Genomic and functional evidence reveals molecular insights into the origin of echolocation in whales

Liu, Zhen; Qi, Fei-Yan; Xu, Dongming; Zhou, Xin; Shi, Peng

doi:10.1126/sciadv.aat8821

Cited by 27 publications

(40 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…通过对回声定位蝙蝠、齿鲸和其他哺乳动物中的Prestin蛋白的编码序列进行系统发育分析, 发现回声定位蝙蝠和齿鲸聚在一起, 表明两个类群的Prestin基因发生了趋同演化 [43,49] . Liu等人 [21,51] [22] 则将研究重点放在回声定位类群的发声器官, 通过对包含有回声定位系统的小棕蝠…”

Section: 回声定位系统是一类非常特殊的听觉机制生物unclassified

“…分子趋同的概念也从编码基因的氨基酸替换趋同扩展到基因丢失趋同、表达调控趋同、表达模式趋同、肠道微生物趋同等多个不同分子层级 [11,13] . 基于不同的研究概念、材料和目的, 分子趋同 [20] ; 利用16个哺乳动物基因组进行祖先序列重建, 回声定位蝙蝠祖先仅与齿鲸祖先的趋同基因显著富集到与听力相关的功能基因, 从分子趋同角度证实齿鲸回声定位特征的独立起源 [21] ; 对30个胎盘类哺乳动物基因组数据比较分析, 发现4个与骨骼肌纤维相关表达基因 (Casq1, Atp2a1, Myh2, Myl1)存在7个保守氨基酸位点的平行替换, 这些基因功能与回声定位类群中高频发声密切相关, 同时新发现三个与高频听力的相关基因(Strc, Tecta, Cabp2)存在平行替换事件 [22] 高海拔极端环境金丝猴属; 食肉目藏獒、藏土狗; 偶蹄目藏羚羊、牦牛;…”

unclassified

See 1 more Smart Citation

Recent progress in convergent molecular evolution of animals based on multi-omics studies

Yu¹,

Cheng²,

Wang³

2019

Sci. Sin.-Vitae

View full text Add to dashboard Cite

show abstract

Section: 回声定位系统是一类非常特殊的听觉机制生物unclassified

unclassified

Recent progress in convergent molecular evolution of animals based on multi-omics studies

Yu¹,

Cheng²,

Wang³

2019

Sci. Sin.-Vitae

View full text Add to dashboard Cite

show abstract

“…This is for instance attested by C4 metabolism in plants [3] and high-altitude adaptations in birds [4]. Traits requiring more advanced genetic rewiring are presumably less likely to evolve repeatedly, an example being echolocation in bats and cetaceans [5].…”

Section: Introductionmentioning

confidence: 99%

Recurrent sequence evolution after independent gene duplication

Dunk

Snel

2020

BMC Evol Biol

View full text Add to dashboard Cite

Background: Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results: We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions: The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

show abstract

“…Traits requiring more advanced genetic rewiring are less likely to evolve repeatedly. Echolocation still evolved independently in bats and cetaceans [5], probably because of its sizable benefit.…”

Section: Introductionmentioning

confidence: 99%

“…Here, recurrent substitutions are used as an umbrella for convergent and parallel substitutions. Bats and cetaceans have fixed a similar set of mutations with respect to their closest relatives during the emergence of echolocation [6,7,5].…”

Section: Introductionmentioning

confidence: 99%

Recurrent Sequence Evolution After Independent Gene Duplication

Dunk

Snel

2020

Preprint

View full text Add to dashboard Cite

Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Genome-wide assessment of recurrent substitutions has only been performed for orthologs. These studies have revealed that the pervasiveness of recurrent substitutions is for a large part explained by purifying selection. At any position in a protein, only a subset of amino acids is allowed, increasing the chance of the same substitution happening in different lineages. ResultsWe developed a framework that detects patterns of recurrent differentiation in paralogs across 90 divergent eukaryotic genomes. A skew in recurrent substitutions serves as a proxy for a recurrent trend in function. We find remarkable examples of recurrent sequence evolution after independent duplication, in some cases involving more than ten different lineages where duplicates show a similar differentiation. We reveal the implicated functional patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. ConclusionsThe presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. The present study uncovers a diverse set of families with recurrent sequence evolution and reveals trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

show abstract

Genomic and functional evidence reveals molecular insights into the origin of echolocation in whales

Abstract: Molecular evolutionary and experimental analyses reject the hypothesis of high-frequency hearing in the archaeocetes.

Cited by 27 publications

References 47 publications

Recent progress in convergent molecular evolution of animals based on multi-omics studies

Recent progress in convergent molecular evolution of animals based on multi-omics studies

Recurrent sequence evolution after independent gene duplication

Recurrent Sequence Evolution After Independent Gene Duplication

Contact Info

Product

Resources

About