Cladistics最新文献

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.

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.

The subtribe Leptoboeinae (Gesneriaceae) has undergone numerous taxonomic revisions due to ambiguous generic boundaries, complicating conservation and utilization efforts. In this study, we employed transcriptomes from a representative clade within the subtribe to construct a low-copy nuclear (LCN) gene data set. Plastid genomes and LCN genes, assembled from 66 samples, were used to investigate the phylogenetic structure, reticulate evolution and divergence times among the species of this subtribe. Firstly, phylogenetic analysis revealed that Boeica is polyphyletic and identified a new genus, Crassicaulis, which forms a sister group to the remaining genera within the subtribe. Secondly, complex cytonuclear conflicts and gene tree incongruence at genus-level nodes were identified. Multiple lines of evidence revealed two reticulate evolutionary events within this lineage, suggesting that Boeica porosa and B. stolonifera, as well as Boeica enpingensis, underwent hybridization during their speciation processes. Finally, divergence time estimation revealed that most genera emerged between 17 and 12 Ma. This study provides a well-resolved phylogenetic framework for the subtribe Leptoboeinae, describes a new genus and elucidates the subtribe's intricate reticulate evolutionary history. Furthermore, we propose that the mid-Miocene East Asian monsoon played a pivotal role in the diversification of this lineage.

Phylogenomic data from enriched informative loci yield higher resolution insights for clarifying taxonomic relationships and reconstructing the evolutionary histories of complex taxa. Section Bromatorrhiza (Allium, Amaryllidaceae), a small taxon of 11 species, has long been plagued by taxonomic controversies and persistent, unresolved phylogenetic incongruence. Here, we collected transcriptome and plastome data from 34 samples representing multiple populations across all species in this section. From these, 1993 low-copy nuclear genes and 110 plastid genes were extracted for phylogenetic reconstruction. Integrating phylogenomic and morphological approaches, we investigated species relationships and the causes of phylogenetic discordance. Our results provide robust clarification of interspecific relationships and identify 10 diagnostic morphological traits in this section. The Allium hookeri Alliance (AHA) was resolved as a monophyletic clade comprising seven species. We elevated Allium hookeri var. muliense to species status, formally describing it as A. muliense, and newly describe a cryptic species as Allium xui Y. Wang, D.F. Xie & X.J. He, sp. nov. Furthermore, we demonstrate that extensive phylogenetic discordance within this section is primarily attributable to incomplete lineage sorting (ILS) and reticulate evolution. By synthesizing phylogenetic and morphological evidence, we propose refined taxonomic treatments. Our findings resolve long-standing taxonomic ambiguities and phylogenetic discordance in section Bromatorrhiza.

Scherotheca is amongst the most diverse earthworm genera within Lumbricidae, exhibiting striking ecomorphological radiation—from small epigeic-like forms to giant anecic species. Accurate systematics is critical for exploring such diversification. We sequenced 16 previously unrepresented species plus additional populations across their range for five molecular markers, inferring phylogenetic relationships via maximum likelihood, Bayesian inference and time-calibrated analyses, as well as ancestral area and character state reconstructions. Scherotheca was recovered as monophyletic, but previous subgeneric divisions were unsupported. With the addition of four new species, Scherotheca currently includes 56 species: Cryptic diversity within Scherotheca aquitania may increase this number upon further research. Biogeographic analyses supported a middle Eocene origin (~47 Mya) on the Corsica–Sardinia–Provence microplate, followed by westward expansion driven by paleogeographic events, such as Pyrenean uplift and marine introgressions. Multiple Corsican clades evolved independently, displaying morphological radiation under insular pressures. Ancestral reconstructions indicated the last common ancestor resembled the mid-sized Scherotheca portcrosana. The radiation of body size was particularly pronounced in Atlantic regions, likely shaped by ecological, climatic and biotic pressures. This study provides the most comprehensive evolutionary framework for Scherotheca, serving as a reference for further research on Western European earthworm diversification, functional trait evolution and biogeographic history.

The genus Merodon (Diptera: Syrphidae) is the most species-rich hoverfly genus in Europe. Recent studies have focused on resolving species-level taxonomy, species delimitation, or phenotypic traits analyses, but only a few authors have dealt with its intra-generic phylogenetic relationships. In this study, we compiled a dataset of adult morphological characters capturing the phylogenetically informative characters for the genus Merodon, as well as the most closely related co-tribal taxa. We also generated molecular data for a set of genes frequently used for molecular systematic studies of insects. Molecular and morphological datasets were analysed together to establish the formal subgeneric classification of Merodon using parsimony and maximum likelihood approaches. For the molecular dataset, the mitochondrial COI and nuclear 28S rRNA and 18S rRNA gene sequences were used, a total of 2947 bp. For the morphological dataset, 204 characters were analysed. The combined analysis involved 3151 characters and 80 taxa. Our analyses supported five subgenera within the genus Merodon described and diagnosed here: Albimerodon subgen. nov., Auremerodon subgen. nov., Avidumerodon subgen. nov., Desutumerodon subgen. nov., and Natamerodon subgen. nov.