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Traditional Taxonomy (traditional + taxonomy)
Selected AbstractsIntegrating DNA data and traditional taxonomy to streamline biodiversity assessment: an example from edaphic beetles in the Klamath ecoregion, California, USADIVERSITY AND DISTRIBUTIONS, Issue 5 2006Ryan M. Caesar ABSTRACT Conservation and land management decisions may be misguided by inaccurate or misinterpreted knowledge of biodiversity. Non-systematists often lack taxonomic expertise necessary for an accurate assessment of biodiversity. Additionally, there are far too few taxonomists to contribute significantly to the task of identifying species for specimens collected in biodiversity studies. While species level identification is desirable for making informed management decisions concerning biodiversity, little progress has been made to reduce this taxonomic deficiency. Involvement of non-systematists in the identification process could hasten species identification. Incorporation of DNA sequence data has been recognized as one way to enhance biodiversity assessment and species identification. DNA data are now technologically and economically feasible for most scientists to apply in biodiversity studies. However, its use is not widespread and means of its application has not been extensively addressed. This paper illustrates how such data can be used to hasten biodiversity assessment of species using a little-known group of edaphic beetles. Partial mitochondrial cytochrome oxidase I was sequenced for 171 individuals of feather-wing beetles (Coleoptera: Ptiliidae) from the Klamath ecoregion, which is part of a biodiversity hotspot, the California Floristic Province. A phylogram of these data was reconstructed via parsimony and the strict consensus of 28,000 equally parsimonious trees was well resolved except for peripheral nodes. Forty-two voucher specimens were selected for further identification from clades that were associated with many synonymous and non-synonymous nucleotide changes. A ptiliid taxonomic expert identified nine species that corresponded to monophyletic groups. These results allowed for a more accurate assessment of ptiliid species diversity in the Klamath ecoregion. In addition, we found that the number of amino acid changes or percentage nucleotide difference did not associate with species limits. This study demonstrates that the complementary use of taxonomic expertise and molecular data can improve both the speed and the accuracy of species-level biodiversity assessment. We believe this represents a means for non-systematists to collaborate directly with taxonomists in species identification and represents an improvement over methods that rely solely on parataxonomy or sequence data. [source] Phylogeny and biogeography of Yellow-headed and Blue-fronted Parrots (Amazona ochrocephala and Amazona aestiva) with special reference to the South American taxaIBIS, Issue 3 2007CAMILA C. RIBAS The Yellow-headed Parrot (Amazona ochrocephala) has a broad Neotropical distribution, ranging from Mexico to the Amazon Basin, and a history of complex taxonomy and controversial species limits. Recent molecular analyses have started to clarify the taxonomic arrangement of the complex, but have not included a representative geographical sampling from South America. These studies have shown that the Yellow-headed complex can be divided into three main lineages, and seems to be paraphyletic, due to the inclusion of the Blue-fronted Parrot (Amazona aestiva) that occurs in central South America. Here we present a phylogenetic analysis based on mitochondrial DNA sequences of 45 representatives of the Yellow-headed complex from South and Central America, plus 13 Blue-fronted individuals from different localities in South America. Our analyses recover the three primary lineages found previously in the Yellow-headed complex, show that there is genetic structure in the South American lineage, which can be divided into two well-supported, closely related clades, and demonstrate that Blue-fronted samples are distributed in both clades. Differentiation of South American Blue-fronted and Yellow-headed Parrot populations does not correspond to the plumage differences used to distinguish the Blue-fronted Parrot from the Yellow-headed Parrot, nor to plumage differences used to distinguish among South American Yellow-headed subspecies. This suggests that traditional taxonomy based on plumage characters needs revision, and that this may be an interesting example of ongoing divergence-with-gene-flow related to the forest/open area ecotone in southern Amazonia. [source] Beyond taxonomy: a review of macroinvertebrate trait-based community descriptors as tools for freshwater biomonitoringJOURNAL OF APPLIED ECOLOGY, Issue 4 2010Salomé Menezes Summary 1.,Species traits have been frequently used in ecological studies in an attempt to develop a general ecological framework linking biological communities to habitat pressures. The trait approach offers a mechanistic alternative to traditional taxonomy-based descriptors. This review focuses on research employing traits as biomonitoring tools for freshwater ecosystems, although the lessons learned have wider application in the assessment of other ecosystem types. 2.,We review the support from ecological theory to employ species traits for biomonitoring purposes (e.g. the habitat templet concept, landscape filtering hypothesis), and the subsequent studies that test the hypotheses arising from these theories, and apply this knowledge under real freshwater biomonitoring scenarios. We also include studies that deal with more specific issues such as trait trade-offs and trait syndromes. 3.,We highlight the functional trait approach as one of the most promising tools emerging for biomonitoring freshwater ecosystems. Several technical issues are addressed and solutions are proposed. We discuss the need for: a broader unified trait biomonitoring tool; a more accurate understanding of the natural variation of community patterns of trait expression; approaches to diminish the effects of trait trade-offs and trait syndromes; additional life history and ecological requirement studies; and the detection of specific impacts under multiple stressor scenarios. 4.,Synthesis and applications. This review provides biologists with the conceptual underpinning for the use of species traits as community descriptors and for freshwater biomonitoring and management. We expect that the functional trait approach will ultimately improve communication to managers and legislators of the importance of protecting freshwater ecosystem functions. [source] Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequencesJOURNAL OF BIOGEOGRAPHY, Issue 8 2006Dekui He Abstract Aim, To test a vicariant speciation hypothesis derived from geological evidence of large-scale changes in drainage patterns in the late Miocene that affected the drainages in the south-eastern Tibetan Plateau. Location, The Tibetan Plateau and adjacent areas. Methods, The cytochrome b DNA sequences of 30 species of the genus Schizothorax from nine different river systems were analysed. These DNA sequences were analysed using parsimony, maximum likelihood and Bayesian methods. The approximately unbiased and Shimodaira,Hasegawa tests were applied to evaluate the statistical significance of the shortest trees relative to alternative hypotheses. Dates of divergences between lineages were estimated using the nonparametric rate smoothing method, and confidence intervals of dates were obtained by parametric bootstrapping. Results, The phylogenetic relationships recovered from molecular data were inconsistent with traditional taxonomy, but apparently reflected geographical associations with rivers. Within the genus Schizothorax, we observed a divergence between the lineages from the Irrawaddy,Lhuit and Tsangpo,Parlung rivers, and tentatively dated this vicariant event back to the late Miocene (7.3,6.8 Ma). We also observed approximately simultaneous geographical splits within drainages of the south-eastern Tibetan Plateau, the Irrawaddy, the Yangtze and the Mekong,Salween rivers in the late Miocene (7.1,6.2 Ma). Main conclusions, Our molecular evidence tentatively highlights the importance of palaeoriver connections and the uplift of the Tibetan Plateau in understanding the evolution of the genus Schizothorax. Molecular estimates of divergence times allowed us to date these vicariant scenarios back to the late Miocene, which agrees with geological suggestions for the separation of these drainages caused by tectonic uplift in south-eastern Tibet. Our results indicated the substantial role of vicariant-based speciation in shaping the current distribution pattern of the genus Schizothorax. [source] Use of microsatellite DNA and amplified fragment length polymorphism for Cherry salmon (Oncorhynchus masou) complex identificationAQUACULTURE RESEARCH, Issue 9 2010Te-Hua Hsu Abstract Formosa landlocked salmon (Oncorhynchus masou formosanus), an endemic, critically endangered subspecies of Cherry salmon (Oncorhynchus masou) complex, is only found in Taiwan. Because the eyed eggs and ungutted carcasses of Pacific salmons (genus Oncorhynchus) are imported for aquaculture and food to Taiwan from overseas every year, the requirement for preventing illegal trade or accidental commercial imports to avoid unwanted fish from contaminating the gene pool of Formosa landlocked salmon and infect them with diseases is critical for the conservation of Formosa landlocked salmon. Traditional morphology-based species identification is impossible for salmon eggs and larvae that lack clearly defined morphological features. In the present study, the genetic differences among four subspecies (Oncorhynchus masou ishikawae, O. masou subsp., Oncorhynchus masou masou and O. masou formosanus) of Cherry salmon complex were determined from microsatellite DNA and amplified fragment length polymorphism analyses. We successfully generated a genetic marker to aid traditional taxonomy and investigate the integrity of the current taxonomic status among members of Cherry salmon complex. Use of molecular markers, in combination with traditional morphological identification, is a promising tool for identifying four closely related subspecies of Cherry salmon complex. [source] A new model Gondwanan taxon: systematics and biogeography of the harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi), with a taxonomic revision of genera from Australia and New ZealandCLADISTICS, Issue 4 2007Sarah L. Boyer The phylogeny of the temperate Gondwanan harvestman family Pettalidae is investigated by means of a new morphological matrix of 45 characters, and DNA sequence data from five markers, including two nuclear ribosomal genes (18S rRNA and 28S rRNA), one nuclear protein coding gene (histone H3), and two mitochondrial genes,one protein coding (cytochrome c oxidase subunit I) and one ribosomal (16S rRNA). Phylogenetic analyses using an array of homology schemes (dynamic and static), criteria (parsimony and maximum likelihood), and sampling strategies (optimal trees versus Bayesian phylogenetics) all agree on the monophyly of Pettalidae as well as several of its subclades, each of which is restricted to a modern landmass. While most genera as traditionally defined are monophyletic, Rakaia and Neopurcellia, distributed across Queensland (Australia) and New Zealand, are not. Instead, the species from Queensland, previously described under three genera, constitute a well-supported clade, suggesting that in this case biogeography prevails over traditional taxonomy. A taxonomic emendation of the genera from Queensland and New Zealand is presented, and the new genus Aoraki is erected to include the species of the New Zealand denticulata group. A biogeographical hypothesis of the relationships of the former temperate Gondwana landmasses (with the exception of Madagascar) is presented, although ambiguity in the deep nodes of the pettalid tree renders such inference provisional. The data suggest that neither the South African fauna, the New Zealand fauna nor the Australian fauna is monophyletic but instead monophyly is found at smaller geographic scales (e.g., Western Australia, Queensland, NE South Africa). © The Willi Hennig Society 2007. [source] | ||||||||||