Advances in the study of the systematics of Actinidia Lindley

Actinidia (Actinidiaceae) is of economic importance for its edible fruits.Traditional taxonomy divided the genus into four sections,Leiocarpae Dunn,Maculatae Dunn,Strigosae Li,and Stellatae Li.However,phylogenetic studies based on morphology and molecular markers have posed challenges to the four-section scheme.It appears that the natural classification of the genus points to the existence of two groups,one comprising Leiocarpae,and the other Maculatae,Strigosae,and Stellatae.Single- or low-copy genes would probably be useful in untangling the perplexity andthe reticulate evolution of the genus.However,any phylogenetic studies must be firmly based on sound taxonomy and identification.Population sampling throughout the distribution range of the taxa should be carried out in order to study the variation pattern of the morphology and,ultimately,to clarify the confusion existing in some taxa.A combination of morphometrics and molecular data is highly desirable for resolving the uncertainty in Actinidia taxonomy.     

Two new species of Phyllonema (Rivulariaceae,Cyanobacteria) with an emendation of the genus

Two untapered, heterocytous species were observed and collected from the intertidal and supratidal zones of the Mexican coastline of the Pacific Ocean near Oaxaca and from the Gulf of Mexico. These populations were highly similar in morphology to the freshwater taxon Petalonema incrustans in the Scytonemataceae. However, 16S rRNA sequence data and phylogenetic analysis indicated that they were sister taxa to the epiphyllic, Brazilian species Phyllonema aveceniicola in the Rivulariaceae, described from culture material. While genetic identity between the two new species was high, they differed significantly in morphology, 16S rRNA gene sequence identity, and sequence and structure of the 16S–23S ITS region. Their morphology differed markedly from the generitype of the previously monotypic Phyllonema, which has tapered, heteropolar, single‐false branched trichomes with very thin or absent sheath. The two new species, Phyllonema ansata and Phyllonema tangolundensis, described from both culture and environmental material, have untapered, isopolar, geminately false branched trichomes with thick, lamellated sheaths, differences so significant that the species would not be placed in Phyllonema without molecular corroboration. The morphological differences are so significant that a formal emendation of the genus is required. These taxa provide a challenge to algal taxonomy because the morphological differences are such that one would logically conclude that they represent different genera, but the phylogenetic evidence for including them all in the same genus is conclusive. This conclusion is counter to the current trend in algal taxonomy in which taxa with minor morphological differences have been repeatedly placed in separate genera based primarily upon DNA sequence evidence.     

Restriction-site variation of PCR-amplified chloroplast DNA regions and its implication for the evolution and taxonomy of Actinidia

 Twenty six restriction sites from five PCR-amplified chloroplast DNA sequences (rbcL, psbA, rpoB, and two spacers flanking the trnL gene) were mapped and analysed in 20 Actinidia taxa, encompassing all four sections into which the genus is divided. At least three species out of the 20 examined have been found to have originated through natural interspecific hybridisation on the basis of the discrepancy between morphological and biochemical traits and the cpDNA profiles of pairs of species. A widely reticulate evolution has therefore been postulated in Actinidia. Wagner and weighted parsimony analysis produced consensus trees that did not match the traditional taxonomy based on morphological characters. The molecular data clearly showed that some taxa, such as A. rufa and A. kolomikta, occupy a wrong position and most, if not all, of the traditional groups represented by sections and series are weakly supported, since they appear as polyphyletic. A. chinensis and A. deliciosa were confirmed to be very closely related. Since chloroplast DNA is paternally inherited in Actinidia, A. chinensis is a paternal progenitor, if not the only one, of A. deliciosa, the domesticated kiwifruit. Received: 18 August 1997 / Accepted: 6 October 1997     

Molecular phylogeny of the blind cavefish <Emphasis Type="Italic">Phreatichthys andruzzii</Emphasis> and <Emphasis Type="Italic">Garra barreimiae</Emphasis> within the family Cyprinidae

The phylogenetic relationships of two cavefish, Phreatichthys andruzzii and Garra barreimiae, belonging to the family Cyprinidae, were investigated by sequencing the mitochondrial cytochrome b gene. These cavefish species are native to Somalia (eastern Africa) and Oman (southeastern Arabian peninsula), respectively, and so far no molecular support to their taxonomy and phylogenetic position was ever provided. The analysis of cytochrome b sequences showed that the species are monophyletic taxa, closely related to each other and to other species of the genus Garra. Molecular clock calculations allowed to date the origin of these hypogaean species back to the Plio-Pleistocene and support the hypothesis that African cyprinids originated from Miocenic immigrations of Asian ancestors.     

Phylogeny of <Emphasis Type="Italic">Litsea</Emphasis> and related genera (Laureae-Lauraceae) based on analysis of <Emphasis Type="Italic">rpb2</Emphasis> gene sequences

The relationship between Litsea and related genera is currently unclear. Previous molecular studies on these taxa using cpDNA and nrITS were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the rpb2 gene as a source of molecular information to better resolve the phylogenetic analysis. Although rpb2 was believed to be a single-copy gene, our cloning results showed that most species examined possessed several copies of these sequences. However, the genetic distance among copies from any one species was low, and these copies always formed monophyletic groups in our molecular trees. Our phylogenetic analyses of rpb2 data resulted in better resolved tree topologies compared to those based on cpDNA or nrITS data. Our results show that monophyly of the genus Litsea is supported only for section Litsea. As a genus, Litsea was shown to be polyphyletic. The genera Actinodaphne and Neolitsea were resolved as monophyletic groups in all analyses. They were also shown to be sisters and closer to the genus Lindera than to the genus Litsea. Our results also revealed that the genus Lindera is not a monophyletic group.     

Characterization of a RAPD fragment unique to species with hairy fruit skin in the genus<Emphasis Type="Italic">Actinidia</Emphasis>

To develop a SCAR primer related to the hairy-fruit trait in the genusActinidia, we took a PCR-RAPD approach using arbitrary 10-mer primers. PCR with the UBC 376 primer generated specific fragments from three species with hairy fruit skin. Those fragments were then cloned to determine their nucleotide sequences. Two SCAR primers were designed from the UBC 376 primer and nucleotide sequences were obtained from the PCR fragments. A SCAR primer, OKC385, specifically amplified a 385-bp fragment from one clone ofActinidia eriantha, four ofActinidia chinensis, and four ofActinidia deliciosa. Deduced amino acid sequences of this fragment showed high sequence homology with plant cellulose synthases, which are involved in the biosynthesis of cellulose, a major cell wall component. The 385-bp fragment was specifically detected only in the seriesPerfectae C.F. Liang of sectionStellatae Li. This type has many hairs on the leaves, fruits, and stems, suggesting that the gene containing the PCR fragment is involved in hair formation in this phylogenetic group. Taken together, our results suggest that the SCAR primer, OKC385, can be used as a specific primer for early selection of the non-hair trait in breeding of the genusActinidia.     

Phylogenetic relationships of the enigmatic ornate shiner,Cyprinella ornata,a species endemic to Mexico (Teleostei: Cyprinidae)

The systematics and taxonomy of North Americancyprinid fishes has historically been said tobe in a chaotic state of affairs. Much of theconfusion as to relationships of species restsin the lack of explicit phylogenetic hypothesesof species and reliance upon degree ofdistinctiveness of taxa or their overallsimilarity for generic placement. Some specieshave had more turbulent or variable taxonomichistories than others. The ornate shiner, Cyprinella ornata, is one of those species,having been placed in the genera Notropis,Codoma, and Cyprinella within the last20 years and found in current texts in any ofthese three genera. Most of the confusionregarding placement of this species has beenrelated to lack of explicit phylogenetichypotheses to formulate its classification, butto a certain degree some researchers haveignored phylogenetic studies and preferred torely upon its morphological distinctiveness orreproductive behavioral traits of questionablehomology to place it in a monotypic genus andalign it with the genera Pimephales andOpsopoeodus.I present a phylogenetic analysis based oncomplete Cytochrome b sequences fromornate shiners, other species of Cyprinella, purported relatives, and severalother species of the Shiner Clade to determinethe phylogenetic affinities of this enigmaticspecies. Molecular analysis reveals the ornateshiner to be more closely related to species ofCyprinella than to a Pimephalesplus Opsopoeodus clade as previouslydiscussed in one morphological analysis, or asargued by Page and Johnston (1990), Johnstonand Page (1992) and Page and Ceas (1989) basedon observations of spawning behaviors andhypotheses of homology between crevice-spawningand egg-clumping behaviors. This molecularanalysis is more consistent with earliermorphological phylogenetic hypotheses of Mayden(1989) wherein these two clades are notconsidered to be closely related and the ornateshiner is a member of the genus Cyprinella.     

Revision and phylogenetic assessment of the rove beetle genus Pseudohesperus Hayashi,with broad reference to the subtribe Philonthina (Coleoptera: Staphylinidae: Staphylinini)

This paper studies the phylogeny of the rove beetle subtribe Philonthina, to test its hypothetical monophyly and to unravel the evolutionary relationships of the subtribe and its included genus‐level taxa, with emphasis on the genus Pseudohesperus and its close‐allied relatives. The phylogenetic analyses are based on 105 adult morphological characters and 66 terminal taxa, i.e., all six members of Pseudohesperus, 51 species to represent 29 other genera of the subtribe Philonthina, seven species to represent the other six subtribes of Staphylinini, one species of the tribes Arrowinini, and one of the Platyprosopini. According to the phylogenetic results obtained, the genus Erichsonius should move out from the hitherto‐defined subtribe Philonthina and thus the monophyly of this taxon is challenged. The phylogenetic tree suggests that the genera Hesperus and Belonuchus might not be monophyletic, but the monophyly of Pseudohesperus and the sister relationship between it and Bisnius are well supported. The species‐level phylogenetic relationships of the genus Pseudohesperus reveal a clear pattern of species diversification that can be correlated well with the species' zoogeographical patterns. The paper also revises the taxonomy of Pseudohesperus and describes five new species from China: Pseudohesperus luteus Li & Zhou sp. nov. , Pseudohesperus pedatiformis Li & Zhou sp. nov. , Pseudohesperus tripartitus Li & Zhou sp. nov. , Pseudohesperus sparsipunctatus Li & Zhou sp. nov. , and Bisnius lubricus Li & Zhou sp. nov. An identification key to the species of Pseudohesperus is provided and their geographical distributions are mapped. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 679–722.     

New insights into and limitations of the molecular phylogeny in the taxon-rich land snail genus Montenegrina (Mollusca: Gastropoda: Clausiliidae)

Rock-dwelling gastropods are usually patchily distributed in limestone habitats, presumably have low active and passive dispersal ability and often represent narrow-ranged endemic taxa. Their current taxonomy is predominantly shell morphology based, and it remains unknown whether the morphologically differentiated and geographically separated populations represent phylogenetic clades. In this study, we analysed the hyperdiverse, terrestrial door snail genus Montenegrina. Based on the current taxonomy defined by shell morphology, it contains 29 species and 106 subspecies distributed in the Balkan region. The constructed phylogenetic tree using three mitochondrial markers was used to test whether it agrees with the current taxonomy. In this comprehensive tree, about half of the species and subspecies are monophyletic. Some of the paraphylies could be reasonably resolved by taxonomic changes; that is, some subspecies should be reassigned or raised to species level. Other incongruencies probably arose due to introgression even between distant clades. The histone genes turned out to be unsuitable for elucidating the phylogeny of Montenegrina. In the species-delimitation tests, considerably more molecular operational taxonomic units were delimited than the number of presently described species. The present data indicate that (a) shell morphology-based taxonomy and taxon recognition can be problematic in such a large and morphologically highly variable genus; (b) the potential error due to incomplete sampling presents a problem in a genus as variable as Montenegrina; (c) multi-locus analyses should be conducted to arrive at a better basis for species delimitation; and (d) integrative approaches including genetic as well as morphological/anatomical data from a comprehensive geographic sample are necessary.     

Numerical analyses of seed morphology and its taxonomic significance in the tribe Nigelleae (Ranunculaceae)

We examined the seed morphology of Nigella, Garidella and Komaroffia to aid systematics and taxonomy. The seeds of 21 taxa in 20 species from Mediterranean and West Asian countries were studied using both zoom stereo and scanning electron microscopy (SEM). Principal coordinate analysis (PCoA) and unweighted average linkage analysis (UPGMA) were performed to assess the contribution of seed characters to the taxonomy of the tribe. Representative pictures from zoom stereo microscopy and SEM studies and measurement of seeds are presented. Most studied species showed unique seed surface sculpturing features, and seed shape, size and surface sculpturing separated the studied taxa into five main groups. However, the variation in seed shape and color were found to be in conflict with the generic taxonomy while macromorphological characters were found more congruent with the sectional taxonomy than with the generic taxonomy. Five main types of seed ornamentations – rugulose + striate, granulate, smooth, rugulose and mucronulate – were identified. Patterns in seed micromorphology strongly supported the sectional level taxonomy of Nigella. Two of the three sections of the genus were found to be well differentiated in terms of seed characters. Furthermore, seed morphology alone provide good support to Garidella as a distinct genus, but shows less taxonomic value for Komaroffia.     

石山苣苔属(苦苣苔科)花形态演化及分类学意义

石山苣苔属(苦苣苔科)约30种,主要分布于我国南部的石灰岩地区.目前该属已知物种数虽少但花形态极其多样,是该科中分类最为困难的类群之一.基于分子证据,其它8个属中花形态迥异的一些物种被并入石山苣苔属.然而,该属花形态的演化趋势缺乏系统性的研究,传统分类对属的界定与分子系统学研究结果相矛盾的原因,以及是否有形态特征支持新界定的石山苣苔属还不清楚.该研究中,总共编码了19种石山苣苔属植物和9种报春苣苔属植物的35个形态特征,其中包括26个花部形态特征,在分子系统树上追踪了它们的演化路径.结果表明:无论属内还是属间,多数花部形态特征,尤其以往属的分类界定特征,在演化过程中变化频繁且发生了高度同塑性演化,这是导致传统形态分类不自然的关键因素.此外,在观察研究的所有特征中,花丝和柱头的差异可能在石山苣苔属植物共同祖先中经历了演变,或可用于区分石山苣苔属与其姐妹报春苣苔属的大多数种类.因此,在苦苣苔科植物的分类学研究中应当慎用这些花部性状作为分类依据,而且应对形态特征进行广泛地观察研究,在密集的取样和分辨率更高、更可靠的系统树上追踪它们的演化规律.更为重要的是,需要进一步研究导致复杂形态性状演化的内在分子调控机理和外在的自然选择动力,最终更加深入地理解石山苣苔属等典型喀斯特植物的演化过程和机理.     

Exon primed intron-crossing (EPIC) markers reveal natural hybridization and introgression in Actinidia (Actinidiaceae) with sympatric distribution

Interspecific hybridization is widespread among plants. Understanding the phylogenetic relationships among species is necessary for revealing the potential hybridization events. Actinidia, best known as kiwifruit genus found throughout a wide range in eastern Asian from Indonesia to Siberia. In this study, phylogenetic relationships of Actinidia species with sympatric distributions were investigated using three chloroplast introns (trnL-F, atpB-rbcL and rpl32-trnL) and three Exon primed intron-crossing (EPIC) markers. Chloroplast phylogeny supports non-monophyly of the five species studied excluding Actinidia fulvicoma var. lanata. The non-monophyly was also revealed by EPIC markers. Our results showed EPIC markers are more variable and informative for phylogenetic inference than that of chloroplast markers. The incongruences between loci from the plastid and nuclear DNA phylogenic trees may stem from incomplete lineage sorting or historical introgression hybridization. Incomplete lineage sorting may explain the non-monophyly between Actinidia chrysantha (section Maculatae) and other four species (section Stellatae), and introgression hybridization and high level of interspecific gene flow may explain the non-monophyly among the species of sect. Stellatae. Thus, natural hybridization and introgression may be common in Actinidia with sympatric distribution.     

Phylogenetic analysis of the genus Hordeum using repetitive DNA sequences

A set of six cloned barley (Hordeum vulgare) repetitive DNA sequences was used for the analysis of phylogenetic relationships among 31 species (46 taxa) of the genus Hordeum, using molecular hybridization techniques. in situ hybridization experiments showed dispersed organization of the sequences over all chromosomes of H. vulgare and the wild barley species H. bulbosum, H. marinum and H. murinum. Southern blot hybridization revealed different levels of polymorphism among barley species and the RFLP data were used to generate a phylogenetic tree for the genus Hordeum. Our data are in a good agreement with the classification system which suggests the division of the genus into four major groups, containing the genomes I, X, Y, and H. However, our investigation also supports previous molecular studies of barley species where the unique position of H. bulbosum has been pointed out. In our experiments, H. bulbosum generally had hybridization patterns different from those of H. vulgare, although both carry the I genome. Based on our results we present a hypothesis concerning the possible origin and phylogeny of the polyploid barley species H. secalinum, H. depressum and the H. brachyantherum complex.     

An integrative approach to species delimitation in Echinodorus (Alismataceae) and the description of two new species

Summary  Taxonomy of the genus Echinodorus is partially revisited in the light of current understanding of the phylogenetic relationships of the genus. As a result of new taxonomy, the species status of some previously synonymised taxa are restored, other names are synonymised, and some nomenclatural problems unnoticed by previous authors are resolved. Two new species, Echinodorus reptilis and E. emersus are described. The subgeneric divisions of the genus are not accepted, and all subspecific taxa are either rejected or established as species. As a result, 28 species based on a phylogenetic species concept are now recognised in Echinodorus and an identification key to these species is provided.     

猕猴桃属十个种的染色体倍性鉴定

猕猴桃属(Actinidia)植物全世界有66种,约有118个种下分类单位(也有新的划分方法将其划分为54种21变种),其中大部分为中国特有。在猕猴桃杂交育种中,不同倍性之间选配不当会出现杂交失败、后代不育等现象,因此倍性鉴定是猕猴桃常规育种亲本选择的前提条件之一。但到目前为止,不少猕猴桃种或亚种的染色体倍性研究并不十分清楚,因而限制了这些资源的进一步开发利用。该研究针对广西植物研究所猕猴桃种质资源圃收集的目前倍性尚不明确的白萼、白花柱果、二色花、临桂、卵圆叶、桃花、宛田、长果、融水和五瓣猕猴桃等10个种类的猕猴桃,使用酸解法制备染色体标本,通过显微镜观察确定其倍性。这10个种类大多为广西特有,其中蕴藏着独特的优良园艺性状,具有很高的生产和开发价值。该研究结果表明这10个种类猕猴桃的染色体倍性均为二倍体(2n=2x=58)。该研究结果进一步丰富了猕猴桃种质资源多样性数据库,为这些猕猴桃资源的合理开发利用奠定了基础。     

Taxonomy and molecular phylogeny of the Neotropical genus Atlantoscia (Oniscidea,Philosciidae): DNA barcoding and description of two new species

Identification to the species level using morphology is challenging when usual diagnostic characters are similar amongst related taxa. Within the Neotropical genus Atlantoscia, differences between nominal species are generally small and restricted to a few characters. Despite the power of DNA sequencing to identify and distinguish between species, molecular phylogenies of terrestrial isopods from the Neotropics have not been determined. In this study, two new species of Atlantoscia were described and molecular markers were used to verify both the validity of the current taxonomy and the relationships amongst the species within this genus. All of the recognized Atlantoscia species were strongly supported in the generated phylogenetic trees. The average congeneric distance was 14.7%, with Atlantoscia ituberasensis and Atlantoscia rubromarginata showing the highest genetic divergence. Our results demonstrate the utility of the cytochrome c oxidase subunit I gene together with DNA barcoding to reliably distinguish Atlantoscia species. They also show that DNA barcoding may be helpful in those cases in which classical taxonomy does not provide clear‐cut species resolution. © 2015 The Linnean Society of London     

Taxonomic revision of the dolphin genus Lagenorhynchus

Evolutionary relationships among cetaceans within the family Delphinidae have been difficult to resolve due to the high number of species and their relatively rapid radiation. This is the case for the dolphin species currently placed in the genus Lagenorhynchus, and their relations to Cephalorhynchus and Lissodelphis species. Phylogenetic relationships among these species have been investigated using multiple lines of evidence, and that evidence consistently suggests that the six species currently assigned to Lagenorhynchus do not form a monophyletic group. Here, we summarize findings from studies of morphology, genetics, historical biogeography, and acoustics that offer insight into the phylogenetics of these taxa. We present the taxonomic basis for revision of Lagenorhynchus, propose retention of Lagenorhynchus albirostris and reassignment of the remaining five species into other existing generic names, namely Leucopleurus acutus, Sagmatias australis, Sagmatias cruciger, Sagmatias obliquidens, and Sagmatias obscurus. Making these revisions now so that the taxonomy better reflects evolutionary relationships among these species will ensure that future studies include the most appropriate taxa for investigating the complex phylogenetic and systematic relationships among cetaceans. However, comprehensive analyses using multiple lines of evidence are still needed to clarify the phylogenetic relationships within and among the Lissodelphininae genera Cephalorhynchus, Lissodelphis, and Sagmatias.