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Dictyocoela microsporidia diversity and co-diversification with their host, a gammarid species complex (Crustacea, Amphipoda) with an old history of divergence and high endemic diversity. Dictyocoela 小孢子虫的多样性及其与宿主的共同多样性,宿主是一种具有古老分化历史和高度地方多样性的伽马类物种群(甲壳动物,两足纲)。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-11-11 DOI: 10.1186/s12862-020-01719-z
Adrien Quiles, Rémi A Wattier, Karolina Bacela-Spychalska, Michal Grabowski, Thierry Rigaud

Background: Although the processes of co-evolution between parasites and their hosts are well known, evidence of co-speciation remains scarce. Microsporidian intracellular parasites, due to intimate relationships with their hosts and mixed mode of transmission (horizontal but also vertical, from mother to offspring), may represent an interesting biological model for investigating co-speciation. Amphipod crustaceans, especially gammarids, are regular hosts of microsporidian parasites, in particular the Dictyocoela spp., which have so far been found limited to these amphipods and are known to use a vertical mode of transmission. The amphipod genus Gammarus has a diversification history spanning the last 50-60 Mya and an extensive cryptic diversity in most of the nominal species. Here, we investigated the degree of co-diversification between Dictyocoela and Gammarus balcanicus, an amphipod with high degrees of ancient cryptic diversification and lineage endemism, by examining the genetic diversity of these parasites over the entire geographic range of the host. We hypothesised that the strong host diversification and vertical transmission of Dictyocoela would promote co-diversification.

Results: Using the parasite SSU rDNA as a molecular marker, analyzing 2225 host specimens from 88 sites covering whole host range, we found 31 haplogroups of Dictyocoela, 30 of which were novel, belonging to four Dictyocoela species already known to infect other Gammarus spp. The relationships between Dictyocoela and gammarids is therefore ancient, with the speciation in parasites preceding those of the hosts. Each novel haplogroup was nevertheless specific to G. balcanicus, leaving the possibility for subsequent co-diversification process during host diversification. A Procrustean Approach to Co-phylogeny (PACo) analysis revealed that diversification of Dictyocoela was not random with respect to that of the host. We found high degrees of congruence between the diversification of G. balcanicus and that of Dictyocoela roeselum and D. muelleri. However, we also found some incongruences between host and Dictyocoela phylogenies, e.g. in D. duebenum, probably due to host shifts between different G. balcanicus cryptic lineages.

Conclusion: The evolutionary history of Dictyocoela and Gammarus balcanicus represents an example of an overall host-parasite co-diversification, including cases of host shifts.

背景:尽管寄生虫与其宿主之间的共同进化过程已广为人知,但有关共同物种形成的证据仍然很少。微孢子虫细胞内寄生虫与其宿主关系密切,而且具有混合传播方式(水平传播,也有垂直传播,从母体传播给后代),因此可能是研究同种异化的一个有趣的生物模型。两足类甲壳动物,特别是伽马类,是微孢子虫寄生虫的固定宿主,特别是 Dictyocoela spp.。片脚类动物(Gammarus)属的多样化历史可追溯到五六千万年前,大多数标称物种都具有广泛的隐性多样性。在这里,我们通过研究这些寄生虫在宿主整个地理范围内的遗传多样性,研究了Dictyocoela和巴卡尼克斯(Gammarus balcanicus)之间的共同多样性程度,巴卡尼克斯是一种具有高度古老隐性多样性和世系特有性的片脚类动物。我们假设,Dictyocoela强烈的宿主多样化和垂直传播将促进共同多样化:使用寄生虫 SSU rDNA 作为分子标记,分析了来自 88 个地点的 2225 份宿主标本,覆盖了整个宿主分布区,我们发现了 31 个 Dictyocoela 单倍群,其中 30 个是新发现的,属于 4 个已知会感染其他伽马类的 Dictyocoela 物种。尽管如此,每一个新的单倍群都是巴卡尼克斯蜚蠊所特有的,因此在宿主多样化的过程中还存在着共同多样化的可能性。共系统进化方法(PACo)分析表明,Dictyocoela 的分化与宿主的分化并不是随机的。我们发现 G. balcanicus 的多样化与 Dictyocoela roeselum 和 D. muelleri 的多样化高度一致。然而,我们也发现了宿主与 Dictyocoela 系统发育之间的一些不一致之处,例如在 D. duebenum 中,这可能是由于宿主在不同的 G. balcanicus 隐蔽世系之间发生了转移:结论:Dictyocoela 和巴尔卡尼氏沼虾的进化史是宿主与寄生虫共同多样化的一个实例,其中包括宿主转移的情况。
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引用次数: 0
Gene flow between diploid and tetraploid junipers - two contrasting evolutionary pathways in two Juniperus populations. 二倍体刺柏和四倍体刺柏之间的基因流动--两个刺柏种群中两种截然不同的进化途径。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-11-09 DOI: 10.1186/s12862-020-01688-3
Perla Farhat, Sonja Siljak-Yakovlev, Nicolas Valentin, Carlos Fabregat, Silvia Lopez-Udias, Carlos Salazar-Mendias, Joaquín Altarejos, Robert P Adams

Background: Gene flow and polyploidy have been found to be important in Juniperus evolution. However, little evidence has been published elucidating the association of both phenomena in juniper taxa in the wild. Two main areas were studied in Spain (Eastern Iberian Range and Sierra de Baza) with both diploid and tetraploid taxa present in sympatry. Gene flow and ploidy level were assessed for these taxa and the resulted offspring.

Results: Twenty-two allo-triploid hybrids between J. sabina var. sabina and J. thurifera were found in the Eastern Iberian Range population. However, in the Sierra de Baza population no triploids were found. Instead, 18 allo-tetraploid hybrids between two tetraploid taxa: J. sabina var. balkanensis and J. thurifera were discovered. High genetic diversity was exhibited among the tetraploid hybrids at Sierra de Baza, in contrast to the genetically identical triploid hybrids at the Eastern Iberian Range; this suggests meiotic difficulties within the triploid hybrids. In addition, unidirectional gene flow was observed in both studied areas.

Conclusion: Polyploidy and hybridization can be complementary partners in the evolution of Juniperus taxa in sympatric occurrences. Juniperus was shown to be an ideal coniferous model to study these two phenomena, independently or in concert.

背景:基因流和多倍体被认为在杜松进化过程中非常重要。然而,很少有证据能阐明这两种现象在野生杜松类群中的关联。我们对西班牙的两个主要地区(伊比利亚山脉东部和巴扎山脉)进行了研究,这些地区同时存在二倍体和四倍体类群。对这些分类群及其后代的基因流和倍性水平进行了评估:结果:在伊比利亚山脉东部种群中发现了 22 个 sabina J. var. sabina 和 thurifera J. 的异源三倍体杂交种。然而,在 Sierra de Baza 种群中没有发现三倍体。相反,在两个四倍体类群中发现了 18 个异源四倍体杂交种:Balkanensis 和 J. thurifera 之间的 18 个异源四倍体杂交种。Sierra de Baza 的四倍体杂交种之间表现出高度的遗传多样性,与东伊比利亚山脉基因相同的三倍体杂交种形成鲜明对比;这表明三倍体杂交种内部存在减数分裂困难。此外,在两个研究地区都观察到了单向基因流动:结论:多倍体和杂交在瞻博树类群的同域进化过程中是互补的。研究表明,瞻博树是研究这两种现象独立或协同作用的理想针叶树模型。
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引用次数: 0
Avian phenotypic convergence is subject to low genetic constraints based on genomic evidence. 根据基因组证据,鸟类表型趋同受到的遗传限制较小。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-11-07 DOI: 10.1186/s12862-020-01711-7
Yu-Chi Chen, Hao-Chih Kuo, Wen-Sui Lo, Chih-Ming Hung

Background: Phenotypic convergence between distinct species provides an opportunity to examine the predictability of genetic evolution. Unrelated species sharing genetic underpinnings for phenotypic convergence suggests strong genetic constraints, and thus high predictability of evolution. However, there is no clear big picture of the genomic constraints on convergent evolution. Genome-based phylogenies have confirmed many cases of phenotypic convergence in birds, making them a good system for examining genetic constraints in phenotypic convergence. In this study, we used hierarchical genomic approaches to estimate genetic constraints in three convergent avian traits: nocturnality, raptorial behavior and foot-propelled diving.

Results: Phylogeny-based hypothesis tests and positive selection tests were applied to compare 16 avian genomes, representing 14 orders, and identify genes with strong convergence signals. We found 43 adaptively convergent genes (ACGs) associated with the three phenotypic convergence cases and assessed genetic constraints in all three cases, from (amino acid) site mutations to genetic pathways. We found that the avian orders shared few site mutations in the ACGs that contributed to the convergent phenotypes, and that these ACGs were not enriched in any genetic pathways. In addition, different pairs of orders with convergent foot-propelled diving or raptorial behaviors shared few ACGs. We also found that closely related orders that shared foot-propelled diving behavior did not share more ACGs than did distinct orders, suggesting that convergence among these orders could not be explained by their initial genomic backgrounds.

Conclusions: Our analyses of three avian convergence events suggest low constraints for phenotypic convergence across multiple genetic levels, implying that genetic evolution is unpredictable at the phylogenetic level of avian order. Ours is one of first studies to apply hierarchical genomic examination to multiple avian convergent cases to assess the genetic constraints in life history trait evolution.

背景:不同物种之间的表型趋同为研究遗传进化的可预测性提供了机会。不相关的物种共享表型趋同的遗传基础,表明遗传约束很强,因此进化的可预测性很高。然而,基因组对趋同进化的制约还没有清晰的全貌。基于基因组的系统进化已经证实了许多鸟类表型趋同的案例,使其成为研究表型趋同中遗传约束的良好系统。在这项研究中,我们使用了分层基因组学方法来估计鸟类三个趋同性状的遗传限制因素:夜行性、猛禽行为和足推式潜水:结果:基于系统发育的假设检验和正选择检验被用于比较代表14个目16个鸟类基因组,并识别出具有强烈趋同信号的基因。我们发现了与三种表型趋同情况相关的 43 个适应性趋同基因(ACGs),并评估了所有三种情况下的遗传限制,包括(氨基酸)位点突变和遗传途径。我们发现,在导致表型趋同的 ACGs 中,禽类各目共享的位点突变很少,而且这些 ACGs 在任何遗传途径中都没有富集。此外,具有趋同的足推动潜水行为或猛禽行为的不同类群共享的 ACG 也很少。我们还发现,与不同的类群相比,具有相同足动力潜水行为的近缘类群并没有共享更多的 ACGs,这表明这些类群之间的趋同不能用它们最初的基因组背景来解释:我们对三个鸟类趋同事件的分析表明,在多个遗传水平上表型趋同的约束较低,这意味着在鸟类的系统发育水平上,遗传进化是不可预测的。我们的研究是首次将分级基因组检查应用于多个鸟类趋同案例以评估生活史性状进化中的遗传限制的研究之一。
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引用次数: 0
New insights into the genetic diversity of the stone crayfish: taxonomic and conservation implications. 石螯虾遗传多样性的新认识:分类和保护意义。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-11-06 DOI: 10.1186/s12862-020-01709-1
Leona Lovrenčić, Lena Bonassin, Ljudevit Luka Boštjančić, Martina Podnar, Mišel Jelić, Göran Klobučar, Martina Jaklič, Valentina Slavevska-Stamenković, Jelena Hinić, Ivana Maguire

Background: Austropotamobius torrentium is a freshwater crayfish species native to central and south-eastern Europe, with an intricate evolutionary history and the highest genetic diversity recorded in the northern-central Dinarides (NCD). Its populations are facing declines, both in number and size across its entire range. By extanding current knowledge on the genetic diversity of this species, we aim to assist conservation programmes. Multigene phylogenetic analyses were performed using different divergence time estimates based on mitochondrial and, for the first time, nuclear DNA markers on the largest data set analysed so far. In order to reassess taxonomic relationships within this species we applied several species delimitation methods and studied the meristic characters with the intention of finding features that would clearly separate stone crayfish belonging to different phylogroups.

Results: Our results confirmed the existence of high genetic diversity within A. torrentium, maintained in divergent phylogroups which have their own evolutionary dynamics. A new phylogroup in the Kordun region belonging to NCD has also been discovered. Due to the incongruence between implemented species delimitation approaches and the lack of any morphological characters conserved within lineages, we are of the opinion that phylogroups recovered on mitochondrial and nuclear DNA are cryptic subspecies and distinct evolutionary significant units.

Conclusions: Geographically and genetically isolated phylogroups represent the evolutionary legacy of A. torrentium and are highly relevant for conservation due to their evolutionary distinctiveness and restricted distribution.

背景:Austropotamobius torrentium是一种原产于欧洲中部和东南部的淡水小龙虾,具有复杂的进化历史,在Dinarides (NCD)中北部有最高的遗传多样性记录。它的种群数量和规模在整个范围内都面临着下降。通过扩大对该物种遗传多样性的现有知识,我们的目标是协助保护计划。多基因系统发育分析使用基于线粒体和核DNA标记的不同分化时间估计进行,这是迄今为止分析的最大数据集上的第一次。为了重新评价石螯虾的分类学关系,我们采用了几种物种划分方法,并对石螯虾的分生性状进行了研究,以期找到能够明确区分石螯虾属于不同种群的特征。结果:我们的研究结果证实了A. torrentium内部存在高度的遗传多样性,在不同的种群中保持着各自的进化动力。在Kordun地区还发现了一个属于非传染性疾病的新系统群。由于物种划分方法的不一致性和谱系内缺乏任何形态特征的保守性,我们认为在线粒体和核DNA上恢复的系统群是隐藏的亚种和独特的进化重要单位。结论:地理上和遗传上分离的种群代表了A. torrentium的进化遗产,由于它们的进化独特性和有限分布,它们与保护高度相关。
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引用次数: 21
Four myriapod relatives - but who are sisters? No end to debates on relationships among the four major myriapod subgroups. 四个多足动物亲戚——但谁是姐妹?关于四种主要多足亚群之间关系的争论没有结束。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-11-04 DOI: 10.1186/s12862-020-01699-0
Nikolaus U Szucsich, Daniela Bartel, Alexander Blanke, Alexander Böhm, Alexander Donath, Makiko Fukui, Simon Grove, Shanlin Liu, Oliver Macek, Ryuichiro Machida, Bernhard Misof, Yasutaka Nakagaki, Lars Podsiadlowski, Kaoru Sekiya, Shigekazu Tomizuka, Björn M Von Reumont, Robert M Waterhouse, Manfred Walzl, Guanliang Meng, Xin Zhou, Günther Pass, Karen Meusemann

Background: Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data.

Results: We generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda.

Conclusions: Our best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal.

背景:多足亚群中足足亚群、双足亚群、合足亚群和足足亚群之间的系统发育关系尚未得到明确的解决。第一个涵盖所有亚群的系统发育研究与形态学证据一致地解决了系统发育关系,但与大多数先前发表的基于不同分子数据的系统发育树存在冲突。外群体选择和长分支吸引效应被认为是这些不一致的可能解释。在这项研究中,我们通过使用转录组数据扩展多足类和外类群取样来解决这些问题。结果:我们获得了42种全节肢动物的转录组数据,包括所有4个多足亚群和额外的外群分类群。我们的分类群样本与已发表的转录组和基因组数据相补充,形成了覆盖59个物种的超基质。我们编制了两个数据集,第一个是每个物种基因的完整覆盖(292个单拷贝蛋白质编码基因),第二个是不太严格的覆盖(988个基因)。我们使用不同的数据类型、树推理和四重奏计算方法来推断多足类动物之间的系统发育关系。我们的结果明确支持单系的下颌目和多足目。我们的分析清楚地表明,对于单一的无根拓扑有很强的信号,但内部根的位置对外群的选择有敏感性。然而,我们观察到强有力的证据表明一个进化分支为保足纲+合足纲,以及一个进化分支为七足纲+双足纲。结论:我们的最佳四重奏拓扑结构与另一项系统基因组学研究支持的当前形态系统发生不一致。AU测试和四重奏映射拒绝四重奏拓扑与用形态特征推断的树一致。此外,四重奏映射表明,数据集中存在的混杂信号足以解释由形态特征导出的四重奏拓扑的弱信号。虽然外群体选择会影响结果,但我们的研究可以将可能的树缩小到单个四重奏拓扑的导数。对于高度争议的关系,我们建议应用一系列测试(AU和四重奏映射),因为这些测试的结果可以缩小可能的关系并排除混淆信号。
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引用次数: 12
Hidden paths to endless forms most wonderful: Complexity of bacterial motility shapes diversification of latent phenotypes. 通往无尽形式的隐藏路径最奇妙:细菌运动的复杂性塑造了潜在表型的多样化。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-11-04 DOI: 10.1186/s12862-020-01707-3
Olaya Rendueles, Gregory J Velicer

Background: Evolution in one selective environment often latently generates phenotypic change that is manifested only later in different environments, but the complexity of behavior important to fitness in the original environment might influence the character of such latent-phenotype evolution. Using Myxococcus xanthus, a bacterium possessing two motility systems differing in effectiveness on hard vs. soft surfaces, we test (i) whether and how evolution while swarming on one surface-the selective surface-latently alters motility on the alternative surface type and (ii) whether patterns of such latent-phenotype evolution depend on the complexity of ancestral motility, specific ancestral motility genotypes and/or the selective surface of evolution. We analysze an experiment in which populations established from three ancestral genotypes-one with both motility systems intact and two others with one system debilitated-evolved while swarming across either hard or soft agar in six evolutionary treatments. We then compare motility-phenotype patterns across selective vs. alternative surface types.

Results: Latent motility evolution was pervasive but varied in character as a function of the presence of one or two functional motility systems and, for some individual-treatment comparisons, the specific ancestral genotype and/or selective surface. Swarming rates on alternative vs. selective surfaces were positively correlated generally among populations with one functional motility system but not among those with two. This suggests that opportunities for pleiotropy and epistasis generated by increased genetic complexity underlying behavior can alter the character of latent-phenotype evolution. No tradeoff between motility performance across surface types was detected in the dual-system treatments, even after adaptation on a surface on which one motility system dominates strongly over the other in driving movement, but latent-phenotype evolution was instead idiosyncratic in these treatments. We further find that the magnitude of stochastic diversification at alternative-surface swarming among replicate populations greatly exceeded diversification of selective-surface swarming within some treatments and varied across treatments.

Conclusion: Collectively, our results suggest that increases in the genetic and mechanistic complexity of behavior can increase the complexity of latent-phenotype evolution outcomes and illustrate that diversification manifested during evolution in one environment can be augmented greatly by diversification of latent phenotypes manifested later.

背景:在一种选择性环境中的进化往往会潜在地产生表型变化,而这种变化只会在不同的环境中表现出来,但原始环境中对适应度很重要的行为的复杂性可能会影响这种潜在表型进化的特征。利用黄粘球菌(一种在硬、软表面上具有不同运动系统的细菌),我们测试了(i)在一个表面(选择性表面)聚集时的进化是否以及如何潜在地改变了另一个表面类型的运动,(ii)这种潜在表型进化的模式是否取决于祖先运动的复杂性,特定的祖先运动基因型和/或进化的选择性表面。我们分析了一项实验,在该实验中,由三种祖先基因型建立的种群-一种具有完整的运动系统,另两种具有一个系统衰弱-在六种进化处理中通过硬琼脂或软琼脂进行进化。然后,我们比较了选择性和可选表面类型的运动表型模式。结果:潜在运动进化是普遍存在的,但由于存在一个或两个功能性运动系统,并且在一些个体治疗比较中,特定的祖先基因型和/或选择性表面,其特征有所不同。在具有一个功能运动系统的种群中,选择性和选择性表面上的蜂群率普遍呈正相关,而在具有两个功能运动系统的种群中则不呈正相关。这表明,由潜在行为的遗传复杂性增加所产生的多效性和上位性的机会可以改变潜在表型进化的特征。在双系统处理中,没有检测到跨表面类型的运动性能之间的权衡,即使在一种运动系统在驱动运动方面强于另一种运动系统的表面适应之后,但潜在表型进化在这些处理中是特殊的。我们进一步发现,在重复种群中,交替表面群体的随机多样化程度在某些处理中大大超过了选择表面群体的多样化程度,并且在不同处理中有所不同。结论:总的来说,我们的研究结果表明,行为的遗传和机制复杂性的增加可以增加潜在表型进化结果的复杂性,并说明在一个环境中进化过程中表现出的多样性可以通过随后表现出的潜在表型多样化而大大增强。
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引用次数: 15
Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum. 43种植物C-repeat结合因子/脱水响应元件结合1 (CBF/DREB1)蛋白家族的进化历史及龙葵CBF/DREB1蛋白的特征
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-11-03 DOI: 10.1186/s12862-020-01710-8
Wan Li, Yue Chen, Minghui Ye, Haibin Lu, Dongdong Wang, Qin Chen

Background: Plants are easily affected by temperature variations, and high temperature (heat stress) and low temperature (cold stress) will lead to poor plant development and reduce crop yields. Therefore, it is very important to identify resistance genes for improving the ability of plants to resist heat stress or cold stress by using modern biotechnology. Members of the C-repeat binding factor/Dehydration responsive element-binding 1 (CBF/DREB1) protein family are related to the stress resistance of many plant species. These proteins affect the growth and development of plants and play vital roles during environmental stress (cold, heat, drought, salt, etc.). In this study, we identified CBF/DREB1 genes from 43 plant species (including algae, moss, ferns, gymnosperms, angiosperms) by using bioinformatic methods to clarify the characteristics of the CBF/DREB1 protein family members and their functions in potato under heat and cold stresses.

Results: In this study, we identified 292 CBF/DREB1 proteins from 43 plant species. However, no CBF/DREB1 protein was found in algae, moss, ferns, or gymnosperms; members of this protein family exist only in angiosperms. Phylogenetic analysis of all the CBF/DREB1 proteins revealed five independent groups. Among them, the genes of group I do not exist in eudicots and are found only in monocots, indicating that these genes have a special effect on monocots. The analysis of motifs, gene duplication events, and the expression data from the PGSC website revealed the gene structures, evolutionary relationships, and expression patterns of the CBF/DREB1 proteins. In addition, analysis of the transcript levels of the 8 CBF/DREB1 genes in potato (Solanum tuberosum) under low-temperature and high-temperature stresses showed that these genes were related to temperature stresses. In particular, the expression levels of StCBF3 and StCBF4 in the leaves, stems, and roots significantly increased under high-temperature conditions, which suggested that StCBF3 and StCBF4 may be closely related to heat tolerance in potato.

Conclusion: Overall, members of the CBF/DREB1 protein family exist only in angiosperms and plays an important role in the growth and development of plants. In addition, the CBF/DREB1 protein family is related to the heat and cold resistance of potato. Our research revealed the evolution of the CBF/DREB1 family, and is useful for studying the precise functions of the CBF/DREB1 proteins when the plants are developing and are under temperature stress.

背景:植物容易受到温度变化的影响,高温(热胁迫)和低温(冷胁迫)会导致植物发育不良,降低作物产量。因此,利用现代生物技术鉴定抗性基因对提高植物抗热胁迫或冷胁迫能力具有重要意义。C-repeat结合因子/脱水反应元件结合1 (CBF/DREB1)蛋白家族成员与许多植物物种的抗逆性有关。这些蛋白质影响植物的生长发育,在环境胁迫(冷、热、干旱、盐等)中发挥重要作用。本研究采用生物信息学方法,对43种植物(藻类、苔藓、蕨类、裸子植物、被子植物)的CBF/DREB1基因进行了鉴定,阐明了CBF/DREB1蛋白家族成员的特征及其在高温和低温胁迫下在马铃薯中的功能。结果:从43种植物中鉴定出292个CBF/DREB1蛋白。然而,在藻类、苔藓、蕨类植物或裸子植物中未发现CBF/DREB1蛋白;这种蛋白家族的成员只存在于被子植物中。所有CBF/DREB1蛋白的系统发育分析显示了五个独立的组。其中,I组基因不存在于单子房中,只存在于单子房中,说明这些基因对单子房有特殊作用。通过分析基序、基因重复事件和来自PGSC网站的表达数据,揭示了CBF/DREB1蛋白的基因结构、进化关系和表达模式。此外,对低温和高温胁迫下马铃薯(Solanum tuberosum) 8个CBF/DREB1基因的转录水平分析表明,这些基因与温度胁迫有关。特别是高温条件下,StCBF3和StCBF4在马铃薯叶、茎和根中的表达量显著增加,这表明StCBF3和StCBF4可能与马铃薯的耐热性密切相关。结论:总体而言,CBF/DREB1蛋白家族成员仅存在于被子植物中,并在植物的生长发育中发挥重要作用。此外,CBF/DREB1蛋白家族与马铃薯的耐热性和抗寒性有关。我们的研究揭示了CBF/DREB1家族的进化,为研究CBF/DREB1蛋白在植物发育和温度胁迫下的确切功能提供了有用的信息。
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引用次数: 19
Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago. 三刺鱼在日本群岛的多波淡水殖民。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-11-03 DOI: 10.1186/s12862-020-01713-5
Ryo Kakioka, Seiichi Mori, Tomoyuki Kokita, Takuya K Hosoki, Atsushi J Nagano, Asano Ishikawa, Manabu Kume, Atsushi Toyoda, Jun Kitano

Background: The three-spined stickleback (Gasterosteus aculeatus) is a remarkable system to study the genetic mechanisms underlying parallel evolution during the transition from marine to freshwater habitats. Although the majority of previous studies on the parallel evolution of sticklebacks have mainly focused on postglacial freshwater populations in the Pacific Northwest of North America and northern Europe, we recently use Japanese stickleback populations for investigating shared and unique features of adaptation and speciation between geographically distant populations. However, we currently lack a comprehensive phylogeny of the Japanese three-spined sticklebacks, despite the fact that a good phylogeny is essential for any evolutionary and ecological studies. Here, we conducted a phylogenomic analysis of the three-spined stickleback in the Japanese Archipelago.

Results: We found that freshwater colonization occurred in multiple waves, each of which may reflect different interglacial isolations. Some of the oldest freshwater populations from the central regions of the mainland of Japan (hariyo populations) were estimated to colonize freshwater approximately 170,000 years ago. The next wave of colonization likely occurred approximately 100,000 years ago. The inferred origins of several human-introduced populations showed that introduction occurred mainly from nearby habitats. We also found a new habitat of the three-spined stickleback sympatric with the Japan Sea stickleback (Gasterosteus nipponicus).

Conclusions: These Japanese stickleback systems differ from those in the Pacific Northwest of North America and northern Europe in terms of divergence time and history. Stickleback populations in the Japanese Archipelago offer valuable opportunities to study diverse evolutionary processes in historical and contemporary timescales.

背景:三棘棘鱼(Gasterosteus aculeatus)是研究从海洋生境向淡水生境过渡过程中平行进化的遗传机制的重要物种。尽管之前大多数关于棘鱼平行进化的研究主要集中在北美太平洋西北部和北欧的冰川后淡水种群,但我们最近使用日本棘鱼种群来调查地理上遥远种群之间的适应和物种形成的共同和独特特征。然而,我们目前缺乏一个全面的日本三刺鱼的系统发育,尽管一个好的系统发育对于任何进化和生态学研究都是必不可少的。在这里,我们对日本群岛的三棘棘鱼进行了系统基因组分析。结果:我们发现淡水定殖发生在多个波中,每个波可能反映不同的间冰期隔离。据估计,来自日本大陆中部地区的一些最古老的淡水种群(hariyo种群)在大约17万年前定居淡水。下一波殖民浪潮可能发生在大约10万年前。几个人类引进种群的推断起源表明,主要是从附近的栖息地引进的。我们还发现了与日本海棘鱼(Gasterosteus nipponicus)同属的三刺棘鱼的新栖息地。结论:日本棘鱼系统与北美太平洋西北和北欧的棘鱼系统在分化时间和历史上存在差异。日本群岛的棘鱼种群为研究历史和当代时间尺度上的不同进化过程提供了宝贵的机会。
{"title":"Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago.","authors":"Ryo Kakioka,&nbsp;Seiichi Mori,&nbsp;Tomoyuki Kokita,&nbsp;Takuya K Hosoki,&nbsp;Atsushi J Nagano,&nbsp;Asano Ishikawa,&nbsp;Manabu Kume,&nbsp;Atsushi Toyoda,&nbsp;Jun Kitano","doi":"10.1186/s12862-020-01713-5","DOIUrl":"https://doi.org/10.1186/s12862-020-01713-5","url":null,"abstract":"<p><strong>Background: </strong>The three-spined stickleback (Gasterosteus aculeatus) is a remarkable system to study the genetic mechanisms underlying parallel evolution during the transition from marine to freshwater habitats. Although the majority of previous studies on the parallel evolution of sticklebacks have mainly focused on postglacial freshwater populations in the Pacific Northwest of North America and northern Europe, we recently use Japanese stickleback populations for investigating shared and unique features of adaptation and speciation between geographically distant populations. However, we currently lack a comprehensive phylogeny of the Japanese three-spined sticklebacks, despite the fact that a good phylogeny is essential for any evolutionary and ecological studies. Here, we conducted a phylogenomic analysis of the three-spined stickleback in the Japanese Archipelago.</p><p><strong>Results: </strong>We found that freshwater colonization occurred in multiple waves, each of which may reflect different interglacial isolations. Some of the oldest freshwater populations from the central regions of the mainland of Japan (hariyo populations) were estimated to colonize freshwater approximately 170,000 years ago. The next wave of colonization likely occurred approximately 100,000 years ago. The inferred origins of several human-introduced populations showed that introduction occurred mainly from nearby habitats. We also found a new habitat of the three-spined stickleback sympatric with the Japan Sea stickleback (Gasterosteus nipponicus).</p><p><strong>Conclusions: </strong>These Japanese stickleback systems differ from those in the Pacific Northwest of North America and northern Europe in terms of divergence time and history. Stickleback populations in the Japanese Archipelago offer valuable opportunities to study diverse evolutionary processes in historical and contemporary timescales.</p>","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2020-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12862-020-01713-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38562935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly. Steganinae果蝇(双翅目:果蝇科)的系统基因组研究:强大的基因树异质性和单系性证据。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-11-02 DOI: 10.1186/s12862-020-01703-7
Guilherme Rezende Dias, Eduardo Guimarães Dupim, Thyago Vanderlinde, Beatriz Mello, Antonio Bernardo Carvalho

Background: The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous genes present in all species (> 1,000,000 bp). This dataset includes three genera that broke the monophyly of the subfamilies in previous works. To investigate possible biases introduced by small sample sizes and automatic gene annotation, we used the same methods to infer species trees from a set of 10 manually annotated genes that are commonly used in phylogenetics.

Results: Most of the 1,028 gene trees depicted Steganinae as paraphyletic with distinct topologies, but the most common topology depicted it as monophyletic (43.7% of the gene trees). Despite the high levels of gene tree heterogeneity observed, species tree inference in ASTRAL, in PhyloNet, and with the concatenation approach strongly supported the monophyly of both subfamilies for the 1,028-gene dataset. However, when using the concatenation approach to infer a species tree from the smaller set of 10 genes, we recovered Steganinae as a paraphyletic group. The pattern of gene tree heterogeneity was asymmetrical and thus could not be explained solely by incomplete lineage sorting (ILS).

Conclusions: Steganinae was clearly a monophyletic group in the dataset that we analyzed. In addition to ILS, gene tree discordance was possibly the result of introgression, suggesting complex branching processes during the early evolution of Drosophilidae with short speciation intervals and gene flow. Our study highlights the importance of genomic data in elucidating contentious phylogenetic relationships and suggests that phylogenetic inference for drosophilids based on small molecular datasets should be performed cautiously. Finally, we suggest an approach for the correction and cleaning of BUSCO-derived genomic datasets that will be useful to other researchers planning to use this tool for phylogenomic studies.

背景:果蝇科传统上分为两个亚科:果蝇科和隐蝇科。这种划分是基于形态特征,在大多数文献中,这两个亚科被认为是单系的,但一些分子系统发育表明Steganinae是副系的。为了验证这一假说,我们使用了8个果蝇科(3个剑蝇科和5个果蝇科)和2个剑蝇科(外群)物种的基因组序列,并基于所有物种(> 1,000,000 bp)中存在的1,028个同源基因数据集推断了该群体的系统发育。该数据集包括三个属,打破了以往工作中亚科的单一性。为了研究小样本量和自动基因注释可能带来的偏差,我们使用相同的方法从一组10个系统发育中常用的人工注释基因中推断物种树。结果:在1028个基因树中,大多数将Steganinae描述为具有不同拓扑结构的副葡萄系,但最常见的拓扑结构将其描述为单系(43.7%)。尽管观察到高水平的基因树异质性,但ASTRAL、PhyloNet和连接方法中的物种树推断强烈支持1,028个基因数据集中两个亚科的单系性。然而,当使用串联方法从较小的10个基因集推断物种树时,我们恢复了Steganinae作为一个副类群。基因树异质性的模式是不对称的,因此不能完全用不完全谱系分类(ILS)来解释。结论:在我们分析的数据集中,Steganinae显然是一个单系类群。除ILS外,基因树不一致可能是基因渗入的结果,表明果蝇在早期进化过程中存在复杂的分支过程,物种形成间隔短,基因流动频繁。我们的研究强调了基因组数据在阐明有争议的系统发育关系中的重要性,并表明基于小分子数据集的果蝇系统发育推断应谨慎进行。最后,我们提出了一种校正和清理busco衍生基因组数据集的方法,这将对其他计划使用该工具进行系统基因组学研究的研究人员有用。
{"title":"A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly.","authors":"Guilherme Rezende Dias,&nbsp;Eduardo Guimarães Dupim,&nbsp;Thyago Vanderlinde,&nbsp;Beatriz Mello,&nbsp;Antonio Bernardo Carvalho","doi":"10.1186/s12862-020-01703-7","DOIUrl":"https://doi.org/10.1186/s12862-020-01703-7","url":null,"abstract":"<p><strong>Background: </strong>The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous genes present in all species (> 1,000,000 bp). This dataset includes three genera that broke the monophyly of the subfamilies in previous works. To investigate possible biases introduced by small sample sizes and automatic gene annotation, we used the same methods to infer species trees from a set of 10 manually annotated genes that are commonly used in phylogenetics.</p><p><strong>Results: </strong>Most of the 1,028 gene trees depicted Steganinae as paraphyletic with distinct topologies, but the most common topology depicted it as monophyletic (43.7% of the gene trees). Despite the high levels of gene tree heterogeneity observed, species tree inference in ASTRAL, in PhyloNet, and with the concatenation approach strongly supported the monophyly of both subfamilies for the 1,028-gene dataset. However, when using the concatenation approach to infer a species tree from the smaller set of 10 genes, we recovered Steganinae as a paraphyletic group. The pattern of gene tree heterogeneity was asymmetrical and thus could not be explained solely by incomplete lineage sorting (ILS).</p><p><strong>Conclusions: </strong>Steganinae was clearly a monophyletic group in the dataset that we analyzed. In addition to ILS, gene tree discordance was possibly the result of introgression, suggesting complex branching processes during the early evolution of Drosophilidae with short speciation intervals and gene flow. Our study highlights the importance of genomic data in elucidating contentious phylogenetic relationships and suggests that phylogenetic inference for drosophilids based on small molecular datasets should be performed cautiously. Finally, we suggest an approach for the correction and cleaning of BUSCO-derived genomic datasets that will be useful to other researchers planning to use this tool for phylogenomic studies.</p>","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2020-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12862-020-01703-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38557779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
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 : 2020-10-31 DOI: 10.1186/s12862-020-01712-6
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.

背景: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。结论: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,&nbsp;Junli Yan","doi":"10.1186/s12862-020-01712-6","DOIUrl":"https://doi.org/10.1186/s12862-020-01712-6","url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2020-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12862-020-01712-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38550114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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