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1.
    
Cryptic species are present in many animal groups and they may be best detected through large sample sizes collected over broad geographic ranges. Fine‐scale local adaptation has been hypothesized to occur in armoured scale insects (Hemiptera: Diaspididae) and a consequence of this process may be multiple cryptic species. We estimate species diversity of pine‐feeding Chionaspis scale insects across North America by inferring species boundaries using genealogical concordance across allele genealogies of two nuclear loci and one mitochondrial locus. Our ingroup sample includes 366 individual insects from 320 localities and 51 host species within the Pinaceae. We also conducted a morphological survey of all insect specimens and assigned them as either one of the two currently recognized pine‐feeding species, Ch. heterophyllae, Ch. Pinifoliae, or with undescribed morphology. Using maximum likelihood allele genealogies in a majority‐rule consensus to assess congruence, we conservatively detect ten species in this group. Most of these species are robust to alternative methods of genealogical inference (Bayesian inference, maximum parsimony) and a few are robust to the use of strict consensus to assess congruence. Species show both narrow and more widespread ranges where almost half of the individuals sampled belong to a single very widespread polyphagous species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 47–62.  相似文献   

2.
Species Delimitation is a plugin to the Geneious software to support the exploration of species boundaries in a gene tree. The user assigns taxa to putative species and the plugin computes statistics relating to the probability of the observed monophyly or exclusivity having occurred by chance in a coalescent process. It also assesses the within and between species genetic distances to infer the probability with which members of a putative species might be identified successfully with tree-based methods.  相似文献   

3.
    
Sponges are among the most species‐rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model‐based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single‐copy nuclear protein‐coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax, C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera, C. longissima, C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model‐based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.  相似文献   

4.
    
Developmental plasticity is often correlated with diversity and has been proposed as a facilitator of phenotypic novelty. Yet how a dimorphism arises or how additional morphs are added is not understood, and few systems provide experimental insight into the evolution of polyphenisms. Because plasticity correlates with structural diversity in Pristionchus nematodes, studies in this group can test the role of plasticity in facilitating novelty. Here, we describe three new species, Pristionchus fukushimae sp. nov. , Pristionchus hoplostomus sp. nov. , and the hermaphroditic Pristionchus triformis sp. nov. , which are characterized by a novel polymorphism in their mouthparts. In addition to showing the canonical mouth dimorphism of diplogastrid nematodes, comprising a stenostomatous (‘narrow‐mouthed’) and a eurystomatous (‘wide‐mouthed’) form, the new species exhibit forms with six, 12, or intermediate numbers of cheilostomatal plates. Correlated with this polymorphism is another trait that varies among species: whereas divisions between plates are complete in P. triformis sp. nov. , which is biased towards a novel ‘megastomatous’ form comprising 12 complete plates, the homologous divisions in the other new species are partial and of variable length. In a reconstruction of character evolution, a phylogeny inferred from 26 ribosomal protein genes and a partial small subunit rRNA gene supported the megastomatous form of P. triformis sp. nov. as the derived end of a series of split‐plate forms. Although split‐plate forms were normally only observed in eurystomatous nematodes, a single 12‐plated stenostomatous individual of P. hoplostomus sp. nov. was also observed, suggesting independence of the two types of mouth plasticity. By introducing these new species to the Pristionchus model system, this study provides further insight into the evolution of polymorphisms and their evolutionary intermediates. © 2013 The Linnean Society of London  相似文献   

5.
    
An isolate of rare actinobacteria strain Amycolatopsis sp. HCa1 obtained from the gut of grasshopper produced seven different metabolites in vitro. The metabolites isolated from its mycelia cakes were characterized by NMR and MS analyses. Actinotetraose hexatiglate (or tigloside; 1 ) with nonreducing glucotetraose skeleton was isolated as a major constituent; three new tetrasaccharide derivatives actinotetraoses I–K ( 2 – 4 , resp.) and three known actinotetraoses A–C ( 5 – 7 , resp.) were also isolated.  相似文献   

6.
    
A time‐calibrated phylogenetic tree indicates that the evolution of sympatric, montane, endemic species from closely related, co‐distributed lineages of the Hemiphyllodactylus harterti group were not the result of rapid, forest‐driven, climatic oscillations of the Last Glacial Maximum, but rather the result of infrequent episodes of environmental fluctuation during the Late Miocene. This hypothesis is supported by genetic divergences (based on the mitochondrial gene ND2) between the three major lineages of the H. harterti group (17.5–25.1%), their constituent species (9.4–14.3%), and the evolution of discrete, diagnostic, morphological, and colour pattern characteristics between each species. Sister species pairs from two of the three lineages occur in sympatry on mountain tops from opposite sides of the Thai–Malay Peninsula, but the lineages to which each pair belongs are not sister lineages. A newly discovered species from Gunung Tebu, Terengganu State, H emiphyllodactylus bintik sp. nov. , is described. © 2015 The Linnean Society of London  相似文献   

7.
    
Species delimitation among closely related species is challenging because traditional phenotype‐based approaches, for example, using morphology, ecological, or chemical characteristics, may not coincide with natural groupings. With the advent of high‐throughput sequencing, it has become increasingly cost‐effective to acquire genome‐scale data which can resolve previously ambiguous species boundaries. As the availability of genome‐scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, for example, hybridization/introgression and incomplete lineage sorting, and computational limitations. Here, we investigate species boundaries and the potential for micro‐endemism in a lineage of lichen‐forming fungi, Niebla Rundel & Bowler, in the family Ramalinaceae by analyzing single‐locus and genome‐scale data consisting of (a) single‐locus species delimitation analysis using ASAP, (b) maximum likelihood‐based phylogenetic tree inference, (c) genome‐scale species delimitation models, e.g., BPP and SNAPP+BFD, and (d) species validation using the genealogical divergence index (gdi). We specifically use these methods to cross‐validate results between genome‐scale and single‐locus datasets, differently sampled subsets of genomic data and to control for population‐level genetic divergence. Our species delimitation models tend to support more speciose groupings that were inconsistent with traditional taxonomy, supporting a hypothesis of micro‐endemism, which may include morphologically cryptic species. However, the models did not converge on robust, consistent species delimitations. While the results of our analysis are somewhat ambiguous in terms of species boundaries, they provide a valuable perspective on how to use these empirical species delimitation methods in a nonmodel system. This study thus highlights the challenges inherent in delimiting species, particularly in groups such as Niebla, with complex, relatively recent phylogeographic histories.  相似文献   

8.
  总被引：2，自引：0，他引：2  
To critically examine the relationship between species recognized by phylogenetic and reproductive compatibility criteria, we applied phylogenetic species recognition (PSR) to the fungus in which biological species recognition (BSR) has been most comprehensively applied, the well-studied genus Neurospora. Four independent anonymous nuclear loci were characterized and sequenced from 147 individuals that were representative of all described outbreeding species of Neurospora. We developed a consensus-tree approach that identified monophyletic genealogical groups that were concordantly supported by the majority of the loci, or were well supported by at least one locus but not contradicted by any other locus. We recognized a total of eight phylogenetic species, five of which corresponded with the five traditional biological species, and three of which were newly discovered. Not only were phylogenetic criteria superior to traditional reproductive compatibility criteria in revealing the full species diversity of Neurospora, but also significant phylogenetic subdivisions were detected within some species. Despite previous suggestions of hybridization between N. crassa and N. intermedia in nature, and the fact that several putative hybrid individuals were included in this study, no molecular evidence in support of recent interspecific gene flow or the existence of true hybrids was observed. The sequence data from the four loci were combined and used to clarify how the species discovered by PSR were related. Although species-level clades were strongly supported, the phylogenetic relationships among species remained difficult to resolve, perhaps due to conflicting signals resulting from differential lineage sorting.  相似文献   

9.
    
Some of the effects of past climate dynamics on plant and animal diversity make‐up have been relatively well studied, but to less extent in fungi. Pleistocene refugia are thought to harbour high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In addition, high extinction rates and genetic erosion are expected in previously glaciated regions. Some of the consequences of past climate dynamics might involve changes in range and population size that can result in divergence and incipient or cryptic speciation. Many of these dynamic processes and patterns can be inferred through phylogenetic and coalescent methods. In this study, we first delimit species within a group of closely related edible ectomycorrhizal Amanita from North America (the American Caesar's mushrooms species complex) using multilocus coalescent‐based approaches; and then address questions related to effects of Pleistocene climate change on the diversity and genetics of the group. Our study includes extensive geographical sampling throughout the distribution range, and DNA sequences from three nuclear protein‐coding genes. Results reveal cryptic diversity and high speciation rates in refugia. Population sizes and expansions seem to be larger at midrange latitudes (Mexican highlands and SE USA). Range shifts are proportional to population size expansions, which were overall more common during the Pleistocene. This study documents responses to past climate change in fungi and also highlights the applicability of the multispecies coalescent in comparative phylogeographical analyses and diversity assessments that include ancestral species.  相似文献   

10.
Serpula himantioides (Boletales, Basidiomycota) produces thin resupinate basidiocarps on dead coniferous wood worldwide and causes damage in buildings as well. In this study, we present evidence for the existence of at least three phylogenetically defined cryptic species (referred to as Sib I-III) within the morphospecies S. himantioides, a conclusion based on analyses of sequence data from four DNA regions and amplified fragment length polymorphisms (AFLPS). A low degree of shared sequence polymorphisms was observed among the three lineages indicating a long-lasting separation. The AFLPs revealed two additional subgroups within Sib III. Results from mating studies were consistent with the molecular data. In Sib III, no correspondence between genetic and geographical distance was observed among isolates worldwide, presumably reflecting recent dispersal events. Our results indicate that at least two of the lineages (Sib II and Sib III) have wide sympatric distributions. A population genetic analysis of Sib III isolates, scoring sequence polymorphisms as codominant SNP markers, indicates that panmictic conditions exist in the Sib III group. This study supports the view that cryptic speciation is a common phenomenon in basidiomycete fungi and that phylogenetic species recognition can be a powerful inference to detect cryptic species. Furthermore, this study shows that AFLP data are a valuable supplement to DNA sequence data in that they may detect a finer level of genetic variation.  相似文献   

11.
    
The males of four species of the Asian frog genus Limnonectes [Limnonectes dabanus (Smith, 1922a), Limnonectes gyldenstolpei (Andersson, 1916), Limnonectes macrognathus (Boulenger, 1917), and Limnonectes plicatellus (Stoliczka, 1873)] exhibit remarkable ornamentation in the form of a swollen, or cap‐like, structure (caruncle) on the top of their heads. These caruncles vary in their appearance among species, and neither their function nor their actual systematic value is known. We compared their anatomy via dissections, morphometrics, radiography, and histology, and analysed the available mitochondrial DNA sequences as well as new data to place these species within the context of a larger phylogenetic hypothesis for Limnonectes. Despite the externally different morphology, the underlying histological structure is virtually identical. Beneath skin that is densely packed with mucous glands lies a pad of connective tissue overlaying the parietal bone. The actual function of the caruncle, however, remains enigmatic. In addition to the presence of the caruncle, independent evidence from osteological characters and molecular data support the monophyly of a clade comprising of L. dabanus, L. gyldenstolpei, L. macrognathus, and L. plicatellus. The caruncles are therefore interpreted as a robust autapomorphy for this clade, and suggest that the subgenus Elachyglossa should be restricted to the four species in question. © 2014 The Linnean Society of London  相似文献   

12.
    
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13.
    
Seven new polyoxygenated cembranoids possessing an α‐methylene‐γ‐lactone group, crassocolides G–M ( 1 – 7 , resp.), have been isolated from the AcOEt extract of the Formosan soft coral Sarcophyton crassocaule. The structures of compounds 1 – 7 were established by detailed spectroscopic analyses, including 2D‐NMR spectroscopy (1H,1H‐COSY, HMQC, HMBC, and NOESY), while the absolute configuration of 1 was determined using a modified reaction of Mosher's method. The cytotoxicity of compounds 1 – 7 against a limited panel of cancer cell lines was also determined.  相似文献   

14.
    
Nucleotide sequences from the mitochondrial cytochrome c oxidase subunit I (COI) gene, comprising the standard barcode segment, were used to examine genetic differentiation, systematics, and population structure of cactus flies (Diptera: Neriidae: Odontoloxozus) from Mexico and south‐western USA. Phylogenetic analyses revealed that samples of Odontoloxozus partitioned into two distinct clusters: one comprising the widely distributed Odontoloxozus longicornis (Coquillett) and the other comprising Odontoloxozus pachycericola Mangan & Baldwin, a recently described species from the Cape Region of the Baja California peninsula, which we show is distributed northward to southern California, USA. A mean Kimura two‐parameter genetic distance of 2.8% between O. longicornis and O. pachycericola, and eight diagnostic nucleotide substitutions in the COI gene segment, are consistent with a species‐level separation, thus providing the first independent molecular support for recognizing O. pachycericola as a distinct species. We also show that the only external morphological character considered to separate adults of the two species (number of anepisternal bristles) varies with body size and is therefore uninformative for making species assignments. Analysis of molecular variance indicated significant structure among populations of O. longicornis from three main geographical areas, (1) Arizona, USA and Sonora, Mexico; (2) Santa Catalina Island, California, USA; and (3) central Mexico (Querétaro and Guanajuato), although widely‐separated populations from Arizona and Sonora showed no evidence of structure. A TCS haplotype network showed no shared haplotypes of O. longicornis among the three main regions. The potential roles of vicariance and isolation‐by‐distance in restricting gene flow and promoting genetic differentiation and speciation in Odontoloxozus are discussed. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 245–256.  相似文献   

15.
    
Chemical investigation of the Taiwanese soft coral Asterospicularia laurae has led to the isolation of three new xenicane diterpenoids, named asterolaurins K–M ( 1 – 3 , resp.). Their chemical structures were determined through extensive spectroscopic analyses (1H‐ and 13C‐NMR, 1H,1H‐COSY, HMBC, and NOESY). Compound 2 exhibited cytotoxic activity against HEp‐2, Daoy, MCF‐7, and WiDr tumor cells.  相似文献   

16.
    
Four new drimane‐type sesquiterpenoid ethers of isocitric acid, named cryptoporic acids J–M, were isolated from the fruiting bodies of Cryptoporus sinensis, together with six known cryptoporic acids. Their structures were elucidated on the basis of extensive spectroscopic analyses. Among them, cryptoporic acid D showed strong inhibition against nitric oxide (NO) production in macrophages with an IC50 of 45.8±3.6 μM , comparable to the positive control of hydrocortisone (IC50 of 40.6±2.5 μM ).  相似文献   

17.
    
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18.
    
Begomoviruses are a major group of plant viruses, transmitted exclusively by Bemisia tabaci (Gennadius) in a persistent circulative non‐propagative manner. The information regarding molecular and cellular basis underlying Begomovirus – whitefly interaction is very scarce. Evidences have suggested that the insect gut possesses some crucial protein receptors that allow specific entry of virus into the insect haemolymph. We have performed yeast two hybrid gut cDNA expression library screening against coat protein of Tomato leaf curl New Delhi virus (ToLCV) and Cotton leaf curl Rajasthan virus (CLCuV) as bait. Midgut protein (MGP) was the common protein found interacting with both ToLCV and CLCuV. MGP was localized in whole mount B. tabaci as well as in dissected guts through confocal microscopy. Pull down and dot blot assays confirmed in vitro interaction between ToLCV/CLCuV coat protein and MGP. Immunolocalization analysis also showed colocalization of ToLCV/CLCuV particles and MGP within insect's gut. Finally, anti‐MGP antibody fed B. tabaci, exhibited 70% reduction in ToLCV transmission, suggesting a supportive role for MGP in virus transmission.  相似文献   

19.
    
Six new triterpenoids, meliasenins S–X ( 1 – 6 , resp.), were isolated from the stem bark of Melia toosendan. Their structures were elucidated by mass spectrometry, NMR experiments, and comparison with the known compounds. Particularly, the absolute configuration at C(24) in new compounds was determined through their CD spectra of the [Pr(FOD)3] complex (fod=1,1,1,2,2,3,3,7,7,7‐decafluoroheptane‐4,6‐dione) in CCl4, as well as by using Mosher's method.  相似文献   

20.
    
We present five case studies among articulate (rhynchonelliform) brachiopods, i.e. of Rhynchonellida, Cancellothyridoidea, Terebratuloidea, Dyscolioidea, Laqueoidea, and various terebratulids with modified long‐loops, in an attempt to illustrate and better understand congruence and conflict between morpho‐classification and rDNA‐based molecular clade structure, having been prompted to address these issues by difficulties encountered when describing the newly collected brachiopod, E biscothyris bellonensis gen. et sp. nov. The five studies reveal dramatic conflict in the Rhynchonellida and Terebratuloidea/Dyscolioidea, good congruence in the Cancellothyridoidea and Laqueoidea, and fair congruence (albeit with weak phylogenetic signal) in the long‐looped terebratulids. We suggest that the leading cause of the observed conflict lies in the use of inadequately specific morphological characters and morpho‐classification. Phylogenetic systematic (cladistic) analyses of Rhynchonellida also conflict markedly with the rDNA gene tree, leading us to recognize that such analyses are not only conceptually circular (using morphological characters to assess a morphological classification) but also to propose that they are biased by the act of classification that necessarily precedes the identification of putatively homologous characters; when the prior classification does not reflect evolutionary history, phylogenetic analysis will do likewise. In addition, we propose that the brachiopod community has overlooked the significance of two sources of morphological homoplasy affecting brachiopod systematics: (1) the loss of co‐adapted genomic complexes caused by mass extinctions at the end of the Permian; and (2) the pervasive consequences of developmental integration and constraint resulting from the integrated roles of the outer mantle epithelium in shell deposition and growth that underly the determination of form and the shell‐based classification. © 2015 The Linnean Society of London  相似文献   

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