Genome-wide signatures of convergent evolution in echolocating mammals

Genome-wide signatures of convergent evolution in echolocating mammals


Joe Parker, Georgia Tsagkogeorga, James A Cotton, Yuan Liu, Paolo Provero, Elia Stupka, Stephen J Rossiter

Nature (2013/10/10) 502(7470):228-231

Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes1, 2, 3. However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures4, 5. Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level6, 7, 8, 9. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution9, 10, although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.


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DOI: 10.1038/nature12511

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From Jack the Ripper to epidemiology and ecology

From Jack the Ripper to epidemiology and ecology


Steven C Le Comber, Mark D Stevenson

Trends in Ecology and Evolution (2012/4/9) 27(6):307

In many areas of biology – for example invasion biology, dispersal and epidemiology – understanding the ways in which animals, plants or pathogens spread outwards from a central source is of considerable interest. Models of these processes are both common and highly sophisticated [1], and can be used to generate risk maps in epidemiology, or to predict the effect of global climate change on the spread of invasive species. In all of these fields, though, much less attention is paid to models that run backwards in time, using …


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DOI: 10.1016/j.tree.2012.03.004

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The genome of the fire ant Solenopsis invicta

The genome of the fire ant Solenopsis invicta


Yannick Wurm, John Wang, Oksana Riba-Grognuz, Miguel Corona, Sanne Nygaard, Brendan G Hunt, Krista K Ingram, Laurent Falquet, Mingkwan Nipitwattanaphon, Dietrich Gotzek, Michiel B Dijkstra, Jan Oettler, Fabien Comtesse, Cheng-Jen Shih, Wen-Jer Wu, Chin-Cheng Yang, Jerome Thomas, Emmanuel Beaudoing, Sylvain Pradervand, Volker Flegel, Erin D Cook, Roberto Fabbretti, Heinz Stockinger, Li Long, William G Farmerie, Jane Oakey, Jacobus J Boomsma, Pekka Pamilo, Soojin V Yi, J�rgen Heinze, Michael AD Goodisman, Laurent Farinelli, Keith Harshman, Nicolas Hulo, Lorenzo Cerutti, Ioannis Xenarios, DeWayne Shoemaker, Laurent Keller

Proceedings of the National Academy of Sciences (2011/4/5) 108(14):5679

Ants have evolved very complex societies and are key ecosystem members. Some ants, such as the fire ant Solenopsis invicta, are also major pests. Here, we present a draft genome of S. invicta, assembled from Roche 454 and Illumina sequencing reads obtained from a focal haploid male and his brothers. We used comparative genomic methods to obtain insight into the unique features of the S. invicta genome. For example, we found that this genome harbors four adjacent copies of vitellogenin. A phylogenetic analysis …


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DOI: 10.1073/pnas.1009690108

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Cetaceans on a molecular fast track to ultrasonic hearing

Cetaceans on a molecular fast track to ultrasonic hearing


Yang Liu, Stephen J Rossiter, Xiuqun Han, James A Cotton, Shuyi Zhang

Current Biology (2010/10/26) 20(20):1834-1839

The early radiation of cetaceans coincides with the origin of their defining ecological and sensory differences [1, 2]. Toothed whales (Odontoceti) evolved echolocation for hunting 36-34 million years ago, whereas baleen whales (Mysticeti) evolved filter feeding and do not echolocate [2]. Echolocation in toothed whales demands exceptional high-frequency hearing [3], and both echolocation and ultrasonic hearing have also evolved independently in bats [4, 5]. The motor protein Prestin that drives the electromotility of the outer hair cells ( …


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Convergent sequence evolution between echolocating bats and dolphins

Convergent sequence evolution between echolocating bats and dolphins


Yang Liu, James A Cotton, Bin Shen, Xiuqun Han, Stephen J Rossiter, Shuyi Zhang

Current Biology (2010/1/26) 20(2):R53-R54

Cases of convergent evolution – where different lineages have evolved similar traits independently – are common and have proven central to our understanding of selection. Yet convincing examples of adaptive convergence at the sequence level are exceptionally rare [1]. The motor protein Prestin is expressed in mammalian outer hair cells (OHCs) and is thought to confer high frequency sensitivity and selectivity in the mammalian auditory system [2]. We previously reported that the Prestin gene has undergone sequence convergence …


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Contrasting evolutionary dynamics between angiosperm and mammalian genomes

Contrasting evolutionary dynamics between angiosperm and mammalian genomes


Eduard Kejnovsky, Ilia J Leitch, Andrew R Leitch

Trends in ecology & evolution (2009/10/31) 24(10):572-582

Continuing advances in genomics are revealing substantial differences between genomes of major eukaryotic lineages. Because most data (in terms of depth and phylogenetic breadth) are available for angiosperms and mammals, we explore differences between these groups and show that angiosperms have less highly compartmentalized and more diverse genomes than mammals. In considering the causes of these differences, four mechanisms are highlighted: polyploidy, recombination, retrotransposition and genome …


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The genetic code has a �shift�key

The genetic code has a �shift�key


SC Le Comber

Heredity (2009/4/22) 103(3):189-189

The genetic code has attracted the attention of scientists, including biologists, chemists, physicists and mathematicians for more than 40 years (Crick, 1968). Some of this work is among the most beautiful in all of biology – for example, Marshall Nirenberg’s early experiments using poly-U RNA in cell-free systems to show that the triplet UUU in an RNA transcript codes for the amino acid phenylalanine (Nirenberg and Matthaei, 1961). This is true even of ideas subsequently shown to be incorrect, such as the comma-free code …


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DOI: 10.1038/hdy.2009.40

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Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae)

Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae)


K Yoong Lim, Douglas E Soltis, Pamela S Soltis, Jennifer Tate, Roman Matyasek, Hana Srubarova, Ales Kovarik, J Chris Pires, Zhiyong Xiong, Andrew R Leitch

PLoS One (2008/10/9) 3(10):e3353

Background Polyploidy, frequently termed ‘whole genome duplication’, is a major force in the evolution of many eukaryotes. Indeed, most angiosperm species have undergone at least one round of polyploidy in their evolutionary history. Despite enormous progress in our understanding of many aspects of polyploidy, we essentially have no information about the role of chromosome divergence in the establishment of young polyploid populations. Here we investigate synthetic lines and natural populations of two recently and recurrently …


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The hearing gene Prestin reunites echolocating bats

The hearing gene Prestin reunites echolocating bats


Gang Li, Jinhong Wang, Stephen J Rossiter, Gareth Jones, James A Cotton, Shuyi Zhang

Proceedings of the National Academy of Sciences (2008/9/16) 105(37):13959

Abstract The remarkable high-frequency sensitivity and selectivity of the mammalian auditory system has been attributed to the evolution of mechanical amplification, in which sound waves are amplified by outer hair cells in the cochlea. This process is driven by the recently discovered protein prestin, encoded by the gene Prestin. Echolocating bats use ultrasound for orientation and hunting and possess the highest frequency hearing of all mammals. To test for the involvement of Prestin in the evolution of bat echolocation, we …


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