基于线粒体COⅠ基因部分序列的长江口舌鳎科鱼类系统分类研究

为了确定线粒体COⅠ基因在长江口舌鳎科鱼类系统分类及物种鉴定中的作用,本实验采用线粒体COⅠ基因特异扩增测序及GenBank已有序列联合配对分析的方法,对长江口舌鳎科2属9种鱼类39个COⅠ基因片段的序列进行比较和系统进化研究。采用MEGA 5.0软件进行统计分析,舌鳎科鱼类该片段的平均AT含量高于GC含量,第1密码子位点含量最高(51.8%～57.3%,平均53.8%),第2密码子的含量稳定,均为42.0%,第3密码子变化范围最大(28.1%～37.8%,平均32.4%)。依据Kimura-2-parameter模型,9种舌鳎科鱼类种间遗传距离平均值为0.191,种内为0.003,种间遗传距离是种内的63.7倍。采用最大简约法(MP) 和邻接法(NJ)构建系统发育树,显示长江口舌鳎科鱼类为明显的单系群,但舌鳎科鱼类内部的系统发育关系与形态分类划分的亚属并不完全一致,其中须鳎属的日本须鳎(Paraplagusis japonica)与拟舌鳎亚属的宽体舌鳎(Cynoglossus robustus)聚为一支。虽然三线舌鳎亚属的种类均可聚为独立的分支,但短吻三线舌鳎(C. abbreviatus)与紫斑舌鳎(C. purpureomaculatus)、长吻红舌鳎(C. lighti)与短吻红舌鳎(C. joyneri),两组间种间遗传距离分别为0.002和0.007,两组物种间均存在同种异名现象。本研究表明,线粒体COⅠ基因作为分子标记除了能筛选出同种异名种类外,还能够对舌鳎科鱼类进行有效的物种鉴定和系统进化分析,线粒体COⅠ基因作为分类条形码是可行的。     

短吻红舌鳎鱼卵、仔鱼的DNA条形码和形态学鉴定

为了准确鉴定2015年7–10月青岛崂山青山湾鱼类浮游生物调查中采集的依形态学初步鉴定为某种舌鳎属的鱼卵、仔鱼样本,本实验同时采集青岛胶州湾短吻红舌鳎(Cynoglossus joyneri)和长吻红舌鳎(C.lighti)的成鱼样本为参照,通过线粒体COI基因测序分析,以及同山东半岛海域分布的6种舌鳎属鱼类的COI基因序列比对,开展了该舌鳎属鱼卵、仔鱼种类的鉴别分析,以期为今后舌鳎属鱼类的分类及其鱼卵、仔鱼的鉴别提供参考资料。形态学研究结果显示:鱼卵为圆球形浮性卵,直径0.68–0.87 mm(0.73±0.03 mm,n=50),卵膜单层,较薄、光滑透明,卵周隙较大,卵膜及卵黄囊均无特殊构造,油球6–15个,直径0.04–0.10 mm(0.07±0.01 mm,n=50),圆形,大小不一,多位于卵黄囊中与胚体相对的一侧,既有聚集分布也有分散分布;仔鱼的2条冠状幼鳍及右眼移位过程中体长、色素分布等的特征和变化是此鱼种仔鱼鉴别的最明显特征。遗传学分析结果显示:该种舌鳎属样品(Cynoglossus sp.)与短吻红舌鳎和长吻红舌鳎的遗传距离最为接近,三者K2P遗传距离为0.006–0.009;短吻三线舌鳎(C.abbreviatus)与紫斑舌鳎(C.purpureomaculatus)亲缘关系最近,两者K2P遗传距离仅为0.002。以带纹条鳎(Zebrias zebra)为外类群构建的NJ系统发育树显示,该种舌鳎属样品与短吻红舌鳎和长吻红舌鳎以及短吻三线舌鳎与紫斑舌鳎分别聚为一支,其他种类各聚为一支。综合形态特征和COI基因比对结果,确定该舌鳎属鱼卵、仔鱼样品为短吻红舌鳎。     

鳇亚科棒花鱼属鱼类的分类与系统发育关系

逗亚科棒花鱼属鱼类的分类与系统发育关系尚未解决。研究选择线粒体Cyt b基因和核基因RAG1、MLH3及MSH6作为分子标记, 重建了棒花鱼属鱼类的系统发育关系, 并结合形态证据对该属鱼类进行了分类厘定。结果表明: 棒花鱼与钝吻棒花鱼是单系种。拉林棒花鱼与辽宁棒花鱼是并系种, 一起形成单系群。拉林棒花鱼+辽宁棒花鱼一起嵌套在小鳔逗属鱼类内部, 钝吻棒花鱼嵌套在片唇逗属鱼类内部。拉林棒花鱼+辽宁棒花鱼+钝吻棒花鱼+片唇逗属+胡逗属+小鳔逗属+琵琶逗属鱼类组成单系群, 它们一起与棒花鱼形成姊妹群关系。可量性状与可数性状均不能区分拉林棒花鱼和辽宁棒花鱼。结合系统发育关系与形态证据, 棒花鱼属鱼类的分类厘定如下: 棒花鱼属鱼类包括棒花鱼和平江棒花鱼(未取样); 辽宁棒花鱼是拉林棒花鱼的同物异名, 后者的分类位置有待进一步校订; 钝吻棒花鱼校订为钝吻片唇逗。     

基于线粒体COⅠ基因的凤蝶亚科部分物种系统发育关系

通过对凤蝶亚科Papilioninae11属27种的线粒体细胞色素c氧化酶Ⅰ基因(COⅠ)序列测定,以阿波罗绢蝶Parnassius apollo为外群,分别采用邻接法(NJ)、最大简约法(MP)和最大似然法(ML)构建凤蝶亚科的系统发育树,初步探讨了其系统发育关系。结果显示,凤蝶亚科11属27个物种分为4个主要的分支,分别是裳凤蝶族Troidini、凤蝶族Papilionini、燕凤蝶族Lampropterini和喙凤蝶族Teinopalpini,与传统分类学观点一致。其中,燕凤蝶族构成凤蝶亚科系统发育树基部的一个独立分支,且为单系发生。凤蝶属Papilio中美凤蝶亚属Menelaides和翠凤蝶亚属Princeps首先相聚,华凤蝶亚属Sinoprinceps和凤蝶亚属Papilio亲缘关系较近,随后两分支再聚为一支,构成凤蝶属。本研究结果从分子水平验证了凤蝶亚科传统的形态分类地位,并为澄清凤蝶亚科物种间系统发育关系提供了基础资料。     

基于线粒体COⅠ基因的沙鳅亚科鱼类DNA条形码及其分子系统发育研究

选择线粒体COⅠ基因作为分子标记,进行沙鳅亚科鱼类（Botiinae）DNA条形码及其分子系统发育研究。研究获得了沙鳅亚科7属19种共131个个体的COⅠ基因序列,利用MEGA5.0软件分析了沙鳅亚科鱼类COⅠ基因的序列特征,计算了种内及种间遗传距离。沙鳅亚科鱼类的分子系统发育关系的重建分别采用NJ法和Bayesian法。研究发现,沙鳅亚科COⅠ基因的碱基组成为: A 24.4%、T 29.5%、G 18.0%、C 28.1%。沙鳅亚科鱼类种内平均遗传距离为0.0020.000,种间平均遗传距离为0.1480.008。DNA条形码研究结果显示,所分析的19种沙鳅鱼类各自分别聚成单系分支,表明COⅠ基因在本研究中具有100%的物种鉴别率。同时,系统发育分析支持各属的单系性,并且结果显示沙鳅亚科鱼类聚为两个分支,其中一支由薄鳅属和副沙鳅属构成,另一分支则包括: （沙鳅属、色鳅属）和 中华沙鳅属、（缨须鳅属、安彦鳅属）。因此,COⅠ基因可以作为有效的分子标记对沙鳅亚科进行DNA条形码研究以及分子系统发育研究。       

基于线粒体Cytb基因序列探讨中国斑翅蝗科部分种类的系统发育关系

基于斑翅蝗科14种的线粒体Cytb基因462 bp序列,使用MEGA2和PAUP4.0b软件包进行分析,显示Cytb基因序列具有明显的高A、T偏向性和距离依赖的TS/TV值.采用邻接法(NJ)、最大似然法(MP)和极似然法(ML)分别构建斑翅蝗科4亚科8属的系统发育树,不同算法构建的系统发育树均支持分为四大分支(亚科):A(绿纹蝗属)、B(束颈蝗属)、C((飞蝗属+车蝗属)+小车蝗属)、D((痂蝗属+异痂蝗属)+皱膝蝗属);红胫小车蝗和黄胫小车蝗作为两个种比较合适;痂蝗亚科和异痂蝗亚科应该合并为一个亚科;飞蝗亚科与斑翅蝗亚科的分类关系尚未解决,需要进一步的研究进行分析验证.     

多基因联合分析棒束孢属Isaria（Ascomycota,Cordycipitaceae）系统发育关系

对棒束孢属Isaria及近缘属物种开展5基因（nrSSU、nrLSU、tef-1α、rpb1和 rpb2）测序并联合分析,结合GenBank相关类群序列,探讨棒束孢属系统发育关系,最终获得95个菌株、58个明确分类群的2-5基因序列。利用MEGA和MrBayes软件进行多基因聚类分析,结果表明棒束孢属多系起源于虫草菌科中,分3个不同分支。A支主要由Isaria cicadae、I. teniupes、I. coleopterorum、I. fumosorosea和I. cateniannulata等组成;B支包括I. poprawkii、I. locustica、I. javanica、I. amoenerosea和I. cateniobliqua;C支仅有I. farinosa。分支间被Cordyceps militaris、C. ninchukispora、C. pruinosa等隔开。棒束孢在形态上,主要以瓶梗基部膨大、尖端变细及孢子呈链状等特征与其他类群分开,但同时也发现有棒状分生孢子梗和单孢子类型。基于节点的分歧时间预测分析,推测棒束孢属首次分化于70Mya,但棒束孢属主要物种形成却在60-55Mya,且3个分支的棒束孢物种为快速同时形成,而后大多数类群表现遗传稳定。同时发现,与Isaria Clade A较近一支有粉被玛利亚霉Mariannaea pruinosa（C. pruinosa无性型）和蛹草蚧霉Lecanicillium militaris（C. militaris无性型）;与粉棒束孢距离最近一支有Akanthomyces aculeatus（C. tuberculata无性型）和L. attenuatum（C. confragosa无性型）,是两个不同的属征分类群,且相互间遗传距离较近。根据棒束孢属及其近缘种属形态特征的复杂性推测,棒束孢属在快速物种形成中,其近缘类群存在一定程度的丢失和选择性演化。     

基于四个线粒体基因片段的银鱼科鱼类系统发育

银鱼科鱼类是我国重要的经济鱼类,但其属间系统发育关系与属、种的界定尚存争议。研究使用线粒体12S/16S核糖体RNA、细胞色素c氧化酶亚基Ⅰ(COⅠ)基因部分序列以及NADH脱氢酶亚基1全长序列重建银鱼科属间的系统发育。结果显示银鱼科鱼类是单系群,白肌银鱼属在银鱼系统发育的基部,"大银鱼属+新银鱼属"、"间银鱼属+银鱼属"形成两个单系亚群,但日本银鱼属的位置没有很好解决。基于COI基因序列计算的"短吻-陈氏-太湖-近太湖新银鱼复合群"种间遗传距离为0—0.19%、"乔氏-寡齿新银鱼复合群"种间遗传距离为0%。整合研究结果与前人形态、分子证据,详细地讨论了银鱼的属、种分类。     

中国鲿科鱼类线粒体DNA控制区结构及其系统发育分析

采用PCR技术获得了中国鲿科鱼类代表种类线粒体DNA控制区基因的全序列,对控制区基因结构进行了分析,并选用粒鲇科的中华粒鲇,鮡科的三线纹胸鮡作为外类群,用最大简约法(MP)和邻接法(NJ)构建了系统发育树。结果显示鲿科鱼类中控制区基因适于系统发育分析,鲿科鱼类构成一个单系类群;圆尾拟鲿应该放入鮠属里。     

基于稳定同位素研究海州湾短吻红舌鳎的摄食生态

根据2018年春季和秋季在海州湾海域进行底拖网调查采集的样品,基于碳氮稳定同位素分析,对海州湾短吻红舌鳎的摄食生态进行研究。结果表明: 海州湾短吻红舌鳎的δ¹³C值平均值为(-17.79±1.00)‰,其范围在-20.75‰～-15.91‰;δ¹⁵N值平均值为(9.37±1.33)‰,其范围在5.98‰～12.02‰。Pearson相关分析表明,海州湾短吻红舌鳎δ¹³C值与体长呈显著负相关,δ¹⁵N值与体长呈显著正相关。根据δ¹⁵N值计算得出海州湾短吻红舌鳎的平均营养级为(3.43±0.97),且营养级与体长呈显著正相关。海州湾短吻红舌鳎摄食的饵料生物有鱼类、蟹类、虾类、软体动物、多毛类、浮游生物和颗粒有机物等,其中虾类的营养贡献率最高。秋季鱼类、蟹类、虾类对短吻红舌鳎的营养贡献率较春季有所增高。本研究将有助于揭示短吻红舌鳎在海州湾生态系统物质循环和能量流动中的地位和作用,为其资源保护和合理利用提供科学依据。     

蛹虫草线粒体基因型快速检测体系的构建及线粒体遗传稳定性的初步研究

本研究的目的是建立一种快速确定蛹虫草菌株线粒体基因型的技术体系,并探讨蛹虫草连续传代培养后线粒体的遗传稳定性。从已知线粒体基因组的蛹虫草菌株中扩增线粒体内含子位点,将扩增产物混合并制作出两套DNA分子量标准,即在8个内含子位点分别具有内含子的8条扩增条带组成的M-I和在6个内含子位点分别缺失内含子的6条扩增条带组成的M-II。从待检测的蛹虫草菌株（包括3个已知和2个未知线粒体基因组的菌株）中扩增同样的（假定）内含子位点,然后通过琼脂糖凝胶电泳分别与制备好的两个DNA分子量标准进行比较,能够准确判断蛹虫草菌株的线粒体内含子分布模式,从而验证了所构建的线粒体基因型快速检测体系的有效性。选择10个蛹虫草组织分离菌株和8个单分生孢子菌株连续转接培养15代,没有发现线粒体内含子分布模式发生改变。本研究成功构建了快速检测蛹虫草线粒体基因型的技术体系,并发现蛹虫草线粒体具有很高的遗传稳定性,为开展蛹虫草线粒体遗传规律的研究奠定了基础。     

Species of Colletotrichum on Agavaceae

Species of Colletotrichum cause diseases on a wide range of hosts, frequently infecting plants in the Agavaceae (monocotyledons: Liliales). Three species of Colletotrichum restricted to the Agavaceae were detected through morphological studies of specimens and molecular sequence analyses of the LSU of the nu-rDNA and the ITS region of the nu-rDNA from cultures. Colletotrichum agaves on Agave is fully described and illustrated. Colletotrichum dracaenophilum is described as a new species for isolates having long conidia and occurring on Dracaena sanderiana from China. Colletotrichum phormii and Glomerella phormii are determined to be the correct scientific names for the asexual and sexual states, respectively, of a species commonly referred to as C. rhodocyclum and G. phacidiomorpha occurring mainly on Phormium. In addition, C. gloeosporioides and C. boninense were isolated from plants in the Agavaceae. All species of Colletotrichum described on Agavaceae were evaluated based on type specimens. A key to the five species of Colletotrichum on Agavaceae is included. This paper includes one new species, Colletotrichum dracaenophilum, and three new combinations, Colletotrichum phormii, Glomerella phormii, and Phaeosphaeriopsis phacidiomorpha.     

Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica

Interspecific hybridization events have played a major role in plant speciation, yet the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production. We estimated genetic distances between C. arabica and all species that are known to be closely related to C. arabica using genotyping-by-sequencing (GBS) data. In addition, we reconstructed a time-calibrated multilabeled phylogenetic tree of 24 species to estimate the age of the C. arabica hybridization event. Ancestral states of self-compatibility were also inferred to shed new light on the evolution of self-compatibility in Coffea. Coffea canephora and C. eugenioides were confirmed as the putative progenitor species of C. arabica. These species most likely hybridized between 1.08 million and 543 000 years ago, coinciding with periods of environmental upheaval, which may have induced range shifts of the progenitor species that facilitated the emergence of C. arabica.     

Delineation of Chondrus (Gigartinales, Florideophyceae) in China and the origin of C. crispus inferred from molecular data

Complete nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences were obtained for 18 Chondrus populations collected at 15 sites from eight countries worldwide. Pairwise comparisons with the multiple alignment revealed that intraspecific divergences of ITS sequences ranged from 0.3 to 1.8% in C. crispus Stackhouse (except for the entity SVLH from France) and from 0.0 to 0.6% in C. ocellatus Holmes, whereas interspecific divergences in Chondrus varied from 1.4 to 5.0%. Three phylogenetic methods (neighbour joining, maximum parsimony and maximum likelihood) confirmed three main lineages: the North Atlantic lineage containing entities of C. crispus from Canada, France, Germany, England, Portugal, Ireland and Wales; a second lineage comprising three species: C. sp. 1, C. armatus (Harvey) Yamada et Mikami, and C. pinnulatus (Harvey) Okamura from the Northern Pacific; and a third lineage containing just one species: C. ocellatus from the Northern Pacific. Chondrus yendoi Yamada et Mikami separated from other Chondrus species singly. nrDNA ITS data indicate that a previous assignment of C. sp. 2 to Mazzaella japonica (Mikami) Hommersand may be incorrect, and additional evidence is needed to resolve the generic placement of this entity. It is inferred from the nrDNA ITS data that three Chondrus species are presently known in China with two, C. ocellatus and C. nipponicus, in Qingdao and two, C. armatus and C. nipponicus, in Dalian. We hypothesize that the ancestor of North Atlantic C. crispus had a Pacific origin, and that the present distribution of C. crispus in the Atlantic Ocean correlates with a trans-Arctic dispersal and vicariance events associated with Pleistocene glaciation maxima.     

Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes)

The Teloschistaceae is a widespread family with considerable morphological and ecological heterogeneity across genera and species groups. In order to provide a comprehensive molecular phylogeny for this family, phylogenetic analyses were carried out on sequences from the nuclear ribosomal ITS region obtained from 114 individuals that represent virtually all main lineages of Teloschistaceae. Our study confirmed the polyphyly of Caloplaca, Fulgensia and Xanthoria, and revealed that Teloschistes is probably non-monophyletic. We also confirm here that species traditionally included in Caloplaca subgenus Gasparrinia do not form a monophyletic entity. Caloplaca aurantia, C. carphinea and C. saxicola s. str. groups were recovered as monophyletic. The subgenera Caloplaca and Pyrenodesmia were also polyphyletic. In the subgenus Caloplaca, the traditionally recognized C. cerina group was recovered as monophyletic. Because this study is based solely on ITS, to maximize taxon sampling, the inclusion of phylogenetic signal from ambiguously aligned regions in MP (recoded INAASE and arc characters) resulted in the most highly supported phylogenetic reconstruction, compared with Bayesian inference restricted to alignable sites.     

Systematics of Mukdenia and Oresitrophe (Saxifragaceae): Insights from genome skimming data

Oresitrophe and Mukdenia (Saxifragaceae) are epilithic sister genera used in traditional Chinese medicine. The taxonomy of Mukdenia, especially of M. acanthifolia, has been controversial. To address this, we produced plastid and mitochondrial data using genome skimming for Mukdenia acanthifolia and Mukdenia rossii, including three individuals of each species. We assembled complete plastomes, mitochondrial CDS and nuclear ribosomal ETS/ITS sequences using these data. Comparative analysis shows that the plastomes of Mukdenia and Oresitrophe are relatively conservative in terms of genome size, structure, gene content, RNA editing sites and codon usage. Five plastid regions that represent hotspots of change (trnH-psbA, psbC-trnS, trnM-atpE, petA-psbJ and ccsA-ndhD) are identified within Mukdenia, and six regions (trnH-psbA, petN-psbM, trnM-atpE, rps16-trnQ, ycf1 and ndhF) contain a higher number of species-specific parsimony-informative sites that may serve as potential DNA barcodes for species identification. To infer phylogenetic relationships between Mukdenia and Oresitrophe, we combined our data with published data based on three different datasets. The monophyly of each species (Oresitrophe rupifraga, M. acanthifolia and M. rossii) and the inferred topology ((M. rossii, M. acanthifolia), O. rupifraga) are well supported in trees reconstructed using the complete plastome sequences, but M. acanthifolia and M. rossii did not form a separate clade in the trees based on ETS + ITS data, while the mitochondrial CDS trees are not well-resolved. We found low recovery of genes in the Angiosperms353 target enrichment panel from our unenriched genome skimming data. Hybridization or incomplete lineage sorting may be the cause of discordance between trees reconstructed from organellar and nuclear data. Considering its morphological distinctiveness and our molecular phylogenetic results, we strongly recommend that M. acanthifolia be treated as a distinct species.     

宁夏兽类两新纪录——川西缺齿鼩和小纹背鼩鼱

<正>川西缺齿鼩(Chodsigoa hypsibia)(De Winton andStyan,1899)和小纹背鼩鼱(Sorexbedfordiae)(Thomas, 1911)同属于劳亚食虫目(Eulipotyphla)鼩鼱科(Soricidae)。缺齿鼩鼱属(Chodsigoa,Kastschenko, 1907)全世界目前已知10个物种(Wilson and Mittermeier, 2018; Chen et al., 2022)，其中川西缺齿鼩为中国特有，     

Morphology and germination characteristics of the cysts of Chattonella ovata (Raphidophyceae), a novel red tide flagellate in the Seto Inland Sea, Japan

To elucidate the mechanism of bloom outbreaks of Chattonella ovata (Raphidophyceae), we investigated the cysts of C. ovata and succeeded in finding them from the bottom sediments of Hiroshima Bay. The morphology of the cysts was mostly hemispherical in shape, with a diameter of ca. 30 μm and height of ca. 20 μm. The cysts were usually adhering to solid materials, such as diatom frustules, yellow-greenish in color and had several dark brown grains. The cyst wall was smooth and had no ornamentation. Because the morphological characteristic of the cysts was in general agreement with those of Chattonella antiqua and Chattonella marina, it was difficult to differentiate the cysts of these three species. Germination of the cysts of C. ovata was observed at temperatures from 17.5 to 30 °C, but not at 15 °C or below. The number of the germinated cysts increased with increasing temperature and the optimum temperature for germination was 30 °C. Although cysts of C. antiqua and C. marina germinated at temperatures from 15 to 30 °C, optimum temperature of germination was 22.5 °C. The lower limit and optimum temperatures for germination of C. ovata cysts was higher than for C. antiqua and C. marina. The role of cysts in the population dynamics of C. ovata is discussed.     

A systematic study of North American Angelica species (Apiaceae) based on nrDNA ITS and cpDNA sequences and fruit morphology

Angelica is a taxonomically complex genus widespread throughout the North Temperate Zone. Previous phylogenetic studies of the genus have focused primarily on its East Asian species. The relationships among its North American members, the monophyly of these species, and the value of fruit morphology in circumscribing its taxa have yet to be examined. This study represents the most comprehensive sampling of Angelica to date (100 species) and includes all 26 species in North America. Relationships are inferred using Bayesian inference, maximum likelihood, and maximum parsimony analyses of ITS sequences and, for multiple accessions of each North American species, cpDNA ndhF-rpl32, rpl32-trnL, and psbM-psbD sequences. The fruit morphological characters examined were those considered phylogenetically important in East Asian Angelica. The results revealed that the North American species fell into three major clades: North American Angelica clade, Archangelica clade, and the Eurasian Angelica clade. Angelica dawsonii has affinities with Lomatium brandegeei. Fourteen species within the North American Angelica clade were strongly supported as monophyletic. Two paraphyletic species resulted in new combinations in A. lineariloba and A. venenosa. Conflict between the ITS-derived and cpDNA-derived phylogenies and the lack of resolution in portions of the trees may be due to chloroplast capture and rapid species radiation. Fruit morphology supported some interspecific relationships based on molecular data, and relationships revealed by ITS and cpDNA data were roughly in accordance with fruit classification type and geographic distribution region, respectively. A diagnostic key based on fruit morphology is provided for the identification of the North American Angelica taxa.     

Phylogenetic relationships within Pyrenodesmia sensu lato and the role of pigments in its taxonomic interpretation

Most lichens of the family Teloschistaceae (Ascomycota) produce yellow-orange-red anthraquinone pigments. However, the genus Pyrenodesmia encompasses species in which anthraquinones are absent and replaced by a gray pigment Sedifolia-gray. It was shown recently that these species are related to taxa with both anthraquinones and Sedifolia-gray (Caloplaca xerica group, C. haematites group, and C. cretensis) and to species with a brown pigment instead of both anthraquinones and Sedifolia-gray (C. demissa, C. obscurella, and C. reptans). Nevertheless, relationships between mentioned anthraquinone-containing and anthraquinone-lacking species remained unclear. In total, 8 DNA loci from 41 species were used here to resolve these uncertainties. We concluded that C. demissa, C. obscurella, and C. reptans are rather distant from the core of Pyrenodesmia, and we place them outside of Pyrenodesmia sensu lato. Within Pyrenodesmia sensu lato, three lineages were revealed and recognized on a generic level: the genus Pyrenodesmia sensu stricto (21 species), the genus Kuettlingeria (14 species), which is resurrected here, and the genus Sanguineodiscus (4 species), which is newly described here. The genus Pyrenodesmia includes taxa that never contain anthraquinones, but Sedifolia-gray. It matches with the former C. variabilis group. Taxa of the genera Kuettlingeria and Sanguineodiscus have anthraquinones in their apothecia and Sedifolia-gray in their thalli. The genus Kuettlingeria includes the former C. xerica group plus C. cretensis and C. diphyodes. The genus Sanguineodiscus includes the former C. haematites group and C. bicolor. The identity of Kuettlingeria (Caloplaca) diphyodes was clarified and the name Pyrenodesmia helygeoides was resurrected. Twenty-four new combinations were proposed.