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Category Archives: Evolution

Empowering Women: The Evolution and Innovation of coto Social Platform – CXOToday.com

Posted: March 14, 2024 at 12:14 am

CXOToday has engaged in an exclusive interview with Mr. Tarun Katial, Founder & CEO, coto.

What began as a simple tool to communicate and interact with friends, share pixelated images, or even exchange likes and shares, social media has come far from its roots today. It is not just a buzzword anymore, as it is constantly evolving and helping individuals and brands find a voice. However, what also cannot be ignored is the attention span of users on social media is fleeting and competition for engagement is on the edge. As creators often find themselves caught in the whirlwind of algorithm changes staying relevant and trendy feels like a tipping point. These constant shifts can make it feel like a guessing game, leaving creators wondering whether their content will ever truly reach their intended audience.

coto, is a social community platform for women, actively working towards this and understanding that every user is unique. Unlike other platforms that may offer a one-size-fits-all approach, coto lets users take the reins. Users select their interests and communities, and the algorithm does the rest. By understanding users preferences, interests, and engagement history, coto presents them with content that truly resonates. Hence users spend less time scrolling through irrelevant content and more time engaging with what matters most to them. Their journey through coto is as individual as they are, giving them the discoverability and authority they desire and deserve respectively. Soon there will be live commerce integration into the platform facilitating a unique monetisation ecosystem. The traditional social media do not give creators an opportunity to monetise and the amount of effort they put into creating content is a need left unmet. Whereas women creators on coto can monetize their expertise, fostering economic independence and creating a supportive community for women entrepreneurs. It will be a single marketplace to avail of paid consultations on topics like mental health, menstrual health, sexual health, astrology, food and nutrition including the users pregnancy journey, astro-science, coaching, and relationships through live streaming.

During the development of coto, we identified a unique opportunity to promote participative ownership, in line with the decentralised principles of Web3. Our key focus was ensuring that all communities on the platform were collectively owned by women. By integrating Blockchain technology, we established a secure and trustless environment where smart contracts guarantee that women collaborating to build these communities are governed by a sustainable framework for the long term. Alongside our goal of establishing a secure environment for women, our mission extended to providing them with an equitable monetisation opportunity to derive value from their efforts and expertise.

The platforms unique blend of community engagement and live commerce has positioned it as a leader in digital entrepreneurship for women, demonstrating the power of a community-driven, secure online space. Currently, social media platforms lack robust loyalty or referral programs. coto, however, incentivizes community creators with referral points and bonuses for every new member they bring to the platform. Any action you take to contribute to the platforms growth is duly recognized and rewarded.

Let us have a look at some of the remarkable features of the platform are as follows:

At coto, our goal is to actively empower women and with this thought, we have built features that enhance user experience and community engagement through innovative technologies. One of the most remarkable features is the introduction of an AI-powered Q&A feature, a groundbreaking initiative in the digital space for women. By harnessing Open AI technology, coto has unlocked new avenues in content creation, engagement, and learning for women creators.

The AI-powered Q&A feature seamlessly blends sophisticated technology with user-centric design. It introduces innovative tools like anonymous posting and responding, enabling users to engage freely without the constraints of identity, and a unique text edit mode that boosts creativity and personalization. The tagging experts functionality adds a new dimension to community interaction, facilitating easier access to topic-based experts.

More than just facilitating interaction, this feature cultivates a culture of curiosity and continuous learning. It encourages exploration, questioning, and growth through various mediums, including text, images, videos, and anime.

Since its launch, the AI-powered Q&A feature has shown significant success as user engagement on the platform has dramatically increased, bolstered by the integration of personalization, recommendation, and intuitive tools. The features availability on both Android and iOS has expanded platform use, boosting visibility and engagement.

The new and upcoming live commerce feature will cater to a diverse group of women across the world. Women from all levels of society can access the platform and avail of professional consultancy services from subject matter experts across vital women-centric topics. They will get a single marketplace to avail of paid consultations on topics like mental health, menstrual health, sexual health, astrology, food, and nutrition including the users pregnancy journey, astro-science, coaching, and relationships. Customers will find their relevant consultants/ experts directly through recommendations based on their availability, experience, and ratings by searching on the platform directly. They can also have a best-in-class live streaming experience coupled with ease of navigating through the app with AI-based tools, recommendations, and discovery.

We are counting on the invaluable support of our global womens community members and experts to ensure the success of integrating live commerce into our app. Building on the positive response we received from our communities regarding the recent Q&A feature, were optimistic that this addition will drive even greater engagement. By incorporating live commerce into our platform, we anticipate a significant increase in user interaction, strengthened community bonds, enhanced monetization opportunities, personalised experiences, economic empowerment, and financial inclusion of women across the globe. It will surely provide a new dimension to womens digital entrepreneurship at a larger scale which will also narrow the gender gap in the technology world for women.

At coto, user feedback plays a crucial role in shaping the platforms features and ensuring they cater to the needs of its community. coto maintains an ongoing research program to collect feedback from community members and community administrators. Armed with user feedback and data insights, coto embraces an iterative design and development process.

With technology being an integral part of our daily lives, cotos mission transcends mere resonance with womenit seeks to empower them actively. This commitment is evident in our pioneering efforts to enhance user experience and community engagement through innovative technology like the newly launched AI-powered Q&A and the upcoming live commerce. cotos facial recognition technology ensures the safety and security of its members, which is crucial for a community platform designed exclusively for women. The app will soon include more features within the digital services space to help experts grow. The platform is going to launch professional live consultation services around mental health, menstrual health, relationships/sexual health, and astrology, and these categories will only grow over the period. Through the initiative of live monetisation services, coto is revolutionizing the professional journey of aspiring as well as seasoned women entrepreneurs through a tech-enabled inclusive approach backed by the support of influential leaders and subject matter experts on the platform.

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The Evolution of Da’Vine Joy Randolph – The Root

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Deleted Scene: Beth Looks for Loretta - The Lost City

Its a thankless job being the best friend in a rom-com. You have to be on board with whatever crazy adventure your friend is going on, while simultaneously keeping things somewhat believable. Randolph is endlessly interesting as Beth, the only person in this world who seems to understand whats going on at any given moment.

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The Evolution of Da'Vine Joy Randolph - The Root

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Study on mating behaviors offers clues into the evolution of attraction – Phys.org

Posted: at 12:14 am

Study on mating behaviors offers clues into the evolution of attraction  Phys.org

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Study on mating behaviors offers clues into the evolution of attraction - Phys.org

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Dragonball Evolutions live-action Goku says goodbye to Toriyama: Sorry we messed up – AS USA

Posted: at 12:14 am

Justin Chatwin, the actor who played Goku in the 2009 live-action movie adaptation, Dragonball Evolution, has shared his regret on social networks after the sad news of the passing of Akira Toriyama, creator of Dragon Ball and many more famous and influential anime and manga. The interpreter took advantage of the occasion to apologize (once again) for his performance as Goku in said film, highly criticized by critics and fans for its poor quality.

Despite the overwhelming success of the famous manga and anime franchise around the world, the brand created by Toriyama also has one of the worst live action adaptations in history; the film has 14% on Rotten Tomatoes. And for its leading actor, it is still a cross that he must deal with, despite having asked for forgiveness on numerous occasions. And he did it again while saying goodbye to Akira Toriyama:

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Rest in peace brother. And sorry we messed up that adaptation so badly, wrote Justin Chatwin on his Instagram account along with an image of Goku and another with the news of the mangakas death. Dragonball Evolution was harshly criticized, with a story that barely rescued anything from the original work, a high school student Goku, a ridiculous Mutenroshi and a Piccolo who looked like a bad cosplay, in addition to having more than questionable visual effects.

Justin Chatwin himself has always been a declared fan of Goku and his adventures, although his performance as Goku was ultimately forgettable. Even Akira Toriyama at the time stated that said film Didnt even deserve to be called Dragon Ball, with producers who refused to listen to the mangakas advice to make a film more faithful to the original manga.

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Investec, evolution of SMEs in the materials handling sector – Leasing Life

Posted: at 12:14 am

The past decade has been marked by many challenges and uncertainties for SMEs from interest rate fluctuations and supply chain disruption to a global pandemic, geopolitical conflicts, and extreme weather. And lets not forget the game-changing rise of artificial intelligence, reshaping business right before our eyes.

The unexpected has become expected a given, almost. What is surprising, though, is the resilience the materials handling sector has demonstrated despite all this. This industry has become a reliable cornerstone for businesses needing warehousing and distribution.

As we celebrate the 10th anniversary of Investecs presence in the UK materials handling market, we reflect on five megatrends that have shaped the recent past and consider the challenges and opportunities they are likely to present for businesses needing asset financing in future.

The surge in e-commerce has been a transformative force for materials handling and asset finance more generally. The shift in consumer spending towards online shopping has propelled internet sales[1]from 11.3% in 2014 to a staggering 26.6% in 2024, with the UK e-commerce market expected to reach $750.80 billion by 2029[2]. The demand for efficient warehousing and distribution solutions has skyrocketed as a result, leading to a substantial increase in forklift sales globally.

Financing has been and will continue to be key in empowering businesses to adapt to this changing retail landscape and capitalise on opportunities.

In the current challenging economic environment, we expect tailored financing solutions, including stage payments, to prove instrumental in addressing cashflow challenges and play a crucial role in securing good deals, particularly when purchasing overseas assets.

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Against the backdrop of a global shortage of skilled labour, the materials handling industry embraced automation to streamline processes and reduce operational costs. Conveyor systems and automated robots have become the norm and projections paint a promising picture for the UKs robotics market, estimating a revenue of US$1.48bn by 2024[3]. The use of automated robots in warehouses to enable just-in-time production is set to rise, promising increased productivity, accuracy, and safety.

End consumers now expect everything to be frictionless and speedy as standard. SMEs therefore need the same from their lending partner to be able to deliver. Recognising this, Investec has invested significantly to ensure our teams can turn around deals as quickly as possible in days or sometimes hours.

When it comes to financing investment in automation, bespoke debt structures, including asset-based lending and cashflow strategies, or a combination of both, should be considered. A strategic financial partner can assist in effectively navigating through these challenges.

The integration of the Internet of Things (IoT) and data analytics has revolutionised how materials handling operations are managed. Real-time tracking, predictive maintenance, and data-driven decision-making have become integral components of the industry.

For example, Investec gathers data on behalf of its clients that helps to protect and promote their business. We can show them every deal theyve done with us, who the customer was, whether any are in arrears and how their portfolio has performed over time.

SMEs who fail to make the most of the information available to them will struggle to remain competitive in this data-centric era.

At the same time, environmental concerns have risen towards the top of the business agenda. With warehouses among the biggest emitters of fossil fuels, companies in materials handling are stepping up replacing equipment and shifting to sustainable practices.

We hear from our clients that this move is not just about meeting regulatory standards but also about responding to consumer demands and internal expectations.

As a result, Investec Asset Finance is seeing increasing demand from clients for financing initiatives that improve green credentials, diversify their business, and save on energy costs. This includes investments in solar panels, biomass energy, onshore wind, and heat pumps, and more.

The materials handling industry has grappled with supply chain disruptions in recent years. In such a dynamic environment, financial partners need to be nimble in swiftly adapting to changing circumstances for their clients.

For example, when the Covid-19 pandemic broke out, Investec promptly offered a six-month forbearance to clients to help mitigate the impact of supply chain challenges. This kind of responsiveness is especially crucial during a period marked by economic instability and global unrest, where rising prices and trading obstacles are increasingly prevalent.

While these five trends will continue to be key in driving change within materials handling businesses must be prepared for others to join that list. Trying to predict which new technologies or black swan events will shape the industry in future is a fools game. Instead, both SMEs and their lending partners should focus on ensuring they are nimble enough and resilient enough to meet any challenge and finding within that the opportunities.

Notes:

[1]UK State of Commerce ecommerce trends report 2023 | Signifyd

[2]Internet sales as a percentage of total retail sales (ratio) (%) Office for National Statistics (ons.gov.uk)

[3]https://www.statista.com/outlook/tmo/robotics/united-kingdom#revenue

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Pride & Prejudice and the evolution of the female gaze on screen – Yahoo News UK

Posted: March 6, 2024 at 3:57 pm

Colin Firth and Matthew Macfadyen as Mr Darcy in the 1995 TV series and 2005 film adaptations of Pride & Prejudice. (BBC/United International Pictures)

Pride and Prejudice, for many, is the pinnacle of romantic literature, but Jane Austen's creation has also served as a key turning point on screen too: the evolution of the female gaze.

The 'female gaze' refers to a number of things in theory, for one it's the representation of the viewpoint of women both on and off screen ie female directors, writers, and viewers. It can also represent the connection that an audience has with the story, especially if it emphasises the idea of a woman being desired and the idea of a man being the object of desire.

The tale of Elizabeth Bennet and Mr Darcy's romance is ripe ground for the depiction of the female gaze on the silver screen, something that is well represented by the 1995 TV show when Colin Firth's Mr Darcy walked around in a wet shirt after a swim in a lake (which has now been sold at auction for 20,000).

Joe Wright's 2005 film also provided plenty of scenarios that made viewers swoon, and have since become significant cultural moments in their own right. Matthew Macfadyen might be best known for his award-winning role in Succession for some, but for many women it is his depiction of Mr Darcy that stands out thanks to his line delivery, his longing gazes at Keira Knightley's Elizabeth, and of course his infamous hand flex.

These moments all represent the female gaze in some way, the 1995 TV series shows Firth in a desirable fashion, while Macfadyen's depiction of Mr Darcy oozes with attraction the moment he crosses paths with Knightley's strong-willed Elizabeth. In both scenarios female viewers can imagine themselves in Elizabeth's shoes, as the desirer and the desired.

Since then this notion of the female gaze has only grown stronger as time has gone on. Just look at the success of Netflix's Bridgerton to see how successful romance can be on the silver screen the show, like Austen's work and its depictions, focuses on love stories that highlight the woman being courted more so than the men they're involved with.

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Bridgerton even pays homage to Pride & Prejudice in its second season, when Jonathan Bailey's Anthony falls into a lake and is left completely soaked, allowing his romantic interest Kate Sharma (Simone Ashley) to pine for him because of his state of undress.

Romance novels and period dramas have also given way to Byronic heroes, men who have gloomy personalities but are capable of strong passion towards their romantic interest. Characters like Heathcliff in Emily Bront's Wuthering Heights serve as an apt example of this, and these kinds of characters are also ones that serve the female gaze well in cinema.

Shows like Poldark and Outlander have made actors Aidan Turner and Sam Heughan stars overnight because of their depictions of romantic heroes. While chick flicks have also long been used as a way to represent the female gaze over the years.

It's not just films and dramas aimed at women that have highlighted the female gaze, it can also happen in those predominantly aimed at men the James Bond franchise for one. 2006's Casino Royale famously features a scene in which Daniel Craig's 007 emerges from the ocean in slow-motion. It's a scene that feels tailor-made to entice female viewers. For a movie franchise with a long history of objectifying women, it was a refreshing change of pace.

Desire and desirability aside, films focused on women also represent the female gaze onscreen. Greta Gerwig's hugely successful blockbuster Barbie shared the plight that all women face in a patriarchal society with wit and wisdom unexpected for a film about a doll.

It quickly became a cultural phenomenon and earned more than 1bn at the box office, while for some this might make it seem like films about toys are the future the real takeaway should be this movies about women and for women are worth telling.

1995's Pride & Prejudice is streaming on BBC iPlayer.

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Joe Wong’s Musical Evolution – Shepherd Express

Posted: at 3:57 pm

Joe Wongs musical evolution has taken him from the streets of Milwaukee to composing the music for the Netflix series The Russian Doll to having legendary drummer Jim Keltner play on his album,Mere Survival, which was released in February.

Wongs podcast The Trap Set began with a focus on drummers but has expanded to include singers, guitarists, bassists, keyboardists and harpists. The series has aired over 300 episodesconversations reallywith Wong using music as a springboard to detour into the backroads that make creative people tick.

The blurb on Wongs new album reads, Wong finds wonder in the muck, spinning rare beauty into outsized songs of redemption and reconciliation.Chock full of tasteful Zombies-inspired orchestrated pop, standout track Ordinary Light suggests a collaboration of Harry Nilsson and Beach Boys. He cites Love and The Walker Brothers as favorites as well.

Wong took time recently to chat. He broached the task of taking his band on the road. The challenge with me is that I have 20 people in my band (laughs), the drummer is also in Pearl Jam, the guitar player Mary Timony has a busy career, the harpist Mary Lattimore has a busy career. So, we have to plan stuff pretty far out. But Ive tried to figure out how to put together different bands for different types of shows, so I dont need to play with the same folks or as many folks.

The first time he sang was at the end of 2019; Wong had finished his first album, but it hadnt been released. I wanted to play a show to see how the songs translated live. After soundcheck I was sitting behind the drums, which belonged to Matt Cameron, I was feeling comfortable and then remembered I wasnt going to be playing drums and that I had to go out and sing.

Wong says he got so nervous he blacked out and doesnt recall much of the show other than it felt really good. I think my conscious mind had to just shut down and let my subconscious drive the bus.

In the time since, Wong has gotten more comfortable as a singer, some of it from rehearsing for tours that kept getting cancelled during Covid; not to mention the thousands of shows he has played as a drummer. He says the nervousness before each show is a healthy sign that he is pushing himself into a period of growth.

With over 300 episodes and counting, it is safe to say Wong has engaged some legendary musicians. He relates to them on a personal level as well as a musical one.

He began the podcast about a decade ago because he was touring and not feeling the visceral joy he associated with playing music. I was trying to figure out what was going on and thought maybe I was stuck in a loveless marriage with music.

Listening to podcasts instead of music, he was drawn to the longform detailed conversations. He used Marc Marons podcast as a template. The feeling Wong had lost re-emerged and importantly, he figured out a lot of people go through similar periods of ennui.

He has spoken to genre-defining geniuses, but Wongs own brilliance was the initial focus on drummers. Drummers are often the least interviewed members of any band. Even if they are great. There is a lot of untapped gold there.

He said the Keltner recording session came about when the legendary drummer, who had been a podcast guest, offered his services. Wong didnt have anything written but he thought it would be stupidnotto write songs for him to play on. So, I wrote a couple songs with him in mind.

The session was booked at the studio owned by Foo Fighters. It was easy get other musicians to play on that session because everyone wants to play with Jim. That session was recorded live to tape to capture Keltners innate groove.

Back to his idea for the podcast, Wong says he wanted to strike a balance between Marons freewheeling non-agenda and the preparedness of Terry Gross, host of NPRs Fresh Air. I was desperate to know the information I was asking people anyway. As a fan and music geek he gets to ask questions many of us have itched to delve into.

Wongs day job is writing music for film and television. Over the 20 years he has gotten comfortable staring at a blank screen knowing something will come by the time it is due.

When he began working on material for his first album, 2021sNite Creatures, he struggled with drowning in his own neuroses and couldnt finish anything.

Before the era of smart phones, he would call his own answering machine to leave ideas. Writing both albums was a blend of spontaneous ideas but also setting aside time every day to sit and let something happen.

He began using the tools he learned as a composer and applied them to his songwriting. Even if that was just five or 10 minutes in the morning. You can write a song in five minutesor at least the basic idea of the song. The person who writes the song and the person who decides to develop, and record it are two different versions of yourself. The editor is one aspect, and the creator is another aspect of yourself.

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A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer – Nature.com

Posted: at 3:57 pm

Genome selection and pangenome generation

We based our analysis on the proGenomes v.2.2 dataset containing 82,400 genomes grouped into 11,562 species (that is, specI clusters) that were defined based on 40 single-copy marker genes20. The corresponding species tree generated based on concatenated marker gene sequences was kindly provided by the authors of the proGenomes article20.

From this initial selection, we filtered out metagenome-assembled genomes, single-amplified genomes, genomes flagged as chimeric by GUNC39, genomes that were not taxonomically cohesive with the rest of the specI cluster according to GTDB26, genomes with no 16S rRNA gene sequence detected and genomes we could not confidently map to the MicrobeAtlas database (see Mapping genomes to MicrobeAtlas database OTUs below). The species tree was pruned to remove these genomes using the ETE Toolkit v.3 (ref. 40). As a result, we obtained 78,315 genomes grouped into 8,790 species. For each species, a pangenome was generated by clustering all gene sequences on 95% nucleotide sequence identity as described in ref. 41.

All gene sequences were clustered using MMseqs2 (ref. 42) with minimum overlap of 50%, minimum identity threshold of 80% and clustering mode 0. The rest of the parameters were left as default. For each gene cluster, whenever sequences originated from more than one genome within a species, we only retained sequences that were most similar to those from other species within the gene cluster. We then proceeded with gene clusters containing sequences from at least five different species. Sequences were then aligned using the automatic strategy selection option in MAFFT v.7.471 (ref. 43), with all other parameters left as default. On the basis of the multiple sequence alignment, a gene tree was generated using FastTree v.2.1.11 (ref. 44) using the generalised time-reversible model45 of nucleotide evolution, with all parameters left as default.

Before performing tree reconciliation, we subsampled the species tree using ETE Toolkit v.3 (ref. 40) to decrease computational requirements in the following manner: for each gene cluster, the species tree node corresponding to the last common ancestor of all species within the gene cluster was selected. Clades within the species tree not containing any genes from the gene cluster were collapsed for computational efficiency. Subsequently, the subsampled species tree was used to root the gene tree using the OptRoot module from RANGER-DTL v.2.0 (ref. 23). We then ran RANGER-DTL with default settings to perform gene and species tree reconciliation for a total of 500. Gene clusters in which more than 50 optimal roots were detected were not considered further. Reconciliations from each optimal root were aggregated using the AggregateRanger_recipient module from RANGER-DTL v.2.0. We used a custom script to aggregate results across optimal roots and detect tree nodes that were labelled as transfers. For downstream analysis, we considered only transfer events detected in 80% reconciliations that contained gene pairs with 0.5 minimum branch support in the gene tree. In addition, all multifurcations containing 100% identical genes from different species were considered to be transfer events.

For each genome, we counted a gene as having undergone transfer as long as its pangenome-representative gene was involved in a transfer event. For the denominator (that is, total number of genes assessed), we only considered genes if their pangenome-representative genes had passed all steps described above in HGT event detection. The number of genes transferred was then divided by the total number of genes assessed and the average based on all genomes within a species was calculated. For the examples mentioned in the main text, we used data from specI_v3_Cluster259 for A. baumannii and data from specI_v3_Cluster712 for L. monocytogenes.

The NCBI Sequence Read Archive46 was searched for samples and studies containing any of the keywords metagenomic, microb*, bacteria or archaea in their metadata. The corresponding raw sequence data (as of 7 March 2020) were downloaded and quality filtered. To assign OTU labels, quality filtered data were mapped to MAPref v.2.2.1 using MAPseq v.1.0 at a 0.5 confidence level47. We then filtered out samples containing less than 1,000 reads and/or less than 20 OTUs defined at 97% 16S rRNA gene identity and retained samples with at least 90% community coverage (calculated based on the formula in ref. 48).

NCBI Sequence Read Archive sample metadata were parsed to classify every sample into four general environments: animal, aquatic, plant and soil. Subsequently, we calculated BrayCurtis distances between all samples in the dataset and compared community compositions in samples from independent studies. When a sample was consistently similar to samples assigned to a different environment, we adjusted its environment label. In cases where samples with similar community compositions had no general agreement between assigned environments, we removed the environmental label.

We used barrnap49 with default settings to predict 16S rRNA gene sequences in the genome selection, proceeding with sequences of 50% of expected length. The sequences were then mapped to MAPref v.2.2.1 using MAPseq v.1.0 (ref. 47), retaining only sequences that mapped to an OTU with a 0.3 confidence level. Genomes containing multiple 16S rRNA gene copies were mapped to OTUs based on a majority rule (50% copies) or high confidence (at least one copy with a 0.98 confidence level). Species containing multiple genomes were mapped to OTUs based on majority (50% genomes).

For each OTU within the dataset, the average abundance was calculated separately for all samples assigned to the animal, aquatic, plant and soil environments. The OTU was then assigned to its preferred environment based on the highest of the four numbers.

Distances between gene and species pairs were extracted from the corresponding trees using the dist function in ETE Toolkit v.3 (ref. 40). To plot the distribution in Fig. 2a, only gene pairs with 0.5 minimum branch support values and 50% sequence overlap within the multiple sequence alignment were considered. Gene pairs with and without transfer events were normalized with respect to species distance by splitting the species distance distributions into 80 bins and subsampling the group with the larger number of pairs in each bin (either transfer detected or no transfer detected) to the number of pairs in the second group in the corresponding bin (either no transfer detected or transfer detected). The same procedure was performed for normalizing gene pairs with and without transfer events with respect to gene distance. After normalization, the resulting distributions were compared using the two-sided MannWhitney U-test.

To calculate gene ubiquity, we counted the number of genomes represented by a gene in each pangenome versus the total number of genomes in the species. For subsequent analysis, only species encompassing ten or more genomes were considered. We used previously defined thresholds25 to distinguish extended core genes (90% gene ubiquity) and cloud genes (15% gene ubiquity). In the species pair participating in HGT, the species with the higher gene ubiquity was labelled as the putative donor, whereas the species with the lower gene ubiquity was labelled as the putative recipient. To compare extended core and cloud genes with or without transfer events, a two-sided Fishers exact test was performed.

We used the COG category and KEGG pathway functional annotations provided by the proGenomes database after running eggNOG-mapper for eggNOG 5.0 (ref. 35). Each gene cluster was annotated to the corresponding functional categories based on the union of all gene annotations within the cluster. To analyse genes associated with the mobilome, we looked up which terms corresponded to the XMobilome: phages, transposons category in the database of COGs50,51 (mobilome, curated, in Extended Data Fig. 4). In addition, we extracted terms that contained the following keywords in the annotations provided by the proGenomes database: phage, transposon, transposase, transposition, transposable, mobile, mobilization, integrase, integration, plasmid, conjugative, conjugation, transformation and competence (mobilome, uncurated, in Extended Data Fig. 4). To analyse genes associated with transcription regulation, we extracted terms from the transcription category that contained the following keywords in the annotations provided by the proGenomes database: regulation and regulator (transcription regulation, uncurated, in Extended Data Fig. 4). We calculated a functional categorys background expectation fraction by counting the total number of genes that passed the pipeline that were annotated to this category divided by the total number of genes that passed the pipeline.

For each detected transfer event, we calculated the average species and gene distance by taking all average pairwise distances between left descendants and right descendants of the transfer event (for gene distance calculations, only gene pairs with 50% sequence overlap were considered). The resulting distribution of species and gene distances can be seen in Fig. 2e. For functional enrichment analysis, minimum and maximum species and gene distance cut-offs were selected in such a way that there were no bins without observations, with the resulting area divided into thirds. We also looked specifically at transfer events at the 0.01 and 0.05 gene distance cut-offs (approximately 99% and 95% sequence identity, respectively) as these results would be more comparable to previous studies that detected HGT events based on nearly identical sequences. We then counted the number of transfer events annotated to each functional category divided by the total number of transfer events in the area. The observed fraction of events annotated to a specific function was then tested with a two-sided binomial test against the fraction of all genes on which the pipeline was run that were annotated to this function. Resulting P values were corrected for multiple testing using the HolmSidak method.

A similar procedure was performed using KEGG ortholog annotations, grouping them into KEGG pathway maps (0910109145) for Extended Data Fig. 5 and antimicrobial resistance genes (BR:ko01504) for Extended Data Fig. 6.

We compared our functional enrichment analysis results with those from refs. 9,13,18,28,29,30,31,32,33,34. In most of these studies, functional categories were based on the COG database, with the exception of ref. 13 (with categories based on the SEED52) and refs. 9,28 (both with categories based on TIGRFAMs53). The mapping between COG categories and KEGG pathways (used in our study), SEED and TIGRFAMs can be found in Supplementary Table 1.

For our study, we considered enrichment data from the most recent transfers, that is, gene distance bins 0.000.01, 0.000.05 and 0.000.25. These three gene distance bins together with three species distance bins provided us with nine data points to consider for each functional category. We assigned a functional category to have strong evidence for enrichment or depletion in transfers if at least seven of the nine data points showed significant enrichment or depletion. We assigned a functional category to have weak evidence for enrichment or depletion in transfers if most data points showed enrichment or depletion but this was not always statistically significant.

For ref. 18, we considered the results depicted in Fig. 8d and Supplementary Table 13 of the article. We calculated the first and third quartiles of the HGT index using all genes in Supplementary Table 13. We assigned a functional category to have strong evidence for enrichment in transfers if the median HGT index from genes in this category was greater than the third quartile. We assigned a functional category to have strong evidence for depletion in transfers if the median HGT index from genes in this category was less than the first quartile. Only functional categories containing at least five genes were considered.

For ref. 34, we considered the results depicted in Fig. 9 of the article. We considered only recent HGT events (99% nucleotide sequence identity). We assigned a functional category to have strong evidence for enrichment in transfers if the median recent HGTs in this category was greater than the third quartile. We assigned a functional category to have strong evidence for depletion in transfers if the median recent HGTs in this category was less than the first quartile.

For ref. 32, we considered the results depicted in Fig. 4a (HTgenes row) of the article. We considered a functional category to have strong evidence for enrichment or depletion in transfers if the observed-to-expected ratio of orthologous groups was significantly different from one.

For ref. 31, we considered the results depicted in Supplementary Fig. 7 of the article. We considered a functional category to have strong evidence for enrichment or depletion in transfers if the relative proportion of transferred genes was significantly over- or underrepresented when compared with the set of all bacterial genes.

For ref. 30, we considered the results depicted in the first two columns of Table 3 of the article. We considered a functional category to be enriched in transfers if its relative transferability was higher than one, and to be depleted in transfers if its relative transferability was lower than one. We used a P value cut-off of 0.05 to distinguish strong and weak evidence for enrichment or depletion.

For ref. 33, we considered the results depicted in Table 2 of the article. In the table, functional categories were listed that significantly differed from the background of all gene families. We used a P value cut-off of 0.05 to distinguish strong and weak evidence for enrichment or depletion.

For ref. 29, we considered the results depicted in Fig. 4b of the article. We used Z-score cut-offs of 2 and 2 to distinguish strong and weak evidence for enrichment or depletion.

For ref. 13, we considered the results depicted in Supplementary File 6 (SEED level 1 and SEED level 2) of the article. We used a P value cut-off of 0.05 to distinguish strong and weak evidence for enrichment or depletion. We downweighted depletion evidence for the transcription (regulatory) and signal transduction categories as they both mapped to regulation and cell signalling in the SEED. For COG categories that mapped to multiple categories in the SEED, we indicated evidence based on the consensus from these categories.

For ref. 28, we considered the results depicted in Table 2 of the article. We downweighted depletion evidence for cell cycle control and mitosis and cell motility as they both mapped to the cellular processes in TIGRFAMs. We also downweighted enrichment evidence for carbohydrate transport and metabolism as there was no one-to-one mapping for this category.

For ref. 9, we considered the results depicted in Fig. 2 of the article. We considered a functional category to be enriched in transfers if the proportion of transferred genes was greater than 10%, and to be depleted in transfers if the proportion of transferred genes was less than 3%.

An OTU was detected as present in a given sample if its relative abundance was at least 0.01%. To calculate the co-occurrence between two OTUs, we counted the number of samples in which both OTUs were present and divided it by the number of samples in which the less prevalent OTU was present. Phylogenetic distances between OTUs were retrieved from the MicrobeAtlas database 16S rRNA tree using the dist function in ETE Toolkit v.3 (ref. 40).

For modelling the relationship between co-occurrence and phylogenetic distance, we only considered OTUs that exchanged at least 1 gene with 30 other OTUs and OTU pairs in which both OTUs were present in at least 20 environmental samples. The power law equation (1) is as follows:

$${{rm{CO}} approx ktimes {rm{PD}}^{a},}$$

(1)

where CO stands for co-occurrence, PD stands for phylogenetic distance, and k and a are parameters fitted using the nlstools package in R54. Model residuals were then used to calculate Spearman correlations with the number of genes transferred. To generate the background distribution, the number of genes was shuffled before calculating Spearman correlations. The resulting distributions of Spearman correlations generated based on raw co-occurrence (precorrection), model residuals (postcorrection) or background were compared with each other using the two-sided MannWhitney U-test.

The analysis depicted in Fig. 4bd has been performed using a similar set-up as described in Gene and species distance normalization. We used the 7 genes transferred cut-off to denote OTU pairs with many transfer events as this corresponded to the 80% quantile of OTU pairs with at least 1 gene transferred.

Global networks of predicted interactions were computed with FlashWeave v.0.19.0 (ref. 38). This method uses the local-to-global learning approach55 to learn the skeleton of a Bayesian network encoding putative ecological relationships between species adjusted for ecological or technical confounders. To this end, FlashWeave uses an interleaved testing scheme that (1) heuristically determines likely confounding variables for each pair of species (based on univariate associations and previous iterations of the algorithm), and (2) subsequently tests whether the focal association holds when conditioned on these candidate confounders.

The parameters used for running FlashWeave were as follows: sensitive=false, heterogeneous=true, and max_k=3 (with confounder correction) or max_k=0 (without confounder correction). With these settings, FlashWeave converts non-zero read counts to centred log-ratio-transformed values to account for compositionality and discretizes these values. Mutual information tests are then run on the discretized values. We used co-occurrence data from all 95,422 OTUs contained within the environmental sample dataset, filtering the resulting network for edges between the 4,380 OTUs for which transfer event data were generated. OTU pairs with a score higher than zero were considered as interacting. To normalize for differences in phylogenetic distance and co-occurrence distributions between species with at least seven genes transferred and species with zero or one gene transfer, the procedure described in Gene and species distance normalization was performed with simultaneous subsampling on phylogenetic distance and co-occurrence for 8080 bins.

We used the same relative abundance numbers as calculated in Preferred habitat assignment. For each OTU, we only considered its abundance within its preferred environment, denoting high-abundance OTUs as those whose abundance was above the 80% quantile in this environment. In contrast, we denoted low-abundance OTUs as those whose abundance was below the 20% quantile in this environment. OTU pairs were then sorted based on phylogenetic distance and the fraction of OTU pairs with at least one transfer event detected was calculated for each phylogenetic distance bin. Error bands were calculated using Bernoullis principle of uncertainty. Resulting fractions were then pairwise compared between the highhigh, highlow and lowlow groups using a one-sided Wilcoxon rank-sum test. Resulting P values were corrected for multiple testing using the BenjaminiHochberg method.

We computed a generalism index for each OTU reflecting its environmental flexibility. This index was calculated based on the entropy of the OTUs abundance values across the four major environments (animal, aquatic, soil and plant). OTUs with similar abundances across environments had higher entropy. OTUs with uneven abundances across environments (a higher abundance in one or a few of the environments compared with the rest) had lower entropy.

To compare inter-environmental transfers, we selected 200 OTUs assigned to each environment (see Preferred habitat assignment) that displayed the highest entropy (generalists) and 200 OTUs that displayed the lowest entropy (specialists). OTU pairs were then subsampled in such a way that phylogenetic distance distributions were equal between all environments and between generalists, specialists and all species. We then counted the fraction of OTU pairs with at least one transfer event detected. To generate the background expectation, OTU pairs from all species were subsampled to the target phylogenetic distance distribution 1,000. We then fit a normal distribution to the generated data using the fitdistr function in R56 to get an estimate of the expected mean, s.d. and range of transfer rates between different environments.

Data from Figs. 2 and 4b,c and Extended Data Figs. 16 were visualized using seaborn v.0.11.2 (ref. 57) and matplotlib v.3.5.1 (ref. 58) in Python v.3.7.4. Data from Figs. 3, 4a, and 5 and Extended Data Fig. 7 were visualized using ggplot2 v.3.3.5 (ref. 59) in R v.4.1.1.

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.

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A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer - Nature.com

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Redefining Intelligence: Chimpanzees Break Through the Cultural Evolution Barrier – Medriva

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Redefining Intelligence: Chimpanzees Break Through the Cultural Evolution Barrier  Medriva

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Redefining Intelligence: Chimpanzees Break Through the Cultural Evolution Barrier - Medriva

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Mollusk Eyes Reveal How Future Evolution Depends on the Past – Quanta Magazine

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All light-sensing structures on the chiton shell, Varney explained, are attached to nerves, which pass through the shell slits to connect to the bodys main nerves. The slits function as cable organizers, bundling sensory neurons together. More slits mean more openings through which nerves can run.

It so happens that the number of slits is standard information that is recorded anytime somebody describes a new chiton species. The information was out there, but without the context of a phylogeny to map it back to, it didnt have any meaning, Varney said. So I went and looked at this and started seeing this pattern.

Varney saw that twice, independently, lineages with 14 or more slits in the head plate evolved eyespots. And twice, independently, lineages with 10 or fewer slits evolved shell eyes. She realized that the number of slits locked into place which kind of eye type could evolve: A chiton with thousands of eyespots needs more slits, whereas a chiton with hundreds of shell eyes needs fewer. In short, the number of shell slits determined the evolution of the creatures visual systems.

The findings lead to a new set of questions. One that the researchers are actively investigating is why the number of slits constrains the type of eye that can evolve. Answering that will require work to elucidate the circuitry of the optic nerves and how they process signals from hundreds or thousands of eyes.

Alternatively, the relationship between eye type and the number of slits might be driven not by the needs of vision but by the way the plates develop and grow in different lineages, Sumner-Rooney suggested. Shell plates grow from the center outward by accretion, and eyes are added throughout the chitons life as the edge grows. The oldest eyes are those in the middle of the animal, and the most recently are added at the edges, Sumner-Rooney said. As a chiton, you might start life with 10 eyes and finish your life with 200 eyes.

As a consequence, the growing edge of a shell plate has to leave holes for new eyes many small holes for the eyespots, or fewer larger holes for the shell eyes. Too many or too-big holes could weaken a shell to its breaking point, so structural factors might limit which eyes are possible.

Much remains to be discovered about how chitons see the world, but in the meantime, their eyes are primed to become biologists new favorite example of path-dependent evolution, Nilsson said. Examples of path dependence that can be really well demonstrated, as this case [is], are rare even though the phenomenon is not only common, its the standard way things happen.

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Mollusk Eyes Reveal How Future Evolution Depends on the Past - Quanta Magazine

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