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Population continuity and change in Africa’s far south 非洲最南端人口的延续与变化
IF 13.9 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-19 DOI: 10.1038/s41559-024-02537-y
Peter Mitchell
Ancient human genomic data from Oakhurst Rockshelter in South Africa push back the earliest reported ancient DNA from the subcontinent to the start of the Holocene, revealing surprising genetic continuity and raising questions about the nature of regional cultural change.
来自南非奥克赫斯特岩石栖息地的古人类基因组数据,将非洲大陆最早的古人类 DNA 报告推回到全新世开始的时期,揭示了令人惊讶的基因连续性,并提出了有关地区文化变迁性质的问题。
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引用次数: 0
9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter 奥克赫斯特岩石栖息地展示了非洲最南端 9000 年的基因连续性
IF 13.9 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-19 DOI: 10.1038/s41559-024-02532-3
Joscha Gretzinger, Victoria E. Gibbon, Sandra E. Penske, Judith C. Sealy, Adam B. Rohrlach, Domingo C. Salazar-García, Johannes Krause, Stephan Schiffels
Southern Africa has one of the longest records of fossil hominins and harbours the largest human genetic diversity in the world. Yet, despite its relevance for human origins and spread around the globe, the formation and processes of its gene pool in the past are still largely unknown. Here, we present a time transect of genome-wide sequences from nine individuals recovered from a single site in South Africa, Oakhurst Rockshelter. Spanning the whole Holocene, the ancient DNA of these individuals allows us to reconstruct the demographic trajectories of the indigenous San population and their ancestors during the last 10,000 years. We show that, in contrast to most regions around the world, the population history of southernmost Africa was not characterized by several waves of migration, replacement and admixture but by long-lasting genetic continuity from the early Holocene to the end of the Later Stone Age. Although the advent of pastoralism and farming substantially transformed the gene pool in most parts of southern Africa after 1,300 bp, we demonstrate using allele-frequency and identity-by-descent segment-based methods that the ‡Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers, a pattern obscured by recent, extensive non-Southern African admixture. Yet, some southern San in South Africa still preserve this ancient, Pleistocene-derived genetic signature, extending the period of genetic continuity until today. Oakhurst rockshelter in South Africa documents marked cultural change during the Holocene, but genome-wide data from ancient human individuals at the site now demonstrate a remarkable degree of genetic continuity over the last 9,000 years: the contemporary ‡Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers.
南部非洲是人类化石记录最长的地区之一,拥有世界上最丰富的人类遗传多样性。然而,尽管南部非洲与人类的起源和在全球的传播息息相关,但其基因库在过去的形成和发展过程在很大程度上仍不为人所知。在这里,我们展示了从南非的一个遗址--奥克赫斯特岩棚(Oakhurst Rockshelter)采集的九个个体的全基因组序列的时间横断面。这些个体的古DNA跨越了整个全新世,使我们能够重建过去一万年中桑族土著居民及其祖先的人口轨迹。我们的研究表明,与世界上大多数地区不同,非洲最南端的人口历史并不以几波迁徙、更替和融合为特征,而是以从全新世早期到石器时代晚期的长期遗传连续性为特征。尽管在 1300 bp 之后,畜牧业和农耕的出现大大改变了南部非洲大部分地区的基因库,但我们利用等位基因频率和基于世系区段的认同方法证明,南非的‡Khomani San 人和 Karretjiemense 人仍然显示出与 Oakhurst 狩猎采集者的直接亲缘关系,这种模式被近期广泛的非南部非洲混杂所掩盖。然而,南非的一些南部桑人仍然保留着这种源自更新世的古老遗传特征,将遗传连续性延续至今。
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引用次数: 0
Evolutionary shift of a tipping point can precipitate, or forestall, collapse in a microbial community 临界点的进化转变可促使或防止微生物群落崩溃
IF 16.8 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-18 DOI: 10.1038/s41559-024-02543-0
Christopher Blake, Jake N. Barber, Tim Connallon, Michael J. McDonald

Global ecosystems are rapidly approaching tipping points, where minute shifts can lead to drastic ecological changes. Theory predicts that evolution can shape a system’s tipping point behaviour, but direct experimental support is lacking. Here we investigate the power of evolutionary processes to alter these critical thresholds and protect an ecological community from collapse. To do this, we propagate a two-species microbial system composed of Escherichia coli and baker’s yeast, Saccharomyces cerevisiae, for over 4,000 generations, and map ecological stability before and after coevolution. Our results reveal that tipping points—and other geometric properties of ecological communities—can evolve to alter the range of conditions under which our microbial community can flourish. We develop a mathematical model to illustrate how evolutionary changes in parameters such as growth rate, carrying capacity and resistance to environmental change affect ecological resilience. Our study shows that adaptation of key species can shift an ecological community’s tipping point, potentially promoting ecological stability or accelerating collapse.

全球生态系统正在迅速逼近临界点,在这里,微小的变化都可能导致生态的剧烈变化。理论预测,进化可以塑造系统的临界点行为,但缺乏直接的实验支持。在这里,我们研究了进化过程改变这些临界点并保护生态群落免于崩溃的能力。为此,我们将一个由大肠杆菌和面包酵母(Saccharomyces cerevisiae)组成的双物种微生物系统繁殖了 4000 多代,并绘制了共同进化前后的生态稳定性图。我们的研究结果表明,临界点和生态群落的其他几何特性可以通过进化改变微生物群落繁衍生息的条件范围。我们建立了一个数学模型来说明生长率、承载力和对环境变化的抵抗力等参数的进化变化如何影响生态恢复力。我们的研究表明,关键物种的适应可以改变生态群落的临界点,从而有可能促进生态稳定或加速崩溃。
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引用次数: 0
Growth rate as a link between microbial diversity and soil biogeochemistry 生长速度是微生物多样性与土壤生物地球化学之间的纽带
IF 13.9 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-18 DOI: 10.1038/s41559-024-02520-7
Megan M. Foley, Bram W. G. Stone, Tristan A. Caro, Noah W. Sokol, Benjamin J. Koch, Steven J. Blazewicz, Paul Dijkstra, Michaela Hayer, Kirsten Hofmockel, Brianna K. Finley, Michelle Mack, Jane Marks, Rebecca L. Mau, Victoria Monsaint-Queeney, Ember Morrissey, Jeffrey Propster, Alicia Purcell, Egbert Schwartz, Jennifer Pett-Ridge, Noah Fierer, Bruce A. Hungate
Measuring the growth rate of a microorganism is a simple yet profound way to quantify its effect on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production and element transformation—some of the many ways in which organisms affect Earth’s ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favourable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining omics and stable isotope probing enable sensitive measurements of the growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake and ecosystem productivity. Measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry. This Perspective discusses how recent developments in the ability to measure the growth of microbial populations, which provides an indicator of population fitness, can inform ecological and biogeochemical models.
测量微生物的增长率是量化其对世界影响的一种简单而深刻的方法。微生物种群的绝对增长率反映了资源同化、生物量生产和元素转化的速率--这是生物影响地球生态系统和气候的多种方式之一。微生物在环境中的适应能力取决于其在条件有利时快速繁殖的能力,以及在条件恶化时采取生存生理学的能力。在种群水平上,相对生长率是衡量适合度的一个敏感指标,它将生存和繁殖与种群的生态学和进化联系在一起。将全息技术和稳定同位素探测技术相结合,可以灵敏地测量土壤中微生物群落和单个类群的生长率。微生物生态学家可以探索具有已知性状和进化历史的类群的生长率如何对资源可用性、环境条件以及与其他生物的相互作用的变化做出反应。我们预计,有关土壤微生物生长率的定量和可扩展数据与生物地球化学通量的测量结果相结合,将使科学家们能够检验和完善生态学理论,并推进基于过程的碳通量、养分吸收和生态系统生产力模型。对原位微生物生长率的测量有助于深入了解种群生态学,并可用于定量地将微生物多样性与土壤生物地球化学联系起来。
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引用次数: 0
Migratory lifestyle carries no added overall energy cost in a partial migratory songbird 迁徙生活方式不会增加部分迁徙鸣禽的总体能量成本
IF 16.8 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-18 DOI: 10.1038/s41559-024-02545-y
Nils Linek, Scott W. Yanco, Tamara Volkmer, Daniel Zuñiga, Martin Wikelski, Jesko Partecke

Seasonal bird migration may provide energy benefits associated with moving to areas with less physiologically challenging climates or increased food availability, but migratory movements themselves may carry high costs. However, time-dynamic energy profiles of free-living migrants—especially small-bodied songbirds—are challenging to measure. Here we quantify energy output and thermoregulatory costs in partially migratory common blackbirds using implanted heart rate and temperature loggers paired with automated radio telemetry and energetic modelling. Our results show that blackbirds save considerable energy in preparation for migration by decreasing heart rate and body temperature 28 days before departure, potentially dwarfing the energy costs of migratory flights. Yet, in warmer wintering areas, migrants do not appear to decrease total daily energy expenditure despite a substantially reduced cost of thermoregulation. These findings indicate differential metabolic programmes across different wintering strategies despite equivalent overall energy expenditure, suggesting that the maintenance of migration is associated with differences in energy allocation rather than with total energy expenditure.

季节性鸟类迁徙可能会带来能量方面的益处,因为迁徙到的地区气候条件对生理挑战较小或食物供应增加,但迁徙本身也可能带来高昂的成本。然而,自由生活的迁徙鸟类--尤其是小体型鸣禽--的时间动态能量曲线很难测量。在这里,我们使用植入式心率和体温记录仪,配合自动无线电遥测和能量模型,量化了部分迁徙的普通乌鸫的能量输出和体温调节成本。我们的结果表明,黑鸟在出发前28天通过降低心率和体温为迁徙做准备,从而节省了大量能量,这可能使迁徙飞行的能量成本相形见绌。然而,在温暖的越冬地区,尽管体温调节的成本大大降低,迁徙者似乎并没有减少每天的总能量消耗。这些研究结果表明,尽管总体能量消耗相同,但不同越冬策略下的新陈代谢方案不同,这表明维持迁徙与能量分配的差异有关,而不是与总能量消耗有关。
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引用次数: 0
Evolution alters ecological resilience 进化改变生态复原力
IF 16.8 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-18 DOI: 10.1038/s41559-024-02542-1
P. Catalina Chaparro-Pedraza
A long-running coevolution experiment on bacteria and yeasts shows that adaptive evolution can shift the tipping points that trigger critical transitions in a community.
一项关于细菌和酵母菌的长期共同进化实验表明,适应性进化可以改变触发群落关键转变的临界点。
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引用次数: 0
Lake-centred sedentary lifestyle of early Tibetan Plateau Indigenous populations at high elevation 4,400 years ago 4400 年前青藏高原高海拔地区早期土著居民以湖泊为中心的定居生活方式
IF 16.8 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-16 DOI: 10.1038/s41559-024-02539-w
Xiaoyan Yang, Yu Gao, Shargan Wangdue, Jingkun Ran, Qing Wang, Songtao Chen, Jishuai Yang, Tianyi Wang, Zhengquan Gu, Ying Zhang, Peng Cao, Qingyan Dai, Shungang Chen, Yan Tong, Nihanxue Jia, Qingli Sun, Yunzhe Huang, Linda Perry, Jade d’Alpoim Guedes, Xu Han, Feng Liu, Xiaotian Feng, Qi Yang, Yunming Wang, Shihua Hu, Yaofei Tian, Jianglong Guo, Xinwei Liang, Ting You, Yazhong Li, Yunan Zhang, Zhenhua Deng, Ling Qin, Xiaohong Wu, Yijie Zhuang, Yichen Liu, Qiaomei Fu, Fahu Chen

The onset of sedentism on the Tibetan Plateau is often presumed to be associated with the dispersal of agriculture or farmers from archaeological sites located in the low elevation margins of the plateau. Previous studies of the plateau assumed that all foragers were probably mobile, but few systematic excavations at forager sites have been conducted to inform us about their settlement patterns. Here we report the world’s highest elevation sedentary way of living exhibited by the Mabu Co site at 4,446 metres above sea level, deep in the interior of the Tibetan Plateau 4,400–4,000 years ago. Our interdisciplinary study indicates that the site was occupied by Indigenous inhabitants of the plateau, representing the earliest known DNA evidence of foragers who predominantly harbour the southern plateau ancestry. The evidence shows that they had a sedentary lifestyle primarily supported by fishing at nearby lakes, supplemented by mammal and bird hunting, as well as small-scale exchanges of millet and rice crops.

人们通常认为,青藏高原定居现象的出现与位于高原低海拔边缘的考古遗址中农业或农民的扩散有关。以前对高原的研究假设所有觅食者都可能是流动的,但很少对觅食者遗址进行系统发掘,以了解他们的定居模式。在此,我们报告了世界上海拔最高的定居生活方式,即海拔 4446 米的马布错遗址,该遗址位于青藏高原内陆深处,距今 4400-4000 年。我们的跨学科研究表明,该遗址被高原原住民占据,是已知最早的觅食者 DNA 证据,他们主要拥有南部高原的血统。证据显示,他们过着定居的生活方式,主要靠在附近湖泊捕鱼为生,并以狩猎哺乳动物和鸟类以及小规模交换小米和水稻作物为辅。
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引用次数: 0
Author Correction: A policy-driven framework for conserving the best of Earth's remaining moist tropical forests. 作者更正:保护地球上仅存的最佳湿润热带森林的政策驱动框架。
IF 13.9 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-13 DOI: 10.1038/s41559-024-02557-8
Andrew J Hansen, Patrick Burns, Jamison Ervin, Scott J Goetz, Matthew Hansen, Oscar Venter, James E M Watson, Patrick A Jantz, Anne L S Virnig, Kevin Barnett, Rajeev Pillay, Scott Atkinson, Christina Supples, Susana Rodríguez-Buritica, Dolors Armenteras
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引用次数: 0
Evolution of evolvability in rapidly adapting populations 快速适应种群的进化能力
IF 13.9 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-11 DOI: 10.1038/s41559-024-02527-0
James T. Ferrare, Benjamin H. Good
Mutations can alter the short-term fitness of an organism, as well as the rates and benefits of future mutations. While numerous examples of these evolvability modifiers have been observed in rapidly adapting microbial populations, existing theory struggles to predict when they will be favoured by natural selection. Here we develop a mathematical framework for predicting the fates of genetic variants that modify the rates and benefits of future mutations in linked genomic regions. We derive analytical expressions showing how the fixation probabilities of these variants depend on the size of the population and the diversity of competing mutations. We find that competition between linked mutations can dramatically enhance selection for modifiers that increase the benefits of future mutations, even when they impose a strong direct cost on fitness. However, we also find that modest direct benefits can be sufficient to drive evolutionary dead ends to fixation. Our results suggest that subtle differences in evolvability could play an important role in shaping the long-term success of genetic variants in rapidly evolving microbial populations. Evolvability modifier mutations alter the rates and benefits of future mutations, but it is difficult to predict when they will be favoured by natural selection. A mathematical framework shows that competition between linked mutations can drive strong selection for modifiers and that subtle differences in evolvability can affect the long-term success of mutations.
突变可以改变生物体的短期适应性以及未来突变的速率和益处。虽然在快速适应的微生物种群中观察到了大量这些进化性修饰因子的例子,但现有理论却难以预测它们何时会受到自然选择的青睐。在这里,我们建立了一个数学框架,用于预测基因变异体的命运,这些变异体会改变相关基因组区域未来突变的速率和益处。我们推导出分析表达式,显示这些变异的固定概率如何取决于种群规模和竞争变异的多样性。我们发现,链接突变之间的竞争会显著增强对增加未来突变收益的修饰因子的选择,即使这些修饰因子会对适应性造成很高的直接成本。然而,我们也发现,适度的直接收益足以促使进化死胡同固定下来。我们的研究结果表明,在快速进化的微生物种群中,可进化性的细微差别可能在塑造遗传变异的长期成功方面发挥重要作用。
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引用次数: 0
David Penny (1938–2024) 戴维-彭尼(1938-2024)
IF 13.9 1区 生物学 Q1 ECOLOGY Pub Date : 2024-09-10 DOI: 10.1038/s41559-024-02540-3
Matthew J. Phillips, Anthony M. Poole, Patricia A. McLenachan, Peter J. Lockhart, Michael D. Hendy
Theoretical biologist who ‘tamed’ mathematicians and tested the theory of evolution.
理论生物学家,他 "驯服 "了数学家并验证了进化论。
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引用次数: 0
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Nature ecology & evolution
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