Molecular convergence at the sequence level: a genome-wide approach in a novel mammalian model

趋同进化是同一特征在不同生物群体中的独立起源。经典的例子包括脊椎动物的翅膀，它已经独立进化了很多次，例如蝙蝠、鸟类和翼龙，以及脊椎动物和一些无脊椎动物（如鱿鱼）类似的图像形成眼睛。事实上，相似的结构已经进化了好几次，这表明它们进化的功能相似，所以趋同进化是自然选择塑造了这些特征的有力证据——例如，毫无疑问，蝙蝠和鸟类的翅膀都是为了飞行而进化的。然而，尽管趋同的例子在生命之树中极为常见，但我们对趋同进化在基因水平上发生的程度知之甚少，在DNA序列和它们编码的蛋白质中。我们最近发现了几个例子，在不同的回声定位哺乳动物群体中，一套涉及听力的基因明显趋同。回声定位涉及声呐脉冲的产生和回波的处理，用于狩猎和定位，对高频听力提出了特殊的挑战。在蝙蝠和鲸的某些谱系中，这种能力表现得最为复杂。多年来，回声定位蝙蝠与果蝠是分开的；然而，我们解决物种关系的能力的进步提供了无可辩驳的证据，证明一些回声定位蝙蝠实际上与果蝠的关系比它们彼此之间的关系更密切。这一发现导致了对蝙蝠进化关系的修正；这就提出了一个问题，回声定位要么是被果蝠丢失了，要么是通过收敛进化了不止一次。我们研究了蝙蝠和鲸鱼的“听觉基因”，发现基于其中四个基因的进化树都将回声定位蝙蝠归为一个单一但技术上不正确的群体。更令人惊讶的是，其中一个基因导致了一群有回声定位海豚的蝙蝠。这些结果提出了一个有趣的可能性，即解剖学特征的趋同有时可能是由序列水平的趋同所支撑的。任何这种趋同的发现都是令人惊讶的，因为任何基因可能的序列数量都是天文数字。因此，这种情况不太可能偶然发生。据我们所知，在与特定性状相关的许多不同基因中识别趋同分子进化是前所未有的。我们的证据表明，分子趋同可能比目前怀疑的要普遍得多。这可能部分是因为很少有科学家一直在寻找这种趋同，也没有系统的尝试去调查它有多普遍。检测DNA或蛋白质序列收敛性的方法也相对较新。为了证实我们的发现，我们想要在整个基因组中寻找趋同序列，寻找在回声定位蝙蝠群体之间，在具有相似回声定位呼叫的蝙蝠之间，以及在蝙蝠和鲸鱼之间显示趋同的基因。如果在这个系统中趋同是普遍的，它将提高我们对回声定位的认识，例如通过识别可能涉及该系统的一些基因。更重要的是，如果在其他系统中得到证实，它将改变科学家对基因和蛋白质如何进化的看法，这表明进化可以采取的途径可能比以前认为的更受限制，因此，进化可能没有相对较少的好方法来塑造一种蛋白质来完成特定的工作。

Convergent evolution is the independent origin of the same feature in different groups of living things. Classic examples include the vertebrate wing, which has independently evolved a number of times, for example in bats, birds and pterosaurs, and the similar image-forming eyes of vertebrates and some invertebrates such as squid. The fact that similar structures have evolved several times suggests that they evolved to perform similar functions, so convergent evolution is powerful evidence that natural selection has shaped these features - there can be little doubt that bat and bird wings both evolved to allow powered flight, for example. Yet though examples of convergence are extremely common in the tree of life, we understand very little about the extent to which convergent evolution happens at the genetic level, in sequences of DNA and the proteins that they code for. We have recently identified several examples of apparent convergence in a suite of genes involved in hearing in different groups of echolocating mammal. Echolocation involves the production of sonar pulses and processing of the returning echoes for hunting and orientation, and poses particular challenges for high frequency hearing. It is seen at its most sophisticated in some lineages of bats and whales. For many years, echolocating bats were separated from fruit bats; however, advances in our ability to resolve species' relationships provided irrefutable evidence that some echolocating bats were in fact more related to the fruit bats than they were to each other. This finding has led to a revision of bat evolutionary relationships; so raising the issue that echolocation has either been lost by the fruit bats, or has evolved more than once by convergence. We have studied 'hearing genes' in bats and whales, and found that evolutionary trees based on four of these genes all unite echolocating bats into a single but technically incorrect group. Even more surprising, one of these genes leads to a well supported group of these bats with echolocating dolphins. These results raise the intriguing possibility that convergence in anatomical traits might sometimes be underpinned by convergence at the sequence level. Any finding of convergence of this kind is surprising, as the number of possible sequences for any gene is astronomically large. Therefore, such cases are unlikely to arise by chance. The identification of convergent molecular evolution in a number of different genes associated with a particular trait is, to our knowledge, unprecedented. Our evidence suggests that molecular convergence may be far more common than currently suspected. This may be partly because few scientists have been looking for this kind of convergence, and there has been no systematic attempt to investigate how common it might be. Methods to detect convergence in DNA or protein sequences are also relatively new. To confirm our finding, we want to search for convergent sequences across entire genomes, looking for genes that show convergence between the groups of echolocating bats, between bats that share similar echolocation calls, and also between bats and whales. If convergence is common in this system, it will advance our knowledge of echolocation, for example by identifying a number of genes probably involved in this system. More importantly, if confirmed in other systems, it will change the way scientists think about how genes and proteins evolve, suggesting that the pathways that evolution can take may be more constrained than previously thought, so that there may be relatively few good ways for evolution to fashion a protein to do a particular job.