Forest and Demons in the Papua New Guinea Highlands

The Wola people of the Southern Highland Province of Papua New Guinea believe that two kinds of demon spirit inhabit the montane forests of their region. They call them saem and iybtit. When people are attacked by these frightening creatures, they are injured or fall sick, and may die; their relatives perform rituals to drive the demons away and promote their recovery. The attitude of the Wola towards demon spirits expresses something of their ambivalent and enigmatic attitudes towards the forest that covers large areas of their region. They are neither innate conservationists nor reckless destroyers of forest, but something more equivocal, an antipathetic combination of both.     

Systematic and conservation implications of geographic variation in pipits (Anthus: Motacillidae) in New Zealand and some offshore islands

The New Zealand Pipit Anthus novaeseelandiae occurs as a single species in Europe (as Richard's Pipit), Asia, Africa, New Guinea, Australia and New Zealand. In the New Zealand region, subspecific status has been accorded to allopatric populations on the mainland (A. n. novaeseelandiae) , on the Auckland and Campbell Islands (A. n. aucklandicus) , on the Antipodes Islands (A. n. steindachneri) and on the Chatham Islands (A. n. chathamensis) . Analyses of 23 allozyme loci and morphometric variation of populations on mainland New Zealand and on the Auckland, Campbell, Antipodes and Chatham Islands showed an appreciable and significant divergence between mainland and island populations. The magnitude of the allozyme difference is sufficient to suggest full species designation for the island birds, a conclusion supported by morphometric analyses and in sharp contrast to current taxonomy. However, formal taxonomic change will not be undertaken until the two New Zealand groups have been compared with more distant populations of this wideranging genus. The cryptic variation found in this species has conservation management implications for the small offshore populations.     

The Australian monsoon tropics as a barrier for exchange of dragonflies (Insecta: Odonata) between New Guinea and Australia

Recent studies show a remarkable scarcity of faunal exchange events between Australia and New Guinea in the Pleistocene despite the presence of a broad land connection for long periods. This is attributed to unfavourable conditions in the connecting area associated with the long established northern Australian Monsoon Climate. This would be expected to have impacted strongly on freshwater faunas with the following results: (1) limited overlap in species, (2) most higher taxonomic groups present in both areas sharing no species or even genera and (3) shared species dominated by lentic species with high dispersal capacity. Testing these predictions for dragonflies showed the turnover in the family, genus and species composition between Australia and New Guinea to be higher than anywhere in the world with only 50% of families and subfamilies, 33% of the genera and 8% of the species being shared. Only one of the 53 shared species favors lotic waters compared with 64% of the 652 combined Australian–New Guinean species. These results agree with our predictions and indicate that the dragonfly fauna of Australia and New Guinea have effectively been separated during the Pleistocene probably due to the prolonged unfavourable climatic conditions in the intervening areas.     

Using the taxon-specific genes for the taxonomic classification of bacterial genomes

Background

The correct taxonomic assignment of bacterial genomes is a primary and challenging task. With the availability of whole genome sequences, the gene content based approaches appear promising in inferring the bacterial taxonomy. The complete genome sequencing of a bacterial genome often reveals a substantial number of unique genes present only in that genome which can be used for its taxonomic classification.

Results

In this study, we have proposed a comprehensive method which uses the taxon-specific genes for the correct taxonomic assignment of existing and new bacterial genomes. The taxon-specific genes identified at each taxonomic rank have been successfully used for the taxonomic classification of 2,342 genomes present in the NCBI genomes, 36 newly sequenced genomes, and 17 genomes for which the complete taxonomy is not yet known. This approach has been implemented for the development of a tool ‘Microtaxi’ which can be used for the taxonomic assignment of complete bacterial genomes.

Conclusion

The taxon-specific gene based approach provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1542-0) contains supplementary material, which is available to authorized users.     

Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species

Biodiversity studies require species level analyses for the accurate assessment of community structures. However, while specialized taxonomic knowledge is only rarely available for routine identifications, DNA taxonomy and DNA barcoding could provide the taxonomic basis for ecological inferences. In this study, we assessed the community structure of sediment dwelling, morphologically cryptic Chironomus larvae in the Rhine-valley plain/Germany, comparing larval type classification, cytotaxonomy, DNA taxonomy and barcoding. While larval type classification performed poorly, cytotaxonomy and DNA-based methods yielded comparable results: detrended correspondence analysis and permutation analyses indicated that the assemblages are not randomly but competitively structured. However, DNA taxonomy identified an additional species that could not be resolved by the traditional method. We argue that DNA-based identification methods such as DNA barcoding can be a valuable tool to increase accuracy, objectivity and comparability of the taxonomic assessment in biodiversity and community ecology studies.     

Contrasting phylogeographic signatures in two Australo‐Papuan bowerbird species complexes (Aves: Ailuroedus)

The Australo‐Papuan catbird genus Ailuroedus has a complex distribution and a contested taxonomy. Here, we integrate phylogenetic analysis of DNA data and morphology to study the group's biogeography and to re‐examine its taxonomy. We couple phylogeographic and abiotic data to examine differences between the major groups defined in our phylogenetic analysis. Our results are consistent with Ailuroedus catbirds being divided into two species complexes, one distributed in humid forests in the lowlands on New Guinea and another in comparably drier and colder forests mainly in mid‐mountains on New Guinea and Australia. Vicariant events during the Pliocene are surmised to have been the major force in shaping the contemporary phylogeographical signature of this genus. Several previously suggested vicariant events, such as fragmentation of xeric forests in Australia and the uplift of the central mountain range on New Guinea, are reinforced as important Pliocene barriers for tropical forest taxa in this region. Interaction between Pleistocene climatic fluctuations and differences in habitat requirements may explain a higher and more recent population structures in the mid‐mountain catbird complex and the lack of representatives from the lowland clade in the comparably drier Australia. Phylogeographical patterns in both catbird complexes, respectively, both comply and deviate from other lowland and mid‐mountain taxa in the region. This highlights that taxon‐specific properties, such as their historical spatial and ecological distributions, capacity to disperse and tolerance to habitat changes, affect the phylogeographical histories of organisms. Within both species complexes, the genetic differentiation between several geographically isolated populations was found to exceed those commonly observed for avian sister species. As these genetically distinct taxa also were found to be morphological diagnosable, we suggest a revised classification of the genus Ailuroedus, where we recognize three species within the lowland complex and seven species within the mid‐mountain complex.     

Phylogenetic Species Identification in Rattus Highlights Rapid Radiation and Morphological Similarity of New Guinean Species

The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and phylogenetics. The remaining taxonomic complexity highlights the recent and rapid radiation of Rattus in the Australo-Papuan region.     

Infrequent and unidirectional colonization of hyperdiverse Papuadytes diving beetles in New Caledonia and New Guinea

We present a molecular phylogenetic analysis of 2808 aligned bp of rrnL, cox1, cob, H3 and 18S rRNA of all major morphological groups of Papuadytes diving beetles (Coleoptera: Dytiscidae) which are diverse in running water habitats throughout the Australian region. We focus on the origin of the fauna of the megadiverse islands of New Guinea and New Caledonia. Parsimony as well as Bayesian analyses suggest a basal position of Australian species in a paraphyletic series, with more recent nested radiations in New Caledonia and New Guinea. According to molecular clock analyses, both landmasses were colonized during the Miocene, which matches geological data and corroborates similar findings in other taxonomic groups. Our analyses suggest that dispersal played an important role in the formation of these large insular faunas, although successful colonization appears to be a rare event, and, in this case, is unidirectional. Whether or not a lineage is present on an island is due to chance: Papuadytes are absent from Fiji, where related Copelatus have radiated extensively in the same habitats occupied by Papuadytes in New Caledonia and New Guinea, while Copelatus are absent from New Caledonia. Lineages of Papuadytes apparently colonized New Caledonia twice, around 14 and 9 MYA according to the molecular calibration, and both lineages are derived from an Australian ancestor. The older clade is represented only by two apparently relictual mountain species (one morphologically strongly adapted to highly ephemeral habitats), while the younger clade contains at least 18 species exhibiting a great morphological diversity. The 150+ species in New Guinea are monophyletic, apparently derived from an Australian ancestor, and constitute a morphologically rather homogenous group. The tree backbone remains insufficiently supported under parsimony and Bayesian analyses, where shorter branches suggest a rapid sequence of major branching events.     

杨属植物分类的研究进展和展望

自林奈建立杨属（Populus）以来,众多的学者对杨属的分类进行了研究,并建立了较多的分类系统。目前的国际杨属分类,总体上还停留在传统形态分类阶段,存在明显的地域和国别特征。尽管各国在主流上都采用“属—组—种”的分类阶元,但在种、亚种、变种的划分上,却存在很大的不同。中国和美国分别是细分派和聚合派的代表,两国的分类系统存在很大分歧,但各有优点和缺点。即使在国内,杨属分类也还有很多需要解决的问题。新兴的分子系统学研究,为杨属的分类修订提供了一些有益参考,但总体贡献不大。国际杨属分类的趋势和终极目标是建立基于系统发生的统一分类系统。这需要基于种群和综合物种概念,融合形态学、生态学、生物地理学、基因组生物信息学和进化生物学等的综合系统分类来实现。     

Classification of weevils as a data-driven science: leaving opinion behind

Data and explicit taxonomic ranking criteria, which minimize taxonomic change, provide a scientific approach to modern taxonomy and classification. However, traditional practices of opinion-based taxonomy (i.e., mid-20^th century evolutionary systematics), which lack explicit ranking and naming criteria, are still in practice despite phylogenetic evidence. This paper discusses a recent proposed reclassification of weevils that elevates bark and ambrosia beetles (Scolytinae and Platypodinae) to the ranks of Family. We demonstrate that the proposed reclassification 1) is not supported by an evolutionary systematic justification because the apparently unique morphology of bark and ambrosia beetles is shared with other unrelated wood-boring weevil taxa; 2) introduces obvious paraphyly in weevil classification and hence violates good practices on maintaining an economy of taxonomic change; 3) is not supported by other taxonomic naming criteria, such as time banding. We recommend the abandonment of traditional practices of an opinion-based taxonomy, especially in light of available data and resulting phylogenies.     

Revised concept of the genus Euryporus Erichson (Coleoptera, Staphylinidae, Staphylininae) and phylogenetic significance of Staphylinini from New Guinea

The Staphylinini rove beetle genus Euryporus Erichson from the subtribe Quediina is restricted to include only three species from the Western Palearctic region: Euryporus picipes (Paykull, 1800), Euryporus aeneiventris (Lucas, 1846), and Euryporus princeps Wollaston, 1864. Euryporus argentatus Fauvel, 1881, Euryporus warisensis Last, 1987 and Euryporus multicavus Last, 1980, which do not even belong to the subtribe Quediina, are excluded fromthe genus. Of these, two were transferred to different genera: Tympanophorus argentatus (Fauvel, 1881), comb. nov., from Sumatra;and Hesperus warisensis (Last, 1987), comb. nov.,from New Guinea. "Euryporus" multicavus could not be placed to any of the described genera of Staphylinini and is left as incertae sedis pending a broader study of the relevant fauna of this tribe in New Guinea and adjacent regions. The taxonomic history of Euryporus is reviewed, and an updated diagnosis of this genus is provided.     

"Making Twos": Pairing as an Alternative to the Taxonomic Mode of Representation

Melpa-speaking children do very poorly on cognitive tasks, in general, and as compared to children from another traditional society in Papua New Guinea. Causes for this difference are sought in an analysis of the tasks which shows them to require a taxonomic strategy for successful performance and in an analysis of the folk taxonomies of the respective societies which shows them to vary in complexity. Further study of Melpa representation reveals that this can better be represented as a pairing rather than a taxonomizing tendency This finding allows a reinterpretation of the cognitive task results . [Cognition, child development, ethnosemantics, world view, Melpa, Papua New Guinea]     

Prokaryotic taxonomy and nomenclature in the age of big sequence data

The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.Subject terms: Archaea, Bacteria     

Revision of the termite family Rhinotermitidae (Isoptera) in New Guinea

Recently, we completed a revision of the Termitidae from New Guinea and neighboring islands, recording a total of 45 species. Here, we revise a second family, the Rhinotermitidae, to progress towards a full picture of the termite diversity in New Guinea. Altogether, 6 genera and 15 species are recorded, among which two species, Coptotermes gambrinus and Parrhinotermes barbatus, are new to science. The genus Heterotermes is reported from New Guinea for the first time, with two species restricted to the southern part of the island. We also provide the first New Guinea records for six species of the genera Coptotermes and Schedorhinotermes. We briefly describe soldiers and imagoes of each species and provide a key based on soldier characters. Finally, we discuss the taxonomic and biogeographical implication of our results. A replacement name, Schedolimulus minutides Bourguignon, is proposed for the termitophilous staphylinid Schedolimulus minutus Bourguignon, to solve a question of secondary homonymy.     

New World Monkey Nightmares: Science,Art, Use,and Abuse (?) in Platyrrhine Taxonomic Nomenclature

The taxonomy and nomenclature of New World monkeys is becoming precariously unstable and impractical, plagued by revisions aimed at conforming to approaches that reject the Biological Species Concept for narrowly construed reasons and resulting in a hyperinflated taxonomy at species (often) and genus (sometimes) levels. This undermines a major goal of classification at the most basic taxonomic levels to ease communication and facilitate research. Since it is difficult to justify extensive changes in terminology without a deeply justified theoretical purpose or without showing what scientific benefits these alterations can bring, working primatologists need not accept this doctrinaire trend. Knowing as little as we do about what a species actually is, does not justify contorting the value of a species nomenclature so that it reflects nothing more than coat color, a node, or endpoint of a dendrogram. Am. J. Primatol. 74:692‐695, 2012. © 2012 Wiley Periodicals, Inc.     

Classical and non-classical taxonomy: where does the boundary pass?

Rise of non-classical science during XX century had certain influence upon development of biological taxonomy. Scientific pluralism (especially normative naturalism of Laudan), contrary to positivist and early post-positivist treatments, made taxonomy acknowledged scientific discipline of its own right. The present state of some schools of taxonomy makes it possible to consider them as a part of non-classical science and constituting the non-classical taxonomy. The latter is characterized by the following most important features. Ontological substantiation of both classificatory approaches and particular classifications is requested which invalidates such formal approaches as nominalistic and phenetic (numerical) schools. This substantiation takes a form of content-wise background preferably causal models which include certain axioms and presumptions about taxonomic diversity being studied, together with its causes, and thus define initial conditions of classificatory procedures. From this viewoint, phylogenetic classificatory approach is the most developed part of non-classical taxonomy. The entire taxonomic diversity is structured into several aspects of different levels of generality, each being outlined by a particular consideration aspect. The latter makes personal knowledge constituting an irremovable part of any scientific statement about taxonomic diversity, thus opposition of "objectively" and "subjectively" elaborated classifications becomes vague. Interrelation of various species concepts corresponding to its different consideration aspects is described by uncertainty relation principle. Classificatory algorithms are to be compatible with the conditions of a background model to ensure particular classifications obtained by their means are interpretable within the same model: this is provided by the correspondence principle. Classification is considered as a taxonomic hypothesis, i.e. a conjectural judgement about structure of particular fragment of taxonomic diversity considered within given consideration aspect; wich is to be forwarded and tested according to certain rules. Recognition of different aspects of taxonomic diversity makes it "legal" to elaborate several classifications of equal status, each reflecting a particular aspect of a fixed fragment of that diversity. This viewpoint makes classical ideas of the "ultimate" Natural (whatever might be its definition) or the best reference systems futile. In general, any pretension of an approach to be "the best" in reflecting taxonomic divesrity is contr-productive. Instead, elaboration of particular spectra of complementary classifications becomes the main task of non-classical taxonomy which describes in sum the entire taxonomic diversity. So, not opposition but correct mutual interpretation of such classifications and uniting them into the comprehensive picture of taxonomic diversity become focal points of non-classical taxonomy.     

Bivalves in a bottleneck: taxonomy,phylogeography and conservation of freshwater mussels (Bivalvia: Unionoida) in Australasia

The conservation biology of Australasian freshwater mussels is hindered by lack of a taxonomic framework that employs molecular data as a complement to shell characters, larval forms and internal anatomy. The fauna includes more than 32 known species (30+ Hyriidae, 2 Unionidae), but has not been revised for 55 years, despite minor amendments. The hyriids are relics of Gondwana, represented in Australia and New Guinea by the ancestral Velesunioninae and in Australia and New Zealand by the Hyriinae (Tribe Hyridellini). Many taxonomic and phylogeographic issues await resolution, including the relationships between Australasian and South American species, and between Australian and New Zealand species, and the status of species in New Guinea (including uncertain reports of Unionidae) and the Solomon Islands. Once these are clarified, it will be easier to identify threatened species and evaluate the conservation status of the fauna. At present, only seven taxa are named in the IUCN Red List or under national/state legislation, and these are not representative. Threatening processes include altered flow regimes, catchment disturbances, salinisation, pollution and invasive species. While the need for a taxonomic revision is paramount, progress in conservation may depend also upon involving the wider community.     

Spatial congruence in language and species richness but not threat in the world's top linguistic hotspot

Languages share key evolutionary properties with biological species, and global-level spatial congruence in richness and threat is documented between languages and several taxonomic groups. However, there is little understanding of the functional connection between diversification or extinction in languages and species, or the relationship between linguistic and species richness across different spatial scales. New Guinea is the world''s most linguistically rich region and contains extremely high biological diversity. We demonstrate significant positive relationships between language and mammal richness in New Guinea across multiple spatial scales, revealing a likely functional relationship over scales at which infra-island diversification may occur. However, correlations are driven by spatial congruence between low levels of language and species richness. Regional biocultural richness may have showed closer congruence before New Guinea''s linguistic landscape was altered by Holocene demographic events. In contrast to global studies, we demonstrate a significant negative correlation across New Guinea between areas with high levels of threatened languages and threatened mammals, indicating that landscape-scale threats differ between these groups. Spatial resource prioritization to conserve biodiversity may not benefit threatened languages, and conservation policy must adopt a multi-faceted approach to protect biocultural diversity as a whole.     

After the 'affluent society': cost of living in the Papua New Guinea highlands according to time and energy expenditure-income

What is the cost of living in the Papua New Guinea highlands? An answer is sought using a time and energy accounting approach. The subsistence regime of Wola-speaking highlanders, the subjects of this investigation, comprises three components. The principal one is horticulture: people clearing gardens from forest and grassland, with tuberous crops predominating, notably sweet potato. The second component comprises animal rearing, notably of domestic pigs. The third, and least important, is hunting and gathering for food in the forest. The calculated returns on investments in these subsistence domains vary considerably. Gardens return in their crops between ten and fifteen times the energy expended in cultivation. Pigs may also give a good return, of four to five times the energy invested in rearing them, if slaughtered when adult, but people regularly keep animals for years and may incur negative energy returns on their labour investments. This relates to the high cultural premium put on pigs. Foraging for food is also energetically costly, the Wola expending four times more energy on these activities than they gain in return from the food they secure. This analysis of energy gains and losses challenges the relative notion of affluence as applied to foragers, by reviewing it in the comparative context of subsistence horticulture.