Origins of polyploids: an example from peonies (Paeonia) and a model for angiosperms

The majority of tetraploid peonies are allopolyploids derived from crosses between phylogenetically distinct diploid lineages. Tetraploid Paeonia obovata was previously considered to be an autopolyploid because it is morphologically indistinguishable from the diploid of the same species. The presence of the Adh2 gene in tetraploid P. obovata but the inability to amplify the Adh2 gene from Chinese diploids of P. obovata, however, suggests that the tetraploid was not an autotetraploid derivative of the geographically adjacent diploid populations in China. The Adh gene phylogenies rather suggest that the tetraploid originated from crosses between two geographical races of diploid P. obovata distributed in China and Japan. The intermediate status of tetraploid P. obovata between auto‐ and allopolyploidy highlights the need for population genetic analyses of polyploid origins along the continuous range of genomic divergence. Here we present a model that describes the probabilities of polyploid formation and establishment as a function of genomic divergence between diploid progenitors. The probability of polyploid formation (P_f) is obtained from the multiplication of the probability of production of unreduced gametes (P_g) and the probability of ‘hybridization’ (P_h). P_f stays relatively stable when the genomic divergence is low, and then decreases progressively rapidly with the increase of genomic divergence between diploid progenitors. The probability of polyploid establishment (P_e), which depends on the rate of appearance of stable beneficial gene combinations and the rate of fertility restoration, is positively correlated with the genomic divergence of diploid parents. Multiplication of P_f and P_e gives an overall probability of polyploid origins (P_o) that varies continuously along the genomic divergence between diploid progenitors. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82 , 561–571.     

鸻形目15种鸟类线粒体ND6基因序列差异及其系统进化关系

采用PCR和质粒克隆测序方法,首次获得鸻形目l5种鸟类线粒体基因组的ND6基因全长522bp的序列。经对位排列,序列间末见有插入和缺失,共有216个变异位点,种间序列差异为5．17％—19．92％。以白鹤为外群,用NJ法构建15种鸟类的进化关系树。研究结果表明：构建的系统树将鸻形目15种鸟类分为2个支系：第1支系包括蒙古沙鸻、环颈鸻、灰斑鸻和反嘴鹬。第2支系包括红脚鹬、林鹬、青脚鹬、翘嘴鹬、翻石鹬、大滨鹬、尖尾滨鹬、斑尾塍鹬、中杓鹬、大杓鹬和白腰杓鹬,其中鹬属的3个种和杓鹬属的3个种分别组成一个单系;翘嘴鹬和翻石鹬、大滨鹬和尖尾滨鹬分别聚为姊妹群,表现出较近的亲缘关系;斑尾塍鹬独立分支出来。分子证据提示：鹬科中的塍鹬属、鸻科中的斑鸻属应提升为亚科分类阶元;反嘴鹬与鸻科鸟类亲缘关系较近,组成一个单系,将其归入鸻科下属的一个类群更为合理,与核型研究结果及Sibley新分类体系的观点相一致。     

Physical mapping of ribosomal RNA genes in peonies (Paeonia,Paeoniaceae) by fluorescent in situ hybridization: implications for phylogeny and concerted evolution

Physical maps of the 18S–5.8S–26S ribosomal RNA genes (rDNA) were generated by fluorescent in situ hybridization for five diploid Paeonia species, P. delavayi and P. rockii of section Moutan, and P. emodi, P. tenuifolia, and P. veitchii of section Paeonia. Of five pairs of mitotic chromosomes, rDNA loci were mapped near the telomeres of chromosomes 3, 4, and 5 of P. rockii and P. tenuifolia, chromosomes 2, 3, 4, and 5 of P. delavayi, and all five pairs of chromosomes of P. emodi and P. veitchii. Combining this information with the previously obtained rDNA maps of P. brownii and P. californica of section Oneapia, we hypothesized that the most recent common ancestor of extant peony species had three rDNA loci located on chromosomes 3, 4, and 5. Increase in number of rDNA loci occurred later in each of the three sections, and the increase from three to four loci represents a parallel gain of an rDNA locus on chromosome 2 in P. delavayi of section Moutan and P. brownii of section Oneapia. The increase in number of rDNA loci likely resulted from the translocation of rDNA repeats from chromosomes bearing rDNA loci to chromosomes without them; such translocation is probably facilitated by the telomeric location of rDNA loci. For allotetraploid peony species lacking polymorphism in sequences of the internal transcribed spacers (ITS) of rDNA, the rDNAs derived from divergent diploid parents may have been homogenized through concerted evolution among at least six rDNA loci in the allotetraploids. Chromosomal location of rDNA loci has a more substantial impact on the tempo of concerted evolution than the number of loci.     

Molecular analysis of phylogenetic relationships among Myrmecophytic macaranga species (Euphorbiaceae)

Many species of the paleotropical pioneer tree genus Macaranga Thou. (Euphorbiaceae) live in association with ants. Various types of mutualistic interactions exist, ranging from the attraction of unspecific ant visitors to obligate myrmecophytism. In the latter, nesting space and food bodies are exchanged for protection by highly specific ant partners (mainly species of the myrmicine genus Crematogaster). As a first step toward elucidating the coevolution of ant-plant interactions in the Macaranga-Crematogaster system, we have initiated a molecular investigation of the plant partners' phylogeny. Nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were analyzed for 73 accessions from 47 Macaranga species, representing 17 sections or informally described species groups. Three accessions from the putative sister taxon Mallotus Lour, were included as outgroups. Cladograms of the ITS data revealed Macaranga to be nested within Mallotus. ITS sequences are highly similar within section Pachystemon s.str., suggesting a relatively recent and rapid radiation of obligate myrmecophytes within this section. Forty-three accessions, mainly of ant-inhabited species, were additionally investigated by random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) techniques. Phenetic analysis of RAPD and MP-PCR banding profiles generally confirmed the ITS results. Best resolutions for individual clades were obtained when ITS and RAPD/MP-PCR data were combined into a single matrix and analyzed phenetically. The combined analysis suggests multiple (four) rather than a single evolutionary origin of myrmecophytism, at least one reversal from obligate myrmecophytism to nonmyrmecophytism, and one loss of mutualistic specifity.     

Molecular phylogenetic relationships of family Haemulidae (Perciformes: Percoidei) and the related species based on mitochondrial and nuclear genes

Haemulidae species are morphologically diversified fishes with wondrous and changeable coloration. These species are prevalent in global tropical, subtropical, and temperate inshore reef areas. Previous morphological classification within Haemulidae and some related families was problematic, and no comprehensive molecular evaluation was conducted on these groups. In this study, we revealed the first molecular phylogenetic analysis involving representative species within Haemulidae and the relevant families (Nemipteridae and Teraponidae). The analysis was performed using both mitochondrial DNA (16S rRNA) and nuclear DNA (TMO-4c4) genes to construct maximum parsimony, maximum likelihood, and Bayesian analysis tree topologies. The molecular phylogeny recovered well-resolved relationships within Haemulidae species and the problematic taxa. In the trees, the Haemulidae species (except for genus Hapalogenys) were divided into two distinct sister lineages, including grunts (Haemulinae) and sweetlips (Plectorhynchinae). Hapalogenys was positioned outside the major Haemulidae tribe and formed an independent group, which challenged the traditional taxonomy that Hapalogenys was classified into Haemulidae. The results did agree with most current studies that Hapalogenys was only distantly related to Haemulidae and could potentially be removed from this family. Additionally, the genus Diagramma was observed to be tightly grouped inside the clade Plectorhinchus, indicating its highly close affinity within Plectorhinchus. Regarding interfamily relationships, the phylogenetic constructions suggested distant relationships within two pairs: between Scolopsis and Haemulidae and between Teraponidae and Haemulidae. Scolopsis was revealed to be highly close with Nemipteridae, and Teraponidae was clustered in an independent group, which was in accordance with most current taxonomic studies.     

形目15种鸟类线粒体ND6基因序列差异及其系统进化关系

采用PCR和质粒克隆测序方法 ,首次获得形目 15种鸟类线粒体基因组的ND6基因全长 5 2 2bp的序列。经对位排列 ,序列间未见有插入和缺失 ,共有 2 16个变异位点 ,种间序列差异为 5 17%～ 19 92 %。以白鹳为外群 ,用NJ法构建 15种鸟类的进化关系树。研究结果表明 :构建的系统树将形目 15种鸟类分为 2个支系。第 1支系包括蒙古沙、环颈、灰斑和反嘴鹬。第 2支系包括红脚鹬、林鹬、青脚鹬、翘嘴鹬、翻石鹬、大滨鹬、尖尾滨鹬、斑尾塍鹬、中杓鹬、大杓鹬和白腰杓鹬 ,其中鹬属的 3个种和杓鹬属的 3个种分别组成一个单系 ;翘嘴鹬和翻石鹬、大滨鹬和尖尾滨鹬分别聚为姊妹群 ,表现出较近的亲缘关系 ;斑尾塍鹬独立分支出来。分子证据提示 :鹬科中的塍鹬属、科中的斑属应提升为亚科分类阶元 ;反嘴鹬与科鸟类亲缘关系较近 ,组成一个单系 ,将其归入科下属的一个类群更为合理 ,与核型研究结果及Sibley新分类体系的观点相一致 [动物学报 49(1) :6 1～ 6 7,2 0 0 3]。     

芍药属牡丹组基于形态学证据的系统发育关系分析

对芍药属牡丹组Paeonia L.sect.Moutan DC.（全部野生种）40个居群进行了基于形态学证据的系统学分析,试图建立组内种间的系统发育关系。利用PAUP （4.0）计算机程序分别构建了建立在25个形态学性状基础上的所有研究类群的距离树（UPGMA、NJ）和最大简约树（MP）。所得树的拓扑结构基本一致,差异只发生在距离树和简约树之间,在由形态和细胞学关系都很近的5个种（牡丹P.suffruticosa、矮牡丹P.jishanensis、卵叶牡丹P.qiui、紫斑牡丹P.rockii和凤丹P.o     

Paeonia rotundiloba (D.Y.Hong) D.Y.Hong: A new status in tree peonies (Paeoniaceae)

Paeonia decomposita Hand.-Mazz.subsp,rotundiloba D.Y.Hong is here raised to the specific rank,P.rotundiloba (D.Y.Hong) D.Y.Hong,based on its distinctiveness of four diagnostic characters:number of carpels;height of disk; number of leaflets of the lower leaves,and shape of the terminal leaflets; and unpublished molecular data.Paeonia rotundiloba differs distinctly from P.decomposita in having carpels mostly 3,less often 2 or 4,very rarely 5 (vs.almost always 5,very occasionally 4 or 3),disk 8-15 mm high (vs.4-9.6 mm),leaflets mostly 19-39(vs.29-63) in number,and ratio of length to width of the terminal leaflets 1.09-1.93 (vs.1.81-2.99).     

Hydra of Hawaii: phylogenetic relationships with continental species

The presence of freshwater hydra in the Hawaiian Islands, over 3,700 km from the nearest continental margin, provokes the question of how these animals could reach the islands. We examined three islands for hydra and found two species (the brown hydra, Hydra vulgaris Pallas 1766, and green hydra, H. viridissima Pallas 1766) present at multiple locations on Oahu and Kauai, and at a single site on Hawaii. Phylogenetic analysis based on the internal transcribed spacer (ITS1 and ITS2) regions of ribosomal DNA indicates that all collected strains of brown hydra were closely related to each other—consistent with a single introduced origin. The analysis also shows that all sampled Hawaiian brown hydra fall within a specific clade of H. vulgaris. This clade is sister to a North American clade and nested within a deeper North/Central America clade. The clade with all the Hawaiian brown hydra includes also individuals from Southern California, suggesting a Californian origin for the brown Hawaiian hydra. Hawaiian hydra were probably transported to the islands by man.     

Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared with nuclear data. In this study, we intended to identify a set of desirable nuclear genes for resolving the phylogeny of the temperate woody bamboos. Using two different methodologies, we identified 209 and 916 genes, respectively, as putative single copy orthologous genes. A total of 112 genes was successfully amplified and sequenced by next‐generation sequencing technologies in five species sampled from the tribe. As most of the genes exhibited intra‐individual allele heterozygotes, we investigated phylogenetic utility by reconstructing the phylogeny based on individual genes. Discordance among gene trees was observed and, to resolve the conflict, we performed a range of analyses using BUCKy and HybTree. While caution should be taken when inferring a phylogeny from multiple conflicting genes, our analysis indicated that 74 of the 112 investigated genes are potential markers for resolving the phylogeny of the temperate woody bamboos.     

The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup

The DNA sequences of the Adh genes of three members of the Drosophila melanogaster species subgroup have been determined. This completes the Adh sequences of the eight species of this subgroup. Two species, D. yakuba and D. teissieri, possess processed Adh pseudogenes. In all of the species of the subgroup, a gene of unknown function, Adhr, is located about 300 bp 3' to Adh. Although this gene is experiencing a higher rate of synonymous substitution than Adh, it is more constrained at the amino acid level. Phylogenetic relationships between all eight members of the melanogaster subgroup have been analyzed using a variety of methods. All analyses suggested that the D. yakuba and D. teissieri pseudogenes have a single common ancestor, rather than evolving independently in each species, and that D. melanogaster is the sister species to D. simulans, D. sechellia, and D. mauritiana. The evolutionary relationships of the latter three species remain equivocal.      

Molecular phylogenetic relationships among species of the Malagasy-Comoran gecko genus Paroedura (Squamata: Gekkonidae)

We use approximately 3100bp of mitochondrial (ND2, ND4) and nuclear (RAG1, phosducin) DNA sequence data to recover phylogenetic relationships among 14 of the 16 recognized taxa of the lizard genus Paroedura as well as two undescribed forms. These geckos are endemic to Madagascar and the Comores and are popularly kept and bred by herpetoculturalists. The closest relative of Paroedura is another Indian Ocean leaf-toed gecko, Ebenavia. Both Bayesian inference and maximum parsimony strongly support the monophyly of two major clades within Paroedura that conflict with existing species group assignments based on scale characteristics. Our well-resolved tree elucidates a biogeographic pattern in which eastern Paroedura are most basal and western and south-western species form a monophyletic group. Our data demonstrate the phylogenetic utility of phosducin, a novel marker in squamate phylogenetics, at the intrageneric level.     

Linkage of the alcohol dehydrogenase structural genes in pearl millet (Pennisetum typhoides)

Pearl millet produces three ADH isozymes, Sets I, II, and III. Naturally occurring ADH electrophoretic variants affecting Sets I and II isozymes but not III have been previously described. Analysis of such variants led to the identification of the Adh1 structural gene. The existence of a second Adh structural gene was inferred from dissociation-reassociation studies of Set II. In the present report, a naturally occurring variant affecting the electrophoretic mobility of Sets III and II but not Set I is described. Analysis of this variant confirms the existence of a second structural gene, Adh2. Crosses utilizing this Adh2 marker reveal a dissimilarity with maize and other plants such as sunflower and narrow-leafed lupins. Adh1 and Adh2 of pearl millet do not segregate independently; indeed, no recombinants have been observed. This is the first major difference encountered in an otherwise remarkably similar genetic and environmental control of the ADH isozymes in maize and millet. The organization of the Adh genes of pearl millet may reflect a more primitive arrangement than that of maize.This work was supported by a PHS National Research Service Award Training Grant in Genetics to the Biology Department of the University of Oregon.     

Genetic variation and phylogenetic relationships of a pantropical species group in Polystachya (Orchidaceae)

Amplified fragment length polymorphism (AFLP) markers were used to investigate the relationships among Polystachya accessions from a group of closely related pantropical tetraploids. Before starting with the fingerprinting analyses, the polyploid accessions were first included in a phylogenetic analysis using low‐copy nuclear DNA data to establish their relationships, which confirmed that they belonged to a species group of closely related allotetraploids. Neo‐ and Palaeotropical polyploid accessions formed two hybrid clades with apparently independent origins. Sampling for the AFLP analyses included single accessions from much of the range of the genus and populations from Costa Rica (CR) and Sri Lanka (SL) to compare population structure and genetic diversity in these two areas in more detail. A splits graph of the complete AFLP data showed three major clusters corresponding to three sources of population sampling (P. concreta, SL; P. foliosa, CR; P. masayensis, CR), with individual accessions from Africa and Indian Ocean islands showing a closer relationship to P. concreta from SL than to the two CR species. Individual accessions from the Neotropics occurred in more isolated positions in the splits network, with little resolution. Some P. foliosa accessions clustered with P. masayensis, suggesting some hybridization between the two species, and this was confirmed by Bayesian structure analysis. However, the splits network, structure and analyses of molecular variance indicated a generally high level of genetic divergence between the two CR species, despite their recent hybrid origin, occurrence in largely the same localities and occasional hybridization. Polystachya foliosa from CR had a higher degree of population‐level genetic structure (Φ_ST = 0.291) than P. masayensis from CR (Φ_ST = 0.161) and P. concreta from SL (Φ_ST = 0.138), possibly because of its occurrence within a larger and more environmentally diverse continuous range than the other two species. Genetic divergence between Neo‐ and Palaeotropical members of the pantropical tetraploid group of Polystachya and the nonmonophyly of P. concreta suggested that P. concreta s.l. should be split and the use of this epithet should be confined to the Neotropics (the type is from Martinique). Other names should be used in Africa and the Asian tropics. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 235–250.     

Evolution and phylogenetic relationships within Porinaceae (Ostropomycetidae), focusing on foliicolous species

A phylogeny of the lichen family Porinaceae using mitochondrial SSU rDNA sequences is presented, with special focus on foliicolous taxa. Fifty specimens of 28 mostly tropical species, representing eight species groups of Porina as well as the genus Trichothelium, were analysed together with species of other members of Ostropomycetidae, and using Agyriaceae as outgroup. We performed the phylogenetic analyses with a Bayesian approach and under the criterion of maximum parsimony. Four main clades can be distinguished: the P. nitidula-group s. lat. (including Trichothelium, P. papillifera and P. rubescens), the Porina epiphylla-group s. lat. (including the P. radiata-, the P. nucula-, the P. imitatrix- and the P. epiphylla-group s. str.) and two clades of the P. rufula-group. The genus Porina as understood by all recent concepts is paraphyletic, and Trichothelium is nested within the Porina nitidula-group. The non-setose P. repanda forms a monophyletic clade with Trichothelium. The tree does not support a monophyletic origin of substrate preferences or photobiont selection. Species-specific associations with morphologically different trentepohlioid photobionts mapped on the tree suggest that closely related mycobiont species switch between different types of algae.     

Molecular identification and phylogenetic relationships among the species of the genus Oligoryzomys (Rodentia, Cricetidae) present in Argentina, putative reservoirs of hantaviruses

The systematics and geographical distribution of the species of Oligoryzomys present in Argentina are poorly known. From some of the species different hantavirus genotypes have been recovered. In order to contribute to the accurate identification of those species and to infer their phylogenetic relationships, we analysed data of restriction sites and sequences of the mtDNA d -loop region. The samples used represent almost all Oligoryzomys species known to occur in Argentina. The trees obtained with the two types of data were similar, showing high bootstrap values for the majority of the nodes. Our results support the idea that the specific name Oligoryzomys longicaudatus should be applied only to individuals from the south of Argentina and Chile and confirm that O. nigripes and O. delticola are conspecific. Specimens identified as O. flavescens conform three related clades, probably belonging to a species complex. This study also emphasises that the use of a DNA fragment characterised by a high evolutionary rate compare with other mitochondrial segments as the d -loop, was appropriate to infer the phylogenetic relationships in a group originated by a rapid speciation process. We also suggest the following modifications in the rodent–hantavirus relationships: the only viral genotype associated to O. longicaudatus would be Andes Sout, while O. chacoensis would be the natural host of the genotype Oran. One of the forms of the O. flavescens complex would be the natural host of the genotype Bermejo. Our data are consistent with the hypothesis that each hantavirus genotype is associated with a specific rodent host.     

Paeonia rotundiloba (D. Y. Hong) D. Y. Hong: A new status in tree peonies (Paeoniaceae)

Abstract Paeonia decomposita Hand.‐Mazz. subsp. rotundiloba D. Y. Hong is here raised to the specific rank, P. rotundiloba (D. Y. Hong) D. Y. Hong, based on its distinctiveness of four diagnostic characters: number of carpels; height of disk; number of leaflets of the lower leaves, and shape of the terminal leaflets; and unpublished molecular data. Paeonia rotundiloba differs distinctly from P. decomposita in having carpels mostly 3, less often 2 or 4, very rarely 5 (vs. almost always 5, very occasionally 4 or 3), disk 8–15 mm high (vs. 4–9.6 mm), leaflets mostly 19–39 (vs. 29–63) in number, and ratio of length to width of the terminal leaflets 1.09–1.93 (vs. 1.81–2.99).