Phylogenetic Framework for Trema (Celtidaceae)

We used ITS and trnL sequence data, analyzed separately and combined by MP, to explore species relationships and concepts in Trema (Celtidaceae), a pantropical genus of pioneer trees. Whether Trema is monophyletic or includes Parasponia is still unresolved. Three clades within Trema received moderate to high support, one from the New World and two from the Old World, but their relationships were not resolved. In the New World, specimens of T. micrantha formed two groups consistent with endocarp morphology. Group I, with smaller brown endocarps, is a highly supported clade sister to T. lamarckiana. Group II, with larger black endocarps, is poorly resolved with several subclades, including the highly supported T. integerrima clade. Both Old World clades contain Asian and African species, with three or more species in each region. Trema orientalis is not monophyletic: specimens from Africa formed a highly supported clade sister to T. africana, while those from Asia were sister to T. aspera from Australia.     

Endemic evolutionary radiation of Rhagada land snails (Pulmonata: Camaenidae) in a continental archipelago in northern Western Australia

In the Dampier Archipelago of Western Australia's Pilbara Region, several locally endemic, morphologically distinctive species of Rhagada land snails occur, contrasting with the morphologically conservative species with wider distributions on the adjacent mainland. To test alternative origins of this unusual local diversity in a continental archipelago, we examined sequences of the cytochrome oxidase subunit 1 and 16S mitochondrial genes in 22 described species and eight undescribed forms, including all known morphospecies from the Pilbara Region's Dampier Archipelago and adjacent mainland. Phylogenetic analyses consistently resolved four, deep clades within the Pilbara Region, with a mean sequence divergence of 15–18%. All but one of the species from the Dampier Archipelago formed one of the major clades, indicating that the morphological radiation in the archipelago evolved locally, rather than through multiple, relictual mainland lineages. Morphological divergence spanning almost that of the entire genus was within a subclade with sequence divergence < 4%, highlighting the disconnection between morphological diversification and levels of molecular genetic divergence. This in situ morphological radiation in the Dampier Archipelago, which transcends variation seen over much larger distances on the mainland, is unusual for a continental archipelago, and may relate to local heterogeneity of land forms. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 316–327.     

Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South-East Asian waters

The decapod family Penaeidae comprises most of the economically important marine shrimp species. Its members are widespread throughout the world, with its highest species diversity centred in the Indo-West Pacific region. Despite this importance, their taxonomy, classification and phylogeny are not yet settled due in part to incongruence among hypotheses proposed from molecular versus morphological studies. In this study, using a thorough taxonomic sampling of especially the South-East Asian species, we aim to (a) utilize a reconstructed phylogeny to test the monophyly of the Penaeidae and its currently recognized genera and (b) explore its species diversity in South-East Asian waters. To infer the phylogeny, a combined gene data set (including 109 ingroup and six outgroup taxa) of mitochondrial genes, COI and 16S rRNA, and two nuclear genes, NaK and PEPCK, was utilized. To explore its diversity, another data set that included 371 COI gene sequences (231 newly generated and 140 retrieved from public sources) was compiled and subsequently analysed with two different tools (ABGD and bPTP) for species delimitation. Other than supporting the non-monophyly of the Penaeidae with the Sicyoniidae nested within the penaeid tribe Trachypenaeini, the genera Penaeus, Mierspenaeopsis and Parapenaeopsis were also revealed to be polyphyletic. Our species delimitation analysis inferred that 94 putative species actually existed within the 71 morphospecies reviewed, indicating an underestimated biodiversity in this family and the potential presence of new species within the following morphospecies: Kishinouyepenaeopsis cornuta, K. incisa, Mierspenaeopsis sculptilis, M hardwicki, Parapenaeopsis coromandelica and Penaeus monodon.     

Comparative innervation of cephalic photophores of the loosejaw dragonfishes (Teleostei: Stomiiformes: Stomiidae): Evidence for parallel evolution of long‐wave bioluminescence

Four genera of the teleost family Stomiidae, the loosejaw dragonfishes, possess accessory cephalic photophores (AOs). Species of three genera, Aristostomias, Malacosteus, and Pachystomias, are capable of producing far‐red, long‐wave emissions (>650nm) from their AOs, a character unique among vertebrates. Aristostomias and Malacosteus posses a single far‐red AO, while Pachystomias possesses anterior and posterior far‐red AOs, each with smaller separate photophores positioned in their ventral margins. The purpose of this study was to establish the primary homology of the loosejaw AOs based on topological similarity of cranial nerve innervation, and subject these homology conjectures to tests of congruence under a phylogenetic hypothesis for the loosejaw dragonfishes. On the basis of whole‐mount, triple‐stained specimens, innervation of the loosejaw AOs is described. The AO of Aristostomias and the anterior AO of Pachystomias are innervated by the profundal ramus of the trigeminal (Tpr), while the far‐red AO of Malacosteus and a small ventral AO of Pachystomias are innervated by the maxillary ramus of the trigeminal (Tmx). The largest far‐red AO of Pachystomias, positioned directly below the orbit, and the short‐wave AO of Photostomias are innervated by a branch of the mandibular ramus of the trigeminal nerve. Conjectures of primary homology drawn from these neuroanatomical similarities were subjected to tests of congruence on a phylogeny of the loosejaws inferred from a reanalysis of a previously published morphological dataset. Optimized for accelerated transformation, the AO innervated by the Tpr appears as a single transformation on the new topology, thereby establishing secondary homology. The AOs innervated by the Tmd found in Pachystomias and Photostomias appear as two transformations in a reconstruction on the new topology, a result that rejects secondary homology of this structure. The secondary homology of AOs innervated by the Tmx found in Malacosteus and Pachystomias is rejected on the same grounds. Two short‐wave cephalic photophores present in all four genera, the suborbital (SO) and the postorbital (PO), positioned in the posteroventral margin of the orbit and directly posterior to the orbit, respectively, are innervated by separate divisions of the Tmd. The primary homologies of the loosejaw PO and SO across loosejaw taxa are proposed on the basis of similar innervation patterns. Because of dissimilar innervation of the loosejaw SO and SO of basal stomiiforms, primary homology of these photophores cannot be established. Because of similar function and position, the PO of all other stomiid taxa is likely homologous with the loosejaw PO. Nonhomology of loosejaw long‐wave photophores is corroborated by previously published histological evidence. The totality of evidence suggests that the only known far‐red bioluminescent system in vertebrates has evolved as many as three times in a closely related group of deep‐sea fishes. J. Morphol., 2010. © 2009 Wiley‐Liss, Inc.     

采自祁连山的冷杉侧耳生物学特性及栽培条件探索

以采自甘肃省祁连山国家级自然保护区菌物保育区的野生侧耳作为试验材料,通过形态学及系统发育分析方法将其鉴定为冷杉侧耳Pleurotus abieticola。对该菌株生物学特性及栽培条件进行初步研究,结果表明：菌丝体最适生长温度为25℃;最适pH为7.0;最适碳源为玉米粉;最适氮源为豆粉;在以棉籽壳、木屑和麸皮为栽培料时,可获得子实体。     

毛离褶伞——一种孢子杆状的离褶伞科新属和新种

根据形态和分子系统发育证据,描述采自我国西南的新属和新种毛离褶伞Tricholyophyllum brunneum。与离褶伞科其他属不同,该新属的菌盖表皮为毛皮状,菌柄表皮为不连续的毛皮状,有褶缘囊状体,担孢子长椭圆形至圆柱形。     

中国甘肃省狭义丝盖伞属二新种

依据形态学和分子系统学研究结果,描述了产自中国甘肃省的狭义丝盖伞属2个新种,即拟黄囊丝盖伞Inocybe muricellatoides和甘肃丝盖伞I. gansuensis。对新种的ITS、LSU和rpb2片段进行了测序和分析,并提供了详细描述、线条图、生态照片及与相似种的区别。拟黄囊丝盖伞以菌盖翘起的鳞片、菌柄纤维状、孢子光滑和厚壁的侧生囊状体为主要识别特征。甘肃丝盖伞具有粗壮的子实体、较大的孢子和厚壁侧生囊状体。基于LSU和rpb2联合数据的分子系统发育分析显示这两个新种隶属于狭义丝盖伞属且分别占据独特的分支。     

中国小菇属十个新记录种

报道了小菇科小菇属真菌10个中国新记录种,香菌组：橙盖小菇Mycena aurantiidisca、黄白小菇Mycena flavoalba、粉黄小菇Mycena floridula;棘刺组：异刺小菇Mycena heteracantha;纤柄组：碱味小菇Mycena amygdalina;脆足组：粉被小菇Mycena zephirus;冬生组：绣线菊小菇Mycena speirea、冬生小菇Mycena hiemalis;小菇组：绒柄小菇Mycena flos-nivium,分别来自吉林等11个省份、自治区。提供了每个物种的形态描述和线条图,以及与相近种的讨论。共计90条自测及下载ITS序列,在采用贝叶斯法和最大似然法构建的小菇属系统发育树中,新记录种均得到分子数据支持。凭证标本存放于吉林农业大学菌物标本馆（HMJAU）。     

干皮孔菌属的一个新种和三个组合种

本文报道了产自斯里兰卡的干皮孔菌属一个新种,该种的主要特征是具有平伏反卷或具菌盖的子实体,很小的孔口（每毫米8-10个）,菌丝系统二系,生殖菌丝覆盖有刺状结晶,骨架菌丝橙棕色,细腊肠状担孢子（2.7-3.4×0.5-0.8μm）。基于ITS和nLSU序列的系统发育分析表明该新种属于干皮孔菌属的一个明确的分支。此外,将毛孔菌属组合到干皮孔菌属中,并报道了3个组合种,白边干皮孔菌、印度干皮孔菌和萨彦干皮孔菌。     

Phylogenetic relationships of Cyrtandromoea and Wightia revisited: A new tribe in Phrymaceae and a new family in Lamiales

The familial placements of Cyrtandromoea Zoll. and Wightia Wall., two small and enigmatic South‐East Asian genera, have long been controversial in Lamiales. Here we adopt a two‐step approach to resolve their phylogenetic relationships. We initially reconstructed a large‐scale phylogeny of Lamiales using six chloroplast markers (atpB, matK, ndhF, psbBTNH, rbcL, and rps4). The results showed that both Cyrtandromoea and Wightia emerged in the LMPO clade, including Lamiaceae, Mazaceae, Phrymaceae, Paulowniaceae, and Orobanchaceae. Based on the second set of six chloroplast markers (atpB, matK, ndhF, rbcL, rps16, and trnL‐F) and two nuclear ribosomal regions (external transcribed spacer and internal transcribed spacer) for the analyses focusing on the LMPO clade, our results revealed that Cyrtandromoea was consistently nested within Phrymaceae, whereas Wightia was supported as sister to Phrymaceae by the chloroplast DNA dataset or sister to Paulowniaceae by the nuclear ribosomal DNA dataset. Morphological and anatomical evidence fully supports the inclusion of Cyrtandromoea in Phrymaceae, and an updated tribal classification is done for Phrymaceae with five tribes, that is, Cyrtandromoeeae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Diplaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Leucocarpeae, Mimuleae, and Phrymeae. The conflicting phylogenetic position of Wightia indicated by different genome markers results in difficulty placing the genus in either Phrymaceae or Paulowniaceae. Considering the distinct morphological differences between Wightia and other families in the LMPO clade, we here propose a new family, Wightiaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, fam. nov., to accommodate it, which is the 26th family recognized in Lamiales.