New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK (i)

To date, there is little consensus concerning the phylogenetic relationships among neognath orders, which include all extant birds except ratites and tinamous. Different data sets, both molecular and morphologic, have yielded radically different and often unresolved ordinal topologies, especially within the neoaves clade. This lack of resolution and ongoing conflict indicates a need for additional phylogenetic characters to be applied to the question of higher-level avian phylogeny. In this study, sequences of a single-copy nuclear gene, ZENK, were used to reconstruct an ordinal-level phylogeny of neognath birds. Strong support was indicated for the oldest divergence within Neognathae; the chicken- and duck-like birds formed a clade that was sister to all other modern birds. In addition, many families of traditional taxonomic orders clustered together in the ZENK tree, indicating the gene's general phylogenetic reliability. However, within the neoaves clade, there was little support for relationships among orders, which is a result similar to all other recent molecular studies of higher-level avian phylogeny. This similarity among studies suggests the possibility of a rapid radiation of the major neoaves lineages. Despite the ongoing lack of neoaves resolution, ZENK's sequence divergence and base composition patterns indicate its general utility as a new phylogenetic marker for higher-level avian systematics.     

Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes

Neoaves is the most diverse major avian clade, containing ~95% of avian species, and it underwent an ancient but rapid diversification that has made resolution of relationships at the base of the clade difficult. In fact, Neoaves has been suggested to be a "hard" polytomy that cannot be resolved with any amount of data. However, this conclusion was based on slowly evolving coding sequences and ribosomal RNAs and some recent studies using more rapidly evolving intron sequences have suggested some resolution at the base of Neoaves. To further examine the utility of introns and exons for phylogenetics, we sequenced parts of two unlinked clathrin heavy chain genes (CLTC and CLTCL1). Comparisons of phylogenetic trees based upon individual partitions (i.e. introns and exons), the combined dataset, and published phylogenies using Robinson-Foulds distances (a metric of topological differences) revealed more similarity than expected by chance, suggesting there is structure at the base of Neoaves. We found that introns provided more informative sites, were subject to less homoplasy, and provided better support for well-accepted clades, suggesting that intron evolution is better suited to determining closely-spaced branching events like the base of Neoaves. Furthermore, phylogenetic power analyses indicated that existing molecular datasets for birds are unlikely to provide sufficient phylogenetic information to resolve relationships at the base of Neoaves, especially when comprised of exon or other slowly evolving regions. Although relationships among the orders in Neoaves cannot be definitively established using available data, the base of Neoaves does not appear to represent a hard polytomy. Our analyses suggest that large intron datasets have the best potential to resolve relationships among avian orders and indicate that the utility of intron data for other phylogenetic questions should be examined.     

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.     

Molecular phylogeny of Rhacophoridae (Anura): A framework of taxonomic reassignment of species within the genera Aquixalus, Chiromantis, Rhacophorus, and Philautus

Phylogenetic relationships among representative species of the family Rhacophoridae were investigated based on 2904bp of sequences from both mitochondrial (12S rRNA, 16S rRNA, the complete t-RNA for valine), and nuclear (tyrosinase, rhodopsin) genes. Maximum parsimony, maximum likelihood, and Bayesian analyses were employed to reconstruct the phylogenetic trees. This analysis, combined with previous phylogenetic studies, serves as a framework for future work in rhacophorid systematics. The monophyly of Rhacophorus is strongly confirmed except for the species R.hainanus, which is the sister taxon to A.odontotarsus. The non-monophyly of the newly designated genus Aquixalus by Delorme et al. [Delorme, M., Dubois, A., Grosjean, S., Ohler, A., 2005. Une nouvelle classification générique et subgénérique de la tribu des Philautini (Amphibia, Anura, Ranidae, Rhacophorinae). Bull. Mens. Soc. Linn. Lyon 74, 165-171] is further confirmed. Aquixalus (Aquixalus) forms a well-supported monophyletic group within Kurixalus, whereas, Aquixalus (Gracixalus) is more closely related to species of Rhacophorus, Polypedates, and Chiromantis. Philautus as currently understood, does not form a monophyletic group. Philautus (Kirtixalus) is the sister group to the clade comprising Kurixalus and Aquixalus (Aquixalus), and more remotely related to Philautus (Philautus). Chiromantisromeri does not cluster with species of Chiromantis, and forms a basal clade to all rhacophorids save Buergeria. We propose some taxonomic changes that reflect these findings, but further revision should await more detailed studies, which include combined morphological and molecular analyses, with greater species sampling.     

Molecular phylogeny of songbirds (Aves: Passeriformes) and the relative utility of common nuclear marker loci

While the monophyly of the largest avian order Passeriformes as well as its suborders suboscines (Tyranni) and oscines (Passeri) is well established, lower phylogenetic relationships of this fast radiated taxon have been a continuous matter of debate, especially within the suborder oscines. Many studies analyzing phylogenetic relationships of the Passeriformes using molecular markers have been published, which led to a better resolved phylogeny. Conflicting hypotheses and still remaining uncertainties, especially within the Passerida, have repeatedly stimulated further research with additional new markers. In the present study we used a combination of established molecular markers (RAG‐1, RAG‐2, c‐myc) and the recently introduced ZENK. We accomplished phylogenetic analyses using maximum parsimony, maximum likelihood and Bayesian inference, both separately for all genes and simultaneously. To assess the phylogenetic utility of the different genes in avian systematics we analyzed the influence of each data partition on the phylogenetic tree yielded by the combined approach using partitioned Bremer support. Compared with the other single gene analyses, the ZENK trees exhibited by far the best resolution and showed the lowest amount of homoplasy. Our data indicate that this gene is—at least in passerines—suitable for inference of even old taxonomic splits. Our combined analysis yields well‐supported phylogenetic hypotheses for passerine phylogeny and apart from corroborating recently proposed hypotheses on phylogenetic relationships in the Passeriformes we provide evidence for some new hypotheses. The subdivision of the Passerida into three superfamilies, Sylvioidea, Passeroidea and Muscicapoidea, the first as sister to the two latter groups is strongly supported. We found evidence for a split between Paridae and the remaining Sylvioidea. © The Willi Hennig Society 2007.     

TRENDS IN AVIAN SYSTEMATICS

The classical "new systematics" with its replacement of the monotypic by the polytypic species, and of the morphological by the biological species concept, is now so universally accepted in ornithology that it can hardly be considered any longer as "new". Present trends indicate two areas of avian systematics favourable for active expansion, population systematics and phylogenetic systematics. Instead of describing the population structure of species in terms of subspecies, the trend will be to describe it in terms of "geographical isolates", "population continuats", and "zones of secondary intergradation" of former geographic isolates. Such an analysis can shed much light on the ecological requirements of species and on their former history. The other area of new avian systematics is a re-activated study of the higher categories of birds, with new methods and interpreted by a re-evaluated set of phylogenetic and evolutionary concepts.     

近代鸟类分类与系统发育研究进展

简要综述了宏观和微观领域的鸟类分类学研究进展.宏观领域介绍了传统形态分类学、数值分类学和支序分类学,结合鸣声分析强调支序分类学的应用.微观领域介绍了Sibley分类系统和近年来出现的主要基于mtDNA的鸟类系统学研究.通过对大量研究工作的分析提出该领域今后应进行综合性研究.     

Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea,Mammalia): new data and phylogenetic analyses of Elephantidae

The phylogenetic relationships between recent Elephantidae (Proboscidea, Mammalia), that is to say extant elephants (Asian and African) and extinct woolly mammoth, have remained unclear to date. The prevailing morphological scheme (mammoth grouped with Asian elephant) is either supported or questioned by the molecular results. Recently, the monophyly of woolly mammoths on mitochondrial grounds has been demonstrated (Thomas, et al., 2000), but it conflicts with previous studies (Barriel et al., 1999; Derenko et al., 1997). Here, we report the partial sequencing of two mitochondrial genes: 128 bp of 12S rDNA and 561 bp of cytochrome b for the Lyakhov mammoth, a 49,000-year-old Siberian individual. We use the most comprehensive sample of mammoth (11 sequences) to determine whether the sequences achieved by former studies were congruent or not. The monophyly of a major subset of mammoths sequences (including ours) is recovered. Such a result is assumed to be a good criterion for ascertaining the origin of ancient DNA. Our sequence is incongruent with that of Yang et al. (1996), though obtained for the same individual. As far as the latter sequence is concerned, a contamination by non-identified exogenous DNA is suspected. The robustness and reliability of the sister group relation between Mammuthus primigenius and Loxodonta africana are examined: down-weighting saturated substitutions has no impact on the topology; analyzing data partitions proves that the support of this clade can be assigned to the most conservative phylogenetic signal; insufficient taxonomic and/or characters sampling contributed to former discordant conclusions. We therefore assume the monophyly of "real mammoth sequences" and the (Mammuthus, Loxodonta) clade.     

Epigenetic Variations in Plant Hybrids and Their Potential Roles in Heterosis

Heterosis,one of the most important biological phenomena,refers to the phenotypic superiority of a hybrid over its genetically diverse parents with respect to many traits such as biomass,growth rate and yield.Despite its successful application in breeding and agronomic production of many crop and animal varieties,the molecular basis of heterosis remains elusive.The classic genetic explanations for heterosis centered on three hypotheses:dominance (Davenport,1908;Bruce,1910;Keeble and Pellew,1910;Jones,1917),overdominance (East,1908;Shull,1908) and epistasis (Powers,1944;Yu et al.,1997).However,these hypotheses are largely conceptual and not connected to molecular principles,and are therefore insufficient to explain the molecular basis of heterosis (Birchler et al.,2003).Recently,many studies have explored the molecular mechanism of heterosis in plants at a genome-wide level.These studies suggest that global differential gene expression between hybrids and parental lines potentially contributes to heterosis in plants (e.g.,Swanson-Wagner et al.,2006;Zhang et al.,2008;Wei et al.,2009;Song et al.,2010).Research suggests that genetic components,including cis-acting elements and trans-acting factors,are critical regulators of differential gene expression in hybrids (Hochholdinger and Hoecker,2007;Springer and Stupar,2007;Zhang et al.,2008).However,other research indicates that epigenetic components,the regulators of chromatin states and genome activity,also have the potential to impact heterosis (e.g.,Ha et al.,2009;He et al.,2010;Groszmann et al.,2011;Barber et al.,2012;Chodavarapu et al.,2012;Greaves et al.,2012a;Shen et al.,2012).     

分子生物学手段在植物系统与进化研究中的应用

在植物系统与进化研究中,为了揭示真实本质,必须从分子水平进行研究。植物分子系统学的研究包括两大方面,一是蛋白质与酶,二是核酸。酶电泳是分子水平上研究植物分子遗传学最经济有效的方法,可以有效地揭示自然居群中遗传结构、基因流动、变化系统、选择作用和系统发育等问题。植物核酸系统学的研究倍受青睐,因为核酸分子是最基本的进化单元,几乎不受主观因素影响。相关的核酸分析技术主要有：DNA杂交、DNA限制酶谱分析、RFLP分析、DNA指纹图技术、RAPD分析和核酸序列分析。在植物系统学和进化研究中,结合各方面的生物学证据,才能显示植物分子系统学的独特优势。     

Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals

Background  

Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics, not found in the primary sequence, that give "morphological" information. Despite the number of recent molecular studies on octocorals, there is no consensus opinion about a region that carries enough phylogenetic resolution to solve intrageneric or close species relationships. Moreover, intrageneric morphological information by itself does not always produce accurate phylogenies; intra-species comparisons can reveal greater differences than intra-generic ones. The search for new phylogenetic approaches, such as by RNA secondary structure analysis, is therefore a priority in octocoral research.     

Re-evaluation on the diversity of the polyphyletic genus Metaurostylopsis (Ciliophora, Hypotricha): ontogenetic, morphologic, and molecular data suggest the establishment of a new genus Apourostylopsis n. g

The urostylid genus Metaurostylopsis Song et al., 2001 was considered to be a well-outlined taxon. Nevertheless, recent evidence, including morphological, ontogenetic, and molecular information, have consistently revealed conflicts among congeners, regarding their systematic relationships, ciliature patterns, and origins of ciliary organelles. In the present work, the morphogenetic and morphogenetic features were re-checked and compared, and the phylogeny of nominal species was analysed based on information inferred from the small subunit ribosomal RNA (SS rRNA) gene sequence. In addition, the binary divisional process in a new isolate of Metaurostylopsis struederkypkeae Shao et al., 2008 is described. All results obtained reveal that the genus is a polyphyletic assemblage whose nominal congeners fall into three clades within the core Urostylida, based on SS rRNA gene sequences. These three clades not match the groups inferred from morphological/morphogenetical evidences. Some conflicting data from molecular and ontogenetic studies also indicate that single-gene information might not be consistently reliable in detecting the phylogenetic relationships among closely related groups and comprehensive multi-gene analyses are necessary to give a more exact evaluation for this divergent assemblage. According to our new understandings, five forms are confirmed to be true Metaurostylopsis. The morphotype Metaurostylopsis sinica Shao et al., 2008 should be excluded from the genus and represents a distinct type, and, thus, a new genus Apourostylopsis n. g. with it as the type specie, i.e. Apourostylopsis sinica (Shao et al., 2008) n. comb.     

毛茛科分子系统发育研究进展

毛茛科(Ranunculaceae)在被子植物的系统演化中占有十分重要的地位,其系统位置和科下演化关系一直备受争议。近20多年的分子系统学研究表明,以往基于形态学的分类系统与分子系统学研究结果存在巨大差异。通过形态学性状界定的绝大多数亚科都没有得到分子系统学支持。此外,通过形态学确定的一些属如升麻属(Cimicifuga)、黄三七属(Souliea)、獐耳细辛属(Hepatica)、白头翁属(Pulsatilla)和水毛茛属(Batrachium)等,根据分子系统学研究均应予以归并。而分子系统学研究也确立了一些类群的属级地位,如露蕊乌头属(Gymnaconitum)等。以中国分布的毛茛科植物为例,通过以往分子系统学研究,共有10个属被归并,2个属新被确立。然而,毛茛科分子系统学研究对于科下许多类群之间的关系目前仍然没有得到很好的解决,如毛茛亚科和翠雀族等类群的系统发育关系仍需要进行深入研究后方能确定。该文对近年来国内外有关毛茛科的分子系统学研究进展进行了综述,并对该科尚存的一些问题和未来的研究方向进行了讨论。     

Plant diversity and ecology on the Qinghai–Tibet Plateau

The Qinghai–Tibet Plateau (QTP) comprises a platform (sometimes called the Qinghai–Tibet Plateau sensu stricto), the Himalayas, and Hengduan Mountains (Liang et al.,2018; Mao et al.,2021). The latter two parts and adjacent highlands are also called the Pan-Himalaya. Numerous plants are distributed there with many endemic species, probably because of the high diverse landscapes created by continuous geological and climatic activities (Favre et al.,2015; Mao et al.,2021). As the well known biodiversity hotspot of the alpine plants in the world (Sun et al.,2017), many studies have been conducted on evolutionary origin and ecological adaptation of those species occurring in the QTP (e.g., Wen et al.,2014, 2019; Zhang et al.,2019). In the present special issue, we collected 15 related papers on this topic. Among them, two are invited reviews. Mao et al. (2021) provide a comprehensive review of evolutionary origin of species diversity on the QTP. Especially, they outlined major disputes and likely causes in this research topic, including circumscribing and naming the QTP, the QTP uplifts, dating of molecular phylogenetic trees, non-causal correlations between QTP uplifts and species diversification and the unified ice sheet. The authors also summarized genomic advancements related to high-altitude adaptation of both plants and animals. Tong et al. (2021) reviewed the reproductive strategies of animal-pollinated alpine plants on the QTP, involving pollination system, pollen limitation, self-pollination, and sexual system. In this region, 95.4% of animal-pollinated plants are pollinated by insects (i.e., bees, moths, butterflies, and flies) with only 4% by vertebrates (i.e., bats and birds). Self-pollination through self-compatibility shift from outcrossing has become an effective reproductive strategy to overcome pollen limitation in alpine plants. The other 13 research papers aimed to address origin and adaptation of alpine flora involving three major lines of evidence: genomics, ecology, and paleobotany. We hope that the collection of these papers will increase our understanding of the origin, speciation, and adaptation of alpine species on the QTP.     

宽体金线蛭嗜水气单胞菌感染的病原检验

对河北某宽体金线蛭（Whitmania pigra Whitman）养殖场所养殖的宽体会线蛭发生的病害,进行了发病情况、临床表现、病理变化等方面的枪验。同时,择代表菌株进行了16S rRNA基因的分子鉴定,测定了16S rRNA基因序列、分析了相关细菌相应序列的同源性、构建了系统发生树。结果表明所检病例为由嗜水气单胞菌（Aeronmnas hydrophila）所引起的感染。分离后做纯培养的10株嗜水气申胞菌均为同种血清型菌株;代表菌株对健康宽体金线蛭的人工感染试验表明了相应的原发病原学意义;药敏试验结果显示,对供试37种抗菌药物中的头孢噻肟等高度敏感、对链霉素等敏感、对苯唑青霉素等耐药。     

核基因在两栖爬行动物分子系统学中的研究进展

从DNA水平探索生物进化的理论、生物类群的演化历史具有重要的意义,应用DNA序列研究生物的系统发育和进化规律成为当前分子系统学研究的热点,与线粒体DNA相比,核基因由于包含有更加丰富的生物学信息,运用核基因序列或将核基因序列与线粒体基因序列相结合研究两栖爬行动物的系统发育,正成为分子系统学领域的新的发展趋势.Rag-1、Rag-2、tyrosinase、rhodopsin、C-mos等核基因已在两栖爬行动物分子系统学中得到了广泛的应用.由于目前的技术手段等诸多因素,限制了更多的核基因用于两栖爬行动物分子系统学研究.为此简要介绍了目前核基因在两栖爬行动物分子系统学方面的研究进展,并分析了核基因序列在分子系统学应用上面临的问题和应用前景.     

A genomic schism in birds revealed by phylogenetic analysis of DNA strings

The molecular systematics of vertebrates has been based entirely on alignments of primary structures of macromolecules; however, higher order features of DNA sequences not used in traditional studies also contain valuable phylogenetic information. Recent molecular data sets conflict over the phylogenetic placement of flightless birds (ratites - paleognaths), but placement of this clade critically influences interpretation of character change in birds. To help resolve this issue, we applied a new bioinformatics approach to the largest molecular data set currently available. We distilled nearly one megabase (1 million base pairs) of heterogeneous avian genomic DNA from 20 birds and an alligator into genomic signatures, defined as the complete set of frequencies of short sequence motifs (strings), thereby providing a way to directly compare higher order features of nonhomologous DNA sequences. Phylogenetic analysis and principal component analysis of the signatures strongly support the traditional hypothesis of basal ratites and monophyly of the nonratite birds (neognaths) and imply that ratite genomes are linguistically primitive within birds, despite their base compositional similarity to neognath genomes. Our analyses show further that the phylogenetic signal of genomic signatures are strongest among deep splits within vertebrates. Despite clear problems with phylogenetic analysis of genomic signatures, our study raises intriguing issues about the biological and genomic differences that fundamentally differentiate paleognaths and neognaths.     

Concurrent speciation in the eastern woodland salamanders (Genus Plethodon): DNA sequences of the complete albumin nuclear and partial mitochondrial 12s genes

Salamanders of the North American plethodontid genus Plethodon are important model organisms in a variety of studies that depend on a phylogenetic framework (e.g., chemical communication, ecological competition, life histories, hybridization, and speciation), and consequently their systematics has been intensively investigated over several decades. Nevertheless, we lack a synthesis of relationships among the species. In the analyses reported here we use new DNA sequence data from the complete nuclear albumin gene (1818 bp) and the 12s mitochondrial gene (355 bp), as well as published data for four other genes (Wiens et al., 2006), up to a total of 6989 bp, to infer relationships. We relate these results to past systematic work based on morphology, allozymes, and DNA sequences. Although basal relationships show a strong consensus across studies, many terminal relationships remain in flux despite substantial sequencing and other molecular and morphological studies. This systematic instability appears to be a consequence of contemporaneous bursts of speciation in the late Miocene and Pliocene, yielding many closely related extant species in each of the four eastern species groups. Therefore we conclude that many relationships are likely to remain poorly resolved in the face of additional sequencing efforts. On the other hand, the current classification of the 45 eastern species into four species groups is supported. The Plethodon cinereus group (10 species) is the sister group to the clade comprising the other three groups, but these latter groups (Plethodon glutinosus [28 species], Plethodon welleri [5 species], and Plethodon wehrlei [2 species]) probably diverged from each other at approximately the same time.