Cladistics最新文献

Millions of species remain undescribed, and each eventually will require a species description with a diagnosis. Yet, we lack software that can derive state-specific and contrastive molecular diagnoses and allows the user to validate them based on all available sequences for the taxon under study. Here we introduce UITOTO, which addresses this shortcoming by facilitating the identification, testing, and visualization of diagnostic molecular combinations (DMCs). The software uses a weighted random sampling algorithm based on the Jaccard Index for building candidate DMCs. It then selects DMCs with the highest specificity stability, meeting user-defined thresholds for exclusive character states. If multiple optimal DMCs are identified, UITOTO derives a majority-consensus DMC. To verify whether the generated DMCs are contrastive, UITOTO includes a validation module that tests DMCs against databases, efficiently handling thousands of aligned or unaligned sequences. We here, not only propose UITOTO, but also assess its performance relative to other software that can derive DMCs (e.g. MOLD). For this purpose, we analyse three large empirical datasets: (i) Megaselia (Diptera: Phoridae: 69 species, 2229 training and 30 289 testing barcodes); (ii) Mycetophilidae (Diptera: 118 species, 1456 training, 60 349 testing barcodes); and (iii) European Lepidoptera (49 species, 591 training, 21 483 testing barcodes). Based on classification metrics (e.g. F1 Score), UITOTO's DMCs outcompete DMCs from other software. We furthermore provide guidelines for generating molecular diagnoses and a user-friendly Shiny App-GUI that includes a module for obtaining publication-quality DMC visualizations. Overall, our study confirms that the biggest challenge for generating molecular and morphological diagnoses is similar: balancing specificity and length; short diagnoses often lack specificity, while excessively long DMCs are often so specific that they do not accommodate intraspecific variation.

Advances in Macrodasyida (Gastrotricha) phylogenetics, fuelled by new species discoveries and molecular data, are reshaping taxonomic classifications. Molecular analyses suggest polyphyly in Cephalodasyidae and Macrodasyidae, yet insufficient sampling continues to obscure precise relationships. Our study seeks to enhance the resolution of Macrodasyida's internal phylogeny through expanded taxonomic and molecular sampling. We obtained 63 new sequences from 21 Macrodasyidan species, integrating them with published data. Our dataset includes representatives from nine Macrodasyida families and 21 genera, alongside two chaetonotidans. We analysed the concatenated sequences of three genes (18S, 28S rRNA, COI mtDNA) from 51 terminals using Maximum Parsimony, Maximum Likelihood and Bayesian Inference. Our findings confirm the polyphyly of Cephalodasyidae. Dolichodasys and Paradasys cluster with Redudasyidae, while Cephalodasys and Mesodasys form unrelated lineages. Cephalodasys mahoae is nested within Paradasys rather than Cephalodasys, suggesting an original misidentification. The phylogenetic placement of Pleurodasys remains uncertain. Macrodasyidae is non-monophyletic, with Urodasys forming an independent lineage. The first molecular data ever obtained for Dendrodasys hint that the family Dactylopodolidae is likely polyphyletic as well. We propose an updated classification of Macrodasyida, introducing Mesodasyidae fam. nov., Urodasyidae fam. nov. and Paraurodasys gen. nov. Furthermore, we reassign Dolichodasys and Paradasys to Redudasyidae and Cephalodasys mahoe to Paradasys.

The dispersal pattern of tetrapods across Pangaea is a crucial problem for understanding Permian terrestrial ecosystems. This study describes a rare cross-equatorial record of a dicynodont genus. New fossil material from China can be referred to Dinanomodon, a genus formerly only known from South Africa, although it represents a new species-D. guoi. To investigate the divergence of Bidentalia, a newly assembled dataset was employed to perform maximum parsimony analysis, Bayesian inference and the first tip-dating analysis within the anomodonts. Considering other tetrapod occurrences, we suggest that frequent cross-equatorial dispersal of tetrapods occurred during the Lopingian (late Permian). Based on tetrapod distribution and paleoclimate data, precipitation, rather than temperature, probably represents the major ecological factor influencing corridors for dispersal along the eastern margin of Pangaea.

The Hengduan Mountains (HDM), a biodiversity hotspot in Southwest China, harbour numerous endemic taxa whose diversification has been driven by the complex geological history of this region. This study investigates the diversification of the katydid genus Sichuana, endemic to the HDM, integrating mitochondrial genomics, morphology and biogeography. We sequenced complete mitochondrial genomes of all known geographic populations of Sichuana, revealing four major clades diverging during the Late Miocene (5.06-8.37 Ma). Orogeny-driven vicariance fragmented ancestral populations, while unstable barriers may facilitate mitochondrial introgression, as evidenced by paraphyletic lineages contrasting with distinct morphologies. We describe five new species (S. brevicerca sp. nov., S. fortidens sp. nov., S. qiuzhi sp. nov., S. luqiaoensis sp. nov. and S. pseudomagna sp. nov.) and two subspecies (S. pseudomagna pseudomagna subsp. nov. and S. pseudomagna borealis subsp. nov.), highlighting the taxonomic challenges posed by discordance between mitochondrial DNA-based phylogenies and morphological classifications. This study demonstrates that orogeny-driven vicariance dominates speciation in low-dispersal insects, but transient gene flow complicates species delimitation. Our findings advocate for integrative taxonomy in biodiversity hotspots and highlight the HDM as a model system for studying biogeographic complexity.

Sphaenorhynchini comprises 15 species of small, greenish treefrogs from cis-Andean South America. Araujo-Vieira et al. (2019, A total evidence analysis of the phylogeny of hatch-faced treefrogs [Anura: Hylidae: Sphaenorhynchus], Cladistics 35, 469-486) conducted a total evidence parsimony analysis of DNA sequences and phenotypic data, corroborating the monophyly of Sphaenorhynchus, identifying three species groups, and placing the unusual species S. pauloalvini as sister to all other species. On this basis and numerous phenotypic differences, Araujo-Vieira et al. (2020, A new genus of lime treefrogs [Anura: Hylidae: Sphaenorhynchini], Zool. Anz. 286, 81-89) erected the genus Gabohyla for S. pauloalvini. Subsequently, Pereira et al. (2022, The dispersal between Amazonia and Atlantic Forest during the Early Neogene revealed by the biogeography of the treefrog tribe Sphaenorhynchini [Anura, Hylidae], Ecol. Evol. 12, e8754) performed a Bayesian analysis of a subset of Araujo-Vieira et al.'s (2019) molecular data and found G. pauloalvini to be nested within Sphaenorhynchus, which they attributed exclusively to choice of analytical method. To test this claim, we performed parsimony and Bayesian analyses of the total evidence dataset and the complete and partial molecular datasets with either the entire outgroup sample or a single terminal. The topology from the Bayesian analysis of the complete dataset is almost identical to that of Araujo-Vieira et al. (2019), with G. pauloalvini sister to Sphaenorhynchus, thereby refuting Pereira et al.'s claim. Moreover, the monophyly of Sphaenorhynchus sensu stricto was remarkably robust, being recovered in all analyses except the Bayesian analysis of the partial molecular dataset with a single outgroup terminal (i.e., the analysis performed by Pereira et al.). In addition to supporting the continued recognition of Gabohyla, our results underscore the importance of considering not only the choice of analytical method, but also character and taxon sampling-including outgroup sampling-before rejecting prior findings.

The reliability of biogeographic analyses depends strongly on the type and quality of species distribution data. We compared point-based occurrence records and polygonal range maps for 160 species of the lizard genus Liolaemus, assessing their influence on the identification of areas of endemism across three spatial scales using endemicity analysis. Our results show that range maps consistently overestimate distributions, often identifying broad endemic areas with low species overlap-patterns likely inflated by commission errors. In contrast, occurrence data yield fewer but more localized and compositionally distinct areas of endemism, especially at finer spatial scales, capturing spatial discontinuities and narrow-range endemism more effectively. Occurrence data also proved to be more sensitive to spatial scale, revealing fine-grained biogeographic patterns often missed by range maps, particularly in mountainous or environmentally heterogeneous regions. Despite potential biases from uneven sampling, occurrence data provide a more ecologically meaningful representation of endemism, especially for habitat specialists or narrowly distributed species. These findings highlight that data choice significantly affects the detection of endemism, with direct implications for biodiversity assessments and conservation planning. Researchers should carefully consider data sources in light of their study taxa's ecological and geographic traits to ensure robust and scale-appropriate analyses.

Passive tectonic uplift of populations is being discussed in a growing number of studies from many regions around the world, usually for areas that have undergone dramatic uplift in fold mountains (orogens). It is also proposed in belts of uplift along the margins ("shoulders") of rifts, as in south-eastern Brazil, West Africa and the rift mountains of Central and East Africa. Many groups show signs of having been left stranded inland with the retreat of inland epicontinental seas in the Cretaceous, consistent with the long-term persistence and passive uplift of populations in situ. Passive uplift provides a mechanism in which groups are elevated and also a mode of speciation that can help explain the anomalous, high diversity of areas such as the Andes ("Humboldt's enigma"). We suggest that one focus of future research could be on the location of elevational anomalies in species distributions. Studying these will require good information on the three-dimensional distribution of species, and this is still lacking for most groups. If these data were available, it would be possible to use niche models to identify populations at anomalous elevations.

As our understanding of abiotic factors continues to grow, along with insights into the biological traits of organisms, so too does the sophistication of studies exploring global diversification and spatio-temporal distribution patterns. The global distribution of coastal Cafius rove beetles, combined with the endemic distribution patterns observed in its subclades, suggests repeated colonization of new regions via ocean surface currents, followed by local diversification and speciation. We reached these conclusions by reconstructing the Cafius phylogeny and a time-calibrated Cafius phylogeny, then conducting a spatio-temporal biogeographic analysis. Our study is based on sequences from 10 genetic loci, including six nuclear and four mitochondrial genes (6891 bp). Our findings support the monophyly of Cafius, with an estimated origin in the early Miocene (17.91 Ma) along the coasts of Europe and Australia. From this origin, transoceanic dispersal events led to the colonization of the coasts. These patterns suggest that ancestral Cafius lineages initially migrated to continental coastlines, with subsequent vicariance and in situ speciation. The directionality of these colonization events closely aligns with global ocean surface current patterns and the geological and climatic history of the regions involved. Biological adaptations likely facilitated their survival and subsequent diversification in coastal habitats worldwide.

Family Rhinoceroidae exhibits a complex and debated phylogeny, with fossil records spanning over 50 million years. This study presents a comprehensive phylogenetic total-evidence analysis of Rhinocerotidae to date, integrating morphological, molecular, fossil and paleoclimatic data within maximum parsimony, maximum likelihood, Bayesian and time-calibrated frameworks. A matrix of 106 taxa and 534 morphological characters, including 11 newly defined ones, was assembled through systematic revision of previously ambiguous characters. In contrast to earlier studies, a fossil-based outgroup was selected in place of extant Tapirus to improve character polarity and reduce topological artefacts associated with distant outgroup choice. The resulting cladograms resolve longstanding conflicts in rhinocerotid systematics and identify many supported clades. Analyses of the studied clades revealed an association between lineage diversification and climatic thresholds, which appear to have mediated ecological turnover and the differential persistence of traits. The application of an integrative total-evidence approach illustrates the role of climatic and ecological filters in shaping the evolutionary trajectories of megafaunal lineages and contributes to broader methodological discussions in phylogenetics. The analytical framework developed provides a comparative model applicable to both extinct and extant taxa, reaffirming the value of rigorous cladistic methods in paleobiology and systematics.

Neoprocoela edentata is a fossil anuran collected in Scarritt Pocket, Patagonia, Argentina. This locality provided the first described pre-Neogene batrachofauna of South America, which is also one of the few known to include representatives of extant taxa. Neoprocoela edentata shows an unusual combination of characters, and it has alternatively been related to Bufonidae or to a polyphyletic assemblage including Calyptocephalellidae and Telmatobiidae. In this article, we redescribe the single specimen of N. edentata, complementing the examination with micro-CT scan reconstructions, and expanding its original description. This results in a combination of character states unique to Bufonidae, allowing us to confidently assign N. edentata to this family. Then, we performed a total evidence phylogenetic analysis, including molecular and osteological data, to evaluate the phylogenetic relationships of N. edentata within Bufonidae. This species was recovered in a strongly supported clade with the extant genus Nannophryne; thus, Neoprocoela is considered a junior synonym of this genus, retaining edentata as a valid species. Finally, considering the geographic and stratigraphic provenance of the fossil remains, we discuss its value as evidence of the early evolution of South American toads and as an absolute-age calibration point, something relatively unusual for neobatrachian fossil species of that age.