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Clonal evolution driven by superdriver mutations. 由超级驱动突变驱动的克隆进化。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-20 DOI: 10.1186/s12862-020-01647-y
Patrick Grossmann, Simona Cristea, Niko Beerenwinkel

Background: Tumors are widely recognized to progress through clonal evolution by sequentially acquiring selectively advantageous genetic alterations that significantly contribute to tumorigenesis and thus are termned drivers. Some cancer drivers, such as TP53 point mutation or EGFR copy number gain, provide exceptional fitness gains, which, in time, can be sufficient to trigger the onset of cancer with little or no contribution from additional genetic alterations. These key alterations are called superdrivers.

Results: In this study, we employ a Wright-Fisher model to study the interplay between drivers and superdrivers in tumor progression. We demonstrate that the resulting evolutionary dynamics follow global clonal expansions of superdrivers with periodic clonal expansions of drivers. We find that the waiting time to the accumulation of a set of superdrivers and drivers in the tumor cell population can be approximated by the sum of the individual waiting times.

Conclusions: Our results suggest that superdriver dynamics dominate over driver dynamics in tumorigenesis. Furthermore, our model allows studying the interplay between superdriver and driver mutations both empirically and theoretically.

背景:肿瘤被广泛认为是通过克隆进化,依次获得选择性有利的遗传改变,从而显著促进肿瘤的发生,因此被称为驱动因素。一些癌症驱动因素,如TP53点突变或EGFR拷贝数增加,提供了特殊的适应性增加,这在时间上足以触发癌症的发作,而很少或没有其他遗传改变的贡献。这些关键的变化被称为超级驱动程序。结果:在本研究中,我们采用Wright-Fisher模型来研究肿瘤进展中驱动因子和超级驱动因子之间的相互作用。我们证明了由此产生的进化动力学遵循超驱动器的全局克隆扩展和驱动器的周期性克隆扩展。我们发现肿瘤细胞群中一组超驱动因子和驱动因子累积的等待时间可以近似为个体等待时间的总和。结论:我们的研究结果表明,在肿瘤发生过程中,超级驱动动力学比驱动动力学起主导作用。此外,我们的模型允许从经验和理论上研究超级驱动程序和驱动程序突变之间的相互作用。
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引用次数: 4
Ancient DNA of northern China Hystricidae sub-fossils reveals the evolutionary history of old world porcupines in the Late Pleistocene. 中国北方豪猪亚化石的古DNA揭示了晚更新世旧大陆豪猪的进化史。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-18 DOI: 10.1186/s12862-020-01656-x
Guilian Sheng, Jiaming Hu, Haowen Tong, Bastien Llamas, Junxia Yuan, Xindong Hou, Shungang Chen, Bo Xiao, Xulong Lai

Background: Old World porcupines (Family: Hystricidae) are the third-largest rodents and inhabit southern Europe, Asia, and most regions of Africa. They are a typical indicator of warm climate and their distribution is restricted to tropical and subtropical zones. In China, porcupines are widely distributed in southern areas of the Yangtze River. However, fossil remains have been identified in a few sites in northern China, among which Tianyuan Cave-near Zhoukoudian site-represents the latest known porcupine fossil record. So far, studies have focused mainly on porcupines' husbandry and domestication but little is known about their intrafamilial phylogenetic relationships and evolutionary history.

Results: In this study, we sequence partial mitochondrial 12S rRNA and cyt b genes for seven Late Pleistocene porcupine individuals from Northern, Southern and Central China. Phylogenetic analyses show that the Tianyuan Cave porcupines, which had been morphologically identified as Hystrix subcristata, have a closer relationship to Hystrix brachyura.

Conclusion: Together with morphological adaptation characteristics, associated fauna, and climate change evidence, the molecular results reveal that a Late Quaternary extirpation has occurred during the evolutionary history of porcupines.

背景:东半球豪猪(豪猪科:豪猪科)是世界第三大啮齿类动物,栖息于欧洲南部、亚洲和非洲大部分地区。它们是温暖气候的典型标志,其分布仅限于热带和亚热带地区。在中国,豪猪广泛分布在长江以南地区。然而,在中国北方的一些遗址已经发现了化石遗迹,其中周口店遗址附近的天源洞代表了已知的最新豪猪化石记录。迄今为止,对豪猪的研究主要集中在豪猪的饲养和驯化方面,但对豪猪家族内的系统发育关系和进化历史知之甚少。结果:本研究对来自中国北部、南部和中部的7个晚更新世豪猪个体的部分线粒体12S rRNA和cyt b基因进行了测序。系统发育分析表明,天源洞豪猪与短尾豪猪亲缘关系较近,形态鉴定为下冠豪猪。结论:结合形态适应特征、相关区系和气候变化证据,分子生物学研究结果表明,豪猪在进化史上经历了一次晚第四纪灭绝。
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引用次数: 5
Expansions and contractions in gene families of independently-evolved blood-feeding insects. 独立进化的食血昆虫基因家族的扩张与收缩
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-17 DOI: 10.1186/s12862-020-01650-3
Lucas Freitas, Mariana F Nery

Background: The blood-feeding behavior evolved multiple times in Insecta lineages and it represents an excellent opportunity to study patterns of convergent molecular evolution regarding this habit. In insects the expansion of some gene families is linked with blood-feeding behavior, but a wide study comparing the evolution of these gene families among different lineages is still missing. Here we gathered genomic data from six independently-evolved hematophagous lineages, aiming to identify convergent expansions and/or contractions of gene families in hematophagous lineages of insects.

Results: We found four rapidly evolving gene families shared by at least two hematophagous independently-evolved lineages, including a heat-shock and a chemosensory protein. On the expression of these four rapidly evolving gene families we found more genes expressed in mated individuals compared with virgin individuals in rapidly-expanded families and more genes expressed in non-blood-feeding individuals compared with blood-feeding individuals in rapidly-contracted families.

Conclusion: Our results reveal a new set of candidate genes to be explored in further analysis to help the development of new strategies to deal with blood-feeding vectors and also presents a new perspective to study the evolution of hematophagy identifying convergent molecular patterns.

背景:吸血行为在昆虫系中经历了多次进化,这是研究这一习性的趋同分子进化模式的绝佳机会。在昆虫中,一些基因家族的扩展与吸血行为有关,但目前仍缺乏对这些基因家族在不同品系间的进化进行比较的广泛研究。在此,我们收集了六个独立进化的食血系的基因组数据,旨在确定昆虫食血系中基因家族的趋同性扩张和/或收缩:结果:我们发现至少两个独立进化的噬血系共有四个快速进化的基因家族,包括一个热休克蛋白和一个化学感应蛋白。在这四个快速进化基因家族的表达方面,我们发现在快速扩展的家族中,交配个体比处女个体表达更多的基因;在快速收缩的家族中,非吸血个体比吸血个体表达更多的基因:我们的研究结果揭示了一组新的候选基因,有待进一步分析探讨,以帮助开发新的策略来对付噬血媒介,同时也为研究噬血进化提供了一个新的视角,以识别趋同的分子模式。
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引用次数: 0
Assessing the utility of Hsp90 gene for inferring evolutionary relationships within the ciliate subclass Hypotricha (Protista, Ciliophora). 评估Hsp90基因在推断纤毛虫亚纲(原生动物,纤毛虫)进化关系中的效用。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-16 DOI: 10.1186/s12862-020-01653-0
Qi Zhang, Jiahui Xu, Alan Warren, Ran Yang, Zhuo Shen, Zhenzhen Yi

Background: Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-shock protein 90 gene (Hsp90) as a marker for inferring phylogenetic relationships among hypotrich ciliates.

Results: A total of 87 novel Hsp90 gene sequences of 10 hypotrich species were generated. Of these, 85 were distinct sequences. Phylogenetic analyses based on these data showed that: (1) the Hsp90 gene amino acid trees are comparable to the small subunit rDNA tree for recovering phylogenetic relationships at the rank of class, but lack sufficient phylogenetic signal for inferring evolutionary relationships at the genus level; (2) Hsp90 gene paralogs are recent and therefore unlikely to pose a significant problem for recovering hypotrich clades; (3) definitions of some hypotrich orders and families need to be revised as their monophylies are not supported by various gene markers; (4) The order Sporadotrichida is paraphyletic, but the monophyly of the "core" Urostylida is supported; (5) both the subfamily Oxytrichinae and the genus Urosoma seem to be non-monophyletic, but monophyly of Urosoma is not rejected by AU tests.

Conclusions: Our results for the first time demonstrate that the Hsp90 gene is comparable to SSU rDNA for recovering phylogenetic relationships at the rank of class, and its paralogs are unlikely to pose a significant problem for recovering hypotrich clades. This study shows the value of careful gene marker selection for phylogenomic analyses of ciliates.

背景:尽管系统基因组学分析越来越多地用于揭示纤毛虫之间的进化关系,但相对较少的核蛋白编码基因标记已被测试用于推断该类群的系统发生。在这项研究中,我们研究了热休克蛋白90基因(Hsp90)作为推断低营养纤毛虫之间系统发育关系的标记的效用。结果:共获得10个欠营养种的87条Hsp90新基因序列。其中85个是不同的序列。基于这些数据的系统发育分析表明:(1)Hsp90基因氨基酸树在恢复类级的系统发育关系方面与小亚基rDNA树相当,但在推断属级的进化关系方面缺乏足够的系统发育信号;(2) Hsp90基因同源物是最近发现的,因此不太可能对恢复低营养枝构成重大问题;(3)由于某些亚富目和科的单系性没有得到各种基因标记的支持,需要重新定义;(4)散柄虫目为副虫目,但“核心”尿柄虫目的单系性得到支持;(5)木刺虫亚科和尿瘤属似乎都是非单系的,但尿瘤的单系性并没有被AU测试所拒绝。结论:我们的研究结果首次证明了Hsp90基因与SSU rDNA在恢复类级系统发育关系方面具有可比性,其相似物不太可能对恢复低营养进化支构成重大问题。本研究显示了精心选择基因标记对纤毛虫系统基因组分析的价值。
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引用次数: 0
Directional divergence of Ep300 duplicates in teleosts and its implications 硬骨鱼Ep300复制体的定向分化及其意义
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-15 DOI: 10.21203/rs.3.rs-42120/v1
Xianzong Wang, Junli Yan
Background EP300 is a conserved protein in vertebrates, which serves as a key mediator of cellular homeostasis. Mutations and dysregulation of EP300 give rise to severe human developmental disorders and malignancy. Danio rerio is a promising model organism to study EP300 related diseases and drugs; however, the effect of EP300 duplicates derived from teleost-specific whole genome duplication should not just be neglected. Results In this study, we obtained EP300 protein sequences of representative teleosts, mammals and sauropsids, with which we inferred a highly supported maximum likelihood tree. We observed that Ep300 duplicates (Ep300a and Ep300b) were widely retained in teleosts and universally expressed in a variety of tissues. Consensus sequences of Ep300a and Ep300b had exactly the same distribution of conserved domains, suggesting that their functions should still be largely overlapped. We analyzed the molecular evolution of Ep300 duplicates in teleosts, using branch-site models, clade models and site models. The results showed that both duplicates were subject to strong positive selection; however, for an extant species, generally at most one copy was under positive selection. At the clade level, there were evident positive correlations between evolutionary rates, the number of positively selected sites and gene expression levels. In Ostariophysi, Ep300a were under stronger positive selection than Ep300b; in Neoteleostei, another species-rich teleost clade, the contrary was the case. We also modeled 3D structures of zf-TAZ domain and its flanking regions of Ep300a and Ep300b of D. rerio and Oryzias latipes and found that in either species the faster evolving copy had more short helixes. Conclusions Collectively, the two copies of Ep300 have undoubtedly experienced directional divergence in main teleost clades. The divergence of EP300 between teleosts and mammals should be greater than the divergence between different teleost clades. Further studies are needed to clarify to what extent the EP300 involved regulatory network has diverged between teleosts and mammals, which would also help explain the huge success of teleosts.
EP300是脊椎动物中的一种保守蛋白,在细胞稳态中起着重要的调节作用。EP300的突变和失调导致严重的人类发育障碍和恶性肿瘤。瘤胃瘤胃是研究EP300相关疾病和药物的良好模式生物;然而,来自硬骨鱼特异性全基因组复制的EP300副本的影响不应被忽视。结果本研究获得了具有代表性的硬骨鱼、哺乳动物和蜥脚类动物的EP300蛋白序列,并推断出高度支持的最大似然树。我们观察到Ep300重复序列(Ep300a和Ep300b)在硬骨鱼中广泛保留,并在多种组织中普遍表达。Ep300a和Ep300b的共识序列保守结构域分布完全相同,表明它们的功能仍有很大的重叠。采用分支位点模型、进化枝模型和位点模型分析了硬骨鱼Ep300重复序列的分子进化。结果表明,这两个重复都受到强阳性选择的影响;然而,对于一个现存物种来说,通常最多有一个拷贝处于正选择状态。在支系水平上,进化速率、正选择位点数量与基因表达水平之间存在显著正相关。在牡蛎中,Ep300a比Ep300b受到更强的正选择;在另一个种类丰富的硬骨鱼分支新硬骨鱼中,情况正好相反。我们还模拟了D. rerio和Oryzias latipes的Ep300a和Ep300b的zf-TAZ结构域及其侧翼区域的三维结构,发现在这两个物种中,更快进化的拷贝具有更多的短螺旋。总的来说,Ep300的两个拷贝在硬骨鱼的主要分支中无疑经历了方向性分化。EP300在硬骨鱼和哺乳动物之间的差异应该大于不同硬骨鱼支系之间的差异。需要进一步的研究来阐明EP300参与的调节网络在硬骨鱼和哺乳动物之间的差异程度,这也有助于解释硬骨鱼的巨大成功。
{"title":"Directional divergence of Ep300 duplicates in teleosts and its implications","authors":"Xianzong Wang, Junli Yan","doi":"10.21203/rs.3.rs-42120/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-42120/v1","url":null,"abstract":"Background EP300 is a conserved protein in vertebrates, which serves as a key mediator of cellular homeostasis. Mutations and dysregulation of EP300 give rise to severe human developmental disorders and malignancy. Danio rerio is a promising model organism to study EP300 related diseases and drugs; however, the effect of EP300 duplicates derived from teleost-specific whole genome duplication should not just be neglected. Results In this study, we obtained EP300 protein sequences of representative teleosts, mammals and sauropsids, with which we inferred a highly supported maximum likelihood tree. We observed that Ep300 duplicates (Ep300a and Ep300b) were widely retained in teleosts and universally expressed in a variety of tissues. Consensus sequences of Ep300a and Ep300b had exactly the same distribution of conserved domains, suggesting that their functions should still be largely overlapped. We analyzed the molecular evolution of Ep300 duplicates in teleosts, using branch-site models, clade models and site models. The results showed that both duplicates were subject to strong positive selection; however, for an extant species, generally at most one copy was under positive selection. At the clade level, there were evident positive correlations between evolutionary rates, the number of positively selected sites and gene expression levels. In Ostariophysi, Ep300a were under stronger positive selection than Ep300b; in Neoteleostei, another species-rich teleost clade, the contrary was the case. We also modeled 3D structures of zf-TAZ domain and its flanking regions of Ep300a and Ep300b of D. rerio and Oryzias latipes and found that in either species the faster evolving copy had more short helixes. Conclusions Collectively, the two copies of Ep300 have undoubtedly experienced directional divergence in main teleost clades. The divergence of EP300 between teleosts and mammals should be greater than the divergence between different teleost clades. Further studies are needed to clarify to what extent the EP300 involved regulatory network has diverged between teleosts and mammals, which would also help explain the huge success of teleosts.","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2020-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44159781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Investigating cellular and molecular mechanisms of neurogenesis in Capitella teleta sheds light on the ancestor of Annelida. 研究 Capitella teleta 神经发生的细胞和分子机制有助于了解无脊椎动物的祖先。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-14 DOI: 10.1186/s12862-020-01636-1
A Sur, A Renfro, P J Bergmann, N P Meyer

Background: Diverse architectures of nervous systems (NSs) such as a plexus in cnidarians or a more centralized nervous system (CNS) in insects and vertebrates are present across Metazoa, but it is unclear what selection pressures drove evolution and diversification of NSs. One underlying aspect of this diversity lies in the cellular and molecular mechanisms driving neurogenesis, i.e. generation of neurons from neural precursor cells (NPCs). In cnidarians, vertebrates, and arthropods, homologs of SoxB and bHLH proneural genes control different steps of neurogenesis, suggesting that some neurogenic mechanisms may be conserved. However, data are lacking for spiralian taxa.

Results: To that end, we characterized NPCs and their daughters at different stages of neurogenesis in the spiralian annelid Capitella teleta. We assessed cellular division patterns in the neuroectoderm using static and pulse-chase labeling with thymidine analogs (EdU and BrdU), which enabled identification of NPCs that underwent multiple rounds of division. Actively-dividing brain NPCs were found to be apically-localized, whereas actively-dividing NPCs for the ventral nerve cord (VNC) were found apically, basally, and closer to the ventral midline. We used lineage tracing to characterize the changing boundary of the trunk neuroectoderm. Finally, to start to generate a genetic hierarchy, we performed double-fluorescent in-situ hybridization (FISH) and single-FISH plus EdU labeling for neurogenic gene homologs. In the brain and VNC, Ct-soxB1 and Ct-neurogenin were expressed in a large proportion of apically-localized, EdU+ NPCs. In contrast, Ct-ash1 was expressed in a small subset of apically-localized, EdU+ NPCs and subsurface, EdU- cells, but not in Ct-neuroD+ or Ct-elav1+ cells, which also were subsurface.

Conclusions: Our data suggest a putative genetic hierarchy with Ct-soxB1 and Ct-neurogenin at the top, followed by Ct-ash1, then Ct-neuroD, and finally Ct-elav1. Comparison of our data with that from Platynereis dumerilii revealed expression of neurogenin homologs in proliferating NPCs in annelids, which appears different than the expression of vertebrate neurogenin homologs in cells that are exiting the cell cycle. Furthermore, differences between neurogenesis in the head versus trunk of C. teleta suggest that these two tissues may be independent developmental modules, possibly with differing evolutionary trajectories.

背景:神经系统(NSs)的结构多种多样,如网虫的神经丛或昆虫和脊椎动物的更中枢化的神经系统(CNS),这些结构存在于整个后生动物中,但目前还不清楚是什么选择压力推动了神经系统的进化和多样化。这种多样性的一个基本方面在于驱动神经发生(即从神经前体细胞生成神经元)的细胞和分子机制。在刺胞动物、脊椎动物和节肢动物中,SoxB 和 bHLH proneural 基因的同源物控制着神经发生的不同步骤,这表明某些神经发生机制可能是保守的。然而,目前还缺乏螺旋类群的相关数据:为此,我们描述了螺旋纲环带动物 Capitella teleta 在神经发生不同阶段的 NPCs 及其子代的特征。我们使用胸腺嘧啶类似物(EdU和BrdU)进行静态和脉冲追逐标记,评估了神经外胚层的细胞分裂模式,从而确定了经历多轮分裂的NPCs。发现活跃分裂的脑NPC位于顶部,而活跃分裂的腹侧神经索(VNC)NPC位于顶部、基部和更靠近腹侧中线的位置。我们利用系谱追踪来描述躯干神经外胚层边界变化的特征。最后,为了开始建立遗传层次结构,我们进行了双荧光原位杂交(FISH)和单荧光原位杂交加EdU标记,以寻找神经源基因同源物。在大脑和 VNC 中,Ct-soxB1 和 Ct-neurogenin 在大量顶部定位、EdU+的 NPC 中表达。相反,Ct-ash1在一小部分顶部定位、EdU+的NPC和表面下、EdU-的细胞中表达,但不在Ct-neuroD+或Ct-elav1+细胞中表达,这些细胞也是表面下细胞:我们的数据表明,Ct-soxB1和Ct-neurogenin是一个假定的遗传层次,其次是Ct-ash1,然后是Ct-neuroD,最后是Ct-elav1。 将我们的数据与Platynereis dumerilii的数据进行比较,发现环纹类动物增殖的NPC中有神经原蛋白同源物的表达,这似乎与脊椎动物神经原蛋白同源物在退出细胞周期的细胞中的表达不同。此外,C. teleta头部与躯干神经发生的差异表明,这两个组织可能是独立的发育模块,可能具有不同的进化轨迹。
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引用次数: 0
Molecular evolution of the ATP-binding cassette subfamily G member 2 gene subfamily and its paralogs in birds. 鸟类atp结合盒亚家族G成员2基因亚家族及其类似物的分子进化。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-14 DOI: 10.1186/s12862-020-01654-z
Shengchao Ma, Hehe Liu, Wenqiang Sun, Ahsan Mustafa, Yang Xi, Fajun Pu, Yanying Li, Chunchun Han, Lili Bai, He Hua

Background: ATP-binding cassette (ABC) transporters are involved in the active transportation of various endogenous or exogenous substances. Two ABCG2 gene subfamily members have been identified in birds. A detailed comparative study of the ABCG2 and ABCG2-like genes aid our understanding of their evolutionary history at the molecular level and provide a theoretical reference for studying the specific functions of ABCG2 and ABCG2-like genes in birds.

Results: We first identified 77 ABCG2/ABCG2-like gene sequences in the genomes of 41 birds. Further analysis showed that both the nucleic acid and amino acid sequences of ABCG2 and ABCG2-like genes were highly conserved and exhibited high homology in birds. However, significant differences in the N-terminal structure were found between the ABCG2 and ABCG2-like amino acid sequences. A selective pressure analysis showed that the ABCG2 and ABCG2-like genes were affected by purifying selection during the process of bird evolution.

Conclusions: We believe that multiple members of the ABCG2 gene subfamily exist on chromosome 4 in the ancestors of birds. Over the long course of evolution, only the ABCG2 gene was retained on chromosome 4 in birds. The ABCG2-like gene on chromosome 6 might have originated from chromosome replication or fusion. The structural differences between the N terminus of ABCG2 protein and those of ABCG2-like proteins might lead to functional differences between the corresponding genes.

背景:atp结合盒(ABC)转运体参与多种内源性或外源性物质的主动运输。在鸟类中已鉴定出两个ABCG2基因亚家族成员。对ABCG2和ABCG2样基因进行详细的比较研究,有助于我们在分子水平上了解它们的进化史,并为研究ABCG2和ABCG2样基因在鸟类中的具体功能提供理论参考。结果:首次在41只鸟类基因组中鉴定出77个ABCG2/ABCG2样基因序列。进一步分析表明,ABCG2和ABCG2样基因的核酸和氨基酸序列在鸟类中高度保守,具有高度同源性。然而,ABCG2和ABCG2样氨基酸序列的n端结构存在显著差异。选择压力分析表明,ABCG2和ABCG2样基因在鸟类进化过程中受到纯化选择的影响。结论:我们认为鸟类祖先的4号染色体上存在多个ABCG2基因亚家族成员。在漫长的进化过程中,鸟类的4号染色体上只保留了ABCG2基因。6号染色体上的abcg2样基因可能起源于染色体复制或融合。ABCG2蛋白N端与ABCG2样蛋白N端结构上的差异可能导致相应基因功能上的差异。
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引用次数: 2
Genetic legacy of cultures indigenous to the Northeast Asian coast in mitochondrial genomes of nearly extinct maritime tribes. 几乎灭绝的海上部落线粒体基因组中东北亚海岸土著文化的遗传遗产。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-13 DOI: 10.1186/s12862-020-01652-1
Stanislav V Dryomov, Elena B Starikovskaya, Azhar M Nazhmidenova, Igor V Morozov, Rem I Sukernik

Background: We have described the diversity of complete mtDNA sequences from 'relic' groups of the Russian Far East, primarily the Nivkhi (who speak a language isolate with no clear relatedness to any others) and Oroki of Sakhalin, as well as the sedentary Koryak from Kamchatka and the Udegey of Primorye. Previous studies have shown that most of their traditional territory was dramatically reshaped by the expansion of Tungusic-speaking groups.

Results: Overall, 285 complete mitochondrial sequences were selected for phylogenetic analyses of published, revised and new mitogenomes. To highlight the likely role of Neolithic expansions in shaping the phylogeographical landscape of the Russian Far East, we focus on the major East Eurasian maternal lineages (Y1a, G1b, D4m2, D4e5, M7a2, and N9b) that are restricted to the coastal area. To obtain more insight into autochthonous populations, we removed from the phylogeographic analysis the G2a, G3a2, M8a1, M9a1, and C4b1 lineages, also found within our samples, likely resulting from admixture between the expanding proto-Tungus and the indigenous Paleoasiatic groups with whom they assimilated. Phylogenetic analysis reveals that unlike the relatively diverse lineage spectrum observed in the Amur estuary and northwestern Sakhalin, the present-day subpopulation on the northeastern coast of the island is relatively homogenous: a sole Y1a sublineage, conspicuous for its nodal mutation at m.16189 T > C!, includes different haplotypes. Sharing of the Y1a-m.16189 T > C! sublineages and haplotypes among the Nivkhi, Ulchi and sedentary Koryak is also evident. Aside from Y1a, the entire tree approach expands our understanding of the evolutionary history of haplogroups G1, D4m, N9b, and M7a2. Specifically, we identified the novel haplogroup N9b1 in Primorye, which implies a link between a component of the Udegey ancestry and the Hokkaido Jomon.

Conclusions: Through a comprehensive dataset of mitochondrial genomes retained in autochthonous populations along the coast between Primorye and the Bering Strait, we considerably extended the sequence diversity of these populations to provide new features based on the number and timing of founding lineages. We emphasize the value of integrating genealogical information with genetic data for reconstructing the population history of indigenous groups dramatically impacted by twentieth century resettlement and social upheavals.

背景:我们已经描述了来自俄罗斯远东地区“遗迹”群体的完整mtDNA序列的多样性,主要是Nivkhi(他们说一种与任何其他人没有明确关系的孤立语言)和库页岛的Oroki,以及来自堪察加半岛的定居Koryak和滨海边疆区的Udegey。先前的研究表明,通古斯语群体的扩张极大地改变了他们的大部分传统领土。结果:总的来说,285个完整的线粒体序列被选择用于已发表的、修订的和新的有丝分裂基因组的系统发育分析。为了突出新石器时代扩张在塑造俄罗斯远东地区系统地理景观中的可能作用,我们将重点放在主要的东欧亚母系(Y1a, G1b, D4m2, D4e5, M7a2和N9b)上,这些母系仅限于沿海地区。为了更深入地了解土著群体,我们从系统地理分析中删除了在我们的样本中发现的G2a, G3a2, M8a1, M9a1和C4b1谱系,这些谱系可能是由扩张的原始通古斯人和他们同化的土著古亚洲群体之间的混合造成的。系统发育分析显示,与在阿穆尔河河口和库页岛西北部观察到的相对多样化的谱系谱不同,目前在该岛东北海岸的亚种群相对同质:一个单一的Y1a亚谱系,其在m.16189 T > C处的节点突变很明显!,包括不同的单体型。Y1a-m.16189 T > C的分享!Nivkhi, Ulchi和久坐的Koryak之间的亚谱系和单倍型也很明显。除了Y1a,整个树的方法扩展了我们对单倍群G1, D4m, N9b和M7a2的进化史的理解。具体来说,我们在滨海地区发现了新的单倍群N9b1,这意味着Udegey祖先的一个组成部分与北海道绳纹之间存在联系。结论:通过在滨海边疆区和白令海峡之间沿海地区的本土种群中保留的线粒体基因组的综合数据集,我们大大扩展了这些种群的序列多样性,并根据建立谱系的数量和时间提供了新的特征。我们强调整合家谱信息与遗传数据的价值,以重建受20世纪重新安置和社会动荡严重影响的土著群体的人口历史。
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引用次数: 4
Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea. 末次冰川极盛期导致巴布亚新几内亚高原山地鸣禽辐射的整个族群种群扩张。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-11 DOI: 10.1186/s12862-020-01646-z
Kritika M Garg, Balaji Chattopadhyay, Bonny Koane, Katerina Sam, Frank E Rheindt

Background: Quaternary climate fluctuations are an engine of biotic diversification. Global cooling cycles, such as the Last Glacial Maximum (LGM), are known to have fragmented the ranges of higher-latitude fauna and flora into smaller refugia, dramatically reducing species ranges. However, relatively less is known about the effects of cooling cycles on tropical biota.

Results: We analyzed thousands of genome-wide DNA markers across an assemblage of three closely related understorey-inhabiting scrubwrens (Sericornis and Aethomyias; Aves) from montane forest along an elevational gradient on Mt. Wilhelm, the highest mountain of Papua New Guinea. Despite species-specific differences in elevational preference, we found limited differentiation within each scrubwren species, but detected a strong genomic signature of simultaneous population expansions at 27-29 ka, coinciding with the onset of the LGM.

Conclusion: The remarkable synchronous timing of population expansions of all three species demonstrates the importance of global cooling cycles in expanding highland habitat. Global cooling cycles have likely had strongly different impacts on tropical montane areas versus boreal and temperate latitudes, leading to population expansions in the former and serious fragmentation in the latter.

背景:第四纪的气候波动是生物多样性的动力。众所周知,全球降温周期(如末次冰川极盛期)将高纬度动植物群的活动范围分割成更小的避难所,从而大大缩小了物种的分布范围。然而,人们对降温周期对热带生物群的影响了解相对较少:我们分析了巴布亚新几内亚最高峰威廉山(Mt. Wilhelm)海拔梯度上的山地森林中三种密切相关的林下栖息恙虫(Sericornis 和 Aethomyias; Aves)的数千个全基因组 DNA 标记。尽管在海拔偏好方面存在物种特异性差异,但我们在每个灌丛鹩莺物种内部都发现了有限的分化,但在 27-29 ka 期间发现了同步种群扩张的强烈基因组特征,这与 LGM 的开始时间相吻合:结论:所有三个物种种群扩张的显著同步时间表明了全球冷却周期在扩大高原栖息地方面的重要性。全球降温周期对热带高原地区与北方和温带纬度地区的影响可能截然不同,前者导致了种群扩张,后者则导致了严重的破碎化。
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引用次数: 0
Phylogenetic and spatial distribution of evolutionary diversification, isolation, and threat in turtles and crocodilians (non-avian archosauromorphs). 海龟和鳄目动物(非鸟类古蜥目)进化多样化、隔离和威胁的系统发育和空间分布。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-07-10 DOI: 10.1186/s12862-020-01642-3
Timothy J Colston, Pallavi Kulkarni, Walter Jetz, R Alexander Pyron

Background: The origin of turtles and crocodiles and their easily recognized body forms dates to the Triassic and Jurassic. Despite their long-term success, extant species diversity is low, and endangerment is extremely high compared to other terrestrial vertebrate groups, with ~ 65% of ~ 25 crocodilian and ~ 360 turtle species now threatened by exploitation and habitat loss. Here, we combine available molecular and morphological evidence with statistical and machine learning algorithms to present a phylogenetically informed, comprehensive assessment of diversification, threat status, and evolutionary distinctiveness of all extant species.

Results: In contrast to other terrestrial vertebrates and their own diversity in the fossil record, the recent extant lineages of turtles and crocodilians have not experienced any global mass extinctions or lineage-wide shifts in diversification rate or body-size evolution over time. We predict threat statuses for 114 as-yet unassessed or data-deficient species and identify a concentration of threatened turtles and crocodilians in South and Southeast Asia, western Africa, and the eastern Amazon. We find that unlike other terrestrial vertebrate groups, extinction risk increases with evolutionary distinctiveness: a disproportionate amount of phylogenetic diversity is concentrated in evolutionarily isolated, at-risk taxa, particularly those with small geographic ranges. Our findings highlight the important role of geographic determinants of extinction risk, particularly those resulting from anthropogenic habitat-disturbance, which affect species across body sizes and ecologies.

Conclusions: Extant turtles and crocodilians maintain unique, conserved morphologies which make them globally recognizable. Many species are threatened due to exploitation and global change. We use taxonomically complete, dated molecular phylogenies and various approaches to produce a comprehensive assessment of threat status and evolutionary distinctiveness of both groups. Neither group exhibits significant overall shifts in diversification rate or body-size evolution, or any signature of global mass extinctions in recent, extant lineages. However, the most evolutionarily distinct species tend to be the most threatened, and species richness and extinction risk are centered in areas of high anthropogenic disturbance, particularly South and Southeast Asia. Range size is the strongest predictor of threat, and a disproportionate amount of evolutionary diversity is at risk of imminent extinction.

背景:海龟和鳄鱼的起源以及它们容易辨认的身体形态可以追溯到三叠纪和侏罗纪。尽管它们取得了长期的成功,但与其他陆生脊椎动物群体相比,现存物种多样性很低,濒危程度极高,25种鳄鱼和360种海龟中有65%受到开发和栖息地丧失的威胁。在这里,我们将现有的分子和形态学证据与统计和机器学习算法结合起来,对所有现存物种的多样性、威胁状态和进化独特性进行了系统发育上的全面评估。结果:与化石记录中其他陆生脊椎动物及其自身的多样性相比,最近存在的海龟和鳄鱼谱系没有经历过任何全球大灭绝或谱系范围内多样化率或体型进化的变化。我们预测了114种尚未评估或缺乏数据的物种的威胁状况,并确定了南亚和东南亚、西非和亚马逊东部受威胁的海龟和鳄鱼的集中。我们发现,与其他陆生脊椎动物不同,灭绝风险随着进化独特性的增加而增加:不成比例的系统发育多样性集中在进化上孤立的、处于危险的分类群中,特别是那些地理范围小的分类群。我们的研究结果强调了灭绝风险的地理决定因素的重要作用,特别是那些由人为生境干扰引起的因素,这些因素影响着物种的体型和生态。结论:现存的海龟和鳄鱼保持着独特的、保守的形态,这使它们在全球范围内得到了识别。由于开发和全球变化,许多物种受到威胁。我们使用分类学上完整的、过时的分子系统发育和各种方法来对这两个群体的威胁状态和进化独特性进行全面评估。这两个群体都没有在多样化率或体型进化方面表现出显著的总体变化,也没有在最近现存的谱系中出现任何全球大灭绝的迹象。然而,进化上最独特的物种往往是最受威胁的,物种丰富度和灭绝风险集中在高人为干扰地区,特别是南亚和东南亚。范围大小是威胁的最强预测器,不成比例的进化多样性正面临即将灭绝的危险。
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引用次数: 31
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BMC Evolutionary Biology
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