Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish

Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of the evolutionary mechanisms impending or favouring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (Mallotus villosus). We first assembled a 490‐Mbp draft genome of M. villosus to map our RAD sequence reads. Then, we used a large data set of genome‐wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they probably diverged from 3.8 to 1.8 million years ago and experienced secondary contacts. Within each lineage, our analyses provided evidence for large N_e and high gene flow among spawning sites. Within the Northwest Atlantic lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype–environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that both shared polymorphisms among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.     

The complete chloroplast genome of Myriophyllum spicatum reveals a 4‐kb inversion and new insights regarding plastome evolution in Haloragaceae

Myriophyllum, among the most species‐rich genera of aquatic angiosperms with ca. 68 species, is an extensively distributed hydrophyte lineage in the cosmopolitan family Haloragaceae. The chloroplast (cp) genome is useful in the study of genetic evolution, phylogenetic analysis, and molecular dating of controversial taxa. Here, we sequenced and assembled the whole chloroplast genome of Myriophyllum spicatum L. and compared it to other species in the order Saxifragales. The complete chloroplast genome sequence of M. spicatum is 158,858 bp long and displays a quadripartite structure with two inverted repeats (IR) separating the large single copy (LSC) region from the small single copy (SSC) region. Based on sequence identification and the phylogenetic analysis, a 4‐kb phylogenetically informative inversion between trnE‐trnC in Myriophyllum was determined, and we have placed this inversion on a lineage specific to Myriophyllum and its close relatives. The divergence time estimation suggested that the trnE‐trnC inversion possibly occurred between the upper Cretaceous (72.54 MYA) and middle Eocene (47.28 MYA) before the divergence of Myriophyllum from its most recent common ancestor. The unique 4‐kb inversion might be caused by an occurrence of nonrandom recombination associated with climate changes around the K‐Pg boundary, making it interesting for future evolutionary investigations.     

中国陆地生态系统碳源/汇整合分析

国家尺度陆地生态系统碳收支及其循环过程的研究对于提升地球系统科学与全球变化科学的科技创新能力、提高我国参与应对全球气候变化国际行动和维护国家利益的话语权、保障国家生态安全和改进生态系统管理都具有重要意义。近年来,我国已经在气候变化与陆地生态系统碳循环领域开展了大量的研究工作,主要包括国家清查、生态系统模型模拟、大气反演等手段。然而,由于大尺度陆地生态系统碳源/汇的估算存在很大的不确定性,目前尚未形成国家尺度的陆地生态系统碳源/汇的整合分析。通过搜集已发表的关于中国陆地生态系统及其组分碳源/汇的59篇文献,整合国家清查、生态系统模型模拟、大气反演3种研究手段,分析中国陆地生态系统碳源/汇大小以及时间尺度上的动态变化。结果表明,在1960s-2010s期间中国陆地生态系统碳汇整体呈上升趋势,平均为（0.213±0.030）Pg C/a,其中森林、草地、农田和灌木生态系统碳汇分别为（0.101±0.023）Pg C/a、（0.032±0.007）Pg C/a、（0.043±0.010）Pg C/a和（0.028±0.010）Pg C/a。森林生态系统中的植被碳汇远大于土壤碳汇,然而这种格局在草地和农田生态系统却相反,而且1960s-2010s期间中国主要植被类型的生态系统碳汇总体上随时间呈增加趋势。融合多源数据（地面观测、激光雷达、卫星遥感等）、多尺度数据（样地尺度、站点尺度、区域尺度）以及多手段数据（联网观测、森林清查、模型模拟）,有助于全面准确地评估中国陆地生态系统碳源/汇及其对气候变化的响应。     

联合GF-6和Sentinel-2红边波段的森林地上生物量反演

光谱反射率能反映地物差异,是森林地上生物量（Aboveground Biomass,AGB）遥感反演的理论基础。红边波段处于近红外与红光波段交界处快速变化的区域,能对植被冠层结构和叶绿素含量的微小变化做出快速反应,对植被生长状况较敏感。研究以GF-6和Sentinel-2多光谱影像作为数据源,结合野外调查AGB数据,构建落叶松和樟子松AGB线性和非线性估测模型,通过比较模型精度选择最优模型进行森林AGB反演和空间分布制图。结果表明：GF-6和Sentinel-2影像红边波段反射率与落叶松、樟子松AGB均呈显著相关（P<0.05）,红边波段对AGB估测较敏感。多变量估测模型整体估测效果优于单变量模型,所有模型中多元线性回归模型取得了最优的决定系数（落叶松R²=0.66,樟子松R²=0.65）和最低的均方根误差（落叶松RMSE=31.45 t/hm²,樟子松RMSE=54.77 t/hm²）。相比单个数据源,联合GF-6和Sentinel-2影像构建的多元线性回归模型估测效果得到了显著提升,模型RMSE对于落叶松和樟子松AGB估测分别最大降低了22.9%和11.2%。增加红边波段进行AGB估测能显著提高模型估测精度,三组数据源分别加入红边波段信息后进行建模,模型RMSE得到了显著降低。GF-6拥有800 km观测幅宽和高效的重访周期,可以快速地提供大尺度时间序列数据,在森林地上生物量反演和动态监测方面有着很大潜力。     

Experimental warming shifts coupling of carbon and nitrogen cycles in an alpine meadow

增温对高寒草甸生态系统碳氮循环耦合关系的影响 陆地生态系统碳吸收受土壤氮素可用性的调节。然而,全球变化背景下的不同生态系统组分的碳氮比及其所反映的碳氮循环耦合关系尚不十分清楚。本文运用数据同化的方法,将一个高寒草甸增温试验的14组数据同化到草地生态系统模型中,从而评估了增温如何影响陆地生态系统的碳氮循环耦合关系。研究结果表明,增温提高了土壤氮素的有效性,降低了土壤活性碳库的碳氮比,导致植物对土壤氮的吸收增加。但是由于植物叶片吸收的碳比吸收的氮增加更多,使得叶片中碳氮比增加,而根部的碳输入增加则低于氮的增加,导致根部的碳氮比减少。同时,增温降低了凋落物碳氮比,可能是在土壤高氮有效性的条件下,凋落物氮的固定得到增强;而且增温加速了凋落物的分解。同时增温还增加了慢速土壤有机质的碳氮比,使得该土壤碳库的碳固存潜力增大。由于大多数模型在不同的环境中通常使用相对固定的碳氮比,本研究所发现的气候变暖条件下碳氮比的差异变化可为模型参数化提供一个有效的参考,有利于模型对未来气候变化背景下生态系统碳氮耦合关系响应的预测。     

A large proportion of North American net ecosystem production is offset by emissions from harvested products,river/stream evasion,and biomass burning

Diagnostic carbon cycle models produce estimates of net ecosystem production (NEP, the balance of net primary production and heterotrophic respiration) by integrating information from (i) satellite‐based observations of land surface vegetation characteristics; (ii) distributed meteorological data; and (iii) eddy covariance flux tower observations of net ecosystem exchange (NEE) (used in model parameterization). However, a full bottom‐up accounting of NEE (the vertical carbon flux) that is suitable for integration with atmosphere‐based inversion modeling also includes emissions from decomposition/respiration of harvested forest and agricultural products, CO₂ evasion from streams and rivers, and biomass burning. Here, we produce a daily time step NEE for North America for the year 2004 that includes NEP as well as the additional emissions. This NEE product was run in the forward mode through the CarbonTracker inversion setup to evaluate its consistency with CO₂ concentration observations. The year 2004 was climatologically favorable for NEP over North America and the continental total was estimated at 1730 ± 370 TgC yr^?1 (a carbon sink). Harvested product emissions (316 ± 80 TgC yr^?1), river/stream evasion (158 ± 50 TgC yr^?1), and fire emissions (142 ± 45 TgC yr^?1) counteracted a large proportion (35%) of the NEP sink. Geographic areas with strong carbon sinks included Midwest US croplands, and forested regions of the Northeast, Southeast, and Pacific Northwest. The forward mode run with CarbonTracker produced good agreement between observed and simulated wintertime CO₂ concentrations aggregated over eight measurement sites around North America, but overestimates of summertime concentrations that suggested an underestimation of summertime carbon uptake. As terrestrial NEP is the dominant offset to fossil fuel emission over North America, a good understanding of its spatial and temporal variation – as well as the fate of the carbon it sequesters ─ is needed for a comprehensive view of the carbon cycle.     

Nucleolar organizer regions in Sittasomus griseicapillus and Lepidocolaptes angustirostris (Aves,Dendrocolaptidae): Evidence of a chromosome inversion

Cytogenetic studies in birds are still scarce compared to other vertebrates. Woodcreepers (Dendrocolaptidae) are part of a highly specialized group within the Suboscines of the New World. They are forest birds exclusive to the Neotropical region and similar to woodpeckers, at a comparable evolutionary stage. This paper describes for the first time the karyotypes of the Olivaceous and the Narrow-billed Woodcreeper using conventional staining with Giemsa and silver nitrate staining of the nucleolar organizer regions (Ag-NORs). Metaphases were obtained by fibular bone marrow culture. The chromosome number of the Olivaceous Woodcreeper was 2n = 82 and of the Narrow-billed Woodcreeper, 2n = 82. Ag-NORs in the largest macrochromosome pair and evidence of a chromosome inversion are described herein for the first time for this group.