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解开鸣禽多样性之谜

Solving the Mystery of Songbird Diversity
解开鸣禽多样性之谜
1974字
2019-11-08 21:03
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火星译客

When a 10-kilometer-wide hunk of burning space rock slammed into what is now the Gulf of Mexico 66 million years ago, it touched off widespread destruction, wiping out more than 75 percent of life on Earth. The Chicxulub asteroid, as it is called, is best known as the dinosaur killer. But although it doomed Tyrannosaurus rex and Triceratops, the sauropods and the hadrosaurs, the asteroid actually set one lineage of dinosaurs on a path to glory: that of modern birds.

6600万年前,一块直径为10公里巨型太空岩石以点燃的状态飞向地球大气层并袭击了现在的墨西哥湾,引发了大规模的破坏,地球上75%的生命因此消失。这颗被称为希克苏鲁伯的小行星被认为是恐龙杀手。尽管这颗小行星让霸王龙、三角龙、蜥脚类和鸭嘴龙等恐龙灭亡,但它实际上让曾经的恐龙家族以光荣的姿态步入现代鸟类的阶段。

Birds got their start more than 150 million years ago, evolving from meat-eating dinosaurs called theropods, and they attained an impressive degree of diversity in the first 85 million years or so of their existence. But the ancestors of today's birds—members of the neornithine lineage—were mere bit players compared with archaic birds such as the enantiornithines, which ruled the roost. When the asteroid struck, however, neornithine fortunes shifted. The impact extinguished all of the nonbird dinosaurs and most birds. Only the neornithines made it through that apocalyptic event. This clutch of survivors would give rise to one of the greatest evolutionary radiations of all time.

鸟类起源于1.5亿年前,从食肉恐龙兽脚亚目恐龙进化而来,自其出现的头8500万年左右,鸟类物种的多样性程度就已经令人印象深刻。但是,今天鸟类的祖先——今鸟亚纲族类——与古代鸟类相比只是微不足道的小角色。然而,当小行星撞击地球时,它们的命运发生了转变。这次撞击使得所有的非鸟类恐龙和大多数鸟类彻底灭绝。只有今鸟亚纲得以熬过了这场灾难。这群幸存的鸟类在进化过程中将是有史以来辐射范围最广的物种之一。

Today there are more than 10,000 bird species, making them the second most speciose class of vertebrate creatures alive, outnumbered only by the bony fish. They come in every shape and size—the land-bound ostrich tips the scales at more than 136 kilograms; the ever whirring bee hummingbird, less than two grams. They have colonized virtually every major body of land and water on the planet, from the sweltering tropics to the frozen poles. And they have diversified to fill a vast array of dietary niches, evolving adaptations to eating everything from microscopic algae to large mammals.

今天有超过10000种鸟类,这一强大的家族规模使其成为现存第二大最具物种特征的脊椎动物,其数量仅次于硬骨鱼。它们体型各异——陆生鸵鸟的体重超过136公斤;蜂鸟嗡嗡叫个不停,重量却不到两克。分布范围极广,几乎占领了地球上所有的主要陆地和水域,从潮热的热带到酷冷的两极都可以看到它们的身影。因其多样化的特征,各类饮食性的生态区位都得以填补,它们在进化过程中已经具备适应吃下从微观藻类到大型哺乳动物等一切东西的能力。

Incredibly, roughly half of these species are songbirds, which are characterized by a special voice box. The group includes the warblers, canaries, larks and other mellifluous singers but also the strident (to human ears, anyway) crows and their kin. To put that number in perspective, there are approximately as many living species of songbirds as there are of mammals.

令人难以置信的是,这些物种中大约有一半是鸣禽,它们的特征是都具备声音盒般的美妙歌声。例如,莺、金丝雀、云雀和其他甜美型的鸟中歌唱家,又或者叫声刺耳的乌鸦和它们的同类都属于该群体之列。单看数字记载,鸣禽的现存物种大约和哺乳动物一样多。

How did this particular group of birds come to be so extraordinarily diverse? Biologists have long sought to answer this question, scouring the fossil record and DNA sequences of modern birds for clues. But apart from pinpointing where songbirds originated (Australia), many of these studies produced inconclusive or conflicting results. A detailed picture of where and when the lineages leading to modern songbirds split off from one another—and thus the factors driving this radiation—remained elusive.

这个特殊的鸟类家族是如何进化为如此多元化的群体的?长期以来,生物学家一直在寻找这个问题的答案,他们试图从有记载的现代鸟类化石和DNA序列中寻找线索。但是,除了鸣禽的起源地(澳大利亚)被确定外,这些研究中得出的很多结论都是不确定的或相互矛盾的。关于发展为现代鸣禽的原始谱系在何时何地从某一物种中分化而来的详细情况——以及导致这种进化辐射的因素——仍然是难以捉摸的。

In the absence of conclusive evidence to show how it all transpired, researchers have advanced a number of competing theories for songbird diversification that center variously on climate change, plate tectonics and sexual selection, in which mate preferences spur evolution.

由于未能发现证明上述鸣禽进化过程的确凿依据,研究人员只能转向某些关于鸣禽多样化的竞争理论,这些理论涉及气候变化、板块构造和性选择,其中择偶因素刺激了物种的进化。

Now a new finding has set the field atwitter. All songbirds, it seems, have a weird extra chromosome that does not appear to exist in other birds. The discovery suggests a genetic mechanism for creating barriers to reproduction between populations of a species, which promotes speciation. Much remains to be learned about this auxiliary package of DNA, but already some researchers are wondering whether it just might be the secret of the songbirds' dazzling evolutionary success.

目前,一项新的发现引起了人们的关注。所有的鸣鸟体内似乎都额外存在一条异常染色体,这在其他鸟类中似乎并未发现。这项新发现揭示了一种遗传机制,这种机制会阻碍单一物种种群之间的繁殖交配,从而促进了新物种的形成。关于该DNA的系列辅助基因还存在很多未被发掘的问题,但是一些研究人员已经开始猜测遗传机制导致鸣鸟进化成庞大物种体系的可能性。

Back Pocket Genes

口袋里的基因

The chromosome in question is called the germ-line-restricted chromosome (GRC), so named for its presence in reproductive cells—eggs, sperm and their precursors—but not the rest of the body's cells, called somatic cells. Progenitors of both eggs and sperm contain GRC, but by the time a sperm cell has developed fully, the GRC has been eliminated from it. The chromosome is thus transmitted to offspring via the mother exclusively.

这种引起广泛关注的染色体被称为生殖细胞限制性染色体(GRC),因为它存在于生殖细胞——卵子、精子和它们的前体——而不是身体的其他细胞,即体细胞。卵子和精子的祖细胞都含有GRC,但当一个精子细胞发育完全时,GRC就被从精子中消除了。因此,染色体只通过母亲传给后代。

Until recently the GRC was known only from two songbirds: the zebra finch and its close relative the Bengalese finch. It seemed to be an oddity of these two species, nothing more. But when researchers decided to look for it in other lineages of birds, a striking pattern emerged. In a paper published in the June 11 Proceedings of the National Academy of Sciences USA, Anna Torgasheva and Pavel Borodin of the Russian Academy of Sciences, Denis Larkin of the University of London and their colleagues report that all 16 of the songbird species they examined—a sample that included representatives from across the family tree of songbirds—had the GRC; none of the eight species representing other major bird groups did. What is more, the GRCs they found differed considerably from species to species—even between closely related ones—suggesting that the chromosome has evolved quickly in these different songbird lineages since it first appeared in their common ancestor an estimated 35 million years ago.

直到最近,人们对GRC的了解还仅限于两种鸣鸟:斑胸草雀和它的近亲斑胸草雀。似乎只有这两种动物身上才存在这种异常现象。但当研究人员决定在其他鸟类谱系中寻找这种异常染色体时,一个惊人的模式出现了。在一篇发表于6月11日《美国国家科学院院刊》的报告中,俄罗斯科学院的安娜·托尔加舍瓦和帕维尔鲍罗廷,以及伦敦大学的丹尼斯·拉金及其同事称,他们研究的所有16种鸣鸟——包括整个鸣禽系谱的代表性鸟类体内都有GRC;类属其他主要鸟类群体的八种鸟类体内并未发现GRC的存在。更重要的是,他们发现物种不同,体内的GRC也有很大差异,甚至在亲缘关系很近的物种之间这种差异也同样存在。这表明,自从大约3500万年前,该染色体首次出现在其共同祖先身上以来,染色体在这些不同的鸣禽谱系中进化速度很快。

Cells of other organisms have previously been found to carry extra chromosomes called B chromosomes. But their occurrence is erratic, varying between members of the same species or even between different cells in the same individual. GRC, in contrast, is “an obligatory element in the germ line of song birds,” Larkin says. This ubiquity suggests that GRC is more influential than B chromosomes.

在此之前,人们已经发现其他生物体的细胞携带有称为B染色体的额外染色体。但其存在状况是不稳定的,在同一物种的成员之间甚至在同一个体的不同细胞之间,B染色体也有所不同。相比之下,GRC是“促进鸣禽繁殖体系不断进化的必不可少的元素,”拉金说。这种普遍性表明GRC的影响作用强于B染色体。

Exactly what GRC is influencing is largely a mystery, however—researchers know very little about what its genes actually do. But some hints have come to light. In another recent GRC study, which has been posted to the bioRxiv preprint server but not yet published in a peer-reviewed scientific journal, Cormac M. Kinsella and Alexander Suh of Uppsala University in Sweden and their colleagues found that the zebra finch GRC contains at least 115 genes, including some that have been shown to make proteins and RNA in the ovaries and testes of birds. This expression pattern hints that these genes may help guide the development of sperm and eggs. Other genes on the zebra finch GRC are comparable to genes that are known from mouse studies to be involved in early embryonic development.

然而,由于研究人员对其基因的实际作用知之甚少,GRC究竟在很大程度上对什么造成了影响仍然是一个谜。但某些相关迹象已经浮出水面。在最近另一项刊登在《bioRxiv》预印数据库中但尚未在同行评审的科学期刊上发表的GRC研究中,瑞典乌普萨拉大学的Cormac M. Kinsella和Alexander Suh以及他们的同事发现,斑胸草雀体内的GRC至少包含115个基因,其中一些基因已经被证明可以在鸟类的卵巢和睾丸中制造蛋白质和RNA。这种表达模式暗示这些基因可能有助于指导精子和卵子的发育。斑胸草雀体内的GRC上的其他基因与小鼠研究中发现的参与早期胚胎发育的基因相似。

To Borodin and Larkin, these findings suggest that the GRC may have allowed songbirds to circumvent key constraints on bird evolution. “The avian genome in general is very compact and conserved compared with, for example, the mammalian genome,” Larkin explains. The genomes of today's mammals range in size from less than two picograms to more than eight picograms and are packaged into anywhere from six chromosomes to 102. In the tens of millions of years over which they have been evolving, their chromosomes have been sliced and diced and reshuffled and rejoined many times. These rearrangements have altered gene expression in ways that have produced diverse traits. Birds, in contrast, have genomes ranging from just under one picogram to just over two. And they usually have right around 80 chromosomes, with comparatively little of the “junk” DNA found in most mammals.

对博罗丁和拉金来说,这些发现表明GRC可能使鸣鸟有能力规避限制鸟类进化的关键因素。拉金解释说:“与哺乳动物的基因组相比,鸟类的基因组通常排列紧致且行为模式相对保守。”如今哺乳动物的基因组大小不一,从不到2微克到超过8微克不等,从6条染色体到102条染色体都有。在它们进化的数千万年里,它们的染色体被多次切割、重组和重新结合。这些重排过程改变了基因的表达方式,从而产生了不同的性状。相比之下,鸟类的基因组的大小则从略低于1微微克到略高于2微微克不等。它们通常有大约80条染色体,而在大多数哺乳动物中发现的“垃圾”DNA相对较少。

The reason bird genomes are small and streamlined, some experts surmise, has to do with flight. Flying is an energetically expensive activity. Larger genomes require larger cells, and both are metabolically costlier than their smaller counterparts. The intense metabolic demands of flying may have therefore limited bird genome size. Because the GRC occurs only in germ-line cells and not the far more numerous somatic cells, it could have provided songbirds with a rare chunk of extra DNA—fodder for the evolution of new traits—without the metabolic costs associated with having a larger somatic genome.

一些专家推测,鸟类基因组之所以短小且呈流线型与飞行有关。飞行是一项极其耗费精力的活动。更大的基因组需要更大的细胞,两者的代谢成本都比较小的基因组高。因此,飞行对新陈代谢的强烈需求可能限制了鸟类基因组的大小。因为GRC只发生在生殖细胞系细胞中,而不是数量多得多的体细胞中,它可以为鸣禽额外提供大量罕见的DNA并促进新特性的进化过程,而不需要消耗数量相对更多的体细胞基因组所需的代谢成本。

“Birds need additional copies of germ-cell-specific genes for a very short breeding period only to produce a lot of sperm and load [egg cells] with large amounts of proteins. They have no reason to carry these genes throughout the year and in [the rest of the body's] cells when and where they are of no use,” Borodin says. If songbirds found a way to obtain additional genes on a temporary basis that could work during early stages of development while keeping their basic genome intact, Larkin adds, such an arrangement would be tremendously advantageous and could lead to the huge variety seen in songbirds compared with other bird groups.

“鸟类在极短的繁殖期内需要额外的特异表达于精子细胞的基因,这样才能产生大量的精子,并使(卵细胞)装载大量的蛋白质。它们没有理由全年携带这些基因,也没有理由在它们没有用处的时候、在身体的其他细胞中携带这些基因,”博罗丁说。如果鸣鸟能够寻求临时方法获取额外的基因,那么它们就可以在早期的发展阶段,同时保持其基本基因组的完整性。拉金补充说,这样的安排为鸣鸟极大地区别于其他鸟类群体创造了有利条件。

In theory, the GRC could have created the reproductive isolation needed for new species to evolve by rendering those individuals that carried the extra chromosome unable to interbreed and produce fertile offspring with those that did not. Once the GRC originated in the last common ancestor of songbirds, members of that ancestral species that carried the GRC could produce fertile offspring only with mates that also had the GRC. As the GRC evolved, acquiring new genes, songbirds with a particular variant of GRC could produce fertile offspring only with mates that carried that same GRC variant.

理论上,GRC可以限制携带额外染色体的个体与不携带的个体进行杂交并孕育可育后代,通过这种方法新物种进化提供了所需的生殖隔离。一旦GRC起源和鸣禽来自相同的最终祖先,携带GRC的祖先物种之一只能与携带GRC的配偶杂交才能孕育可育后代。随着GRC的进化,该染色体会获得新的基因,带有特定GRC变体的鸣鸟只能与带有相同GRC变体的配偶孕育可育后代。

Engine of Change?

引擎的改变?

According to Borodin and Larkin, the discovery that GRC is widespread among songbirds and absent in other birds dovetails with the results of another recent study. In April, Carl Oliveros of Louisiana State University and his colleagues reported on the results of their analysis of DNA from dozens of members of the passerine order of birds, which comprises the songbirds and some other, far less speciose groups. Based on the DNA sequences and a handful of fossils of known age, the team reconstructed how the various passerine families were related and when they branched off. It then compared this time line of diversification against climate and geologic records to see if the passerine diversification trends correlated with events in Earth history, as predicted by some hypotheses. On the whole, fluctuations in the diversification rates of these birds did not track changes in global temperature or dispersals of the birds into new continents. The findings prompted the authors to suggest that more complex mechanisms than temperature or ecological opportunity were the main drivers of passerine speciation. “These conclusions are very much in line with our hypothesis of GRC contribution to songbird diversification,” Larkin asserts.

根据博罗丁和拉金的说法,GRC在鸣禽中广泛存在,而在其他鸟类中不存在,这一发现与最近另一项研究的结果相吻合。今年4月,路易斯安那州立大学的卡尔·奥里维罗斯(Carl Oliveros)和他的同事在一项研究报告中称,他们分析了几十种雀形目鸟类的DNA,包括鸣鸟和其他一些种类少得多的鸟类。基于DNA序列和已知的化石年龄,该研究团队对不同的雀形目家族之间的关系,以及它们分化为其他物种的时间进行了重建。然后,为了明确雀形目多样化的趋势是否如预测的那样,与过去发生在地球上的事件相关,他们将这条多样化的时间线与气候和地质记录进行了比较。总的来说,这些鸟类多样化率的波动并没有因为全球温度的变化或鸟类向新大陆的分散而发生变化。考虑到这些新发现,作者提出比温度或生态因素更复杂的机制是导致雀形目物种形成的关键因素。“这些结论非常符合我们关于GRC造成鸣鸟多样化的假设,”拉金断言。

Not everyone is ready to embrace the suggestion that GRC drove songbird diversification, however. “In general, it is hard to establish causation between any one given trait, like the presence of GRCs, and the evolutionary success of a particular group,” Oliveros says. “The presence of the trait could by chance have coincided with another trait—nesting behavior, for example—that may have played a larger role in a group's evolutionary success.”

然而,并非所有人都愿意接受GRC推动鸣鸟多样化的说法。奥利维罗斯说:“一般来说,很难就某个任意的具体特征(比如GRC的存在)和某一特定群体实现成功进化建立因果关系。”“这种特征的出现可能碰巧与另一种特征——例如,筑巢行为——同时发生,这可能在一个群体的进化过程中发挥了更大的作用。”

But other researchers not involved in the new studies find the notion intriguing. “The fact that [GRCs] have been maintained over long evolutionary periods and also contain putatively functional genes ... suggests that they could play a role in reproductive isolation in birds,” observes David Toews of Pennsylvania State University. If the sky-high diversification rate of songbirds compared with that of other birds was promoted by a genomic mechanism such as GRCs, “it would definitely be exciting and not something that I would have predicted,” Toews says. He cautions, though, that “we need to know more about what they are actually doing to make that link with confidence.”

但是其他没有参与新研究的研究人员发现这个概念很有趣。“事实上,(GRCs)在漫长的进化过程中没有出现变化,而且其中还含有假定功能基因……宾夕法尼亚州立大学的戴维·托沃斯说。托沃斯说,如果鸣禽与其他鸟类相比具有极高的多样化率是由诸如GRC这样的基因组机制推动的,“这固然是令人兴奋的新发现,而与我的预测相差甚远。”不过,他还警告“我们需要更多地了解他们实际上在做什么,才能将这种联系与信心相挂钩。”

The work could have implications for understanding organisms beyond birds. “We thought we knew a lot about how bird genomes are organized,” Suh reflects, “but the GRC has been right before our eyes yet has been overlooked.” Scientists have found similar extra chromosomes in hagfishes and some insects. What if GRCs are more widespread in the tree of life, he wonders: “The findings in songbirds open up a bunch of new directions for thinking about evolution and development.”

这项工作可能对了解鸟类以外的生物意义重大。“我们原以为我们对鸟类基因组的组织方式很了解,”苏赫反思道,“但我们却忽视了眼前的GRC(蕴含的巨大作用)。”科学家们在盲鳗和一些昆虫身上发现了类似的额外染色体。如果GRC在自然生命中的存在更为普遍,他想知道:“在鸣禽身上的发现是否为进化和发展的进一步研究指引了许多新方向。”

MORE TO EXPLORE

探究更多信息

Programmed DNA Elimination of Germline Development Genes in Songbirds. Cormac M. Kinsella et al. Posted to Biorxiv preprint server December 22, 2018. www.biorxiv.org/content/10.110¼44364v2

《鸣禽生殖系发育过程中的程序化DNA消除》。作者:Cormac M. Kinsella等人。发布于2018年12月22日。链接:www.biorxiv.org/content/10.110¼44364 v2

Germline-Restricted Chromosome Is Widespread among Songbirds. Anna Torgasheva et al. in Proceedings of the National Academy of Sciences USA, Vol. 116, No. 24, pages 11,845–11,850; June 11, 2019.

《受种系限制的染色体在鸣禽中的广泛分布》。作者:安娜·托尔加舍瓦等。发表期刊:《美国国家科学院院刊》,第116卷,第24期,第11845-11850页;发布于2019年6月11日。

FROM OUR ARCHIVES

出自档案记载

Taking Wing. Stephen Brusatte; January 2017.

《展翅的鸟儿》。作者:斯蒂芬·布鲁塞特;发布于2017年1月。

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