Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae)

The beetle suborder Adephaga is traditionally divided into two sections on the basis of habitat, terrestrial Geadephaga and aquatic Hydradephaga. Monophyly of both groups is uncertain, and the relationship of the two groups has implications for inferring habitat transitions within Adephaga. Here we examine phylogenetic relationships of these groups using evidence provided by DNA sequences from all four suborders of beetles, including 60 species of Adephaga, 4 Archostemata, 3 Myxophaga, and 10 Polyphaga. We studied 18S ribosomal DNA and 28S ribosomal DNA, aligned with consideration of secondary structure, as well as the nuclear protein-coding gene wingless . Independent and combined Bayesian, likelihood, and parsimony analyses of all three genes supported placement of Trachypachidae in a monophyletic Geadephaga, although for analyses of 28S rDNA and some parsimony analyses only if Coleoptera is constrained to be monophyletic. Most analyses showed limited support for the monophyly of Hydradephaga. Outside of Adephaga, there is support from the ribosomal genes for a sister group relationship between Adephaga and Polyphaga. Within the small number of sampled Polyphaga, analyses of 18S rDNA, wingless , and the combined matrix supports monophyly of Polyphaga exclusive of Scirtoidea. Unconstrained analyses of the evolution of habitat suggest that Adephaga was ancestrally aquatic with one transition to terrestrial. However, in analyses constrained to disallow changes from aquatic to terrestrial habitat, the phylogenies imply two origins of aquatic habit within Adephaga.     

Phylogenomic analysis of the beetle suborder Adephaga with comparison of tailored and generalized ultraconserved element probe performance

Adephaga is the second largest suborder of beetles (Coleoptera) and they serve as important arthropod predators in both aquatic and terrestrial ecosystems. The suborder is divided into Geadephaga comprising terrestrial families and Hydradephaga for aquatic lineages. Despite numerous studies, phylogenetic relationships among the adephagan families and monophyly of the Hydradephaga itself remain in question. Here we conduct a comprehensive phylogenomic analysis of the suborder using ultraconserved elements (UCEs). This study presents the first in vitro test of a newly developed UCE probe set customized for use within Adephaga that includes both probes tailored specifically for the suborder, alongside generalized Coleoptera probes previously found to work in adephagan taxa. We assess the utility of the entire probe set, as well as comparing the tailored and generalized probes alone for reconstructing evolutionary relationships. Our analyses recovered strong support for the paraphyly of Hydradephaga with whirligig beetles (Gyrinidae) placed as sister to all other adephagan families. Geadephaga was strongly supported as monophyletic and placed sister to a clade composed of Haliplidae + Dytiscoidea. Monophyly of Dytiscoidea was strongly supported with relationships among the dytiscoid families resolved and strongly supported. Relationships among the subfamilies of Dytiscidae were strongly supported but largely incongruent with prior phylogenetic estimates for the family. The results of our UCE probe comparison showed that tailored probes alone outperformed generalized probes alone, as well as the full combined probe set (containing both types of probes), under decreased taxon sampling. When taxon sampling was increased, the full combined probe set outperformed both tailored probes and generalized probes alone. This study provides further evidence that UCE probe sets customized for a focal group result in a greater number of recovered loci and substantially improve phylogenomic analysis.     

The beetle tree of life reveals that Coleoptera survived end‐Permian mass extinction to diversify during the Cretaceous terrestrial revolution

Here we present a phylogeny of beetles (Insecta: Coleoptera) based on DNA sequence data from eight nuclear genes, including six single‐copy nuclear protein‐coding genes, for 367 species representing 172 of 183 extant families. Our results refine existing knowledge of relationships among major groups of beetles. Strepsiptera was confirmed as sister to Coleoptera and each of the suborders of Coleoptera was recovered as monophyletic. Interrelationships among the suborders, namely Polyphaga (Adephaga (Archostemata, Myxophaga)), in our study differ from previous studies. Adephaga comprised two clades corresponding to Hydradephaga and Geadephaga. The series and superfamilies of Polyphaga were mostly monophyletic. The traditional Cucujoidea were recovered in three distantly related clades. Lymexyloidea was recovered within Tenebrionoidea. Several of the series and superfamilies of Polyphaga received moderate to maximal clade support in most analyses, for example Buprestoidea, Chrysomeloidea, Coccinelloidea, Cucujiformia, Curculionoidea, Dascilloidea, Elateroidea, Histeroidea and Hydrophiloidea. However, many of the relationships within Polyphaga lacked compatible resolution under maximum‐likelihood and Bayesian inference, and/or lacked consistently strong nodal support. Overall, we recovered slightly younger estimated divergence times than previous studies for most groups of beetles. The ordinal split between Coleoptera and Strepsiptera was estimated to have occurred in the Early Permian. Crown Coleoptera appeared in the Late Permian, and only one or two lineages survived the end‐Permian mass extinction, with stem group representatives of all four suborders appearing by the end of the Triassic. The basal split in Polyphaga was estimated to have occurred in the Triassic, with the stem groups of most series and superfamilies originating during the Triassic or Jurassic. Most extant families of beetles were estimated to have Cretaceous origins. Overall, Coleoptera experienced an increase in diversification rate compared to the rest of Neuropteroidea. Furthermore, 10 family‐level clades, all in suborder Polyphaga, were identified as having experienced significant increases in diversification rate. These include most beetle species with phytophagous habits, but also several groups not typically or primarily associated with plants. Most of these groups originated in the Cretaceous, which is also when a majority of the most species‐rich beetle families first appeared. An additional 12 clades showed evidence for significant decreases in diversification rate. These clades are species‐poor in the Modern fauna, but collectively exhibit diverse trophic habits. The apparent success of beetles, as measured by species numbers, may result from their associations with widespread and diverse substrates – especially plants, but also including fungi, wood and leaf litter – but what facilitated these associations in the first place or has allowed these associations to flourish likely varies within and between lineages. Our results provide a uniquely well‐resolved temporal and phylogenetic framework for studying patterns of innovation and diversification in Coleoptera, and a foundation for further sampling and resolution of the beetle tree of life.     

鞘翅目高级阶元分子系统学： 研究现状及存在的问题

鞘翅目是世界上物种最丰富的类群, 分为原鞘亚目（Archostemata Kolbe, 1908）、 藻食亚目（Myxophaga Crowson, 1955）、 肉食亚目（Adephaga Schellenberg, 1806）和多食亚目（Polyphaga Emery, 1886）。随着分子生物学的发展,分子系统学的技术被广泛应用于鞘翅目系统学研究中。本文综述了鞘翅目高级阶元的分子系统学的研究进展及存在问题。基于分子生物学手段, 分子分类学家提出了关于鞘翅目高级阶元分子系统学很多假说, 分子分析结果支持鞘翅目的4个亚目各为单系, 而亚目间的系统关系还不统一。基于分子手段对于亚目内的系统发育关系的研究也有了一定的进展, 比如： 分子系统学结果支持肉食亚目的水生类群和陆生类群分别为单系, 水生类群为一次起源。目前, 鞘翅目高级阶元分子系统学的研究还不够成熟和完善, 主要表现为： 材料选择有限且不均衡、 基因数目和适合度不理想, 以及一些关键节点研究的欠缺。     

Basal relationships of Coleoptera inferred from 18S rDNA sequences

The basal relationships of the hyperdiverse insect order Coleoptera (beetles) have proven difficult to resolve. Examination of beetle suborder relationships using 18S ribosomal DNA reveals a previously unproposed relationship among the four major lineages: [(Archostemata(Myxophaga(Adephaga, Polyphaga)))]. Adding representatives of most other insect orders results in a non-monophyletic Coleoptera. However, constraining Coleoptera and its suborders to be monophyletic, in analyses of beetle and outgroup sequences, also results in the above beetle relationships, with the root placed between Archostemata and the remaining suborders.     

Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’

The beetle suborder Adephaga has been the subject of many phylogenetic reconstructions utilizing a variety of data sources and inference methods. However, no strong consensus has yet emerged on the relationships among major adephagan lineages. Ultraconserved elements (UCEs) have proved useful for inferring difficult or unresolved phylogenies at varying timescales in vertebrates, arachnids and Hymenoptera. Recently, a UCE bait set was developed for Coleoptera using polyphagan genomes and a member of the order Strepsiptera as an outgroup. Here, we examine the utility of UCEs for reconstructing the phylogeny of adephagan families, in the first in vitro application a UCE bait set in Coleoptera. Our final dataset included 305 UCE loci for 18 representatives of all adephagan families except Aspidytidae, and two polyphagan outgroups, with a total concatenated length of 83 547 bp. We inferred trees using maximum likelihood analyses of the concatenated UCE alignment and coalescent species tree methods (astral ii , ASTRID, svdquartets ). Although the coalescent species tree methods had poor resolution and weak support, concatenated analyses produced well‐resolved, highly supported trees. Hydradephaga was recovered as paraphyletic, with Gyrinidae sister to Geadephaga and all other adephagans. Haliplidae was recovered as sister to Dytiscoidea, with Hygrobiidae and Amphizoidae successive sisters to Dytiscidae. Finally, Noteridae was recovered as monophyletic and sister to Meruidae. Given the success of UCE data for resolving phylogenetic relationships within Adephaga, we suggest the potential for further resolution of relationships within Adephaga using UCEs with improved taxon sampling, and by developing Adephaga‐specific probes.     

The number that counts. Phylogenetic implications of the number of nurse cells in ovarian follicles of Coleoptera-Adephaga

The structure of polytrophic ovarioles in both Geadephaga and Hydradephaga is reviewed. Particular attention is paid to the significance of various morphological features and their bearing on the phylogeny of Adephaga. It is concluded that the number of nurse cells in the egg chambers is a valuable character in clarifying the phylogenetic relationships. The comparative analysis of the organization of egg chambers in aquatic and terrestrial adephagans, combined with other data suggests that a relatively small and constant number of nurse cells is a plesiomorphic condition for the Adephaga. This conclusion supports the notion that Haliplidae and Gyrinidae stand close to the ancestral stock of adephagous beetles.     

The morphological evolution of the Adephaga (Coleoptera)

The evolution of the coleopteran suborder Adephaga is discussed based on a robust phylogenetic background. Analyses of morphological characters yield results nearly identical to recent molecular phylogenies, with the highly specialized Gyrinidae placed as sister to the remaining families, which form two large, reciprocally monophyletic subunits, the aquatic Haliplidae + Dytiscoidea (Meruidae, Noteridae, Aspidytidae, Amphizoidae, Hygrobiidae, Dytiscidae) on one hand, and the terrestrial Geadephaga (Trachypachidae + Carabidae) on the other. The ancestral habitat of Adephaga, either terrestrial or aquatic, remains ambiguous. The former option would imply two or three independent invasions of aquatic habitats, with very different structural adaptations in larvae of Gyrinidae, Haliplidae and Dytiscoidea.     

Phylogeny of hydradephagan water beetles inferred from 18S rRNA sequences

Several families in the beetle suborder Adephaga have an aquatic life style and are commonly grouped in the "Hydradephaga," but their monophyly is contentious and relationships between and within these families are poorly understood. Here we present full-length 18S rRNA sequence for 84 species of Hydradephaga, including representatives of most major groups down to the tribal level, and a total of 68 species of the largest family, Dytiscidae. Using a direct optimization method for the alignment of length-variable regions, the preferred tree topology was obtained when the cost of gaps and the cost of nucleotide changes were equal, and three hypervariable regions of 18S rRNA were downweighted by a factor of five. Confirming recent molecular studies, the Hydradephaga were found to be monophyletic, indicating a single colonization of the aquatic medium. The most basal group within Hydradephaga is Gyrinidae, followed in a comb-like arrangement by families Haliplidae, Noteridae, Amphizoidae, and Hygrobiidae plus Dytiscidae. Under most alignment parameters, Hygrobiidae is placed amid Dytiscidae in an unstable position, suggesting a possible data artifact. Basal relationships within Dytiscidae are not well established, nor is the monophyly of subfamilies Hydroporinae and Colymbetinae. In contrast, relationships at the genus level appear generally well supported. Despite the great differences in the rates of change and the significant incongruence of the phylogenetic signal in conserved vs hypervariable regions of the 18S rRNA gene, both contribute to establish relationships at all taxonomic levels.     

Phylogenetic analyses and evolutionary timescale of Coleoptera based on mitochondrial sequence

Coleopteran phylogeny was analysed using mitochondrial genome (mitogenome) sequence. The optimal tree topology was given by the dataset consisted of all coding genes except for the exclusion of the 3rd codon sites (mtDNA12) using Bayesian Inference Method. This topology supports the monophyly of four suborders, and the sister group relationship between Adephaga and Myxophaga and between Polyphaga and Archostemata. In Polyphaga, Cucujiformia and Elateroidea formed independent node respectively, the remaining species grouped together except for Cyphon sp, among which, only Cucujiformia and Scarabaeiformia were supported as monophyletic group, respectively. Within Cucujiformia, the monophyly of Chrysomeloidea, Curculionoidea and Tenebrionoidea were supported respectively, among which Tenebrionoidea occupied the basal position of Cucujiformia. Cleroidea grouped together with Bothrideridae and Coccinellidae, and formed an independent node, which lead to the paraphyly of Cucujoidea. The monophyly of Elateriformia was not supported because of the division of Scirtoidea and Buprestoidea. Furthermore, using a Bayesian relaxed clock calibrated with fossil data, we estimated that most superfamilies within Polyphaga originated in the Jurassic period.     

The mitogenomes of three beetles (Coleoptera: Polyphaga: Cucujiformia): New gene rearrangement and phylogeny

The mitochondrial genome (mitogenome) has been extensively used for studying phylogenetic relationships at different taxonomic levels. Several molecular analyses have been performed, but the phylogenetic relationships among infraorders in Polyphaga have not been well resolved. In this work, three nearly complete mitogenomes of Coleoptera, Sitophilus oryzae, Oryzaephilus surinamensis and Callosobruchus chinensis, were determined. The O. surinamensis and S. oryzae mitogenomes harbor gene content typical of other Polyphaga mitogenomes, while a gene rearrangement (trnQ) was found in the C. chinensis mitogenome. The mitogenomes of these three Coleoptera species each consist of approximately 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one A + T-rich region. Phylogenetic analysis within Polyphaga was carried out based on mitochondrial data. The phylogenetic results within Polyphaga support the basal position of Cyphon sp., which belonged to Scirtoidea, Elateriformia. Within Cucujiformia, monophyletic Curculionoidea, Chrysomeloidea and Tenebrionoidea were confirmed.     

水生肉食亚目(Hydradephaga)系统发育学研究简论

水生肉食亚目(Hydradephaga)属于鞘翅目Coleoptera,是一类具有水生习性的食肉性真正水生甲虫(True water beetles)。在真正水生甲虫的系统分类中存在三种假说,一种是肉食亚目(Adephaga)位于该系统的基部,一种是多食亚目(Polyphaga)位于该系统基部,第三种是藻食亚目(Myxophaga)位于该系统基部。最近研究结果更多倾向第一种假说。目前水生肉食亚目大约有5 500个种,200多个属,含8个科。水生肉食亚目的科间水平系统发育关系虽被广泛研究,但观点仍不统一。有代表意义的有三个假说,一是豉甲科(Gyrinidae)位于系统基部,接下来是龙虱科(Dytiscidae)、两栖甲科(Amphizoidae)、水甲科(Hygrobiidae)、小粒龙虱科(Noteridae)与沼梭科(Haliplidae);二是沼梭科位于系统的基部;三是豉甲科位于系统的基部,接下来是沼梭科和龙虱总科(Dytiscoidea),其中龙虱总科由两栖甲科、水甲科、龙虱科、小粒龙虱科组成。目前根据形态学的分类,并结合分子系统学研究方法,第三种假说更符合水生肉食亚目的系统分类,也支持了水生肉食亚目作为一个单系,其祖先来自陆生的假说。     

Complete mitochondrial genome sequence of the yellow-spotted long-horned beetle <Emphasis Type="Italic">Psacothea hilaris</Emphasis> (Coleoptera: Cerambycidae) and phylogenetic analysis among coleopteran insects

We have determined the complete mitochondrial genome of the yellow-spotted long horned beetle, Psacothea hilaris (Coleoptera: Cerambycidae), an endangered insect species in Korea. The 15,856-bp long P. hilaris mitogenome harbors gene content typical of the animal mitogenome and a gene arrangement identical to the most common type found in insect mitogenomes. As with all other sequenced coleopteran species, the 5-bp long TAGTA motif was also detected in the intergenic space sequence located between tRNA^Ser(UCN) and ND1 of P. hilaris. The 1,190-bp long non-coding A+T-rich region harbors an unusual series of seven identical repeat sequences of 57-bp in length and several stretches of sequences with the potential to form stem-and-loop structures. Furthermore, it contains one tRNA^Arg-like sequence and one tRNA^Lys-like sequence. Phylogenetic analysis among available coleopteran mitogenomes using the concatenated amino acid sequences of PCGs appear to support the sister group relationship of the suborder Polyphaga to all remaining suborders, including Adephaga, Myxophaga, and Archostemata. Among the two available infraorders in Polyphaga, a monophyletic Cucujiformia was confirmed, with the placement of Cleroidea as the basal lineage for Cucujiformia. On the other hand, the infraorder Elateriformia was not identified as monophyletic, thereby indicating that Scirtoidea and Buprestoidea are the basal lineages for Cucujiformia and the remaining Elateriformia.     

The primary structure ofHarpalus rufipes 5S ribosomal RNA

The nucleotide sequence of 5S ribosomal RNA from the beetleHarpalus rufipes was determined and compared with primary structures of other insect 5S rRNAs. Sequence differences between two beetle 5S rRNAs may represent phylogenetic markers specific for two groups of Coleoptera — Adephaga and Polyphaga. Analysis of all insect sequences using parsimony allowed us to infer a phylogenetic tree of insects, which is consistent with morphological and paleobiological data.     

Phylogenetic Relationships of the Suborders of Coleoptera (Insecta)

One hundred seven external and internal characters of larval and adult representatives of 28 genera of the coleopteran suborders were analyzed cladistically. Four groups of Neuropterida were introduced as outgroup. The analysis yielded 18 trees with a minimum of 194 steps (CI 0.691). All trees support the monophyly of all four suborders and a branching pattern (Archostemata + (Adephaga + (Myxophaga + Polyphaga))). The presence of elytra with meso- and metathoracic locking devices, the specific hind-wing folding, the close connection of exposed sclerites, the absence of the mera, the absence of eight thoracic muscles, the reduced abdominal sternite I, and the invagination of terminal segments are autapomorphies of Coleoptera. The monophyly of Coleoptera excl. Archostemata is supported by further transformations of the thoracic sclerites such as absence of the mesothoracic discriminal line and katepisternal joint, by an internalized or absent metathoracic trochantin, by the presence of a bending zone in the hind-wing, and by eight further muscle losses. Fusion of tibia and tarsus and presence of a single claw are larval synapomorphies of Myxophaga and Polyphaga. Adults are characterized by fusion of protrochantin and propleura and by the rigid connection of the meso- and metathoracic ventrites. The eucinetoid lineage of Polyphaga is characterized by the secondary absence of the bending zone of the alae. This results in a distinctly simplified wing folding mechanism. The monophyly of Cucujiformia (+ Bostrichoidea) is supported by the presence of cryptonephric Malpighian tubules. Transformations of fore-and hind-wings, reinforcement and simplification of the thoracic exoskeleton, and an efficient use of a distinctly reduced set of thoracic muscles play an important role in the early evolution of Coleoptera. Many different larval character transformations take place in the earlier Mesozoic within the suborders.     

豉甲科及水生肉食亚目的分子系统发育学分析(昆虫纲：鞘翅目)

利用PAUP和MrBayes软件,对线粒体COⅠ基因序列3个密码子位置的数据模块分别进行了豉甲科(Gyrinidae)和水生肉食亚目(Hydradephaga)在亚科或科水平上的系统发育学分析,结果表明第二密码子数据模块获得了理想的分析结果。由PAUP生成的豉甲科最优树来自第二密码子数据模块的分析,而由MrBayes生成的最优树来自全部密码子数据模块的分析。此外,用对应的氨基酸序列生成的ME和MP树与第二密码子数据模块分析的结果也一致。亚科Orectochilinae和Gyrininae以高的支持率形成了单系。然而,来自亚科Enhydrinae的种Porrorhynchus landaisi landaisi呈现了异常的位置。SH-test检验也支持该异常位置,表明这个种可能代表了一个科。在来自第二密码子数据模块的水生肉食亚目最优ML树中,整个Hydradephaga树呈现单系,豉甲科位于树的基部,表明了该科在水生肉食亚目中是一个早期的分支。在树中还产生了一个单系的Dytiscoidea总科,由Dytiscidae、Hygrobiidae、Noteridae和Amphizoidae 4个科组成,单系的Haliplidae与之成为姐妹群。此外线粒体分子钟的结果表明豉甲科的5对相近种间的分化是一个短时期内发生的(0.01～1.81百万年前),这点可能与它们的特殊地理分布有关。     

Mitochondrial genomes of three Bostrichiformia species and phylogenetic analysis of Polyphaga (Insecta,Coleoptera)

Here we determined mitogenomes of three Bostrichiformia species. These data were combined with 51 previously sequenced Polyphaga mitogenomes to explore the higher-level relationships within Polyphaga by using four different mitogenomic datasets and three tree inference approaches. Among Polyphaga mitogenomes we observed heterogeneity in nucleotide composition and evolutionary rates, which may have affected phylogenetic inferences across the different mitogenomic datasets. Elateriformia, Cucujiformia, and Scarabaeiformia were each inferred to be monophyletic by all analyses, as was Bostrichiformia by most analyses based on two datasets with low heterogeneity. The large series Staphyliniformia was never recovered as monophyletic in our analyses. The Bayesian tree using a degenerated nucleotide dataset (P123_Degen) and a site-heterogeneous mixture model in PhyloBayes was supported as the best Polyphaga phylogeny: (Scirtiformia, (Elateriformia, ((Bostrichiformia, Cucujiformia), (Scarabaeiformia + Staphyliniformia)))). For Cucujiformia, the largest series, we inferred a superfamily-level phylogeny: ((Cleroidea, Coccinelloidea), (Tenebrionoidea, (Cucujoidea + Curculionoidea + Chrysomeloidea))).     

Chromosomes of Trachypachus Motschulsky and the evolution of the ancestral adephagan karyotype (Coleoptera)

The family Trachypachidae is a critical group for understanding the evolution of the coleopteran suborder Adephaga. In this article, we report the first karyotypic data on Trachypachus showing a diploid number of 2n = 36 + X (meioformula n = 18 + X) and a single autosomal localization of the rDNA clusters. The evolutionary dynamics of this karyotype are discussed in the light of recent phylogenetic hypotheses of the order Coleoptera. We conclude that chromosome analysis supports a close relationship between trachypachids and the other Geadephaga and that a male karyotype with 36 + X chromosomes may well be considered ancestral for the whole suborder Adephaga.