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.     

Comparative studies of the population genetic structure of the Brachionus calyciflorus species complex from four inland lakes in Wuhu,China

To study how the population genetic structure in zooplankton respond to environmental conditions, using comparative limnology, the genetic diversity and genetic differentiation of the B. calyciflorus complex collected from four inland lakes in Wuhu City, China were investigated based on the 16S rRNA gene and nuDNA ITS sequences. The results displayed a high genetic diversity, and the nucleotide diversity of the 16S rRNA gene was higher than that of the ITS sequence. The phylogenetic analyses grouped the four populations into two cryptic species (Bc-JT and Bc-FL) with strong support. The two cryptic species were found in lakes with different trophic levels, demonstrating significant ecological specialization. The origins of clone TW12 were not consistent in the phylogenetic trees between two genetic markers, which might be attributed to the effects of male-mediated gene flow on the phylogenetic relationships of rotifers. The nucleotide diversity of the cryptic species Bc-JT was higher than that of Bc-FL, indicating that eutrophication might decrease the genetic diversity of cryptic species. The total phosphorus concentration in water bodies might be the most important factor affecting the genetic diversity of species.     

Population genetic structure of Sorex unguiculatus and Sorex caecutiens (Soricidae, Mammalia) in Hokkaido, based on microsatellite DNA polymorphism

We investigated the genetic structure of Sorex unguiculatus and Sorex caecutiens populations in Hokkaido, Japan, using hypervariable microsatellite DNA markers. We used five microsatellite loci to type 475 S. unguiculatus individuals from 20 localities on the Hokkaido mainland and four localities from each of four offshore islands (and 11 shrews from one locality in southern Sakhalin for a particular analysis). We used six microsatellite loci to type 240 S. caecutiens individuals from 13 localities on the Hokkaido mainland. Genetic variation was high in mainland populations of both species and low in the island populations of S. unguiculatus. Allelic richness and island size were positively correlated for S. unguiculatus, suggesting that genetic drift occurred on those islands due to small population size. In addition, four insular populations of S. unguiculatus were genetically differentiated from the mainland populations, although clear phylogeographic clustering was not confirmed among populations on the Hokkaido mainland for either S. unguiculatus or S. caecutiens. Heterozygosity excess was observed in more than half of the populations including the mainland populations of the two species, suggesting recent bottleneck events in these populations. Population dynamics of the shrews might be explained by a metapopulation scheme. According to autocorrelation analysis, the extent of non-random spatial genetic structure was approximately 100 km. Isolation by distance was observed in S. unguiculatus, but not in S. caecutiens although there is a positive trend. The lack of correlation for S. caecutiens might have been due to small sample size. Thus, no obvious differences in population genetic structure were found between the two species on the Hokkaido mainland in the present study, while previous investigations using mitochondrial DNA sequences inferred that these two species might have rather different biogeographic histories.     

Genetic diversity and geographic distribution of Bemisia tabaci species complex in Nepal

Bemisia tabaci species complex comprises at least 44 cryptic species worldwide. Here, we analyze the nucleotide sequences of mitochondrial cytochrome oxidase subunit 1 (COI) gene obtained from 76 samples of B. tabaci collected from 23 districts in Nepal. This is the first genetic and geographic study of B. tabaci species complex in Nepal. Our phylogenetic study identified the presence of three cryptic species—Asia I, Asia II 1, and Asia II 5—with high interspecific but low intraspecific variations. Among the three cryptic species, Asia II 5 was the most prevalent in Nepal, constituting 64.47% of all the sequenced samples. Based on haplotype network analysis of COI sequences, Asia II 1 was more genetically diversified than the other two cryptic species. Our results provided useful information on the genetic diversity and geographic distribution of B. tabaci in Nepal, which help monitor population changes of B. tabaci at cryptic species level and develop sustainable management strategies for its control.     

中国浙江麝鼩属(劳亚食虫目:鼩鼱科)一新种描记

2017年8月,在浙江省拟建淳安磨心尖省级自然保护区和拟建东阳市东江源省级自然保护区捕获麝鼩属（Crocidura）共5号标本。基于线粒体细胞色素b基因构建的系统发育树显示采集于浙江的麝鼩属样本与大麝鼩（Crocidura lasiura）和日本麝鼩（Crocidura dsinezumi）构成姊妹群,遗传距离最近,而与中国西南部分布的小体型印支小麝鼩（Crocidura indochinensis）、五指山小麝鼩（Crocidura wuchihensis）及东北部分布的山东小麝鼩（Crocidua shantungensis）、北小麝鼩（Crocidua suaveolens）亲缘关系较远,其遗传距离分别为0.114、0.124、0.139和0.144。这些样本与麝鼩属其他物种之间的遗传距离在0.101~0.155之间,最小遗传距离出现在来自浙江的样本和大麝鼩之间,最大遗传距离在浙江样本与中麝鼩之间。形态上,采集于浙江的麝鼩属标本个体小,体长48~61mm（平均：55.60mm）,尾长35~49mm（平均：43.14mm）;尾长与体长之比72.92%~80.36%;尾近乎裸露,尾基1/3~1/2着生稀疏长毛;尾上下双色,背部黑褐色,腹部较淡;颅较短,颅全长15.60~17.16mm（平均：16.46mm）,与中国东北部分布的山东小麝鼩和北小麝鼩相近又有区别,与已知其它麝鼩属物种形态差异较大;综合形态和系统发育关系证实采集于浙江的麝鼩属物种为一新物种,命名为东阳江麝鼩（Crocidura dongyangjiangensis Liu Y, Chen SD, and Liu SY sp. nov.）。本文对其形态、栖息环境和与近缘种的区别进行了详细记述。     

Phylogeny,phylogeography and geographical variation in the Crocidura monax (Soricidae) species complex from the montane islands of Tanzania,with descriptions of three new species

We assess morphological and multilocus genetic variation among 11 isolated montane populations of white‐toothed shrews from Tanzania that have been referred to either Crocidura monax Thomas or C. montis Thomas. The montane sites we sampled represent ‘sky‐islands’ from two geologically distinct archipelagos (Northern Highlands and the Eastern Arc Mountains) and are a significant component of the Eastern Afromontane Biodiversity Hotspot. We used multivariate analyses of morphometric traits and phylogenetic and species‐delimitation analyses of multilocus DNA sequence data to assess species‐level diversity. Our species delimitation analyses included a novel, pairwise validation approach that avoids potential biases associated with specifying a guide tree. These analyses reveal several distinct lineages, which we treat as six allopatric species. Each species is restricted to one, two or four mountains. We use available names to recognize C. monax, C. tansaniana Hutterer and C. usambarae Dippenaar, while naming and describing three new species. Our results demonstrate the effectiveness of combining morphological and genetic data to uncover and describe hidden diversity in a cryptic mammalian system. © 2015 The Linnean Society of London     

Allozyme variation and genetic relationships among species in the Carex willdenowii complex (Cyperaceae)

A taxonomic study by Naczi, Reznicek, and Ford (American Journal of Botany, 85, 434-447, 1998) has determined that three species (Carex willdenowii, C. basiantha, and C. superata) can be recognized within the C. willdenowii complex. To determine the amount of genetic divergence within and between these species, allozyme analyses were conducted on 14 populations distributed from Pennsylvania to eastern Texas. Seventeen loci were surveyed, 13 of which were polymorphic, with all populations being polymorphic at one or more loci. Interspecific genetic identities ranged from 0.560 (C. willdenowii and C. basiantha) to 0.807 (C. basiantha and C. superata). Alleles for the isozymes Aat-1, Dia-1, Idh-2, Mdh-2, Per-1, Pgm-1, and Pgm-2 served to distinguish C. willdenowii from C. basiantha and C. superata. Carex basiantha and C. superata were recognized by alleles of Mdh-2, Pgm-1, and Tpi-2. The genetic identities of populations within species were high and exceeded 0.957. A caespitose growth habit and perigynia in close proximity to the staminate flowers suggest adaptations for selfing and therefore low levels of heterozygosity. Paradoxically, the values for expected heterozygosities (Hexp) were always lower than those obtained by direct count (Hobs): F values were highly negative, indicating heterozygous excess. Disassortative mating and selection are discussed as possible mechanisms for maintaining heterozygous excess within populations.     

Genetic diversity of Bemisia tabaci cryptic species in Nigeria and their relationships with endosymbionts and acquired begomoviruses

Bemisia tabaci is a species complex of at least 44 cryptic species with a worldwide distribution. It is a serious pest of many crop plants as well as a successful vector of at least 100 begomoviruses. Using B. tabaci collected from cassava and tomato fields in the southwestern and north central regions of Nigeria, we determined nucleotide sequences from the mitochondrial cytochrome c oxidase subunit I (COI) of 23 B. tabaci samples, the 16S and 23S ribosomal DNA of endosymbionts, and the coat protein gene of geminiviruses ingested by the whiteflies. The COI analysis identified three different genetic groups including the indigenous Sub-Saharan Africa 1 subgroup 1 (SSA1-SG1) and 5 (SSA1-SG5, which was most prevalent), and an invasive cryptic species (Mediterranean). SSA1 was infected by five known secondary endosymbionts, Arsenophonus, Cardinium, Hamiltonella, Rickettsia, and Wolbachia, and co-infections with two or three endosymbionts were common. Five begomoviruses, okra enation leaf curl virus, squash leaf curl China virus, tobacco curly shoot virus, tomato leaf curl New Delhi virus, and tomato yellow leaf curl virus, were detected from 43.5% of the B. tabaci samples. However, cassava mosaic disease that causes devastating cassava yield losses was not detected in this study. This study improves the current understanding of the genetic diversity of B. tabaci cryptic species, and it reveals their relationships with endosymbionts and geminiviruses in the cassava and tomato fields of Nigeria.     

DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species

Alexandrium species can be very difficult to identify, with A. catenella, A. tamarense, and A. fundyense that compose “Alexandrium tamarense species complex” (Atama complex) as a distinct example. DNA barcoding is promising to offer a solution but remains to be established. In this study, we examined the utility of ITS in resolving the Atama species complex, by analyzing previously studied strains plus unstudied Chinese strains within the LSU- and SSU-rDNA based group/clade frameworks recently established. We further investigated the presence of intragenomic polymorphism and its implications in species delimitation. Similar to the previous SSU and LSU results, our ITS-based phylogenies divided the complex to five clusters, but with longer and evener branch lengths between the clusters. Based on the ITS region, the inter-cluster genetic distances (p = 0.134–0.216) were consistently and substantially greater than intra-cluster genetic distances (p = 0.000–0.066), with an average inter-cluster (species) distance (p = 0.167) 7.6-fold of the average intraspecific difference (p = 0.022), qualifying the approximately 510–520 bp ITS as a DNA barcode for Atama complex. We detected varying levels of intragenomic polymorphism in ITS but found that this did not impact the taxon-resolving power of this gene. With this DNA barcode, the new East and South China Sea strains and one Antarctic strain were placed in Clade IIC/Group IV, even though there were 7–10 polymorphic sites in their ITS, in contrast to none in SSU. Furthermore, our results suggest that the five clusters are recognizable as distinct species according to the phylogenetic species concept. Based on the phylogenetic placements of the type-locality strains of the existing three morphospecies and the dominant localities of other strains, we propose that Group I/Clade I be designated as A. fundyense, Group III/Clade IIB as A. tamarense, Group IV/Clade IIC as A. catenella, Group II/Clade IIA as A. mediterranis, and Group V/Clade IID as A. australis.     

The morphology and relationships of the walking mud spiders of the genus Cryptothele (Araneae: Zodariidae)

We revise the relationships of the spider genus Cryptothele after reexamination of the morphology of the spinnerets, leg tarsal claws and maxillae with scanning electron microscopy. Cryptothele species have a particular conformation of the spinning field of the anterior lateral spigots that is typical of zodariids and close relatives: the field of major ampullate gland spigots, together with their strain sensilla, are invaginated within the field of piriform gland spigots. The implantation of the teeth on the inner side of the leg tarsal claws is also consistent with its placement among zodariids. We added Cryptothele to a morphological dataset of zodariid genera, together with the outgroups Homalonychus (Homalonychidae) and Penestomus (Penestomidae). The phylogenetic analysis concludes that the genus Cryptothele is a member of the subfamily Cydrelinae, which by priority is here considered a junior synonym of Cryptothelinae. Cryptothele specimens cover most of their body with soil particles which become consolidated as mud, and the debris is probably held in place by curved setae covered by long barbs. The spinnerets, which can be retracted and hidden, as well as the booklungs, are surrounded by a crown of thick setae that are densely covered by short barbs, protecting those areas against soil particles. Cryptothele are probably specialized to prey on termites, and their phylogenetic placement indicates that this diet specificity evolved two times independently in zodariids.     

A genetic determination of cryptic species (Copepoda: Calanoida) and their postglacial biogeography in North America

Allozyme electrophoresis of Hesperodiaptomus arcticus (Marsh) sensu lato at subarctic Churchill, Canada revealed significant deviations from random mating in several populations, as shown by the complete absence of certain heterozygous types. A broad geographic survey of 20 enzyme loci in 1077 individuals from 27 ponds at 11 arctic and alpine sites west of Hudson Bay demonstrated that there were three genetically distinct types. Morphological analysis of genetically classified populations uncovered consistent morphological differences that had been ignored previously. These morphological characteristics were used to reclassify preserved museum and private specimens from additional sites from the entire North American distribution of H. arcticus sensu lato. A detailed study of two of the distinct types co-occurring at Churchill showed reproduction timing and habitat differences consistent with reproductive isolation. I concluded that there are three species and each have different distributions. Most regions examined must have been repopulated by dispersal from glacial refugia after deglaciation. The nominal species is apparently restricted to western arctic localities in the vicinity of the Alaskan refugium while the other two putative taxa have dispersed widely into previously glaciated regions.     

Genetic variability in Lycopersicon species and their genetic relationships

Summary Genetic diversity has to be described and measured in order to establish breeding strategies and manage genetic resources. It is also fundamental to develop a comparative intraspecific study before attempting to discuss and conclude any phylogenetic relationship. The genetic variability of Lycopersicon species was studied using starch gel electrophoresis of 11 enzymatic systems in a hierarchical fashion. The species with the greatest genetic variability are L. chilense, L. peruvianum and L. pennellii, mainly due to the within-line component. L. chmielewskii, L. parviflorum and L. pimpinellifolium show an intermediate total variability and their between-component clearly predominates over the within-component. The least variable species are L. cheesmanii and L. esculentum. Cluster analysis resulted in three main groups: one formed by the cultigen, L. pimpinellifolium, L. cheesmanii and L. peruvianum;another by two species with self-incompatibility systems, L. pennelli and L. chilense; and another by two autogamous species L. chmielewskii and L. parviflorum. With respect to L. esculentum the farthest related species is Solanum rickii and the closest, L. pimpinellifolium.     

Isozyme variation and differentiation of morphologically cryptic species in the Brachypodium distachyon complex

Isozyme variation of nine enzymes among three morphologically cryptic species of the Brachypodium distachyon complex was studied with PAGE. Aspartate aminotransferase isozymes AAT-A and AAT-C, aryl alcohol dehydrogenase AAD-B, malate dehydrogenase MDH-A and leucine aminopeptidase LAP-A in the allotetraploid B. hybridum display fixed heterozygosities with codominant expression of homoeozymes corresponding to divergent orthozymes of diploids B. distachyon and B. stacei. The multilocus isozyme genotype inherent to most accessions of B. hybridum combines two divergent multilocus isozyme genotypes characteristic of most accessions of B. distachyon and B. stacei. The maternally inherited chloroplast-encoded RUBISCO isozymes show that B. stacei is a maternal progenitor of B. hybridum, whereas the nuclear-encoded isozymes AAD-B, AAT-A, AAT-C, LAP-A, and MDH-A confirm that B. distachyon is the paternal progenitor. These data provide a new isozyme-based support to the karyological and DNA marker data on the allotetraploid nature of B. hybridum and its origin from diploids B. distachyon and B. stacei.     

Ceratopteris chunii and Ceratopteris chingii(Pteridaceae),two new diploid species from China,based on morphological,cytological,and molecular dataOA

Understanding how natural hybridization and polyploidizations originate in plants requires identifying potential diploid ancestors.However,cryptic plant species are widespread,particularly in Ceratopteris(Pteridaceae).Identifying Ceratopteris cryptic species with different polyploidy levels is a challenge because Ceratopteris spp.exhibit high degrees of phenotypic plasticity.Here,two new cryptic species of Ceratopteris,Ceratopteris chunii and Ceratopteris chingii,are described and illustrated.Ph...     

Taxonomy and phenotypic relationships of the Anastrepha fraterculus complex in the Mesoamerican and Pacific Neotropical dominions (Diptera,Tephritidae)

Previous morphometric studies based on linear measurements of female structures of the aculeus, mesonotum, and wing revealed the existence of seven morphotypes within the Anastrepha fraterculus cryptic species complex along the Neotropical Region. The current research followed linear and geometric morphometric approaches in 40 population samples of the nominal species Anastrepha fraterculus (Wiedemann) spread throughout the Meso-American and Pacific Neotropical dominions (including Mexico, Central America, Venezuela, Colombia, Ecuador, and Peru). The goals were to explore the phenotypic relationships of the morphotypes in these biogeographical areas; evaluate the reliability of procedures used for delimitation of morphotypes; and describe their current distribution. Findings determined that morphotypes previously recognized via the linear morphometrics were also supported by geometric morphometrics of the wing shape. In addition, we found an eighth morphotype inhabiting the highlands of Ecuador and Peru. Morphotypes are related into three natural phenotypic groups nominated as Mesoamerican-Caribbean lineage, Andean lineage, and Brazilian lineage. The hypothesis that lineages are not directly related to each other is discussed, supported by their large morphological divergence and endemicity in these three well-defined biogeographic areas. In addition, this hypothesis of the non-monophyly of the Anastrepha fraterculus complex is also supported by evidence from other authors based on molecular studies and the strong reproductive isolation between morphs from different lineages.     

Analysis of the genetic diversity of garlic (Allium sativum L.) germplasm by SRAP

Cluster analysis and principal component analysis were used to investigate the genetic diversity of 40 garlic germplasms analyzed with 23 sequence-related amplified polymorphism (SRAP) primer combinations. A total of 130 polymorphic loci were detected among these germplasms, with an average of 5.65 polymorphic loci per SRAP primer combination. The percentage of polymorphic loci was 69.1%, whereas the mean effective number of alleles, the mean Nei's gene diversity, and the mean Shannon's information index were 1.4446, 0.2788, and 0.4365, respectively. Cluster analysis revealed that the 40 germplasms could be divided into 3 groups. The results of principal component analysis were consistent with those of unweighted pair-group method with arithmetic averages (UPGMA) clustering analysis. The Shannon-Weaver information index ranged from 0.2419 to 0.4202, indicating that the garlic germplasms had high genetic diversity.     

27份花生种质资源的主成份分析及遗传距离测定

摘要：本文对27份花生种质资源的10个主要农艺性状表现进行了变异和主成份分析,结果表明：单株秕果数、单株结果数、主茎高与单株双仁果数变异系数较大;前4个主成份对变异的累计贡献率达84.98%。根据各种质资源的主成份值判断其表现特点,选出了综合性状比较理想的10份品种作为育种亲本。利用各种质资源的前4个主成份值计算各品种间的遗传距离,按遗传距离大小在D2=3.21水平下将27份种质资源聚类划分为6大类群,其中Ⅱ类群品种数最多(16份),该类群品种综合性状也表现较好,大多可为育种亲本利用或推广种植提供选择。     

Systematics of the Osteocephalus buckleyi species complex (Anura,Hylidae) from Ecuador and Peru

We present a new phylogeny, based on DNA sequences of mitochondrial and nuclear genes, for frogs of the genus Osteocephalus with emphasis in the Osteocephalus buckleyi species complex. Genetic, morphologic, and advertisement call data are combined to define species boundaries and describe new species. The phylogeny shows strong support for: (1) a basal position of Osteocephalus taurinus + Osteocephalus oophagus, (2) a clade containing phytotelmata breeding species, and (3) a clade that corresponds to the Osteocephalus buckleyi species complex. Our results document a large proportion of hidden diversity within a set of populations that were previously treated as a single, widely distributed species, Osteocephalus buckleyi. Individuals assignable to Osteocephalus buckleyi formed a paraphyletic group relative to Osteocephalus verruciger and Osteocephalus cabrerai and contained four species, one of which is Osteocephalus buckleyi sensu stricto and three are new. Two of the new species are shared between Ecuador and Peru (Osteocephalus vilmae sp. n. and Osteocephalus cannatellai sp. n.) and one is distributed in the Amazon region of southern Peru (Osteocephalus germani sp. n.) We discuss the difficulties of using morphological characters to define species boundaries and propose a hypothesis to explain them.