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.

Oxidative stress, triggered by hypoxia during repetitive diving, represents a notable environmental adaptation of marine mammals. Glutathione (GSH) is a widely acknowledged antioxidant that protects crucial cellular elements from damage by reactive oxygen species (ROS). Nevertheless, the role of the glutathione metabolism pathway in shaping the adaptation to oxidative stress in marine mammals is not fully elucidated. In this study, we conducted evolutionary analyses on 37 genes related to GSH metabolism pathway in marine and terrestrial mammals. We found that in comparison with their terrestrial relatives, marine mammals showed convergently accelerated evolution on the core modules of GSH metabolism. Specifically, we identified a total of 16 genes with significant evolution signals unique to marine mammals, and several genes (e.g., accelerated evolution genes: RRM1 and SMS, positively selected genes: ANPEP and GCLC) were shared in marine mammal lineages. Eight genes were discovered to possess specific amino acid modifications that are common among all marine mammals. Functional assays of marine mammal GCLC showed a downregulation of HIF-1α and enhanced GSH levels under hypoxic conditions, suggesting heightened protection of marine mammals against oxidative stress induced by hypoxia. Our study identified key genes with significant evolutionary signals in marine mammals, providing genomic and functional support for convergent hypoxia adaptation mechanisms within this taxon.

Understanding the genetic diversity and genetic load of endangered species is essential for developing effective conservation strategies, particularly in ecologically sensitive regions such as the Himalayas. Cupressus austrotibetica, a rare conifer and the tallest recorded tree in Asia, reaching up to 101.2 m, faces substantial anthropogenic and environmental threats. To evaluate its genetic status, we sequenced transcriptomes of 54 individuals sampled across its restricted range and compared them with 96 individuals of C. gigantea, a closely related endangered species with broader distribution at higher elevations. Our analysis reveals that C. austrotibetica exhibits higher genetic diversity (π = 0.0091) compared to C. gigantea (π = 0.0042). Demographic analyses identified three historical bottleneck events in C. austrotibetica and two in C. gigantea, with two of these events coinciding with Quaternary climatic oscillations. Despite its relatively high genetic diversity, C. austrotibetica has a smaller effective population size based on Stairway Plot 2 (Nₑ ≈ 7200) than C. gigantea (Nₑ ≈ 17 600). Furthermore, C. austrotibetica harbors a higher proportion of severe deleterious mutations, while C. gigantea retains more moderate deleterious variants. These findings indicate that a recent anthropogenic bottleneck event has likely driven the reduced population size and increased genetic load in C. austrotibetica, emphasizing the urgent need for conservation priorities for this imperiled species.

The peppered moth Biston betularia L., widely distributed across the Northern Hemisphere, represents an ideal organism for exploring phylogeographic pattern and evolutionary history. In this study, we integrated molecular, morphological, and distributional data of this species to reconstruct its phylogenetic relationships, estimate divergence times, infer the geographic origin, and trace dispersal routes. Molecular analyses identified six monophyletic lineages (HM, NC, HD, E, NA I, and NA II). With the exception of the sympatric North American lineages NA I and NA II, the remaining lineages exhibit allopatric distributions across Eurasia. Ancestral area reconstruction and approximate Bayesian computation (ABC) analyses supported a southern Xizang origin within the Himalayan Mountains, consistent with the ‘Xizang-origin hypothesis’. The colonization of North America occurred twice via the Bering Land Bridge during the Pleistocene glaciation. Collectively, the current genetic pattern is best explained by gradual allopatric differentiation following long-distance dispersal and subsequent isolation. Furthermore, we reconstructed the global dispersal history of B. betularia. These results indicated that in situ speciation within the Himalaya may be more common than previously recognized, challenging the notion that Himalayan fauna are predominantly considered ‘immigrant’. This study enhances our understanding of Himalayan zoogeography and biodiversity through the resolved evolutionary history of a widely distributed species.