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Abstract Background Floodplains harbor highly biodiverse ecosystems, which have been strongly affected by both past climate change and by recent human activities, resulting in a high prevalence of many endangered species in these habitats. Understanding the history of floodplain species over a wide range of timescales can contribute to effective conservation planning. We reconstructed the population formation history of the Itasenpara bitterling Acheilognathus longipinnis, an endangered floodplain fish species in Japan, over a broad timescale based on phylogenetic analysis, demographic modeling, and historical demographic analysis using mitogenome and whole-genome sequences. A genome sequence was newly assembled as a reference for the resequencing analysis. This bitterling is distributed in three plains separated by high mountain ranges and exhibits ecological characteristics well adapted to floodplain environments. Results Our analyses revealed an unexpected population branching pattern, gene flow, and timing of the differentiation that occurred within a few hundred thousand years, i.e., long after the mountain uplift that was assumed to be the primary geological cause of the population differentiation. The analyses also showed that all local populations experienced a severe decline during the last glacial and post-glacial periods. Conclusions Our results suggest that the floodplain bitterling was able to disperse through unknown routes after mountain uplift and that its populations were strongly influenced by climatic and geographic changes in glacial–interglacial cycles and subsequent human activities, probably related to its floodplain-dependent ecology. The genomic data highlight the unanticipated distribution process of this species and the magnitude of the impact of human activities, with important implications for its conservation.

Abstract Background Developing evolutionary literacy is an important component of post-secondary students’ education and is a primary goal for evolution educators. However, as obstacles exist to students’ acceptance of evolution, more information needs to be obtained about what type of evidence students find compelling (or do not) that supports evolution to explain the diversity of life on Earth. Using the lens of conceptual ecologies, this study aimed to determine what lines of evidence senior university biology students found compelling. We examined six semesters of Pre-Post survey data taken at the beginning and end of the semester from 2014 to 2021 to categorize the types of evidence students claimed to find compelling. Results We identified seven categories of evidence that senior university biology students found compelling: New from Old, Comparative Biology, Structural Homology, Demonstration of Natural Section, Adaptation, Molecular Biology, and Not Convinced. A Chi-Square test of Independence indicated a significant difference in the categories that were most frequently discussed between the Pre- and Post surveys. Demonstration of Natural Selection had the highest percentage of student responses in the Pre-survey, while Molecular Biology ranked the highest in the Post. We parsed out the particular types of evidence nested within the Molecular Biology category to see which students found more compelling in the Post-survey. We also found that participation in a one-semester course decreased the percentage of students who answered Not Convinced from Pre to Post every semester. Conclusions Results from this study can offer suggestions for evolution education, such as including more examples of Molecular Biology evolution, as students found this category most compelling in the Post-survey. These types of examples can be used throughout evolution courses or focused on more deeply to support student understanding.

Abstract This study introduces a participatory science-inspired approach to teaching and curriculum design, involving undergraduate students directly in active research. Using a case study on dinosaur eye size, integrated into a first-year undergraduate course in Geology and Palaeontology at a UK university, this study presents the advantages and disadvantages of this approach for both teachers and learners. As part of the study, 22 undergraduate students were involved in data collection, analysis, and the subsequent publication processes, emphasizing active student participation in research. A subsequent survey demonstrated high student engagement and perceived relevance of this participatory science-style teaching approach. Results indicate that students found the approach appealing, engaging, and beneficial for understanding scientific concepts and methods. The case study shows that a participatory science approach through a course-based research experience can enhance student engagement and learning by providing meaningful, hands-on research experiences. This approach allowed students to apply theoretical knowledge in a realistic context, fostering their understanding of evolutionary theory through active data collection and analysis. However, care should be taken concerning data accuracy and ethical aspects, such as exploitation of labour and the recognition of knowledge creators and participants. Despite these challenges, the benefits of integrating such approaches into higher education curricula can be substantial, offering a valuable model for teaching evolutionary theory and related topics.

Abstract Background Phylogenetics is one of the main methodologies to understand cross-cutting principles of evolution, such as common ancestry and speciation. Phylogenetic trees, however, are reportedly challenging to teach and learn. Furthermore, phylogenetics teaching methods traditionally rely solely on visual information, creating inaccessibility for people with visual impairment. Sensory learning style models advocate for tailoring teaching to individual preferred sensory learning style. However, recent research suggests that optimal learning, independently of preferred learning style, depends on the types of transmitted information and learning tasks. The lack of empirically-supported education into the effectiveness of teaching phylogenetics through alternative sensory modalities potentially hinders learning. The aim of this study was to determine whether phylogenetic trees could be better understood if presented in kinaesthetic or multisensory teaching modalities. Results Participants (N = 52) self-assessed personal learning style and were randomly assigned to: visual, kinaesthetic or multisensory learning conditions. Phylogeny reading performance was better for both kinaesthetic and multisensory teaching conditions, compared to the visual teaching condition. There was no main effect and no interaction effect of personal learning style. Conclusions This study establishes a baseline for further research by suggesting that easy-to-implement kinaesthetic teaching modalities might support phylogenetic tree learning and reading. This has practical implications for evolution education and accessibility for students with visual impairment, underscoring the need to shift from vision-centric teaching paradigms towards evidence-based instructional strategies that accommodate sensory diversity.

Abstract Background Panarthropods, a major group of invertebrate animals comprised of arthropods, onychophorans, and tardigrades, are the only limb-bearing members of Ecdysozoa. The complexity and versatility of panarthropod paired limbs has prompted great interest in their development to better understand the formation of these structures and the genes involved in this process. However, studies of limb patterning and development are overwhelmingly focused on arthropods, followed by select work on onychophorans but almost entirely lacking for tardigrades. This model organism bias is inherently limited and precludes a comparative analysis of how panarthropod legs originated, have evolved, and the likely limb patterning genes present in the earliest panarthropod ancestors. In this study, we investigated tardigrade homologs of seven arthropod distal limb patterning genes (apterous, aristaless, BarH1, clawless, Lim1, rotund, and spineless) to better characterize tardigrade limb development in a comparative context. Results We detected homologs of all seven genes in the eutardigrade Hypsibius exemplaris and heterotardigrade Echiniscoides cf. sigismundi suggesting their conservation in both tardigrade lineages. Hybridization chain reaction experiments in H. exemplaris reveal a regionalized expression pattern for the genes aristaless, BarH1, clawless, rotund and spineless. Conclusion The observed regionalized expression of the distal limb patterning genes in H. exemplaris might reflect the external morphological features of tardigrade legs, such as the distal claws, sensory organs in the proximal region, and specific muscle attachment sites. The comparison between the expression of these limb patterning genes in H. exemplaris relative to other panarthropods suggests their conserved role in the last common panarthropod ancestor, such as establishing the distal limb end and the distribution of sensory structures. Our results support the hypothesis that tardigrade legs are homologous to the distal region of other panarthropod limbs, as suggested by previous work on the expression of leg gap genes in H. exemplaris.

Abstract Understanding the interplay between genetic drift, natural selection, gene flow, and demographic history in driving phenotypic and genomic differentiation of insular populations can help us gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study repeated evolution and identify shared patterns in their genomic landscapes of differentiation. We selected four species of passerine birds (Common Chaffinch Fringilla coelebs/canariensis, Red-billed Chough Pyrrhocorax pyrrhocorax, House Finch Haemorhous mexicanus and Dark-eyed/island Junco Junco hyemalis/insularis) that have both mainland and insular populations. Changes in body size between island and mainland populations were consistent with the island rule. For each species, we sequenced whole genomes from mainland and insular individuals to infer their demographic history, characterize their genomic differentiation, and identify the factors shaping them. We estimated the relative (F st ) and absolute (d xy ) differentiation, nucleotide diversity (π), Tajima’s D, gene density and recombination rate. We also searched for selective sweeps and chromosomal inversions along the genome. All species shared a marked reduction in effective population size (Ne) upon island colonization. We found diverse patterns of differentiated genomic regions relative to the genome average in all four species, suggesting the role of selection in island-mainland differentiation, yet the lack of congruence in the location of these regions indicates that each species evolved differently in insular environments. Our results suggest that the genomic mechanisms involved in the divergence upon island colonization—such as chromosomal inversions, and historical factors like recurrent selection—differ in each species, despite the highly conserved structure of avian genomes and the similar selective factors involved. These differences are likely influenced by factors such as genetic drift, the polygenic nature of fitness traits and the action of case-specific selective pressures.

Abstract The ecological importance of great apes is widely recognised, yet few studies have highlighted the role of protecting great apes’ habitats in mitigating climate change, particularly through carbon sequestration. This study used GIS tools to extract data from various sources, including the International Union for Conservation of Nature database, to examine carbon quantity and great ape abundance in African great ape habitats. Subsequently, we employed a generalised linear model to assess the relationship between locally measured great ape populations abundance and carbon storage across areas with different levels of protection. Our findings showed a positive relationship between the abundance of great apes in their habitats and carbon storage, likely since conservation efforts in great apes habitats may be strengthened with higher great ape populations. The results reveal that gorilla habitats exhibited higher carbon storage than chimpanzee habitats. Specifically, the areas inhabited by gorillas are associated with a mean increase of 27.47 t/ha in carbon storage. Additionally, we observed a positive association between highly protected areas and carbon storage within great ape habitats. Our model indicates that highly protected areas increase the mean carbon stored by 1.13 t/ha compared to medium protected areas, which show a reduction of 15.49 t/ha. This highlights the critical role that protected areas play in both species conservation and carbon sequestration, contributing significantly to climate mitigation efforts. Furthermore, our study underscores the significant contribution of great ape habitats, extending beyond protected areas, to carbon storage, highlighting the potential for synergistic conservation strategies targeting both great apes and carbon sequestration. Protecting great apes is vital for reducing carbon emissions from deforestation and boosting tropical forest carbon sinks. Since nearly 90% of great apes live outside protected areas, targeted conservation in these low-protected areas is also crucial.

Abstract Geographic distribution, as well as evolutionary and biogeographic processes and patterns of marine invertebrate benthic species are strongly shaped by dispersal ability during the life cycle. Remote oceanic islands lie at the brink of complex biotic and abiotic interactions which have significantly influenced the biodiversity patterns we see today. The interaction between geological environmental change and taxon-specific dispersal modes can influence species evolutionary patterns, eventually delimiting species-specific biogeographic regions. In this study, we compare the population genetic patterns of the marine bivalve Cardita calyculata in the northeast Atlantic, discussing the role of Macaronesian islands during past climatic cycles. The genetic structure and diversity patterns were outlined based on SSR-GBAS loci of 165 individuals and on the mitochondrial COI marker of 22 individuals from the Canary Islands, Madeira, Azores and the Mediterranean. The highly structured genetic pattern found among regions and within archipelagos suggests the central role of oceanic islands in promoting the divergence of the species in both the NE Atlantic and the Mediterranean. The high degree of divergence in the COI dataset (> 7%) suggests the existence of potential cryptic speciation that needs to be further explored with a more comprehensive sampling. Such patterns are only congruent with a scenario where C. calyculata populations were maintained during glacial/interglacial cycles, supporting the role of the studied archipelagos as drivers of diversity for marine biota. We stress the importance of developing studies for species with various life history and dispersal modes. In such a way, a more profound understanding of the biogeographic and evolutionary significance of oceanic islands can catalyse directed conservation efforts, especially in the context of the ongoing climate crisis.

Abstract A terrace in a phylogenetic tree space is a region where all trees contain the same set of subtrees, due to certain patterns of missing data among the taxa sampled, resulting in an identical optimality score for a given data set. This was first investigated in the context of phylogenetic tree estimation from sequence alignments using maximum likelihood (ML) and maximum parsimony (MP). It was later extended to the species tree inference problem from a collection of gene trees, where a set of equally optimal species trees was referred to as a “pseudo” species tree terrace which does not consider the topological proximity of the trees in terms of the induced subtrees resulting from certain patterns of missing data. In this study, we mathematically characterize species tree terraces and investigate the mathematical properties and conditions that lead multiple species trees to induce/display an identical set of locus-specific subtrees owing to missing data. We report that species tree terraces are agnostic to gene tree heterogeneity. Therefore, we introduce and characterize a special type of gene tree topology-aware terrace which we call “peak terrace”. Moreover, we empirically investigated various challenges and opportunities related to species tree terraces through extensive empirical studies using simulated and real biological data. We demonstrate the prevalence of species tree terraces and the resulting ambiguity created for tree search algorithms. Remarkably, our findings indicate that the identification of terraces could potentially lead to advances that enhance the accuracy of summary methods and provide reasonably accurate branch support.

Abstract Background This review compiles and synthesises the existing information concerning non-native poeciliid introductions to Africa. The recent upsurge in research on invasive poeciliids has revealed their widespread occurrence in Africa. Results Within the 87 relevant articles, 74% reported on the presence of Gambusia spp., 33% on P. reticulata, 19% on X. hellerii, 11% on X. maculatus, and 5% on other ornamental poeciliids. Overall, poeciliids have been documented as introduced to 25 different countries in Africa. With Gambusia spp. being introduced to 16 countries and P. reticulata to 19 countries. Our results are representative of the current state of research on invasive poeciliids in Africa. There was a concentration of studies in South Africa, with limited research elsewhere. Current distribution data is relatively patchy, although widespread surveys of multiple river systems in Morocco and South Africa, confirmed widespread and abundant established poeciliid populations. The ecological impacts of invasive poeciliids in Africa remain understudied but evidence indicates deleterious effects on native fish, invertebrates, and amphibians, many of which are critically endangered or endemic. Conclusion Current research is limited in reporting from certain countries and ecological impacts. An increased effort to monitor species composition in vulnerable waterbodies, especially in the many African countries where invasive poeciliids are reported, should be completed to reveal further established populations. Future research should prioritise quantifying the ecological impacts of invasive poeciliids in the field and identifying both vulnerable and resistant native ecosystems to guide future management decisions.

Abstract Background Montane ecosystems play crucial roles as global biodiversity hotspots. However, climatic changes and anthropogenic pressure increasingly threaten the stability of montane community dynamics, such as diversity-elevation interactions, creating a challenge in understanding species biogeography and community ecology dynamics in these crucial conservation areas. We examined how varying sampling spatial grains influence small mammal diversity patterns within Kenya’s tallest montane ecosystems. Methods Employing a combination of multidimensional alpha diversity metrics and multisite beta diversity characteristics (species richness, phylogenetic and functional diversity and divergence, and multisite beta diversity) alongside spatial generalized additive multivariate regression analyses, we tested how spatial scaling influences elevational diversity gradient patterns and their associations with environmental and human activity variables. Results The diversity-elevation associations were generally homogeneous across spatial grains; however, idiosyncratic patterns emerged across mountains. The total (taxonomic, phylogenetic, and functional) beta diversity, nestedness, and turnover resultant components monotonically increased or decreased with varying spatial grains. The associations between the diversity patterns and the environmental and human footprint variables increased with spatial grain size but also presented variations across mountains and indices. Species richness and phylogenetic and functional richness indices were more strongly influenced by spatial scale variations than were the divergence and community structure indices in both the diversity distribution patterns and their associations with the environmental and human variables. Conclusions The diversity-elevation and diversity-environment (including human activity pressure) relationships across spatial grains suggest that montane small mammal diversity patterns portray subtle but systematic sensitivity to sampling spatial grain variation and underscore the importance of geographical context in shaping these elevational diversity gradients. For improved effectiveness, conservation efforts should consider these spatial effects and the unique geographical background of individual montane ecosystems.

Abstract Dancing to music is ancient and widespread in human cultures. While dance shows great cultural diversity, it often involves nonvocal rhythmic movements synchronized to musical beats in a predictive and tempo-flexible manner. To date, the only nonhuman animals known to spontaneously move to music in this way are parrots. This paper proposes that human-parrot similarities in movement to music and in the neurobiology of advanced vocal learning hold clues to the evolutionary foundations of human dance. The proposal draws on recent research on the neurobiology of parrot vocal learning by Jarvis and colleagues and on a recent cortical model for speech motor control by Hickock and colleagues. These two lines of work are synthesized to suggest that gene regulation changes associated with the evolution of a dorsal laryngeal pitch control pathway in ancestral humans fortuitously strengthened auditory-parietal cortical connections that support beat-based rhythmic processing. More generally, the proposal aims to explain how and why the evolution of strong forebrain auditory-motor integration in the service of learned vocal control led to a capacity and proclivity to synchronize nonvocal movements to the beat. The proposal specifies cortical brain pathways implicated in the origins of human beat-based dancing and leads to testable predictions and suggestions for future research.

Abstract Each commentary on my article raises important points and new ideas for research on rhythmic processing in humans and other species. Here I respond to points concerning the role of social factors in the ontogeny of beat synchronization, the neural connectivity underlying beat synchronization, the evolution of this connectivity, and the mechanisms by which evolutionary changes in the strength of one white matter tract (driven by natural selection) can have knock-on effects on the structure of an adjacent tract.

Abstract Rosavirus is a newly discovered member of the family Picornaviridae that was initially detected in wild rodents and subsequently in children with diarrhoea. Nevertheless, there is a significant gap in our understanding of the geographical distribution, phylogenetic relationships, evolutionary patterns, and transmission of rosaviruses. To address these issues, we analysed 434 rodents and shrews from five different species that were collected in southern China. Using PCR screening of faecal samples, we detected rosaviruses in Norway rats (Rattus norvegicus) and identified two previously undocumented host species: tanezumi rats (Rattus tanezumi) and Asian house shrews (Suncus murinus). Rosaviruses were particularly common in these animals, with an overall prevalence rate of 32.49% (141/434). For genetic and evolutionary analyses, we selected six representative positive samples to amplify the complete genomes of rosaviruses. Bayesian phylogenetic analysis suggested that our sequences clustered within the genus Rosavirus, where genotype B sequences are the closest relatives. The elevated nonsynonymous-to-synonymous ratios observed in rosavirus B may be attributed to relaxed selection pressures driven by virus spillover events. On the basis of the available data, it is hypothesized that the genus Rosavirus may have originated from Norway rats around the year 1339. In summary, these findings provide valuable insights into the complex evolutionary history of rosaviruses and underscore the urgent need for ongoing surveillance of this virus.

Abstract The evolution of cancer cells parallels species evolution in numerous ways. Variations arise and spread under the pressure of competition between cancer cells. Current investigations of tumor evolution echo earlier debates between biologists. These include the role of non-Darwinian mechanisms, the contribution of neutral evolution, and life history dynamics. The trade-off between proliferation and metastasis is the most well-studied application of life history theory to cancer evolution. This article briefly introduces some parallels between cancer and species evolution, focusing on the life history of evolving tumors. Next, we review evidence from simulation and experimental studies supporting task specialization and trade-offs in cancer. We also cover recent work on inferring tumor tasks from data. We then turn to the implications of multi-tasking and the utility of the theory in explaining critical aspects of tumor heterogeneity. Finally, we discuss some of the criticism and future directions of this research topic.

Abstract Background Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification. Results The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity. Conclusions Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.

Abstract Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.

Abstract The Western honey bee (Apis mellifera) subspecies exhibit local adaptive traits that evolved in response to the different environments that characterize their native distribution ranges. An important trait is the cuticular hydrocarbon (CHC) profile, which helps to prevent desiccation and mediate communication. We compared the CHC profiles of six European subspecies (A. m. mellifera, A. m. carnica, A. m. ligustica, A. m. macedonica, A. m. iberiensis, and A. m. ruttneri) and investigated potential factors shaping their composition. We did not find evidence of adaptation of the CHC profiles of the subspecies to the climatic conditions in their distribution range. Subspecies-specific differences in CHC composition might be explained by phylogenetic constraints or genetic drift. The CHC profiles of foragers were more subspecies-specific than those of nurse bees, while the latter showed more variation in their CHC profiles, likely due to the lower desiccation stress exerted by the controlled environment inside the hive. The strongest profile differences appeared between nurse bees and foragers among all subspecies, suggesting an adaptation to social task and a role in communication. Foragers also showed an increase in the relative amount of alkanes in their profiles compared to nurses, indicating adaptation to climatic conditions.

Abstract In order to clarify the chloroplast genomes and structural features of ten Ilex species and provide insights into the phylogeny and genome evolution of the genus Ilex, we conducted a comparative analysis of chloroplast genomes using bioinformatics methods. The chloroplast genomes of ten Ilex species were obtained, and their structural features and variations were compared. The results indicated that all chloroplast genomes in the genus Ilex exhibit a double-stranded circular structure, with sizes ranging from 157,356 to 158,018 bp, showing minimal differences in size. The chloroplast genomes of the ten Ilex species have a relatively conservative gene count, with a total of 134 to 135 genes, including 88 or 89 protein-coding genes, and a conserved number of 8 rRNA genes. Each chloroplast genome contains 3 to 123 SSR (Simple Sequence Repeat) sites, predominantly composed of mononucleotide and trinucleotide repeats, with no detection of pentanucleotide or hexanucleotide repeats. The variation in dispersed repeat sequences among Ilex species is minimal, with a total repeat sequence number ranging from 1 to 14, concentrated in the length range of 30 to 42 base pairs. The expansion and contraction of chloroplast genome boundaries among Ilex species are relatively stable, with only minor variations observed in individual species. Variations in non-coding regions are more pronounced than those in coding regions, with the variability in the Large Single Copy region (LSC) being the highest, while the variability in the Inverted Repeat region A (IRa) is the lowest. The divergence time among Ilex species was estimated using the MCMC-tree module, revealing the evolutionary relationships among these species, their common ancestors, and their differentiation throughout the evolutionary process. The research findings provide a valuable reference for the systematic study and molecular marker development of Ilex plants.

Abstract Background Continuously growing teeth are an important innovation in mammalian evolution, yet genetic regulation of continuous growth by stem cells remains incompletely understood. Dental stem cells responsible for tooth crown growth are lost at the onset of tooth root formation. Genetic signaling that initiates this loss is difficult to study with the ever-growing incisor and rooted molars of mice, the most common mammalian dental model species, because signals for root formation overlap with signals that pattern tooth size and shape (i.e., cusp patterns). Bank and prairie voles (Cricetidae, Rodentia, Glires) have evolved rooted and unrooted molars while retaining similar size and shape, providing alternative models for studying roots. Results We assembled a de novo genome of Myodes glareolus, a vole with high-crowned, rooted molars, and performed genomic and transcriptomic analyses in a broad phylogenetic context of Glires (rodents and lagomorphs) to assess differential selection and evolution in tooth forming genes. Bulk transcriptomics comparisons of embryonic molar development between bank voles and mice demonstrated overall conservation of gene expression levels, with species-specific differences corresponding to the accelerated and more extensive patterning of the vole molar. We leverage convergent evolution of unrooted molars across the clade to examine changes that may underlie the evolution of unrooted molars. We identified 15 dental genes with changing synteny relationships and six dental genes undergoing positive selection across Glires, two of which were undergoing positive selection in species with unrooted molars, Dspp and Aqp1. Decreased expression of both genes in prairie voles with unrooted molars compared to bank voles supports the presence of positive selection and may underlie differences in root formation. Conclusions Our results support ongoing evolution of dental genes across Glires and identify candidate genes for mechanistic studies of root formation. Comparative research using the bank vole as a model species can reveal the complex evolutionary background of convergent evolution for ever-growing molars.

Abstract The two-component system (TCS) consists of histidine kinase (HK), histidine phosphate transfer protein (HP), and response regulatory factor (RR). It is one of the most crucial components of signal transduction in plants, playing a significant role in regulating plant growth, development, and responses to various abiotic stresses. Although TCS genes have been extensively identified in a variety of plants, the genome-wide recognition and examination of TCS in switchgrass remain unreported. Accordingly, this study identified a total of 87 TCS members in the genome of switchgrass, comprising 20 HK(L)s, 10 HPs, and 57 RRs. Detailed analyses were also conducted on their gene structures, conserved domains, and phylogenetic relationships. Moreover, this study analysed the gene expression profiles across diverse organs and investigated their response patterns to adverse environmental stresses. Results revealed that 87 TCS genes were distributed across 18 chromosomes, with uneven distribution. Expansion of these genes in switchgrass was achieved through both fragment and tandem duplication. PvTCS members are relatively conservative in the evolutionary process, but the gene structure varies significantly. Various cis-acting elements, varying in types and amounts, are present in the promoter region of PvTCSs, all related to plant growth, development, and abiotic stress, due to the TCS gene structure. Protein-protein interaction and microRNA prediction suggest complex interactions and transcriptional regulation among TCS members. Additionally, most TCS members are expressed in roots and stems, with some genes showing organ-specific expression at different stages of leaf and inflorescence development. Under conditions of abiotic stress such as drought, low temperature, high temperature, and salt stress, as well as exogenous abscisic acid (ABA), the expression of most TCS genes is either stimulated or inhibited. Our systematic analysis could offer insight into the characterization of the TCS genes, and further the growth of functional studies in switchgrass.

Abstract In last 100 years or so, much information has been accumulated on avian karyology, genetics, physiology, biochemistry and evolution. The chicken genome project generated genomic resources used in comparative studies, elucidating fundamental evolutionary processes, much of it funded by the economic importance of domestic fowl (which are also excellent model species in many areas). Studying karyotypes and whole genome sequences revealed population processes, evolutionary biology, and genome function, uncovering the role of repetitive sequences, transposable elements and gene family expansion. Knowledge of the function of many genes and non-expressed or identified regulatory components is however still lacking. Birds (Aves) are diverse, have striking adaptations for flight, migration and survival and inhabit all continents most islands. They also have a unique karyotype with ~ 10 macrochromosomes and ~ 30 microchromosomes that are smaller than other reptiles. Classified into Palaeognathae and Neognathae they are evolutionarily close, and a subset of reptiles. Here we overview avian molecular cytogenetics with reptilian comparisons, shedding light on their karyotypes and genome structure features. We consider avian evolution, then avian (followed by reptilian) karyotypes and genomic features. We consider synteny disruptions, centromere repositioning, and repetitive elements before turning to comparative avian and reptilian genomics. In this context, we review comparative cytogenetics and genome mapping in birds as well as Z- and W-chromosomes and sex determination. Finally, we give examples of pivotal research areas in avian and reptilian cytogenomics, particularly physical mapping and map integration of sex chromosomal genes, comparative genomics of chicken, turkey and zebra finch, California condor cytogenomics as well as some peculiar cytogenetic and evolutionary examples. We conclude that comparative molecular studies and improving resources continually contribute to new approaches in population biology, developmental biology, physiology, disease ecology, systematics, evolution and phylogenetic systematics orientation. This also produces genetic mapping information for chromosomes active in rearrangements during the course of evolution. Further insights into mutation, selection and adaptation of vertebrate genomes will benefit from these studies including physical and online resources for the further elaboration of comparative genomics approaches for many fundamental biological questions.

Abstract Background Sanniang Bay (SNB) and Dafeng River (DFR), located in the northern Beibu Gulf, is well-known as one of the eight habitats for humpback dolphins in China. This region is representative of typical estuarine and bay ecosystems and produce complex hydrodynamic seawater conditions. Moreover, anthropogenic pressure, such as eutrophication and large-scale infrastructure projects, have caused ongoing habitat deterioration and loss. It is urgent to know the phytoplankton community and their relationships with environmental factors in this region. Results In this study, we assessed the diversity and assembly mechanisms of phytoplankton communities, as well as their relationship with the physicochemical characteristics of seawater in SNB and DFR region using 18 S rDNA metabarcoding analysis. The results showed that seasonal changes markedly impacted the alpha diversity of the phytoplankton community. From March to July, with the average temperature increasing from 25.2℃ to 28.1℃,the Shannon or Species Richness were negatively correlated with temperature. During hot season (in Sep, average temperature 32.1℃), phytoplankton diversity was negatively correlated with nutrients (NH4 +, NO3 −, PO4 3−, TN). Additionally, during the rainy season, the Bray-Curtis similarity of the phytoplankton community was significantly lower than during the dry season. In March, the distance among the sampling sites was most strongly and positively correlated with the Bray-Curtis dissimilarity. Stochastic processes, specifically dispersal limitation and ecological drift, are the primary drivers of community assembly, while deterministic assembly processes (mainly heterogeneous selection) contribute a relatively minor portion (

Abstract Background Heelwalkers possess a highly modified tarsal attachment system. All extant species lift the distalmost tarsomere permanently off the substrate and primarily use their euplantulae for locomotion. The combination of a smooth adhesive pad (arolium) on the pretarsus and fibrillary attachment pads on the euplantulae offers valuable insights for translational approaches, but its infra-order diversity remains unexplored. Results We explored the morphology of the tarsal attachment apparatus of Mantophasmatodea based on a representative taxon sampling spanning a large fraction of species of this group and compared morphological differences in the specialized morphology of this system across species and sexes. Our scanning electron microscope investigation of the tarsi of 11 species (52% of all described extant species) revealed an overall very consistent ground pattern and almost no specific adaptations. There are only minor, but mostly clade-specific differences in the shape of the adhesive setae on the tarsal euplantulae and in the morphology and density of the acanthae on the pretarsal arolium. Both features differ primarily between Austrophasmatidae in comparison to the remaining Mantophasmatodea taxa. Conclusion We conclude that the strong specialization of the mantophasmatodean tarsal attachment sufficiently copes with the diversity of substrates the insects are exposed to.

Abstract Background Evolution continues to be one of the most difficult biological topics to teach, warranting innovative pedagogical tools and assessment strategies for enhancing evolutionary instruction. A major advance in measuring the evolution knowledge of undergraduate students came with the development of the Conceptual Assessment of Natural Selections (CANS). In this study, we use the CANS to measure knowledge and learning of natural selection in a large (N > 6000) sample of undergraduate students to expand upon prior validity testing of this instrument and advance knowledge of student evolutionary reasoning. We apply the Rasch measurement framework to examine if the CANS productively measures the intended construct and investigate the patterns of knowledge and learning about evolution among students with different backgrounds and demographic characteristics. Results While a unidimensional Rasch model demonstrated acceptable reliabilities and fit for most of the CANS items, some items showed problematic fit statistics and were resistant to instruction. The instrument items also did not span the full range of student abilities, which suggests relatively low measurement precision. Our large sample also allowed rigorous tests of multidimensionality, revealing the presence of multiple dimensions or constructs, some of which may not be intentional. These results generated specific item-level recommendations for improving this instrument. Using Rasch measures to examine learning patterns, we found that pre-test evolution knowledge was low but that there were high learning gains by the end of the course. However, some concept categories were found to be more difficult than others, suggesting the need for more attention to these areas by instructors. We also identified pre-test disparities in evolutionary knowledge by socially defined race and biological sex, yet students from all groups achieved comparable learning gains at the end of the course. Conclusion The CANS holds great potential to generate critical insights about student evolutionary reasoning and provide information about which instructional approaches most effectively mitigate the notable knowledge disparities among students. We leverage the findings of this study to propose tangible ways in which this instrument may be improved in order to better achieve both of these goals.

Abstract Background Early embryogenesis is characterized by dramatic cell proliferation and movement. In most insects, early embryogenesis includes a phase called the uniform blastoderm, during which cells evenly cover the entirety of the egg. However, the embryo of the German cockroach, Blattella germanica, like those of many insects within the super order Polyneoptera, does not have a uniform blastoderm; instead, its first cells condense rapidly at the site of a future germband. We investigated early development in this species in order to understand how early gene expression is or is not conserved in these insect embryos with distinct early cell behaviors. Results We present a detailed time series of nuclear division and distribution from fertilization through germband formation and report patterns of expression for the early patterning genes hunchback, caudal, and twist in order to understand early polarization and mesoderm formation. We show a detailed time course of the spatial expression of two genes involved in the segmentation cascade, hedgehog and even-skipped, and demonstrate two distinct dynamics of the segmentation process. Conclusions Despite dramatic differences in cell distribution between the blastoderms of many Polyneopteran insects and those of more well-studied developmental models, expression patterns of early patterning genes are mostly similar. Genes associated with axis determination in other insects are activated relatively late and are probably not maternally deposited. The two phases of segmentation—simultaneous and sequential—might indicate a broadly conserved mode of morphological differentiation. The developmental time course we present here should be of value for further investigation into the causes of this distinct blastoderm type.

Abstract Background The snake genera Atropoides, Cerrophidion, and Metlapilcoatlus form a clade of neotropical pit vipers distributed across Mexico and Central America. This study evaluated the myotoxic and neurotoxic effects of nine species of Atropoides, Cerrophidion, and Metlapilcoatlus, and the neutralising efficacy of the ICP antivenom from Costa Rica against these effects, in the chick biventer cervicis nerve-muscle preparation. Given the prominence of PLA2s within the venom proteomes of these species, we also aimed to determine the neutralising potency of the PLA2 inhibitor, varespladib. Results All venoms showed myotoxic and potential neurotoxic effects, with differential intra-genera and inter-genera potency. This variation was also seen in the antivenom ability to neutralise the muscle damaging pathophysiological effects observed. Variation was also seen in the relative response to the PLA2 inhibitor varespladib. While the myotoxic effects of M. mexicanus and M. nummifer venoms were effectively neutralised by varespladib, indicating myotoxicity is PLA2 mediated, those of C. godmani and M. olmec venoms were not, revealing that the myotoxicity is driven by non-PLA2 toxin types. Conclusions This study characterises the myotoxic and neurotoxic venom activity, as well as neutralisation of venom effects from the Atropoides, Cerrophidion, and Metlapilcoatlus clade of American crotalids. Our findings contribute significant clinical and evolutionary knowledge to a clade of poorly researched snakes. In addition, these results provide a platform for future research into the reciprocal interaction between ecological niche specialisation and venom evolution, as well as highlighting the need to test purified toxins to accurately evaluate the potential effects observed in these venoms.

Abstract Background With the advances in high-throughput sequencing and bioinformatic pipelines, mitochondrial genomes have become increasingly popular for phylogenetic analyses across different clades of invertebrates. Despite the vast rise in available mitogenomic datasets of molluscs, one class of aplacophoran molluscs – Solenogastres (or Neomeniomorpha) – is still neglected. Results Here, we present six new mitochondrial genomes from five families of Solenogastres (Amphimeniidae, Gymnomeniidae, Proneomeniidae, Pruvotinidae, Simrothiellidae), including the first complete mitogenomes, thereby now representing three of the four traditional orders. Solenogaster mitogenomes are variable in size (ranging from approximately 15,000 bp to over 17,000 bp). The gene order of the 13 protein coding genes and two rRNA genes is conserved in three blocks, but considerable variation occurs in the order of the 22 tRNA genes. Based on phylogenetic analyses and reconstruction of ancestral mitochondrial genomes of Aculifera, the position of (1) trnD gene between atp8 and atp6, (2) trnT and P genes between atp6 and nad5, and (3) trnL1 gene between G and E, resulting in a ‘MCYWQGL1E’-block of tRNA genes, are all three considered synapomorphies for Solenogastres. The tRNA gene block ‘KARNI’ present in Polyplacophora and several conchiferan taxa is dissolved in Solenogastres. Conclusion Our study shows that mitogenomes are suitable to resolve the phylogenetic relationships among Aculifera and within Solenogastres, thus presenting a cost and time efficient compromise to approach evolutionary history in these clades.

Abstract Background Isolating phylogenetic signal from morphological data is crucial for accurately merging fossils into the tree of life and for calibrating molecular dating. However, subjective character definition is a major limitation which can introduce biases that mislead phylogenetic inferences and divergence time estimation. The use of quantitative data, e.g., geometric morphometric (GMM; shape) data can allow for more objective integration of morphological data into phylogenetic inference. This systematic review describes the current state of the field in using continuous morphometric data (e.g., GMM data) for phylogenetic reconstruction and assesses the efficacy of these data compared to discrete characters using the PRISMA-EcoEvo v1.0. reporting guideline, and offers some pathways for approaching this task with GMM data. A comprehensive search string yielded 11,123 phylogenetic studies published in English up to Oct 2023 in the Web of Science database. Title and abstract screening removed 10,975 articles, and full-text screening was performed for 132 articles. Of these, a total of twelve articles met final inclusion criteria and were used for downstream analyses. Results Phylogenetic performance was compared between approaches that employed continuous morphometric and discrete morphological data. Overall, the reconstructed phylogenies did not show increased resolution or accuracy (i.e., benchmarked against molecular phylogenies) as continuous data alone or combined with discrete morphological datasets. Conclusions An exhaustive search of the literature for existing empirical continuous data resulted in a total of twelve articles for final inclusion following title/abstract, and full-text screening. Our study was performed under a rigorous framework for systematic reviews, which showed that the lack of available comparisons between discrete and continuous data hinders our understanding of the performance of continuous data. Our study demonstrates the problem surrounding the efficacy of continuous data as remaining relatively intractable despite an exhaustive search, due in part to the difficulty in obtaining relevant comparisons from the literature. Thus, we implore researchers to address this issue with studies that collect discrete and continuous data sets with directly comparable properties (i.e., describing shape, or size).

Abstract Drought stress poses a critical threat to global crop yields and sustainable agriculture. The GASA genes are recognized for their pivotal role in stress tolerance and plant growth, but little is known about how they function in sunflowers. The investigation aimed to identify and elucidate the role of HaGASA genes in conferring sunflowers with drought tolerance. Twenty-seven different HaGASA gene family members were found in this study that were inconsistently located across eleven sunflower chromosomes. Phylogeny analysis revealed that the sunflower HaGASA genes were divided into five subgroups by comparing GASA genes with those from Arabidopsis, peanut, and soybean, with members within each subgroup displaying similar conserved motifs and gene structures. In-silico evaluation of cis-regulatory elements indicated the existence of specific elements associated with stress-responsiveness being the most abundant, followed by hormone, light, and growth-responsive elements. Transcriptomic data from the NCBI database was utilized to assess the HaGASA genes expression profile in different sunflower varieties under drought conditions. The HaGASA genes expression across ten sunflower genotypes under drought stress, revealed 14 differentially expressed HaGASA genes, implying their active role in the plant’s stress response. The expression in different organs revealed that HaGASA2, HaGASA11, HaGASA17, HaGASA19, HaGASA21 and HaGASA26 displayed maximum expression in the stem. Our findings implicate HaGASA genes in mediating sunflower growth maintenance and adaptation to abiotic stress, particularly drought. The findings, taken together, provided a basic understanding of the structure and potential functions of HaGASA genes, setting the framework for further functional investigations into their roles in drought stress mitigation and crop improvement strategies.

Abstract Background Achieving cost-competitiveness remains challenging for industrial biomanufacturing. With whole-cell biocatalysis, inefficiency presents when individual cells vary in their production levels. The problem exacerbates when the basis for such production heterogeneity is heritable. Here, evolution selects for the low- and non-producers, as they have lowered/abolished the cost of bioproduction to fitness. With the scale of population expansion required for industrial bioproduction, the asymmetrical enrichment can be severe enough to compromise the performance, and hence commercial viability of the bioprocess. Clearly, addressing production heterogeneity is crucial, especially in improving the stability of bioproduction across the cell generations. In this respect, we designed a growth-coupling strategy for terpenoid bioproduction in Escherichia coli. By knocking out the native 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) gene and introducing the heterologous mevalonate pathway, we created a chassis that relies solely on the latter for synthesis of all terpenoids. We hypothesise that the need to sustain the biosynthesis of endogenous life-sustaining terpenoids will impose a minimum level of productivity, which concomitantly improves the bioproduction of our target terpenoid. Results Following the confirmation of lethality of a dxr knockout, we challenged the strains with a continuous plasmid-based bioproduction of linalool. The Δdxr strain achieved an improved productivity profile in the first three days post-inoculation when compared to the parental strain. Productivity of the Δdxr strain remained observable near the end of 12 days, and after a disruption in nutrient and oxygen supply in a separate run. Unlike the parental strain, the Δdxr strain did not evolve the same deleterious mutations in the mevalonate pathway, nor a viable subgroup that had lost its resistance to the antibiotic selection pressure (a plausible plasmid loss event). We believe that this divergence in the evolution trajectories is indicative of a successful growth-coupling. Conclusion We have demonstrated a proof of concept of a growth-coupling strategy that improves the performance, and stability of terpenoid bioproduction across cell generations. The strategy is relatively broad in scope, and easy to implement in the background as a ‘fail-safe’ against a fall in productivity below the imposed minimum. We thus believe this work will find widespread utility in our collective effort towards industrial bioproduction.

Abstract Background Few animal populations have been studied under the framework of the OCBIL theory, which addresses the ecology and evolution of biodiversity on old climatically buffered infertile landscapes. Available genetic data challenge the low connectivity and high genetic differentiation predicted for isolated tepui-summit vertebrate communities, suggesting potential dispersal among summits. However, the OCBIL theory posits reduced dispersibility, enhanced resilience to habitat fragmentation and inbreeding due to small populations. We tested these hypotheses by conducting the first analytic evaluation of the spatial ecology and population biology of a tepui-summit vertebrate at multiple spatial scales. Results We used harmonic radar tracking (100 individuals/448 points of contact) and capture-mark-recapture data (596 individuals captured/52 recaptured) to reveal the temporal niche, microhabitat use, population size, and dispersal abilities of the tepui-summit endemic toad Oreophrynella quelchii on Roraima-tepui. Abundance was determined using a closed population model incorporating sources of variation in capture probability. We tested the relative influence of biotic and abiotic variables on distances moved through model selection. Our data indicate that the population size of O. quelchii is remarkably large (ca. 12 million individuals), with strong seasonal demographic fluctuations. Ecology and observed limited spatial movements challenge the likelihood of active dispersal among tepui tops in this species. Our results are counter to those predicted by the available genetic data but support two hypotheses of the OCBIL theory: reduced dispersibility and enhanced resilience. However, they do not support the expectation of a small refugial population size. Conclusion We postulate that the insular, hostile tepui-summit environment tends to produce robust demographic populations, likely to buffer stochastic adverse environmental effects, rather than diversity, as observed in much younger post-Pleistocene Neotropical landscapes. Our results draw attention to the value of faunal studies using an OCBIL framework to better understand the ecology and evolution of this unique biota worldwide.

Abstract Background White forsythia (Abeliophyllum distichum) is an endangered Korean Peninsula endemic that has been subjected to recent population genomics studies using SNPs via RAD sequencing. Here, we primarily employed the often underutilized haplotype information from RAD loci to further describe the species’ previously uninvestigated haplotype-based genomic variation and structure, and genetic-geographic characteristics and gene flow patterns among its five earlier identified genetic groups. We also inferred the time of past events that may have impacted the effective population size of these groups, as well as the species’ potential future distribution amidst the warming climate and anthropogenic threats. Results Our findings emphasized the recognition of the species’ regional patterns of genetic structure, and the role of topography and its associated gene flow patterns as some of the possible factors that may have influenced the species’ present-day fragmented population distribution. The inferred bottleneck events during the Anthropocene, some of which aligned with the time of historical catastrophic events on the Peninsula (e.g., the Korean War), were revealed to have contributed to the generally low effective population size of its five lineages, particularly those with marginal distributional range. Future distribution under both optimistic and pessimistic climatic scenarios suggests unlikely suitable habitats for these populations to expand from their current range limits, at least in the next 80 years. Conclusions The small effective population size and landscape-driven limited gene flow among white forsythia populations will remain a big challenge for the conservation management of the species’ already fragmented population distribution. To help mitigate these impacts, the merging of various research approaches and the use of genomic data to their full potential is recommended to provide the optimized knowledge-based tools for the conservation of this endangered species, and other similar plants under pressure.

Abstract Invasive species such as Xanthium strumarium L., can disrupt ecosystems, reduce crop yields, and degrade pastures, leading to economic losses and jeopardizing food security and biodiversity. To address the challenges posed by invasive species such as X. strumarium, this study uses species distribution modeling (SDM) to map its potential distribution in Pakistan and assess how it might respond to climate change. This addresses the urgent need for proactive conservation and management strategies amidst escalating ecological threats. SDM forecasts a species’ potential dispersion across various geographies in both space and time by correlating known species occurrences to environmental variables. SDMs have the potential to help address the challenges posed by invasive species by predicting the future habitat suitability of species distributions and identifying the environmental factors influencing these distributions. Our study shows that seasonal temperature dependence, mean temperature of wettest quarter and total nitrogen content of soil are important climatic factors influencing habitat suitability of X. strumarium. The potential habitat of this invasive species is likely to expand beyond the areas it currently colonizes, with a notable presence in the Punjab and Khyber Pakhtunkhwa regions. These areas are particularly vulnerable due to threats to agriculture and biodiversity. Under current conditions, an estimated 21% of Pakistan’s land area is infested by X. strumarium, mainly in upper Punjab, central Punjab and Khyber Pakhtunkhwa. The range is expected to expand in most regions except Sindh. The central and northeastern parts of the country are proving to be particularly suitable habitats for X. strumarium. Effective strategies are crucial to contain the spread of X. strumarium. The MaxEnt modeling approach generates invasion risk maps by identifying potential risk zones based on a species’ climate adaptability. These maps can aid in early detection, allowing authorities to prioritize surveillance and management strategies for controlling the spread of invasive species in suitable habitats. However, further research is recommended to understand the adaptability of species to unexplored environments.

Abstract Some snakes emit hissing calls which are imitated by birds to deter potential predators. However, the effect of these snake and bird hisses on anuran risk recognition is not yet explored. Here we hypothesize that these hisses may advertise dangers to frogs and evoke their anti-predator responses. We used little torrent frogs (Amolops torrentis) as subjects and conducted sound playbacks to test their anti-predator behaviors. We found that little torrent frogs changed their calling behaviors during sympatric snake hiss playbacks, but showed no response to white noise and allopatric snake hiss playbacks. They did not respond to sympatric avian hiss that has low acoustic similarity with snake sounds. However, they decreased calling activity in response to sympatric avian hiss that has high acoustic similarity with snakes. As compared to other treatments, more individuals ceased calling during the playbacks of the highly similar bird hiss. These results suggest that frogs may recognize risks from snake and snake-like hissing calls and perform anti-predator responses.

Abstract The common pochard (Aythya ferina) is a freshwater diving duck found in the Palearctic region that has been classified as vulnerable by the IUCN due to continuous and rapid population declines across their distribution. To gain a better understanding of its genetic mechanism of adaptive evolution, we successfully sequenced and assembled the first high-quality chromosome-level genome of A. ferina using Illumina, Nanopore and Hi-C sequencing technologies. A total assembly length of 1,130.78 Mbp was obtained, with over 98.81% (1,117.37Mbp) of sequence anchored to 35 pseudo-chromosomes. We predicted 17,232 protein-coding genes, 95.9% of which were functionally annotated. We identified 339 expanded and 937 contracted gene families in the genome of A. ferina, and detected 95 genes that have been positively selected. The significantly enriched Gene Ontology and enriched pathways were related to energy metabolism, immune, nervous, and sensory systems, suggests that these factors likely played an important role in its evolution. Importantly, we recovered signatures of positive selection on genes related to vasoconstriction that may be associated with thermoregulatory adaptations of A. ferina for underwater diving. Overall, the high-quality genome assembly and annotation in this study provides valuable genomic resources for ecological and evolutionary studies, as well as toward the conservation of A. ferina.

Abstract Avida-ED is a model system that lets students explore evolution and the nature of science by observing and manipulating the evolutionary dynamics of digital organisms. Over 5 years, we ran eight 2.5-day in-person professional development workshops for 105 primarily college biology instructors to introduce them to Avida-ED and digital evolution and to help them to plan implementations. In this paper, based upon 60-min interviews with 46 of the attendees, we describe what they found to be of value in the workshop itself and the implementations of Avida-ED that they subsequently carried out. The Active LENS workshops were universally valued by the interviewees as a professional development experience; they valued the overall experience of the workshops, their organization and content, and the instructor support materials. Of the 46 teachers that we interviewed, 41 implemented Avida-ED in their classrooms, in 66 separate implementations. We characterized these with respect to the nature of the implementation and its duration, and examined the data in relation to course type, course level, and stated learning goals of the instructors. The most common use was to have students learn evolutionary concepts by observing them in action. A smaller fraction used it to provide a complete research experience.

Abstract Background Previous studies have reported that periderm (the outer ectodermal layer) in zebrafish partially expands into the mouth and pharyngeal pouches, but does not reach the medial endoderm, where the pharyngeal teeth develop. Instead, periderm-like cells, arising independently from the outer periderm, cover prospective tooth-forming epithelia and are crucial for tooth germ initiation. Here we test the hypothesis that restricted expansion of periderm is a teleost-specific character possibly related to the derived way of early embryonic development. To this end, we performed lineage tracing of the periderm in a non-teleost actinopterygian species possessing pharyngeal teeth, the sterlet sturgeon (Acipenser ruthenus), and a sarcopterygian species lacking pharyngeal teeth, the axolotl (Ambystoma mexicanum). Results In sturgeon, a stratified ectoderm is firmly established at the end of gastrulation, with minimally a basal ectodermal layer and a surface layer that can be homologized to a periderm. Periderm expands to a limited extent into the mouth and remains restricted to the distal parts of the pouches. It does not reach the medial pharyngeal endoderm, where pharyngeal teeth are located. Thus, periderm in sturgeon covers prospective odontogenic epithelium in the jaw region (oral teeth) but not in the pharyngeal region. In axolotl, like in sturgeon, periderm expansion in the oropharynx is restricted to the distal parts of the opening pouches. Oral teeth in axolotl develop long before mouth opening and possible expansion of the periderm into the mouth cavity. Conclusions Restricted periderm expansion into the oropharynx appears to be an ancestral feature for osteichthyans, as it is found in sturgeon, zebrafish and axolotl. Periderm behavior does not correlate with presence or absence of oral or pharyngeal teeth, whose induction may depend on ‘ectodermalized’ endoderm. It is proposed that periderm assists in lumenization of the pouches to create an open gill slit. Comparison of basal and advanced actinopterygians with sarcopterygians (axolotl) shows that different trajectories of embryonic development converge on similar dynamics of the periderm: a restricted expansion into the mouth and prospective gill slits.

Abstract Background Hybrids are expected to show greater phenotypic variation than their parental species, yet how hybrid phenotype expression varies with genetic distances in closely-related parental species remains surprisingly understudied. Here, we investigate pelage and morphometric trait variation in anthropogenic hybrids between four species of Brazilian Callithrix marmosets, a relatively recent primate radiation. Marmoset species are distinguishable by pelage phenotype and morphological specializations for eating tree exudates. In this work, we (1) describe qualitative phenotypic pelage differences between parental species and hybrids; (2) test whether significant quantitative differences exist between parental and hybrid morphometric phenotypes; and (3) determine which hybrid morphometic traits show heterosis, dysgenesis, trangression, or intermediacy relative to the parental trait. We investigated cranial and post-cranial morphometric traits, as most hybrid morphological studies focus on the former instead of the latter. Finally, we estimate mitogenomic distances between marmoset species from previously published data. Results Marmoset hybrid facial and overall body pelage variation reflected novel combinations of coloration and patterns present in parental species. In morphometric traits, C. jacchus and C. penicillata were the most similar, while C. aurita was the most distinct, and C. geoffroyi trait measures fell between these species. Only three traits in C. jacchus x C. penicillata hybrids showed heterosis. We observed heterosis and dysgenesis in several traits of C. penicillata x C. geoffroyi hybrids. Transgressive segregation was observed in hybrids of C. aurita and the other species. These hybrids were also C. aurita-like for a number of traits, including body length. Genetic distance was closest between C. jacchus and C. penicillata and farthest between C. aurita and the other species. Conclusion We attributed significant morphometric differences between marmoset species to variable levels of morphological specialization for exudivory in these species. Our results suggest that intermediate or parental species-like hybrid traits relative to the parental trait values are more likely in crosses between species with relatively lesser genetic distance. More extreme phenotypic variation is more likely in parental species with greater genetic distance, with transgressive traits appearing in hybrids of the most genetically distant parental species. We further suggest that fewer developmental disturbances can be expected in hybrids of more recently diverged parental species, and that future studies of hybrid phenotypic variation should investigate selective pressures on Callithrix cranial and post-cranial morphological traits.

Abstract Complexity is inherent in most biological phenomena, yet there is little effort to teach biological complexity per se in the classroom. Levels of organization and hierarchical complexity are familiar features of living systems and taken for granted in most instructional materials including the Next Generation Science Standards (NGSS) of the United States. However, the evolution of the hierarchical organization of life is not being taught because there has been no instructional framework for doing so until now. We seek to address this gap in instruction by translating recent research on evolutionary transitions in individuality (ETI theory) into an integrative, instructional framework for teaching the hierarchy of life that aligns with the three dimensions of the NGSS. ETI theory presents an evolutionary framework for teaching hierarchical complexity using the social principles of cooperation and conflict. These principles are intuitive for students because they are analogous to many of the social situations in their lives. By making use of the ETI framework, instructors can explicitly teach the evolution of the hierarchical organization of life, the organizing framework for all of biology.

Abstract Background Cotton is one of the topmost fiber crops throughout the globe. During the last decade, abrupt changes in the climate resulted in drought, heat, and salinity. These stresses have seriously affected cotton production and significant losses all over the textile industry. The GhAGC kinase, a subfamily of AGC group and member of serine/threonine (Ser/Thr) protein kinases group and is highly conserved among eukaryotic organisms. The AGC kinases are compulsory elements of cell development, metabolic processes, and cell death in mammalian systems. The investigation of RNA editing sites within the organelle genomes of multicellular vascular plants, such as Gossypium hirsutum holds significant importance in understanding the regulation of gene expression at the post-transcriptional level. Methods In present work, we characterized twenty-eight GhAGC genes in cotton and constructed phylogenetic tree using nine different species from the most primitive to the most recent. Results In sequence logos analyses, highly conserved amino acid residues were found in G. hirsutum, G. arboretum, G. raimondii and A. thaliana. The occurrence of cis-acting growth and stress-related elements in the promoter regions of GhAGCs highlight the significance of these factors in plant development and abiotic stress tolerance. Ka/Ks levels demonstrated that purifying selection pressure resulting from segmental events was applied to GhAGC with little functional divergence. We focused on identifying RNA editing sites in G. hirsutum organelles, specifically in the chloroplast and mitochondria, across all 28 AGC genes. Conclusion The positive role of GhAGCs was explored by quantifying the expression in the plant tissues under abiotic stress. These findings help in understanding the role of GhAGC genes under abiotic stresses which may further be used in cotton breeding for the development of climate smart varieties in abruptly changing climate.

Abstract Tadpoles serve as crucial evidence for testing systematic and taxonomic hypotheses. Suctorial tadpoles collected in Guyana were initially assigned to Rhaebo nasicus through molecular phylogeny. Subsequent analysis of larval and adult morphological traits revealed synapomorphies within the clade encompassing R. nasicus and R. ceratophrys, prompting the recognition of a new genus described herein as Adhaerobufo. The new genus is distinguished from other bufonids by specific phenotypic traits including an enlarged, suctorial oral disc with distinct papillae arrangements, and the presence of certain muscles and narial vacuities at the larval stage. However, only a few adult external characteristics (e.g., enlarged eyelids, infraocular cream spot), seem to be reliably discriminative from related genera. This study underscores the significance of larval morphology in anuran systematics and offers new insights into the evolution of suctorial and gastromyzophorous larvae within bufonids.

Abstract Background Muslim Indonesian prospective biology teachers have different views on evolution theory. Muslim prospective biology teachers suspect that differences in their understanding of the theory of evolution stem from their religious beliefs. This study aims to investigate Muslim Indonesian prospective biology teachers’ acceptance and typology of evolution theory. Methods An explanatory sequential design was combined with mixed techniques. Out of 185 potential biology teachers, 153 (16 males and 137 females) completed the questionnaire during the quantitative phase. We interviewed 5 males and 28 females in the qualitative phase to determine the typology of engagement, and all participants filled out an open-ended questionnaire to complete the previous data. Results The findings demonstrated the validity and reliability of the tools employed, as well as the high degree of acceptance of evolution among Muslim Indonesian aspiring biology teachers. The results also showed that there is a predominant typology of engagement reconciliation among Muslim Indonesian prospective biology teachers, with few explorers and resistors. Conclusions Muslim Indonesian prospective biology teachers do not differ in their conceptual understanding of theory evolution from their religious beliefs.

Abstract Background Spiders evolved different types of eyes, a pair of primary eyes that are usually forward pointing, and three pairs of secondary eyes that are typically situated more posterior and lateral on the spider’s head. The best understanding of arthropod eye development comes from the vinegar fly Drosophila melanogaster, the main arthropod model organism, that also evolved different types of eyes, the larval eyes and the ocelli and compound eyes of the imago. The gene regulatory networks that underlie eye development in this species are well investigated revealing a conserved core network, but also show several differences between the different types of eyes. Recent candidate gene approaches identified a number of conserved genes in arthropod eye development, but also revealed crucial differences including the apparent lack of some key factors in some groups of arthropods, including spiders. Results Here, we re-analysed our published scRNA sequencing data and found potential key regulators of spider eye development that were previously overlooked. Unlike earlier research on this topic, our new data suggest that Hedgehog (Hh)-signalling is involved in eye development in the spider Parasteatoda tepidariorum. By investigating embryonic gene expression in representatives of all main groups of spiders, we demonstrate that this involvement is conserved in spiders. Additionally, we identified genes that are expressed in the developing eyes of spiders, but that have not been studied in this context before. Conclusion Our data show that single-cell sequencing represents a powerful method to gain deeper insight into gene regulatory networks that underlie the development of lineage-specific organs such as the derived set of eyes in spiders. Overall, we gained deeper insight into spider eye development, as well as the evolution of arthropod visual system formation.

Abstract Hox genes are transcriptional regulators that elicit cell positional identity along the anterior–posterior region of the body plan across different lineages of Metazoan. Comparison of Hox gene expression across distinct species reveals their evolutionary conservation; however, their gains and losses in different lineages can correlate with body plan modifications and morphological novelty. We compare the expression of 11 Hox genes found within Streblospio benedicti, a marine annelid that produces two types of offspring with distinct developmental and morphological features. For these two distinct larval types, we compare Hox gene expression through ontogeny using hybridization chain reaction (HCR) probes for in situ hybridization and RNA-seq data. We find that Hox gene expression patterning for both types is typically similar at equivalent developmental stages. However, some Hox genes have spatial or temporal differences between the larval types that are associated with morphological and life-history differences. This is the first comparison of developmental divergence in Hox gene expression within a single species and these changes reveal how body plan differences may arise in larval evolution.

Abstract Mollusca is a morphologically diverse phylum, exhibiting an immense variety of calcium carbonate structures. Proteomic studies of adult shells often report high levels of rapidly-evolving, ‘novel’ shell matrix proteins (SMPs), which are hypothesized to drive shell diversification. However, relatively little is known about the phylogenetic distribution of SMPs, or about the function of individual SMPs in shell construction. To understand how SMPs contribute to shell diversification a thorough characterization of SMPs is required. Here, we build tools and a foundational understanding of SMPs in the marine gastropod species Crepidula fornicata and Crepidula atrasolea because they are genetically-enabled mollusc model organisms. First, we established a staging system of shell development in C. atrasolea for the first time. Next, we leveraged previous findings in C. fornicata combined with phylogenomic analyses of 95 metazoan species to determine the evolutionary lineage of its adult SMP repertoire. We found that 55% of C. fornicata’s SMPs belong to molluscan orthogroups, with 27% restricted to Gastropoda, and only 5% restricted at the species level. The low percentage of species-restricted SMPs underscores the importance of broad-taxon sampling and orthology inference approaches when determining homology of SMPs. From our transcriptome analysis, we found that the majority of C. fornicata SMPs that were found conserved in C. atrasolea were expressed in both larval and adult stages. We then selected a subset of SMPs of varying evolutionary ages for spatial-temporal analysis using in situ hybridization chain reaction (HCR) during larval shell development in C. atrasolea. Out of the 18 SMPs analyzed, 12 were detected in the larval shell field. These results suggest overlapping larval vs. adult SMP repertoires. Using multiplexed HCR, we observed five SMP expression patterns and three distinct cell populations within the shell field. These patterns support the idea that modular expression of SMPs could facilitate divergence of shell morphological characteristics. Collectively, these data establish an evolutionary and developmental framework in Crepidula that enables future comparisons of molluscan biomineralization to reveal mechanisms of shell diversification.

Abstract Background Volvocales in green algae have evolved by multicellularity of Chlamydomonas-like unicellular ancestor. Those with various cell numbers exist, such as unicellular Chlamydomonas, four-celled Tetrabaena, and Volvox species with different cell numbers (~1,000, ~5,000, and ~10,000). Each cell of these organisms shares two cilia and an eyespot, which are used for swimming and photosensing. They are all freshwater microalgae but inhabit different fluid environments: unicellular species live in low Reynolds-number (Re) environments where viscous forces dominate, whereas multicellular species live in relatively higher Re where inertial forces become non-negligible. Despite significant changes in the physical environment, during the evolution of multicellularity, they maintained photobehaviors (i.e., photoshock and phototactic responses), which allows them to survive under changing light conditions. Results In this study, we utilized high-speed imaging to observe flash-induced changes in the ciliary beating manner of 27 Volvocales strains. We classified flash-induced ciliary responses in Volvocales into four patterns: “1: temporal waveform conversion”, “2: no obvious response”, “3: pause in ciliary beating”, and “4: temporal changes in ciliary beating directions”. We found that which species exhibit which pattern depends on Re, which is associated with the individual size of each species rather than phylogenetic relationships. Conclusions These results suggest that only organisms that acquired different patterns of ciliary responses survived the evolutionary transition to multicellularity with a greater number of cells while maintaining photobehaviors. This study highlights the significance of the Re as a selection pressure in evolution and offers insights for designing propulsion systems in biomimetic micromachines.

Abstract Background The evolution of extracellular matrix is tightly linked to the evolution of organogenesis in metazoans. Tenascins are extracellular matrix glycoproteins of chordates that participate in integrin-signaling and morphogenetic events. Single tenascins are encoded by invertebrate chordates, and multiple tenascin paralogs are found in vertebrates (designated tenascin-C, tenascin-R, tenascin-W and tenascin-X) yet, overall, the evolution of this family has remained unclear. Results This study examines the genomes of hemichordates, cephalochordates, tunicates, agnathans, cartilaginous fishes, lobe-finned fishes, ray-finned fishes and representative tetrapods to identify predicted tenascin proteins. We comprehensively assess their evolutionary relationships by sequence conservation, molecular phylogeny and examination of conservation of synteny of the encoding genes. The resulting new evolutionary model posits the origin of tenascin in an ancestral chordate, with tenascin-C-like and tenascin-R-like paralogs emerging after a whole genome duplication event in an ancestral vertebrate. Tenascin-X appeared following a second round of whole genome duplication in an ancestral gnathostome, most likely from duplication of the gene encoding the tenascin-R homolog. The fourth gene, encoding tenascin-W (also known as tenascin-N), apparently arose from a local duplication of tenascin-R. Conclusions The diversity of tenascin paralogs observed in agnathans and gnathostomes has evolved through selective retention of novel genes that arose from a combination of whole genome and local duplication events. The evolutionary appearance of specific tenascin paralogs coincides with the appearance of vertebrate-specific cell and tissue types where the paralogs are abundantly expressed, such as the endocranium and facial skeleton (tenascin-C), an expanded central nervous system (tenascin-R), and bone (tenascin-W).

Abstract Background Terniopsis yongtaiensis, a member of the Podostemaceae family, is an aquatic flowering plant displaying remarkable adaptive traits that enable survival in submerged, turbulent habitats. Despite the progressive expansion of chloroplast genomic information within this family, mitochondrial genome sequences have yet to be reported. Results In current study, the mitochondrial genome of the T. yongtaiensis was characterized by a circular genome of 426,928 bp encoding 31 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNA genes. Our comprehensive analysis focused on gene content, repeat sequences, RNA editing processes, intracellular gene transfer, phylogeny, and codon usage bias. Numerous repeat sequences were identified, including 130 simple sequence repeats, 22 tandem repeats, and 220 dispersed repeats. Phylogenetic analysis positioned T. yongtaiensis (Podostemaceae) within the Malpighiales order, showing a close relationship with the Calophyllaceae family, which was consistent with the APG IV classification. A comparative analysis with nine other Malpighiales species revealed both variable and conserved regions, providing insights into the genomic evolution within this order. Notably, the GC content of T. yongtaiensis was distinctively lower compared to other Malpighilales, primarily due to variations in non-coding regions and specific protein-coding genes, particularly the nad genes. Remarkably, the number of RNA editing sites was low (276), distributed unevenly across 27 PCGs. The dN/dS analysis showed only the ccmB gene of T. yongtaiensis was positively selected, which plays a crucial role in cytochrome c biosynthesis. Additionally, there were 13 gene-containing homologous regions between the mitochondrial and chloroplast genomes of T. yongtaiensis, suggesting the gene transfer events between these organellar genomes. Conclusions This study assembled and annotated the first mitochondrial genome of the Podostemaceae family. The comparison results of mitochondrial gene composition, GC content, and RNA editing sites provided novel insights into the adaptive traits and genetic reprogramming of this aquatic eudicot group and offered a foundation for future research on the genomic evolution and adaptive mechanisms of Podostemaceae and related plant families in the Malpighiales order.

Abstract Background Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) plays a critical role in the ecology and economy of Western North America. This conifer species comprises two distinct varieties: the coastal variety (var. menziesii) along the Pacific coast, and the interior variety (var. glauca) spanning the Rocky Mountains into Mexico, with instances of inter-varietal hybridization in Washington and British Columbia. Recent investigations have focused on assessing environmental pressures shaping Douglas-fir’s genomic variation for a better understanding of its evolutionary and adaptive responses. Here, we characterize range-wide population structure, estimate inter-varietal hybridization levels, identify candidate loci for climate adaptation, and forecast shifts in species and variety distribution under future climates. Results Using a custom SNP-array, we genotyped 540 trees revealing four distinct clusters with asymmetric admixture patterns in the hybridization zone. Higher genetic diversity observed in coastal and hybrid populations contrasts with lower diversity in inland populations of the southern Rockies and Mexico, exhibiting a significant isolation by distance pattern, with less marked but still significant isolation by environment. For both varieties, we identified candidate loci associated with local adaptation, with hundreds of genes linked to processes such as stimulus response, reactions to chemical compounds, and metabolic functions. Ecological niche modeling revealed contrasting potential distribution shifts among the varieties in the coming decades, with interior populations projected to lose habitat and become more vulnerable, while coastal populations are expected to gain suitable areas. Conclusions Overall, our findings provide crucial insights into the population structure and adaptive potential of Douglas-fir, with the coastal variety being the most likely to preserve its evolutionary path throughout the present century, which carry implications for the conservation and management of this species across their range.