Bird eggs can be spherical, ellipsoid, ovoid, or pear-shaped (pyriform), the latter being the most complex. There is however no unambiguous evolutionary/adaptive explanation for this final, exotic shape. We hypothesized that pyriform eggs have a larger surface area-to-volume ratio (S/V) that may be a criterion for increased embryo metabolism. By integrating mathematical approaches, we confirmed this to be the case and developed a model of the egg metabolic rate defined as the ratio of S/V to its maximum possible value, depending on egg length. We found this to be inversely proportional to the egg incubation period and concluded that the complex pyriform shape is most likely due to embryo metabolism increase and, as a result, a reduction in the incubation period and shortened hatching time. As a result of this study, we conclude that some avian eggs are pyriform as this may attain a larger S/V ratio making them grow and hatch quicker.

It is commonly admitted that the continuous development of human infrastructure (HI), resulting in natural habitat fragmentation, affects farmland birds by misleading their strategies of nest site selection. Here, we examined how HI in agricultural landscape (AL) could be affecting nest habitat selection of Barbary partridge (BP; Alectoris barbara). A total of 160 BP nests were monitored during 4 years (2017, 2018, 2021, and 2022) in eight Moroccan agricultural zones. We used the generalized linear mixed models and variation partitioning methods to quantify the effects of AL and HI on BP nest occurrence. This occurrence increased with track density (within 300 m of sampled nests) and decreased with built-up area cover (50 m). Nest occurrence was also associated with the cover of agricultural areas (300 m), distances to the nearest agricultural area, the nearest human settlement, and the nearest track. However, the effect of these covariates depended on distance to the nearest paved road, being close to roads located far away from agricultural areas and tracks and near human settlements and tracks. Overall, our results highlighted a trend to nest close to HI when agricultural areas were relatively remote or less represented. For the effective conservation and management of the Moroccan BP populations, it is critical to keep human infrastructures at a level that allows for maintaining the relative dominance of the agricultural landscape. Further fragmentation of this landscape will impact the ability of this farmland species to select its nesting sites flexibly.

Birds exhibit remarkable variations in body size, making them an ideal group for the study of adaptive evolution. However, the genetic mechanisms underlying body size evolution in avian species remain inadequately understood. This study investigates the evolutionary patterns of avian body size by analyzing 15 body-size-related genes, including GHSR, IGF2BP1, and IGFBP7 from the growth hormone/insulin-like growth factor axis, EIF2AK3, GALNS, NCAPG, PLOD1, and PLAG1 associated with tall stature, and ACAN, OBSL1, and GRB10 associated with short stature, four genes previously reported in avian species: ATP11A, PLXDC2, TNS3, and TUBGCP3. The results indicate significant adaptive evolution of body size-related genes across different avian lineages. Notably, in the IGF2BP1 gene, a significant positive correlation was observed between the evolutionary rate and body size, suggesting that larger bird species exhibit higher evolutionary rates of the IGF2BP1 gene. Furthermore, the IGFBP7 and PLXDC2 genes demonstrated accelerated evolution in large- and medium-sized birds, respectively, indicating distinct evolutionary patterns for these genes among birds of different sizes. The branch-site model analysis identified numerous positively selected sites, primarily concentrated near functional domains, thereby reinforcing the critical role of these genes in body size evolution. Interestingly, extensive convergent evolution was detected in lineages with larger body sizes. This study elucidates the genetic basis of avian body size evolution for the first time, identifying adaptive evolutionary patterns of body size-related genes across birds of varying sizes and documenting patterns of convergent evolution. These findings provide essential genetic data and novel insights into the adaptive evolution of body size in birds.

Urbanization processes modulate the immunological challenges faced by animals. Urban habitat transformations reshape pathogen diversity and abundance, while high population density—common in urban exploiter species—promotes disease transmission. Responses to urbanization may include adaptive adjustments of constitutive innate immune defenses (e.g. complement system and natural antibodies [NAbs]), which serve as first-line protection against infections. Here, we investigated associations of habitat urbanization and host population density with complement and NAbs in an urban bird, the feral pigeon Columba livia domestica. To do so, we employed the hemolysis–hemagglutination assay to analyze nearly 200 plasma samples collected across urbanization and pigeon population density gradients in five major cities in Poland. We found a negative association between urbanization score and hemagglutination (i.e. NAbs activity), but not hemolysis (i.e. complement activity), indicating either immunosuppression or adaptive downregulation of this immune defense in highly transformed urban landscape. Population density was not significantly related to either immune parameter, providing no evidence for density-dependent modulation of immune defenses. At the same time, there was a negative association of hemolysis with condition (scaled mass index), suggesting resource allocation trade-offs or contrasting effects of the urban environment on immune defenses and body condition. The results demonstrate that habitat structure can be an important factor shaping the immune defenses of the feral pigeon, although these associations were not mediated by variation in population density. Our study highlights the complexity of the links between immune defenses in wildlife and urbanization and reinforces the need for comprehensive ecoimmunological studies on urban animals.

The soybean pod borer, Leguminivora glycinivorella (Matsumura), is an important tortricid pest species widely distributed in most parts of China and its adjacent regions. Here, we analyzed the genetic diversity and population differentiation of L. glycinivorella using diverse genetic information including the standard cox1 barcode sequences, mitochondrial genomes (mitogenomes), and single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Based on a comprehensive sampling (including adults or larvae of L. glycinivorella newly collected at 22 of the total 30 localities examined) that covers most of the known distribution range of this pest, analyses of 543 cox1 barcode sequences and 60 mitogenomes revealed that the traditionally recognized and widely distributed L. glycinivorella contains two sympatric and widely distributed genetic lineages (A and B) that were estimated to have diverged ∼1.14 million years ago during the middle Pleistocene. Moreover, low but statistically significant correlations were recognized between genetic differentiation and geographic or environmental distances, indicating the existence of local adaptation to some extent. Based on SNPs, phylogenetic inference, principal component analysis, fixation index, and admixture analysis all confirm the two divergent sympatric lineages. Compared with the stable demographic history of Lineage B, the expansion of Lineage A had possibly made the secondary contact of the two lineages probable, and this process may be driven by the climate fluctuation during the late Pleistocene as revealed by ecological niche modeling.

Urban environments often present environmental conditions that facilitate the introduction and establishment of nonnative and invasive species. These can expand their range into areas with unfavorable climates by taking advantage of the ecological and climatic homogenization of cities, bypassing the ecological barriers presented by the surrounding environment. One way to monitor the expansion of these species is using potential distribution models. We used as a model species the Argentine ant, Linepithema humile (Hymenoptera: Formicidae) whose invasion has caused serious consequences for biodiversity and economic losses worldwide. We used the average result of six different algorithms and used climatic variables and population density as a proxy for the urbanization level in the Western Palearctic to build the predictive model. The model indicates this ant prefers to inhabit areas with Mediterranean and Temperate Oceanic climates and that its suitability depends on two main factors: the continentality (temperature annual range) and the degree of urbanization. The species is predicted to be absent in areas with large temperature contrasts throughout the year, particularly in rural and peri-urban areas (i.e. adjacent to urban areas) of inland regions. Conversely, the species has a predilection for coastal and urban areas where environmental conditions are attenuated by the influence of the sea or the “urban heat island” effect in the case of inland cities. In this sense, cities act as “bioclimatic islands” facilitating the establishment of the Argentine ant as a reservoir, enlarging its distribution into climatically nonoptimal areas, and promoting its future expansion in a scenario of global warming and socioeconomic change.

Chiroptera (bats) presents a fascinating model due to its remarkable variation in chromosome numbers, which range from 14 to 62. This astonishing diversity makes bats an excellent subject for studying chromosome evolution. The black-bearded tomb bat (Taphozous melanopogon) occupies a pivotal phylogenetic position within Chiroptera, emphasizing its crucial role in the systematic examination of bat chromosome evolution. In this study, we present the first chromosome-level genome of T. melanopogon within the family Emballonuridae. Together with previously published genomes, we construct a strongly supported phylogenetic tree of bats, which supports that Emballonuridae forms a basal group within Yangochiroptera. Furthermore, we reconstruct ancestral karyotypes at key nodes along the bat phylogeny and conduct a synteny analysis among the genomes of 12 bat species. Our findings identified evolutionary breakpoint regions (EBRs) that are of particular interest. Notably, some bat genomes exhibit an enrichment of genes related to host defense against microbial pathogens within EBRs. Remarkably, one species possesses multiple copies of some β-defensin genes, while six other species have experienced the loss of some β-defensin genes due to EBRs. Furthermore, some olfactory receptor genes are located in EBRs of 12 species, 4 of which have a significant enrichment in sensory perception of smell. Together, our comparative genomic analysis underscores the potential link between chromosome rearrangements and the adaptation of bats to defend against microbial pathogens.

Variations in skin structures can possibly reflect local adaptation to distinct environmental factors. As the primary interface with the surrounding environment, amphibian skin undergoes phenotypic innovations that play a key role in protection, water absorption, and respiration. However, the effects of environmental factors on skin structures have been examined in only a limited number of species. Here, we conducted a comparative analysis of the skin structures of 102 Chinese anuran species across varying geographical distributions and habitat types. Our results revealed that the total volume of granular glands and capillary density in the dorsal skin significantly increased with increasing latitude. We also found that the thickness of calcified layers in both dorsal and ventral skin was positively correlated with annual temperature and negatively correlated with humidity. Additionally, terrestrial species exhibited the largest dorsal granular gland, whereas arboreal species had the smallest one. Likewise, the largest dorsal mucous gland was observed in aquatic species, while the smallest was found in terrestrial species. These results highlighted the importance of understanding the relationship between skin phenotypes and environmental variables and thus providing conservation strategies based on the evolutionary adaptations in anurans. Our study can contribute to the broader knowledge of evolutionary biology in anurans by demonstrating how specific skin traits are linked to survival and fitness across various ecological contexts.

Many animal species show considerable intraspecific phenotypic variation. For species with broad distributions, this variation may result from heterogeneity in the strength and agents of selection across environments and could contribute to reproductive isolation among populations. Here, we examined interpopulation variation in a morphological trait related to chemical communication, femoral pore number (FP), using 3437 individuals from 55 Pyrenean populations of the common wall lizard (Podarcis muralis). Specifically, we tested the relative roles of genetic relatedness and gene flow, and adaptation to local conditions in generating this variation, with particular interest in the influence of climate and the socio-sexual environment (i.e., the intensity of sexual selection, estimated using sexual size dimorphism [SSD] and adult sex ratio as proxy measures). We found significant interpopulation variation and sexual dimorphism in FP, as well as high genomic differentiation among populations driven by both geographic and environmental distances. Specifically, FP differences across populations were best predicted by a combination of positive allometry and the local intensity of sexual selection, as determined by SSD, or local climatic conditions. Higher FP in more male-competitive environments, or with higher temperature and vegetation complexity, is consistent with adaptation to maintaining signaling efficacy of territorial scent marks. These results suggest that adaptation to local conditions contributes to interpopulation divergence in FP and thus environmental changes can potentially impact the fine-tuning of chemical communication mediating social and sexual behavior.

Diamondback terrapins (Malaclemys terrapin centrata) exhibit strong environmental adaptability and live in both freshwater and saltwater. However, the genetic basis of this adaptability has not been the focus of research. In this study, we successfully constructed a ∼2.21-Gb chromosome-level genome assembly for M. t. centrata using high-coverage and high-depth genomic sequencing data generated on multiple platforms. The M. t. centrata genome contains 25 chromosomes and the scaffold N50 of ∼143.75 Mb, demonstrating high continuity and accuracy. In total, 53.82% of the genome assembly was composed of repetitive sequences, and 22 435 protein-coding genes were predicted. Our phylogenetic analysis indicated that M. t. centrata was closely related to the red-eared slider turtle (Trachemys scripta elegans), with divergence approximately ∼23.6 million years ago (Mya) during the early Neogene period of the Cenozoic era. The population size of M. t. centrata decreased significantly over the past ∼14 Mya during the Cenozoic era. Comparative genomic analysis indicated that 36 gene families related to ion transport were expanded and several genes (AQP3, solute carrier subfamily, and potassium channel genes) underwent specific amino acid site mutations in the M. t. centrata genome. Changes to these ion transport-related genes may have contributed to the remarkable salinity adaptability of diamondback terrapin. The results of this study not only provide a high-quality reference genome for M. t. centrata but also elucidate the possible genetic basis for salinity adaptation in this species.

The Yarlung Tsangpo River on the Tibetan Plateau provides a unique natural environment for studying fish evolution and ecology. However, the genomes and genetic diversity of plateau fish species have been rarely reported. Schizopygopsis younghusbandi, a highly specialized Schizothoracine species and economically important fish inhabiting the Yarlung Tsangpo River, is threatened by overfishing and biological invasion. Herein, we generated a chromosome-level genome of S. younghusbandi and whole-genome resequencing data for 59 individuals from six locations of the river. The results showed that the divergence time between S. younghusbandi and other primitive Schizothoracine species was ∼4.2 Mya, coinciding with the major phase of the Neogene Tibetan uplift. The expanded gene families enriched in DNA integration and replication, ion binding and transport, energy storage, and metabolism likely contribute to the adaption of this species. The S. younghusbandi may have diverged from other highly specialized Schizothoracine species in the Zanda basin during the Pliocene epoch, which underwent major population reduction possibly due to the drastic climate change during the last glacial period. Population analysis indicated that the ancient population might have originated upstream before gradually adapting to evolve into the populations inhabiting the mid-stream and downstream regions of the Yarlung Tsangpo River. In conclusion, the chromosome-level genome and population diversity of S. younghusbandi provide valuable genetic resources for the evolution, ecology, and conservation studies of endemic fishes on the Tibetan Plateau.

Pancreatic ribonuclease (RNase1), a digestive enzyme produced by the pancreas, is associated with the functional adaptation of dietary habits and is regarded as an attractive model system for studies of molecular evolution. In this study, we identified 218 functional genes and 48 pseudogenes from 114 species that span all four Cetartiodactyla lineages: two herbivorous lineages (Ruminantia and Tylopoda) and two non-herbivorous lineages (Cetancodonta and Suoidea). Multiple RNase1 genes were detected in all species of the two herbivorous lineages, and phylogenetic and genomic location analyses demonstrated that independent gene duplication events occurred in Ruminantia and Tylopoda. In Ruminantia, the gene duplication events occurred in the ancestral branches of the lineage in the Middle Eocene, a time of increasing climatic seasonality during which Ruminantia rapidly radiated. In contrast, only a single RNase1 gene was observed in the species of the two non-herbivorous lineages (Cetancodonta and Suoidea), suggesting that the previous Cetacea-specific loss hypothesis should be rejected. Moreover, the duplicated genes of RNase1 in the two herbivorous lineages (Ruminantia and Tylopoda) may have undergone functional divergence. In combination with the temporal coincidence between gene replication and the enhanced climatic seasonality during the Middle Eocene, this functional divergence suggests that RNase1 gene duplication was beneficial for Ruminantia to use the limited quantities of sparse fibrous vegetation and adapt to seasonal changes in climate. In summary, the findings indicate a complex and intriguing evolutionary pattern of RNase1 in Cetartiodactyla and demonstrate the molecular mechanisms by which organisms adapt to the environment.

Oceans’ absorption of human-related CO₂ emissions leads to a process called ocean acidification (OA), consisting of the decrease of the seawater pH with negative consequences for many marine organisms. In this study, we investigate the microbial community of two species of polychaetes found in naturally acidified CO₂ vents: the nereid Platynereis massiliensis complex and the syllid Syllis prolifera. Animals were collected in the CO₂ vents of Castello Aragonese (Gulf of Naples, Ischia, Italy) in three zones at decreasing pH. For the analysis of the microbiome, the V3-V4 hypervariable region of the 16S ribosomal RNA gene of 40 worm samples was sequenced on an Illumina MiSeq platform. No difference in the microbial alpha diversity of both species was highlighted. On the contrary, the microbial composition of worms collected in the site at normal pH was different from that of the individuals obtained from the sites at lower pH. This effect was evident also in samples from the site with a slight, but relevant, degree of acidification. Amplicon sequence variants showing a significant variation among the groups of samples collected from different pH zones were reported for both polychaetes, but no common trend of variation was observed. The present study deepens our knowledge about the composition of polychaete microbiome in marine naturally acidified sites. Our results stress the importance of future investigations about the connection between the variation of environmental and polychaete microbial communities induced by OA and about the effect of these variations on polychaete key biological and ecological traits.

Acute environmental changes cause stress during conventional deep-sea biological sampling without in situ fixation and affect gene expressions of samples collected. However, the degree of influence and underlying mechanisms are hardly investigated. Here, we conducted comparative transcriptomic analyses between in situ and onboard fixed gills and between in situ and onboard fixed mantles of deep-sea mussel Gigantidas haimaensis to assess the effects of incidental sampling stress. Results showed that transcription, translation, and energy metabolism were upregulated in onboard fixed gills and mantles, thereby mobilizing rapid gene expression to tackle the stress. Autophagy and phagocytosis that related to symbiotic interactions between the host and endosymbiont were downregulated in the onboard fixed gills. These findings demonstrated that symbiotic gill and nonsymbiotic mantle responded differently to sampling stress, and symbiosis in the gill was perturbed. Further comparative metatranscriptomic analysis between in situ and onboard fixed gills revealed that stress response genes, peptidoglycan biosynthesis, and methane fixation were upregulated in the onboard fixed endosymbiotic Gammaproteobacteria inside the gills, implying that energy metabolism of the endosymbiont was increased to cope with sampling stress. Furthermore, comparative analysis between the mussel G. haimaensis and the limpet Bathyacmaea lactea transcriptomes resultedidentified six transcription factor orthologs upregulated in both onboard fixed mussel mantles and limpets, including sharply increased early growth response protein 1 and Kruppel-like factor 5. They potentially play key roles in initiating the response of sampled deep-sea macrobenthos to sampling stress. Our results clearly show that in situ fixed biological samples are vital for studying deep-sea environmental adaptation.

A possible explanation for ocean acidification-induced changes in fish behavior is a systemic effect on the nervous system. Three biological barriers at the blood–brain interface effectively separate the brain from the body fluids. It is not known whether fish brain regions in contact with these barriers are affected by acidification. Here, we studied structural changes in medaka (Oryzias melastigma) brain regions contacting cerebrospinal fluid (CSF) after short-term (7 days) CO₂ exposure. The brain water content decreased significantly and the superficial structure of the pia mater was changed, but there was no obvious damage to the internal structures of the brain after seawater acidification. Seawater acidification also led to an increase in apoptosis and a decrease in the number of proliferative cells in brain areas contacting CSF. These results indicate that the structure of CSF-contacting brain regions in medaka was affected by seawater acidification, and the brain responded to seawater acidification stress by increasing apoptosis and reducing proliferation.

Since ancient times, zoology, as the branch of biology dealing with animals, has been a cornerstone of natural science and has developed substantially over the last century. We conducted a bibliometric analysis using structural topic modeling (STM) to determine changes in the representation of principal zoological subdisciplines in the literature between 1960 and 2022. We collated a corpus of 217 414 articles from 88 top-ranked zoology journals and identified three main fields: (i) ecology, (ii) evolution, and (iii) applied research. Within these, we identified 10 major subdisciplines. The number of studies published per year grew from 118 in 1960 to 6635 in 2022. Macroscale-related subdisciplines increased while classical and traditional subdisciplines decreased. Mammals (34.4%) and insects (18.1%) were the dominant taxa covered, followed by birds (15.2%) and fish (8.0%). Research on mammals, insects, and fish involved a broad range of subdisciplines, whereas studies of birds focused on ecological subdisciplines. Most publications were from the United States, followed by the United Kingdom, Germany, Canada, Australia, China, and Japan, with two developing countries, China and South Africa among the top 15 countries. There were different subdiscipline biases between countries, and the gross domestic product of each country correlated positively with its publication output (R² = 0.681). We discuss our findings in the context of advances in technological innovations and computing power, as well as the emergence of ecology as a formal sister discipline, driven by changing environmental pressures and societal values. We caution that valuable publications from traditional zoological fields must not be completely supplanted by more contemporary topics and increasingly sophisticated analyses.