内容来源：https://www.quantamagazine.org/the-sudden-surges-that-forge-evolutionary-trees-20250828/

内容总结：

【进化论新模型揭示生命演化存在“爆发式跃进”】
近日，《皇家学会学报B》发表的一项研究提出全新数学模型，证实生物进化并非始终匀速渐进，而是在物种分化的关键节点出现剧烈爆发式演变。这一发现为1972年古生物学家提出的“间断平衡”理论提供了强有力证据。

研究表明，从章鱼等头足类动物的触手演化，到人类语言的谱系分化，乃至病毒变异过程，均呈现出“分支盐跃演化”（saltative branching）规律：即物种在进化树分叉时刻会爆发性加速演变，而非传统认为的缓慢渐进。研究团队通过分析蛋白质家族、化石记录及语言演变等十余组数据发现，头足类动物5亿年演化中99%的显著特征形成于分支爆发期，而非渐进积累。

该模型同时整合了已灭绝物种的“幽灵分支”数据，揭示即使分支消失，其进化痕迹仍会影响现有物种演化路径。英国雷丁大学进化生物学家马克·佩格尔评价称，这一发现将微观进化与宏观进化置于统一框架，是“科学哲学中的优美篇章”。

尽管该模型仍需更多化石与分子数据验证，但已为解释生物与文化演进中的爆发式变革提供了新范式。正如研究者所言：“若要真正理解进化，就必须重视这种爆发式进程。”

（根据《皇家学会学报B》研究报道）

中文翻译：

演化树上的爆发式跃变
引言
在过去的五亿年间，乌贼、章鱼及其头足类亲属的演化轨迹宛如一场烟火表演：在漫长的酝酿停顿间，不时迸发出剧烈的爆发式演变。头足动物之所以能演化出如此多样的腕足形态，关键在于演化动力在物种分化的关键时刻全力迸发——渐进式演变带来的缓慢积累只占其演化历程的极小部分。

这种现象并非孤例。纵观生命演化的各个尺度，每当出现基于遗传变异的分支系统时，演化树的分叉处总会迸发突发性加速，这种动态模式是传统演化模型未曾探讨的。

这一洞见源于《皇家学会学报B辑》发布的新数学模型，该框架旨在描述演化变革的节奏。作为近五十年来对演化节奏重新认知的重要组成部分，新模型植根于古生物学家尼尔斯·埃尔德里奇与斯蒂芬·杰伊·古尔德于1972年提出的"间断平衡"理论。

"物种在化石记录中会保持数百万年的静止状态，然后突然——砰！——转变成全新形态，"英国雷丁大学演化生物学家马克·佩格尔解释道。

间断平衡理论最初颇具争议。它挑战了延续百年的主流观点——即演化始终遵循达尔文渐进主义的缓慢稳定节奏，认为物种通过难以察觉的微量调整逐渐演变成新物种。该理论揭示了一种令人困惑的可能性：推动种群内部微观演化的选择机制，与驱动物种级以上宏观演化的长期广域变革机制之间，可能存在本质断层。

过去数十年间，随着数据积累，研究者持续争论这些观点：古生物学家通过化石数据集追溯远古谱系的宏观演化，分子生物学家则通过DNA及蛋白质编码在更压缩的时间尺度上重构微观演化。

如今已有足够数据来全面检验这些演化理论。近期，科学家团队整合多种演化模型的洞见与新方法，构建出能更准确反映真实演化过程的数学框架。当他们将这套工具应用于精选的演化数据集（包括对远古蛋白质家族的研究数据）时，发现演化爆发不仅普遍存在，而且以可预测的方式聚集在演化树的分叉节点。

模型显示蛋白质在分化时期会加速自我重构；人类语言在谱系分叉处剧烈演变；头足类软体动物同样在分化节点快速演化出腕足与吸盘。

未参与该研究的佩格尔指出，这项新研究为间断平衡现象提供了进一步支持。不过这种快速演化行为并非如埃尔德里奇和古尔德所言是独立于自然选择的过程，而是由极端快速适应期推动的演化变革。

"这堪称科学哲学领域的精彩篇章，"佩格尔评价道。

幻影爆发
堪培拉澳大利亚国立大学的演化生物学家乔丹·道格拉斯痴迷于遗传密码的起源之谜。为探究生命演化的初始阶段，他专注于研究氨酰-tRNA合成酶（aaRS）——这类对蛋白质合成至关重要的酶家族，其存在甚至可能早于地球所有生命的最后共同祖先。

"这些酶通过协助将RNA翻译成能复制RNA的蛋白质，构建出自然自我复制的反射逻辑链，"道格拉斯解释道。

道格拉斯管理着不断扩大的aaRS结构与序列数据库，通过与同事分析这些数据，重构了这个蛋白质家族约40亿年的演化史。通过序列研究，他发现这些酶必然经历了快速爆发式演化。虽然这些分子本身并非物种，但它们随时间推移以分叉树状模式演变——类似生物种群的分化方式——新形态会形成具有准物种特征的分支。这种演化树模式令道格拉斯团队联想到关于间断平衡的争论。

团队深入"兔子洞"（意指深入探索），系统评估支持埃尔德里奇与古尔德理论的各项证据：从哺乳动物体型演化数据集，到澳洲鹦鹉吸食花蜜的特化消化系统，再到新冠病毒的早期全球传播数据。他们试图构建统一模型，揭示间断平衡在酶类及其他生命形式与尺度中的形成机制，尤其关注物种一分为二的神秘时刻。

其方法论的核心是引入"爆发值"参数，用于衡量分支出现时的变革强度。"这是该算法对系统发育学的独创贡献，"道格拉斯强调。传统系统发育学认为演化不仅缓慢渐进，且新物种形成分支后往往独立演变。经典假设认为物种分化后，两个新形态会像海上脱锚的浮标般被动漂离，但道格拉斯认为现实演化并非总是如此——可能存在"分化即加速"的动态机制。

"当群体分裂为二时，仿佛存在某种磁力推进瞬间驱使它们分离，"他描述道，"此后才会进入缓慢的独立演化阶段。"

新模型还纳入了现今不可见的远古分支事件。若某个谱系曾分叉但因灭绝而被抹去，现代数据可能完全无法呈现其存在。道格拉斯特将这种演化中的"幻影爆发"称为"存根"。"尽管分支已消失，但它留下了足迹，"他指出。

该方法借鉴了佩格尔等学者的成果——后者在2010年共同开发了追溯灭绝物种失落分支的方法。佩格尔认为道格拉斯团队的模型比前人更普适，允许研究者构建演化速率可变的发展树。"这项研究以精妙方式融合了诸多碎片化发现，"他称赞道。

解释力
团队开发新模型后，在十多个不同研究领域的演化数据集上进行了测试。

应用于aaRS酶自身研究时，模型显示出演化树分支周围的快速变革聚集。与传统渐进模型对比显示，虽然谱系关系相似，但新模型的爆发值使演化树长度缩短了30%，表明从远古祖先到分支末端的演化时间更短，酶演化速度更快。

团队还重新分析了头足类特征数据集（涵盖27个现存物种和52个化石的触手发生与体型演化）。结果显示五亿年来渐进演化对头足类体型塑造的贡献微乎其微，99%的演化发生在分支分叉附近的爆发式跃变中。

道格拉斯团队将这种谱系分裂时的突发加速称为"跃变分支"，并发现该现象不仅限于生物演化。他们将其应用于印欧语系谱系的树状演变分析，通过计算语言演化早期的爆发性变革，推算出该语系在欧亚大陆的起源时间。

"这些结果表明间断平衡在演化的多重维度中具有相当程度的普遍性，"道格拉斯总结道，"忽视这个过程就难以建立对演化的完整认知。"跃变分支可能是生物演化与文化演化的共同基础。

时间检验
该研究融合了古生物学与分子生物学在演化节奏方面长期存在且时常冲突的观点。主要研究化石形态数据的古生物学家更常观察到间断平衡现象。"古生物学家难以准确把握物种形成时实际发生的精细化过程，"未参与研究的史密森尼国家自然历史博物馆演化古生物学家吉恩·亨特指出。物种形成过程的细节在化石记录中难以捕捉，恰恰因为该过程发生得极其迅速。

与此同时，遗传与分子数据对此现象的定义较为模糊——这些数据往往揭示物种分化时更微妙渐进的差异。"分子生物学家曾明确表示古尔德错了或他不理解分子数据，"未参与研究的东南路易斯安那大学统计系统发育学家艾普丽尔·赖特表示，"因此在分子数据中检测到这种（爆发式演化）模式确实令人振奋。"

何种条件会改变分叉点的演化节奏？当生物群体进入新环境或面临新演化压力时，可能发生物理分离并快速积累差异。人类及其文化或语言从初始大群体中隔离时也可能出现类似现象。

"可能是新环境刺激，也可能是群体发展过程中适应了不同文化规范，"赖特分析道，"在节点处观测到相同的变革聚集特征完全合乎逻辑。"

这些演化爆发也可等同于分裂或物种形成事件。佩格尔认为物种多数时候处于临时静态平衡，环境变化会周期性打破这种稳定，促使种群快速演化出新的生存方式以占据生态位新 niche。

该框架仍需进一步验证。亨特指出目前仅十余项研究用于评估新模型，但仅古生物学领域就有数百个数据集可用这些工具分析，分子演化数据更是不计其数。"海量现存数据可供使用，"他表示。无人能预知哪些测试会推动这个跃变分支模型迈向下一轮演化突破。

英文来源：

The Sudden Surges That Forge Evolutionary Trees
Introduction
Over the last half-billion years, squid, octopuses and their kin have evolved much like a fireworks display, with long, anticipatory pauses interspersed with intense, explosive changes. The many-armed diversity of cephalopods is the result of the evolutionary rubber hitting the road right after lineages split into new species, and precious little of their evolution has been the slow accumulation of gradual change.
They aren’t alone. Sudden accelerations spring from the crooks of branches in evolutionary trees, across many scales of life — seemingly wherever there’s a branching system of inherited modifications — in a dynamic not examined in traditional evolutionary models.
That’s the perspective emerging from a new mathematical framework published in Proceedings of the Royal Society B that describes the pace of evolutionary change. The new model, part of a roughly 50-year-long reimagining of evolution’s tempo, is rooted in the concept of punctuated equilibrium, which was introduced by the paleontologists Niles Eldredge and Stephen Jay Gould in 1972.
“Species would just sit still in the fossil record for millions of years, and then all of a sudden — bang! — they would turn into something else,” explained Mark Pagel, an evolutionary biologist at the University of Reading in the United Kingdom.
Punctuated equilibrium was initially a controversial proposal. The theory diverged from the dominant, century-long view that evolution adhered to a slow, steady pace of Darwinian gradualism, in which species incrementally and almost imperceptibly developed into new ones. It opened the confounding possibility that there was a discontinuity between the selection processes behind the microevolutionary changes that occur within a population and those driving the long-term, broad-scale changes that take place higher than the species level, known as macroevolution.
In the decades since, researchers have continued to debate these views as they’ve gathered more data: Paleontologists have accumulated fossil datasets tracing macroevolutionary changes in ancient lineages, while molecular biologists have reconstructed microevolution on a more compressed timescale — in DNA and the proteins they encode.
Now there are enough datasets to more fully test the theories of evolutionary change. Recently, a team of scientists blended insights from several evolutionary models with new methods to build a mathematical framework that better captures real evolutionary processes. When the team applied their tools to a selection of evolutionary datasets (including their own data from research into an ancient protein family), they found that evolutionary spikes weren’t just common, but somewhat predictably clustered at the forks in the evolutionary tree.
Their model showed that proteins contort themselves into new iterations more rapidly around the time they diverge from each other. Human languages twist and recast themselves at the bifurcations in their own family tree. Cephalopods’ soft bodies sprout arms and bloom with suckers at these same splits.
The new study adds to previous support for the punctuated equilibrium phenomenon, said Pagel, who wasn’t involved in the project. However, the rapid evolutionary behavior isn’t a unique process separate from natural selection, as Eldredge and Gould suggested, but rather the result of periods of extremely rapid adaptation propelling evolutionary change.
“This is really a rather beautiful story in the philosophy of science,” Pagel said.
Phantom Bursts
Jordan Douglas, an evolutionary biologist at the Australian National University in Canberra, is fascinated by the origins of the genetic code. To understand those first stages of life’s evolution, he studies aminoacyl-tRNA synthetases (aaRSs), a family of enzymes essential to building proteins. The aaRS enzymes appear to predate the last universal common ancestor for all life on the planet.
“These enzymes are responsible for creating that kind of reflexive logic that nature uses to build itself, by helping to translate RNA into proteins which copy RNA, which build more proteins, which copy more RNA,” Douglas said.
Marcelo Cortes
Douglas administers a growing database of aaRS structures and sequences from across the tree of life, which he and his colleagues use to reconstruct the protein family’s roughly 4-billion-year evolutionary history. Studying the sequences, he observed that these enzymes must have evolved in very fast bursts. Although the molecules are not species per se, they changed through time in a bifurcating treelike pattern, much like populations of organisms, as their new forms created branches with quasi-species. Their evolutionary tree pattern reminded Douglas and his colleagues of the debate about punctuated equilibrium.
The team went down a “rabbit hole,” Douglas said, to surface and assess any evidence in support of Eldredge and Gould’s theory — datasets on everything from the evolution of mammalian body size to Australasian parrots’ specialized digestive system for slurping nectar, to the early global spread of the virus behind the Covid-19 pandemic. They wanted to build a cohesive model of how punctuated equilibria take shape across many forms and scales of life, including and beyond enzymes. They were especially curious about those elusive moments where one species becomes two.
A key part of their approach introduced “spikes,” a model parameter that measures the amount of change that occurs every time a branch appears. “[The spike is] a novel contribution of this algorithm that is not usually done in phylogenetics,” Douglas said.
The paradigm in phylogenetics (the study of evolutionary relationships), he said, is that changes happen not only slowly and gradually, but often independently once a new species forms its own branch. The assumption was that when one species splits from another, the two new forms passively evolve away from each other, drifting solo on their evolutionary paths like two untethered buoys at sea. But Douglas doesn’t think this is how evolution always plays out in reality — he thinks there can be a split-and-hit-the-gas dynamic.
“When one group or population splits into two, it’s like there’s often this magnetic propulsion that immediately drives them apart,” Douglas said. “Then afterwards they go through a kind of slow, independent evolution.”
The new model also incorporates past branching events that we can’t see today. If a lineage branches, but that branch is cut short — sliced off millions of years ago when the lineage went extinct — then it may not appear at all in modern data. Douglas and his team accounted for what he called “phantom bursts” of evolution, termed “stubs” in their model. “Even though the branch is gone, it’s left behind a footprint,” Douglas said.
The approach builds on the insights of other evolutionary biologists, including Pagel, who in 2010 co-developed a method to account for lost branches of extinct species. Douglas’s team’s model is more general than previous approaches, Pagel said, allowing researchers to develop trees where the rate of evolution varies throughout. “There’s a lot of little bits of this story that come together in a really nice way,” he said.
Explanatory Power
Once the team developed their new model, they tested it on over a dozen evolutionary datasets across multiple fields of study.
When the researchers applied the model to their own research on aaRS enzymes they saw rapid changes accumulate around the branches of the evolutionary tree. When they compared their aaRS tree to others that assumed more gradual changes, they saw that the relationships between lineages were similar. However, the new model’s evolutionary spikes made the new trees 30% shorter with respect to gradual change, which suggested that less time had passed between the earliest ancestors and the tips of the branches, and that the enzymes had evolved more quickly.
Douglas and his colleagues also reanalyzed a dataset on cephalopod traits, such as the emergence of tentacles and evolution of body shapes, from 27 living species and 52 fossils. The results showed what the researchers describe as being a trivial contribution of gradual evolution toward the physical shape of cephalopods over some 500 million years, with 99% of the evolution occurring in spectacular bursts near the forking of branches.
Jaap Bleijenberg/Alamy
This sudden acceleration when lineages split — termed “saltative branching” by Douglas and his colleagues — isn’t limited to the evolution of living things. They found that it also applies to systems that living things create. The team turned their model loose on the series of treelike modifications and convolutions in the Indo-European family of languages. By accounting for early bursts in language evolution, the team developed an time estimate for the family’s origins in Eurasia.
The lesson from these results, Douglas said, is that punctuated equilibria are “quite pervasive, quite general” across many different faces of evolution. “It’s difficult to build up a solid understanding of evolution without accounting for this process,” he said. Saltative branching may be fundamental across biological and cultural evolution.
The Test of Time
The study merges the long-standing, and often conflicting, perspectives of paleontologists and molecular biologists when it comes to the pacing of evolution. Paleontologists — who primarily work with long-term morphological data from fossils — more often encounter punctuated equilibria. “What paleontologists have been much less able to get at is the whole narrowing down that actually happens at speciation,” said Gene Hunt, an evolutionary paleontologist at the Smithsonian National Museum of Natural History who was not involved in the new research. The details surrounding species emergence are difficult to capture in the fossil record simply because the process happens so quickly, he said.
Meanwhile, the phenomenon is less defined in genetic and molecular data, which tends to reveal more subtle, incremental differences as species diverge. “[Molecular biologists] definitely expressed the perspective that Gould was wrong or he didn’t understand molecular data,” said April Wright, a statistical phylogeneticist at Southeastern Louisiana University who was not involved in the new research. “So it’s definitely interesting to see this pattern [of abrupt evolution] getting measured in molecular data.”
What conditions could change the evolutionary tempo where trees fork? After spending time in new surroundings or experiencing new evolutionary pressures, two groups of organisms may split apart physically and quickly accumulate differences. The same may occur when humans and their cultures or languages become isolated from an initial, larger group.
“Maybe they’re in a new environment. Maybe they’re just adapting different sets of cultural norms as they grow as a group,” Wright said. “That would make a lot of sense, that you would see that same signature of change cluster at the nodes.”
These evolutionary bursts could also be equated with splitting or speciation events. Pagel describes species mostly being held in a kind of temporary stasis. Every so often, that stability is perturbed by environmental changes, and populations quickly evolve new ways to survive, occupying a different niche in their ecosystem.
The framework needs to be tested further. Just over a dozen studies were used in evaluating the new model, Hunt said. But there are probably hundreds of paleontological datasets alone that could be analyzed by these new tools, plus more on molecular evolution. “There’s a huge amount of data sitting around that could be used for this,” he said. There’s no telling which of those tests could perturb this new saltative branching model into its next evolutionary spike.