基于ITS和matK基因对牡丹组序列分析及其亲缘关系的研究

以芍药属牡丹组全部9个野生种、5个紫斑牡丹栽培品种及3个中原牡丹品种为试材,进行核糖体内转录间隔区（ITS）和叶绿体成熟酶K （matK）基因片段测序分析,探讨ITS和matK序列为牡丹组所有野生种种间关系提供分子证据。从GeneBank中选取了1个牡丹及3个外类群芍药、川赤芍和草芍药的ITS及matK序列。对试验样品进行DNA提取、PCR扩增并双向测序得到44条序列,人工校正后将所得44条序列进行比对;计算碱基组成频率、变异位点、简约信息位点数、转换/颠换比率、种内及种间遗传距离,以邻接法进行系统发育分析。结果表明,牡丹组所有个体ITS序列长度在750~800 bp,含有86个多态位点,74个简约信息位点,转换/颠换比率（R）为1.2;而matK序列含有20个简约信息位点,转换/颠换比率（R）为1.7。ITS序列分析将牡丹组野生种分为两大枝,稷山牡丹、紫斑牡丹、卵叶牡丹和杨山牡丹聚为一枝,狭叶牡丹、滇牡丹、黄牡丹和大花黄牡丹聚为另一枝,这两枝分别与革质花盘亚组和肉质花盘亚组相对应,而四川牡丹位于革质花盘亚组最底端,支持前人研究将四川牡丹归为革质花盘亚组。matK序列分析的牡丹组野生种间遗传距离结果不理想,未能清晰的表明野生种之间的亲缘关系。由此说明,ITS序列更适合牡丹组野生种间亲缘关系的研究分析。     

基于线粒体基因组控制区序列的中国冰清绢蝶遗传分化和谱系生物地理研究

【目的】分析中国冰清绢蝶Parnassius glacialis遗传多样性和遗传分化情况及其系统发生关系,推测其起源及分歧时间,并探讨其历史生物地理分布格局的成因。【方法】以2008-2016年采集于中国13个地区的冰清绢蝶的325头及绢蝶属其他11个种的11头个体样品,对其线粒体基因组的AT富集区(控制区)序列进行PCR扩增和序列测定,采用MEGA 6.0, Dna SP 5.1和Arlequin 3.5等软件分析其遗传多样性和遗传分化情况;以其他近缘绢蝶种类作为外类群,采用PhyML3.0, MrBayes 3.2和BEAST V1.8.3等软件重建冰清绢蝶的系统发生树,并利用宽松分子钟和校准方法推测中国冰清绢蝶的起源和分歧时间;同时结合现今冰清绢蝶的地理分布特点和第四纪以来的地球环境事件,分析其扩散路径,探讨其历史生物地理分布格局及成因。【结果】冰清绢蝶AT富集区序列长度介于487～495 bp之间,平均为491 bp,其长度的差异主要体现在Poly(T)或Poly(A)的数目差异,A+T平均含量为95.76%。供试冰清绢蝶13个地理居群325头个体中,共检测出基于线粒体基因组AT富集区序列的239个单倍型,单倍型多样性Hd为0.9971;核苷酸多态性指数π值为0.02948, Theta (per site)Eta值为0.06594。系统发生分析和分子定年显示,冰清绢蝶和白绢蝶P.stubbendorfii为近缘姊妹种,二者在距今7.52百万年(Ma)的中新世晚期开始分化。冰清绢蝶的祖先可能起源于我国西南地区(现今横断山脉-喜马拉雅附近的青藏高原东北缘)距今1.53 Ma的更新世时期,先由起源地先期扩散到达小陇山、秦岭一带;后来,由于第四纪的冰期-间冰期轮回事件和扩散路径的不同而分化出2大支系,但两个支系之间存在少量的单倍型相互混杂现象;随后,2大支系继续向低海拔、低纬度地区扩散,即通过伏牛山脉向东北方向扩散到嵩山、泰山、昆嵛山一带,经大别山系向东南方向扩散到琅琊山、紫金山和天目山一带。【结论】中国13个居群的冰清绢蝶没有形成明显的地理分化格局,其遗传变异主要来自居群内部,居群间的遗传分化现象尚不明显;冰清绢蝶起源于更新世时期的较高海拔地区,由于第四纪的冰期-间冰期轮回事件以及扩散路径的不同而形成2大支系并向中国东部和南部低海拔和低纬度地区扩散。     

Phylogenetic relationships and biogeographic history of the unique Saxifraga sect. Irregulares (Saxifragaceae) from eastern Asia

Saxifraga L. is the largest genus in Saxifragaceae and a characteristic component of the herbaceous flora of the temperate and alpine mountains in the Northern Hemisphere. Section Irregulares is a small group of 15–20 species, representing one of the early‐diverged lineages in the genus characterized with unique zygomorphic flowers. We used both nuclear internal transcribed spacer and chloroplast DNA regions (psbA‐trnH, trnL‐F, and matK) to reconstruct its species relationships, estimate divergence times, and infer its historical biogeography. Our phylogenetic results corroborate the monophyly of sect. Irregulares and its sister relationship to sect. Heterisia from North America. The section was well resolved into two lineages corresponding to their morphological features and biogeographic distributions. One represents ser. Stoloniferae including S. stolonifera Curtis and S. nipponica Makino with long‐creeping stolons/rhizomes and small petals with spots and the other comprises the remaining taxa (ser. Rufescentes) which lack long‐creeping rhizomes. Spots on leaves (abaxially spotted vs. abaxially without spots) and spots on petals (without spots vs. with spots) are inferred to be phylogenetically informative within ser. Rufescentes. Divergence time estimates and ancestral area analysis suggested a western North American origin of sect. Irregulares with migration into East Asia by way of the Bering land bridge in the Middle Oligocene. The development of drying and desertification belt in the late Miocene could have played an important role in the subsequent restriction and separation of the north and south lineages within eastern Asia.     

Phylogeny and taxonomy of Afrocayratia,a new genus of Vitaceae from continental Africa and Madagascar

The genus Cayratia Juss. in the traditional sense (i.e., Cayratia s.l.) of the grape family has been shown to be non‐monophyletic. Previous studies supported the splitting of Cayratia s.l. into three genera, that is, Cayratia s.s., Causonis Raf., and a new genus representing the African Cayratia clade. However, the morphology of the African Cayratia clade has not been studied carefully and its phylogenetic position within Vitaceae remains unclear. Our study integrates molecular, distributional, and morphological data and supports the recognition of the new genus Afrocayratia from continental Africa and Madagascar. Phylogenetic analyses strongly support the monophyly of Afrocayratia and resolve it as a sister of Cayratia s.s. based on the chloroplast data, but it is placed sister to Cyphostemma based on the internal transcribed spacer dataset. Molecular dating suggests that Afrocayratia split with Cayratia s.s. during the Paleocene, but that the extant species of Afrocayratia did not diversify until the early Miocene. Afrocayratia differs from its allied genera in having short stigmas and seeds with subcircular ventral infold cavities in cross‐section. Three clades are detected within Afrocayratia, with A. debilis (Baker) J.Wen & L.M.Lu as the first diverged lineage. The second diverged lineage includes A. delicatula (Willems) J.Wen & Z.D.Chen and A. gracilis (Guill. & Perr.) J.Wen & Z.D.Chen. The third diverged lineage includes A. imerinensis (Baker) J.Wen & L.M.Lu, A. longiflora (Desc.) J.Wen & Rabarijaona, and A. triternata (Baker) J.Wen & Rabarijaona from Madagascar, which form a monophyletic group that diverged from the second lineage in the middle Miocene. Combining the morphological and molecular evidence, we formally describe the new genus Afrocayratia, make seven new combinations, and provide a key to species of the genus.     

Phylogenomics and biogeography of Wisteria: Implications on plastome evolution among inverted repeat-lacking clade (IRLC) legumes

The genus Wisteria (Fabaceae) is disjunctly distributed in eastern Asian and eastern North American temperate deciduous forests, and it is widely cultivated around the world as spectacular garden plants. It is a member of inverted repeat-lacking clade (IRLC). The IRLC Species are characterized by the loss of an IR region in their plastomes, which has long been of great interest. In this research, we report whole plastome sequences from all four Wisteria species and a Wisteriopsis japonica, combining these with existing data to explore phylogenetic relationships and biogeography of Wisteria, as well as plastome evolution of IRLC species. Phylogenetic analyses recognized a clade containing Glycyrrhiza–Wisteriopsis–Wisteria as sister to the remaining genera of IRLC. North American Wisteria frutescens and the three Asian species formed reciprocal clades, and Wisteria brachybotrys was sister to Wisteria floribunda and Wisteria sinensis. Wisteria may have originated in Japan near the boundary of the Oligocene and Miocene. The disappearance of Bering Land Bridge in the late Miocene might lead to the Eastern Asian–Eastern North American disjunction of Wisteria. Allopatric speciation of Wisteria between the Japanese archipelago and the Asian continent in the Quaternary increased the species richness of eastern Asia in comparison with eastern North America. Synonymous substitution rates (d_S) of protein-coding genes in the IRLC species were around 2-fold (SC genes) or 11-fold (IR genes) higher than those of non-IRLC species. For both SC and IR genes, herbaceous legumes have around 3-fold higher d_S than woody ones. Both loss of one IR region and herbaceous habit elevated substitution rates of the plastomes.     

Phylogeny and biogeography of the alpine newt Mesotriton alpestris (Salamandridae, Caudata), inferred from mtDNA sequences

In this paper, we performed phylogenetic analyses of Mesotriton alpestris populations from the entire range of species distribution, using fragments of two mtDNA genes, cytochrome b (309bp) and 16S rRNA ( approximately 500bp). Sequence diversity patterns and phylogenetic analyses reveal the existence of a relict lineage (Clade A) of late Miocene origin, comprising populations from south-eastern Serbia. This lineage is proposed to be ancestor to a western and an eastern lineage, which diverged during the middle Pliocene. The western lineage is further divided in two clades (Clades B, C) of middle Pliocene origin that represent populations from Italy (B) and populations from central Europe and Iberia (C). Further subdivision, dated back to the middle-late Pliocene, was found within the eastern lineage, representing southern (Clade D) and central-northern (Clade E) Balkan populations, respectively. Extensive sequence divergence, implying greater isolation in multiple refugia, is found within eastern clades, while the western clades seem to have been involved in the colonization of central, western and north-eastern Europe from a hypothetical refugium in central Europe. The extent of divergence does not support the current taxonomy indicating cryptic speciation in the Balkans, while paedomorphic lineages were found to have been evolved during early-middle Pleistocene probably as a response to the ongoing dramatic climatic oscillations.     

Evolution of mitochondrial relationships and biogeography of Palearctic green toads (Bufo viridis subgroup) with insights in their genomic plasticity

Taxa involving three bisexually reproducing ploidy levels make green toads a unique amphibian system. We put a cytogenetic dataset from Central Asia in a molecular framework and apply phylogenetic and demographic methods to data from the entire Palearctic range. We study the mitochondrial relationships of diploids to infer their phylogeography and the maternal ancestry of polyploids. Control regions (and tRNAs between ND1 and ND2 in representatives) characterize a deeply branched assemblage of twelve haplotype groups, diverged since the Lower Miocene. Polyploidy has evolved several times: Central Asian tetraploids (B. oblongus, B. pewzowi) have at least two maternal origins. Intriguingly, the mitochondrial ancestor of morphologically distinctive, sexually reproducing triploid taxa (B. pseudoraddei) from Karakoram and Hindukush represents a different lineage. We report another potential case of bisexual triploid toads (B. zugmayeri). Identical d-loops in diploids and tetraploids from Iran and Turkmenistan, which differ in morphology, karyotypes and calls, suggest multiple origins and retained polymorphism and/or hybridization. A similar system involves diploids, triploids and tetraploids from Kyrgyzstan and Kazakhstan where green toads exemplify vertebrate genomic plasticity. A new form from Sicily and its African sister species (B. boulengeri) allow internal calibration and divergence time estimates for major clades. The subgroup may have originated in Eurasia rather than Africa since the earliest diverged lineages (B. latastii, B. surdus) and earliest fossils occur in Asia. We delineate ranges, contact and hybrid zones. Phylogeography, including one of the first non-avian datasets from Central Asian high mountains, reflects Quaternary climate and glaciation.     

Rediscovery of the lost little dogwood Cornus wardiana (Cornaceae)—Its phylogenetic and morphological distinction and implication in the origin of the Arctic‐Sino‐Himalayan disjunction

The dwarf dogwoods (subgenus Arctocrania) have been widely known to consist of three circumboreal species Cornus suecica, Cornus canadensis, and Cornus unalaschkensis. A fourth putative species was discovered from the northern Myanmar in 1937, but it had never been formally reported on. Here, we formally report the species on the basis of phylogenetic and morphological evidence and name it Cornus wardiana Rushforth & Wahlsteen (sp. nov.). We conducted phylogenetic and morphometric analyses to determine its evolutionary relationship and differentiation from the existing relatives. We dated the phylogeny using molecular data and conducted a biogeographic analysis to gain insights into the evolution and biogeography of the Arctic‐Sino‐Himalayan disjunction. The phylogenetic analysis used sequences of the nrITS and plastid matK and rbcL genes and included all four dwarf dogwoods and 20 other species representing the three other major lineages of Cornus and the outgroup. The morphometric analyses included 60 populations and 102 specimens of dwarf dogwood, representing the entire range of the subgenus. The results showed that C. wardiana diverged first within subgenus Arctocrania in the Miocene, from a wide‐spread ancestor. Results from principal component analysis and discriminant analysis also showed that the Myanmar samples are well separated from the others. Taken together, these results suggest that the dwarf dogwood lineage split from the big‐bracted dogwoods in Asia or Asia‐western North America during the late Paleocene and spread widely to form a Eurasia‐North America distribution; the Arctic‐Sino‐Himalayan disjunction was the result of southward migration in the Miocene followed by extinction in the intervening highland areas.     

Plastid and nuclear phylogenomic incongruences and biogeographic implications of Magnolia s.l. (Magnoliaceae)

Magnoliaceae, an assemblage of early diverged angiosperms, comprises two subfamilies, speciose Magnolioideae with approximately 300 species in varying numbers of genera and monogeneric Liriodendroideae with two species in Liriodendron L. This family occupies a pivotal phylogenetic position with important insights into the diversification of early angiosperms, and shows intercontinentally disjunct distribution patterns between eastern Asia and the Americas. Widespread morphological homogeneity and slow substitution rates in Magnolia L. s.l. resulted in poorly supported phylogenetic relationships based on morphology or molecular evidence, which hampers our understanding of the genus’ temporal and spacial evolution. Here, based on the newly generated genome skimming data for 48 Magnolia s.l. species, we produced robust Magnolia phylogenies using genome-wide markers from both plastid genomes and single nucleotide polymorphism data. Contrasting the plastid and nuclear phylogenies revealed extensive cytonuclear conflicts in both shallow and deep relationships. ABBA-BABA and PhyloNet analyses suggested hybridization occurred within sect. Yulania, and sect. Magnolia, which is in concordance with the ploidy level of the species in these two sections. Divergence time estimates and biogeographic reconstruction indicated that the timing of the three tropical Magnolia disjunctions coincided with the mid-Eocene cooling climate and/or late Eocene climate deterioration, and two temperate disjunctions occurred much later, possibly during the warm periods of the Miocene, hence supporting the boreotropical flora concept of Magnolia s.l.     

Species richness in plant genera disjunct between temperate eastern Asia and North America

The species richness of 109 amphi-Pacific disjunct genera was examined in eastern Asia and North America. Although the entire flora of eastern Asia contains approximately one-third more species than that of North America, the difference in species richness among disjunct taxa is less. When woody and herbaceous genera are considered separately, the former exhibit a strong diversity bias favouring eastern Asia whereas there is no significant difference in diversity between continents among herbaceous genera. This result is not due to habitat differences between woody and herbaceous genera, because the disjunct herbs inhabit primarily moist forests and woodlands. This result is also not related to relative phylogenetic advancement, even though older major lineages of plants tend to have a predominance of woody taxa. Woody genera are distributed in lower latitudes than herbaceous genera on both continents, and both woody and herbaceous genera are distributed in lower latitudes in eastern Asia than in North America. The North American temperate flora is primarily a relict of a flora form 7 more widespread throughout the Northern Hemisphere. Contemporary patterns of diversity suggest that the effects of climate changes in the late Tertiary were less severe in eastern Asia and promoted diversification, but were more severe in North America and may have caused widespread extinction. The difference in the effect of climate change on diversity in herbaceous and woody lineages reflects the different ecological relationships of species having these contrasting life forms. Clearly, the contemporary floras of eastern Asia and North America bear the imprint of history and emphasize the important interface between ecological relationships and evolutionary responses.     

山西关帝山森林群落物种、谱系和功能多样性海拔格局

探索和揭示生物多样性的空间格局和维持机制是生态学和生物地理学研究的热点内容, 但综合物种、系统进化和功能属性等方面的多样性海拔格局研究很少。该文以关帝山森林群落为研究对象, 综合物种、谱系和功能α和β多样性指数, 旨在初步探讨关帝山森林群落多样性海拔格局及其维持机制。研究结果表明: 随着海拔的升高(1 409-2 150 m), 关帝山森林群落物种丰富度指数(S)、谱系多样性指数(PD)和功能丰富度指数(FRic)整体上表现出上升的趋势, 特别是海拔1 800 m以上区域。随着海拔的升高, 总β多样性(β_total)和更替(β_repl)上升趋势明显, 而丰富度差异(β_rich)则逐渐下降。不同生活型植物的物种、谱系和功能多样性海拔格局差异较大。随着海拔的升高, 草本植物S和物种多样性指数(H′)上升趋势高于木本植物。影响草本植物S分布的主要因素是地形因子, 而影响木本植物S分布的主要因素是历史过程。随着海拔的升高, 木本植物β_total上升趋势要比草本植物明显。随着海拔的升高, 木本植物β_repl和β_rich分别表现出单峰格局和“U”形格局, 而草本植物β_repl和β_rich则分别表现出单调递增和单调递减的格局。随着环境差异和地理距离的增加, 群落间物种、谱系和功能β多样性显著增加。环境差异(环境过滤)对木本植物的β多样性具有相对较强的作用; 而环境差异(环境过滤)和地理距离(扩散限制)共同作用于草本植物的β多样性。     

The Peniophorella praetermissa species complex (Basidiomycota)

The corticioid basidiomycete Peniophorella praetermissa has long been regarded as a morphologically variable species complex. An ITS-based phylogenetic study based on a worldwide sampling was carried out using parsimony and Bayesian inference. The resulting trees feature three major clades, further divided into well-supported subclades. These could be considered as distinct species, a contention that is further supported by crossing test data. Only two out of the eight phylogenetic lineages identified can be distinctly morphologically characterized: P. odontiaeformis and P. subpraetermissa. P. odontiaeformis is an odontioid species with a paleotropical distribution whereas the taxa in the remaining subclades have smooth basidiomata and are distributed in temperate areas. P. subpraetermissa is known only from the type collection and is distinguished microscopically by its reddish brown apically encrustated cystidia. Taxa in the remaining subclades are impossible to distinguish from each other morphologically, and therefore, are viewed as a species complex, P. praetermissa s. lat. One of the subclades, which is widely distributed but restricted to the Northern hemisphere, is proposed to represent P. praetermissa s. str. An epitype is selected from the same area as the holotype, among the specimens studied here. However, the geographically most widespread clade with many representatives from both hemispheres is here referred to as P. pertenuis, a taxon that was previously considered a synonym to P. praetermissa.     

Phylogenetic relationships and the maternal donor of Roegneria (Triticeae: Poaceae) based on three nuclear DNA sequences (ITS,Acc1, and Pgk1) and one chloroplast region (trnL-F)

Roegneria is a polyploid perennial genus in the tribe Triticeae. Some species of Roegneria are morphologically similar to genus Elymus and have been classified in Elymus. To investigate the delimitation and phylogenetic relationships of Roegneria, nuclear (ITS, Acc1, and Pgk1) and chloroplast (trnL–trnF) DNA regions were sequenced for 38 allopolyploid species and 32 diploid species of Triticeae. Phylogenetic analyses of nuclear DNA revealed that all Roegneria species were included in the St and Y genome clades, and that the Y genome was closely related to the V and Xp genomes. The chloroplast DNA dataset showed that Roegneria species were grouped with Pseudoroegneria species. The Pseudoroegneria species from the Middle East (P. libanotica and P. tauri) and Central Asia (P. strigosa) were more closely related to Roegneria species. The results suggested that: (i) the species containing the St and Y genomes should be segregated from Elymus and treated as a distinct genus, Roegneria, based on the genomic constitution; (ii) P. libanotica, P. tauri, and/or P. strigosa potentially served as the maternal donor of the St genome in Roegneria; (iii) The Y genome of Roegneria originated from a diploid Y genome species, and the V and Xp genomes may have contributed to Y genome formation; (iv) among Roegneria species of previously uncertain genomic constitution, R. seriotina was tetraploid and possessed the StY genomes, E. calcicolus was hexaploid with the StYH genomic constitution and should be classified in Campeiostachys, R. glaucifolia possessed the StStY genomes, and R. tschimganica had the genomic constitution St₁St₂Y.     

Analysis of phylogenetic relationships of Potamogeton species in China based on chloroplast trnT-trnF sequences

Sequences of the chloroplast trnT-trnF region were analyzed for species of the genus Potamogeton distributed in China to reconstruct phylogenetic relationships. The phylogenetic analyses showed that the genus Potamogeton could be divided into two clades. Eighteen species formed a monophyletic clade while the remaining four formed a second, distinguishable one, supporting the conventional treatment that the genus Potamogeton contains the submerged linear-leaved group and the submerged broad-leaved group. The first clade, which represented the subgenus Potamogeton, could be further divided into two subclades. The second clade, which represented the subgenus Coleogeton, displayed a close phylogenetic relationship with the subgenus Potamogeton and occupied a unique position within the genus Potamogeton. This finding suggested that the treatment of the subgenus Coleogeton, which was once regarded as the genus Stuckenia Börner, may need to be reconsidered. Furthermore, identification of maternal donors of some hybrids was successfully applied based on sequence of maternally inherited chloroplast genome. The female parents of three putative hybrids, P. × malainoides, P. × anguillanus, and P. × orientalis, were proved to be accordant with previous morphological conclusions.     

Molecular phylogeny and historical biogeography of the Holarctic wetland leaf beetle of the genus Plateumaris

Leaf beetles of the genus Plateumaris inhabit wetlands across the temperate zone of the Holarctic region. To explore the phylogeographic relationships among North American, East Asian, and European members of this genus and the origin of the species endemic to Japan, we studied the molecular phylogeny of 20 of the 27 species in this genus using partial sequences of mitochondrial cytochrome oxidase subunit I (COI) and the 16S and nuclear 28S rRNA genes. The molecular phylogeny revealed that three species endemic to Europe are monophyletic and sister to the remaining 11 North American and six Asian species. Within the latter clade, North American and Asian species did not show reciprocal monophyly. Dispersal-vicariance analysis and divergence time estimation revealed that the European and North America-Asian lineages diverged during the Eocene. Moreover, subsequent differentiation occurred repeatedly between North American and Asian species, which was facilitated by three dispersal events from North America to Asia and one in the opposite direction during the late Eocene through the late Miocene. Two Japanese endemics originated from different divergence events; one differentiated from the mainland lineage after differentiation from the North American lineage, whereas the other showed a deep coalescence from the North American lineage with no present-day sister species on the East Asian mainland. This study of extant insects provides molecular phylogenetic evidence for ancient vicariance between Europe and East Asia-North America, and for more recent (but pre-Pleistocene) faunal exchanges between East Asia and North America.     

Phylogenetic perspectives on diversification and character evolution in the species‐rich genus Erysimum (Erysimeae; Brassicaceae) based on a densely sampled ITS approach

Erysimum includes 150–350 species distributed in the Northern Hemisphere, with Eurasia being the centre of greatest diversity. It is well known for its taxonomic complexity as a result of overlapping morphological characters. We present the first densely sampled phylogenetic analysis of Erysimum using internal transcribed spacer (ITS) DNA sequences from c. 85% of the species (117 for the first time), representing the full range of morphological variation and geographical distribution. We used several approaches to reconstruct phylogenetic relationships, dating of diversification and patterns of evolution of morphological characters in the genus. Ancestral‐state reconstructions of four morphological diagnostic characters were performed using maximum parsimony, maximum likelihood and Bayesian methods. Our phylogenetic framework strongly supports the monophyly of Erysimum and recovers some well‐supported clades that are geographically, rather than morphologically, correlated. Our study confirms the placement of Erysimum in lineage I and reveals two Malcolmia spp. (M. maritima and M. orsiniana) as its sister taxa. The results suggest that the biennial duration and caespitose habit (vs. annual or perennial duration and herbaceous or woody habit) and large, yellow, glabrous (vs. small, non‐yellow, pubescent) petals are ancestral in Erysimum. The ancestral‐state reconstruction results show that annual vs. perennial and woody vs. herbaceous features have been independently derived several times. The dating analyses suggest an early radiation of Erysimum during the late Pliocene or early Pleistocene. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 497–522.     

Revisiting of Carex sect. Confertiflorae s.l. (Cyperaceae): New data from molecular and morphological evidence and first insights on Carex biogeography in East Asia

Carex sect. Confertiflorae s.l. is a medium-sized species group (ca. 40 species) with its center of diversity in E Asia (China and Japan). According to morphological traits, the section has been proposed to split into two sections (sects. Confertiflorae sensu Ohwi and Molliculae Ohwi) up to five different ones (sects. Confertiflorae s.s., Molliculae, Dispalatae Ohwi, Ischnostachyae Ohwi, and Alliiformes Akiyama). Recent phylogenetic reconstructions showed Confertiflorae s.l. not to be monophyletic, as species traditionally considered part of it were found to belong to other clades, whereas species traditionally ascribed to other sections were nested within it. In this study, we investigated the phylogenetic structure, morphological affinities, and biogeographic history of sect. Confertiflorae s.l. We employed a taxon-based approach to explore the morphological affinities of the species considered in sect. Confertiflorae and compared the micromorphology of the nutlets of almost all the taxa using SEM. We included 40 samples representing 31 species/subspecies of sect. Confertiflorae s.l. and used two nuclear (ETS and ITS) and three plastid (trnL-F, matK, and rpl32-trnL ^UAG) molecular markers to reconstruct the phylogeny of the group. The phylogenetic analyses confirmed the polyphyly of sect. Confertiflorae s.l., whose representatives were found within five distinct clades. From these, two clades, sect. Confertiflorae and sect. Molliculae, were found to be closely related and contained the majority of the species. The composition of the two clades agreed with the morphological structure of the group, and we confirmed an exclusive combination of features (namely color of basal sheaths, presence of bract sheath, peduncle of lowest spike, inflorescence sex distribution, shape of pistillate glume apex, and color and veins of utricle, among others) characterizing each of the two clades. The origin of the two clades was found to be in the early Pliocene; however, the majority of the diversification events within each clade took place during the Pleistocene. This illustrates that although Asia has been regarded as having little potential ecological space for Carex to diversify due to its climate stability, groups of sedges sub-endemic from that area may have a fairly recent origin related to glaciations. We proposed the rearrangement of sect. Confertiflorae as previously conceived as three independent sections: the monotypic Alliiformes, sect. Molliculae, and sect. Paludosae.     

Polyphyly and species delimitation of Picea brachytyla (Pinaceae) based on population genetic data

Accurate species delimitation is fundamental to biodiversity conservation. The endangered spruce Picea brachytyla (Franch.) E. Pritz. was suggested to be polyphyletic based on a limited number of samples in previous studies. To evaluate polyphyly of P. brachytyla, we sampled 139 individuals from 16 populations across most of its distributional range, plus representatives of two related species, Picea likiangensis (Franch.) E. Pritz. and Picea wilsonii Mast. We sequenced 13 nuclear loci and three chloroplast and two mitochondrial loci for the following species delimitation. Phylogenetic analyses of nuclear loci grouped all individuals of P. brachytyla from Sichuan and Chongqing into one distinct lineage and those from Yunnan and Tibet (southern distribution) nested within the P. likiangensis species complex. Structure analyses confirmed this result. Networks of chloroplast DNA haplotypes similarly showed that P. brachytyla from the southern distribution nested within the P. likiangensis species complex, whereas haplotypes for the northern distribution comprised a separate and well-supported lineage. These results suggest that P. brachytyla from the southern distribution is a part of the P. likiangensis species complex and should be removed from P. brachytyla. Our study highlights the utility of population genetic evidence in delimitating endangered species and understanding the conservation status of such species.