Histopathological, molecular, and phylogenetic analyses of Echinococcus species isolated from humans in Mongolia, 2010-2024.

A comprehensive workflow for resolving Gryllidea phylogeny using universal single-copy orthologs.

Potentilla sensu lato, a taxonomically complex genus within the Rosaceae, comprises approximately 300 taxa worldwide. Thirteen taxa, each restricted to limited localities, are currently recognized as endemic to the Mongolian flora. Therefore, the conservation of Potentilla faces significant challenges due to habitat loss caused by climate change and overharvesting. In this study, we explore the phylogenetic relationships and local evolutionary patterns of five endemic Potentilla species in Mongolia based on their complete chloroplast genomes. We utilized high-throughput sequencing of complete chloroplast genomes and conducted comparative analyses. The complete chloroplast genomes ranged from 156,273 to 156,395bp long and exhibited a typical quadripartite structure. Genome annotation revealed 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Two intergenic regions (ndhF-rpl32 and rpl32-trnL) in the SSC region showed markedly high diversity among chloroplast genomes. Analysis of selection signatures identified two genes (rpoC1 and ycf1) under positive selection. These genes may play important roles in the adaptation of these species to specific geographical environments. Phylogenetic analysis placed all five newly sequenced species within the Argentea clade, and divergence time estimation indicated that diversification within this clade occurred from the late Miocene to the Pleistocene. This study provides valuable genomic resources for endemic Potentilla species in Mongolia, offers insights into their evolutionary history, and lays a foundation for future phylogenetic research and molecular marker development. Furthermore, this study fills a geographic gap in chloroplast genomes sampling of Potentilla in Central Asia.

Phylogenomics, reticulate evolution, and taxonomic revision of East Asian Cardamine (Brassicaceae) in the Hengduan biodiversity hotspot.

ABSTRACTCatfishes of the genus Hypancistrus are among the most emblematic endemic species of the Xingu River rapids, a biodiversity hotspot of the Amazon Basin. In the unique Volta Grande region, the distribution of Hypancistrus zebra, Hypancistrus seideli, and Hypancistrus yudja overlap, creating a potential zone of biological interaction, and previous morphological analyses suggest the occurrence of hybridization between H. seideli and H. yudja. We investigated maternal inheritance and phylogenetic relationships among the three species and hybrids using complete mitochondrial genomes and nuclear genome size estimates. Phylogenetic analyses revealed that hybrids carried maternal lineages exclusively from H. zebra and H. seideli, with no evidence of contribution from H. yudja. Nuclear genome size analyses support this pattern, with hybrids exhibiting intermediate values consistent with additive inheritance. Divergence time estimates indicated a very recent evolutionary radiation (< 0.5 Ma), explaining the persistence of reproductive compatibility among the species. These findings raise conservation concerns, particularly for the zebra pleco H. zebra, a critically endangered species at risk of genetic introgression. Our study provides the first complete mitochondrial genome data for these species and emphasizes the importance of integrating morphological and genomic approaches to understand hybridization dynamics and guide conservation strategies in the Xingu River.

Rafflesiaceae (Malpighiales) is an iconic parasitic plant clade of species that occur west of Wallace's line in tropical Southeast Asia. This clade has been notoriously difficult to place phylogenetically and is nested within an explosive ancient radiation in Malpighiales, rendering one of the thorniest nodes across the angiosperm Tree of Life. The parasitic family Apodanthaceae has recently been positioned as sister to Rafflesiaceae, offering hope of stabilizing their placements. Here, using a data set of 2135 genes and complex methods for species tree inference, we aimed to resolve the phylogenetic placement and divergence time of Rafflesiaceae and Apodanthaceae. We also applied computational simulation to investigate the impact of incomplete lineage sorting (ILS) and long-branch attraction on resolving this ancient radiation. The clade comprising Rafflesiaceae and Apodanthaceae was variously placed with Euphorbiaceae, Peraceae, Putranjivaceae, and Pandaceae by coalescent and concatenation methods. Such unstable placements appear to be the result of excessive levels of rate heterogeneity and ILS, which contribute to a phylogenetic "danger zone" where simulation suggests that current methods and genomic data may never provide a tidy species tree. Despite the topological uncertainty, our divergence time estimation identified a mid-Cretaceous origin of stem group Rafflesiaceae and Apodanthaceae, not only making them the oldest parasitic plant lineage reported to date, but also suggesting a likely Gondwana vicariance scenario that explains their initial disjunct distribution in Northern India, Australia, South America, and Africa.

Fallen Leaves to Their Roots: genome-wide evidence for two independent colonizations of the Taiwan island by Mogera moles.

IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelihood. Here, we present IQ-TREE version 3, the third major release of the software. IQ-TREE 3 significantly extends version 2 with new features, including mixture models as an alternative to partitioned models, gene and site concordance factors to quantify discordance between genomic regions, integration with phylogenomic divergence time estimation, and a fully-featured sequence simulator. The IQ-TREE 3 source code is available at https://github.com/iqtree/iqtree3.

Limitations of molecular dating using constant birth-death rate priors in deep time reflected in Brachiopoda evolution.

Out of North Africa: Evolution and biogeography of Afro-Arabian dwarf tarantulas (Theraphosidae, Ischnocolinae).

Repurposing genome skimming data for non-model plant functional phylogenetics: A case study in Rhodiola.

The Neotropical cichlid genus Apistogramma represents one of the most taxonomically diverse and ecologically significant groups of South American freshwater fishes, yet its evolutionary history and species boundaries remain poorly understood due to a lack of comprehensive genomic resources. To address this gap, this study investigated the complete mitogenomic characteristics of six representative Apistogramma species (A. agassizii, A. allpahuayo, A. baenschi, A. nijsseni, A. resticulosa, and A. cacatuoides) to establish a robust molecular framework for species identification and phylogenetic reconstruction. The results showed that Apistogramma mitogenomes are highly conserved. All six Apistogramma species exhibited significant AT bias. Selection pressure analysis revealed that the Ka/Ks ratios for all 13 protein-coding genes were between 0 and 1, indicating that these genes were under purifying selection. Differential site analysis identified nad5, cox1, and nad4 as ideal molecular markers for rapid Apistogramma species identification owing to higher proportions of variable sites. Phylogenetic analysis recovered Apistogramma as a strongly supported monophyletic clade (BP = 100, PP = 1.00), within which A. nijsseni clustered with A. baenschi and A. cacatuoides with A. agassizii. These internal phylogenetic relationships are consistent with the calculated genetic distances and previous morphological groupings. These findings provide an important theoretical basis and data support for rapid species identification, genetic evolutionary research, and divergence time estimation within Apistogramma.

Phenotypes serve as the interface between organisms and their environments and are thus pivotal for comprehensive biological understanding. However, comparative analyses of species' phenotypes must account for the non-independence of characters imposed by the branching pattern of macroevolution. Methods to account for this phylogenetic non-independence have historically been conceived of as their own subfield: phylogenetic comparative methods (PCMs). In this conceptualization, a researcher takes a pre-existing phylogeny and uses it to correct for the non-independence of the character data that they wish to analyze. Here we argue that parallel developments in scientific philosophy, data availability, computational capacity, and model development have enabled a new paradigm of character evolution, where patterns of character evolution are seen as intrinsically related to the diversification process, and thus should be inferred jointly with the tree rather than reconstructed on an existing phylogeny in a two-step process. In the context of this paradigm shift, we review historical milestones in studies of character macroevolution and discuss major recent conceptual and methodological advances, with an emphasis on the opportunities and insights provided by the joint-inference perspective. We include primers on current topics in character evolution where joint inference is particularly effective, including: (1) state-dependent speciation and extinction models and the importance of cladogenetic change; (2) jointly modeling discrete and continuous characters; (3) accounting for hidden process variation in character evolution; (4) joint inference in divergence-time estimation; (5) joint inference of phylogeny and ancestral states, and; (6) joint inference of alignment and phylogeny. The article concludes with a reflection on the future trajectory of these methods, emphasizing the interconnectedness of character evolution with broader processes in biology.

ABSTRACT Aim Lacustrine systems generally exhibit greater habitat stability than riverine systems, yet some lakes have experienced substantial lake‐level fluctuations throughout the Pleistocene. These environmental perturbations repeatedly altered habitat availability critical to the evolution of their diverse fish communities. In this context, we inferred phylogenetic relationships and divergence times of lacustrine Synodontis catfishes in Lake Tanganyika. We then focused on three closely related species with distinct ecomorphological specializations ( Synodontis petricola , S. polli , S. irsacae ) to further investigate their evolutionary dynamics and elucidate responses to a temporally dynamic lacustrine environment. Location Lake Tanganyika, East Africa. Taxa Synodontis spp. (Mochokidae). Methods We used mitochondrial genomes for phylogenetic reconstruction and divergence time estimation, mitochondrial COI sequences for haplotype network analysis, and genome‐wide SNPs from ddRADseq to assess population structure, demographic history, and patterns of gene flow. Results Mitochondrial genomes indicate that diversification within lacustrine Synodontis of Lake Tanganyika occurred in two main phases during the Pleistocene (2.5–1.5 Ma and 1.0–0.5 Ma), coinciding with pronounced lake‐level fluctuations and palaeoclimatic shifts. Across three closely related but ecologically distinct species, S. petricola and S. polli exhibited mitonuclear discordance—with distinct mtDNA lineages in the northern and southern lake basins—and also showed strong population structure based on nuclear genomic SNP data, whereas S. irsacae lacked geographically structured mtDNA lineages and displayed weaker nuclear differentiation. Demographic reconstructions revealed asynchronous, species‐specific expansions across lake basins, and gene‐flow modelling indicated introgression across all species following a period of isolation after divergence. Main Conclusions Our results show that—in Lake Tanganyika—complex phylogeographic patterns in lacustrine fishes can arise through combined effects of lake‐level fluctuations, ecological specialization, and spatially variable gene flow. These findings highlight how dynamic environmental histories in lacustrine systems can profoundly shape diversification of their biodiversity.

The Madras hedgehog (Paraechinus nudiventris) is an understudied species endemic to southern India, with limited genetic data available for understanding its evolutionary history. Here, we present the complete mitochondrial genome (17,232 bp), annotated and analysed in comparison with other Erinaceidae species. The mitogenome retains the typical vertebrate structure, comprising 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region, with an A + T rich nucleotide composition. Phylogenetic analyses using Bayesian and maximum-likelihood approaches confirmed the species’ placement within Paraechinus, with divergence from P. micropus estimated during the Pleistocene. Molecular evolutionary analyses revealed selective constraints on oxidative phosphorylation genes, with atp8 showing the highest variability. Our divergence time estimates, incorporating fossil calibrations, refine the evolutionary timeline of Erinaceidae, providing insights into the diversification of hedgehogs in South Asia. By making this annotated mitochondrial genome publicly available, we provide a foundational resource for future studies on the genetic diversity, phylogeography, and conservation of P. nudiventris and its relatives.

Abstract The genus Chelonus Panzer is one of the largest genera within the subfamily Cheloninae with 11 subgenera and more than 1000 valid species. However, the phylogenetic relationships of species within this genus and their coevolutionary relationships with endogenous bracoviriforms (BVfs) remain unclear. Here we provide the first phylogenomic analysis of 42 taxa representing all 11 subgenera of Chelonus and other species within the Cheloninae using 2380 loci of ultraconserved elements (UCEs). The results showed that the subgenus Arichelonus Viereck has an isolated position outside of the rest of Chelonus , while the other 10 subgenera formed a monophyletic group, the traditional genus Chelonus . Four subgenera within Chelonus , that is, Chelonus s. str., Megachelonus Baker, Microchelonus Szépligeti and Parachelonus Tobias are polyphyletic, suggesting that the traditional genus Chelonus could be further divided into 14 clades. Divergence time estimates indicated that the subgenus Arichelonus diverged approximately 35.5 million years ago, while most species within the genus Chelonus diversified &lt;21.9 million years ago. Ancestral state reconstructions revealed morphological innovations of the subfamily, including metasomal curvature, which may be linked to host‐use strategies. Cophylogenetic analyses demonstrated that a strong congruence of parasitoid‐bracoviriform exists and confirmed that BVf nudivirus genes and virulence genes displayed different evolutionary trajectories. Altogether, our findings provide new insights into the evolutionary history of the genus Chelonus and substantiated the coevolutionary relationships between the parasitoids and their associated BVfs.

Diversification and biogeographic history of African dormice (genus Graphiurus) revealed by ultraconserved elements and mitochondrial data.

Mitochondrial genome (mitogenome) has been proposed as a powerful molecular marker for phylogenetic reconstruction, evolutionary genomics, and population-level studies due to its maternal inheritance, relatively conserved structure, and elevated evolutionary rates. Anurans (frogs and toads), comprising 7693 species and ~90% of extant amphibian diversity, exhibit extensive mitogenome variability, yet the evolutionary significance of this structural diversity remains poorly understood. Using 277 anuran mitogenomes (spanning 35 families) and outgroup comparisons, phylogenomic reconstructions and gene order evolution analyses were conducted. Phylogenetic analyses resolved five major clades: Leiopelmatoidea (basal lineage), Discoglossoidea, Pipoidea, Pelobatoidea, and the crown group Neobatrachia. Archaeobatrachians emerged as a paraphyletic group, with sequential divergences of the first four clades. Neobatrachia was monophyletic, with Heleophrynidae and Sooglossidae occupying basal positions. Subsequent diversification revealed two major neobatrachian subclades: one uniting Calyptocephalellidae with Myobatrachoidea and Hyloidea, and another comprising Ranoidea, a topology consistent with recent phylogenomic studies but highlighting persistent conflicts within Hyloidea and Ranoidea. Divergence time estimation traced the origin of Anura to the Early-Late Triassic boundary, with major neobatrachian radiations occurring from the Late Cretaceous through the Early Neogene. CREx-based comparative analyses identified 58 distinct gene arrangement patterns, including lineage-specific synapomorphic rearrangements that were phylogenetically mapped. Our study provides a robust mitogenomic framework for Anura, reconciling deep phylogenetic discordance while revealing novel patterns of gene order evolution. These findings establish critical foundations for future investigation into the mechanisms driving mitogenomic structure diversification and its interplay with the evolutionary success of this ecologically vital vertebrate group.

Phylogenomic and evolutionary analysis of arrowhead (Sagittaria L.) chloroplast genomes.

The Congo River, with the highest diversity of riverine fishes in Africa, only recently established its contemporary outlet into the Atlantic around the Miocene-Pliocene transition (∼5 millions of years ago; Ma). Yet, its role in shaping ichthyofaunal diversification across central Africa through interactions with adjacent Atlantic coastal rivers remains unexplored at both regional and local scales. The African characiform family Alestidae, with lineages distributed across the entire region, offers an ideal system to investigate inland-coastal biogeographic connections. However, phylogenetic relationships within Alestidae remain unresolved, particularly with respect to two key genera, Brachypetersius and Nannopetersius, which inhabit both regions of interest. Applying likelihood and species-tree inferences using 1,759 nuclear ultraconserved elements (UCEs) and 13 protein-coding genes of mitochondrial genomes from 42 alestid taxa, we resolve both Brachypetersius and Nannopetersius as polyphyletic and identify a distinct clade warranting recognition as a new genus: Clavocharax. External morphological and osteological data from museum specimens corroborate this finding by providing diagnostic characters for the new genus. Our molecular and morphological data also support the revalidation of Clupeocharacinae as an inclusive subfamily, encompassing the new genus and seven other West and Central African genera, marking the first phylogenetically supported subfamily within Alestidae. Divergence time estimates suggest that Clavocharax originated in the early Miocene (23.2-15.0Ma), coinciding with climatic shifts and potential river capture events across the region of the Congo River outflow and lower Guinean coastal systems. Ancestral range estimation implicates Miocene climatic and geological events, including the formation of Congo's current Atlantic outlet, in driving repeated geodispersal and diversification across inland and coastal drainages. This study highlights the influence of historical hydrological connectivity on African freshwater fish diversity and resolves previous gaps in our understanding of regional ichthyofaunal evolution and biogeography.