Evolutionary Changes Research Articles

DIGITAL TRANSFORMATION IN FINANCIAL SERVICES: OVERVIEW OF BEFORE AND AFTER THE PANDEMIC

This research examines the significant impact of digital transformation on the financial services sector, focusing on evolutionary changes that occurred before and during the worldwide pandemic. The core goals are to assess the scope of digital transformation in financial institutions, identify important obstacles and possibilities, and examine the techniques used to manage the changing landscape. Data were gathered from a varied group of financial institutions to ensure a complete picture of the sector. The findings show a large increase in digital use before the pandemic, with the pandemic acting as a catalyst for digital activities. Data-driven methods were critical for improving client experiences, increasing operational efficiency, and resolving cyber security issues. The conversation focuses on the industry's resilience in the face of enormous shocks, highlighting the vital role of technology in crisis management. Significant results include a growth in remote banking services, a greater dependence on artificial intelligence for fraud detection, and the adoption of cloud-based solutions for scalability. These findings illustrate the revolutionary impact of digital technology in altering the financial services industry. This comprehensive overview contributes to our understanding of the dynamic relationship between digital transformation and the financial services sector, providing valuable insights for industry stakeholders, policymakers, and researchers. Key Words: World Pandemic, Operational efficiency, Financial Institutions, Stakeholders, Artificial Intelligence

Range of trait variation in prey determines evolutionary contributions to predator growth rates.

Evolutionary and ecological dynamics can occur on similar timescales and thus influence each other. While it has been shown that the relative contribution of ecological and evolutionary change to population dynamics can vary, it still remains unknown what influences these differences. Here, we test whether prey populations with increased variation in their defense and competitiveness traits will have a stronger impact of evolution for predator growth rates. We controlled trait variation by pairing distinct clonal lineages of the green alga Chlamydomonas reinhardtii with known traits as prey with the rotifer Brachionus calyciforus as predator and compared those results with a mechanistic model matching the empirical system. We measured the impact of evolution (shift in prey clonal frequency) and ecology (shift in prey population density) for predator growth rate and its dependency on trait variation using an approach based on a two-way ANOVA. Our experimental results indicated that higher trait variation, i.e., a greater distance in trait space, increased the relative contribution of prey evolution to predator growth rate over 3-4 predator generations, which was also observed in model simulations spanning longer time periods. In our model, we also observed clone-specific results, where a more competitive undefended prey resulted in a higher evolutionary contribution, independent of the trait distance. Our results suggest that trait combinations and total prey trait variation combine to influence the contribution of evolution to predator population dynamics, and that trait variation can be used to identify and better predict the role of eco-evolutionary dynamics in predator-prey systems.

How Parenting Style Varies Between the Sexualities and Cultures in the Aspects of Evolutionary Psychology

From the perspective of evolutionary psychology, the evolution of human parenting styles is delved into, considering various mechanisms and factors influencing it. The primary focus is placed on how these parenting styles have been changed over time and influenced by different cultures.The paper analyzes five key evolutionary mechanisms and their impact on parenting styles.The first mechanism explores how the transition from polygamous mating to normative monogamy in history increased paternal investment in offspring. The second mechanism delves into how cultural differences between Eastern and Western societies have shaped distinct parenting styles. The third evolutionary mechanism examines how different family structures have led to variations in child-rearing approaches.The fourth point discusses how the progress of women's status in society has brought about shifts in marital dynamics and parenting practices. Lastly, building upon the fourth evolutionary mechanism, the paper analyzes the relationship between the advancement of women's status, increased divorce rates, and the consequent influence on parenting styles within single-parent families.The overarching conclusion drawn from this paper is that human parenting styles, from ancient nomadic periods to contemporary societies, have evolved in response to various evolutionary mechanisms and changing environmental factors. Parenting decisions are intricately tied to specific temporal, spatial, and environmental contexts, ultimately serving the goals of reproduction and survival. Valuable insights into the evolution of parenting styles have been provided, emphasizing the importance of considering a variety of influences when studying human behavior.

Understanding microchromosomal organization and evolution in four representative woodpeckers (Picidae, Piciformes) through BAC-FISH analysis.

The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species (Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus, and Picumnus nebulosus) was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from Gallus gallus and Taeniopygia guttata. Findings suggest that P. nebulosus (2n=110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for V. spilogaster (2n=88) and demonstrated microchromosomal rearrangements involving C. campestris plus a single, unique hitherto undescribed rearrangement in V. spilogaster. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of M. candidus is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.

Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes.

The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.

Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat

Key messagePHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development.The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.

Evolvability predicts macroevolution under fluctuating selection.

Heritable variation is a prerequisite for evolutionary change, but the relevance of genetic constraints on macroevolutionary timescales is debated. By using two datasets on fossil and contemporary taxa, we show that evolutionary divergence among populations, and to a lesser extent among species, increases with microevolutionary evolvability. We evaluate and reject several hypotheses to explain this relationship and propose that an effect of evolvability on population and species divergence can be explained by the influence of genetic constraints on the ability of populations to track rapid, stationary environmental fluctuations.

Evolutionary changes in metabolic dysfunction-associated steatotic liver disease and the risk of hepatocellular carcinoma: a nationwide cohort study.

To determine the association between evolutionary changes in metabolic dysfunction-associated steatotic liver disease (MASLD) status and the risk of hepatocellular carcinoma (HCC) in a nationwide population-based cohort. Information on study participants were derived from the Korea National Health Insurance Service database. The study population consisted of 5,080,410 participants who underwent two consecutive biennial health screenings between 2009 and 2012. All participants were followed up until HCC, death, or 31 December 2020. Association of evolutionary changes in MASLD status as assessed by fatty liver index and cardiometabolic risk factors, including persistent non-MASLD, resolved MASLD, incident MASLD, and persistent MASLD, with HCC risk was evaluated using the multivariable-adjusted Cox proportional hazards regression. Among the 5,080,410 participants with 39,910,331 person-years of follow-up, 4,801 participants developed HCC. The incidence of HCC in participants with resolved, incident, and persistent MASLD was approximately 2.2-, 2.3-, and 4.7-fold higher, respectively, than that in those with persistent non-MASLD among the Korean adult population. When stratifying the participants according to the evolutionary change in MASLD status, persistent (adjusted hazard ratio [aHR], 2.94; 95% confidence interval [CI], 2.68-3.21; P<0.001), incident (aHR, 1.85; 95% CI, 1.63-2.10; P<0.001), and resolved MASLD (aHR, 1.33; 95% CI, 1.18-1.50; P<0.001) had an increased risk of HCC than that of persistent non-MASLD. The evolutionary changes in MASLD were associated with the differential risk of HCC independent of metabolic risk factors and concomitant medications, providing additional information on the risk of HCC stratification in patients with MASLD.

New occurrences of mammals from McKay Reservoir (Hemphillian, Oregon)

Abstract Encompassing global cooling, the spread of grasslands, and biogeographic interchanges, the Hemphillian North American Land Mammal Age is an important interval for understanding the factors driving ecological and evolutionary change through time. McKay Reservoir near Pendleton, Oregon is a natural laboratory for analyses of these factors. It is remarkable for its small vertebrate fauna including rodents, bats, turtles, and lagomorphs, but also for its larger mammal fossils like camelids, rhinocerotids, canids, and felids. Despite the importance of the site, few revisions to its faunal list have been published since its original description. We expand on this description by identifying taxa not previously known from McKay Reservoir based on specimens collected during fieldwork and through reidentification of previously collected fossils. Newly identified taxa include the borophagine canid Borophagus secundus (Matthew and Cook, 1909), the camelids Megatylopus Matthew and Cook, 1909 and Pleiolama Webb and Meachen, 2004, a dromomerycid, and the equids Cormohipparion Skinner and MacFadden, 1977 and Pseudhipparion Ameghino, 1904. Specimens previously assigned to Neohipparion Gidley, 1903 and Hipparion de Christol, 1832 lack the features necessary to diagnose these genera, which are therefore removed from the site's faunal list. The presence of Borophagus secundus, Cormohipparion, and Pseudhipparion is especially important, because each occurrence represents a major geographic range extension. This refined understanding of the fauna lays the foundation for future studies of taphonomy, taxonomy, functional morphology, and paleoecology—potentially at the population, community, or ecosystem levels—at this paleobiologically significant Miocene locality.

Centennial-millennial scale global climate-linked monsoonal and non-monsoonal changes in the eastern Arabian Sea during the last 42,800 years

The Arabian Sea significantly impacts the global climate due to its hosting of one of the largest sedimentary bodies in the Modern Ocean basin and thickest oxygen minimum zone. It makes the study of fine-scale evolutionary changes in the Arabian Sea imperative to address the ongoing challenges in developing a strong and cohesive model for predicting rapid climate change in the future. Therefore, this study carried out environmental magnetic, grain size, stable isotope, total organic carbon (TOC), trace elements (TE), and rare earth elements (REE) investigations on a well-dated 2.68 m long sediment core from the eastern Arabian Sea to understand the fluctuation in monsoon and non-monsoon-driven sediment supply and associated primary productivity changes during the late Quaternary. The careful observations of chronological changes in the investigated parameters concerning coeval major global events enabled us to successfully identify the response of major global climatic events that occurred around 42.8–28 ka, 17 ka, 14.5 ka, 11.7 ka, 9.7 ka, 8.2 ka, 4.6–3.9, and 2–0.6 ka. These global events also played a crucial role in co-regulating the water column oxygen conditions in the Arabian Sea. Comparing our record with a sedimentary record from off Chennai, Bay of Bengal, suggests that opposite variations (anti-phasing) between southwest (SW) monsoon and northeast (NE) monsoon is a post-25 ka phenomenon. Pre-25 ka SW and NE monsoon showed similar variations (same phase), and we speculate that this anti-phasing between the SW and NE monsoon was cyclically driven by the earth's axial precession cycle.

Experimental evolution for the recovery of growth loss due to genome reduction.

As the genome encodes the information crucial for cell growth, a sizeable genomic deficiency often causes a significant decrease in growth fitness. Whether and how the decreased growth fitness caused by genome reduction could be compensated by evolution was investigated here. Experimental evolution with an Escherichia coli strain carrying a reduced genome was conducted in multiple lineages for approximately 1000 generations. The growth rate, which largely declined due to genome reduction, was considerably recovered, associated with the improved carrying capacity. Genome mutations accumulated during evolution were significantly varied across the evolutionary lineages and were randomly localized on the reduced genome. Transcriptome reorganization showed a common evolutionary direction and conserved the chromosomal periodicity, regardless of highly diversified gene categories, regulons, and pathways enriched in the differentially expressed genes. Genome mutations and transcriptome reorganization caused by evolution, which were found to be dissimilar to those caused by genome reduction, must have followed divergent mechanisms in individual evolutionary lineages. Gene network reconstruction successfully identified three gene modules functionally differentiated, which were responsible for the evolutionary changes of the reduced genome in growth fitness, genome mutation, and gene expression, respectively. The diversity in evolutionary approaches improved the growth fitness associated with the homeostatic transcriptome architecture as if the evolutionary compensation for genome reduction was like all roads leading to Rome.

Experimental evolution for the recovery of growth loss due to genome reduction

Experimental evolution for the recovery of growth loss due to genome reduction

Unveiling ecological/evolutionary insights in HIV viral load dynamics: Allowing random slopes to observe correlational changes to CpG-contents and other molecular and clinical predictors

In the context of infectious diseases, the dynamic interplay between ever-changing host populations and viral biology demands a more flexible modeling approach than common fixed correlations. Embracing random-effects regression models allows for a nuanced understanding of the intricate ecological and evolutionary dynamics underlying complex phenomena, offering valuable insights into disease progression and transmission patterns. In this article, we employed a random-effects regression to model an observed decreasing median plasma viral load (pVL) among individuals with HIV in Mexico City during 2019-2021. We identified how these functional slope changes (i.e. random slopes by year) improved predictions of the observed pVL median changes between 2019 and 2021, leading us to hypothesize underlying ecological and evolutionary factors. Our analysis involved a dataset of pVL values from 7,325 ART-naïve individuals living with HIV, accompanied by their associated clinical and viral molecular predictors. A conventional fixed-effects linear model revealed significant correlations between pVL and predictors that evolved over time. However, this fixed-effects model could not fully explain the reduction in median pVL; thus, prompting us to adopt random-effects models. After applying a random effects regression model—with random slopes and intercepts by year—, we observed potential "functional changes" within the local HIV viral population, highlighting the importance of ecological and evolutionary considerations in HIV dynamics: A notably stronger negative correlation emerged between HIV pVL and the CpG content in the pol gene, suggesting a changing immune landscape influenced by CpG-induced innate immune responses that could impact viral load dynamics. Our study underscores the significance of random effects models in capturing dynamic correlations and the crucial role of molecular characteristics like CpG content. By enriching our understanding of changing host-virus interactions and HIV progression, our findings contribute to the broader relevance of such models in infectious disease research. They shed light on the changing interplay between host and pathogen, driving us closer to more effective strategies for managing infectious diseases. Significance of the studyThis study highlights a decreasing trend in median plasma viral loads among ART-naïve individuals living with HIV in Mexico City between 2019 and 2021. It uncovers various predictors significantly correlated with pVL, shedding light on the complex interplay between host-virus interactions and disease progression. By employing a random-slopes model, the researchers move beyond traditional fixed-effects models to better capture dynamic correlations and evolutionary changes in HIV dynamics. The discovery of a stronger negative correlation between pVL and CpG content in HIV-pol sequences suggests potential changes in the immune landscape and innate immune responses, opening avenues for further research into adaptive changes and responses to environmental shifts in the context of HIV infection. The study's emphasis on molecular characteristics as predictors of pVL adds valuable insights to epidemiological and evolutionary studies of viruses, providing new avenues for understanding and managing HIV infection at the population level.

Evolutionary Period Changes for 52 Cataclysmic Variables, and the Failure for the Most-fundamental Prediction of the Magnetic Braking Model

The evolution of cataclysmic variables (CVs) is driven by period changes ( Ṗ ), for which the long-venerable consensus is the magnetic braking model (MBM). The MBM has its only distinctive assumption being a power-law “recipe” describing the angular momentum loss (AML) in the binary, producing a single unique evolutionary track with Ṗ as a function of the orbital period. This required prediction can be used to test the most-fundamental assumption of MBM, but it has never been tested previously. In this paper, I collect Ṗ measures for 52 CVs of all types. First, 44% of the CVs have positive Ṗ , with such being impossible in MBM. Second, even among the CVs with negative Ṗ , their Ṗ measures are always more negative than required by MBM, with an average deviation of 110×. Third, three CVs have large chaotic variations in Ṗ that are impossible for MBM, proving that some unknown mechanism exists and is operating that dominates for these systems. Fourth, the MBM does not account for the long-term effects on evolution arising from the large sudden period decreases seen across many nova events, with this unaccounted effect dominating for the majority of nova systems and changing the sign of the overall evolutionary Ṗ . Fifth, three recurrent novae are observed to suddenly change Ṗ by an order of magnitude across a nova event, with this being impossible in the MBM. In all, the required MBM Ṗ predictions all fail for my 52 CVs, usually by orders of magnitude, so the MBM AML-recipe is wrong by orders of magnitude.

Sedimentary facies analysis of a thin-bed-dominated turbidite succession in the Miocene Temburong Formation, Kampung Bebuloh, Labuan Island, Malaysia

Thin-bedded turbidites are important hydrocarbon-bearing reservoirs in many mature fields throughout the world. The type of turbidite depositional setting strongly influences vertical and horizontal continuity of the reservoir. However, distinguishing between lobe and levee associated thin-bedded turbidites remains challenging due to their generally similar facies characteristics. This study aims to contribute some insights to this problem by conducting a detailed bed-scale facies analysis on the Early Miocene Temburong Formation exposed at Kampung Bebuloh, Labuan Island, Malaysia, which may uncover features that can help in differentiating between both depositional types. Six facies are recognized in the Temburong Formation, which are interpreted as low density turbidites (F1 – F4), hybrid event beds (F5), and sustained turbidites (F6). Detailed facies and ichnology analysis reveal features which are consistent with a lobe fringe deposit rather than levee-associated environment interpretation, including tabular bed geometries, presence of hybrid event beds, and the absence of thick-bedded channel-fill sandstones. Five facies associations are identified and interpreted as representing sub-environments within an overall lobe depositional setting. A diverse trace fossil assemblage, comprising the Nereites ichnofacies is consistent with a deep marine environment. Further identification of the Paleodictyon and Nereites sub-ichnofacies indicates a distal turbidite system setting, most likely lobe fringe. Based on the thick accumulation of FA2 and FA3 and no distinct observable vertical trend, the Early Miocene Temburong Formation in Labuan is interpreted as turbidites deposited at the fringes of lobe complexes rather than a single lobe fringe. Earlier works into the Temburong Formation in SW Labuan proposed a middle slope to proximal basin floor setting where the thin-bedded intervals were interpreted as potentially representing either levee deposits or the fringes of confined lobe deposits. Conversely, the Temburong Formation at Kampung Bebuloh exhibits characteristics of an unconfined lobe setting, suggesting an evolutionary change in depositional conditions over time.

Comparative Analysis of Maternal Gene Expression Patterns Unravels Evolutionary Signatures Across Reproductive Modes.

Maternal genes have a pivotal role in regulating metazoan early development. As such their functions have been extensively studied since the dawn of developmental biology. The temporal and spatial dynamics of their transcripts have been thoroughly described in model organisms and their functions have been undergoing heavy investigations. Yet, less is known about the evolutionary changes shaping their presence within diverse oocytes. Due to their unique maternal inheritance pattern, a high degree is predicted to be present when it comes to their expression. Insofar only limited and conflicting results have emerged around it. Here, we set out to elucidate which evolutionary changes could be detected in the maternal gene expression patterns using phylogenetic comparative methods on RNAseq data from 43 species. Using normalized gene expression values and fold change information throughout early development we set out to find the best-fitting evolutionary model. Through modeling, we find evidence supporting both the high degree of divergence and constraint on gene expression values, together with their temporal dynamics. Furthermore, we find that maternal gene expression alone can be used to explain the reproductive modes of different species. Together, these results suggest a highly dynamic evolutionary landscape of maternal gene expression. We also propose a possible functional dichotomy of maternal genes which is influenced by the reproductive strategy undertaken by examined species.

Niche conservatism and spread explain introgression between native and invasive fish.

Hybridisation can be an important driver of evolutionary change, but hybridisation with invasive species can have adverse effects on native biodiversity. While hybridisation has been documented across taxa, there is limited understanding of ecological factors promoting patterns of hybridisation and the spatial distribution of hybrid individuals. We combined the results of ecological niche modelling (ENM) and restriction site-associated DNA sequencing to test theories of niche conservatism and biotic resistance on the success of invasion, admixture, and extent of introgression between native and non-native fishes. We related Maxent predictions of habitat suitability based on the native ranges of invasive Eastern Banded Killifish (Fundulus diaphanus diaphanus Lesueur 1817) and native Western Banded Killifish (Fundulus diaphanus menona Jordan and Copeland 1877) to admixture indices of individual Banded Killifish. We found that Eastern Banded Killifish predominated at sites predicted as suitable from their ENM, consistent with niche conservatism. Admixed individuals were more common as Eastern Banded Killifish habitat suitability declined. We also found that Eastern Banded Killifish were most common at sites closest to the presumed source of this invasion, whereas the proportion of admixed individuals increased with distance from the source of invasion. Lastly, we found little evidence that habitat suitability for Western Banded Killifish provides biotic resistance from either displacement by, or admixture with, invasive Eastern Banded Killifish. Our study demonstrates that ENMs can inform conservation-relevant outcomes between native and invasive taxa while emphasising the importance of protecting isolated Western Banded Killifish populations from invasive conspecifics.

New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves.

Several efforts have been undertaken to predict the response of microbes under climate change, mainly based on short-term microcosm experiments under forced conditions. A common concern is that manipulative experiments cannot properly simulate the response of microbes to climate change, which is a long-term evolutionary process. In this proof-of-concept study with a limited sample size, we demonstrate a novel approach yet to be fully explored in science for accessing genetic information from putative past marine microbes preserved under Antarctic ice shelves before the industrial revolution. This potentially allows us estimating evolutionary changes as exemplified in our study. We advocate for gathering a more comprehensive Antarctic marine ice core data sets across various periods and sites. Such a data set would enable the establishment of a robust baseline, facilitating a better assessment of the potential effects of climate change on key genetic signatures of microbes.

Emx2 underlies the development and evolution of marsupial gliding membranes

Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium—an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.

Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae)

BackgroundCorydalis DC., the largest genus in the family Papaveraceae, comprises > 465 species. Complete plastid genomes (plastomes) of Corydalis show evolutionary changes, including syntenic arrangements, gene losses and duplications, and IR boundary shifts. However, little is known about the evolution of the mitochondrial genome (mitogenome) in Corydalis. Both the organelle genomes and transcriptomes are needed to better understand the relationships between the patterns of evolution in mitochondrial and plastid genomes.ResultsWe obtained complete plastid and mitochondrial genomes from Corydalis pauciovulata using a hybrid assembly of Illumina and Oxford Nanopore Technologies reads to assess the evolutionary parallels between the organelle genomes. The mitogenome and plastome of C. pauciovulata had sizes of 675,483 bp and 185,814 bp, respectively. Three ancestral gene clusters were missing from the mitogenome, and expanded IR (46,060 bp) and miniaturized SSC (202 bp) regions were identified in the plastome. The mitogenome and plastome of C. pauciovulata contained 41 and 67 protein-coding genes, respectively; the loss of genes was a plastid-specific event. We also generated a draft genome and transcriptome for C. pauciovulata. A combination of genomic and transcriptomic data supported the functional replacement of acetyl-CoA carboxylase subunit β (accD) by intracellular transfer to the nucleus in C. pauciovulata. In contrast, our analyses suggested a concurrent loss of the NADH-plastoquinone oxidoreductase (ndh) complex in both the nuclear and plastid genomes. Finally, we performed genomic and transcriptomic analyses to characterize DNA replication, recombination, and repair (DNA-RRR) genes in C. pauciovulata as well as the transcriptomes of Liriodendron tulipifera and Nelumbo nuicifera. We obtained 25 DNA-RRR genes and identified their structure in C. pauciovulata. Pairwise comparisons of nonsynonymous (dN) and synonymous (dS) substitution rates revealed that several DNA-RRR genes in C. pauciovulata have higher dN and dS values than those in N. nuicifera.ConclusionsThe C. pauciovulata genomic data generated here provide a valuable resource for understanding the evolution of Corydalis organelle genomes. The first mitogenome of Papaveraceae provides an example that can be explored by other researchers sequencing the mitogenomes of related plants. Our results also provide fundamental information about DNA-RRR genes in Corydalis and their related rate variation, which elucidates the relationships between DNA-RRR genes and organelle genome stability.