Evolutionary History Research Articles

Innovation investment and performance: the moderating role of university collaborations

Purpose Considering the historical evolution of innovation dynamics, and its paradoxical state, and answering Nelson (2008) and Winter (2014), this paper aims to analyze the dynamics of innovation within the context of the Evolutionary Economic Theory. Specifically, this study looks to unravel the moderating influence of university cooperation on the relationship between innovation expenditure and innovation results. This study aims to provide valuable insights and evidence that can inform strategic decision-making for policymakers and businesses striving to foster innovation-driven economic growth in an ever-evolving global landscape. Design/methodology/approach The quantitative methodology adopted in this study involved harvesting data from the Latin American Innovation Survey (LAIS) database and cleaning it up using Python to ensure data integrity. Subsequently, SPSS, coupled with the PROCESS macro, was employed to conduct moderation analysis. This methodological approach enabled the examination of the intricate interplay between innovation expenditure, university cooperation and innovation outcomes within a large sample of firms, thereby easing a robust exploration of the hypothesis. Findings The research highlights the moderating role of university cooperation, showing that collaborative partnerships amplify the impact of innovation spending on innovation results, advancing the understanding of the impact of university-business collaborations. Additionally, the results revealed a positive relationship between innovation expenditure and innovation results, underscoring the significance of R&D investments. Practical implications This study highlights the role of university-industry collaborations in enhancing innovation investment outcomes in Latin America. It suggests that managers should proactively engage with universities to access advanced research and foster a culture of innovation. These partnerships can significantly boost a firm's competitive edge and innovation success, marking them as crucial in the rapidly evolving economic environment. Originality/value The originality of the paper relies on bridging theoretical concepts from the Evolutionary Economic Theory framework with empirical insights of the moderating role of university cooperation. It addresses a theoretical gap, with a new methodology and offers insights into the complex relationship between universities, businesses and innovation in a constantly changing economic environment, making it clearer how these connections can help boost innovation in practical ways.

Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama.

Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here we conduct range-wide sampling for Pederson's cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates x 45 evolutionary models x 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 million years ago. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.

Evolution of ion channels in cetaceans: a natural experiment in the tree of life

Cetaceans represent a natural experiment within the tree of life in which a lineage changed from terrestrial to aquatic habitats. This shift involved phenotypic modifications, representing an opportunity to explore the genetic bases of phenotypic diversity. Among the different molecular systems that maintain cellular homeostasis, ion channels are crucial for the proper physiological functioning of all living species. This study aims to explore the evolution of ion channels during the evolutionary history of cetaceans. To do so, we created a bioinformatic pipeline to annotate the repertoire of ion channels in the genome of the species included in our sampling. Our main results show that cetaceans have, on average, fewer protein-coding genes and a higher percentage of annotated ion channels than non-cetacean mammals. Signals of positive selection were detected in ion channels related to the heart, locomotion, visual and neurological phenotypes. Interestingly, we predict that the NaV1.5 ion channel of most toothed whales (odontocetes) is sensitive to tetrodotoxin, similar to NaV1.7, given the presence of tyrosine instead of cysteine, in a specific position of the ion channel. Finally, the gene turnover rate of the cetacean crown group is more than three times faster than that of non-cetacean mammals.

Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing.

The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (O. kisutch), and sockeye salmon (O. nerka) from the Fraser River at moderate coverage (∼16x). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1x more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, three Fraser River genetic groups were identified for each species using principal component and admixture analyses, which is consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available.

Income and Sex Moderate the Association Between Population Density and Reproduction: A Multilevel Analysis of Life History Strategies Across 23 Nations.

While previous studies guided by evolutionary life history theory have revealed several important socioecological moderators of the influence of population density (PD) on reproduction, absent is an understanding of how individual-level factors such as personal resources and sex differences might interact and play a role. Using data from a large sample of clients (N = 4,432,440) of an online dating company spanning 317 states nested within 23 countries, we contributed a robust multilevel analysis of life history effects by assessing the interaction between state-level PD and individual-level income on offspring quantity, and we further qualified this analysis by sex. Consistent with previous research, PD was negatively correlated with having children. Consistent with our novel hypotheses, this negative relationship was moderated by income such that the link between PD and low fertility became weaker with increasing levels of income and these patterns were stronger for men than for women. These results held despite controlling for a variety of country-level, state-level, and individual-level confounds. Findings are discussed together with theoretical and practical implications for the management of fertility based on evolutionary life history perspectives.

Cleaner gobies can solve a biological market task when the correct cue is larger

Animal cognition is deeply influenced by interactions with the environment. A notable example of sophisticated cognition in the animal kingdom is described by the mutualistic relationship between cleaner fish and clients, where decision-making processes play a pivotal role in partner choice and fish survival. In this context, while extensive research has explored the cognition of the cleaner wrasse Labroides dimidiatus, it is important to note that studies on the cognition of other wrasse species and on its Caribbean counterparts, Elacatinus spp., are limited. Therefore, to extend our comprehension of cognition in cleaner fish with different evolutionary backgrounds, it is important to focus our attention on the genus Elacatinus spp. In this study, we used plexiglass plates as surrogates for clients and assessed the ability of cleaner gobies, Elacatinus oceanops, to solve a biological market task where prioritizing an ephemeral food plate over a permanent one would double the food reward. We varied cue-based decision-making using both ecologically relevant cues (plate, size, and color) and non-relevant ones (presentation side). Additionally, we tested their capacity for reversal learning, an indicator of complex cognitive abilities. Notably, cleaner gobies were able to solve the biological markets task when the distinguishing cue was a larger plate size. Given that these gobies tend to prioritize larger predatory clients in nature, our results align with their natural inclination. Consequently, further research, including studies involving wild individuals, is essential to elucidate the cognitive abilities of the studied species and their implications in the ecological context and evolutionary history.

Genomic evidence of reproductive isolation among the Semisulcospira snails radiated in the ancient Lake Biwa.

Determining species boundaries within rapidly evolving species flocks is essential to understanding their evolutionary history but is often difficult to achieve due to the lack of clear diagnostic features. Ancient Lake Biwa harbors endemic snails in the genus Semisulcospira, a species flock with 19 described species. However, their morphological and genetic similarity cast doubt on the validity of their species status and their histories of explosive speciation. To evaluate their species boundaries, we examine patterns of gene flow among the sympatric or parapatric nominal Semisulcospira species in Lake Biwa. The principal component analysis and Bayesian structure analysis based on the genome-wide genotyping dataset demonstrated no gene flow between five pairs of the Semisulcospira species. However, we found the hybrids between the closely related species pair, Semisulcospira decipiens and S. rugosa. Despite the presence of hybrids, these nominal species still formed their own genetic clusters. There are variations in the chromosome numbers among these species, potentially providing an intrinsic barrier to panmictic gene flow. Our study showed complete or partial reproductive isolation among the sympatric or parapatric Semisulcospira species, demonstrating that the Semisulcospira snails are real species assemblages radiated in Lake Biwa. Our study provides significant implications for establishing species boundaries among rapidly evolving freshwater species in ancient lakes.

Biogeographic history of pigeons and doves drives the origin and diversification of their parasitic body lice.

Despite their extensive diversity and ecological importance, the history of diversification for most groups of parasitic organisms remains relatively understudied. Elucidating broad macroevolutionary patterns of parasites is challenging, often limited by the availability of samples, genetic resources, and knowledge about ecological relationships with their hosts. In this study, we explore the macroevolutionary history of parasites by focusing on parasitic body lice from doves. Building on extensive knowledge of ecological relationships and previous phylogenomic studies of their avian hosts, we tested specific questions about the evolutionary origins of the body lice of doves, leveraging whole genome data sets for phylogenomics. Specifically, we sequenced whole genomes from 68 samples of dove body lice, including representatives of all body louse genera from 51 host taxa. From these data, we assembled >2,300 nuclear genes to estimate dated phylogenetic relationships among body lice and several outgroup taxa. The resulting phylogeny of body lice was well supported, although some branches had conflicting signal across the genome. We then reconstructed ancestral biogeographic ranges of body lice and compared the body louse phylogeny to phylogeny of doves, and also to a previously published phylogeny of the wing lice of doves. Divergence estimates placed the origin of body lice in the late Oligocene. Body lice likely originated in Australasia and dispersed with their hosts during the early Miocene, with subsequent codivergence and host switching throughout the world. Notably, this evolutionary history is very similar to that of dove wing lice, despite the stronger dispersal capabilities of wing lice compared to body lice. Our results highlight the central role of the biogeographic history of host organisms in driving the evolutionary history of their parasites across time and geographic space.

Study on the Structuring of Music for Buddhist Folk Funeral Rituals in Bijie

I think I have made an in-depth study of folk Buddhist funeral ceremony music in Bijie area, which aims to explore the origin, development, evolution of folk Buddhist funeral ceremony music in Bijie area, as well as its position and role in society and culture, and education. This study adopts a variety of research methods such as field survey, literature study, and music analysis. A large amount of musical materials were collected through field surveys and recordings of different folk Buddhist funeral ceremony music in the Bijie area. Relevant historical documents, folklore and oral history materials were also sorted out and analyzed to understand the historical origin and cultural background of funeral ceremony music. The results of the study show that the folk Buddhist funeral ceremony music in the Bijie area has a long history and a unique style. These musical compositions usually consist of elements such as Buddhist scriptures, mantras, Buddhist music and folk music, forming a unique musical form. In funeral ceremonies, these musical compositions are used to pay homage to the deceased, transcend the spirits of the dead, and protect the living, etc., and they have both religious ceremonial and social functions (ethics and morals, Buddhist education, and rituals). In addition, the study also found that folk Buddhist funeral ritual music in the Bijie area was influenced by a variety of factors during its evolution, such as regional culture, religious sects, and social change. With the development and change of society, the funeral ceremony music also evolved and innovated, gradually forming unique local characteristics. In general, the music of BiJie folk Buddhist funeral rituals is characterized by its solemnity, solemnity, sadness, and mourning, and adds a unique atmosphere to the funeral rituals through various forms of Buddhist scripture recitation, gatha and music performance, so that people are more able to feel the presentation of cultural phenomena such as memorialization and prayers for the deceased, and expectations and teachings for the living, and so on. It reveals the historical origin, cultural background and evolution process of the music of Bijie folk Buddhist funeral ceremony, and provides theoretical and practical guidance for the protection and inheritance of this unique music culture.

When a name changes everything: taxonomy and conservation of the Atlantic bushmaster (Lachesis Daudin, 1803) (Serpentes: Viperidae: Crotalinae)

The South American bushmaster Lachesis muta is currently considered a valid taxon with no recognized subspecies. However, its wide distribution with discontinuous populations, the restricted sampling of molecular data in previous studies, and the inherent difficulty in obtaining diagnostic data, preclude a detailed evaluation of the taxonomic status of this taxon. In this study, we use high-resolution genomics, as well as venomic, morphological, and ecological data to infer the speciation processes involved in the evolutionary history of L. muta populations. Our data recognize the Amazon populations as L. muta and the Atlantic Forest populations as L. rhombeata. Lachesis rhombeata has lower genetic diversity than L. muta and we recommend a critical evaluation to include this species in the national and international red lists of endangered species. Moreover, we propose classifying the L. rhombeata population from the Baturité massif (Ceará state) as an evolutionarily significant unit (ESU) for conservation and we also found genetic substructure within L. muta populations. We expect our results will contribute to the taxonomic stability of the Neotropical fauna and highlight the urgency of protecting Atlantic Forest populations of Lachesis species and, consequently, the landscape that this species and related biota inhabit.

Phylogeny predicts sensitivity in aquatic animals for only a minority of chemicals.

There are substantial gaps in our empirical knowledge of the effects of chemical exposure on aquatic life that are unlikely to be filled by traditional laboratory toxicity testing alone. One possible alternative of generating new toxicity data is cross-species extrapolation (CSE), a statistical approach in which existing data are used to predict the effect of a chemical on untested species. Some CSE models use relatedness as a predictor of chemical sensitivity, but relatively little is known about how strongly shared evolutionary history influences sensitivity across all chemicals. To address this question, we conducted a survey of phylogenetic signal in the toxicity data from aquatic animal species for a large set of chemicals using a phylogeny inferred from taxonomy. Strong phylogenetic signal was present in just nine of thirty-six toxicity datasets, and there were no clear shared properties among those datasets with strong signal. Strong signal was rare even among chemicals specifically developed to target insects, meaning that these chemicals may be equally lethal to non-target taxa, including chordates. When signal was strong, distinct patterns of sensitivity were evident in the data, which may be informative when assembling toxicity datasets for regulatory use. Although strong signal does not appear to manifest in aquatic toxicity data for most chemicals, we encourage additional phylogenetic evaluations of toxicity data in order to guide the selection of CSE tools and as a means to explore the patterns of chemical sensitivity across the broad diversity of life.

Bayesian phylogenetic analysis of pitch-accent systems based on accentual class merger: a new method applied to Japanese dialects

Abstract Unlike studies of the evolutionary relationship between languages, the dialect-level variation within a language has seldom been studied within the framework of a phylogenetic tree, because frequent lexical borrowing muddles the evidence of shared ancestry. The phonological history of Japanese is an exceptional case study where the phenomenon called accentual class merger enables the phylogenetic analysis of dialectal pitch-accent systems in a way that is not subject to borrowing. However, previous studies have lacked statistical analysis and failed to evaluate the relative credence of alternative hypotheses. Here we developed a novel substitution model that describes the mutation of pitch-accent systems driven by accentual class merger and integrated the model into the framework of Bayesian phylogenetic inference with geographical diffusion. Applying the method to data on the pitch-accent variation in modern Japanese dialects and historical documents collected from literature, we reconstructed the evolutionary history and spatial diffusion of pitch-accent systems. Our result supports the monophyly of each of three groups of pitch-accent systems in conventional categorization, namely Tokyo type, Keihan type, and N-kei (N-pattern) type of Kyushu, whereas the monophyly of the Tokyo type has been highly controversial in previous studies. The divergence time of the mainland pitch-accent systems was estimated to be from mid-Kofun to early Heian period. Also, it is suggested that the modern Kyoto dialect did not inherit its accent patterns from Bumoki but from an unrecorded lineage which survived from the Muromachi period. Analyses on geographical diffusion suggest that the most recent common ancestor (MRCA) of all the taxa and that of Keihan type were located in or around the Kinki region, whereas the MRCA of N-kei type was located in northern to central Kyushu. The geographical location of the MRCA of Tokyo type remains unclear, but the Kinki and Kanto regions are the most plausible candidates.

The past, present and future developments in mariculture in the coastal waters of mainland Tanzania

AbstractMarine coastal resources are crucial to Tanzania's socio‐economic development and are a lifeline for the livelihoods and incomes of coastal communities. This study provides an overview of the coastal development of mariculture in mainland Tanzania and suggests future development strategies. The review article covers extensive reports available through field interviews, government policy documents, library literature searches and field work carried out by the authors. Despite the immense potential of mariculture to improve food security for localcommunities, its development has been uneven. Specifically only seaweed farming has advanced to commercial‐scale production. Other mariculture activities, such as finfish farming (e.g. milkfish, silver pompano), shellfish farming (e.g. prawn, mud crab and half‐pearl) and sea cucumber farming, are underdeveloped and confined to small‐scale operations. Locally consumed finfish, such as milkfish and pompano, have not attracted investors out of fear that the recovery of investment may not be achieved due to the low prices offered in the market. In this context, the sustainable use of coastal resources through mariculture becomes paramount to alleviating poverty and facilitating controlled migration from rural to urban. This comprehensive review explores the historical evolution and current status of mariculture initiatives in the coastal waters of mainland Tanzania, which presents a crucial aspect of the socio‐economic development of the nation. With declining global capture fisheries production and a growing demand for fish protein, Tanzania has strategically embraced mariculture as a viable alternative. The article traced the development of mariculture since the 1970s, highlighting past and current initiatives managed by government agencies, non‐government organizations and the private sector. Notable successes, such as seaweed culture, are highlighted along with the challenges that hinder the growth of marine farming activities. The review integrates insights from a comprehensive survey in coastal Tanzania, focusing on mariculture activities and collecting information on people who have stopped such practices, elucidating reasons for quitting. By consolidating experiences from past and present mariculture initiatives, this review provides valuable guidance for decision‐making towards promoting sustainable mariculture that supports coastal communities while preserving marine biodiversity.

Phylogenetic relationships and plant life stage but not biogeographic history mediate priority effects of European grassland plants

Abstract The timing and order of species arrival have been shown to be a significant factor in the assembly of biotic communities. Therefore, understanding priority effects, which refer to the impact of an early‐arriving species on a later‐arriving one, can help us better predict community assembly processes. However, little is known about the role of phylogenetic distance (PD) in priority effects and how they are mediated by the biogeographic history (BH) and the life stages (LSs) of interacting species. To shed light on the role of PD in priority effects, we conducted a multispecies greenhouse experiment. We created 10 allopatric and 10 sympatric species pairs, representing a PD gradient between early‐ and late‐arriving species from 5 to 270 Myr in evolutionary history and tested the priority effect of early‐arriving species on the late‐arriving species at multiple LSs. We found evidence of stronger competition between closely related species, as late‐arriving plants produced less above‐ground biomass when the PD was low. However, priority effects varied across the development of late‐arriving plants, as there were no effects on seedling emergence and survival, independent of PD. Regardless of PD, the pairs of allopatric and sympatric species did not differ in their responses. Synthesis. While many studies have produced contradictory results regarding the effect of PD on plant–plant interactions, our study provides experimental evidence that priority effects can be stronger when PD is small. This effect was independent of BH but varied across different LSs of late‐arriving plants. The dependence of the effect of PD on the LS of late‐arriving species highlights the importance of the timing of interactions for the assembly of plant communities, which could also have significant implications for the fields of invasion and restoration ecology.

Ecological niche modeling of the Leopardus tigrinus complex sheds light on its elusive evolutionary history

Abstract The evolutionary history and taxonomy of the Leopardus tigrinus species complex have been studied based on several approaches, mostly employing genetic and morphological data, leading to distinct classification schemes. We approached this problem from an ecological perspective, with 2 main goals: (i) to evaluate ecological niche differences among regional L. tigrinus populations to determine the extent of ecological divergence among them; and (ii) to identify environmental barriers to historical dispersal that could have driven differentiation among the proposed groups. We modeled the ecological niche of all taxonomic/geographic groups proposed so far to comprise the L. tigrinus complex using the Maximum Entropy algorithm, and evaluated geographic and ecological niche differences among them. Furthermore, we investigated possible environmental barriers to historical dispersal that could have driven differentiation among regional groups. We evaluated 4 hypothetical barriers across 3 time periods to assess their potential historical effect. We found high ecological divergence between northeastern tigrina populations and the northern Andean and Central American tigrinas. Other groups within the L. tigrinus complex are less divergent. In addition, the Guiana Shield tigrina, where the type locality of the species is located, seems to be ecologically similar to populations from northeastern Brazil while also showing some overlap with Andean populations. The Panama center, the Llanos of Colombia and Venezuela, and the Amazon region were identified as historical barriers for tigrina dispersal across all time periods. The inferred historical barriers and ecological divergence observed in this study contribute to the inference of evolutionary differentiation among geographic groups comprising the L. tigrinus complex, revealing areas of consistently low habitat suitability that have likely contributed to divergence among regional populations.

Evolution Characteristics of Cultivated Land Protection Policy in China Based on Smith Policy Implementation

(1) Background: In the context of the Sustainable Development Goals (SDGs) and based on the historical evolution of cultivated land protection policy, we used the Smith model to address the problem of policy implementation bias and provide recommendations on how to ensure that cultivated land protection policy does not deviate in the implementation process. (2) Methods: The historical evolution process of China’s cultivated land protection policy was elucidated using literature analysis and the inductive deduction method; moreover, the issues regarding local evolution were investigated. In addition, utilizing the Smith model, which has an important role in policy implementation, the restoration direction of cultivated land protection in China was summarized. (3) Project: China’s cultivated land protection policy has demonstrated success in two stages of its historical development—from the basic stage of pursuing equal quantity and quality to the new stage of the trinity of “quantity–quality–ecology” of cultivated land. However, the trend of cultivated land protection policy development based on the regional division of labor in China still has some problems, i.e., the total quantity of cultivated land is insufficient, the quality is low, and the implementation of the trinity is unclear. These regional divisions depend on solving the balance of China’s grain security, and using the Smith model to solve the problem of policy implementation has become an important measure to resolve the issue of grain security and achieve the goal of cultivated land protection. (4) Conclusions: The Smith model is suitable for the implementation of China’s cultivated land protection policy. By utilizing the Smith model, the policy target group was found to be conducive to contributing to the maturity of and improvement in China’s cultivated land protection policy.

Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of salmonellosis, and the emergence of multidrug-resistant pathovariants has become a growing concern. Here, we investigate a distinct rough colony variant exhibiting a strong biofilm-forming ability isolated in China. Whole-genome sequencing on 2,212 Chinese isolates and 1,739 publicly available genomes reveals the population structure and evolutionary history of the rough colony variants. Characterized by macro, red, dry, and rough (mrdar) colonies, these variants demonstrate enhanced biofilm formation at 28 °C and 37 °C compared to typical rdar colonies. The mrdar variants exhibit extensive multidrug resistance, with significantly higher resistance to at least five classes of antimicrobial agents compared to non-mrdar variants. This resistance is primarily conferred by an IncHI2 plasmid harboring 19 antimicrobial resistance genes. Phylogenomic analysis divides the global collections into six lineages. The majority of mrdar variants belong to sublineage L6.5, which originated from Chinese smooth colony strains and possibly emerged circa 1977. Among the mrdar variants, upregulation of the csgDEFG operons is observed, probably due to a distinct point mutation (−44G > T) in the csgD gene promoter. Pangenome and genome-wide association analyses identify 87 specific accessory genes and 72 distinct single nucleotide polymorphisms associated with the mrdar morphotype.

Exploring the Evolutionary History and Phylogenetic Relationships of Giant Reed (Arundo donax) through Comprehensive Analysis of Its Chloroplast Genome

Exploring the Evolutionary History and Phylogenetic Relationships of Giant Reed (Arundo donax) through Comprehensive Analysis of Its Chloroplast Genome

Functional and regulatory diversification of Period genes responsible for circadian rhythm in vertebrates.

The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular rhythms through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes at the copy number and sequence levels, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events of Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa.

A systematic analysis of GASA family members in the Salix matsudana genome: Characterization, expression profile, and putative function in antioxidation

The gibberellic acid stimulated Arabidopsis (GASA) gene family, specific to plants, plays a pivotal role in growth, development, and response to diverse environmental stresses. Despite their importance, GASA genes in willow trees have been little studied. Here, 35 SmGASAs were identified from the Salix matsudana genome, which exhibited similar physical and chemical proprieties to GASAs in other species. A phylogenetic analysis revealed that GASAs from Populus trichocarpa, Vitis vinifera, Nicotiana tabacum, Oryza sativa, Arabidopsis thaliana, and S. matsudana are categorized into three distinct subfamilies. It appeared that polyploidization and segmental duplication have contributed to the expansion and diversification of the SmGASA family. These genes were significantly enriched in response to GA and oxygen-containing compounds. The diverse expression patterns observed across willow varieties suggested functional variation of SmGASAs throughout their evolutionary history. The expression profiles of SmGASAs were further analyzed in response to different treatments (i.e., salt, submergence, and polyethylene glycol (PEG)), indicating a potential role for SmGASAs in adapting to these stressors in willows. Remarkably, SmGASAs were shown to detoxify hydrogen peroxide (H2O2), highlighting their potent antioxidant properties. Overall, the comprehensive genomic analysis of willow SmGASAs shed light on their role in stress responses, offering valuable insights for future research and supporting the hypothesis of their involvement in stress adaptation mechanisms.