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In ecological speciation, incipient species diverge due to natural selection that is ecologically based. In flowering plants, different pollinators could mediate that selection (pollinator-mediated divergent selection) or other features of the environment that differ between habitats of 2 species could do so (environment-mediated divergent selection). Although these mechanisms are well understood, they have received little rigorous testing, as few studies of divergent selection across sites of closely related species include both floral traits that influence pollination and vegetative traits that influence survival. This study employed common gardens in sites of the 2 parental species and a hybrid site, each containing advanced generation hybrids along with the parental species, to test these forms of ecological speciation in plants of the genus Ipomopsis. A total of 3 vegetative traits (specific leaf area, leaf trichomes, and photosynthetic water-use efficiency) and 5 floral traits (corolla length and width, anther insertion, petal color, and nectar production) were analyzed for impacts on fitness components (survival to flowering and seeds per flower, respectively). These traits exhibited strong clines across the elevational gradient in the hybrid zone, with narrower clines in theory reflecting stronger selection or higher genetic variance. Plants with long corollas and inserted anthers had higher seeds per flower at the Ipomopsis tenuituba site, whereas selection favored the reverse condition at the Ipomopsis aggregata site, a signature of divergent selection. In contrast, no divergent selection due to variation in survival was detected on any vegetative trait. Selection within the hybrid zone most closely resembled selection within the I. aggregata site. Across traits, the strength of divergent selection was not significantly correlated with width of the cline, which was better predicted by evolvability (standardized genetic variance). These results support the role of pollinator-mediated divergent selection in ecological speciation and illustrate the importance of genetic variance in determining divergence across hybrid zones.

The amount of standing variation present within populations is a fundamental quantity of interest in population genetics, commonly represented by calculating the average number of differences between pairs of nucleotide sequences (nucleotide diversity, π). It is well understood that both background and positive selection can cause reductions in nucleotide diversity, but less clear how local adaptation affects it. Depending on the assumptions and parameters, some theoretical studies have emphasized how local adaptation can reduce nucleotide diversity, while others have shown that it can increase it. Here, we explore how local adaptation shapes genome-wide patterns in within-population nucleotide diversity, extending previous work to study the effects of polygenic adaptation, genotypic redundancy, and population structure. We show that local adaptation produces two very different patterns depending on the relative strengths of migration and selection, either markedly decreasing or increasing within-population diversity at linked sites at equilibrium. At low migration, regions of depleted diversity can extend large distances from the causal locus, with substantially more diversity eroded than expected with background selection. With higher migration, peaks occur over much smaller genomic distances but with much larger magnitude changes in diversity. Across spatially extended environmental gradients, both patterns can be found within a single species, with increases in diversity at the center of the range and decreases towards the periphery. Our results demonstrate that there is no universal diagnostic signature of local adaptation based on within-population nucleotide diversity, so it will not be broadly useful for explaining increased FST. However, given that neither background nor positive selection inflate diversity, when peaks are found they suggest local adaptation may be acting on a causal allele in the region. [ABSTRACT FROM AUTHOR]

The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. Understanding the extent to which genetics × environment plays a role in shaping individual strategies to environmental challenges is of considerable interest for future selection of more resilient animals. The objective of this study was to evaluate the metabolic responses of goats, selected for functional longevity, to a nutritional challenge. This evaluation was based on plasma metabolites and was repeated across 2 experimental farms over 2 years. We carried out 6 different experimental trials from 2018 to 2022 (4 trials on site Bourges, 2018–2021 and 2 trials on site Grignon, 2021–2022) in which 267 first kidding goats, daughters of Alpine bucks divergently selected for functional longevity, longevity plus (n = 137), and longevity minus (n = 130), were exposed to a 2-d nutritional challenge in early lactation. The experiments consisted of a 5 or 7-d control period (prechallenge) on a standard lactation diet followed by a 2-d nutritional challenge with straw-only feeding, and then a 7- or 10-d recovery period on a standard lactation diet, for site Bourges and Grignon, respectively. During the challenge plasma metabolite composition was measured. Linear mixed models were used to analyze all traits, considering the individual as a random effect and the 2 × 2 treatments (i.e., genetic line and year nested in site) and litter size as fixed effects. The linear mixed-effects model using a piecewise arrangement was used to analyze the response/recovery profiles to the nutritional challenge. The estimates of the random effect for each individual, using the mixed models without the fixed effects of genetic line, were used in a sparse partial least square discriminant analysis (sPLS-DA) to compare the goat metabolism response to the challenge on a multivariate scale. The plasma glucose, BHB, nonesterified fatty acids (NEFA), and urea concentrations significantly responded to the 2-d nutritional challenge. Selection for functional longevity did not affect plasma glucose, NEFA, BHB, and urea response/recoveries to a 2-d nutritional challenge. However, site, trial, and litter size significantly affected these responses. Moreover, the plasma metabolites seem not to fully recover to prechallenge levels after the recovery phase. The sPLS-DA analysis did not discriminate between the 2 longevity lines. We observed meaningful between-individuals variability in plasma BHB, especially on the prechallenge and rate of response and rate of recovery from the 2-d nutritional challenge (CV = 26.2%, 36.1%, and 41.2%, repeatability = 0.749, 0.322, and 0.741, respectively). Plasma NEFA recovery from challenge also demonstrated high between-individuals variability (CV = 16.4%, repeatability = 0.323). Selection for functional longevity did not affect plasma metabolites responses to a 2-d nutritional challenge in dairy goats. Plasma NEFA and BHB response and recovery presented high between-individuals variability, indicating that individual adaptative characteristics to nutritional challenges are not related to the environmental conditions but to inherent individual characteristics. [ABSTRACT FROM AUTHOR]

Understanding the drivers of community assembly is critical for predicting the future of biodiversity and ecosystem services. Ecological selection ubiquitously shapes communities by selecting for individuals with the most suitable trait combinations. Detecting selection types on key traits across environmental gradients and over time has the potential to reveal the underlying abiotic and biotic drivers of community dynamics. Here, we present a model‐based predictive framework to quantify the multidimensional trait distributions of communities (community trait spaces), which we use to identify ecological selection types shaping communities along environmental gradients. We apply the framework to over 3600 boreal forest understory plant communities with results indicating that directional, stabilizing, and divergent selection all modify community trait distributions and that the selection type acting on individual traits may change over time. Our results provide novel and rare empirical evidence for divergent selection within a natural system. Our approach provides a framework for identifying key traits under selection and facilitates the detection of processes underlying community dynamics. [ABSTRACT FROM AUTHOR]

ABSTRACT: Understanding the extent to which genetics × environment plays a role in shaping individual strategies to environmental challenges is of considerable interest for future selection of more resilient animals. The objective of this study was to evaluate the metabolic responses of goats, selected for functional longevity, to a nutritional challenge. This evaluation was based on plasma metabolites and was repeated across 2 experimental farms over 2 years. We carried out 6 different experimental trials from 2018 to 2022 (4 trials on site Bourges, 2018–2021 and 2 trials on site Grignon, 2021–2022) in which 267 first kidding goats, daughters of Alpine bucks divergently selected for functional longevity, longevity plus (n = 137), and longevity minus (n = 130), were exposed to a 2-d nutritional challenge in early lactation. The experiments consisted of a 5 or 7-d control period (prechallenge) on a standard lactation diet followed by a 2-d nutritional challenge with straw-only feeding, and then a 7- or 10-d recovery period on a standard lactation diet, for site Bourges and Grignon, respectively. During the challenge plasma metabolite composition was measured. Linear mixed models were used to analyze all traits, considering the individual as a random effect and the 2 × 2 treatments (i.e., genetic line and year nested in site) and litter size as fixed effects. The linear mixed-effects model using a piecewise arrangement was used to analyze the response/recovery profiles to the nutritional challenge. The estimates of the random effect for each individual, using the mixed models without the fixed effects of genetic line, were used in a sparse partial least square discriminant analysis (sPLS-DA) to compare the goat metabolism response to the challenge on a multivariate scale. The plasma glucose, BHB, nonesterified fatty acids (NEFA), and urea concentrations significantly responded to the 2-d nutritional challenge. Selection for functional longevity did not affect plasma glucose, NEFA, BHB, and urea response/recoveries to a 2-d nutritional challenge. However, site, trial, and litter size significantly affected these responses. Moreover, the plasma metabolites seem not to fully recover to prechallenge levels after the recovery phase. The sPLS-DA analysis did not discriminate between the 2 longevity lines. We observed meaningful between-individuals variability in plasma BHB, especially on the prechallenge and rate of response and rate of recovery from the 2-d nutritional challenge (CV = 26.2%, 36.1%, and 41.2%, repeatability = 0.749, 0.322, and 0.741, respectively). Plasma NEFA recovery from challenge also demonstrated high between-individuals variability (CV = 16.4%, repeatability = 0.323). Selection for functional longevity did not affect plasma metabolites responses to a 2-d nutritional challenge in dairy goats. Plasma NEFA and BHB response and recovery presented high between-individuals variability, indicating that individual adaptative characteristics to nutritional challenges are not related to the environmental conditions but to inherent individual characteristics.

Understanding population genetic structure and its possible causal factors is critical for utilizing genetic resources and genetic breeding of economically important plants. Although Torreya grandis is an important conifer producing nuts in China, little is known about its population structure, let alone the causal factors that shaped its genetic variation pattern and population structure. In this work, we intended to characterize the genetic variation pattern and population structure of the nut-yielding conifer T. grandis throughout its whole geographical distribution and further explore the potentially causal factors for the population structure using multiple approaches. A moderate level of genetic diversity and a novel population structure were revealed in T. grandis based on eleven robust EST-SSR loci and three chloroplast fragments. Alien genetic composition derived from the closely related species T. nucifera endemic to Japan was detected in the Kuaiji Mountain area, where the seed quality of T. grandis is considered the best in China. Demography history and niche modeling were inferred and performed, and the contribution of geographic isolation to its population structure was compared with that of environmental isolation. Significant demographic changes occurred, including a dramatic population contraction during the Quaternary, and population divergence was significantly correlated with geographic distance. These results suggested that early breeding activities and demographic changes significantly contributed to the population structure of T. grandis. In turn, the population structure was potentially associated with the excellent variants and adaptation of cultivars of T. grandis. The findings provide important information for utilizing genetic resources and genetic breeding of T. grandis in the future. [ABSTRACT FROM AUTHOR]

SUMMARY: Understanding the genetic basis of population divergence and adaptation is an important goal in population genetics and evolutionary biology. However, the relative roles of demographic history, gene flow, and/or selective regime in driving genomic divergence, climatic adaptation, and speciation in non‐model tree species are not yet fully understood. To address this issue, we generated whole‐genome resequencing data of Liquidambar formosana and L. acalycina, which are broadly sympatric but altitudinally segregated in the Tertiary relict forests of subtropical China. We integrated genomic and environmental data to investigate the demographic history, genomic divergence, and climatic adaptation of these two sister species. We inferred a scenario of allopatric species divergence during the late Miocene, followed by secondary contact during the Holocene. We identified multiple genomic islands of elevated divergence that mainly evolved through divergence hitchhiking and recombination rate variation, likely fostered by long‐term refugial isolation and recent differential introgression in low‐recombination genomic regions. We also found some candidate genes with divergent selection signatures potentially involved in climatic adaptation and reproductive isolation. Our results contribute to a better understanding of how late Tertiary/Quaternary climatic change influenced speciation, genomic divergence, climatic adaptation, and introgressive hybridization in East Asia's Tertiary relict flora. In addition, they should facilitate future evolutionary, conservation genomics, and molecular breeding studies in Liquidambar, a genus of important medicinal and ornamental values. Significance Statement: We assembled a chromosome‐scale genome of Liquidambar formosana and resequenced 160 individuals of L. formosana and its high‐altitude sister species L. acalycina. Benefiting from advanced analytical methods and robust evidence, we found that multiple "genomic islands" mainly evolved as a result of divergence hitchhiking and recombination rate variation, as likely fostered by long‐term refugial isolation and recent differential introgression in low‐recombination genomic regions; and identified some candidate genes associated with climatic adaptation and reproductive isolation. [ABSTRACT FROM AUTHOR]

In ecological speciation, incipient species diverge due to natural selection that is ecologically based. In flowering plants, different pollinators could mediate that selection (pollinator-mediated divergent selection) or other features of the environment that differ between habitats of 2 species could do so (environment-mediated divergent selection). Although these mechanisms are well understood, they have received little rigorous testing, as few studies of divergent selection across sites of closely related species include both floral traits that influence pollination and vegetative traits that influence survival. This study employed common gardens in sites of the 2 parental species and a hybrid site, each containing advanced generation hybrids along with the parental species, to test these forms of ecological speciation in plants of the genus Ipomopsis. A total of 3 vegetative traits (specific leaf area, leaf trichomes, and photosynthetic water-use efficiency) and 5 floral traits (corolla length and width, anther insertion, petal color, and nectar production) were analyzed for impacts on fitness components (survival to flowering and seeds per flower, respectively). These traits exhibited strong clines across the elevational gradient in the hybrid zone, with narrower clines in theory reflecting stronger selection or higher genetic variance. Plants with long corollas and inserted anthers had higher seeds per flower at the Ipomopsis tenuituba site, whereas selection favored the reverse condition at the Ipomopsis aggregata site, a signature of divergent selection. In contrast, no divergent selection due to variation in survival was detected on any vegetative trait. Selection within the hybrid zone most closely resembled selection within the I. aggregata site. Across traits, the strength of divergent selection was not significantly correlated with width of the cline, which was better predicted by evolvability (standardized genetic variance). These results support the role of pollinator-mediated divergent selection in ecological speciation and illustrate the importance of genetic variance in determining divergence across hybrid zones. [ABSTRACT FROM AUTHOR]

Runs of homozygosity (ROH) are defined as long continuous homozygous stretches in the genome which are assumed to originate from a common ancestor. It has been demonstrated that divergent selection for variability in mice is possible and that low variability in birth weight is associated with robustness. To analyse ROH patterns and ROH‐based genomic inbreeding, two mouse lines that were divergently selected for birth weight variability for 26 generations were used, with: 752 individuals for the high variability line (H‐Line), 766 individuals for the low variability line (L‐Line) and 74 individuals as a reference population. Individuals were genotyped using the high density Affymetrix Mouse Diversity Genotyping Array. ROH were identified using both the sliding windows (SW) and the consecutive runs (CR) methods. Inbreeding coefficients were calculated based on pedigree (FPED) information, on ROH identified using the SW method (FROHSW) and on ROH identified using the CR method (FROHCR). Differences in genomic inbreeding were not consistent across generations and these parameters did not show clear differences between lines. Correlations between FPED and FROH were high, particularly for FROHSW. Moreover, correlations between FROHSW and FPED were even higher when ROH were identified with no restrictions in the number of heterozygotes per ROH. The comparison of FROH estimates between either of the selected lines were based on significant differences at the chromosome level, mainly in chromosomes 3, 4, 6, 8, 11, 15 and 19. ROH‐based inbreeding estimates that were computed using longer homozygous segments had a higher relationship with FPED. Differences in robustness between lines were not attributable to a higher homozygosis in the L‐Line, but maybe to the different distribution of ROH at the chromosome level between lines. The analysis identified a set of genomic regions for future research to establish the genomic basis of robustness. [ABSTRACT FROM AUTHOR]

Color polymorphic species provide an excellent opportunity to investigate the ecology and evolution of intraspecific niche differences. The red‐backed salamander, Plethodon cinereus, is a fully terrestrial lungless salamander with two common color forms, striped and unstriped. Previous research suggests the morphs may be differentially adapted to surface and subsurface microhabitats, with the unstriped morph being more fossorial. This hypothesis predicts that the unstriped morph should be more sensitive to the risks of surface activity (e.g., thermal stress, dehydration, predation), and therefore be more selective than striped morphs when choosing soil surface microhabitats. To test this hypothesis, we experimentally manipulated leaf litter mass in small forest patches (~0.45 m2). Leaf litter addition reduced soil temperatures, buffered against changes in air temperature, and likely provided physical protection from predators. Over 3 years, we found that unstriped adults responded positively to leaf litter addition, but striped adults did not. In addition, unstriped morphs spent significantly more time in protective refuges (opaque, moistened tubes) than striped morphs in laboratory assays. Taken together, the field and laboratory results support the hypothesis that the unstriped morph is more sensitive to the risks of surface activity, and therefore is more likely to be fossorial. This difference in microhabitat use, combined with spatiotemporal variation in leaf litter accumulation on the forest floor, may play an important role in the maintenance of the polymorphism. [ABSTRACT FROM AUTHOR]

Norway spruce is expected to suffer from drought stress and other manifestations of climate change. This study relies on a manipulative experiment with drought-stressed and well-watered (control) seedlings, comprising five provenances of Norway spruce distributed along a steep elevational transect from 550 to 1,280 m a.s.l. within the natural range. Seedlings were subjected to measurement of physiological traits (content of phytohormones and monoterpenes, slow and fast chlorophyll a fluorescence kinetics, gas exchange, hyperspectral indices), and genotyping at 8 nuclear microsatellite loci. Comparison of the coefficient of differentiation at neutral loci (FST) vs. differentiation at phenotypic traits (PST) was used to identify traits underlying divergent selection. In total, 18 traits exhibited a significant PST – FST difference. However, the consistency in differentiation patterns between drought-stressed and control plants was limited, only three traits exhibited signals of selection under both treatments. This outcome indicates that the identified differentiation patterns can only be interpreted in the context of environmental setup of the experiment, and highlights the importance of common gardens in adaptation research, as they allow both elimination of environment-induced phenotypic variation and studying genotype-by-environment interaction in physiological responses to environmental stresses.

Understanding population genetic structure and its possible causal factors is critical for utilizing genetic resources and genetic breeding of economically important plants. Although Torreya grandis is an important conifer producing nuts in China, little is known about its population structure, let alone the causal factors that shaped its genetic variation pattern and population structure. In this work, we intended to characterize the genetic variation pattern and population structure of the nut-yielding conifer T. grandis throughout its whole geographical distribution and further explore the potentially causal factors for the population structure using multiple approaches. A moderate level of genetic diversity and a novel population structure were revealed in T. grandis based on eleven robust EST-SSR loci and three chloroplast fragments. Alien genetic composition derived from the closely related species T. nucifera endemic to Japan was detected in the Kuaiji Mountain area, where the seed quality of T. grandis is considered the best in China. Demography history and niche modeling were inferred and performed, and the contribution of geographic isolation to its population structure was compared with that of environmental isolation. Significant demographic changes occurred, including a dramatic population contraction during the Quaternary, and population divergence was significantly correlated with geographic distance. These results suggested that early breeding activities and demographic changes significantly contributed to the population structure of T. grandis. In turn, the population structure was potentially associated with the excellent variants and adaptation of cultivars of T. grandis. The findings provide important information for utilizing genetic resources and genetic breeding of T. grandis in the future.

Introgressive hybridization may erode phenotypic divergence along environmental gradients, collapsing locally adapted populations into a hybrid swarm. Alternatively, introgression may promote phenotypic divergence by providing variation on which natural selection can act. In freshwater fishes, water flow often selects for divergent morphological traits in lake versus stream habitats. We tested the effects of introgression on lake-stream morphological divergence in the minnow Owens Tui Chub (Siphateles bicolor snyderi), which has been rendered endangered by introgession from the introduced Lahontan Tui Chub (Siphateles bicolor obesa). Using geometric morphometric analysis of 457 individual Tui Chub from thirteen populations, we found that both native and introgressing parent taxa exhibited divergent body and caudal fin shapes in lake versus stream habitats, but their trajectories of divergence were distinct. In contrast, introgressed populations exhibited intermediate body and caudal fin shapes that were not differentiated by habitat type, indicating that introgression has eroded phenotypic divergence along the lentic-lotic gradient throughout the historic range of the Owens Tui Chub. Individuals within hybrid populations were less morphologically variable than those within parent populations, suggesting hybrid adaptation to selective agents other than water flow or loss of variance by drift.

Abstract Background The time between the appearance of successive leaves, or phyllochron, characterizes the vegetative development of annual plants. Hypothesis testing models, which allow the comparison of phyllochrons between genetic groups and/or environmental conditions, are usually based on regression of thermal time on the number of leaves; most of the time a constant leaf appearance rate is assumed. However regression models ignore auto-correlation of the leaf number process and may lead to biased testing procedures. Moreover, the hypothesis of constant leaf appearance rate may be too restrictive. Methods We propose a stochastic process model in which emergence of new leaves is considered to result from successive time-to-events. This model provides a flexible and more accurate modeling as well as unbiased testing procedures. It was applied to an original maize dataset collected in the field over three years on plants originating from two divergent selection experiments for flowering time in two maize inbred lines. Results and conclusion We showed that the main differences in phyllochron were not observed between selection populations but rather between ancestral lines, years of experimentation and leaf ranks. Our results highlight a strong departure from the assumption of a constant leaf appearance rate over a season which could be related to climate variations, even if the impact of individual climate variables could not be clearly determined.

Abstract Color polymorphic species provide an excellent opportunity to investigate the ecology and evolution of intraspecific niche differences. The red‐backed salamander, Plethodon cinereus, is a fully terrestrial lungless salamander with two common color forms, striped and unstriped. Previous research suggests the morphs may be differentially adapted to surface and subsurface microhabitats, with the unstriped morph being more fossorial. This hypothesis predicts that the unstriped morph should be more sensitive to the risks of surface activity (e.g., thermal stress, dehydration, predation), and therefore be more selective than striped morphs when choosing soil surface microhabitats. To test this hypothesis, we experimentally manipulated leaf litter mass in small forest patches (~0.45 m2). Leaf litter addition reduced soil temperatures, buffered against changes in air temperature, and likely provided physical protection from predators. Over 3 years, we found that unstriped adults responded positively to leaf litter addition, but striped adults did not. In addition, unstriped morphs spent significantly more time in protective refuges (opaque, moistened tubes) than striped morphs in laboratory assays. Taken together, the field and laboratory results support the hypothesis that the unstriped morph is more sensitive to the risks of surface activity, and therefore is more likely to be fossorial. This difference in microhabitat use, combined with spatiotemporal variation in leaf litter accumulation on the forest floor, may play an important role in the maintenance of the polymorphism.

This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (FNEJ), Li and Horvitz (FL&H), Van Raden method 1 (FVR1) and method 2 (FVR2), and Yang (FYAN). Inbreeding based on runs of homozygosity (FROH) and pedigree inbreeding (FPED) were also computed. FROH, FNEJ, and FL&H were also adjusted for their average values in the first generation of selection and named FROH0, FNEJ0, and FL&H0. ∆F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (∆FPEDt) and individual increases in inbreeding (∆FPEDi). Moreover, individual ∆F was calculated from the different molecular inbreeding coefficients (∆FNEJ0, ∆FL&H, ∆FL&H0, ∆FVR1, ∆FVR2, ∆FYAN, and ∆FROH0). The Ne was obtained from different ∆F, such as NePEDt, NePEDi, NeNEJ0, NeL&H, NeL&H0, NeVR1, NeVR2, NeYAN, and NeROH0. Comparing with FPED, FROH, FNEJ and FVR2 overestimated inbreeding while FNEJ0, FL&H, FL&H0, FVR1 and FYAN underestimated inbreeding. Correlations between inbreeding coefficients and ∆F were calculated. FROH had the highest correlation with FPED (0.89); FYAN had correlations >0.95 with all the other molecular inbreeding coefficients. NePEDi was more reliable than NePEDt and presented similar behaviour to NeL&H0 and NeNEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation NePEDi was 42.20, NeL&H0 was 45.04 and NeNEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively FROH presented the highest correlation with FPED, which addresses the identity by descent probability (IBD). The evolution of NeL&H0 and NeNEJ0 was the most similar to that of NePEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.

The Sebastes inermis complex includes three sympatric species (Sebastes cheni, viz Sebastes inermis, and Sebastes ventricosus) with clear ecomorphological differences, albeit incomplete reproductive isolation. The presence of putative morphological hybrids (PMH) with plausibly higher fitness than the parent species indicates the need to confirm whether hybridization occurs within the complex. In this sense, we assessed the dynamics of genetic divergence and hybridization within the species complex using a panel of 10 microsatellite loci, and sequences of the mitochondrial control region (D-loop) and the intron-free rhodopsin (RH1) gene. The analyses revealed the presence of three distinct genetic clusters, large genetic distances using D-loop sequences, and distinctive mutations within the RH1 gene. These results are consistent with the descriptions of the three species. Two microsatellite loci had signatures of divergent selection, indicating that they are linked to genomic regions that are crucial for speciation. Furthermore, nonsynonymous mutations within the RH1 gene detected in S. cheni and "Kumano" (a PMH) suggest dissimilar adaptations related to visual perception in dim-light environments. The presence of individuals with admixed ancestry between two species confirmed hybridization. The presence of nonsynonymous mutations within the RH1 gene and the admixed ancestry of the "Kumano" morphotype highlight the potential role of hybridization in generating novelties within the species complex. We discuss possible outcomes of hybridization within the species complex, considering hybrid fitness and assortative mating. Overall, our findings indicate that the genetic divergence of each species is maintained in the presence of hybridization, as expected in a scenario of speciation-with-gene-flow. [ABSTRACT FROM AUTHOR]

Simple Summary: Ten generations of divergent selection for intramuscular fat (IMF) content was performed in rabbits. Through the generations, the IMF content has improved. Different Bayesian animal models were used to assess the importance of maternal genetic effects on the genetic control of IMF and fatty acid composition of the two rabbit lines divergently selected for IMF content. Additionally, maternal genome-wide association studies were carried out in these lines to identify genomic regions affecting the IMF and intramuscular fatty acid composition of the offspring. The maternal genetic variance explained an important part of the phenotypic variance of the IMF and intramuscular fatty acid composition. Potential candidate genes were identified on the associated genomic regions related to the traits under study. Maternal genetic effects (MGE) could affect meat quality traits such as intramuscular fat (IMF) and its fatty acid composition. However, it has been scarcely studied, especially in rabbits. The objectives of the present study were, first, to assess the importance of MGE on intramuscular fat and fatty acid composition by applying a Bayesian maternal animal model in two rabbit lines divergently selected for IMF. The second objective was to identify genomic regions and candidate genes of MGE that are associated with the traits of these offspring, using Bayesian methods in a Genome Wide Association Study (GWAS). Quantitative analyses were performed using data from 1982 rabbits, and 349 animals from the 9th generation and 76 dams of the 8th generation with 88,512 SNPs were used for the GWAS. The studied traits were IMF, saturated fatty acids (total SFA, C14:0; myristic acid, C16:0; palmitic acid and C18:0; stearic acid), monounsaturated fatty acids (total MUFA, C16:1n-7; palmitoleic acid and C18:1n-9; oleic acid), polyunsaturated fatty acids (total PUFA, C18:2n-6; linoleic acid, C18:3n-3; α-linolenic acid and C20:4n-6; arachidonic acid), MUFA/SFA and PUFA/SFA. The proportion of phenotypic variance explained by the maternal genetic effect ranged from 8 to 22% for IMF, depending on the model. For fatty acid composition, the proportion of phenotypic variance explained by maternal genetic effects varied from 10% (C18:0) to 46% (MUFA) in a model including both direct and additive maternal genetic effects, together with the common litter effect as a random variable. In particular, there were significant direct maternal genetic correlations for C16:0, C18:1n9, C18:2n6, SFA, MUFA, and PUFA with values ranging from −0.53 to −0.89. Relevant associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU5 and OCU19 containing some relevant candidates (TANC2, ACE, MAP3K3, TEX2, PRKCA, SH3GL2, CNTLN, RPGRIP1L and FTO) related to lipid metabolism, binding, and obesity. These regions explained about 1.2 to 13.9% of the total genomic variance of the traits studied. Our results showed an important maternal genetic effect on IMF and its fatty acid composition in rabbits and identified promising candidate genes associated with these traits. [ABSTRACT FROM AUTHOR]

Abstract Invasive species often possess a great capacity to adapt to novel environments in the form of spatial trait variation, as a result of varying selection regimes, genetic drift, or plasticity. We explored the geographic differentiation in several phenotypic traits related to plant growth, reproduction, and defense in the highly invasive Centaurea solstitialis by measuring neutral genetic differentiation (FST), and comparing it with phenotypic differentiation (PST), in a common garden experiment in individuals originating from regions representing the species distribution across five continents. Native plants were more fecund than non‐native plants, but the latter displayed considerably larger seed mass. We found indication of divergent selection for these two reproductive traits but little overall genetic differentiation between native and non‐native ranges. The native versus invasive PST–FST comparisons demonstrated that, in several invasive regions, seed mass had increased proportionally more than the genetic differentiation. Traits displayed different associations with climate variables in different regions. Both capitula numbers and seed mass were associated with winter temperature and precipitation and summer aridity in some regions. Overall, our study suggests that rapid evolution has accompanied invasive success of C. solstitialis and provides new insights into traits and their genetic bases that can contribute to fitness advantages in non‐native populations.

Background: The time between the appearance of successive leaves, or phyllochron, characterizes the vegetative development of annual plants. Hypothesis testing models, which allow the comparison of phyllochrons between genetic groups and/or environmental conditions, are usually based on regression of thermal time on the number of leaves; most of the time a constant leaf appearance rate is assumed. However regression models ignore auto-correlation of the leaf number process and may lead to biased testing procedures. Moreover, the hypothesis of constant leaf appearance rate may be too restrictive. Methods: We propose a stochastic process model in which emergence of new leaves is considered to result from successive time-to-events. This model provides a flexible and more accurate modeling as well as unbiased testing procedures. It was applied to an original maize dataset collected in the field over three years on plants originating from two divergent selection experiments for flowering time in two maize inbred lines. Results and conclusion: We showed that the main differences in phyllochron were not observed between selection populations but rather between ancestral lines, years of experimentation and leaf ranks. Our results highlight a strong departure from the assumption of a constant leaf appearance rate over a season which could be related to climate variations, even if the impact of individual climate variables could not be clearly determined. [ABSTRACT FROM AUTHOR]

Abstract Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. Results Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) F ST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). Conclusion Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.

Invasive species often possess a great capacity to adapt to novel environments in the form of spatial trait variation, as a result of varying selection regimes, genetic drift, or plasticity. We explored the geographic differentiation in several phenotypic traits related to plant growth, reproduction, and defense in the highly invasive Centaurea solstitialis by measuring neutral genetic differentiation (FST), and comparing it with phenotypic differentiation (PST), in a common garden experiment in individuals originating from regions representing the species distribution across five continents. Native plants were more fecund than non‐native plants, but the latter displayed considerably larger seed mass. We found indication of divergent selection for these two reproductive traits but little overall genetic differentiation between native and non‐native ranges. The native versus invasive PST–FST comparisons demonstrated that, in several invasive regions, seed mass had increased proportionally more than the genetic differentiation. Traits displayed different associations with climate variables in different regions. Both capitula numbers and seed mass were associated with winter temperature and precipitation and summer aridity in some regions. Overall, our study suggests that rapid evolution has accompanied invasive success of C. solstitialis and provides new insights into traits and their genetic bases that can contribute to fitness advantages in non‐native populations. [ABSTRACT FROM AUTHOR]

Improving our knowledge of how past climate‐driven selection has acted on present‐day trait population divergence is essential to understand local adaptation processes and improve our predictions of evolutionary trajectories in the face of altered selection pressures resulting from climate change. In this study, we investigated signals of selection on traits related to drought tolerance and growth rates in two Mediterranean oak species (Quercus faginea and Q. lusitanica) with contrasting distribution ranges and climatic niches. We genotyped 182 individuals from 24 natural populations of the two species using restriction‐site‐associated DNA sequencing and conducted a thorough functional characterization in 1602 seedlings from 21 populations cultivated in common garden experiments under contrasting watering treatments. Our genomic data revealed that both Q. faginea and Q. lusitanica have very weak population genetic structure, probably as a result of high rates of pollen‐mediated gene flow among populations and large effective population sizes. In contrast, common garden experiments showed evidence of climate‐driven divergent selection among populations on traits related to leaf morphology, physiology and growth in both species. Overall, our study suggests that climate is an important selective factor for Mediterranean oaks and that ecophysiological traits have evolved in drought‐prone environments even in a context of very high rates of gene flow among populations. [ABSTRACT FROM AUTHOR]

BackgroundGlucosinolates (GSLs) constitute a characteristic group of secondary metabolites present in the Brassica genus. These compounds confer resistance to pests and diseases. Moreover, they show allelopathic and anticarcinogenic effects. All those effects are dependent on the chemical structure of the GSL. The modification of the content of specific GSLs would allow obtaining varieties with enhanced resistance and/or improved health benefits. Moreover, the attainment of varieties with the same genetic background but with divergent GSLs concentration will prompt the undertaking of studies on their biological effects.Objective and MethodsThe objective of this study was to evaluate the efficacy of two divergent mass selection programs to modify GSL content in the leaves of two Brassica species: nabicol (Brassica napus L.), selected by glucobrassicanapin (GBN), and nabiza (Brassica rapa L.), selected by gluconapin (GNA) through several selection cycles using cromatographic analysis.ResultsThe response to selection fitted a linear regression model with no signs of variability depletion for GSL modification in either direction, but with higher efficiency in reducing the selected GSL than in the increasing. The selection was also effective in other parts of the plant, suggesting that there is a GSL translocation in the plant or a modification in their synthesis pathway that is not-organ specific. There was an indirect response of selection in other GSL; thus this information should be considered when designing breeding programs. Finally, populations obtained by selection have the same agronomic performance or even better than the original population.ConclusionTherefore, mass selection seems to be a good method to modify the content of specific GSL in Brassica crops.

ABSTRACT: The population dynamics of 2 lines of chickens from a long-term (59 generations) selection experiment were assessed based on pedigree data. These lines were propagated from phenotypic selection for low and high 8-wk BW in White Plymouth Rock chickens. Our objective was to determine whether the 2 lines maintained similar population structures over the selection horizon to allow meaningful comparisons of their performance data. A complete pedigree of 31,909 individuals, consisting of 102 founders, 1,064 from the parental generation, and 16,245 low weight (LWS) and 14,498 high weight (HWS) select chickens, was available. Inbreeding (F) and average relatedness (AR) coefficients were computed. Average F per generation and AR coefficients were 1.3 (SD 0.8) % and 0.53 (SD 0.001) for LWS, and 1.5 (SD 1.1) % and 0.66 (SD 0.001) for HWS. Mean F for the entire pedigree was 0.26 (0.16) and 0.33 (0.19), and maximum F was 0.64 and 0.63, in LWS and HWS, respectively. Based on Wright's fixation index, at generation 59, substantial genetic differences were established between lines. The effective population size was 39 in LWS and 33 in HWS. The effective number of founders was 17 and 15, effective number of ancestors were 12 and 8, and genome equivalents were 2.5 and 1.9 in LWS and HWS, respectively. About 30 founders explained the marginal contribution to both lines. By generation 59, only 7 male and 6 female founders contributed to both lines. Moderately high levels of inbreeding and low effective population sizes were inevitable, as this was a closed population. However, effects on the fitness of the population were expected to be less substantial because founders were a combination of 7 lines. The effective numbers of founders and ancestors were relatively low compared to the actual number of founders, as few ancestors contributed to descendants. Based on these evaluations, it can be inferred that LWS and HWS had similar population structures. Comparisons of selection responses in the 2 lines therefore should be reliable.

ABSTRACT: This study aimed to assess the effect of inbreeding on production traits using a long-term closed-line population recorded for residual feed intake (RFI). The study first used data from a previously reported population to determine the appropriate period of divergent selection for RFI. The results showed that RFI had similar moderate heritability estimates (0.28–0.34) during the fast-growing period (7–12 wk), and RFI at 7 to 10 wk had the highest heritability (0.34). Therefore, divergent selection was performed in a Chinese broiler population for RFI at 7 to 10 wk; the total sample size from generations zero (G0) to 13 was 9050. The divergence between the 2 lines increased steadily throughout generations, resulting in G13 with average RFI values of 304.55 in high RFI (HRFI) males, −160.31 in low RFI (LRFI) males, 296.30 in HRFI females and −157.55 in LRFI females. The feed intake (FI) and feed conversion ratio were almost higher in HRFI broilers than in LRFI broilers, and the magnitude of the difference in FI increased from approximately 4% for both sexes in G1 to approximately 33% in G13. Body weight gain was irregular from G1 to G13 and higher in LRFI broilers than in HRFI broilers after G10. Indeed, the HRFI broilers consumed more food, but they were lighter than LRFI broilers. In G13, LRFI males had heavier slaughter weight, longer cecum length, more white blood cells (WBC), red blood cells (RBC) and hemoglobin (HGB), but triglycerides, lower dressed percentage, percentage of half eviscerated yield, and eviscerated yield than HRFI males. LRFI females had a higher percentage of breast muscle and gizzard yield, longer cecum length, and more WBCs, RBCs and HGB but less abdominal fat and serum total cholesterol than HRFI females. This study was the first to verify that long-term divergent selection for RFI in Chinese broiler chickens is positive and beneficial.

Background: The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. Results: Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) FST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). Conclusion: Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation. [ABSTRACT FROM AUTHOR]

Introduction: Due to long-term domestication, breeding and divergent selection, a vast genetic diversity in poultry currently exists, with various breeds being characterized by unique phenotypic and genetic features. Assuming that differences between chicken breeds divergently selected for economically and culturally important traits manifest as early as possible in development and growth stages, we aimed to explore breed-specific patterns and interrelations of embryo myogenesis, nitric oxide (NO) metabolism and post-hatch growth rate (GR). Methods: These characteristics were explored in eight breeds of different utility types (meat-type, dual purpose, egg-type, game, and fancy) by incubating 70 fertile eggs per breed. To screen the differential expression of seven key myogenesis associated genes (MSTN, GHR, MEF2C, MYOD1, MYOG, MYH1, and MYF5), quantitative real-time PCR was used. Results: We found that myogenesis associated genes expressed in the breast and thigh muscles in a coordinated manner showing breed specificity as a genetic diversity signature among the breeds studied. Notably, coordinated ("accord") expression patterns of MSTN, GHR, and MEFC2 were observed both in the breast and thigh muscles. Also, associated expression vectors were identified for MYOG and MYOD1 in the breast muscles and for MYOG and MYF5 genes in the thigh muscles. Indices of NO oxidation and post-hatch growth were generally concordant with utility types of breeds, with meat-types breeds demonstrating higher NO oxidation levels and greater GR values as compared to egg-type, dual purpose, game and fancy breeds. Discussion: The results of this study suggest that differences in early myogenesis, NO metabolism and post-hatch growth are breed-specific; they appropriately reflect genetic diversity and accurately capture the evolutionary history of divergently selected chicken breeds. [ABSTRACT FROM AUTHOR]

In animal-pollinated plants, the growth environment and pollination environment are two important agents of natural selection. However, their simultaneous effects on plant speciation remain underexplored. Here, we report a theoretical finding that if plants' local adaptation to the growth environment increases their floral rewards for pollinators, it can strongly facilitate ecological speciation in plants. We consider two evolving plant traits, vegetative and floral signal traits, in a population genetic model for two plant populations under divergent selection from different growth environments. The vegetative trait determines plants' local adaptation. Locally adapted plants reward pollinators better than maladapted plants. By associative learning, pollinators acquire learned preferences for floral signal traits expressed by better-rewarding plants. If pollinators' learned preferences become divergent between populations, floral signal divergence occurs and plants develop genetic associations between vegetative and floral signal traits, leading to ecological speciation via a two-allele mechanism. Interestingly, speciation is contingent on whether novel floral signal variants arise before or after plant populations become locally adapted to the growth environment. Our results suggest that simultaneous selection from growth and pollination environments might be important for the ecological speciation of animal-pollinated plants. [ABSTRACT FROM AUTHOR]

Habitat choice is an important behavior for maximizing fitness. One of the factors involved in habitat choice is preference for habitat substrates. In the context of predatory avoidance, it is adaptive to prefer substrates that are matched to own body color. The ground cricket Dianemobius csikii (Bolívar, 1901) occurs on sandy beaches. The body color of D. csikii resembles the sand of their habitat, which could be a form of crypsis. If D. csikii is not able to choose a suitable habitat background that matches their body color, the crickets incur a high risk of predation. The risk could result in population decline of the cricket. To examine whether D. csikii shows preference for substrates that match its body color, we undertook a two‐choice test of sand or soil substrates after controlling the type of flooring substrates used during rearing. The crickets did not show preference for sand. There was no significant effect of flooring substrates during the nymph stage on the preference. These results suggest that when habitats are fragmented, crickets do not actively choose a cryptic background. There were significant differences in the substrate preference between sexes. These results reflect differences in the reproductive strategies of males and females. [ABSTRACT FROM AUTHOR]

Aim: Species living in a shared environment face similar selective pressures and often evolve adaptive divergence to avoid competition. Quantifying phenotypic divergence and its genetic parallelism among sympatric species is important for understanding of ecologically moderated biodiversity. Here, we integrate ecologic, phenotypic and genomic datasets to study to what extent three sympatrically snowfinches (Montifringilla adamsi, Pyrgilauda ruficollis and Onychostruthus taczanowskii) differ in their adaptations in order to co‐exist in a shared environment. Location: Qinghai–Tibetan Plateau. Methods: We used principal component analysis to summarize and compare environmental and phenotypic divergence. We compared phenotypes relevant to body and beak sizes (n = 68) because they are indicators of niche and food segregation, thus critical for establishing co‐existence of sympatric birds. We used comparative genomics (n = 33) to identify genetic loci that are highly divergent between species as well as loci unique for each of species. Using vector analyses, we integrated correlation and permutation to quantify parallelism between phenotypic and genetic divergences. Results: We found that body and beak sizes are significantly different among three snowfinches. The phenotypic differentiations are greater in species that share similar ecological conditions than in those that do not. We showed that genes related to developmental process are over‐represented within highly divergent genomic regions and unique genetic loci of each species. We found that the extent of phenotypic divergence between snowfinch pairs is more strongly correlated with the magnitude of divergence in developmental genes than in the whole genome. Main conclusions: Adaptive divergence of sympatric snowfinches is highly constrained on developmental genes. As this genetic divergence is strongly correlated with divergence of the traits related to segregation in niche and food resources, this correlation reflects either causal effects or indirect consequences of ecological mediated changes. Our study provides novel insights into the mechanisms underlying evolutionary versatility and ecological success among sympatric species. [ABSTRACT FROM AUTHOR]

Within-species, biodiversity can be organized in units, ranging from subspecies to evolutionarily significant units (ESUs), populations and social groups. To define ESUs, researchers often focus on the concordant distribution of traits that exhibit likely adaptive significance, including genetic and ecological variation. Caribou is a Species at Risk in Canada, and are conserved at the level of both subspecies and designatable units (DUs), which are conceptually similar to ESUs. However, the use of genomics has been suggested to provide better delineation of units that are based upon variation of genes—not just neutral genetic markers. Here, we analyzed single nucleotide polymorphisms (SNPs) for 190 caribou belonging to two recognized subspecies and four DUs found throughout western Canada. We confirmed two major genetic clusters, which we refer to as the Northern Caribou and Southern Caribou, characterized by divergence at numerous SNPs and genes with known functions in other mammals. Notably, the distribution of these two clusters did not fully overlap with currently recognized subspecies. A discrepancy with current classification was detected for Mountain DUs, which were thought to belong to the Woodland subspecies, but with significant northern-type ecological traits described in the literature, indicating more work is needed to refine our understanding of this transitional zone. We also detected genetic signals of male-biased dispersal, which may be natural or affected by habitat fragmentation effects on females. This work illustrates the value of genomics in rethinking subspecies and conservation unit designations and better conserve biodiversity within terrestrial species at risk. [ABSTRACT FROM AUTHOR]

Maternal genetic effects (MGE) could affect meat quality traits such as intramuscular fat (IMF) and its fatty acid composition. However, it has been scarcely studied, especially in rabbits. The objectives of the present study were, first, to assess the importance of MGE on intramuscular fat and fatty acid composition by applying a Bayesian maternal animal model in two rabbit lines divergently selected for IMF. The second objective was to identify genomic regions and candidate genes of MGE that are associated with the traits of these offspring, using Bayesian methods in a Genome Wide Association Study (GWAS). Quantitative analyses were performed using data from 1982 rabbits, and 349 animals from the 9th generation and 76 dams of the 8th generation with 88,512 SNPs were used for the GWAS. The studied traits were IMF, saturated fatty acids (total SFA, C14:0; myristic acid, C16:0; palmitic acid and C18:0; stearic acid), monounsaturated fatty acids (total MUFA, C16:1n-7; palmitoleic acid and C18:1n-9; oleic acid), polyunsaturated fatty acids (total PUFA, C18:2n-6; linoleic acid, C18:3n-3; α-linolenic acid and C20:4n-6; arachidonic acid), MUFA/SFA and PUFA/SFA. The proportion of phenotypic variance explained by the maternal genetic effect ranged from 8 to 22% for IMF, depending on the model. For fatty acid composition, the proportion of phenotypic variance explained by maternal genetic effects varied from 10% (C18:0) to 46% (MUFA) in a model including both direct and additive maternal genetic effects, together with the common litter effect as a random variable. In particular, there were significant direct maternal genetic correlations for C16:0, C18:1n9, C18:2n6, SFA, MUFA, and PUFA with values ranging from −0.53 to −0.89. Relevant associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU5 and OCU19 containing some relevant candidates (TANC2, ACE, MAP3K3, TEX2, PRKCA, SH3GL2, CNTLN, RPGRIP1L and FTO) related to lipid metabolism, binding, and obesity. These regions explained about 1.2 to 13.9% of the total genomic variance of the traits studied. Our results showed an important maternal genetic effect on IMF and its fatty acid composition in rabbits and identified promising candidate genes associated with these traits.

Introduction: Due to long-term domestication, breeding and divergent selection, a vast genetic diversity in poultry currently exists, with various breeds being characterized by unique phenotypic and genetic features. Assuming that differences between chicken breeds divergently selected for economically and culturally important traits manifest as early as possible in development and growth stages, we aimed to explore breed-specific patterns and interrelations of embryo myogenesis, nitric oxide (NO) metabolism and post-hatch growth rate (GR).Methods: These characteristics were explored in eight breeds of different utility types (meat-type, dual purpose, egg-type, game, and fancy) by incubating 70 fertile eggs per breed. To screen the differential expression of seven key myogenesis associated genes (MSTN, GHR, MEF2C, MYOD1, MYOG, MYH1, and MYF5), quantitative real-time PCR was used.Results: We found that myogenesis associated genes expressed in the breast and thigh muscles in a coordinated manner showing breed specificity as a genetic diversity signature among the breeds studied. Notably, coordinated (“accord”) expression patterns of MSTN, GHR, and MEFC2 were observed both in the breast and thigh muscles. Also, associated expression vectors were identified for MYOG and MYOD1 in the breast muscles and for MYOG and MYF5 genes in the thigh muscles. Indices of NO oxidation and post-hatch growth were generally concordant with utility types of breeds, with meat-types breeds demonstrating higher NO oxidation levels and greater GR values as compared to egg-type, dual purpose, game and fancy breeds.Discussion: The results of this study suggest that differences in early myogenesis, NO metabolism and post-hatch growth are breed-specific; they appropriately reflect genetic diversity and accurately capture the evolutionary history of divergently selected chicken breeds.

Evidence for adaptation to different climates in the model species Arabidopsis thaliana is seen in reciprocal transplant experiments, but the genetic basis of this adaptation remains poorly understood. Field-based quantitative trait locus (QTL) studies provide direct but low-resolution evidence for the genetic basis of local adaptation. Using high-resolution population genomic approaches, we examine local adaptation along previously identified genetic trade-off (GT) and conditionally neutral (CN) QTLs for fitness between locally adapted Italian and Swedish A. thaliana populations [Ågren J, et al. (2013) Proc Natl Acad Sci USA 110:21077-21082]. We find that genomic regions enriched in high FST SNPs colocalize with GT QTL peaks. Many of these high FST regions also colocalize with regions enriched for SNPs significantly correlated to climate in Eurasia and evidence of recent selective sweeps in Sweden. Examining unfolded site frequency spectra across genes containing high FST SNPs suggests GTs may be due to more recent adaptation in Sweden than Italy. Finally, we collapse a list of thousands of genes spanning GT QTLs to 42 genes that likely underlie the observed GTs and explore potential biological processes driving these trade-offs, from protein phosphorylation, to seed dormancy and longevity. Our analyses link population genomic analyses and field-based QTL studies of local adaptation, and emphasize that GTs play an important role in the process of local adaptation.

Divergent selection of KNR6 maximizes grain production by balancing the flowering-time adaptation and ear size in maize Keywords: flowering time; grain yield; trade-off; divergent selection; maize EN flowering time grain yield trade-off divergent selection maize 1311 1313 3 06/22/23 20230701 NES 230701 Domestication and improvement have led to dramatic changes in the plant architecture and inflorescence in maize. Collectively, we found that I KNR6 i underwent divergent selection during maize breeding to extend adaptation and increase grain yield, and offered a knowledge-driven strategy for engineering I KNR6 i to maximize maize grain production. [Extracted from the article]

Coupling of multiple barriers to gene‐flow, such as divergent local adaptation and reproductive isolation, facilitates speciation. However, alleles at loci that contribute to barrier effects can be dissociated by recombination. Models of linkage between diverging alleles often consider elements that reduce recombination, such as chromosomal inversions and alleles that modify recombination rate between existing loci. In contrast, here, we consider the evolution of linkage due to the close proximity of loci on the same chromosome. Examples of such physical linkage exist in several species, but in other cases, strong associations are maintained without physical linkage. We use an individual‐based model to study the conditions under which the physical linkage between loci controlling ecological traits and mating preferences might be expected to evolve. We modelled a single locus controlling an ecological trait that acts also as a mating cue. Mating preferences are controlled by multiple loci, formed by mutations that are randomly placed in the "genome", within varying distances from the ecological trait locus, allowing us to examine which genomic architectures spread across the population. Our model reveals that stronger physical linkage is favoured when mating preferences and selection are weaker. Under such conditions mating among divergent phenotypes is more frequent, and matching ecological trait and mating preference alleles are more likely to become dissociated by recombination, favouring the evolution of genetic linkage. While most theoretical studies on clustering of divergent loci focus on how physical linkage influences speciation, we show how physical linkage itself can arise, establishing conditions that can favour speciation. [ABSTRACT FROM AUTHOR]

Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed QST‐FST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait‐climate and plasticity‐climate regressions. Three major findings emerged: (1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. (2) Based on QST‐FST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. (3) Traits and/or their plasticity were often correlated with population source climate (R2 up to.77 and.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change. [ABSTRACT FROM AUTHOR]

Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry. [ABSTRACT FROM AUTHOR]

Simple Summary: The purpose of the investigation was to determine the effect of the selection for the total fat content of the rabbit body on the fat content and fatty acid composition of different meat cuts. The higher the fat content of the given meat, the more effective the selection was. Authors found that the meat of fatter rabbits is healthier, which can be used in the production of baby food. The present research studied the potential of a four-generation divergent selection (Pannon maternal rabbit lines) based on the total body fat content to create two rabbit lines with different meat attributes: a Fat line to deliver greater amounts of healthy fatty acids for newborns and infants, and a Lean line intended to provide lean meat for everyday consumption. Selection was based on the fat index calculated in 10-week-old live rabbits by means of computed tomography (CT). For each generation, 60 rabbits/line were fed ad libitum with commercial pellet from weaning (5 weeks) to slaughter (11 weeks). A total of 15 rabbits/line were randomly selected for meat quality evaluations: the longissimus thoracis et lumborum muscles (LTLs), hind legs (HLs), forelegs (FLs) and abdominal wall (AW) were analyzed for their proximate composition and fatty acid (FA) profile. FA contents were also calculated. Results highlighted that it was possible to obtain leaner meat for everyday consumption in most meat portions starting from generation 4 (7.93 vs. 11.9, 5.10 vs. 5.98 and 7.26 vs. 10.9 g of lipids/100 g of meat in Lean and Fat groups for the FLs, HLs and AW, respectively). The sole exception was the LTLs, which were not affected by the divergent selection. The total PUFA amount increased in FL and AW (p < 0.05) portions of the Fat line only, attributable to a greater n-3 amount (151 vs. 216 and 73 vs. 143 mg/100 g of meat in Lean and Fat groups for the FLs and AW, respectively). [ABSTRACT FROM AUTHOR]

Summary: Sympatric genetic divergence is the most appealing and controversial pattern in the theory of ecological speciation. Examples that support sympatric genetic divergence in plant species are extremely rare. Solid evidence of sympatric genetic divergence will provide deep insights for revealing the underlying mechanisms of ecological speciation.We analysed the total genomic DNA sequences of 120 weedy rice (WR; Oryza sativa f. spontanea) plants, representing three WR population pairs separately from three early‐ and late‐season rice fields, in comparison with those of the co‐occurring rice cultivars and other rice materials.We detected substantial genetic divergence within the pairs of the sympatric early‐ and late‐season WR populations, although genetic divergence was unevenly distributed across the genomes. Restricted gene flow was determined between the sympatric WR populations, resulting in their distinct genetic structures. We also detected relatively low genetic diversity that was likely to be associated with stronger selection in early‐season WR populations.Our findings provide strong evidence for sympatric genetic divergence between the WR populations in the same fields but in different seasons. We conclude that temporal isolation plays an important role in creating genetic divergence between sympatric populations/species in plants. [ABSTRACT FROM AUTHOR]

Abstract Introgressive hybridization may erode phenotypic divergence along environmental gradients, collapsing locally adapted populations into a hybrid swarm. Alternatively, introgression may promote phenotypic divergence by providing variation on which natural selection can act. In freshwater fishes, water flow often selects for divergent morphological traits in lake versus stream habitats. We tested the effects of introgression on lake–stream morphological divergence in the minnow Owens Tui Chub (Siphateles bicolor snyderi), which has been rendered endangered by introgession from the introduced Lahontan Tui Chub (Siphateles bicolor obesa). Using geometric morphometric analysis of 457 individual Tui Chub from thirteen populations, we found that both native and introgressing parent taxa exhibited divergent body and caudal fin shapes in lake versus stream habitats, but their trajectories of divergence were distinct. In contrast, introgressed populations exhibited intermediate body and caudal fin shapes that were not differentiated by habitat type, indicating that introgression has eroded phenotypic divergence along the lentic–lotic gradient throughout the historic range of the Owens Tui Chub. Individuals within hybrid populations were less morphologically variable than those within parent populations, suggesting hybrid adaptation to selective agents other than water flow or loss of variance by drift.

Because of ongoing climate change, populations of organisms are being subjected to stressful temperatures more often. This is especially problematic for ectothermic organisms, which are likely to be more sensitive to changes in temperature. Therefore, we need to know if ectotherms have adapted to environmental temperature and, if so, what are the evolutionary mechanisms behind such adaptation. Here, we use the nematode Pristionchus pacificus as a case study to investigate thermal adaptation on the Indian Ocean island of La Réunion, which experiences a range of temperatures from coast to summit. We study the evolution of high‐temperature tolerance by constructing a phylogenetic tree of strains collected from many different thermal niches. We show that populations of P. pacificus at low altitudes have higher fertility at warmer temperatures. Most likely, this phenotype has arisen recently and at least twice independently, consistent with parallel evolution. We also studied low‐temperature tolerance and showed that populations from high altitudes have increased their fertility at cooler temperatures. Together, these data indicate that P. pacificus strains on La Réunion are subject to divergent selection, adapting to hot and cold niches at the coast and summit of the volcano. Precisely defining these thermal niches provides essential information for models that predict the impact of future climate change on these populations. [ABSTRACT FROM AUTHOR]

The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies. [ABSTRACT FROM AUTHOR]

Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa. [ABSTRACT FROM AUTHOR]

Uniformity, understood as a similar performance in relevant livestock traits, such as birth weight within the litter, is being included as one of the selection objectives in breeding programmes, especially for polytocous livestock species. A divergent selection experiment for birth weight within‐litter variability in mice during 23 generations showed that homogeneous animals were better for litter size, survival and feed efficiency but less heavy than heterogeneous animals. The aim of this study was to compare the reproductive longevity in both divergent lines as time to the end of the reproductive period. Two generations from both lines with an initial number of 43 females and 43 males were mated one to one and stayed together to have consecutive parturitions until the end of the reproductive life. Females were discarded when the time elapsed from the last parturition was longer than 63 days. The time to the end of the reproductive period between both lines was compared by fitting a Cox proportional hazard regression model adjusting for line, generation and its interaction. The rate of parturitions in both lines was also compared using a Prentice–Williams–Peterson model adjusted for the same effects. The low variability line was associated with a higher parturition rate, e.g., adjusted hazard ratio was 2.93 (95% CI 2.17–3.94). The Cox model showed that the low variability females also presented benefits of time to the end of the reproductive period, with an adjusted hazard ratio of 0.26 (95% CI 0.16–0.41). The median of reproductive days was 55.50 in the high variability line whilst the median was 252.50 days for the low variability females. The homogeneous line presented important reproductive advantages suggesting higher robustness and animal welfare. Further research should confirm whether the findings presented here of a better performance in the low variability line could be properly applied to some livestock species. [ABSTRACT FROM AUTHOR]

Background and Aims The timing of seed dispersal determines the environmental conditions that plants face during early life stages. In seasonal environments, selection is expected to favour dispersal timing that is matched to environmental conditions suitable for successful recruitment. Our aim here was to test whether the timing of seed dispersal influences seedling establishment success in two populations of Euterpe edulis that are located at contrasting altitudes, have different seed-dispersal phenologies and are subjected to distinct climatic conditions. Methods We sowed E. edulis seeds in contrasting altitudes on different dates, and monitored seed germination, emergence and seedling establishment at each altitude over 4 years. At the high-altitude site, five seed-dispersal cohorts were established during the natural dispersal period. At the low-altitude site, three seed-dispersal cohorts were established during natural dispersal, and two were established either before or after natural dispersal. Key Results At the high-altitude site, seed-dispersal timing did not affect seed germination, seedling emergence or seedling establishment success. In contrast, at the low-altitude site, late seed dispersal near the end of the wet season resulted in a lower probability of seedling establishment, possibly due to the exposure of seeds, germinants and seedlings to unfavourable drought conditions. In addition, at the low-altitude site, the natural seed-dispersal period was poorly matched to favourable environmental conditions for seedling establishment. Conclusions The greater effect of seed-dispersal timing on seedling establishment at the low-altitude site is probably related to a more seasonal and drought-prone environment that favours a restricted period of seed dispersal. The magnitude of the effect of dispersal timing on seedling establishment success was modulated by environmental conditions that vary across altitude. Furthermore, reproductive phenology appears to be subject to more intense selection at the lower limit of the altitudinal range, due to a more restrictive window of opportunity for successful seedling establishment. [ABSTRACT FROM AUTHOR]

Simple Summary: Atlantic salmon is a diadromous species that has the particularity that it returns to reproduce to its river of birth. This means that, in most cases, each river can be considered a population and that these populations can be adapted to the characteristics of the river. The Atlantic Salmon in the rivers of the Iberian Peninsula has been in decline since the 80's of the last century. At that time, to alleviate the decline in the number of individuals, the rivers were stocked with salmon from Scotland and other northern European rivers, but the result was not positive. In this work, we studied eight salmon populations using a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations, which may be the cause of the failure of restocking programs. In addition, by performing a review of previous studies, we demonstrated that, as suggested, NADP-dependent malic enzyme-2 is a candidate for local adaptation in salmon from the Iberian Peninsula. Pollution and other anthropogenic effects have driven a decrease in Atlantic salmon (Salmo salar) in the Iberian Peninsula. The restocking effort carried out in the 1980s, with salmon from northern latitudes with the aim of mitigating the decline of native populations, failed, probably due to the deficiency in adaptation of foreign salmon from northern Europe to the warm waters of the Iberian Peninsula. This result would imply that the Iberian populations of Atlantic salmon have experienced local adaptation in their past evolutionary history, as has been described for other populations of this species and other salmonids. Local adaptation can occur by divergent selections between environments, favoring the fixation of alleles that increase the fitness of a population in the environment it inhabits relative to other alleles favored in another population. In this work, we compared the genomes of different populations from the Iberian Peninsula (Atlantic and Cantabric basins) and Scotland in order to provide tentative evidence of candidate SNPs responsible for the adaptive differences between populations, which may explain the failures of restocking carried out during the 1980s. For this purpose, the samples were genotyped with a 220,000 high-density SNP array (Affymetrix) specific to Atlantic salmon. Our results revealed potential evidence of local adaptation for North Spanish and Scottish populations. As expected, most differences concerned the comparison of the Iberian Peninsula with Scotland, although there were also differences between Atlantic and Cantabric populations. A high proportion of the genes identified are related to development and cellular metabolism, DNA transcription and anatomical structure. A particular SNP was identified within the NADP-dependent malic enzyme-2 (mMEP-2*), previously reported by independent studies as a candidate for local adaptation in salmon from the Iberian Peninsula. Interestingly, the corresponding SNP within the mMEP-2* region was consistent with a genomic pattern of divergent selection. [ABSTRACT FROM AUTHOR]

Understanding the role of divergent host‐use in promoting population differentiation among herbivorous insects provides valuable insight into the origin of diversity in this species‐rich group. A strong signature of divergent selection in promoting population differentiation is provided by parallel phenotypic divergence across multiple insect species adapting to the same set of divergent host plants.In this study, we explored whether a key phenotype of gall‐forming insects—gall size—exhibits parallel patterns of divergence across a community of gall‐forming insect species because of adaptation to different host plant species. A previous study found parallel divergence in gall morphology across two gall‐forming insect species adapted to two sister species of oaks (Fagaceae). Here, we expand this question to four additional members of the gall‐forming insect community that specialise on the same two host plant species: Quercus geminata (Qg) and Quercus virginiana (Qv).Consistent with the previous result, all four additional gall‐forming species tended to induce larger galls on Qg than on Qv, with two of the four species exhibited statistically significant differences and one species showed marginally significant differences. Moreover, we found gall size was similar for two gall‐forming species when cross‐reared on natural versus planted hosts, ruling out environmental causes of parallel host‐associated gall size difference across multiple species.Our study documents parallel divergence in a key phenotype of gall‐forming insects associated with different host environments, shedding light on the important role of divergent host use in driving the evolution of gall morphology. [ABSTRACT FROM AUTHOR]