Evolutionary Relationships Of Species Research Articles

A generalized framework to expand incomplete phylogenies using non‐molecular phylogenetic information

AbstractAimThe increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the world's biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. This prospect has urged the development of software to expand phylogenies based on non‐molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms.InnovationHere, we present a completely generalized and flexible framework to expand incomplete phylogenies. The framework is implemented in the R package “randtip”, a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. Although randtip can generate fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the “blind” expansion of phylogenies using “quick‐and‐dirty” approaches often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step‐by‐step tutorial that was designed to provide guidelines to non‐specialist users.Main ConclusionsPhylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete phylogenies and thereby account for phylogenetic uncertainty in quantitative analyses.

Macroecological links between the Linnean, Wallacean, and Darwinian shortfalls

Species are the currency of most biodiversity studies. However, many shortfalls and biases remain in our biodiversity estimates, preventing a comprehensive understanding of the eco-evolutionary processes that have shaped the biodiversity currently available on Earth. Biased biodiversity estimates also jeopardize the effective implementation of data-driven conservation strategies, ultimately leading to biodiversity loss. Here, we delve into the concept of the Latitudinal Taxonomy Gradient (LTG) and show how this new idea provides an interesting conceptual link between the Linnean (i.e., our ignorance of how many species there are on Earth), Darwinian (i.e., our ignorance of species evolutionary relationships), and Wallacean (i.e., our ignorance on species distribution) shortfalls. More specifically, we contribute to an improved understanding of LTGs and establish the basis for the development of new methods that allow us to: (i) better account for the integration between different shortfalls and, (ii) estimate how these interactions may affect our understanding about the evolutionary components of richness gradients at macroecological scales.

Molecular phylogenetic analysis of Tulipa (Liliaceae) from Aksu-Zhabagly Nature Reserve

Barcodes are conserved sequences of genomic, plastid and mitochondrial DNA that can be utilized to uniquely identify an unidentified specimen to its species when conventional identification methods are inapplicable. Among prokaryotic and eukaryotic species, nuclear ribosomal internal transcribed spacer (ITS) sections are one of the most often utilized DNA markers in DNA barcoding and phylogenetic research. In addition to the ribosomal genes, the plastid genes are the most suitable for identifying plant species. The Aksu-Zhabagly Nature Reserve is the oldest nature reserve in Central Asia and is home to 1,312 vascular plant species, 44 of which are categorized as threatened or endangered in Kazakhstan's red data book. In this study, a collection of specimens of uncommon tulip species was compiled, along with their morphological identification and DNA barcoding. The ITS region and parts of the matK and ycf1b genes of tulip plastid DNA were sequenced. The evolutionary link between species of tulips was investigated. Phylogenetic study predicted two Tulipa subclades. Tulipa species have substantially preserved MatK genes. Tulips' ycf1b gene has evolved more slowly than other Liliaceae family members. Nuclear and plastid DNA sequences investigated Tulipa species evolutionary relationships. The findings about the ITS region of nuclear DNA were more definite. Overall, our work shows that genetic data will be important in determining species concepts in this genus, however, even with a molecular perspective pulling apart closely related taxa can be extremely challenging.

Phylogeny, infrageneric classification and historical biogeography of Mesochila Rivalier, 1969 (Coleoptera: Cicindelidae), with the performance of different phylogenetic inferences using morphological data compared

In this study, we aim to understand the boundaries and the species evolutionary relationships in Mesochila, which includes 20 species arranged into three subgenera. We also conducted a biogeographic analysis that allowed us to identify the major events that shaped the currently disjunct distribution of the group. Our analyses were performed employing four major phylogenetic algorithms: equal and implied weight parsimony, maximum likelihood and Bayesian inference. Phylogenetic analyses, including 25 taxa (all 20 species in the genus plus five outgroups) and 37 characters, indicated that Mesochila is a monophyletic group composed of four strongly supported lineages, although no consensus was attained regarding relationships between lineages. Bayesian inference resulted in the less resolved topology, whereas implied weight parsimony yielded the most different tree when using a low k value (1). We present a new infrageneric classification for the group with the description of Mesochila (Neomesochila)subgen. nov. to accommodate M. (N.) brevipennis, M. (N.) drechseli, M. (N.) moraveci, and M. (N.) prepusula. Furthermore, we transfer M. (M.) distincta from M. (Eumesochila) back to M. (Mesochila). The biogeographical analysis suggested a South American origin for the group, in Chacoan/Paraná dominions (Atlantic rainforest/Cerrado biomes), with subsequent dispersions to Central America and Amazonia.

Phylogeny and Biogeography of Acaena (Rosaceae) and its Relatives: Evidence of Multiple Long-Distance Dispersal Events Across the Globe

Abstract— Acaena (Rosaceae) is the most complex and ecologically variable genus in Sanguisorbinae. Although it has been the subject of several taxonomic treatments, the largest phylogenetic analysis to date only sampled a small fraction of the total global diversity (five to seven out of 45 to 50 species). This study included most of the species to elucidate the phylogenetic relationships of Acaena and biogeographic patterns in Sanguisorbinae. Phylogenetic analyses of non-coding nuclear (ITS region) and chloroplast (trnL-F) DNA sequence markers using maximum likelihood and Bayesian analyses suggested that Acaena is a paraphyletic group with species of Margyricarpus and Tetraglochin nested within it. We identified strong support for eight subclades that are geographically or taxonomically structured. Nevertheless, the species-level relationships within subclades are still uncertain, which may be due to rapid diversification and lack of informative characters in the markers used. Sanguisorbinae, a primarily Southern Hemisphere clade, exhibits a classic Gondwana disjunct distribution. This current distribution is explained primarily by eight long-distance dispersal events. Our results suggested that Sanguisorbinae split into Cliffortia and Acaena around 13.6 mya. While Cliffortia diversified in southern South Africa, Acaena experienced several migration events in the Southern Hemisphere. Our estimation of the ancestral range suggested that Acaena likely originated in South Africa, followed by migration and subsequent diversification into southern South America. From there, the genus migrated to New Zealand, throughout the Andes, and to tropical areas in Central America, reaching as far north as California. Chile and New Zealand are the main sources of propagules for dispersal as well as the greatest diversity for the genus. The evolutionary relationships of species in Acaena combine a history of rapid diversifications, long-distance dispersals, and genetic variation within some taxa. Further research should be undertaken to clarify the infraspecific classification of A. magellanica.

Analysis of gut microbiota in three species belonging to different genera (Hemitragus, Pseudois, and Ovis) from the subfamily Caprinae in the absence of environmental variance.

This study aimed to identify the effects of host species on the gut microbial flora in three species (Hemitragus jemlahicus, Pseudois nayaur, and Ovis orientalis) from the subfamily Caprinae, by excluding the impact of environment factors. We investigated the differences in intestinal flora of three species belonging to Caprinae, which were raised in identical conditions. Fecal samples were collected from tahr, mouflon, and bharal, and the V3–V4 region of the 16S ribosomal RNA gene was analyzed by high‐throughput sequencing. The analysis of 16S rRNA gene sequences reveals that fecal samples were mainly composed of four phyla: Firmicutes, Bacteroidetes, Spirochaetes, and Proteobacteria. The most abundant phyla included Firmicutes and Bacteroidetes accounting for >90% of the bacteria, and a higher Firmicutes/Bacteroidetes ratio was observed in tahrs. Moreover, significant differences existed at multiple levels of classifications in the relative abundance of intestinal flora, differing greatly between species. Phylogenetic analyses based on 16S rRNA gene indicated that mouflon is closely related to bharal, and it is inconsistent with previous reports in the species evolutionary relationships. In this study, we demonstrated that the gut microbiota in tahr had a stronger ability to absorb and store energy from the diet compared with mouflon and bharal, and the characteristics of host–microbiome interactions were not significant.

Complete mitochondrial genome of Coscinodiscus granii (Coscinodiscophyceae, Bacillariophyta)

Coscinodiscus is a genus common in marine phytoplankton, with some species thought to have a significant negative ecological impact. However, the availability of their genome sequences is rather limited. Here, we assembled and annotated the first complete mitochondrial genome (mtDNA) of the species Coscinodiscus granii L.F.Gough 1905, as part of our efforts to gain a better understanding of the genetic characteristics of Coscinodiscus taxa at a genomic level. The circular mtDNA was 34,970 bp in length and encoded 60 genes, including 32 protein-coding genes (PCGs), 24 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and two conserved open reading frames (orfs). The overall GC content of C. granii mtDNA was 24.30%, which was slightly lower than that of C. wailesii (25.00%), the first species in the genus Coscinodiscus whose mtDNA has been reported, and higher than that of Melosira undulata (21.60%), the first species in the class Coscinodiscophyceae whose mtDNA has been reported. As expected for congeneric species, phylogenetic analysis using concatenated amino acid sequences of 27 shared PCGs suggested that C. granii has a closer evolutionary relationship with C. wailesii. Coscinodiscus was found to be monophyletic in the phylogeny. The complete mtDNAs of more Coscinodiscus species will facilitate the exploration of the evolutionary relationships of species in the Class Coscinodiscophyceae.

Phylogenetic regionalization of tree assemblages reveals novel patterns of evolutionary affinities in the Atlantic Forest

AbstractAimWe used a phylogenetic approach to group assemblages of woody plant into major vegetation units in the Atlantic Forest, thus for the first time incorporating information on species evolutionary relationships into a bioregionalization of this critical hotspot. A phylogenetic regionalization will provide a spatially explicit framework for answering many basic and applied questions in biogeography, ecology and conservation.LocationAtlantic Forest.TaxonAngiospermsMethodsOur data set comprises 614 genera and 116 families, spread over 1,755 assemblages. To place assemblages in a multivariate evolutionary composition space, we used a phylogenetically informed ordination analysis, and to determine what the main phylogenetic groups of assemblages were, we used K‐means clustering based on phylogenetic dissimilarity of assemblages. To quantify how well environmental variables distinguish the phylogenetic groups found, we implemented classification tree approaches. Then, to explore the evolutionary turnover between the phylogenetic groups, we calculated phylogenetic beta diversity. Finally, we determined the lineages that are most strongly associated with individual phylogenetic groups using an indicator analysis for lineages.ResultsOur analyses suggest that there are seven principal groups, in terms of evolutionary lineage composition, in the Atlantic Forest. The greatest turnover of phylogenetic lineage composition separates tropical evergreen rain forest and semideciduous assemblages from subtropical and highland assemblages. The mixed subtropical forest showed the lowest phylogenetic compositional similarity values with other groups. Tropical rain forest had the highest number of significant indicator lineages, and the highest values of the indicator statistic for lineages.Main conclusionsWe found that the most pronounced evolutionary division separates southern and highland tree assemblages from those occurring under more tropical climates and at lower elevations. Our phylogenetic analyses point to an environmentally driven compositional division, likely based on the regular occurrence of freezing versus non‐freezing temperatures. Precipitation and edaphic regimes that assemblages experience had less definitive effects on their evolutionary lineage composition.

A new graph-theoretic approach to determine the similarity of genome sequences based on nucleotide triplets

Methods of finding sequence similarity play a significant role in computational biology. Owing to the rapid increase of genome sequences in public databases, the evolutionary relationship of species becomes more challenging. But traditional alignment-based methods are found inappropriate due to their time-consuming nature. Therefore, it is necessary to find a faster method, which applies to species phylogeny. In this paper, a new graph-theory based alignment-free sequence comparison method is proposed. A complete-bipartite graph is used to represent each genome sequence based on its nucleotide triplets. Subsequently, with the help of the weights of edges of the graph, a vector descriptor is formed. Finally, the phylogenetic tree is drawn using the UPGMA algorithm. In the present case, the datasets for comparison are related to mammals, viruses, and bacteria. In most of the cases, the phylogeny in the present case is found to be more satisfactory as compared to earlier methods.

An integrative approach to the study of Helicotylenchus (Nematoda: Hoplolaimidae) Colombian and Brazilian populations associated with Musa crops.

In total, 10 populations of Helicotylenchus associated with Musa spp., six from Colombia, and four from Brazil were identified to the species level. Morphological and morphometric data were recorded for each population, performed a principal components analysis (PCA), a conglomerate, along with consensus sequences of D2 to D3 expansion segment of the large subunit of ribosomal DNA (28S) for different populations. Identify of species were performed using the basic local alignment search tool (BLAST), and the evolutionary relationships of species were explored using a phylogeny study. Four species of Helicotylenchus were identified based on morphological and morphometric data: H. multicinctus, H. dihystera, H. erythrinae, and H. californicus. PCA and conglomerate analysis clearly separated these species. BLAST and phylogenetic analysis confirmed the presence of these species associated with Musa spp. crops. This is the first report of these species in Colombia through integrative taxonomy.

An approximation algorithm for genome sorting by reversals to recover all adjacencies

Genome rearrangement problems have been extensively studied for more than two decades, intended to understand the species evolutionary relationships in terms of the long range genetic mutations at the genome level. While most earlier studies focus on the simplified genomes ignoring gene duplicates, thousands of whole genome sequencing projects reveal that a genome typically carries multiple gene duplicates distributed in various ways along the genome. Given a source genome and a target genome such that one is a re-ordering of the genes in the other, we measure the evolutionary distance by the minimum number of reversals applied on the source genome to recover all the gene adjacencies in the target genome. We define this optimization problem as sorting by reversals to recover all adjacencies, or SBR2RA in short. We show that SBR2RA is APX-hard and uncover some similarities and differences to the classic counterpart, the sorting by reversals problem. From the approximability perspective, we present a \(2 \alpha \)-approximation algorithm, where \(\alpha \in [1, 2]\) is the best approximation ratio for a related optimization problem which is suspected to be NP-hard.

Tongues on the EDGE: language preservation priorities based on threat and lexical distinctiveness.

Languages are being lost at rates exceeding the global loss of biodiversity. With the extinction of a language we lose irreplaceable dimensions of culture and the insight it provides on human history and the evolution of linguistic diversity. When setting conservation goals, biologists give higher priority to species likely to go extinct. Recent methods now integrate information on species evolutionary relationships to prioritize the conservation of those with a few close relatives. Advances in the construction of language trees allow us to use these methods to develop language preservation priorities that minimize loss of linguistic diversity. The evolutionarily distinct and globally endangered (EDGE) metric, used in conservation biology, accounts for a species’ originality (evolutionary distinctiveness—ED) and its likelihood of extinction (global endangerment—GE). Here, we use a similar framework to inform priorities for language preservation by generating rankings for 350 Austronesian languages. Kavalan, Tanibili, Waropen and Sengseng obtained the highest EDGE scores, while Xârâcùù (Canala), Nengone and Palauan are among the most linguistically distinct, but are not currently threatened. We further provide a way of dealing with incomplete trees, a common issue for both species and language trees.

Evolutionary distinctness of Important Bird Areas (IBAs) of Sri Lanka: Do the species-rich wet zone forests safeguard Sri Lanka’s genetic heritage?

Different components of biodiversity cannot be treated equally due to the limitations of knowledge and resources, and the heterogeneity in the distribution of biodiversity in the landscape. Therefore, biodiversity should be prioritized in effective site-based conservation. Parameters related to ecology, sociology and economics are primarily used for this prioritization process. Genetic and evolutionary history is broadly ignored. Using Important Bird Areas (areas of high avian diversity or density, defined based on several key criteria of species richness and abandons) as a model, here we attempted to use several key evolutionary tools in biodiversity prioritization with the aim of testing their applicability in an island nation where evolutionary relationships of species are yet to be fully appreciated. We developed a DNA-based phylogenetic tree for the 342 total species of birds recorded in Sri Lanka’s 71 IBAs. We used DNA sequence archives at www.birdtree.org for closely-related crown nodes of Sri Lankan species and higher-order phylogenetic backbone for represented taxonomic orders to construct the phylogenetic tree. Using this tree, we calculated the Phylogenetic Diversity (PD), Evolutionary Distinctness (ED) and the extinction risk of deep lineages (EDGE scores) for each IBA. Batrachostomus moniliger (Ceylon Frogmouth) is the most ED species while Otus thilohoffmanni (Serendib Scopes-owl) is the most EDGE species for Sri Lanka. Sri Lanka’s premier dry zone National Parks, Yala, Bundala and Udawalawe are the top ranked IBAs in PD, ED and EDGE scores. Except Sinharaja MAB Reserve and Knuckles, all other wet zone IBAs, which are characterized by their high endemicity and biodiversity were not ranked among the top ten IBAs for above evolutionary parameters. Mixing of both continental and insular lineages in the dry zone due to its proximity to mainland, the presence of wetlands that support migratory lineages and the movement of wet zone taxa along the riverine forests towards the dry zone could have increased the PD and ED scores in dry zone IBAs. However, wet zone IBAs are better at keeping the avian genetic composition that is unique to Sri Lanka by holding most of the avian endemics. For islands like Sri Lanka, global indices do not reflect the local evolutionary and conservation status. Effective site-based conservation programs that are aimed at preventing local extinctions therefore, must recognize the heterogeneity of biodiversity across the landscape. Our results show that the evolutionary parameters such as PD, ED and EDGE score are effective tools to refine the conventional indices used in habitat prioritization for Sri Lanka.

Resident-invader phylogenetic relatedness, not resident phylogenetic diversity, controls community invasibility.

A central goal of invasion biology is to elucidate mechanisms regulating community invasibility. Darwin's naturalization hypothesis, one of the oldest hypotheses in invasion biology, emphasizes the importance of phylogenetic relatedness (PR) between resident and invader species for predicting invasibility. Alternatively, a recent extension of the diversity-invasibility hypothesis predicts that phylogenetic diversity (PD) of resident communities influences invasibility. Neither of these hypotheses has undergone rigorous experimental testing, and the relative contributions of PR and PD to community invasibility are unknown, in part because their effects tend to be confounded with each other. Here we consider both perspectives together by independently manipulating PR and PD in laboratory bacterial assemblages. We found that, although invader abundance decreased significantly as PR increased, it was unaffected by PD. Likewise, we found that resident-invader functional similarity, not functional diversity of resident communities, was a significant predictor of invader abundance. Nevertheless, invader abundance was better predicted by PR than by functional similarity. These results highlight the importance of considering species evolutionary relationships, especially the PR between resident and invader species, for the prediction, prevention, and management of biological invasions.

Interspecific tests of allelism reveal the evolutionary timing and pattern of accumulation of reproductive isolation mutations.

Despite extensive theory, little is known about the empirical accumulation and evolutionary timing of mutations that contribute to speciation. Here we combined QTL (Quantitative Trait Loci) analyses of reproductive isolation, with information on species evolutionary relationships, to reconstruct the order and timing of mutations contributing to reproductive isolation between three plant (Solanum) species. To evaluate whether reproductive isolation QTL that appear to coincide in more than one species pair are homologous, we used cross-specific tests of allelism and found evidence for both homologous and lineage-specific (non-homologous) alleles at these co-localized loci. These data, along with isolation QTL unique to single species pairs, indicate that >85% of isolation-causing mutations arose later in the history of divergence between species. Phylogenetically explicit analyses of these data support non-linear models of accumulation of hybrid incompatibility, although the specific best-fit model differs between seed (pairwise interactions) and pollen (multi-locus interactions) sterility traits. Our findings corroborate theory that predicts an acceleration (‘snowballing’) in the accumulation of isolation loci as lineages progressively diverge, and suggest different underlying genetic bases for pollen versus seed sterility. Pollen sterility in particular appears to be due to complex genetic interactions, and we show this is consistent with a snowball model where later arising mutations are more likely to be involved in pairwise or multi-locus interactions that specifically involve ancestral alleles, compared to earlier arising mutations.

К изучению рода Auricularia (Auriculariales, Basidiomycota) в России

The paper covers the study of the genus Auricularia in Russia. The taxonomic history of the genus and problems of its morphological systematics are described in details. The evolutionary relationships of species and species complexes were revealed based on a comparative study of the nucleotide sequences of nrDNA (ITS, rpb2). The occurrence of A. auricula-judae only in European of Russia part was confirmed by molecular data, whereas the morphologically similar species A. americana had the Far Eastern distribution in Russia. In total, 7 taxa of Auricularia have so far been recorded from Russia: known species A. mesenterica, A. minor, A. cornea, A. americana, A. auricula-judae, newly described species — A. villosula and undescribed Auricularia sp. An identification key to the studied Auriculariaspecies and its morphological descriptions are also provided.

Trees, thickets, or something in between? Recent theoretical and empirical work in cultural phylogeny

Anthropology has always had as one of its goals the explanation of human cultural diversity across space and through time. Over the past several decades, there has been a growing appreciation among anthropologists and other social scientists that the phylogenetic approaches that biologists have developed to reconstruct the evolutionary relationships of species are useful tools for building and explaining patterns of human diversity. Phylogenetic methods offer a means of creating testable propositions of heritable continuity – how one thing is related to another in terms of descent. Such methods have now been applied to a wide range of cultural phenomena, including languages, projectile points, textiles, marital customs, and political organization. Here we discuss several cultural phylogenies and demonstrate how they were used to address long-standing anthropological issues. Even keeping in mind that phylogenetic trees are nothing more than hypotheses about evolutionary relationships, some researchers have argued that when it comes to cultural behaviors and their products, tree building is theoretically unwarranted. We examine the issues that critics raise and find that they in no way sound the death knell for cultural phylogenetic work.

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot.

BackgroundSpecies number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.Methodology/Principal FindingsHere we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.Conclusions/SignificanceAs first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.

Phylogenetic inferences in Avena based on analysis of FL intron2 sequences

The development and application of molecular methods in oats has been relatively slow compared with other crops. Results from the previous analyses have left many questions concerning species evolutionary relationships unanswered, especially regarding the origins of the B and D genomes, which are only known to be present in polyploid oat species. To investigate the species and genome relationships in genus Avena, among 13 diploid (A and C genomes), we used the second intron of the nuclear gene FLORICAULA/LEAFY (FL int2) in seven tetraploid (AB and AC genomes), and five hexaploid (ACD genome) species. The Avena FL int2 is rather long, and high levels of variation in length and sequence composition were found. Evidence for more than one copy of the FL int2 sequence was obtained for both the A and C genome groups, and the degree of divergence of the A genome copies was greater than that observed within the C genome sequences. Phylogenetic analysis of the FL int2 sequences resulted in topologies that contained four major groups; these groups reemphasize the major genomic divergence between the A and C genomes, and the close relationship among the A, B, and D genomes. However, the D genome in hexaploids more likely originated from a C genome diploid rather than the generally believed A genome, and the C genome diploid A. clauda may have played an important role in the origination of both the C and D genome in polyploids.

Proposals for classification methods dedicated to biological data

The number of available genomic sequences is growing very fast, due to the development of massive sequencing techniques. Sequence classification is needed and contributes to the assessment of gene and species evolutionary relationships. Classification methods are thus necessary to carry out these identification operations in an accurate and fast way. We develop a classification method dedicated to homologous sequence family databases, allowing the attribution of a new sequence to a cluster using similarity measures. We used this classification method to implement two applications, Homologous Sequence Identification (HoSeqI) and MultiHoSeqI. Lately, we developed a chimera detection method and implemented an application, Chimeric Sequence Identification (ChiSeqI) to automate the processes of classification of specific biological data, the bacterial 16S ribosomal RNA sequences, and of detection of chimeric sequences.