Cavefishes display pronounced troglomorphic adaptations, such as visual degeneration, depigmentation, and scale reduction, as specialized responses to subterranean environments. Among these, the cave loaches (CLS) of the family Nemacheilidae represent China’s second-most diverse cavefish group; however, their evolutionary history remains poorly understood. To bridge this knowledge gap, we conducted whole-genome resequencing of 62 CLS species and two closely related taxa, complementing these data with published genomic resources. The reconstructed phylogeny identified ancient introgression as the primary driving force behind phylogenetic discordance, with incomplete lineage sorting as a secondary contributor. Pleistocene climatic fluctuations, coupled with species-specific genetic architectures, generated four distinct demographic trajectories across populations. Additionally, we delineated four distinct phases of lineage diversification in CLS, shaped by tectonic–climatic interactions, with alternating periods of acceleration and decline synchronized with the Asian orogenic and monsoonal cycles. This study provides the first integrated genomic perspective on the evolution of the CLS, demonstrating how biotic and abiotic factors have collectively shaped subterranean biodiversity.

Species descriptions in taxonomy have become increasingly comprehensive, yet disparities persist across taxa and regions. We assess temporal trends in mammal species descriptions (1990–2025) using four proxies of comprehensiveness—counts of examined specimens and compared taxa, number of pages (only from the Methods/Results sections), and number of evidence lines (i.e., analytical tools and techniques). Using generalized linear models, we assessed how these proxies are explained by factors associated with species’ biology, geography, and taxonomic practice. Most new species derive from tropical regions, particularly rodents and bats, reflecting global discovery hotspots. Descriptions have grown more rigorous over time, with expanded specimen sampling, broader taxonomic comparisons, and integrative methods. However, disparities emerge along geographic and biological axes: descriptions from temperate regions incorporate more evidence lines, while small-bodied and tropical species (especially bats) remain understudied due to sampling biases and resource limitations. Body size inversely correlates with description length, as smaller species often require advanced diagnostics. Species-rich genera show greater comprehensiveness, likely due to heightened diagnostic scrutiny. Our findings highlight progress in taxonomic rigor but underscore persistent gaps tied to geography, body size, and accessibility of analytical tools. Addressing these disparities requires targeted investments in local capacity, equitable collaboration, and accessible methodologies to strengthen global taxonomic infrastructure and support conservation priorities.

Magnoliaceae, a typical boreotropical relict lineage, exhibits striking species richness in tropical regions, making it an important model for testing the time-for-speciation and diversification rate hypotheses for present-day diversity patterns. Here, we reconstructed a time-calibrated phylogeny using plastomes from 123 species, representing Liriodendron and all 15 sections of Magnolia, and investigated its colonization and diversification history. Our results reveal that Magnoliaceae likely experienced peak extinction during the mid-Eocene, accompanied by a range contraction from high latitudes to the amphi-Pacific tropics, followed by the rise of tropical clades with rapid diversification. Phylogenetic generalized least squares analysis demonstrates that diversification rate explains clade-level diversity variation more strongly than time-for-speciation. Tropical regions, such as South America and Southeast Asia, with high Magnoliaceae diversity consistently exhibit elevated diversification rates and shorter time for speciation. These results indicate that higher diversification rate, rather than longer time for speciation, explains the high diversity of Magnoliaceae in tropical clades and regions. Our findings not only shed light on the evolutionary history of Magnoliaceae but also provide important insights into the broader processes that shape tropical biodiversity.

While sex-biased gene expression and its evolutionary dynamics across taxa have been extensively investigated, systematic separate characterization of the evolutionary patterns in transcriptome divergence between male and female lineages remains underexplored. Here, we analyze a comprehensive RNA-seq dataset from the house mouse complex, spanning multiple organs across subspecies and species, to delineate the evolutionary trajectories of gene expression in males and females in intra- and inter-species contrasts. For both sexes, we find specific gene expression divergence patterns across the surveyed organs, with a particularly high divergence rate at early evolutionary stages of separation. Comparative analysis between sexes demonstrates male reproductive organs, particularly the testis, displaying accelerated evolutionary rates of expression divergence. Strikingly, testicular long non-coding RNA genes exhibit the most pronounced acceleration with differences emerging already after a few thousand years of population separation. In contrast, somatic organs and female reproductive auxiliary tissues show no major sex-specific evolutionary dynamics. Genes with sex-biased expression substantially contribute to differentially expressed genes across evolutionary transitions, though without predominant directional bias toward either sex. Notably, these differentially expressed genes display significant over-representation on autosomes. A general functional divergence process is found between male and female transcriptomes across organs mainly driven by sex-specific differentially expressed genes. Collectively, our findings establish a new evolutionary framework for sex-specific expression divergence and provide novel insights into the role of reproductive constraints in shaping transcriptome evolution in mammals.

A major obstacle to biodiversity conservation is that thousands, if not millions, of plant and animal species have yet to be discovered and described, even in historically well-explored regions. Carex sect. Lupulinae (Cyperaceae; “sedges”) is a small group of six showy Eastern North American species that until recently was thought to be well understood. However, a DNA barcoding study of North American Carex undertaken over a decade ago serendipitously revealed unsuspected molecular diversity, including one potentially undescribed cryptic species. Here, we test the hypothesis that this entity is a species on a separate evolutionary trajectory by expanding barcoding results with an integrative approach that combines a densely-sampled molecular phylogeny (five plastid and two nuclear markers, 112 sequenced specimens), morphometric analyses (93 characters, >300 measured specimens), ecological field surveys, and common greenhouse observations. Results all support the recognition of a new, abundant species common in the southeastern United States’ Coastal Plain that we name Carex gator. This study highlights how integrative taxonomy can help to describe cryptic plant species revealed by DNA barcoding. We provide illustrations, a distribution map and an identification key, and discuss how C. gator may be one rare example of homoploid sympatric speciation in plants.

Body size is among the key subjects in macroecology and macroevolution with important implications for conservation. Two major rules have been proposed to explain how body size changes over evolutionary time (Cope’s rule) and across temperature gradients (Bergmann’s rule). To date, however, the applicability of both rules to global terrestrial vertebrates (tetrapod) remains elusive. Here, using the newly available data, we comparatively examined the temporal variation in species body size of the world’s extant tetrapod species (tetrapoda as a whole) and of each class, amphibians (Amphibia), reptiles (Reptilia), mammals (Mammalia), and birds (Aves), through the Cenozoic Era. When all four classes were considered together, the species’ body size had increased over time and was negatively correlated with global surface temperature. However, separate analyses on each of the four classes showed that reptiles and mammals tended to support Cope’s rule while birds and amphibians did not. Also, we found no clear difference in temporal body size variation between endothermic and ectothermic species. Overall, the support for Bergmann’s rule was much stronger than that for Cope’s rule. Future research using more complete and compatible body size data from fossils is needed to better understand how species’ body size evolves over time and across space.

Mazie is amongst the most agriculturally and economically important crops to human beings. It was domesticated from a wild relative called teosinte. During domestication, maize has experienced drastic morphological transformations, such that it produces fewer ears, each of which bears much more kernels covered by soft and reduced glumes. The striking differences between maize and teosinte make the origin of maize ear a fascinating question, which has been fiercely and actively debated for more than a century. Over the past few decades, the discovery of numerous key genes and genetic pathways has greatly deepened our understanding of the mechanisms underlying maize ear development and domestication. In this review, by providing an overview of the morphogenetic processes of maize and teosinte ears, and molecular mechanisms of maize ear development, we highlight key morphodynamical distinctions between maize and teosinte ears. By recapitulating historical accounts and summarizing recent advance regarding maize domestication, we present current understanding and propose a model for the origin of maize ear.

Encephalartos, an African endemic genus within the Zamiaceae, comprises 65 extant species whose phylogenetic relationships have remained unresolved due to limited genetic differentiation observed in previous studies. This research reconstructs the evolutionary history of Encephalartos utilizing 3,545 single-copy nuclear genes derived from transcriptomes of 64 species. The study estimates divergence times and reconstructs ancestral states for 12 key morphological traits. Phylogenetic analyses definitively resolve eight major clades, supported by both molecular and morphological evidence. Although these clades partially align with previous morphology- and geography-based classifications, the genomic data provides novel insights, necessitating a revised infrageneric system. Biogeographic reconstructions indicate that Encephalartos originated in southern Africa during the Oligocene (~26.3 Ma), subsequently dispersing into eastern and northern Africa through the Zimbabwe-Mozambique corridor during the Miocene, followed by expansion into Central Africa. Speciation rates decreased markedly during the Pliocene and Pleistocene, potentially due to intensified climatic drying and cooling. Morphological character mapping identified ancestral traits including aerial stems, green leaves, and red sarcotesta. Specific transitions—such as subterranean stems in clade IV and bluish-green leaves in clades II and V—further substantiate clade differentiation. These findings resolve long-standing taxonomic uncertainties and emphasize the Oligocene-Miocene as a crucial period for Encephalartos diversification, influenced by Cenozoic climate change. This research establishes a robust framework for future systematic and conservation studies while demonstrating the effectiveness of transcriptome data in resolving phylogenies of slowly evolving lineages.

The evolutionary arms race between insects and their predators has fueled remarkable defensive adaptations, offering insights into ecological dynamics across deep time. Fossils provide critical evidence for studying the evolution of defense strategies. Here, we describe a new lineage of Clambidae from mid-Cretaceous Kachin amber, Scutacalyptus kolibaci gen. et sp. nov. Scutacalyptus stands out within the family due to the flattened body and fully explanate body margins. The diversity of defensive morphotypes in Cretaceous Clambidae, including conglobators like Sphaerothorax, semi-flattened forms like Acalyptomerus, and shield-formers like Scutacalyptus, highlights their developmental plasticity and suggests ecological differentiation in response to varied predation pressures during the late Mesozoic. This morphological divergence reflects niche partitioning in the Cretaceous forest floor ecosystem, driven by a diverse predator array including spiders, ants, lizards, and birds. The coexistence of clambids with spines or explanate margins parallels adaptations in the modern, unrelated Cassidinae, where tortoise beetles use explanate margins and some leaf-mining beetles use spines, each tailored to counter specific predation pressures. These parallel strategies reveal how different defenses likely addressed distinct ecological challenges in the mid-Cretaceous.