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1.
    
The hypothesis of phylogenetic niche conservatism proposes that most extant members of a clade remain in ancestral environments because expansion into new ecological space imposes a selectional load on a population. A prediction that follows is that local assemblages contain increasingly phylogenetically clustered subsets of species with increasing difference from the ancestral environment of a clade. We test this in Australian Meliphagidae, a continental radiation of birds that originated in wet, subtropical environments, but subsequently spread to drier environments as Australia became more arid during the late Cenozoic. We find local assemblages are increasingly phylogenetically clustered along a gradient of decreasing precipitation. The pattern is less clear along a temperature gradient. We develop a novel phyloclimatespace to visualise the expansion of some lineages into drier habitats. Although few species extend into arid regions, those that do occupy larger ranges and thus local species richness does not decline predictably with precipitation.  相似文献   

2.
    
High‐throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well‐supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer‐mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well‐understood ecosystems, and will propel both theoretical and applied soil science.  相似文献   

3.
    
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4.
    
Fire is thought to profoundly change the ecology of the sagebrush steppe. The Idaho National Laboratory provides an ideal setting to compare the effects of fire and physical disturbance on plant diversity in high‐native‐cover sagebrush steppe. Seventy‐eight 1‐hectare transects were established along paved, green‐striped, gravel, and two‐track roads, in overgrazed rangeland, and within sagebrush steppe involving different fire histories. Transects were sampled for the diversity and abundance of all vascular plants. Alpha, beta, and phylogenetic beta diversity were analyzed as a response to fire and physical disturbance. Postfire vegetation readily rebounds to prefire levels of alpha plant diversity. Physical disturbance, in contrast, strongly shapes patterns of alpha, beta, and especially phylogenetic beta diversity much more profoundly than fire disturbance. If fire is a concern in the sagebrush steppe then the degree of physical‐disturbance should be more so. This finding is probably not specific to the study area but applicable to the northern and eastern portions of the sagebrush biome, which is characterized by a pulse of spring moisture and cold mean minimum winter temperatures. The distinction of sagebrush steppe from Great Basin sagebrush should be revised especially with regard to reseeding efforts and the control of annual grasses.  相似文献   

5.
    
Scleractinian corals have demonstrated the ability to shuffle their endosymbiotic dinoflagellate communities (genus Symbiodinium) during periods of acute environmental stress. This has been proposed as a mechanism of acclimation, which would be increased by a diverse and flexible association with Symbiodinium. Conventional molecular techniques used to evaluate Symbiodinium diversity are unable to identify genetic lineages present at background levels below 10%. Next generation sequencing (NGS) offers a solution to this problem and can resolve microorganism diversity at much finer scales. Here we apply NGS to evaluate Symbiodinium diversity and host specificity in Acropora corals from contrasting regions of Western Australia. The application of 454 pyrosequencing allowed for detection of Symbiodinium operational taxonomic units (OTUs) occurring at frequencies as low as 0.001%, offering a 10 000‐fold increase in sensitivity compared to traditional methods. All coral species from both regions were overwhelmingly dominated by a single clade C OTU (accounting for 98% of all recovered sequences). Only 8.5% of colonies associated with multiple clades (clades C and D, or C and G), suggesting a high level of symbiont specificity in Acropora assemblages in Western Australia. While only 40% of the OTUs were shared between regions, the dominance of a single OTU resulted in no significant difference in Symbiodinium community structure, demonstrating that the coral‐algal symbiosis can remain stable across more than 15° of latitude and a range of sea surface temperature profiles. This study validates the use of NGS platforms as tools for providing fine‐scale estimates of Symbiodinium diversity and can offer critical insight into the flexibility of the coral‐algal symbiosis.  相似文献   

6.
    
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7.
  1. The upstream migration of juvenile amphidromous shrimps has been proposed as a source of marine or estuarine‐derived nutrients into fresh water. Little is known about the size and ecological importance of any such subsidy as there have been few observational or empirical studies on the topic.
  2. We investigated the upstream migration of the amphidromous shrimp, Macrobrachium spinipes (Palaemonidae) in the Daly River, of tropical northern Australia, to determine migration phenology, estimate migration biomass and determine whether migrating shrimps transport marine‐derived energy and nutrients upstream.
  3. Field observations over 2 years revealed that juvenile M. spinipes migrate upstream en masse during extended periods of declining discharge over a period of 4–6 weeks during the wet season (March–May). In addition, juvenile atyid shrimps from the genus Caridina were also observed migrating upstream during the same period.
  4. Fine‐scale sampling using fyke nets over 2 years (2013 and 2014) consistently found discharge to be the strongest predictor of M. spinipes and Caridina spp. biomass, while moon illumination and cloud cover were also important predictors. An estimated 10–20 million shrimps migrated upstream during each wet season, transporting c. 100 kg of carbon and c. 28 kg of nitrogen per year.
  5. Muscle sulphur stable isotopes (δ34S) and exoskeleton strontium isotope ratios (87Sr/86Sr) were used to establish if marine carbon was transported upstream by the juvenile M. spinipes. Isotope data from migratory M. spinipes were compared to the non‐migratory freshwater Macrobrachium bullatum. No evidence of a marine signature in body tissue or exoskeleton was found using either technique, suggesting very rapid turnover of body tissues
  6. This study provides key insights into the migration phenology of amphidromous shrimps and, importantly, suggests that migrating M. spinipes do not transport significant amounts of marine‐derived energy and nutrients across the marine/freshwater ecotone.
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8.
    
Beet yellows virus (BYV), a member of the Closteroviridae family, is one of the most important sugar beet yellowing viruses. The nine ORFs of BYV genome encode different proteins required for BYV life cycle. We sequenced a part of the genome of BYV Iranian isolate consisting of ORF6, ORF7 and ORF8. The primer pair BYVA/Z was used for amplification of this region in RT‐PCR. The amplicon (1615 bp) was cloned and sequenced. Comparisons showed the amplified segment is corresponding to ORF6, ORF7 and ORF8 of BYV genome encoding coat protein, p20 and p21 proteins, respectively. The ORF7 of BYV Iranian isolate overlaps with ORF6 and ORF8 in four and 26 nucleotides at 5′ and 3′ ends, respectively. The ORF7 of Iranian isolate of BYV was sequenced completely. However, approximately 24 nt. from the beginning of ORF6 and 23 nt. from end of ORF8, including the stop codon, were not determined. ORF6, ORF7 and ORF8 showed the highest similarity at nucleotide (98.3, 99.4 and 99.2%) and amino acid (97.4, 98.9 and 100%) sequence levels, with BYV Ukrainian isolate. Phylogenetic analysis of the deduced amino acid sequences of ORF6, ORF7 and ORF8 revealed closer relationship of Iranian isolate of BYV with BYV Ukrainian isolate than other BYV isolates available at GenBank.  相似文献   

9.
    
The genus Ditylenchus contains more than 80 recognized nematode species with a very wide host range. The most serious species are Ditylenchus dipsaci and Ditylenchus destructor. Populations of D. dipsaci species complex were collected from Allium cepa, Cichorium endivia and Phlox paniculata in Poland. The Ditylenchus gigas population was collected from Vicia faba minor, and populations of D. destructor, from Solanum tuberosum spp. tuberosum. Analyses of the rDNA sequences spanning both ITS1 and ITS2 fragment regions were carried out on the collected populations. The obtained DNA sequences were compared with those DNA sequences deposited in GenBank of populations isolated in other countries. Phylogenetic analysis was performed using the data obtained from the DNA sequence comparisons. The results indicated that there is no clear distinction between European and non‐European populations within D. dipsaci. The results also showed no clear distinction between populations isolated from different host plant species, including populations found in Poland. The populations of D. destructor described here constitute a common group together with American and Chinese populations belonging to the haplotype C of the D. destructor species. On the other hand, the D. gigas population was localized separately from those populations that have been described up until now, from Europe and Africa. This is also the first report on the occurrence of D. gigas in Poland.  相似文献   

10.
    
During the year 2008 to 2009, a new disease of stem canker was noticed in most red‐fleshed dragon fruit (Hylocereus polyrhizus) plantations in Malaysia. The symptoms observed were small circular sunken orange spot, black pycnidia and rotted stem. This study was conducted to determine the occurrence of the stem canker on H. polyrhizus in Malaysia, subsequently to isolate, identify and characterize the fungal pathogen based on morphology and molecular characteristics and pathogenicity test. From the surveyed 20 plantations in Malaysia, stem canker was detected in all the plantations. A total of 40 isolates of Scytalidium‐like fungus were isolated and identified as Neoscytalidium dimidiatum based on morphological characteristics and ITS region sequences, which showed 99% similarity to N. dimidiatum (FJ648577). From the phylogenetic analysis using maximum‐likelihood tree, isolates of N. dimidiatum from stem canker of H. polyrhizus were grouped together and did not show any sequence variation. From pathogenicity test, all 40 isolates of N. dimidiatum were pathogenic causing stem canker on H. polyrhizus. To our knowledge, this is the first report of stem canker of H. polyrhizus caused by N. dimidiatum in Malaysia.  相似文献   

11.
  总被引：2，自引：0，他引：2  
Orchids are some of the most important ornamental flowers. Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) are the most prevalent and economically important viruses affecting orchids in China. In this study, 20 CymMV and 28 ORSV isolates were selected for genetic diversity analysis. The CymMV isolates shared 84.6–100% and 89.5–100% identities of coat protein (CP) at the nucleotide (nt) and amino acid (aa) levels, respectively. The identities of ORSV isolates were 96.4–100% (nt) and 92.5–99.4% (aa). The CP genes of CymMV were found to have genetic diversity, and the CP genes of ORSV were genetically conservative. These results can aid in designing effective disease‐control strategies.  相似文献   

12.
    
Understanding what processes drive community structure is fundamental to ecology. Many wild animals are simultaneously infected by multiple parasite species, so host–parasite communities can be valuable tools for investigating connections between community structures at multiple scales, as each host can be considered a replicate parasite community. Like free‐living communities, within‐host–parasite communities are hierarchical; ecological interactions between hosts and parasites can occur at multiple scales (e.g., host community, host population, parasite community within the host), therefore, both extrinsic and intrinsic processes can determine parasite community structure. We combine analyses of community structure and assembly at both the host population and individual scales using extensive datasets on wild wood mice (Apodemus sylvaticus) and their parasite community. An analysis of parasite community nestedness at the host population scale provided predictions about the order of infection at the individual scale, which were then tested using parasite community assembly data from individual hosts from the same populations. Nestedness analyses revealed parasite communities were significantly more structured than random. However, observed nestedness did not differ from null models in which parasite species abundance was kept constant. We did not find consistency between observed community structure at the host population scale and within‐host order of infection. Multi‐state Markov models of parasite community assembly showed that a host's likelihood of infection with one parasite did not consistently follow previous infection by a different parasite species, suggesting there is not a deterministic order of infection among the species we investigated in wild wood mice. Our results demonstrate that patterns at one scale (i.e., host population) do not reliably predict processes at another scale (i.e., individual host), and that neutral or stochastic processes may be driving the patterns of nestedness observed in these communities. We suggest that experimental approaches that manipulate parasite communities are needed to better link processes at multiple ecological scales.  相似文献   

13.
    
The primary Afrotropical malaria mosquito vector Anopheles gambiae sensu stricto has a complex population structure. In west Africa, this species is split into two molecular forms and displays local and regional variation in chromosomal arrangements and behaviors. To investigate patterns of macrogeographic population substructure, 25 An. gambiae samples from 12 African countries were genotyped at 13 microsatellite loci. This analysis detected the presence of additional population structuring, with the M‐form being subdivided into distinct west, central, and southern African genetic clusters. These clusters are coincident with the central African rainforest belt and northern and southern savannah biomes, which suggests restrictions to gene flow associated with the transition between these biomes. By contrast, geographically patterned population substructure appears much weaker within the S‐form.  相似文献   

14.
    
The Near East endemic vetch Vicia montbretii is a taxonomically controversial species because it has been also treated either as Ervum kotschyanum or Lens montbretii. The phylogenetic affinity and taxonomic treatment of Lens species in relation to Vicia has become debatable. We studied variation of morphological and isozyme characters in V. montbretii, Lens odemensis, L. orientalis and L. nigricans in comparison to 19 species of Vicia subgenus Cracca and three Lathyrus outgroup species in order to get evidence about their systematic and phylogenetic position. The cladistic analysis of morphology revealed that V. montbretii is tightly connected with Lens species and the Ervum group. The cladistic analysis of isozymes placed V. montbretii and the three Lens species in subgenus Cracca as divergent subclades. V. montbretii differs from the Lens species in ten isozymes out of 16 analysed. Vicia montbretii appears sister to Vicia sections Cracca, Panduratae and Pedunculatae, whereas the Lens subclade is linked to the subclade of Vicia sections Ervoides, Ervilia and Lenticula. The consistencies and differences between the morphological and molecular characters (isozymes plus DNA sequences) are discussed.  相似文献   

15.
    
Members of the Nanorana genus (family Dicroglossidae) are often referred to as excellent model species with which to study amphibian adaptations to extreme environments and also as excellent keystone taxa for providing insights into the evolution of the Dicroglossidae. However, a complete mitochondrial genome is currently only available for Nanorana pleskei. Thus, we analyzed the complete mitochondrial genomes of Nanorana parkeri and Nanorana ventripunctata to investigate their evolutionary relationships within Nanorana and their phylogenetic position in the family Dicroglossidae. Our results showed that the genomes of N. parkeri (17,837 bp) and N. ventripunctata (18,373 bp) encode 13 protein‐coding genes (PCGs), two ribosomal RNA genes, 23 transfer RNA (tRNA) genes, and a noncoding control region. Overall sequences and genome structure of the two species showed high degree of similarity with N. pleskei, although the motif structures and repeat sequences of the putative control region showed clear differences among these three Nanorana species. In addition, a tandem repeat of the tRNA‐Met gene was found located between the tRNA‐Gln and ND2 genes. On both the 5′ and 3′‐sides, the control region possessed distinct repeat regions; however, the CSB‐2 motif was not found in N. pleskei. Based on the nucleotide sequences of 13 PCGs, our phylogenetic analyses, using Bayesian inference and maximum‐likelihood methods, illustrate the taxonomic status of Nanorana with robust support showing that N. ventripunctata and N. pleskei are more closely related than they are to N. parkeri. In conclusion, our analyses provide a more robust and reliable perspective on the evolutionary history of Dicroglossidae than earlier analyses, which used only a single species (N. pleskei).  相似文献   

16.
    
  1. The structure of a community is governed by a complex combination of processes whose relative importance varies over time and space. Larval dynamics, settlement and recruitment are thought to be important processes limiting adult abundance and distribution of benthic invertebrates with planktonic larvae.
  2. Two invasive molluscs with similar morphology and resource needs, the Eurasian zebra mussel Dreissena polymorpha and the quagga mussel Dreissena rostriformis bugensis, co‐occur in several North American lakes and rivers but often differ in their adult distribution over depth. Following establishment, the quagga mussel typically replaces the zebra mussel in abundance, particularly in deeper waters. A field sampling programme conducted over 3 years in a lotic system (the Soulanges Canal connected to the St. Lawrence River) examined the extent to which adult distribution and the differential dominance of these two species are determined by larval supply (i.e. larval abundance near settlement sites), settlement and recruitment.
  3. Total dreissenid larval abundance in the water column at two depths was determined weekly, and larval competence (size) and species‐specific larval composition was estimated, during the main settlement period over three consecutive years. The pattern of total dreissenid settlement over the depth gradient was determined by deployment of settlement plates at both depths. Total abundance and proportional abundance of zebra mussel and quagga mussel juveniles and adults in each depth zone were determined monthly from July to September each year.
  4. Mean dreissenid larval size did not differ between depths and the supply of late‐stage larvae was generally low, but total larval abundance was consistently greater in deeper water. This differential larval abundance established settlement and recruitment patterns in the canal but contrasted predictions based on total adult dreissenid abundance – which was higher in the shallow zone. Therefore, the significant factor dictating the abundance of adult mussels in these two depth zones must be post‐recruitment mortality, rather than larval supply, settlement or recruitment.
  5. Despite a strong species‐specific adult depth zonation, larvae and juveniles showed no consistent differences in species proportions over the depth gradient. In fact, zebra mussels dominated larval abundance at both depths for c. 50% of the sampling dates and dominated juvenile abundance at both depths throughout most of the sampling period. In contrast, the proportional abundance of zebra mussels in the adult dreissenid community was consistently 4–5 times higher in the shallow zone.
  6. These results indicate that larval supply, settlement and recruitment processes are not responsible for determining total adult dreissenid distribution or species dominance. Rather, these patterns appear to be governed by post‐recruitment factors that manifest themselves in later stages of mussel development and growth.
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17.
The red seaweed Asparagopsis taxiformis embodies five cryptic mitochondrial lineages (lineage 1–5) introduced worldwide as a consequence of human mediated transport and climate change. We compared globally collected mitochondrial cox2‐3 intergenic spacer sequences with sequences produced from multiple Australian locations and South Korea to identify Asparagopsis lineages and to reveal cryptic introductions. We report A. taxiformis lineage 4 from Cocos (Keeling) Islands, Australia, and the highly invasive Indo‐Pacific Mediterranean lineage 2 from South Korea and Lord Howe Island, Australia. Phylogeographic analysis showed a clear haplotype and geographic separation between western Australian and Great Barrier Reef (GBR) isolates belonging to the recently described lineage 5. The same lineage, however, was characterized by a substantial genetic and geographic break between the majority of Australian specimens and Asparagopsis collections from South Solitary Island, Southern GBR, Lord Howe Island, Kermadec Islands, Norfolk Island, New Caledonia and French Polynesia. The disjunct geographic distribution and sequence divergence between these two groups supports the recognition of a sixth cryptic A. taxiformis mitochondrial lineage. As climatic changes accelerate the relocation of biota and offer novel niches for colonization, periodic surveys for early detection of cryptic invasive seaweeds will be critical in determining whether eradication or effective containment of the aliens are feasible.  相似文献   

18.
    
The tommotiid Paterimitra pyramidalis Laurie, 1986, is redescribed based on well‐preserved material from the lower Cambrian Wilkawillina, Wirrapowie and Ajax limestones of the Flinders Ranges, South Australia. The material shows that the scleritome of Paterimitra pyramidalis includes three sclerite morphotypes (S1, S2 and L). Detailed shell microstructure studies show striking similarities with both the paterinid brachiopod Askepasma toddense and the tommotiid Eccentrotheca helenia, which strengthens the suggested evolutionary link between tommotiids and brachiopods. Based on the partly articulated specimens and similarities in shell microstructure and sclerite morphology with Eccentrotheca, Paterimitra pyramidalis is reconstructed as a tube‐dwelling, epifaunal, sessile, filter‐feeder with an organic pedicle‐like attachment structure. The proposed reconstruction of the scleritome comprises a basal unit composed of one S1 and one S2 sclerite, as well as an unresolved number of L sclerites lining a coniform tubular structure.  相似文献   

19.
    
Understanding the earliest events in speciation remains a major challenge in evolutionary biology. Thus identifying species whose populations are beginning to diverge can provide useful systems to study the process of speciation. Drosophila aldrichi, a cactophilic fruit fly species with a broad distribution in North America, has long been assumed to be a single species owing to its morphological uniformity. While previous reports either of genetic divergence or reproductive isolation among different D. aldrichi strains have hinted at the existence of cryptic species, the evolutionary relationships of this species across its range have not been thoroughly investigated. Here we show that D. aldrichi actually is paraphyletic with respect to its closest relative, Drosophila wheeleri, and that divergent D. aldrichi lineages show complete hybrid male sterility when crossed. Our data support the interpretation that there are at least two species of D. aldrichi, making these flies particularly attractive for studies of speciation in an ecological and geographical context.  相似文献   

20.
The phylogenies derived from housekeeping gene sequence alignments, although mere evolutionary hypotheses, have increased our knowledge about the Aeromonas genetic diversity, providing a robust species delineation framework invaluable for reliable, easy and fast species identification. Previous classifications of Aeromonas, have been fully surpassed by recently developed phylogenetic (natural) classification obtained from the analysis of so‐called ‘molecular chronometers’. Despite ribosomal RNAs cannot split all known Aeromonas species, the conserved nature of 16S rRNA offers reliable alignments containing mosaics of sequence signatures which may serve as targets of genus‐specific oligonucleotides for subsequent identification/detection tests in samples without culturing. On the contrary, some housekeeping genes coding for proteins show a much better chronometric capacity to discriminate highly related strains. Although both, species and loci, do not all evolve at exactly the same rate, published Aeromonas phylogenies were congruent to each other, indicating that, phylogenetic markers are synchronized and a concatenated multigene phylogeny, may be ‘the mirror’ of the entire genomic relationships. Thanks to MLPA approaches, the discovery of new Aeromonas species and strains of rarely isolated species is today more frequent and, consequently, should be extensively promoted for isolate screening and species identification. Although, accumulated data still should be carefully catalogued to inherit a reliable database.  相似文献   

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