molecular phylogenetics

分子系统发育学
  • 文章类型: Journal Article
    Connaraceae是一个大约200种的泛热带家族,其中包含藤本植物和小树,具有明显不同的花卉多态性。包括苦恼,琐碎的,友好地,还有Dioecy.迄今为止,家族内的关系尚未使用靶向分子系统发育治疗进行调查,严重限制了对性状进化的系统理解和重建。因此,他们最后的家族下分类仅基于形态学数据。这里,我们使用了使用Angiosperms353核靶序列捕获探针获得的系统基因组数据,对所有部落和几乎所有属进行抽样,完全来自植物标本室标本,修订家族下系分类,研究异型系的演变。所得到的分子系统发育树的骨架几乎完全被解析。仙人掌科由两个分支组成,一个仅包含非洲属Manotes(4或5种),我们在亚家族层面上新认识到的。建议为Manotoideae提供营养和生殖突触。在Connaroideae内,Connareae已扩展到包括前Jollydoreae。Cnestideae的骨干,其中包含了一半以上的孔雀科物种,仍然没有完全解决。提出了生殖系统进化的重建,初步支持作为家庭的祖先状态,有多个并行损失,与先前的假设一致,加上可能的重新收益。然而,样式多态性的多样性及其系统发育不稳定性排除了明确的答案。总的来说,这项研究加强了植物标本室系统基因组学的实用性,并解锁了Connaraceae的生殖多样性,作为复杂生物学现象进化的模型系统。
    在线版本包含补充材料,可在10.1007/s00606-024-01909-y获得。
    Connaraceae is a pantropical family of about 200 species containing lianas and small trees with remarkably diverse floral polymorphisms, including distyly, tristyly, homostyly, and dioecy. To date, relationships within the family have not been investigated using a targeted molecular phylogenetic treatment, severely limiting systematic understanding and reconstruction of trait evolution. Accordingly, their last infrafamilial classification was based only on morphological data. Here, we used phylogenomic data obtained using the Angiosperms353 nuclear target sequence capture probes, sampling all tribes and almost all genera, entirely from herbarium specimens, to revise infrafamilial classification and investigate the evolution of heterostyly. The backbone of the resulting molecular phylogenetic tree is almost entirely resolved. Connaraceae consists of two clades, one containing only the African genus Manotes (4 or 5 species), which we newly recognize at the subfamily level. Vegetative and reproductive synapomorphies are proposed for Manotoideae. Within Connaroideae, Connareae is expanded to include the former Jollydoreae. The backbone of Cnestideae, which contains more than half of the Connaraceae species, remains incompletely resolved. Reconstructions of reproductive system evolution are presented that tentatively support tristyly as the ancestral state for the family, with multiple parallel losses, in agreement with previous hypotheses, plus possible re-gains. However, the great diversity of stylar polymorphisms and their phylogenetic lability preclude a definitive answer. Overall, this study reinforces the usefulness of herbarium phylogenomics, and unlocks the reproductive diversity of Connaraceae as a model system for the evolution of complex biological phenomena.
    UNASSIGNED: The online version contains supplementary material available at 10.1007/s00606-024-01909-y.
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  • 文章类型: Journal Article
    CampanulaL.是高加索生态区特有数量最多的属之一。一组以高加索为中心的具有短单花茎的有吸引力的高山和亚高山多年生莲座丛植物被视为Campanulasubg。龙舌兰或其他等级,具有相当大的界限和分类。三个质体DNA区域的分子系统发育分析(trnK/matK,petaD,rpl16)的强扩展采样,由27个普遍接受的分类单元中的23个(85%)组成,其中330个物种建立在我们先前对该组的研究结果的基础上,并以此为指导,证实了C.subg的多样性。在其任何限制范围内的龙舌兰。该组的核心进化枝专门包括高加索地区的地方病和近地方病,在这里被视为C.sect。Tridentatae在修订的限制中。概述了Scapiflorae组其他不同元素的系统发育关系。
    Campanula L. is among the genera with the highest number of endemics in the Caucasus ecoregion. A group of attractive alpine and subalpine perennial rosette plants with short single-flowered stems centred in the Caucasus has been treated as Campanulasubg.Scapiflorae or at other ranks, with considerably varying circumscription and classification. Molecular phylogenetic analysis of three plastid DNA regions (trnK/matK, petD, rpl16) of a strongly extended sampling, comprising 23 of the 27 commonly accepted taxa (85%) with 330 accessions built on and guided by the results of our previous study of the group, confirmed the polyphyly of C.subg.Scapiflorae in any of its circumscriptions. The core clade of the group comprises exclusively endemics and near-endemics of the Caucasus and is treated here as C.sect.Tridentatae in a revised circumscription. The phylogenetic relationships of the disparate other elements of the Scapiflorae group are outlined.
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  • 文章类型: Journal Article
    浮游甲藻原甲藻在温暖和温带海域广泛分布。鉴定为P.cf.compressumBEA0681B从大加那利岛隔离,东北大西洋,显示rDNA/ITS系统发育相对于P.compressum的差异。加那利菌株是椭圆形的,平均长宽比为1.35,光滑的皮层表面,小于150个皮层孔,包括斜毛孔,有时有分叉的开口。相比之下,P.压缩更圆,长宽比<1.2,网状中心凹装饰,每个瓣膜有200-300个孔。我们提出了卡那利甲原。11月。这些物种聚集为进化枝中最早分支的谱系。虽然这个进化枝主要含有浮游物种,近亲是底栖动物P.tsawwassenense和P.elegans。有趣的是,P.压缩和P.canariensesp。11月。广泛分布在温带和温暖的海洋中,对浮游生命没有明显的形态适应。两个同心透明粘液壁的形成可能有助于这一成功。我们讨论了使用Proorocentrumbidens来解决P.compressum的命名问题,该问题以硅藻为同义词。
    The planktonic dinoflagellate Prorocentrum compressum is widespread in warm and temperate seas. A strain identified as P. cf. compressum BEA 0681B isolated from the island of Gran Canaria, NE Atlantic Ocean, showed a divergence in rDNA/ITS phylogenies with respect to P. compressum. The Canarian strain was oval, with an average length-to-width ratio of 1.35, smooth thecal surface with less than 150 thecal pores, including oblique pores, sometimes with a bifurcated opening. In contrast, P. compressum was rounder, with a length-to-width ratio < 1.2, with reticulate-foveate ornamentation and 200-300 pores per valve. We propose Prorocentrum canariense sp. nov. These species clustered as the most early-branching lineage in the clade Prorocentrum sensu stricto. Although this clade mainly contains planktonic species, the closer relatives were the benthic species P. tsawwassenense and P. elegans. Interestingly, P. compressum and P. canariense sp. nov. are widely distributed in temperate and warm seas without an apparent morphological adaptation to planktonic life. The formation of two concentric hyaline mucilaginous walls could contribute to this success. We discuss the use of Prorocentrum bidens to solve the nomenclature issue of P. compressum that was described citing a diatom as basionym.
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  • 文章类型: Journal Article
    双壳类动物是渔业和文物的重要资源。双壳类动物系统发育学有着悠久的传统,使用形态和分子特征,和基因组资源可用于许多商业上重要的物种。然而,双壳类动物家族之间的关系一直不稳定,有丝分裂基因组学和基于Sanger的扩增子测序或基因转录组学的结果之间存在重大冲突.在这里,我们设计并测试了Bivalvia类的超保守元件探针组,目的是使用数百个基因座,而无需对完整的基因组或转录组进行测序。分析起来既昂贵又复杂,并为博物馆标本打开双壳类动物系统发育学。我们的探针组成功捕获了1,513个UCE,总计263,800bp,每个UCE的平均长度为174.59±3.44(范围为28至842bp)。使用不同的数据矩阵和系统发育推断方法,在Bivalvia和Donacidae家族中对该UCE探针进行的系统发育测试在多个分类学水平上显示了有希望的结果。此外,我们的探头能够捕获1900年之前收集的博物馆标本的大量UCE。总的来说,这构成了双壳类动物系统发育的新的和有用的资源。
    Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.
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  • 文章类型: Journal Article
    一个新的抗病珊瑚家族,美洲科(Cnidaria:Anthozoa:Antipatharia),为美国拟真菌藻Opresko&Horowitz建立,gen.等sp.11月。就息肉和触手的形态以及珊瑚的羽状分支而言,该新科类似于Myripathidae和Stylopathidae。使用741个保守元件基因座的基因组数据集进行的系统发育分析表明,新家族是含有肌病科的进化枝的姐妹,Stylopathidae,抗病科,和阿班迪亚科。
    A new family of antipatharian corals, Ameripathidae (Cnidaria: Anthozoa: Antipatharia), is established for Ameripathespseudomyriophylla Opresko & Horowitz, gen. et sp. nov. The new family resembles Myriopathidae and Stylopathidae in terms of the morphology of the polyps and tentacles and the pinnulate branching of the corallum. Phylogenetic analysis using a genomic data set of 741 conserved element loci indicates that the new family is sister to a clade containing the Myriopathidae, Stylopathidae, Antipathidae, and Aphanipathidae.
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  • 文章类型: Journal Article
    我们报告了一种新的陆地蜗牛物种,代表了浙江山区的一个新属,中国。蜗牛有一个凹陷的壳,整个表面都有颗粒。新分类单元的柔软部分的特征是存在地幔叶,其形式在本文中对各种螺旋体蜗牛进行了回顾,有发育的上金属乳头,没有阴茎鞘,飞镖囊装置和鞭毛.如基于分子的系统发育(16S+ITS2)所示,新分类单元深深嵌套在东亚卡马尼德属中,与分布在华中地区的卡马尼德有密切关系。
    We report a new land snail species representing a new genus from the mountainous area of Zhejiang, China. The snail has a depressed shell with granules all over the surface. The soft part of the new taxon is characterized by the presence of a mantle lobe whose form is reviewed herein across a wide range of helicoid snails, the presence of a developed epiphallic papilla, and the absence of a penial sheath, a dart sac apparatus and a flagellum. As indicated by a molecular-based phylogeny (16S + ITS2), the new taxon is deeply nested in the eastern Asian camaenid genera and shows a close relationship with the camaenids distributed in Central China.
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  • 文章类型: Journal Article
    尽管是最普遍的水泡甲虫亚科,Nemognathinae在中国的研究不足。在这项研究中,一个新的属和物种,阴经,来自中国北方的描述和说明。天线,elytra,后翅,和新属的爪子形成了一组真正独特的特征,在NemognathiniLaportedeCastelnau的其他属中从未观察到,1840.新记录并说明了来自中国的三个物种:Megatrachelussibiricus(Tauscher,1812),Zonitomorphadollei(Fairmaire1889),和StenoderadjakonoviAksentjev,1978.OreomeloeTan属,1981年,从梅洛尼·吉伦哈尔部落转移过来,1910年,根据对类型的检查,对Nemognathini进行了检查。为了测试新属的基于形态学的位置,我们使用两个线粒体(COI,16S)和三个核标记(28S,CAD,ITS2)。结果证实了我们对新属的部落分配,并支持由Sinostenoriagen组成的进化枝。n.,LongizonitisPan和博洛尼亚,2018年,斯泰诺里亚参见。grandiceps,和Ctenopuscf.persicus.
    Despite being the most widespread blister beetle subfamily, Nemognathinae is unfairly understudied in China. In this study, a new genus and species, Sinostenoria yangi Pan, from northern China is described and illustrated. The antennae, elytra, hind wings, and claws of the new genus form a truly unique set of characteristics never observed in other genera of Nemognathini Laporte de Castelnau, 1840. Three species from China are newly recorded and illustrated: Megatrachelus sibiricus (Tauscher, 1812), Zonitomorpha dollei (Fairmaire 1889), and Stenodera djakonovi Aksentjev, 1978. The genus Oreomeloe Tan, 1981, is transferred from the tribe Meloini Gyllenhal, 1910, to Nemognathini based on an examination of the types. Aiming to test the morphology-based placement of the new genus, we conducted molecular phylogenetic analyses using two mitochondrial (COI, 16S) and three nuclear markers (28S, CAD, ITS2). The results confirm our tribal assignment of the new genus and support a clade that consists of Sinostenoriagen. n., Longizonitis Pan and Bologna, 2018, Stenoria cf. grandiceps, and Ctenopus cf. persicus.
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  • 文章类型: Journal Article
    Kgaria被描述为Boletaceae的一种新的类似卟啉的属,以适应Tylopiluscyanogranulifer,深棕色至暗淡的淡紫色/紫罗兰色,或者很少,几乎是黑色的bolete,一系列的氧化反应从蓝色到红色,然后几乎是黑色和深棕色的孢子沉积物。特殊的蓝绿色色素结壳(氰颗粒)和位于菌毛和柄表面的菌丝的类似颜色的反应也是诊断性的。核大亚基rDNA(nrLSU)的系统发育分析,平移延伸因子1-α(tef-1),RNA聚合酶II(rpb2)的第二大亚基推断Kgaria是具有两个物种的独特通用谱系,其中一个是新描述的(K.similis).橄榄Tylopilusolivaceporus,最初同时描述,与T.cyanogranulifer不同,似乎与后者有关。巴西最近描述了一些具有类似氧化反应的深色分类群,圭亚那,形态学和分子数据进一步支持了中国,它们是Boletoideae亚科不同属中的离散谱系。引文:HallingRE,FechnerNA,福尔摩斯G,达沃迪安N(2023年)。Kgaria(Boletaceae,Boletoideae)gen。11月。在澳大利亚:既不是Tylopilus也不是Porphyrellus。真菌系统学和进化12:31-45。doi:10.3114/fuse.2023.12.02。
    Kgaria is described as a new porphyrellus-like genus of Boletaceae to accommodate Tylopilus cyanogranulifer, a dark brown to dull lilac/violet, or rarely, nearly black bolete with a series of oxidation reactions progressing from blue to red then nearly black and a dark brown spore deposit. Idiosyncratic blue-green pigment encrustations (cyanogranules) and a similarly colored reaction of the hyphae located on pileus and stipe surfaces are also diagnostic. Phylogenetic analyses of nuclear large-subunit rDNA (nrLSU), translation elongation factor 1-alpha (tef-1), and the second largest subunit of RNA polymerase II (rpb2) infer Kgaria as a unique generic lineage with two species, one of which is newly described (K. similis). Tylopilus olivaceoporus, originally described at the same time and as distinct from T. cyanogranulifer, appears to be conspecific with the latter. Some darkly pigmented taxa with similar oxidation reactions that were recently described from Brazil, Guyana, and China are further supported by morphology and molecular data as discrete lineages in separate genera in subfamily Boletoideae. Citation: Halling RE, Fechner NA, Holmes G, Davoodian N (2023). Kgaria (Boletaceae, Boletoideae) gen. nov. in Australia: Neither a Tylopilus nor a Porphyrellus. Fungal Systematics and Evolution 12: 31-45. doi: 10.3114/fuse.2023.12.02.
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  • 文章类型: Journal Article
    几个直翅目类群的进化,尤其是在蝗虫家族中,仍然知之甚少。对于Gomphocerinae亚科尤其如此,其中包括隐秘的同胞和同位物种。以前的线粒体研究强调了分类学和系统发育假设之间的主要差异,从而强调全基因组方法的必要性。在这项研究中,我们采用双消化限制性位点相关DNA测序(ddRADseq)来重建中欧Chorthippus和假Chorthippus物种的进化,尤其是C.Smadai,P.tatrae和C.biguttulus组.我们的系统基因组分析恢复了与线粒体DNA条形码的深度不一致,强调其在孔雀科蝗虫中的不可靠性。具体来说,我们的数据有力地区分了C.biguttulus组,并证实了C.eisentrauti的独特性,也揭示了它在贝希特斯加登阿尔卑斯山的存在。此外,我们的结果支持将C.smardai重新分类为假chrothippus属,将P.tatrae重新分类为Chorthippus属。我们的研究证明了高通量基因组方法的效率,例如RADseq,无需事先优化即可阐明具有直接分类学意义的蝗虫辐射的复杂进化。虽然RADseq主要用于人口基因组学和属内系统发育组学,它的应用扩展到解决代表不同属的深度发散的进化枝之间的关系。
    The evolution of several orthopteran groups, especially within the grasshopper family Acrididae, remains poorly understood. This is particularly true for the subfamily Gomphocerinae, which comprises cryptic sympatric and syntopic species. Previous mitochondrial studies have highlighted major discrepancies between taxonomic and phylogenetic hypotheses, thereby emphasizing the necessity of genome-wide approaches. In this study, we employ double-digest restriction site-associated DNA sequencing (ddRADseq) to reconstruct the evolution of Central European Chorthippus and Pseudochorthippus species, especially C.smardai, P.tatrae and the C.biguttulus group. Our phylogenomic analyses recovered deep discordance with mitochondrial DNA barcoding, emphasizing its unreliability in Gomphocerinae grasshoppers. Specifically, our data robustly distinguished the C.biguttulus group and confirmed the distinctiveness of C.eisentrauti, also shedding light on its presence in the Berchtesgaden Alps. Moreover, our results support the reclassification of C.smardai to the genus Pseudochorthippus and of P.tatrae to the genus Chorthippus. Our study demonstrates the efficiency of high-throughput genomic methods such as RADseq without prior optimization to elucidate the complex evolution of grasshopper radiations with direct taxonomic implications. While RADseq has predominantly been utilized for population genomics and within-genus phylogenomics, its application extends to resolve relationships between deeply-diverged clades representative of distinct genera.
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  • 文章类型: Journal Article
    在显微镜领域,大量黑暗的生物多样性仍在等待被发现。在这里,没有装甲的植物特别被忽视,因为它们只呈现不起眼的特征。在一个偏远的德国地方,我们收集了细胞,从中建立了单克隆菌株,使用光学和电子显微镜研究形态学,并从rRNA操纵子获得DNA序列。并行,我们通过DNA-metabarcoding(18SrRNA基因的V4区域)在慕尼黑-Nymphenburg植物园的池塘中检测到单细胞真核生物,在一年的时间里每周采样一次。菌株GeoK*077被证明是Borghiella的一种新物种,在分子系统学中具有独特的地位,卵形的特征性球形细胞是最重要的诊断特征。博格希拉卵细胞,sp.11月。,也存在于植物园的人工池塘中,并且是样品中检测到的第二丰富的植物。更具体地说,博格希拉卵细胞,sp.11月。,显示出明显的季节性,在冬季月份频率很高,在夏季月份完全缺席。这项研究强调了评估生物多样性的必要性,特别是更雄心勃勃的显微镜领域,即使是常见的物种,例如以前的Borghiella卵,也是科学未知的。
    In the microscopy realm, a large body of dark biodiversity still awaits to be uncovered. Unarmoured dinophytes are particularly neglected here, as they only present inconspicuous traits. In a remote German locality, we collected cells, from which a monoclonal strain was established, to study morphology using light and electron microscopy and to gain DNA sequences from the rRNA operon. In parallel, we detected unicellular eukaryotes in ponds of the Botanical Garden Munich-Nymphenburg by DNA-metabarcoding (V4 region of the 18S rRNA gene), weekly sampled over the course of a year. Strain GeoK*077 turned out to be a new species of Borghiella with a distinct position in molecular phylogenetics and characteristic coccoid cells of ovoid shape as the most important diagnostic trait. Borghiella ovum, sp. nov., was also present in artificial ponds of the Botanical Garden and was the second most abundant dinophyte detected in the samples. More specifically, Borghiella ovum, sp. nov., shows a clear seasonality, with high frequency during winter months and complete absence during summer months. The study underlines the necessity to assess the biodiversity, particularly of the microscopy realm more ambitiously, if even common species such as formerly Borghiella ovum are yet unknown to science.
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