Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick‐billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick‐billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome‐wide markers mapped to a newly assembled thick‐billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non‐breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.     

Oxygen consumption of East Siberian cod: no support for the metabolic cold adaptation theory

Standard metabolic rate ( R _s) at 2°C of eight East Siberian cod Arctogadus borisovi , caught in West Greenland, body mass of 601.5 ± 147.6 g (mean ± s.D.), was 40.9 ± 5.9 mg O₂ kg^-1 h^-1 and 59.0 ± 6.6mg O₂ kg^-1 h^-1 when extrapolated to a standardized 100 g fish. R _s was compared with three other Gadidae, to test the theory of metabolic cold adaptation (MCA). There was no evidence of MCA in the family.     

Oxygen equilibria of cathodic eel hemoglobin analysed in terms of the MWC model and Adair's successive oxygenation theory

Allosteric effects of erythrocytic NTP and proton concentrations on cathodic eel Hb were investigated by precise measurement of Hb-O₂ equilibria (including extreme saturation values) and analysis in terms of the MWC two-state model and the Adair four-step oxygenation theory. Stripped cathodic Hb shows a reverse Bohr effect and high sensitivities to ATP and GTP that extend to high pH values (>8.5). A decrease in pH raises K _T and lowers the allosteric constant L; compared to opposite effects in normal Bohr effect Hbs. Phosphates even at low concentrations (GTP/Hb=0.5) annihilate the reverse Bohr effect. GTP exerts a reater effect than ATP due to greater changes in K _T and L, and NTP slightly reduces K _R. In the absence of NTP, about 1.1 protons are released on deoxygenation at pH 8.15 (where most protons are released), indicating a pK value of the reverse Bohr group of approximately 8.2 (higher in oxy-Hb and lower in deoxy-Hb). The pH and NTP dependence of the Adair association constants and calculated fractional populations of Hb molecules in different oxygenation stages show that NTP effectors stabilise the T structure and postpone the T-R transition, whereas protons in the absence of NTP have the opposite effect. A molecular mechanism for the reverse Bohr effect is suggested.Abbreviations DPG 2,3 diphosphoglycerate - EPLC fast protein liquid chromatography - Hb hemoglobin - HEPES N-2-hydroxymethyl-piperazine-N-2-ethanesulfonic acid - K _T and K _R O₂ association equilibrium constants of Hb in the deoxy- and oxy-states, respectively - k ₁, k ₂, k ₃ and k ₄ Adair affinity constants for binding of the four O₂ molecules to Hb - L allosteric constant - NTP nucleoside triphosphate - P _m medium O₂ pressure - n ₅₀ Hill's cooperativity coefficient at P ₅₀ - P ₅₀ half-satutarion O₂ tension - TRIS tris(hydroxymethyl)aminomethane     

The effects of wintertime undernutrition on plasma leptin and insulin levels in an arctic ruminant, the reindeer

We examined the effects of prolonged undernutrition on plasma leptin and insulin levels and some serum protein metabolites in reindeer (Rangifer tarandus tarandus L.) during winter and spring. The reindeer (male < 1 year) were fed their preferred winter feed, low-protein lichen ad libitum for 5 weeks, followed by 40% restriction of energy for 8 weeks and refeeding with high-protein pellets for 6 weeks. The control group received high-protein reindeer pellets ad libitum throughout the experiment. Plasma leptin decreased by 46% and insulin by 54% in the lichen group already during the ad libitum period between January and February, with parallel decreases in body weight, serum total proteins, albumin and urea. Leptin remained low during most of the energy restriction period in March and April, but increased at the end of April while body weight decreased. During the refeeding period in May and June, the body weight and insulin of the lichen group increased in parallel with total proteins and urea, but leptin remained unchanged. Similar significant reductions in plasma leptin (40%) as in the lichen group also took place in the control group fed high-protein pellets ad libitum in January and February, although their feed intake, serum total proteins and body weight remained unchanged. The results show that leptin decreases in reindeer during mid-winter, independent of food or protein intake, and suggest that the decrease may be cued by seasonal factors such as the short photoperiod.     

Perinatal adaptation in mammals: the impact of metabolic rate

Mammalian birth is accompanied by profound changes in metabolic rate that can be described in terms of body size relationship (Kleiber's rule). Whereas the fetus, probably as an adaptation to the low intrauterine pO₂, exhibits an “inappropriately” low, adult-like specific metabolic rate, the term neonate undergoes a rapid metabolic increase up to the level to be expected from body size. A similar, albeit slowed, “switching-on” of metabolic size allometry is found in human preterm neonates whereas animals that are normally born in a very immature state are able to retard or even suppress the postnatal metabolic increase in favor of weight gain and O₂ supply. Moreover, small immature mammalian neonates exhibit a temporary oxyconforming behavior which enhances their hypoxia tolerance, yet is lost to the extent by which the size-adjusted metabolic rate is “locked” by increasing mitochondrial density. Beyond the perinatal period, there are no other deviations from metabolic size allometry among mammals except in hibernation where the temporary “switching-off” of Kleiber's rule is accompanied by a deep reduction in tissue pO₂. This gives support to the hypothesis that the postnatal metabolic increase represents an “escape from oxygen” similar to the evolutionary roots of mitochondrial respiration, and that the overall increase in specific metabolic rate with decreasing size might contribute to prevent tissues from O₂ toxicity.     

Using connectivity to identify climatic drivers of local adaptation

Understanding the climatic drivers of local adaptation is vital. Such knowledge is not only of theoretical interest but is critical to inform management actions under climate change, such as assisted translocation and targeted gene flow. Unfortunately, there are a vast number of potential trait–environment combinations, and simple relationships between trait and environment are ambiguous: representing either plastic or evolved variation. Here, we show that by incorporating connectivity as an index of gene flow, we can differentiate trait–environment relationships reflecting genetic variation vs. phenotypic plasticity. In this way, we rapidly shorten the list of trait–environment combinations that are of significance. Our analysis of an existing data set on geographic variation in a tropical lizard shows that we can effectively rank climatic variables by the strength of their role in local adaptation. The promise of our method is a rapid and general approach to identifying the environmental drivers of local adaptation.     

Population differentiation in an annual legume: local adaptation

Abstract. Studies of many plants species have demonstrated adaptive genetic differentiation to local environmental conditions. Typically these studies are conducted to evaluate adaptation to contrasting environments. As a consequence, although local adaptation has been frequently demonstrated, we have little information as to the spatial scale of adaptive evolution. We evaluated adaptive differentiation between populations of the annual legume Chamaecrista fasciculata using a replicated common-garden design. Study sites were established in three field locations that are home to native populations of C. fasciculata . Each location was planted for two years with seed from the population native to the study site (home population) and populations located six distances (0.1-2000 km) from each site (transplanted populations). Seeds were planted into the study sites with minimum disturbance to determine the scale of local adaptation, as measured by a home-site fitness advantage, for five fitness components: germination, survival, vegetative biomass, fruit production, and the number of fruit produced per seed planted (an estimate of cumulative fitness). For all characters there was little evidence for local adaptation, except at the furthest spatial scales. Patterns of adaptive differentiation were fairly consistent in two of the three sites, but varied between years. Little genetic variation was expressed at the third site. These results, combined with previous estimates of limited gene flow, suggest that metapopulation processes and temporal environmental variation act together to reduce local adaptation, except over long distances.     

Morphological adaptation to water uptake and transport in the poikilohydric moss Tortula ruralis

Abstract

In this paper different water-holding and transport adaptations to face the uneven and intermittent distribution of water in the ectohydric moss Tortula ruralis are referred to.

The external conduction of water is operated by different and efficient systems (spaces between adjacent shoots, between leaves, leaves and stems, leaves and rhizoids, life form, etc.) which facilitate absorption and transport of solutions.

Also epi-organ capillary systems (bases and revoluted margin of leaves, a groove, a close network of capillary channels determined by the papillae), intra-organ capillary systems (hyalocysts) and certain amount of internal conduction (conducting parenchyma, stereoma) co-operante to absorb and distribute water to the whole gametophyte.

In addition, some adaptations to xerophytism and heliophytism (life form, disposition of phylloids, hair-points) are discussed.     

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.     

Floral adaptation to local pollinator guilds in a terrestrial orchid

Background and Aims

Studies of local floral adaptation in response to geographically divergent pollinators are essential for understanding floral evolution. This study investigated local pollinator adaptation and variation in floral traits in the rewarding orchid Gymnadenia odoratissima, which spans a large altitudinal gradient and thus may depend on different pollinator guilds along this gradient.

Methods

Pollinator communities were assessed and reciprocal transfer experiments were performed between lowland and mountain populations. Differences in floral traits were characterized by measuring floral morphology traits, scent composition, colour and nectar sugar content in lowland and mountain populations.

Key Results

The composition of pollinator communities differed considerably between lowland and mountain populations; flies were only found as pollinators in mountain populations. The reciprocal transfer experiments showed that when lowland plants were transferred to mountain habitats, their reproductive success did not change significantly. However, when mountain plants were moved to the lowlands, their reproductive success decreased significantly. Transfers between populations of the same altitude did not lead to significant changes in reproductive success, disproving the potential for population-specific adaptations. Flower size of lowland plants was greater than for mountain flowers. Lowland plants also had significantly higher relative amounts of aromatic floral volatiles, while the mountain plants had higher relative amounts of other floral volatiles. The floral colour of mountain flowers was significantly lighter compared with the lowland flowers.

Conclusions

Local pollinator adaptation through pollinator attraction was shown in the mountain populations, possibly due to adaptation to pollinating flies. The mountain plants were also observed to receive pollination from a greater diversity of pollinators than the lowland plants. The different floral phenotypes of the altitudinal regions are likely to be the consequence of adaptations to local pollinator guilds.     

Evidence of local adaptation to coarse-grained environmental variation in Arabidopsis thaliana

Plants can achieve an appropriate phenotype in particular conditions either constitutively or plastically, depending in part on the grain size of the environmental conditions being considered. Coarse-grained environmental variation should result in selection for local adaptation and no selection on plasticity to novel levels of the coarse-grained environmental factors. We tested the hypotheses that natural populations of the well-studied model system Arabidopsis thaliana are locally adapted to spatially coarse-grained environmental variation, and that the photoperiodic regime per se is at least partially responsible for that local adaptation, by exposing natural populations to photoperiodic regimes characteristic of their native and foreign (novel) environments. We also tested the hypothesis that plasticity to novel photoperiodic regimes should appear random. We found that populations showed evidence of local adaptation at a spatially coarse grain, although not to photoperiodic regime per se. We also found that the plasticities to novel photoperiodic regimes appeared random and did not generally show evidence of adaptive divergence. Our study highlights the need for caution in extrapolating from the finding of local adaptation to the causes of local adaptation.     

Genomic signatures of local adaptation in the Drosophila immune response

As environments and pathogen landscapes shift, host defenses must evolve to remain effective. Due to this selection pressure, among-species comparisons of genetic sequence data often find immune genes to be among the fastest evolving genes across the genome. The full extent and nature of these immune adaptations, however, remain largely unexplored. In a recent study, we analyzed patterns of selection within distinct components of the Drosophila melanogaster immune pathway. While we found evidence of positive selection within some immune processes, immune genes were not universally characterized by signatures of strong selection. On the contrary, we even found that some immune functions show greater than expected constraint. Overall these results highlight 2 major factors that appear to play an outsize role in determining a gene's evolutionary rate: the type of pathogen the gene targets and the gene's position within the immune network. These results join a growing body of literature that highlight the complexity of immune adaptation. Rather than there being uniformly strong selection across all immune genes, a combination of pathogen-specificity and host genetic constraints appear to play key roles in determining each immune gene's individual evolutionary trajectory.     

Extreme adaptive life-cycle in a high arctic aphid, Acyrthosiphon svalbardicum

Abstract.

• 1 The year-round biology of a high arctic aphid is described for the first time.
• 2 The life-cycle is shown to be genetically determined, and thus markedly different to temperate species where the observed polymorphism is governed primarily by external environmental cues.
• 3 The fundatrix, which emerges from the overwintering egg, gives birth directly to sexual morphs, a phenomenon previously undescribed in the Aphidinae. This process is essentially prevented in temperate aphids by an endogenous mechanism, the interval timer.
• 4 In addition to the sexual morphs, the fundatrix produces a small number of parthenogenetic individuals (viviparae) that give rise to a third generation. This last generation consists exclusively of oviparae and males that would increase the number of overwintering eggs provided there is sufficient thermal budget for them to mature and oviposit before conditions become adverse.
• 5 The position of particular morphs in the birth sequences of the second and third generations maximize the chances of survival in harsh conditions, whilst enhancing the likelihood that individuals from the third generation will add to the number of overwintering eggs.
• 6 Guaranteed egg production combined with an in-built flexibility to produce an extra generation in particularly favourable seasons, confer adaptations to the high arctic environment, and ideally suit this aphid to exploit elevated temperatures in an era of climate change.

     

全球北极底栖生物研究文献计量分析

以Thomson Reuters的Web of Science信息平台提供的SCI-E数据库为数据源,检索到从1991年至2012年期间全球北极底栖生物研究论文2127篇,利用Note Express软件,分析22年间论文发表的年度、国家、机构、作者、期刊和学科等方面的分布特征,结果表明:1)全球北极底栖生物研究论文数量、篇均作者数和篇均参考文献数都在逐年增加;2)研究论文涉及58个国家或地区,位于前7位的国家依次是美国、德国、加拿大、挪威、俄罗斯、英国和丹麦;美国、加拿大、挪威和丹麦是该领域国际合作研究最主要的国家;3)论文涉及1364个机构,前20名的研究机构中,美国有6家,德国、加拿大和挪威各有3家,俄罗斯和丹麦各有2家,波兰有1家。俄罗斯、丹麦、波兰、德国和挪威超过60%的研究力量集中在位列前20位的相关机构中。俄罗斯科学院论文总量排列首位,德国阿尔弗雷德魏格纳极地与海洋研究中心和基尔大学论文的h指数最高为32;4)论文涉及最多的4个学科是海洋与淡水生物学、生态学、海洋学和多学科地球科学。Polar Biology和Marine Ecology Progress Series是发表该领域最核心的期刊。还对中国在该领域的研究现状进行了简要的分析。从文献计量学角度揭示了全球北极底栖生物研究现状,为提升我国该领域研究的国际竞争力提供科学参考。     

Evolution of polygenic traits under global vs local adaptation

Observations about the number, frequency, effect size, and genomic distribution of alleles associated with complex traits must be interpreted in light of evolutionary process. These characteristics, which constitute a trait’s genetic architecture, can dramatically affect evolutionary outcomes in applications from agriculture to medicine, and can provide a window into how evolution works. Here, I review theoretical predictions about the evolution of genetic architecture under spatially homogeneous, global adaptation as compared with spatially heterogeneous, local adaptation. Due to the tension between divergent selection and migration, local adaptation can favor “concentrated” genetic architectures that are enriched for alleles of larger effect, clustered in a smaller number of genomic regions, relative to expectations under global adaptation. However, the evolution of such architectures may be limited by many factors, including the genotypic redundancy of the trait, mutation rate, and temporal variability of environment. I review the circumstances in which predictions differ for global vs local adaptation and discuss where progress can be made in testing hypotheses using data from natural populations and lab experiments. As the field of comparative population genomics expands in scope, differences in architecture among traits and species will provide insights into how evolution works, and such differences must be interpreted in light of which kind of selection has been operating.     

Change of ruminal sodium transport in sheep during dietary adaptation

Rumen adaptation plays an important role in the productive cycle of dairy cattle. In this study, the time course of functional rumen epithelium adaptation after a change from hay feeding (ad libitum) to a mixed hay/concentrate diet was monitored by measuring Na⁺ transport rates in Ussing chamber experiments. A total of 18 sheep were subjected to different periods of mixed hay/concentrate feeding ranging from 0 weeks (control; hay ad libitum) to 12 weeks (800 g hay plus 800 g concentrate per day in two equal portions). For each animal, the net absorption of sodium was measured following the mixed hay/concentrate feeding period. Net Na transport, J_net, significantly rose from 2.15 ± 0.43 (control) to 3.73 ± 1.02 μeq · cm^?2 · h^?1 after one week of mixed hay/concentrate diet, reached peak levels of 4.55 ± 0.50 μEq · cm^?2 · h^?1 after four weeks and levelled out at 3.92 ± 0.36 μeq · cm^?2 · h^?1 after 12 weeks of mixed feeding. Thus, 73% of functional adaptation occurred during the first week after diet change. This is in apparent contrast to findings that morphological adaptation takes approximately six weeks to reach peak levels. Hence, early functional adaptation to a mixed hay/concentrate diet is characterised by enhanced Na absorption rates per epithelial cell. Absorption rates are likely to be further enhanced by proliferative effects on the rumen epithelium (number and size of papillae) when concentrate diets are fed over longer periods of time. Early functional adaptation without surface area enlargement of the rumen epithelium appears to be the first step in coping with altered fermentation rates following diet change.     

Limits to local adaptation in six populations of the annual plant Diodia teres

* Local adaptation is common, but tests for adaptive differentiation frequently compare populations from strongly divergent environments, making it unlikely that any influence of stochastic processes such as drift or mutation on local adaptation will be detected. Here, the hypothesis that local adaptation is more likely to develop when the native environments of populations are more distinct than when they are similar was tested. * A reciprocal transplant experiment including two populations from each of three habitats was conducted to determine the pattern of local adaptation. In addition to testing for local adaptation at the population level, the hypothesis was tested that local adaptation is more common between populations from different habitats than between populations from the same habitat. * Local adaptation was not common, but more evidence was found of local adaptation between populations from different habitats than between populations from the same habitat. Two instances of foreign genotype fitness advantage confirm that stochastic processes such as drift can limit local adaptation. * These results are consistent with the hypothesis that stochastic processes can inhibit local adaptation but are more likely to be overwhelmed by natural selection when populations occur in divergent environments.