Cladistics最新文献

Life radiated in aquatic environments worldwide. Brackish waters, however, seemingly hinder diversification as their physiologically demanding environmental stochasticity favours transient and impoverished communities assembled from widespread generalist species. Yet, the Ponto-Caspian basin (Aral, Azov, Black and Caspian seas) defies this rule, its rich endemic biota representing the only brackish biodiversity hotspot on Earth. Nevertheless, its origin, age and biogeographic history remain contentious. Here, we reconstruct the evolutionary timescale and diversification dynamics of gammaroidean amphipods, the most diverse Ponto-Caspian faunal group. We show that amphipods started radiating 11 Myr ago when the Paratethys Sea became isolated from the global ocean and stable brackish conditions ensued. Diversification proceeded steadily despite the subsequent water level fluctuations that persisted towards the end of the Miocene. The final Paratethyan Pliocene dissolution into the isolated Black and Caspian seas, followed by their brief intermittent connections during the mid-late Pleistocene, sparked further diversification via dispersal-vicariance pulses. Lastly, a five times faster mitochondrial substitution rate was estimated relative to the typical arthropod rate. Despite the significant geo-environmental upheaval, amphipods show a remarkably continuous evolutionary history shaped by a unique interplay between marine and inland biogeographical processes, highlighting that brackish water can support diverse and enduring evolutionary radiations.

Oedipodinae (Acrididae) is a species-rich and globally distributed subfamily of grasshoppers, currently comprising 807 valid species assigned to 138 genera in 16 tribes. Resolving the phylogeny of Oedipodinae has proven difficult, owing to their extensive species diversity, disjunct geographic distribution and the scarcity of informative molecular markers. To establish a more robust phylogenetic framework, we conducted a mitochondrial phylogenomic analysis of 143 mitogenomes. This dataset includes 103 Oedipodinae species representing all 16 currently recognized tribes, of which 86 mitogenomes from nine tribes were newly sequenced in this study. Divergence times and ancestral areas were also inferred to investigate evolutionary trends within this subfamily. The phylogenetic analysis supports the monophyly of nine tribes within Oedipodinae: Acrotylini, Anconiini, Bryodemini, Chortophagini, Machaerocerini, Psinidiini, Trilophidiini, Trimerotropini and Tropidolophini. Based on these results, we propose taxonomic revisions. The tribe Tropidolophini Otte, 1995 is removed from Oedipodinae and provisionally placed in Acrididae, incertae sedis. In addition, the genus Ceracris Walker, 1870 is removed from Parapleurini and placed in Acridinae, incerta sedis. Divergence time estimation suggests that Oedipodinae originated during the Eocene, approximately 49 Mya. The biogeographic reconstruction supports a Holarctic origin of Oedipodinae, with the Palaearctic region as the principal center of diversification, followed by subsequent dispersal into North America, the Oriental region and Africa. These patterns highlight the role of dispersal in shaping the global distribution of the subfamily.

We herein present a phylogenetic and population genetic analysis of a Tasmanian Mountain Shrimp clade, based on ddRAD and cytochrome oxidase subunit-1 data sets. Our data show that the morphologically well-delineated and widespread Anaspides richardsoni Ahyong, 2016 is paraphyletic with respect to four other species (A. eberhardi Ahyong, 2016, A. spinulae Williams, 1965 and two undescribed species). These four species all form discrete (monophyletic) lineages and exhibit clear morphological distinctions in relation to A. richardsoni and to one another. However, we detect signals of introgression between some populations of A. richardsoni, A. spinulae and an undescribed species. We also find two instances of syntopic occurrences without evidence for interbreeding. Also, A. richardsoni is split into several allopatric and comparably old lineages. Anaspides spinulae from Lake St. Clair, however, seems to be a young species that might have differentiated only after the last glacial maximum of central Tasmania (22 000–17 000 years ago). Moreover, we analyse the present population structure and recolonization of the Central Plateau and Western Mountain Ranges in regard to their glacial history. We distinguish several glacial refugia and show that the recolonization most likely occurred only from one or two of these.

The era of molecular systematics has had a tremendous impact on taxonomy, with the increasing availability of phylogenetic trees allowing the recircumscription of higher taxa, particularly through the application of the monophyletic principle. Whether molecular phylogenetics has caused taxonomic instability has not been objectively assessed. Here, we used the flora of New Caledonia to monitor the evolution of the taxonomy of a tropical flora through four time windows from 1911 to 2024. This Pacific island's flora is renowned for its high species richness and endemism and includes 42% of the currently accepted flowering plant families, including the endemic Amborellaceae. We found that taxonomic changes, including changes in genera and families, have always been common, even in the pre-molecular era. If family changes were more important between 2001 and 2012, following the application of the classification proposed by the Angiosperm Phylogeny Group (APG), changes since then have been reduced to almost zero. Since the latest versions of the APG classification are almost identical, it seems that this classification can now be safely applied outside the world of scientific publication. Greater efforts are needed to achieve a stable generic classification, where collectives similar to APG could target such goals.

Cynoglossoideae is the largest subfamily of Boraginaceae, and Cynoglosseae is its largest tribe, with the eponymous subtribe Cynoglossinae (ca. 200 spp.) being the most taxonomically challenging group. Cynoglossum remains problematic, especially regarding its relationships to a range of satellite genera (e.g. Paracaryum, Lindelofia, Mattiastrum, Rindera). We aim to elucidate the evolutionary relationships among Cynoglossinae and their historical biogeography by analyzing ca. 80 species of the subtribe. We employed PacBio sequencing of four plastid markers (trnL–trnF, rps16, rpl16, trnK–psbA) and one nuclear marker (nrITS), and reconstructed molecular phylogenies utilizing maximum parsimony, maximum likelihood, and Bayesian inference. Our analyses demonstrated a more highly resolved tree for the major clades of Cynoglossinae, strongly supporting a broader taxonomic circumscription of Cynoglossum. Our biogeographic reconstruction suggests that Cynoglossinae diverged from its sister group, Bothriosperminae, during the late Oligocene in East Asia and likely originated during the middle Miocene in an extensive area encompassing East Asia and the Irano-Turanian region. The lineage rapidly diversified, expanding its range towards Europe, including the Mediterranean region, and Africa, as well as southward to Australia from the middle Miocene to Pleistocene. The data indicate that the epichorous fruits of Cynoglossum have significantly contributed to multiple long-distance dispersal events and subsequent diversification.

Understanding when and how habitat transitions occurred is essential for a comprehensive insight into the succession of marine ecosystem and biodiversity. Here we investigated the evolutionary process of an ancient, widespread and ecologically diversified lineage of marine benthic fauna, the ghost and mud shrimps (Decapoda: Axiidea). To reconstruct a robust, time-calibrated phylogeny of this intractable group, we sampled more comprehensively than in previous studies and utilized three types of sequencing data: Sanger, genome-skimming and ultra-conserved elements (UCEs). The UCEs tree supports a monophyletic Axiidea sister to the ‘Gebiidea + (Brachyura + Anomura)’ clade. Our findings reveal the monophyletic status of Callianideidae and Micheleidae, whereas Axiidae and Strahlaxiidae as presently understood are shown to be non-monophyletic. Axiidae s.s. is now restricted to four genera, Strahlaxiidae to one genus, with most former “axiid” genera reclassified under Calocarididae. We determine that crown axiidean shrimps diverged in the Middle Triassic, with a significant habitat transition from epibenthic to endobenthic during the Middle to Late Jurassic, possibly in response to environmental changes and available ecological niche. We hypothesize that the extreme morphological and behavioural adaptations to the obligate/subsurface burrowing life facilitated the radiation and diversification of ghost shrimps, despite some instances of adaptive convergence.

Vesicomyid clams in the subfamily Pliocardiinae are chemosymbiotic and specific to deep-sea chemosynthetic ecosystems with wide bathymetric and geographic ranges, making them a suitable model to study molecular adaptation and biogeography. Its phylogeny, however, still remains contentious due to limited molecular markers. Here, we elucidate the evolutionary relationships among pliocardiines based on phylogenomics data. By testing a wide range of matrices with methods including maximum likelihood, maximum parsimony, Bayesian inference, and a coalescent approach, we present a robust phylogenomic tree at the genus level supported by AU-test and GLS analyses. We revise the genus-level taxonomy of pliocardiines updating from Johnson et al. (Syst. Biodivers. 2017, 15, 346) synonymising a number of species in the “gigas-group” with Archivesica—also supported by a mitogenome phylogeny. Our fossil-calibrated tree based on the phylogenomic backbone reveals that Pliocardiinae originated earlier than [41.06, 42.00] Ma in the middle Eocene, while its diversification has been concurrent with global climatic cooling events. Ancestral state reconstruction analyses found two independent invasions into the abyssal zone, and a shift from harbouring the Ca. Ruthia symbionts to Ca. Vesicomyosocius symbionts. Our results present a solid backbone for future investigations into molecular adaptation, biogeography and symbiosis in this fascinating group of molluscs.

The hylid genus Bokermannohyla comprises 31 species distributed across the Atlantic Forest, Caatinga and Cerrado domains, and their transition zones in Brazil. These species are currently included in three species groups (the B. circumdata, B. martinsi and B. pseudopseudis groups). In this paper, we present the results of a molecular phylogenetic analysis that includes 30 of the 31 species of the genus. Our results indicate that the currently recognized species groups are polyphyletic. To remedy this, we recognize four well-supported species groups—the B. astartea, B. izecksohni, B. nanuzae and B. oxente groups—and leave B. alvarengai, B. saxicola, B. ibitiguara and B. sazimai unassigned to any group. The new phylogenetic hypothesis allowed us to examine the evolution of oviposition sites, revealing that oviposition in water retained in restricted aquatic spaces (rock crevices, natural or male-modified basins or male-excavated tunnels) evolved from oviposition in streams during the evolutionary history of Bokermannohyla. Finally, our results support the hypothesis that this genus initially diversified in the Campos Rupestres (highland rocky fields) of the Serra do Espinhaço, with a subsequent, major diversification in the Atlantic Forest.

Delineating Areas of Endemism (AEs) is crucial for identifying priority areas for biodiversity conservation in a spatial planning framework. Endemicity Analysis in the NDM/VNDM software is one of the primary methodologies for its delineation. Larger grid sizes have been employed to yield higher endemicity scores for AEs, recovering more endemic species and enhancing their conservation appeal. Compiling a robust geographic distribution dataset for 399 freshwater fish species from Southern Brazil, we identified AEs by conducting endemicity analyses with three different grid sizes. We also developed a spatial conservation Priority Index incorporating three grid-size-dependent attributes. We identified 153 AEs, each varying in endemicity scores, species richness, and threatened species. These variations were influenced by the analysed grid size and spatial overlap with specific freshwater ecoregions. The recovered AEs show freshwater fish distribution patterns corroborating significant vicariance events and faunal exchanges between river basins in distinct bordering ecoregions. We found an almost 50% reduction in spatial area when ranking Endemicity and Priority Index scores. This finding demonstrates the effectiveness of the Priority Index in highlighting similar sets of endemic, sympatric, and threatened species within smaller areas. This approach can effectively reconcile attributes easily extracted from the NDM/VNDM program when prioritizing spatial conservation.

Compared to plastid genomes, plant mitochondrial genomes have been less frequently used for species discrimination and phylogenetic studies due to assembly challenges, lower substitution rates and rapid structural evolution. However, this study demonstrates that mitochondrial genome fragments can be valuable for both molecular species identification and phylogenetic analysis in grasses of the tribe Stipeae. To explore this potential, we first assembled the complete mitochondrial genome of Nassella tenuissima—the first fully described mitogenome in Stipeae—which served as a reference for selecting 29 aligned mitochondrial genome fragments totalling 139 680 bp. These fragments were then analysed across 49 representatives of the tribe, including 43 Stipa species and six other taxa. The mitochondrial fragments achieved a species discrimination efficiency of 75%, slightly exceeding the 71% efficiency observed for plastid super-barcodes. Additionally, comparative phylogenetic analyses using plastid and mitochondrial genomes underscored the utility of mitochondrial data in resolving phylogenetic relationships within Stipeae. Our findings provide a valuable resource for future research in transcriptomics, comparative genomics, phylogenomics and phylogeography of grasses.