The evolution of coexisting highly divergent line-1 subfamilies within the rodent genus Peromyscus

Summary Two distinct members of the LINE-1 (L1) family in Peromyscus were characterized. The two clones, denoted L1Pm55 and L1Pm62, were 1.5 kb and 1.8 kb in length, respectively, and align to the identical region of the L1 sequence of Mus domesticus. Sequence similarity was on the order of 70% between L1Pm55 and L1Pm62, which approximates that between either Peromyscus sequence and Mus Ll. L1Pm62 represents a more prevalent subfamily than L1Pm55. L1Pm62 exists in about 500 copies per haploid genome, while L1Pm55 exists in about 100 copies. The existence of major and minor subpopulations of L1 within Peromyscus is in contrast to murine rodents and higher primates, where L1 copy number is on the order of 20,000 to 100,000, and where levels of intraspecific divergence among L1 elements are typically less than 15–20%. Additional Peromyscus clones are similarly divergent from both L1Pm62 and LIPm55, implying the existence of more than two distinct L1 subfamilies. The highly divergent L1 subfamilies in Peromyscus apparently have been evolving independently for more than 25 million years, preceding the divergence of cricetine and murine rodents. Investigations of the evolution of L1 within Peromyscus by restriction and Southern analysis was performed using species groups represented by the partially interfertile species pairs P. maniculatus-P. polionotus, P. leucopus-P. gossypinus, and P. truei-P. difficilis of the nominate subgenus and P. californicus of the Haplomylomys subgenus. Changes in L1 and species group taxonomic boundaries frequently coincided. The implications for phylogeny are discussed.     

Analysis of Orthologous Retrovirus-Like Elements in the White-Footed Mouse,Peromyscus leucopus

Three loci in the genome of the white-footed mouse, Peromyscus leucopus, were examined for the presence or absence of orthologous copies of the retrovirus-like element mys using polymerase chain reaction. We examined these loci in 28 mice collected throughout the P. leucopus species range. Mys insertions were present in only one of the individuals examined at the mys-1 and mys-7 loci. Conversely, the mys-6 element was found in several individuals, but the presence of this element was limited to northern latitudes. Because the long terminal repeats (LTRs) of a given element are expected to be identical at the time of retrotransposition into the genome, and to accumulate changes over evolutionary time, within-element LTR sequence comparisons can be used to estimate the relative age of insertions. Within-element LTR differences are greater in mys-6 than in mys-1 or mys-7. The LTRs from orthologous mys-6 elements of six mice were sequenced. The alignment revealed 13 of the 22 differences between the right and left LTRs that were shared by all orthologous mys-6 sites, suggesting that relative to its time of insertion into the genome, mys-6 has only recently spread across the northern part of the species range. Received: 23 January 1996 / Accepted: 24 April 1996     

BoS: A Large and Diverse Family of Short Interspersed Elements (SINEs) in Brassica oleracea

Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at ∼2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.     

A cladistic analysis ofAnisopappus (Asteraceae: Inuleae)

A cladistic analysis of the genusAnisopappus (Asteraceae: Inuleae) has been undertaken. A hypothesis of species interrelationships in the genus is presented for the first time. The analysis also includedArctotis (Arctoteae), used as outgroup, and five additional genera from theInuleae: Geigeria, Calostephane, Asteriscus, Buphthalmum, Pulicaria, andInula. It is concluded thatAnisopappus is a monophyletic group situated at the base of the tribe, diagnosed by, e.g., their obtuse stylar sweeping-hairs. The species with acute sweeping-hairs were found to be derived within the genus. Problems concerning species delimitation, biogeography and character evolution in the genus are briefly discussed.     

Genetic diversity of SIRE-1 retroelements in annual and perennial glycine species revealed using SSAP

Sequence Specific Amplification Polymorphisms (SSAP) were used to measure the distribution and structure of SIRE-1 retroelement populations in annual and perennial Glycine species. For SSAP analysis, primers corresponding to a region immediately upstream of the 3’LTR of the soybean retroelement SIRE-1 were chosen. Analysis reveals that SIRE-1 is present throughout the Glycine genus and shows that the annual species have similar SIRE-1 populations whilst the perennial species have much more distinct and diverse populations. The high number of species-specific subgroups suggest that SIRE-1 has been active and evolving independently in each species during the course of Glycine evolution.     

Biogeography and evolution of flower color in Veratrum (Melanthiaceae) through inference of a phylogeny based on multiple DNA markers

Veratrum (Melanthiaceae) comprises ca. 27 species with highly variable morphology. This study aims to construct the molecular phylogeny of this genus to infer its floral evolution and historical biogeography, which have not been examined in detail before. Maximum parsimony, maximum likelihood, and Bayesian analyses were performed on the separate and combined ITS, trnL-F, and atpB-rbcL sequences to reconstruct the phylogenetic tree of the genus. All Veratrum taxa formed a monophyletic group, within which two distinct clades were distinguished: species with white-to-green perianth formed one highly supported clade, and the species with black-purple perianth constituted another highly supported clade. Phylogenetic inference on flower color evolution suggested that white-to-green perianth was a plesiomorphic state and black-purple perianth was apomorphic for Veratrum. When species distribution areas were traced as a multi-state character, parsimonious optimization inferred that Veratrum possibly originated in East Asia. Our study confirmed previous phylogenetic and taxonomic suggestions on this genus and provided a typical example of plant radiation across the Northern Hemisphere.     

沉香属的化学分类学研究

为探讨瑞香科沉香亚科的分类学地位,结合其他亚科植物的化学成分类型,对从沉香属植物分离到的各类化学成分进行了综述。从二萜和黄酮(烷)的成分类型判断,沉香亚科的进化地位低于瑞香亚科;从三萜成分类型来看,其地位又比Gonystyloideae亚科稍高;同时2-(2-苯乙基)色酮类和二苯基甲酮类成分为沉香属甚至沉香亚科的特征性成分。因此,沉香亚科是瑞香科中进化程度相对较低的类群,处于瑞香亚科和Gonystyloideae亚科之间。     

《广西植物志》秋海棠属(Begonia L.)增订

秋海棠属(Begonia L.)隶属于葫芦目(Cucurbitales)秋海棠科(Begoniaceae),有1 800余种,是世界第六大属,主要分布于美洲、非洲和亚洲的热带和亚热带地区,具有极高的观赏价值,亦可作为药用、食用、饮料和饲料等。我国有秋海棠属植物近300种,主要分布于我国的云南和广西等长江以南地区,其中云南有秋海棠属植物100余种。近年来,随着广西地区秋海棠属植物野外调查的不断深入,陆续发现并发表了大量秋海棠属新类群,使得广西产秋海棠属植物数目已超出1991年《广西植物志》(第一卷)收录的19种,因此亟需对发表于不同期刊中的类群进行系统地整理和汇总。鉴于此,该文通过查阅文献资料和考证标本信息,整理并汇总了广西产秋海棠属植物共84种,包括2个变种、11个亚种和46个特有种,新增的65种为《广西植物志》(第一卷)中未收录的类群,并补充了这些类群的特征集要、凭证标本信息和属下分组概况,为今后开展秋海棠属植物的分类修订以及系统学、进化生物学和保护生物学等研究提供了参考依据。     

双花木属植物潜在分布区模拟与分析

气候变化直接影响着物种的分布范围。了解气候变化对濒危物种分布区的影响,是开展保护生物学研究的基础。双花木属(Disanthus Maxim.) 1种1变种,隶属金缕梅科(Hamamelidaceae),为东亚特有濒危物种和典型的中-日间断分布成分,在研究东亚植物区系地理演化方面具有重要的科学价值。本研究基于双花木属植物19个当前居群分布点的气候变量,运用MaxEnt模型预测双花木属植物在末次盛冰期(约22000年前)、当前(1950—2000年)和未来(2060—2080年)气候情景下的潜在分布区的结果显示,受试者工作特征曲线下的面积(AUC=0.9999±0.0001)接近于1,表明MaxEnt模型的预测准确度极高;气候变量贡献率和Jackknife检验评估的结果显示,制约双花木属植物分布的主导气候变量是最湿月降水量和最干月降水量。采用ArcGIS 10.0中的ArcToolbox空间分析工具定量分析比较双花木属的分布动态,基于生境稳定性(N_(stab))、当前与其他时期分布区面积比(N_a)和扩张/收缩程度(N_e)的分析结果揭示,在双花木属植物进化过程中,分布范围经历了收缩过程;未来的温室气体排放量升高程度不同,其适生区呈现不同程度(30%—65%)收缩,特别是RCP 8.5气候情景下,我国武夷山山脉的潜在分布区有可能会丧失。探讨双花木属植物对不同时期气候变化的响应,重建冰期以来该属植物地理分布的变迁历史,分析限制其潜在地理分布的主导气候变量,可为双花木属植物保育措施的制定和东亚地区植物区系物种形成演化的研究提供理论参考。     

Phylogeny of the avian genus Pitohui and the evolution of toxicity in birds

Bird species in the avian genus Pitohui contain potent neurotoxic alkaloids that may be used for defense. The genus comprises multiple species that are endemic to New Guinea and were presumed to belong to the family Pachycephalidae or Colluricinclidae, within the core corvoidea, an ancient Australasian radiation of crow-like birds. In order to understand the evolution of toxicity within the genus Pitohui, we sequenced three mitochondrial and two nuclear gene segments and reconstructed a phylogeny of the genus Pitohui and its putative relatives. We show that the genus Pitohui is polyphyletic, and consists of five different lineages. Using Bayesian ancestral state reconstruction, we estimate that toxicity likely evolved multiple times within this group. Furthermore, because the morphological and behavioral similarity among these poisonous birds appears to have evolved convergently, we hypothesize that this may be a possible example of Müllerian mimicry in birds. The Morningbird of Palau, Micronesia, that has often been included in the genus Pitohui, actually belongs in the genus Pachycephala and offers an intriguing case of pronounced evolution on a remote oceanic island.     

Competition,niche specialization and the evolution of brain size in the genus Peromyscus

Previous studies of relative brain size in mammals have suggested an association with complex habitats and with low reproductive rate. In order to examine the causal relationships more thoroughly, a detailed examination of relative brain size variation in the genus Peromyscus was undertaken. Endocranial volumes were used to estimate brain weight for 32 species including 161 subspecies, and relative brain size calculated as the species deviation from the allometric relationship between brain and body size. The intrageneric allometric coefficient was higher than most values previously reported from low taxonomic levels, but intraspecific coefficients were generally lower than this. Island species, and relict species isolated on mountain tops, which may be ecological ‘islands’, had consistently small relative brain sizes, but peninsular species were large brained. Among the remaining species there were significant correlations between litter size and relative brain size, and between the number of competitor species and relative brain size. Species with many competitor species have relatively large brains and small litters. It is concluded that the nature of the geographical distribution, the pattern of species formation and habitat complexity all influence relative brain size in existing forms.     

Molecular Evolution of Satellite DNA CLsat in Lizards from the Genus Darevskia (Sauria: Lacertidae): Correlation with Species Diversity

The structure and evolution of a satellite DNA family was examined in lizards from the genus Darevskia(family Lacertidae). Comparison of tandem units of repeated DNA (satDNA), CLsat, in all species from the genus Darevskiahas shown that their variability is largely explained by single-nucleotide substitutions, which form about 50 diagnostic positions underlying classification of the family into three subfamilies. Maximum differences between the subfamilies reached 25%. At this level of tandem unit divergence in the subfamilies, no cross-hybridization between them was observed (at 65°C). The individual variability within one subfamily within the species was on average 5% while the variability between species consensuses within a subfamily was 10%. The presence of highly conserved regions in all monomers and some features of their organization show that satellites of all Darevskia species belong to one satDNA family. The organization of unit sequences of satellites CLsat and Agi160 also detected by us in another lizard genus, Lacerta s. str. was compared. Similarity that was found between these satellites suggests their relatedness and common origin. A possible pathway of evolution of these two satDNA families is proposed. The distribution and content of CLsat repeat subfamilies in all species of the genus was examined by Southern hybridization. Seven species had mainly CLsatI (83 to 96%); three species, approximately equal amounts of CLsatI and CLsatIII (the admixture of CLsatII was 2–5%); and five species, a combination of all three subfamilies in highly varying proportions. Based on these results as well as on zoogeographic views on the taxonomy and phylogeny of theDarevskia species, hypotheses on the evolution of molecular-genetic relationships within this genus are advanced.     

Retrotransposition of a plant SINE into the wx locus during evolution of rice

A new type of plant retroposon, p-SINE1, has been found in the wx locus of rice (Oryza sativa). It has some structural characteristics similar to those of mammalian SINEs, such as members of the Alu or Bl family. In order to estimate the time at which the integration of p-SINE1 into a single locus occurred during rice evolution, we examined the distribution of two members of p-SINE1 in several species of the Oryza genus by the polymerase chain reaction (PCR). We found that one member of p-SINE1 (p-SINE1-r2) in the ninth intron of the wx ⁺ gene was present only in two closely related species, O. sativa and O. rufipogon, and was not present in the other species carrying the AA genome within the Oryza genus. This result indicates that p-SINE1-r2 was integrated into the wx locus after O. sativa and O. rufipogon had diverged from other species with the AA genome. In contrast to p-SINE1-r2, another member (p-SINE1-rl) located in the untranslated 5-region of the wx ⁺ gene was present not only in all species with the AA genome but also in species with a different genome (CCDD). This result suggests that p-SINE1-rl was integrated into that position prior to the genomic divergence. Thus, it appears that each member of p-SINE1 was retroposed at a specific site at a different time during rice evolution.Correspondence to: Y. Sano     

Distribution,Taxonomy, and Conservation Status of the Perote Mouse <Emphasis Type="Italic">Peromyscus bullatus</Emphasis> (Rodentia: Muridae) in México

The Perote deer mouse Peromyscus bullatus is a rare species known only from a few specimens. It is endemic to the plains surrounding the Oriental Basin in the states of Veracruz and Puebla, Mexico, in the area where the Sierra Madre Oriental and the eastern end of the Transverse Volcanic Range merge. In past studies, a small area within the basin provided the only known habitat. During two recent surveys adjacent to this area, in habitats that matched the area in the state of Puebla where P. bullatus was previously found, we made new surveys. This mouse is differentiable from other species of the genus, mainly in the large of the auditory and the size of the ear. Intrinsic factors are highly discriminating in choice of habitat, low densities, and has restricted distribution, as well as the extrinsic factor of habitat deterioration, indicates a serious conservation problem.     

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.     

Relaxed purifying selection of rhodopsin gene within a Chinese endemic cavefish genus <Emphasis Type="Italic">Sinocyclocheilus</Emphasis> (Pisces: Cypriniformes)

The cyprinid fish genus Sinocyclocheilus, as the most cavefish rich genus, includes many species showing striking adaptation to caves and convergent reduction or even loss of eyes and pigmentation. RH1 is responsible for dim vision. In order to explore the evolution of RH1 gene in this genus, we sequenced the complete gene from 28 individuals of 16 representative species of Sinocyclocheilus, with cave and surface species included. Phylogenetic analyses supported the monophyly of Sinocyclocheilus and polyphyly of the cave species. Codon models implemented in PAML were used to infer the evolution of RH1. We found that Sinocyclocheilus had a significantly higher evolutionary rate for amino acids than other cyprinid fishes compared, which might be the result of relaxation of purifying selection and could be ascribed to cave habit of this genus. In contrast to previous hypotheses, both cave and surface lineages exhibited a similar rate of molecular evolution, so the RH1 of cave species may still be functional, although these species were highly adapted to cave environment. Two amino acid substitutions (D83G and E122V) that were not reported before were found, which may be useful for site-directed mutagenesis in the future. Handling editor: Christian Sturmbauer     

Discrimination of snipefish Macroramphosus species and boarfish Capros aper morphotypes through multivariate analysis of body shape

The existence of two species of the genus Macroramphosus Lacepède 1803, has been discussed based on morphometric characters, diet composition and depth distribution. Another species, the boarfish Capros aper (Linnaeus 1758), caugth along the Portuguese coast, shows two different morphotypes, one type with smaller eyes and a deeper body than the other, occurring with intermediate forms. In both snipefish and boarfish no sexual dimorphism was found with respect to shape and length relationships. However, females in both genera were on average bigger than males. A multidimensional scaling analysis was performed using Procrustes distances, in order to check if shape geometry was effective in distinguishing the species of snipefish as well as the morphotypes of boarfish. A multivariate discriminant analysis using morphometric characters of snipefish and boarfish was carried out to validate the visual criteria for a distinction of species and morphotypes, respectively. Morphometric characters revealed a great discriminatory power to distinguish morphotypes. Both snipefish and boarfish are very abundant in Portuguese waters, showing two well-defined morphologies and intermediate forms. This study suggests that there may be two different species in each genus and that further studies on these fish should be carried out to investigate if there is reproductive isolation between the morphotypes of boarfish and to validate the species of snipefish.     

Re-evaluation of the systematics of the endemic corals of Brazil by molecular data

Recent genetic work on various coral genera has shown that morphological convergence between Atlantic and Pacific corals obscures evolutionary relationships and inferred levels of endemicity between the regions. Based on DNA sequences from nuclear and mitochondrial loci that provide higher resolution than those previously presented, this study shows that relationships within parts of the Atlantic coral fauna are also in need of substantial revision. The data presented here indicate that (1) the endemic Brazilian genus Mussismilia is a monophyletic clade, (2) Mussismilia is more closely related to the Caribbean Faviidae than Mussidae, the family in which it is currently placed, (3) the Brazilian endemic coral Favia leptophylla is much more closely related to Mussismilia than other species of Favia and has most likely been incorrectly placed in the genus Favia and (4) the other endemic Favia species found in Brazil, Favia gravida, is genetically distinct from Favia fragum, a Caribbean congener with which it is frequently synonymized. The nuclear data also suggest the possible presence of a cryptic species within Mussismilia, but additional sampling and morphological information is required to confirm this finding.     

桑黄孔菌属的研究进展

历来"桑黄"的种类混淆不清,直至近年来才被确定为桑树桑黄,与其亲缘性相近的物种也一同被划分入广义纤孔菌属的新分支—桑黄孔菌属。本文整理曾被当作"桑黄"的物种,阐述其正名和桑黄孔菌属确立的过程,对目前该属内物种的生物活性和栽培研究进展进行综述,旨在为桑黄孔菌属真菌资源的研究开发提供参考。     

小柱芥属植物分类及地理分布研究

小柱芥属(Microstigma Trautv.)为十字花科(Brassicaceae)一寡种属,目前由于缺乏系统研究,存在属内物种划分不明确,地理分布不确定等问题.该文通过在甘肃、内蒙古的标本采集,以及GBIF的标本记载和相关文献的查阅,对小柱芥属植物的形态特征和地理分布进行了详细描述,确定了小柱芥属内的物种数目并编...