High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam

We studied the phylogeography of Chinese yew (Taxus wallichiana), a tree species distributed over most of southern China and adjacent regions. A total of 1235 individuals from 50 populations from China and North Vietnam were analysed for chloroplast DNA variation using polymerase chain reaction-restriction fragment length polymorphism of the trnL-F intron-spacer region. A total of 19 different haplotypes were distinguished. We found a very high level of population differentiation and a strong phylogeographic pattern, suggesting low levels of recurrent gene flow among populations. Haplotype differentiation was most marked along the boundary between the Sino-Himalayan and Sino-Japanese Forest floristic subkingdoms, with only one haplotype being shared among these two subkingdoms. The Malesian and Sino-Himalayan Forest subkingdoms had five and 10 haplotypes, respectively, while the relatively large Sino-Japanese Forest subkingdom had only eight. The strong geography-haplotype correlation persisted at the regional floristic level, with most regions possessing a unique set of haplotypes, except for the central China region. Strong landscape effects were observed in the Hengduan and Dabashan mountains, where steep mountains and valleys might have been natural dispersal barriers. The molecular phylogenetic data, together with the geographic distribution of the haplotypes, suggest the existence of several localized refugia during the last glaciation from which the present-day distribution may be derived. The pattern of haplotype distribution across China and North Vietnam corresponded well with the current taxonomic delineation of the three intraspecific varieties of T. wallichiana.     

DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species

There is currently international interest in the application of DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of five candidate plant DNA barcoding regions [rbcL, matK, trnH-psbA, trnL-F and internal transcribed spacer (ITS)] in Eurasian yews. This group of species is taxonomically difficult because of a lack of clear-cut morphologically differences between species and hence represents a good test case for DNA barcoding. Forty-seven accessions were analysed, representing all taxa treated in current floristic works and covering most of the distribution range of Taxus in Eurasia. As single loci, trnL-F and ITS showed the highest species discriminatory power, each resolving 11 of 11 lineages (= barcode taxa). Species discrimination using matK, trnH-psbA and rbcL individually was lower, with matK resolving 8 of 10, trnH-psbA 7 of 11 and rbcL 5 of 11 successfully sequenced lineages. The proposed CBOL core barcode (rbcL + matK) resolved 8 of 11 lineages. Combining loci generally increased the robustness (measured by clade support) of the barcoding discrimination. Based on overall performance, trnL-F and ITS, separately or combined, are proposed as barcode for Eurasian Taxus. DNA barcoding discriminated recognized taxa of Eurasian Taxus, namely T. baccata, T. cuspidata, T. fuana and T. sumatrana, and identified seven lineages among the T. wallichiana group, some with distinct geographical distributions and morphologies, and potentially representing new species. Using the proposed DNA barcode, a technical system can be established to rapidly and reliably identify Taxus species in Eurasia for conservation protection and for monitoring illegal trade.     

Factors limiting seed production of Taxus brevifolia (Taxaceae) in Western Oregon

Seed production of Pacific yew (Taxus brevifolia), an understory conifer, was studied at four sites in western Oregon over 2 yr. The effects of pollen supplementation, overstory canopy, and predator exclusion on ovule attrition were examined. Supplemental hand-pollination of ten trees at two sites resulted in significantly increased rates of ovule development and a doubling of seed efficiency (ratio of seeds to ovules). However, seed efficiency still averaged <15% on branches receiving supplemental pollen, so pollination was not a primary factor limiting seed production. The number of developing ovules was positively associated with overstory openness, but seed production was not. Seed efficiency was negatively associated with overstory openness. Branches bagged to exclude vertebrate seed predators had higher seed production than unbagged branches at three of four sites for 2 yr. In contrast to unbagged branches, seed production on bagged branches was positively associated with overstory openness, as was the effectiveness of bagging. Therefore, both vertebrate predation and overstory were important in limiting seed production, and these factors interacted. Factors limiting seed production varied in importance among the four sites and between years, illustrating the importance of examining multiple limiting factors over several sites and years.     

红豆杉的胚珠发育,传粉滴形成和传粉过程

观察了红豆杉（Ｔａｘｕｓ ｃｈｉｎｅｎｓｉｓ （Ｐｉｌｇ．）Ｒｅｈｄ）的花粉形态和水合特性及胚珠发育、传粉滴形成与传粉过程。成熟花粉为单细胞,无气吓,形状不规则,外壁表面具大量乌氏体。花粉水合时,内壁膨胀,外壁开裂。通常情况下,外壁保留在水滴或传粉滴的表面,而花粉的其他部分进入水滴或传粉滴内。在８月下旬,可观察到下弯的雌性生殖芽。下弯这一特性是雌性生殖芽区别于营养芽的重要特征。这一时期的雌性生殖芽     

黄美乳菇(红菇目,红菇科),中国首个乳菇属变红乳菇亚属中乳汁变黄的物种

红菇属变红乳菇亚属的乳汁常变为红色,变黄的乳汁较为少见.在中国中南部亚热带壳斗科林下发现了一个乳汁迅速变黄色的物种.这是首次在中国发现的变红乳菇亚属中乳汁变黄的物种,其独特的乳汁、褐色的菌盖、稀疏的菌褶和大的具极高翼状纹饰的孢子能将其与其他已知种区分开来,在此将其描述为新种,黄美乳菇L.mirus.本研究提供了该新种的...     

Morphometric analysis of the Bersama abyssinica Fresen. complex (Melianthaceae) in East Africa

 The morphological variation of the Bersama abyssinica complex in East Africa is analysed. A wide range of characters was examined both on specimens collected for this study and on a selection of type material. The character distribution of each character was examined individually. The ratios of some of the characters were calculated, and selected characters were plotted in pairwise combinations. Non-metric multidimensional scaling and principal component analysis were employed in the multivariate analyses. On the basis of the patterns observed in the numerical analyses as well as those in the field, a new combination, Bersama abyssinica Fresen. ssp. rosea (Hoyle) Mikkelsen is proposed. The presence of the two flower types described by White: (a) male flowers, with long stamens and short gynoecium and (b) female flowers, with short, abortive stamens and long gynoecium is confirmed, but found to be taxonomically insignificant. Received May 12, 2000 Accepted February 13, 2001     

Genetic diversity and population structure of the endangered conifer Taxus wallichiana var. mairei (Taxaceae) revealed by Simple Sequence Repeat (SSR) markers

Taxus wallichiana var. mairei is an endangered conifer with important medicinal value in southern China. Nuclear SSR markers were employed to assess genetic diversity and structure of 13 geographically disjunct populations. The present study revealed a moderate genetic diversity (H_E = 0.538) and low genetic differentiation (F_ST = 0.159). And most populations encountered in severe inbreeding and bottleneck effect. No significant genetic structure was detected by IBD and Structure analysis, which was supported by AMOVA analysis. The present results could be ascribed to an earlier period of more pronounced gene flow when the species had a more continuous distribution. However, the 13 studied populations were divided into four clusters based on the UPGMA dendrogram; these clusters were almost congruent with their geographical distributions. Vital areas such as southern mountains of Sichuan basin, Nanling Mts. and the margin of this yew's distribution range had a high priority for conservation.     

Species delimitation methods reveal cryptic diversity in the Hypnea cornuta complex (Cystocloniaceae,Rhodophyta)

The simple and convergent morphologies of many red algae make these species difficult to identify using traditional morphological characters. Many cryptic species have been described in recent years based on molecular datasets, and this has led to the application of an integrative taxonomy approach in species delimitation. Here, we performed several species delimitation methods (mBGD, ABGD, SPN, PTP, GMYCs and GMYCm) based on two different loci (COI-5P and rbcL) in species of the Hypnea cornuta complex. These methods were combined with morphological and phylogenetic data, extensive sampling, analysis of topotype material, and historically relevant herbarium samples. Our findings demonstrate that the groups morphologically assigned to H. cornuta and H. stellulifera consist of five different cryptic species. H. cornuta is a polyphyletic taxon composed of three well-separated lineages, thus requiring sequencing of type or topotype specimens to determine which one is Hypnea cornuta sensu stricto. We have revealed that the distribution of H. stellulifera is limited to Asia, while the Brazilian specimens initially assigned to this species were clarified as a new endemic species: Hypnea cryptica sp. nov. Our results indicated that only an integrative approach combining several lines of evidence, including morphology, nomenclature history, molecular data, biogeography and ecology can correctly solve the taxonomic status of widely distributed cryptic species.     

A new species and geographical variation in the Telmatochromis temporalis complex (Teleostei, Cichlidae) from Lake Tanganyika

Telmatochromis brachygnathus sp.n. is described from the southern and central parts of Lake Tanganyika. It can be distinguished from the similar T. temporalis mainly by its smaller mouth. Morphological distinct populations were found in both species.     

Multivariate morphometric analysis of the Potamogeton compressus group (Potamogetonaceae)

The Potamogeton compressus group is a complex of three to five closely related species with a circumpolar distribution in the Northern Hemisphere. Multivariate morphometric analyses (principal component analysis, cluster analysis, canonical and classificatory discriminant analyses) were used to elucidate the patterns of variation within this group and to test the morphological differentiation of the species recognized in the current literature. From the entire distribution range, 156 specimens of the group were included in the numerical methods. Results from morphological comparison are discussed in relation to molecular data, reproductive behaviour and geographical distribution. Morphometric analyses provided evidence that this complex can be clearly divided into three groups, one of which was subdivided mainly on the basis of allopatric occurrence and genetic differentiation. These groups correspond to four species accepted here: P. acutifolius (temperate regions of Europe), P. compressus (boreal and temperate regions of Europe and Asia), P. manchuriensis (northeastern China and Russian Far East) and P. zosteriformis (boreal and temperate regions of North America). Two species, P. acutifolius and P. compressus, are partly sympatric, but clearly differentiated morphologically and genetically, and effectively isolated reproductively. Endemic P. manchuriensis is characterized by a unique combination of characters and an occurrence in a limited geographical area. Allopatric P. zosteriformis is weakly differentiated morphologically from P. compressus, but differs markedly in molecular markers correlated with geographical differentiation. It may represent a cryptic species. In contrast, a recently suggested concept of southern Siberian P. henningii was not supported by our analyses. Plants so named are considered here as slender phenotypes of the widespread and variable P. compressus. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 112–130.     

Isolation and characterization of microsatellite loci in <Emphasis Type="Italic">Taxus sumatrana</Emphasis> (Taxaceae) using PCR-based isolation of microsatellite arrays (PIMA)

Taxus sumatrana (Miq.) de Laub. (Taxaceae) is an endangered conifer with a scattered distribution in central Taiwan. In this study, we described the development of 12 microsatellite loci in T. sumatrana for genetic studies. These new markers were tested in nine individuals of the rare species. The number of alleles ranged from 3 to 13 and expected heterozygosity from 0.627 to 0.948. Eleven of twelve loci are significantly deviated from Hardy–Weinberg expectations due to the heterozygote deficiency.     

Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and use multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include structure , principal components analysis and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large‐scale ecological data for niche‐based distribution modelling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic‐scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.     

Jenynsia lineata species complex,revision and new species description (Cyprinodontiformes: Anablepidae)

The Jenynsia lineata species complex comprises J. lineata from Montevideo, Uruguay and Jenynsia multidentata, from coastal basins of Brazil, Uruguay and Argentina up to 1200 m a.s.l. Taxonomic divisions within this group were tested using three different species delimitation methods, which found the two existing names to be synonyms and revealed a new cryptic species. Jenynsia darwini sp. nov. is distinguished from all congeners by having a unique combination of character states, including the shape of the dorsal postcleithrum (three times higher than wide v. less than two times higher than wide) and female colour pattern in the half of the caudal peduncle with rows of chromatophores segmented in unaligned spots (v. aligned spots forming lines). The new species also differs from J. lineata by having 26 nucleotide substitutions in the mitochondrial gene cytochrome c oxidase I (coI). Phylogenetic analysis of the genus based on morphological characters proposed by previous studies corroborates monophyly of the subgenera Plesiojenynsia and Jenynsia, with the new species being allocated to the subgenus Jenynsia as the sister group of J. lineata.     

中国竹类植物馆藏标本现状与地理分布

馆藏标本是分类学研究的主要凭证, 对特定类群标本的采集信息进行细致整理和分析, 有助于理解该类群研究的历史、现状和不足。此外, 结合最新的系统学研究成果和相应的环境数据构建生态位模型, 可以加深人们对特定类群分类与分布状况的认识。被子植物的分类鉴定常基于繁殖性状进行, 然而, 竹类植物一般进行克隆繁殖, 只有在经过长期的营养生长之后, 才会进行有性生殖并同时死亡。因此, 国内的竹类标本大多仅记录了营养性状, 具有繁殖性状的标本数量稀少。由于这一特殊的生物学习性, 竹类植物是当今分类学研究中最为困难的类群之一。本研究基于全国竹类植物馆藏标本的采集数据, 分析了我国竹类标本的采集和保藏现状; 利用比值法和斜率法从采集地理偏差和采集类群偏差两方面评估了竹类植物标本的采集完整度; 结合气候数据, 利用模型模拟的方法分析了影响不同竹类分支分布的主要因素。采集信息分析结果表明, 国内标本馆对竹类标本的收集和保藏存在很大的不均衡性, 且对研究团队具有较高的依赖性; 其次竹类标本的采集量的变化较好地反映了国内植物分类学研究的历史; 而对类群和地理采集完整度的评估结果表明, 中国竹类标本的采集和整理工作仍任重道远。模型模拟结果表明, 温度限定了竹类植物两大分支各自的分布北界, 水分对温带木本竹类分支(temperate woody bamboos, TWB)的限制作用比旧世界热带木本竹类分支(paleotropical woody bamboos, PWB)强, 而温度对PWB的限制性更强。生态位模拟的结果进一步显示, 中国温带和旧世界热带木本竹类两大分支的适生区出现了明显的分化, 但在亚热带区域仍有部分重叠。植物标本记录了特定类群在时间和空间上的分布格局, 相关的信息一方面可以促进物种灭绝风险评估、可持续利用和综合保护, 另一方面也可助力大尺度生物多样性分布格局及全球变化对多样性的影响研究。     

A new species of Exostyles (Leguminosae, Papilionoideae, Swartzieae s.l.), from Paraná State, Brazil

A new species Exostyles godoyensis Soares-Silva & Mansano (Leguminosae, Papilionoideae, Swartzieae), endemic to Paraná state in southern Brazil, is described and illustrated. The new species is distinct from all the other species of Exostyles in having a leaf with up to five leaflets, while the other species have at least seven leaflets per leaf. The new species is distinct from Exostyles amazonica Yakovlev in its longer stamen filaments and ovary stipe and from E. glabra Vogel and E. venusta Schott by its shorter anthers. In addition to these morphological characters E. godoyensis has a disjunct geographical distribution.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 103–106.     

Plastome phylogenomic analysis of Torreya (Taxaceae)

Torreya Arn., a small genus of Taxaceae, consists of six species occurring in North America and eastern Asia. Several phylogenetic studies have previously been undertaken to reveal relationships within this genus, although only a few DNA segments or species were used. In the present study, we sequenced five Torreya plastomes and combined these with two existing plastomes from the genus to investigate plastome evolution and phylogenetic relationships within Torreya. All sequenced Torreya plastomes shared the same complement of 82 protein‐coding genes, 4 ribosomal RNA genes, and 31 transfer RNA genes. Phylogenetic inference using a maximum likelihood framework consisted of an 82‐gene, 17‐taxon dataset, including all species of Torreya, resolved Torreya as a monophyletic clade. Strongly supported relationships within the genus include the position of the early diverging T. jackii Chun, the two sister pairs T. fargesii Franch.–T. nucifera (L.) Siebold & Zucc. and T. grandis Fortune ex Lindl.–T. californica Torr., and the monophyly of the clade including T. fargesii var. yunnanensis, T. fargesii, and T. nucifera. In addition to the inference of species relationships, divergence time estimation and biogeographical analysis were carried out. The diversification of Torreya was estimated to be approximately 8.9 Ma. Ancestral state reconstruction of the geographical area suggested China/eastern North America as the most likely ancestral region for the six extant Torreya species.     

中国中剑水蚤属种类记述

记录了目前分布在中国的中剑水蚤属共计10个种：刘氏中剑水蚤Mesocyclops leuckarti（Claus,1857）、温中剑水蚤M．thermocyclopoides Harada,1931、特异中剑水蚤M．dissimilis Defaye＆Kawabata,1993、北碚中剑水蚤M．pehpeiensis Hu,1943、奥贡中剑水蚤M.ogunnus Onabamiro,1957、邬氏中剑水蚤M．woutersi Van de Velde,1987、糙角中剑水蚤M．aspericornis（Daday,1906）、玛丽中剑水蚤M．mariae Guo,2000、深圳中剑水蚤M．shenzhenensis Guo,2000、蒙古中剑水蚤M．mongoliensis Kiefer,1981。对每一种的主要形态特征和地理分布分别做了详尽描述,给出了如何鉴定这10个种的检索表。同时还讨论和更正了过去一些学者对分布在中国的中剑水蚤属个别种诸如同物异名或同名异物的错误。