leveraging recent findings from molecular genetics, we construct a number of polygenic scores (PGSs) of behavioural traits and examine their associations with rice cultivation based on a sample of 4101 individuals recently collected from mainland China. A total of nine polygenic traits and genotypes are investigated in this study, including PGSs of height, body mass index, depression, time discounting, reproduction, educational attainment, risk preference, ADH1B rs1229984 and ALDH2 rs671. Two-stage least-squares estimates of the county-level percentage of cultivated land devoted to paddy rice on the PGS of age at first birth (b = −0.029, p = 0.021) and ALDH2 rs671 (b = 0.182, p < 0.001) are both statistically significant and robust to a wide range of potential confounds and alternative explanations. These findings imply that rice farming may influence human evolution in relatively recent human history.

Understanding the population dynamics of highly mobile, widely distributed, oceanic sharks, many of which are overexploited, is necessary to aid their conservation management. We investigated the global population genomics of tiger sharks (Galeocerdo cuvier), a circumglobally distributed, apex predator displaying remarkable behavioral versatility in its diet, habitat use (near coastal, coral reef, pelagic), and individual movement patterns (spatially resident to long-distance migrations). We genotyped 242 tiger sharks from 10 globally distributed locations at more than 2000 single nucleotide polymorphisms. Although this species often conducts massive distance migrations, the data show strong genetic differentiation at both neutral (F ST = 0.125–0.144) and candidate outlier loci (F ST = 0.570–0.761) between western Atlantic and Indo-Pacific sharks, suggesting the potential for adaptation to the environments specific to these oceanic regions. Within these regions, there was mixed support for population differentiation between northern and southern hemispheres in the western Atlantic, and none for structure within the Indian Ocean. Notably, the results demonstrate a low level of population differentiation of tiger sharks from the remote Hawaiian archipelago compared with sharks from the Indian Ocean (F ST = 0.003–0.005, P < 0.01). Given concerns about biodiversity loss and marine ecosystem impacts caused by overfishing of oceanic sharks in the midst of rapid environmental change, our results suggest it imperative that international fishery management prioritize conservation of the evolutionary potential of the highly genetically differentiated Atlantic and Indo-Pacific populations of this unique apex predator. Furthermore, we suggest targeted management attention to tiger sharks in the Hawaiian archipelago based on a precautionary biodiversity conservation perspective. [ABSTRACT FROM AUTHOR]

Premise: Adaptive traits can be dramatically altered by genome duplication. The study of interactions among traits, ploidy, and the environment are necessary to develop an understanding of how polyploidy affects niche differentiation and to develop restoration strategies for resilient native ecosystems. Methods: Growth and fecundity were measured in common gardens for 39 populations of big sagebrush (Artemisia tridentata) containing two subspecies and two ploidy levels. General linear mixed‐effect models assessed how much of the trait variation could be attributed to genetics (i.e., ploidy and climatic adaptation), environment, and gene–environment interactions. Results: Growth and fecundity variation were explained well by the mixed models (80% and 91%, respectively). Much of the trait variation was attributed to environment, and 15% of variation in growth and 34% of variation in seed yield were attributed to genetics. Genetic trait variation was mostly attributable to ploidy, with much higher growth and seed production in diploids, even in a warm‐dry environment typically dominated by tetraploids. Population‐level genetic variation was also evident and was related to the climate of each population's origin. Conclusions: Ploidy is a strong predictor growth and seed yield, regardless of common‐garden environment. The superior growth and fecundity of diploids across environments raises the question as to how tetraploids can be more prevalent than diploids, especially in warm‐dry environments. Two hypotheses that may explain the abundance of tetraploids on the landscape include selection for drought resistance at the seedling stage, and greater competitive ability in water uptake in the upper soil horizon. [ABSTRACT FROM AUTHOR]

BackgroundPowdery mildew, caused by the obligate biotrophic fungus Erysiphe necator, is an economically important disease of grapevines worldwide. Large quantities of fungicides are used for its control, accelerating the incidence of fungicide-resistance. Copy number variations (CNVs) are unbalanced changes in the structure of the genome that have been associated with complex traits. In addition to providing the first description of the large and highly repetitive genome of E. necator, this study describes the impact of genomic structural variation on fungicide resistance in Erysiphe necator.ResultsA shotgun approach was applied to sequence and assemble the genome of five E. necator isolates, and RNA-seq and comparative genomics were used to predict and annotate protein-coding genes. Our results show that the E. necator genome is exceptionally large and repetitive and suggest that transposable elements are responsible for genome expansion. Frequent structural variations were found between isolates and included copy number variation in EnCYP51, the target of the commonly used sterol demethylase inhibitor (DMI) fungicides. A panel of 89 additional E. necator isolates collected from diverse vineyard sites was screened for copy number variation in the EnCYP51 gene and for presence/absence of a point mutation (Y136F) known to result in higher fungicide tolerance. We show that an increase in EnCYP51 copy number is significantly more likely to be detected in isolates collected from fungicide-treated vineyards. Increased EnCYP51 copy numbers were detected with the Y136F allele, suggesting that an increase in copy number becomes advantageous only after the fungicide-tolerant allele is acquired. We also show that EnCYP51 copy number influences expression in a gene-dose dependent manner and correlates with fungal growth in the presence of a DMI fungicide.ConclusionsTaken together our results show that CNV can be adaptive in the development of resistance to fungicides by providing increasing quantitative protection in a gene-dosage dependent manner. The results of this work not only demonstrate the effectiveness of using genomics to dissect complex traits in organisms with very limited molecular information, but also may have broader implications for understanding genomic dynamics in response to strong selective pressure in other pathogens with similar genome architectures.

Directed evolution is an approach that mimics natural evolution in the laboratory with the goal of modifying existing enzymatic activities or of generating new ones. The identification of mutants with desired properties involves the generation of genetic diversity coupled with a functional selection or screen. Genetic diversity can be generated using PCR or using in vivo methods such as chemical mutagenesis or error-prone replication of the desired sequence in a mutator strain. In vivo mutagenesis methods facilitate iterative selection because they do not require cloning, but generally produce a low mutation density with mutations not restricted to specific genes or areas within a gene. For this reason, this approach is typically used to generate new biochemical properties when large numbers of mutants can be screened or selected. Here we describe protocols for an advanced in vivo mutagenesis method that is based on error-prone replication of a ColE1 plasmid bearing the gene of interest. Compared to other in vivo mutagenesis methods, this plasmid-targeted approach allows increased mutation loads and facilitates iterative selection approaches. We also describe the mutation spectrum for this mutagenesis methodology in detail, and, using cycle 3 GFP as a target for mutagenesis, we illustrate the phenotypic diversity that can be generated using our method. In sum, error-prone Pol I replication is a mutagenesis method that is ideally suited for the evolution of new biochemical activities when a functional selection is available.

Copy number variations (CNVs) are a major source of structural variation in mammalian genomes. Here, we characterized the genome-wide CNV in 2059 sheep from 67 populations all over the world using the Ovine Infinium HD (600K) SNP BeadChip. We tested their associations with distinct phenotypic traits by conducting multiple independent genome-wide tests. In total, we detected 7547 unique CNVs and 18,152 CNV events in 1217 non-redundant CNV regions (CNVRs), covering 245 Mb (∼10%) of the whole sheep genome. We identified seven CNVRs with frequencies correlating to geographical origins and 107 CNVRs overlapping 53 known quantitative trait loci (QTLs). Gene ontology and pathway enrichment analyses of CNV-overlapping genes revealed their common involvement in energy metabolism, endocrine regulation, nervous system development, cell proliferation, immune, and reproduction. For the phenotypic traits, we detected significantly associated (adjusted P < 0.05) CNVRs harboring functional candidate genes, such as SBNO2 for polycerate; PPP1R11 and GABBR1 for tail weight; AKT1 for supernumerary nipple; CSRP1, WNT7B, HMX1, and FGFR3 for ear size; and NOS3 and FILIP1 in Wadi sheep; SNRPD3, KHDRBS2, and SDCCAG3 in Hu sheep; NOS3, BMP1, and SLC19A1 in Icelandic; CDK2 in Finnsheep; MICA in Romanov; and REEP4 in Texel sheep for litter size. These CNVs and associated genes are important markers for molecular breeding of sheep and other livestock species.

Different environmental conditions may lead to diverse morphological, behavioral, and physiological adaptations of different populations of the same species. Lighting conditions, for example, vary vastly especially between aquatic habitats, and have been shown to elicit adaptations. The availability of short-wave ultraviolet (UV) light is especially fluctuating, as UV wavelengths are attenuated strongly depending on water properties. The island of North Uist, Scotland, comprises 2 differential habitat types, tea-stained and clear-water lakes, varying considerably in UV transmission. In previous studies, wild-caught 3-spined stickleback Gasterosteus aculeatus populations (3 populations of each habitat type) were tested with respect to their shoaling and mate preferences for fish viewed under UV-present and UV-absent conditions. The results revealed a habitat-dependent preference of UV cues during shoal choice (tea-stained populations: preference for UV-absent condition in tea-stained water; clear-water populations: no preference in clear-water) but an overall preference for UV-present conditions during mate choice. To assess genetic influences on these behavioral patterns, similar experiments were conducted with lab-bred F1-generations of the same stickleback populations that were raised in a common environment (i.e. standardized clear-water conditions). Offspring of sticklebacks from tea-stained lakes tended to prefer shoals viewed under UV-absent conditions (only in tea-stained water), while sticklebacks from clear-water lakes showed a significant preference for the shoal viewed under UV-present conditions in clear-water but not in tea-stained water. Mate-preference experiments demonstrated that females from the tea-stained lakes significantly preferred and females from the clear-water lakes preferred by trend the male viewed under UV-present conditions in the clear-water treatment. The results for both shoaling- and mate-preference tests were largely similar for wild-caught and lab-bred sticklebacks, thus hinting at a genetic basis for the preference patterns. [ABSTRACT FROM AUTHOR]

Copy number variations (CNVs) are a major source of structural variation in mammalian genomes. Here, we characterized the genome-wide CNV in 2059 sheep from 67 populations all over the world using the Ovine Infinium HD (600K) SNP BeadChip. We tested their associations with distinct phenotypic traits by conducting multiple independent genome-wide tests. In total, we detected 7547 unique CNVs and 18,152 CNV events in 1217 non-redundant CNV regions (CNVRs), covering 245 Mb (∼10%) of the whole sheep genome. We identified seven CNVRs with frequencies correlating to geographical origins and 107 CNVRs overlapping 53 known quantitative trait loci (QTLs). Gene ontology and pathway enrichment analyses of CNV-overlapping genes revealed their common involvement in energy metabolism, endocrine regulation, nervous system development, cell proliferation, immune, and reproduction. For the phenotypic traits, we detected significantly associated (adjusted P < 0.05) CNVRs harboring functional candidate genes, such as SBNO2 for polycerate; PPP1R11 and GABBR1 for tail weight; AKT1 for supernumerary nipple; CSRP1 , WNT7B , HMX1 , and FGFR3 for ear size; and NOS3 and FILIP1 in Wadi sheep; SNRPD3 , KHDRBS2 , and SDCCAG3 in Hu sheep; NOS3 , BMP1 , and SLC19A1 in Icelandic; CDK2 in Finnsheep; MICA in Romanov; and REEP4 in Texel sheep for litter size. These CNVs and associated genes are important markers for molecular breeding of sheep and other livestock species. [ABSTRACT FROM AUTHOR]

Genetic adaptation and phenotypic plasticity facilitate the migration into new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibrio bacteria) stressor using six different populations of the broad-nosed pipefish Syngnathus typhle that originated from either high [14–17 Practical Salinity Unit (PSU)] or low (7–11 PSU) saline environments along the German coastline of the Baltic Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected with Vibrio alginolyticus bacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life-history traits of fathers and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenges encountered at low salinity. Offspring from parents with low saline origin survived better at low salinity suggesting genetic adaptation to low salinity. In addition, gene expression analyses of juveniles indicated patterns of local adaptation, trans-generational plasticity and developmental plasticity. In conclusion, our study suggests that pipefish are locally adapted to the low salinity in their environment, however, they are retaining phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens.

The resistance of pest species to chemical controls has vast ecological, economic, and societal costs. In most cases, resistance is only detected after spreading throughout an entire population. Detecting resistance in its incipient stages, by comparison, provides time to implement preventative strategies. Incipient resistance can be detected by coupling standard toxicology assays with large‐scale gene expression experiments. We apply this approach to a system where an invasive parasite, sea lamprey (Petromyzon marinus), has been treated with the highly effective pesticide 3‐trifluoromethyl‐4‐nitrophenol (TFM) for 60 years. Toxicological experiments revealed that lamprey from treated populations did not have higher survival to TFM exposure than lamprey from untreated populations, demonstrating that full‐fledged resistance has not yet evolved. In contrast, we find hundreds of genes differentially expressed in response to TFM in the population with the longest history of exposure, many of which relate to TFM's primary mode of action, the uncoupling of oxidative phosphorylation, and subsequent depletion of ATP. Three genes critical to oxidative phosphorylation, ATP5PB, PLCB1, and NDUFA9, were nearly fixed for alternative alleles in comparisons of SNPs between treated and untreated populations (FST > 5 SD from the mean). ATP5PB encodes subunit b of ATP synthase and an additional subunit, ATP5F1B, was canalized for high expression in treated populations, but remained plastic in response to TFM treatment in individuals from the untreated population. These combined genomic and transcriptomic results demonstrate that an adaptive, genetic response to TFM is likely driving incipient resistance in a damaging pest species. [ABSTRACT FROM AUTHOR]