Taxonomic Inference Research Articles

The complete mitochondrial genome of Parotis chlorochroalis (Hampson, 1912) (Lepidoptera: Crambidae)

The complete mitochondrial genome of the Parotis chlorochroalis was sequenced, revaeling a length of 15239 bp with 37 genes and an A + T-rich region. All c13 PCGs begin with typical ATN codons, except COI gene, which starts with CGA. Eleven genes terminate with TAA, two with T–. All 22 tRNA genes exhibit typical cloverleaf structure except for trnS1 P. chlorochroalis has two relatively conserved intergenic regions and two relatively conserved overlapping regions. Phylogenetic analysis support P. chlorochroalis belongs to subfamily Spilomelinae, the topologies of Crambidae are highly congruent with previous studies. This newly sequences mitochondrial genome provides valuable resources for taxonomic inference and evolutionary studies of genus Parotis.

Persistent Gene Flow Suggests an Absence of Reproductive Isolation in an African Antelope Speciation Model.

African antelope diversity is a globally unique vestige of a much richer world-wide Pleistocene megafauna. Despite this, the evolutionary processes leading to the prolific radiation of African antelopes are not well understood. Here, we sequenced 145 whole genomes from both subspecies of the waterbuck (Kobus ellipsiprymnus), an African antelope believed to be in the process of speciation. We investigated genetic structure and population divergence and found evidence of a mid-Pleistocene separation on either side of the eastern Great Rift Valley, consistent with vicariance caused by a rain shadow along the so-called 'Kingdon's Line'. However, we also found pervasive evidence of both recent and widespread historical gene flow across the Rift Valley barrier. By inferring the genome-wide landscape of variation among subspecies, we found 14 genomic regions of elevated differentiation, including a locus that may be related to each subspecies' distinctive coat pigmentation pattern. We investigated these regions as candidate speciation islands. However, we observed no significant reduction in gene flow in these regions, nor any indications of selection against hybrids. Altogether, these results suggest a pattern whereby climatically driven vicariance is the most important process driving the African antelope radiation, and suggest that reproductive isolation may not set in until very late in the divergence process. This has a significant impact on taxonomic inference, as many taxa will be in a gray area of ambiguous systematic status, possibly explaining why it has been hard to achieve consensus regarding the species status of many African antelopes. Our analyses demonstrate how population genetics based on low-depth whole genome sequencing can provide new insights that can help resolve how far lineages have gone along the path to speciation.

Nest traits for the world's birds

AbstractMotivationA well‐constructed nest is a key element of successful reproduction in most species of birds, and nest morphology varies widely across the class. Macroecological and macroevolutionary studies tend to group nest design into a small number of discrete categories, often based on taxonomic inference. In reality, however, many species display considerable intraspecific variation in their nest‐building behaviour, and broad‐level categories may include several functionally distinct nest types. To address this imprecision in the literature and facilitate future studies of broad‐scale variation in avian parental care, we here introduce a detailed, global comparative database of nest building in birds, together with preliminary correlations between these traits and species‐level environmental variables.Main types of variables containedWe present species‐level data for nest structure, location, height, material composition, sex of builder, building time and nest dimensions.Spatial location and grainGlobal. Maps are presented at the 10 × 10 level.Time period and grainIncluded species are generally extant, although we present some data for recently extinct taxa. The data were collected in 2017–2021 and was drawn from secondary sources published in 1992–2021.Major taxa and level of measurementPartial or complete trait data is presented for 8601 species of birds, representing 36 of 36 orders and 239 of 243 families.Software formatData have been uploaded as Supplementary Material in .csv format and are separated by species and source for all traits (Dataset , and Metadata) as well as summarized at the species level for the major structure and location variables (Dataset , and Metadata).

Quantifying the ability of imaging sonar to identify fish species at a subtropical artificial reef

Abstract Imaging sonars (ISs) are high-frequency acoustic devices that are increasingly being used to study fish in marine and freshwater habitats. Acoustic devices are limited in quantifying species richness, and previous attempts to identify fish species using IS have mostly focused on assemblages of low species richness or high morphological diversity. This study aimed to determine the ability of IS for identifying fish species at a subtropical artificial reef off Perth, Western Australia. Several fish traits that could be defined using IS were identified and described for all fish species observed with simultaneous optical footage. These traits were used to create a clustering algorithm to infer the species identity of IS detections of the five most abundant species at the reef. The identities of all fish from two species (Chromis westaustralis and Neatypus obliquus) were inferred with 100% success, though no individuals from the remaining three species (Seriola dumerili, Coris auricularis, and Pempheris klunzingeri) were correctly identified. An alternative clustering-based approach to categorising fish detected by IS independent of taxonomic inference was also implemented. Overall, this study demonstrates that IS can identify reef fish with variable success, and proposes an alternative method for describing fish assemblages irrespective of species identity.

PepGM: A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores.

Inferring taxonomy in mass spectrometry-based shotgun proteomics is a complex task. In multi-species or viral samples of unknown taxonomic origin, the presence of proteins and corresponding taxa must be inferred from a list of identified peptides which is often complicated by protein homology: many proteins do not only share peptides within a taxon but also between taxa. However, correct taxonomic inference is crucial when identifying different viral strains with high sequence homology-considering, e.g., the different epidemiological characteristics of the various strains of SARS-CoV-2. Additionally, many viruses mutate frequently, further complicating the correct identification of viral proteomic samples. We present PepGM, a probabilistic graphical model for the taxonomic assignment of virus proteomic samples with strain-level resolution and associated confidence scores. PepGM combines the results of a standard proteomic database search algorithm with belief propagation to calculate the marginal distributions, and thus confidence scores, for potential taxonomic assignments. We demonstrate the performance of PepGM using several publicly available virus proteomic datasets, showing its strain-level resolution performance. In two out of eight cases, the taxonomic assignments were only correct on the species level, which PepGM clearly indicates by lower confidence scores. PepGM is written in Python and embedded into a Snakemake workflow. It is available on https://github.com/BAMeScience/PepGM.

Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts.

Modern microbial taxonomy generally relies on the use of single marker genes or sets of concatenated genes to generate a framework for the delineation and classification of organisms at different taxonomic levels. However, given that DNA is the 'blueprint of life', and hence the ultimate arbiter of taxonomy, classification systems should attempt to use as much of the blueprint as possible to capture a comprehensive phylogenetic signal. Recent analysis of whole-genome sequences from coral reef symbionts (dinoflagellates of the family Symbiodiniaceae) and other microalgal groups has uncovered extensive divergence not recognised by current algal taxonomic approaches. In the era of 'sequence everything', we argue that whole-genome data are pivotal to guide informed taxonomic inference, particularly for microbial eukaryotes.

INaturalist is useful at enhancing biodiversity studies as evident from southern African freshwater crabs (Decapoda: Brachyura: Potamonautidae)

Abstract The value of the citizen science platform iNaturalist was explored using photographic observations of southern African freshwater crabs (Potamonautidae Bott, 1970, among two genera Potamonautes sensu stricto MacLeay, 1838 and MartimonautesCumberlidge & Daniels, 2022) in combination with specimen data deposited in the South African Museum (Iziko Museums of Cape Town, South Africa). Species identification of photographic observations were assessed, and the identification of taxa corrected where necessary. From these records, the habitat type and distribution of the species were noted. The area of occupancy (AOO) and the extent of occurrence (EOO) were calculated where range extensions for species were observed. The results demonstrate that riverine/mountain stream freshwater crabs are over-represented in their frequency but species occurring in swamps/forests were under-represented. Using iNaturalist spatial data for South Africa we can identify several unsampled gaps in the country which included the Free State and North West, Gauteng and the Northern Cape, followed by Limpopo, Mpumalanga, and the Eastern Cape provinces. The Western Cape and KwaZulu-Natal had the highest number of freshwater crab records on iNaturalist. The remaining southern African countries, Angola, Botswana, Eswatini, Lesotho, Malawi, Mozambique, Namibia, and Zimbabwe, have few iNaturalist records. Range extensions were observed in four South African species based on iNaturalist records (P. clarusGouws, Stewart & Coke, 2000, P. flavusjoDaniels, Phiri, & Bayliss, 2014, P. isimangaliso Peer & Gouws, 2015, and P. mariepskoppieDaniels, Barnes, Marais & Gouws, 2021) with increases in AOO and EOO. We also observed a new undescribed freshwater crab on iNaturalist and corroborated this observation by sequencing these specimens for the cytochrome oxidase one subunit (COI) locus. Photographic quality is critical for taxonomic inference. Citizen science ­platforms such as iNaturalist can be invaluable for the discovery and documentation of biodiversity and provide new spatial data for species distributions that in turn can aid conservation tools.

Nuclear and Mitochondrial Data on Trichuris from Macaca fuscata Support Evidence of Host Specificity

Whipworms are parasitic intestinal nematodes infecting mammals, and traditionally humans and other primates that have so far been considered infected by Trichuris trichiura. Recent molecular studies report a more complex scenario suggesting the presence of a species complex with several Trichuris taxa specifically infecting only one primate species as well as taxa able to infect a range of primate species. The systematics of the group is important for taxonomic inference, to estimate the relative zoonotic potential, and for conservation purposes. In fact, captive animals living in zoological gardens are usually infected by persistent monoxenous intestinal parasites. Here, two Japanese macaques living in the Bioparco Zoological Garden of Rome were found infected by Trichuris sp. Nematodes were characterized at the molecular level using nuclear (btub and 18S) and mitochondrial (16S and cytb) markers and then compared to Trichuris collected previously in the same location, and to other Trichuris infecting primates. Evidences from mitochondrial and nuclear markers allowed for the identification of Trichuris sp. specific to Macaca fuscata. Results obtained here also described a uniform taxonomic unit of Trichuris, separated but closely related to Trichuris trichiura, thus, emphasizing its zoonotic potential for workers and visitors.

Disentangling the Genetic Relationships of Three Closely Related Bandicoot Species across Southern and Western Australia

The taxonomy of Australian Isoodon bandicoots has changed continuously over the last 20 years, with recent genetic studies indicating discordance of phylogeographic units with current taxonomic boundaries. Uncertainty over species relationships within southern and western Isoodon, encompassing I. obesulus, I. auratus, and I. fusciventer, has been ongoing and hampered by limited sampling in studies to date. Identification of taxonomic units remains a high priority, as all are threatened to varying extents by ongoing habitat loss and feral predation. To aid diagnosis of conservation units, we increased representative sampling of I. auratus and I. fusciventer from Western Australia (WA) and investigated genetic relationships of these with I. obesulus from South Australia (SA) and Victoria (Vic) using microsatellite markers and mitochondrial DNA. mtDNA analysis identified three major clades concordant with I. obesulus (Vic), I. auratus, and I. fusciventer; however, I. obesulus from SA was polyphyletic to WA taxa, complicating taxonomic inference. Microsatellite data aided identification of evolutionarily significant units consistent with existing taxonomy, with the exception of SA I. obesulus. Further, analyses indicated SA and Vic I. obesulus have low diversity, and these populations may require more conservation efforts than others to reduce further loss of genetic diversity.

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome.

ABSTRACTCarbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and carbadox communities were distinct 2 days after carbadox introduction. This effect was driven by carbadox-associated lower expression of FIGfams (n = 66) related to microbial respiration, carbohydrate utilization, and RNA metabolism (q < 0.1), suggesting bacteriostatic or bactericidal effects within certain populations. Interestingly, carbadox treatment caused greater expression of FIGfams related to all stages of the phage lytic cycle 2 days following the introduction of carbadox (q ≤0.07), suggesting the carbadox-mediated induction of prophages and phage DNA recombination. These effects were diminished by 7 days of continuous carbadox in the feed, suggesting an acute impact. Additionally, the viromes included a few genes that encoded resistance to tetracycline, aminoglycoside, and beta-lactam antibiotics but these did not change in frequency over time or with treatment. The results show decreased bacterial growth and metabolism, prophage induction, and potential transduction of bacterial fitness genes in swine gut bacterial communities as a result of carbadox administration.

Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e. enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

Phylogenetic analysis of the genus Argia Rambur, 1842 (Odonata: Coenagrionidae), based on morphological characters of larvae and mitochondrial DNA sequences

The study of the evolutionary interrelationships among the species encompassed in the Neotropical genus Argia (Zygoptera: Coenagrionidae) has been neglected. The goal of this study is to infer the phylogenetic relationships among 36 species of Argia Rambur, 1842, using complementary data sets (i.e., larval morphology and mitochondrial DNA). The morphological data set comprises 76% of the larvae currently described for this genus and includes 97 morphological characters. From those, 47 characters have not been previously used in taxonomic studies involving dragonflies’ larvae. This is the first cladistic study based on larvae morphology for species within the suborder Zygoptera. Data partitions were analyzed individually, as well as total evidence, using parsimony and Bayesian inference as criteria for optimal-tree selection. The results support the monophyly of the North American species of Argia. This genus can be identified by the combination of eight synapomorphies, four of which are exclusively found in Argia. According to the optimal trees, the individual data sets (i.e., morphology and DNA sequences) have a high level of homoplasy, resulting in soft polytomies and low support for several nodes. The specific relationships of the terminal units differ between the phylogenies; nonetheless, there is historical congruence among them. Within Argia, five clades were consistently recovered. Most of those clades have been identified, at least in part, in previous phylogenetic and taxonomic studies. Indubitably, the morphological characters from larvae have historical signal useful for cladistic and taxonomic inference. Therefore, it should be a priority to pay more attention to this source of characters.

Semiconductor Sequencing Reveals the Diversity of Bacterial Communities in an Amazonian Reservoir

The reservoir of the Tucurui hydropower plant has been reported to be a source of methane by several studies. These results question the Brazilian energy policy that plans to establish many other plants similar to Tucurui in the Amazon region. In this study, we used a next-generation sequencing platform, the Ion Torrent Personal Genome Machine, and employed a barcode library to investigate the bacterial diversity along a 70-m deep water column in the proximity of the dam. One-litre water samples were taken at each 10 m from the surface to extract total DNA. A total of 1,505,461 reads were generated. The alpha diversity analyses showed 2,733, 2,280, 1,354, 1,338, 2,726, 2,134, 2,017, 1,885 operational taxonomic units (OTUs; 3% cutoff) at depths of 0, 10, 20, 30, 40, 50, 60 and 70 m, respectively. Taxonomic inference analyses identified the most abundant phyla as being Proteobacteria, Cyanobacteria, Bacteroidetes, Acidobacteria and Actinobacteria, but others phyla were also found. This water column seems to produce oxygen in the upper layers due to abundance of Cyanobacteria. In the deeper layers, most of Proteobacterial sequences were assigned to Methanotrophic bacteria, showing that a significant amount of methane is consumed by these communities.

Use of Ancient Sedimentary DNA as a Novel Conservation Tool for High‐Altitude Tropical Biodiversity

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited.

Thinking about biology. Modular constraints on categorization and reasoning in the everyday life of Americans, Maya, and scientists

This essay explores the universal cognitive bases of biological taxonomy and taxonomic inference using cross-cultural experimental work with urbanized Americans and forest-dwelling Maya Indians. A universal, essentialist appreciation of generic species appears as the causal foundation for the taxonomic arrangement of biodiversity, and for inference about the distribution of causally-related properties that underlie biodiversity. Universal folkbiological taxonomy is domain-specific: its structure does not spontaneously or invariably arise in other cognitive domains, like substances, artifacts or persons. It is plausibly an innately-determined evolutionary adaptation to relevant and recurrent aspects of ancestral hominid environments, such as the need to recognize, locate, react to, and profit from many ambient species. Folkbiological concepts are special players in cultural evolution, whose native stability attaches to more variable and difficult-to-learn representational forms, thus enhancing the latter's prospects for regularity and recurrence in transmission within and across cultures. This includes knowledge that cumulatively enriches (folk expertise), overrides (religious belief) or otherwise transcends (science) the commonsense ontology prescribed by folkbiology. Finally, the studies summarized here indicate that results gathered from “standard populations” in regard to biological categorization and reasoning more often than not fail to generalize in straightforward ways to humanity at large. This suggests the need for much more serious attention to cross-cultural research on basic cognitive processes.

A bird's eye view: biological categorization and reasoning within and across cultures

Many psychological studies of categorization and reasoning use undergraduates to make claims about human conceptualization. Generalizability of findings to other populations is often assumed but rarely tested. Even when comparative studies are conducted, it may be challenging to interpret differences. As a partial remedy, in the present studies we adopt a ‘triangulation strategy’ to evaluate the ways expertise and culturally different belief systems can lead to different ways of conceptualizing the biological world. We use three groups (US bird experts, US undergraduates, and ordinary Itza’ Maya) and two sets of birds (North American and Central American). Categorization tasks show considerable similarity among the three groups’ taxonomic sorts, but also systematic differences. Notably, US expert categorization is more similar to Itza’ than to US novice categorization. The differences are magnified on inductive reasoning tasks where only undergraduates show patterns of judgment that are largely consistent with current models of category-based taxonomic inference. The Maya commonly employ causal and ecological reasoning rather than taxonomic reasoning. Experts use a mixture of strategies (including causal and ecological reasoning), only some of which current models explain. US and Itza’ informants differed markedly when reasoning about passerines (songbirds), reflecting the somewhat different role that songbirds play in the two cultures. The results call into question the importance of similarity-based notions of typicality and central tendency in natural categorization and reasoning. These findings also show that relative expertise leads to a convergence of thought that transcends cultural boundaries and shared experiences.

CHARACTERIZATION OF MICROSATELLITE FLANKING SEQUENCES IN VITIS SPECIES

Simple sequence repeats (SSRs) or microsatellites have become an important source of highly polymorphic genetic markers. They are widely used in the genetic analysis of populations, the construction of linkage maps, in cultivar fingerprinting and pedigree construction. The SSR unique flanking sequences were used in several eukaryotic taxa for transferring microsatellites isolated from a source species to a related species. Cross-species transportability of microsatellite markers is very attractive in Vitis, as non-V. vinifera species and inter-specific hybrids are commonly used as rootstocks and raw material in breeding programs. This work provides new insights into (1) the transportability of microsatellites isolated from Vitis vinifera to different Vitis species and (2) the possibility of using microsatellite flanking sequences for taxonomic and phylogenetic inference. Eleven microsatellites isolated from grapevine (Vitis vinifera) were used to assay the conservation of priming sites in 14 non-V. vinifera species, including relevant taxa for breeding and Parthenocissus quinquefolia as a representative of a related genus. Cross-species amplification was obtained in 94% of the 176 genotype x locus tested combinations. Sequencing of PCR products was performed for three microsatellite loci amplified in 10 different species. A microsatellite repeat was found to be present in all the cases. The repeat region was often longer in V. vinifera than in non-source species whose repetitive sequences showed frequent interruptions of the core repeat. In spite of these constraints, which could reduce the polymorphism of microsatellites in non-source species, the results demonstrate the possibility of extending the use of microsatellite markers to wild germplasm and inter-specific hybrids. Point mutations have been found in microsatellite flanking regions and these variations have been used to investigate the genetic relationship among taxa. The Neighbour-joining tree obtained on the base of 10 nucleotide variations, showed that there is no clear dividing line between American, Asian and European species and that the actual taxonomy which reflects the geographical distribution of species should be revised.

Genetic variation in seven goby species (Perciformes: Gobiidae) assessed by electrophoresis and taxonomic inference

Data on the electrophoretic patterns of 20 enzyme loci were used to investigate relationships among seven Mediterranean goby species. The study evidenced different levels of genetic variability among the species. On the whole, the degrees of genetic differentiation were consistent with the current taxonomic recognition of species and genera. Phenetic and phylogenetic analyses agreed in clustering the samples in three groups, i.e. the Gobius (including Zosterisessor ophiocephalus), the Lesueurigobius species and Pomatoschiarua minutus. The taxa analysed probably evolved following the complex geological and climatic events that have been affecting the Mediterranean basin ever since the Miocene.

Chromosomal Studies in the Egyptian Flora V. Chromosomal relationships in the genus Astragalus L. (Fabaceae) and their taxonomic inference.

The karyotypes of 17 taxa representing eleven species of Astragalus have been described and their taxonomic inferences are discussed. A diploid chromosome number of 2n =16, with a basic number of x = 8, was recorded in A. eremophilus, two samples of A. peregrinus, A. sieberi, A. sinaicus and A. trigonus. Polyploid numbers, also based on x = 8, were scored, 2n = 32 in A. hamosus and 2n = 40 in A. hamosus v. buceras. Meanwhile, a diploid number of 2n = 14, with a basic number of x = 7 was found in three samples of A. annularis and three varieties of A. tribuloids. A. boeticus was found cytologically distinguished with 2n = 30, and A. tenuirugis with 2n = 24, while A. trimestris has 2n = 12 and x = 6. The chromosomes in the genus Astragalus are relatively samll, among the examined species the largest were found in A. annularis (mean length = 1.7-1.75 gm) and the smallest were recorded in A. boeticus (mean length = 0.95 μm). In general the karyotype of the genus show a relatively high degree of symmetry as reflected by r-value and the TF%. Infra and inter-specific variations, in these criteria, have been recorded among the studied taxa.The preponderance of species with a basic number of x = 8 among the studied taxa agree with the assumption that this number is the primary number in Astragalus, x = 7 and x = 6 could have been evolved by aneuploid loss of chromosomes. This situation is only found in the Old World species of the genus. In the New World species, however basic numbers of x =11, 12, 13, 14 and 15 have been often encountered, these numbers may have been evolved from x = 8 through polyploidy followed by loss of 1-4 chromosomes. Discussion of chromosomal relationships in this large and complex genus chould take into account that only about 25% of the species have been cytologically examined. Moreover chromosomal changes should not be discussed independent of other criteria particularly those of morphology. Among the examined taxa chromosomal features provide evidence for the differentiation of some taxa which share mophological similarities, meanwhile some other taxonomically related species were found to have similar karyotype features.

On taxonomic reasoning in conceptual design

Taxonomic reasoning is a typical task performed by many AI knowledge representation systems. In this paper, the effectiveness of taxonomic reasoning techniques as an active support to knowledge acquisition and conceptual schema design is shown. The idea developed is that by extending conceptual models with defined concepts and giving them rigorous logic semantics, it is possible to infer isa relationships between concepts on the basis of their descriptions. From a theoretical point of view, this approach makes it possible to give a formal definition for consistency and minimality of a conceptual schema. From a pragmatic point of view it is possible to develop an active environment that allows automatic classification of a new concept in the right position of a given taxonomy, ensuring the consistency and minimality of a conceptual schema. A formalism that includes the data semantics of models giving prominence to type constructors (E/R, TAXIS, GALILEO) and algorithms for taxonomic inferences are presented: their soundness, completeness, and tractability properties are proved. Finally, an extended formalism and taxonomic inference algorithms for models giving prominence to attributes (FDM, IFO) are given.