Genetic diversity and genomic signatures of selection among cattle breeds from Siberia,eastern and northern Europe

Domestication in the near eastern region had a major impact on the gene pool of humpless taurine cattle (Bos taurus). As a result of subsequent natural and artificial selection, hundreds of different breeds have evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian B. taurus breeds from different biogeographic and production conditions, which exhibit different demographic histories and have been under artificial selection at various intensities, were investigated using the Illumina BovineSNP50 panel to understand their genetic diversity and population structure. In addition, we scanned genomes from eight breeds for signatures of diversifying selection. Our population structure analysis indicated six distinct breed groups, the most divergent being the Yakutian cattle from Siberia. Selection signals were shared (experimental P‐value < 0.01) with more than four breeds on chromosomes 6, 7, 13, 16 and 22. The strongest selection signals in the Yakutian cattle were found on chromosomes 7 and 21, where a miRNA gene and genes related to immune system processes are respectively located. In general, genomic regions indicating selection overlapped with known QTL associated with milk production (e.g. on chromosome 19), reproduction (e.g. on chromosome 24) and meat quality (e.g. on chromosome 7). The selection map created in this study shows that native cattle breeds and their genetic resources represent unique material for future breeding.     

Combined effect of elevated UVB,elevated temperature and fertilization on growth,needle structure and phytochemistry of young Norway spruce (Picea abies) seedlings

Simultaneously with warming climate, other climatic and environmental factors are also changing. Here, we investigated for the first time the effects of elevated temperature, increased ultraviolet‐B (UVB) radiation, fertilization and all combinations of these on the growth, secondary chemistry and needle structure of 1‐year‐old Norway spruce (Picea abies (L.) Karst.) seedlings in an outdoor experiment. After one growing season, elevated temperature increased root : shoot ratio and concentrations of needle piperidine alkaloids, while concentrations of needle catechins and acetophenones and bark flavonoids decreased compared with ambient temperature seedlings. UVB‐radiation increased concentrations of bark condensed tannins, while fertilization increased total biomass and concentrations of needle catechins. In addition to the main effects, concentrations of some individual phenolic compounds showed UV × temperature or UV × temperature × fertilization interactions, and fertilization modified temperature response on root : shoot ratio. All the treatments described here affected the defence chemistry profiles of the seedlings, which may imply some changes in plant‐herbivore interactions in connection with changing climate. The interactions between treatments indicate a need for further experiments involving several simultaneously affecting environmental changes.     

Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor–derivative spruces (Picea mariana × P. rubens)

The genic species concept implies that while most of the genome can be exchanged somewhat freely between species through introgression, some genomic regions remain impermeable to interspecific gene flow. Hence, interspecific differences can be maintained despite ongoing gene exchange within contact zones. This study assessed the heterogeneous patterns of introgression at gene loci across the hybrid zone of an incipient progenitor–derivative species pair, Picea mariana (black spruce) and Picea rubens (red spruce). The spruce taxa likely diverged in geographic isolation during the Pleistocene and came into secondary contact during late Holocene. A total of 300 SNPs distributed across the 12 linkage groups (LG) of black spruce were genotyped for 385 individual trees from 33 populations distributed across the allopatric zone of each species and within the zone of sympatry. An integrative framework combining three population genomic approaches was used to scan the genomes, revealing heterogeneous patterns of introgression. A total of 23 SNPs scattered over 10 LG were considered impermeable to introgression and putatively under diverging selection. These loci revealed the existence of impermeable genomic regions forming the species boundary and are thus indicative of ongoing speciation between these two genetic lineages. Another 238 SNPs reflected selectively neutral diffusion across the porous species barrier. Finally, 39 highly permeable SNPs suggested ancestral polymorphism along with balancing selection. The heterogeneous patterns of introgression across the genome indicated that the speciation process between black spruce and red spruce is young and incomplete, albeit some interspecific differences are maintained, allowing ongoing species divergence even in sympatry. The approach developed in this study can be used to track the progression of ongoing speciation processes.     

Disentangling the effects of acidic air pollution,atmospheric CO2, and climate change on recent growth of red spruce trees in the Central Appalachian Mountains

In the 45 years after legislation of the Clean Air Act, there has been tremendous progress in reducing acidic air pollutants in the eastern United States, yet limited evidence exists that cleaner air has improved forest health. Here, we investigate the influence of recent environmental changes on the growth and physiology of red spruce (Picea rubens Sarg.) trees, a key indicator species of forest health, spanning three locations along a 100 km transect in the Central Appalachian Mountains. We incorporated a multiproxy approach using 75‐year tree ring chronologies of basal tree growth, carbon isotope discrimination (?¹³C, a proxy for leaf gas exchange), and δ¹⁵N (a proxy for ecosystem N status) to examine tree and ecosystem level responses to environmental change. Results reveal the two most important factors driving increased tree growth since ca. 1989 are reductions in acidic sulfur pollution and increases in atmospheric CO₂, while reductions in pollutant emissions of NO_x and warmer springs played smaller, but significant roles. Tree ring ?¹³C signatures increased significantly since 1989, concurrently with significant declines in tree ring δ¹⁵N signatures. These isotope chronologies provide strong evidence that simultaneous changes in C and N cycling, including greater photosynthesis and stomatal conductance of trees and increases in ecosystem N retention, were related to recent increases in red spruce tree growth and are consequential to ecosystem recovery from acidic pollution. Intrinsic water use efficiency (iWUE) of the red spruce trees increased by ~51% across the 75‐year chronology, and was driven by changes in atmospheric CO₂ and acid pollution, but iWUE was not linked to recent increases in tree growth. This study documents the complex environmental interactions that have contributed to the recovery of red spruce forest ecosystems from pervasive acidic air pollution beginning in 1989, about 15 years after acidic pollutants started to decline in the United States.     

Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)

Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long‐term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false‐positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.     

Genomic organization of molecular differentiation in Norway spruce (Picea abies)

Diversity and differentiation among three populations representing the geographical domains commonly recognized within the natural distribution area of Picea abies were analysed by using a set of 292 AFLP (amplified fragment length polymorphism), SSR (single sequence repeat) and ESTP (expressed sequence tags polymorphism) markers. As usually observed in forest trees, results showed high within-population diversity (H(S) reaching 0.79) and low among-population differentiation (G(ST) approximately 2%). The genomic organization of differentiation was then investigated on the basis of a subsample of 150 AFLP, SSR and ESTP mapped markers. The number of the loci differentiating the Baltico-Nordic from the central European populations (25 loci) and, within the central European populations, the Alpine from the Hercyno-Carpathian populations (12 loci), were different. These 37 differentiated loci, with individual G(ST) values ranging from 0.008 to 0.20, were evenly distributed on all linkage groups and mostly followed the neutral expectations, suggesting genome-wide effects on differentiation. Nine of them however behave as 'outlier' loci indicating possible locus-specific selective effects. Contribution of ongoing evolutionary forces and historical effects to the geographical differentiation of the species are discussed.     

Carbon dioxide assimilation and growth of red spruce (Picea rubens Sarg.) seedlings in response to ozone,precipitation chemistry,and soil type

Summary The influence of ozone, mist chemistry, rain chemistry, and soil type on CO₂ assimilation and growth of red spruce (Picea rubens Sarg.) seedlings was investigated over a 4-month period under controlled laboratory and glasshouse conditions. Growth was evaluated through interval estimates of aboveground relative growth rates (RGR) and the partitioning of biomass components at harvest to root, stem, and needle fractions. Precipitation chemistry treatments and O₃ exposure dynamics were based on reported characteristics of air chemistry and/or deposition in high-elevation forests of eastern North America. The two soils were collected from Camels Hump in the Green Mountains of Vermont and Acadia National Park on the Maine coast. Soil from Acadia had higher organic content, higher levels of extractable base cations, and lower levels of extractable aluminum and heavy metals. The only treatment variables that consistently influenced the growth of P. rubens were soil type and rain chemistry. In comparison with seedlings grown in soil from Acadia National Park, those grown in Camels Hump soil had significantly less needle (27%), stem (33%), and root (26%) biomass at harvest and statistically lower aboveground RGR within 2 months after initiation of the treatments. Seedlings grown in Camels Hump soil had significantly higher levels of aluminum (6.5X), copper (1.4X), and nickel (2.7X) in new needle tissue. The only influence of precipitation chemistry on the growth of P. rubens was a pattern of greater root and shoot biomass in seedlings experiencing the more acidic rain treatments. Interactive effects among the main treatment variables (e.g., acidic mist and O₃, acidic rain and soil type) on seedling growth were not notable. Rates of CO₂ assimilation and transpiration on a per gram needle dry weight basis [mol·g^-1·s^-1] were not influenced by any of the main treatment variables or their interaction. Because neither soil type nor precipitation chemistry influenced the efficiency of CO₂ assimilation per gram dry weight of needle tissue, the physiological mechanism underlying the growth response of P. rubens is attributed to a change in either whole-plant allocation of carbon resources or a direct toxic effect in the rhizosphere on root growth.     

Divergent selection and heterogeneous migration rates across the range of Sitka spruce (Picea sitchensis)

Gene flow and effective population size (N(e)) should depend on a population's position within its range: those near the edges are expected to have smaller N(e) and lower relative emigration rates, whereas those nearer the centre should have larger N(e) and higher relative emigration rates. In species with continuous ranges, this phenomenon may limit the ability of peripheral populations to respond to divergent selection. Here, we employ Sitka spruce as a model to test these predictions. We previously genotyped 339 single nucleotide polymorphisms (SNPs) in 410 individuals from 13 populations, and used these data to identify putative targets of divergent selection, as well as to explore the extent to which central-peripheral structure may impede adaptation. Fourteen SNPs had outlier F(ST) estimates suggestive of divergent selection, of which nine were previously associated with phenotypic variation in adaptive traits (timing of autumn budset and cold hardiness). Using coalescent simulations, we show that populations from near the centre of the range have higher effective populations sizes than those from the edges, and that central populations contribute more migrants to marginal populations than the reverse. Our results suggest that while divergent selection appears to have shaped allele frequencies among populations, asymmetrical movement of alleles from the centre to the edges of the species range may affect the adaptive capacity of peripheral populations. In southern peripheral populations, the movement of cold-adapted alleles from the north represents a significant impediment to adaptation under climate change, while in the north, movement of warm-adapted alleles from the south may enhance adaptation.     

Microtubule organization in germinated pollen of the conifer Picea abies (Norway spruce,Pinaceae)

The organization of microtubules in germinated pollen of the conifer Picea abies (Norway spruce, Pinaceae) was examined using primarily confocal microscopy. Pollination in conifers differs from angiosperms in the number of mitotic divisions between the microspore and the sperm and in the growth rate of the pollen tube. These differences may be orchestrated by the cytoskeleton, and this study finds that there are important functional differences in microtubule organization within conifer pollen compared to the angiosperm model systems. Pollen from P. abies contains two degenerated prothallial cells, a body cell, a stalk cell, and a vegetative cell. The body cell produces the sperm. In the vegetative cell, microtubules form a continuous network from within the pollen grain, out through the aperture, and down the length of the tube to the elongating tip. Within the grain, this network extends from the pollen grain wall to the body and stalk cell complex. Microtubules within the body and stalk cells form a densely packed array that enmeshes amyloplasts and the nucleus. Microtubule bundles can be traced between the body and stalk cells from the cytoplasm of the body cell to the adjoining cell wall and into the cytoplasm of the stalk cell. Body and stalk cells are connected by plasmodesmata. The organization of microtubules and the presence of plasmodesmata suggest that microtubules form a path for intercellular communication by projecting from the cytoplasm to interconnecting plasmodesmata. Microtubules in the elongating tube form a net axial array that ensheathes the vegetative nucleus. Microtubules are enriched at the elongating tip, where they form an array beneath the plasma membrane that is perpendicular to the direction of tube growth. This enriched region extends back 20 μm from the tip. There is an abrupt transition from a net perpendicular to a net axial organization at the edge of the enriched region. In medial sections, microtubules are present in the core of the elongating tip. The organization of microtubules in the tip differs from that seen in angiosperm pollen tubes.     

Genetic variation in Tertiary relics: The case of eastern‐Mediterranean Abies (Pinaceae)

The eastern‐Mediterranean Abies taxa, which include both widely distributed species and taxa with minuscule ranges, represent a good model to study the impacts of range size and fragmentation on the levels of genetic diversity and differentiation. To assess the patterns of genetic diversity and phylogenetic relationships among eastern‐Mediterranean Abies taxa, genetic variation was assessed by eight nuclear microsatellite loci in 52 populations of Abies taxa with a focus on those distributed in Turkey and the Caucasus. Both at the population and the taxon level, the subspecies or regional populations of Abies nordmanniana s.l. exhibited generally higher allelic richness, private allelic richness, and expected heterozygosity compared with Abies cilicica s.l. Results of both the Structure analysis and distance‐based approaches showed a strong differentiation of the two A. cilicica subspecies from the rest as well as from each other, whereas the subspecies of A. nordmanniana were distinct but less differentiated. ABC simulations were run for a set of scenarios of phylogeny and past demographic changes. For A. ×olcayana, the simulation gave a poor support for the hypothesis of being a taxon resulting from a past hybridization, the same is true for Abies equi‐trojani: both they represent evolutionary branches of Abies bornmuelleriana.     

Signatures of diversifying selection at EST‐SSR loci and association with climate in natural Eucalyptus populations

Understanding the environmental parameters that drive adaptation among populations is important in predicting how species may respond to global climatic changes and how gene pools might be managed to conserve adaptive genetic diversity. Here, we used Bayesian F_ST outlier tests and allele–climate association analyses to reveal two Eucalyptus EST‐SSR loci as strong candidates for diversifying selection in natural populations of a southwestern Australian forest tree, Eucalyptus gomphocephala (Myrtaceae). The Eucalyptus homolog of a CONSTANS‐like gene was an F_ST outlier, and allelic variation showed significant latitudinal clinal associations with annual and winter solar radiation, potential evaporation, summer precipitation and aridity. A second F_ST outlier locus, homologous to quinone oxidoreductase, was significantly associated with measures of temperature range, high summer temperature and summer solar radiation, with important implications for predicting the effect of temperature on natural populations in the context of climate change. We complemented these data with investigations into neutral population genetic structure and diversity throughout the species range. This study provides an investigation into selection signatures at gene‐homologous EST‐SSRs in natural Eucalyptus populations, and contributes to our understanding of the relationship between climate and adaptive genetic variation, informing the conservation of both putatively neutral and adaptive components of genetic diversity.     

Temporal genetic stability in natural populations of the waterflea Daphnia magna in response to strong selection pressure

Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species’ evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank.     

Responses of white spruce (Picea glauca) to experimental warming at a subarctic alpine treeline

From 2001 to 2004 we experimentally warmed 40 large, naturally established, white spruce [Picea glauca (Moench) Voss] seedlings at alpine treeline in southwest Yukon, Canada, using passive open‐top chambers (OTCs) distributed equally between opposing north and south‐facing slopes. Our goal was to test the hypothesis that an increase in temperature consistent with global climate warming would elicit a positive growth response. OTCs increased growing season air temperatures by 1.8°C and annual growing degree‐days by one‐third. In response, warmed seedlings grew significantly taller and had higher photosynthetic rates compared with control seedlings. On the south aspect, soil temperatures averaged 1.0°C warmer and the snow‐free period was nearly 1 month longer. These seedlings grew longer branches and wider annual rings than seedlings on the north aspect, but had reduced Photosystem‐II efficiency and experienced higher winter needle mortality. The presence of OTCs tended to reduce winter dieback over the course of the experiment. These results indicate that climate warming will enhance vertical growth rates of young conifers, with implications for future changes to the structure and elevation of treeline contingent upon exposure‐related differences. Our results suggest that the growth of seedlings on north‐facing slopes is limited by low soil temperature in the presence of permafrost, while growth on south‐facing slopes appears limited by winter desiccation and cold‐induced photoinhibition.     

Positive selection on the mitochondrial ATP synthase 6 and the NADH dehydrogenase 2 genes across 22 hare species (genus Lepus)

Amino acid changes in mitochondrial (mt) oxidative phosphorylation (OXPHOS) genes have been suggested as a key adaptation to environmental variation. Here, we analyzed 416 sequences of ATPase synthase 6 (MT‐ATP6) and NADH dehydrogenase 2 (MT‐ND2) in 22 different hare (Lepus) species from across a wide range of habitats and climates. We used site‐ and branch‐based methods to test for positive selection on specific codons and lineages. We found four codons in MT‐ATP6 and five in MT‐ND2 under positive selection, affecting several species lineages. We investigated the association of protein variants at each locus with climate zone, using multinomial generalized linear models (glm), including species, regions, historical introgression events, and the co‐occurring protein variant at the other locus as additional explanatory variables. A significant climate effect as based on the “Köppen climate classification” was observed for MT‐ND2 protein variants as translated from our nucleotide sequences. Moreover, MT‐ND2 protein variants were significantly affected by the co‐occurring MT‐ATP6 protein variant in the same mtDNA molecule. Contrary to the expectation for non‐recombining mitochondrial DNA molecules, the presence of an evolutionarily relatively ancestral protein variant at one locus was associated with a relatively derived protein at the other locus in the same mitochondrial molecule, respectively. The relative evolutionary status of a protein variant was evaluated according to its positions relative to the respective out‐group protein variant in a network analysis of nucleotide sequences. All our results suggest a complex effect of various climatic parameters acting on multiple mtOXPHOS genes in a co‐adaptive way, favoring combinations of ancestral and derived variants.     

Sex‐specific selection under environmental stress in seed beetles

Sexual selection can increase rates of adaptation by imposing strong selection in males, thereby allowing efficient purging of the mutation load on population fitness at a low demographic cost. Indeed, sexual selection tends to be male‐biased throughout the animal kingdom, but little empirical work has explored the ecological sensitivity of this sex difference. In this study, we generated theoretical predictions of sex‐specific strengths of selection, environmental sensitivities and genotype‐by‐environment interactions and tested them in seed beetles by manipulating either larval host plant or rearing temperature. Using fourteen isofemale lines, we measured sex‐specific reductions in fitness components, genotype‐by‐environment interactions and the strength of selection (variance in fitness) in the juvenile and adult stage. As predicted, variance in fitness increased with stress, was consistently greater in males than females for adult reproductive success (implying strong sexual selection), but was similar in the sexes in terms of juvenile survival across all levels of stress. Although genetic variance in fitness increased in magnitude under severe stress, heritability decreased and particularly so in males. Moreover, genotype‐by‐environment interactions for fitness were common but specific to the type of stress, sex and life stage, suggesting that new environments may change the relative alignment and strength of selection in males and females. Our study thus exemplifies how environmental stress can influence the relative forces of natural and sexual selection, as well as concomitant changes in genetic variance in fitness, which are predicted to have consequences for rates of adaptation in sexual populations.     

Frequency of somaclonal variation in plants of black spruce (Picea mariana,Pinaceae) and white spruce (P. glauca,Pinaceae) derived from somatic embryogenesis and identification of some factors involved in genetic instability

Plants of black spruce (Picea mariana, N = 7047 individuals) and white spruce (P. glauca, N = 3995 individuals) were regenerated from a total of 87 clones over a 5-yr period by somatic embryogenesis to study factors that might be associated with the appearance of variant phenotypes. Morphological evaluation of the plants showed several types of variation. These variations were grouped into nine types: dwarfism (type A), reduced height with various form anomalies (types B, C, and D), needle fasciation (type E), abnormality in tree architecture (type F), variegata phenotype (type G), and plants with an overall regular morphology but smaller than normal plants (type H). Plagiotropic plants were also observed (type I). Each plant from types A to H (except type C where no plants survived more than 6 mo) had retained its phenotype over 4–5 yr of growth. Some of the variant types could be related to chromosomic instability: chromosome counts showed aneuploid cells for type-A and type-D plants. The type I (plagiotropism) was not related to genetic instability but rather to physiological disorders. In total, spruce variants of types A–H were obtained at relatively low frequencies, i.e., 1.0% (39/3995) for white spruce and 1.6% (110/7047) for black spruce. Statistical analyses, conducted with family, clone, and time in maintenance as variables, showed that clone was the most important source of genetic instability followed by time in maintenance.     

Silver fir and Douglas fir are more tolerant to extreme droughts than Norway spruce in south‐western Germany

Improving our understanding of the potential of forest adaptation is an urgent task in the light of predicted climate change. Long‐term alternatives for susceptible yet economically important tree species such as Norway spruce (Picea abies) are required, if the frequency and intensity of summer droughts will continue to increase. Although Silver fir (Abies alba) and Douglas fir (Pseudotsuga menziesii) have both been described as drought‐tolerant species, our understanding of their growth responses to drought extremes is still limited. Here, we use a dendroecological approach to assess the resistance, resilience, and recovery of these important central Europe to conifer species the exceptional droughts in 1976 and 2003. A total of 270 trees per species were sampled in 18 managed mixed‐species stands along an altitudinal gradient (400–1200 m a.s.l.) at the western slopes of the southern and central Black Forest in southwest Germany. While radial growth in all species responded similarly to the 1976 drought, Norway spruce was least resistant and resilient to the 2003 summer drought. Silver fir showed the overall highest resistance to drought, similarly to Douglas fir, which exhibited the widest growth rings. Silver fir trees from lower elevations were more drought prone than trees at higher elevations. Douglas fir and Norway spruce, however, revealed lower drought resilience at higher altitudes. Although the 1976 and 2003 drought extremes were quite different, Douglas fir maintained consistently the highest radial growth. Although our study did not examine population‐level responses, it clearly indicates that Silver fir and Douglas fir are generally more resistant and resilient to previous drought extremes and are therefore suitable alternatives to Norway spruce; Silver fir more so at higher altitudes. Cultivating these species instead of Norway spruce will contribute to maintaining a high level of productivity across many Central European mountain forests under future climate change.