Die Neanderthaler -brein het groter geword met 'n groter koolhidraatverbruik

Die Neanderthaler -brein het groter geword met 'n groter koolhidraatverbruik

Ongeveer 'n miljoen jaar gelede het die Neanderthal -brein in ongeveer 200 000 jaar verdubbel, wat in evolusionêre terme 'n geringe getal is. Die evolusie van die brein word lankal toegeskryf aan die toenemend gesofistikeerde gebruik van klipgereedskap. Groter breine het Neanderdallers nuwe voordele in wildjag en voer gegee. Hierdie faktore is al lank bekend as die hoofredes vir groter Neanderthal -brein, maar die jongste studie oor hierdie onderwerp het 'n ander faktor in hierdie verandering in breingrootte beklemtoon: koolhidraatverbruik.

'N Nuwe studie gepubliseer in die Verrigtinge van die National Academy of Sciences (PNAS), wat die orale mikrobiome en bakterieë van die tande van Neanderthalers en moderne mense bestudeer het (voor die Landbou -rewolusie 10 000 jaar gelede), werp nuwe lig op waarom die Neanderdal -brein groter word. Die navorsers het bevind dat styselryke en koolhidraatryke voedsel so gereeld verbruik word dat dit die bakterieë in hul liggame verander, hul gedrag en hul breingrootte verander.

"Ons dink ons ​​sien bewyse van 'n baie ou gedrag wat moontlik deel kon wees van enkefalisering - of die groei van die menslike brein," sê professor Christina Warinner, Harvard. "Dit is 'n bewys van 'n nuwe voedselbron wat vroeë mense in die vorm van wortels, styselgroente en sade kon gebruik." Sy het vinnig daarop gewys dat mense wat deel uitmaak van hierdie proses duidelik nie bewus was van die uitwerking wat dit op hul brein sou hê nie.

Grauer se gorilla -eksemplare by die Royal Museum for Central Africa in Tervuren (België), met tipiese tandheelkundige afsettings op die tande wat donker gevlek is, waarskynlik as gevolg van hul plantetende dieet, wat baie stysels en koolhidrate sou bevat. (Katerina Guschanski / Koninklike Museum vir Sentraal -Afrika )

Neanderthal -brein, tandheelkundige gedenkplaat en die orale mikrobioom

Die nuutste studie van die Neanderdal -brein was 'n groot onderneming, wat bestaan ​​uit 'n multidissiplinêre internasionale navorsingspan van 50 wetenskaplikes, uit 13 lande en 41 instellings. Die span is hoofsaaklik gelei deur navorsers van die Max Planck Institute for the Science of Human History, Duitsland en Harvard Universiteit.

Die studie het meer as 7 jaar geduur, terwyl die span die gefossiliseerde tandplak van Neanderthalers en laat-Pleistoseen noukeurig ontleed het aan moderne mense wat die afgelope 100 000 jaar geleef het, en dit vergelyk het met dié van wilde sjimpansees, gorilla's en huilapies.

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"Ons kon aantoon dat bakteriële DNA uit die orale mikrobioom minstens twee keer so lank behou as wat voorheen gedink is," het J. A. F. Yates gesê. Hy was die hoofskrywer van die studie en is tans 'n doktorale kandidaat by die Max Planck Institute for the Science of Human History. "Die gereedskap en tegnieke wat in hierdie studie ontwikkel is, bied nuwe geleenthede vir die beantwoording van fundamentele vrae in mikrobiese argeologie, en sal die intieme verhouding tussen mense en hul mikrobioom verder kan ondersoek."

Die orale mikrobioom is een van die belangrikste aanduiders van menslike gesondheid, biologie en siektes. Baie min is egter bekend oor die rol daarvan in evolusie of diversiteit in verskillende topografieë. Boonop is die vind van miljarde DNA -rye en fragmente, honderde duisende jare oud, 'n ingewikkelde en omslagtige proses.

Argeogenetici moet die stukkende fragmente van antieke genome bymekaarmaak, en dan probeer hulle, met behulp van hoëtegnologiese data en tegnologie, om bakterieë wat reeds dood is, te verstaan. Hulle het geluk met die rekonstruksie van die 100,000 jaar oue mikrobioom van 'n Neanderthaler uit Pešturina-grot in Serwië, wat die ouderdom van die voorheen oudste orale mikrobioom wat herbou is, verdubbel het.

Close -up van 'n inheemse Neanderthaler -grotmanskedel wat duidelik tande toon, en tandplak, wat gebruik is om die orale mikrobioom en die Neanderdal -koolhidraatverbruik te verstaan. ( gerasimov174 / Adobe Stock)

Neanderthalerbreine en tandbakterieë is swak ondersoek

Die ander uitdaging is dat hierdie gebied van studie verbasend swak ondersoek word ten opsigte van die benoeming van die miljoene bakterieë wat in ons mond voorkom. Baie van die orale mikrobiome is verantwoordelik vir lewensbelangrike funksies in die menslike mond, insluitend gesonde tandvleis en tande. Tog bly die meeste van hierdie bakterieë naamloos, wat fundamentele uitdagings vir hedendaagse navorsers bied.

Die bakteriegemeenskappe in die monde van moderne mense voor die landbou en Neanderthalers het sterk op mekaar gelyk, volgens die studie. Moderne mense en Neanderthalers het veral 'n ongewone groep Streptokokke bakterieë in hul mond. Streptokokke het die unieke vermoë om te bind aan 'n volop ensiem in die menslike speeksel genaamd amilase, 'n ensiem wat die hidrolise van stysel in suiker kataliseer.

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Die suikerverbruikende bakterieë is gevind in die plaak -DNA van Neanderthalers en moderne mense, wat dui op 'n definitiewe styselverbruik. Sjimpansees, aan die ander kant, het geen strepbakterieë op hul tande nie. Daarbenewens het die streptokokke teenwoordigheid by beide Neanderthalers en vroeë mense dui op 'n erfenis van mikrobes van algemene voorouers, moontlik 600 000 jaar gelede.

Familie van Neanderthalers of vroeë Homo Sapiens -kookkuns. Die jongste studie toon dat dit nie net vleis op die spyskaart was nie, maar ook toenemende hoeveelhede koolhidrate, wat bygedra het tot breingrootte -uitbreiding. ( Gorodenkoff / Adobe Stock)

Menslike evolusie en mikrobiome

Die gevolge hiervan, in die studie van menslike evolusie, is diep en viervoudig.

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Eerstens is die omvang van die brein-uitbreidingsteorie, wat gesentreer was rondom die ontwikkeling van klipgereedskap en vleisverbruik, uitgebrei vir toekomstige navorsing.

Tweedens, soos Christina Warriner van Harvard University, 'n molekulêre argeoloog en mede-outeur van die studie, dit stel: "... dit stoot die belangrikheid van stysel in die dieet verder terug in tyd."

In die derde plek dui die teenwoordigheid van die amilase -ensiem, wat die doeltreffende vertering van gaar voedsel bevorder, ook daarop aan dat kook ongeveer 600 000 jaar gelede algemeen en wydverspreid word. Dit help die idee dat kook, soos ons dit ken, slegs sinoniem was met die Landbou -rewolusie, wat 'n baie meer onlangse verskynsel is. Die vraag is of kosmaak deel was van die grootbrein-uitbreiding ongeveer 2 miljoen jaar gelede, maar die jurie is nog steeds daaroor.

Uiteindelik het die studie ons kennis van mikrobiome verbeter en die studie daarvan 'n ernstige voorstel gemaak vir huidige en toekomstige historici. Soos Warriner bondig sê: "" Dit toon aan dat ons mikrobioom waardevolle inligting oor ons eie evolusie kodeer, wat ons soms wenke gee oor dinge wat andersins geen spore laat nie. "


Gemors: Mark Bittman se geskiedenis van hoekom ons slegte kos eet

Mark Bittman skryf die manier waarop hy kook: Die bestanddele is gesond, die voorbereiding elegant eenvoudig, die resultate voed in die beste sin van die woord. Hy span hom nooit daar op nie en probeer geen indruk maak nie, maar jy kom vol, tevrede en opgewek weg.

Uit sy magnum opus, Hoe om alles gaar te maak, en sy vele kookboekgenote, na sy resepte vir Die New York TimesIn sy essays oor voedselbeleid het Bittman 'n gierigheid ontwikkel wat die gewig van die politiek en die ekonomie rondom die vervaardiging en verbruik van voedsel omring. In Dier, groente, rommel, sy nuutste boek, bied hy ons sy deeglikste aanval op die korporatiewe magte wat ons voedsel beheer, die evolusie van verbouing en verbruik van die oorspronklike tot die moderne tyd dop en ontwikkel wat waarskynlik sy mees radikale en reguitste argument is oor hoe ons ons moet aanspreek kontemporêre voedselkulture en baie siektes. Maar dit gaan steeds maklik, die broccoli proe goed genoeg sodat jy sekondes gelukkig kan gaan.

Bittman begin Dier, groente, rommel met die vroeë hominiene. Terwyl hierdie menslike voorouers geleer het om regop te loop, het hulle oor groter gebiede begin soek en met gemak vergelyk. Bittman merk op dat hulle ook meer buigsame diëte begin ontwikkel het: & ldquoa verskeidenheid vrugte, blare, neute en diere, insluitend insekte, voëls, weekdiere, skaaldiere, skilpaaie, klein diere & helliprabbits, en vis. & Rdquo Uiteindelik, met die voedingshupstoot hiervan nuwe dieet, het hulle gou geleer hoe om vinniger prooi op te spoor (wat makliker was om in groepe te doen en sodoende meer sosiale gedrag te veroorsaak) en om oor vuur te kook.

Met meer voedingstowwe en meer gevorderde metodes om voedsel in te samel en te kook, het die vroeë hominiene en die groot brein al hoe groter geword. & Hardwired om te eet en wat ons kan, wanneer ons kan, en dat hulle dieet gehad het wat van plek tot plek verskil: & ldquo Sommige mense het 'n hoë dieet gehad in vet en proteïene, en sommige het 'n dieet gehad waarin koolhidrate oorheers het. & rdquo Maar ten spyte van hierdie verskille, het die opkomende voedselkulture en dieet een ding gemeen. Die tydperk van jag en versameling het 'n tydperk van groter lewensduur en algemene gesondheid opgelewer as in bykans enige ander tyd voor of sedertdien. & Rdquo Uiteindelik het dit ook 'n nuwe truuk opgelewer: hoe om op een plek te bly en gewasse te verbou waarvan die oorskot gestoor kan word.

Die oorgang van jag en versameling na landbou was op baie maniere welkom, maar dit het 'n prys opgelewer, skryf Bittman. Ja, dit ondersteun groter bevolkings, maar diëte word eentonig en minder voedsaam, die lewensduur neem af en die werksure neem toe. Bittman is nie die eerste wat hierdie argument voer nie. Jared Diamond noem boerdery onvergeetlik die grootste fout in die geskiedenis van die mensdom, en Bittman het dus nie die punt bedoel nie en aanvaar dat ons nou op 'n planeet leef waar voedsel iets is wat ons bymekaarmaak, nie iets wat ons jag of versamel nie.

Vir Bittman begin die sentrale drama van hierdie verhaal in die loop van die vorige eeu, namate landbou en voedselverwerking massabedrywe geword het, en ons het oorgegaan van twee soorte voedsel (plante en diere) na 'n nuwe derde tipe & mdashone Dit was soortgelyk aan gif

Hierdie gemorskos het, meen Bittman, 'n algemene gesondheidskrisis veroorsaak wat die lewens van miskien die helfte van alle mense kan verminder. die aarde as strookmynbou, verstedeliking, selfs onttrekking van fossielbrandstowwe. & rdquo


Blameer 'n antieke klimaatsverskuiwing.

Tussen 2,6 en 2,5 miljoen jaar gelede het die aarde aansienlik warmer en droër geword. Voor die klimaatsverskuiwing, het ons verre menslike voorouers gesamentlik bekend gestaan ​​as hominieneBestaan ​​meestal op vrugte, blare, sade, blomme, bas en knolle. Namate die temperatuur styg, krimp die welige woude en groot grasvelde floreer. Namate groen plante skaarser geword het, het evolusionêre druk vroeë mense gedwing om nuwe energiebronne te vind.

Die grasveld -savannes wat oor Afrika versprei het, het 'n groeiende aantal weidende herbivore ondersteun. Argeoloë het groot herbivoorbene gevind wat uit 2,5 miljoen jaar gelede dateer met merkbare snymerke van ruwe klipgereedskap. Ons ou hominin -voorouers was nog nie bekwame jagters nie, maar het waarskynlik die vleis uit gevalle karkasse verwyder.

“Meer grasse beteken meer weidende diere, en meer dooie weidingsdiere beteken meer vleis, ”, sê Marta Zaraska, skrywer van Meathooked: die geskiedenis en wetenskap van ons obsessie met vleis van 2,5 miljoen jaar.

As mense eers oorgegaan het na selfs vleisete, het dit nie lank geneem om dit 'n groot deel van ons dieet te maak nie. Zaraska sê daar is genoeg argeologiese bewyse dat die eerste 2 miljoen jaar gelede die eerste was Homo spesies het gereeld aktief vleis geëet.

Neanderthalers jag 'n sebra vir kos.

Peter Bischoff/Getty Images


Hoe eet ons verlede gevorm het en ons toekoms definieer, volgens Mark Bittman

Verskeie taco's van District Taco in Washington DC, Virginia en Philadelphia. 'Ons is nie hier as dit nie vir kos is nie. Voedsel is dus die bepalende faktor vir hoe ons grond gebruik. Dit is waar ons woon, ”sê die skrywer Mark Bittman. Foto deur Brandon Dewey Photography.

Voedsel het 'n belangrike rol gespeel in die geskiedenis en evolusie van die mens. Deur meer kalorieë van hoër gehalte te eet, het ons brein groter geword en het ons slimmer en bedagsamer geword om ons kos te vind en te kweek.

Die reis na kos en die behoefte om te eet het 'n impak gehad op alles, van slawerny en kolonialisme tot hongersnood en volksmoord. Nou bedreig die industriële landbou die volksgesondheid en vererger die klimaatsverandering.

Joanthan Bastian van KCRW praat met die bekende kosskrywer Mark Bittman oor sy nuutste boek, "Animal, Vegetable, Junk: A History of Food, from Sustainable to Suicidal." Hulle kyk na hoe voedsel ons verlede gevorm het, en of ons die impak daarvan in die toekoms kan verander.

Die volgende onderhoud uittreksels is vir die duidelikheid afgekort en geredigeer.

KCRW: In u boek gebruik u voedsel as 'n raam om deur die tyd terug te gaan en te praat oor hoe mense ontwikkel. Hoe het jy gedink dat dit vir ons 'n belangrike manier sou wees om te verstaan ​​hoe ver ons as menslike samelewing gekom het?

Mark Bittman: “Hoekom nie kos nie? Dit is die belangrikste ding wat daar is. U kan argumenteer oor voedsel teenoor suurstof. Maar natuurlik is ons nie hier as dit nie vir kos is nie. Voedsel is dus die bepalende faktor vir hoe ons grond gebruik. Dis waar ons woon. ... Arbeid het begin as landbouarbeid.

Ek dink dit het gebeur nadat ek jare lank gesê het: 'U kan die samelewing nie herstel sonder om die voedselstelsel reg te stel nie, en u kan nie die voedselstelsel regstel sonder om die samelewing reg te stel nie', en om te praat oor die verband tussen voedsel en alles anders. Dit het net tot my deurgedring dat dit altyd die geval was, dat kos begin draai het, en dat dit nooit opgehou het om een ​​van die kragtigste invloede te wees nie. ”

U begin een van die vroeë hoofstukke met 'die terugvoerlus vir voedsel-brein'. Wat is dit?

'Dit beskryf basies die proses waarmee ons uit die bome gekom het. Ons het 'n meer uiteenlopende dieet begin eet. Niemand weet dit regtig nie, maar die vermoede is dat ons brein groter geword het deur meer kalorieë van hoë gehalte te eet. En namate ons brein groter geword het, was ons in staat om slimmer en bedagsamer te wees.

Ons kon meer kos vind, ons het beter geword om kos te vind. En namate ons beter geword het om kos te vind, het ons brein steeds groter geword. En die proses het 'n paar honderdduisend jaar voortgeduur totdat ons ... die Neanderthalers oorskry het en ons die belangrikste Homo sapiens -spesie geword het. "

Kan u die idee van kalorie -inname en breingrootte uitbrei?

'Ek is nie seker of dit soveel kalorieë is as die kwaliteit van die kalorieë nie. ... Daar was 'n aantal veranderinge wat in ons liggame plaasgevind het ten opsigte van die liggame van ons meer aapagtige voorouers. Daardie diere spandeer baie tyd aan kou, en baie tyd om groen en houtagtige stowwe om te skakel in verteerbare voedsel wat dan in aminosure en proteïene gemaak kan word.

Toe ons van die bome afkom, en veral as ons begin jag het, het ons meer direk begin eet. So voedsel wat hoër proteïenbronne was. En ek dink dus dit gaan baie oor proteïenverbruik, dit is 'n groter breingrootte of meer skerp denkvermoëns. En dit het net oor die jare aangehou en aangehou.

Uiteindelik kon ons beter jag. Uiteindelik kon ons kook. En dit het beteken dat ons nog meer voedselbronne tot ons beskikking het, want baie kosse wat eetbaar blyk te wees, is baie, baie moeilik om te kou, of baie, baie moeilik om te verteer, tensy dit gaar is. Die beheer van vuur was dus 'n groot faktor in die bepaling van die rigting wat ons dieet volg. En dieet het oor die algemeen beter en beter rigtings geneem, veral tot die koms van die landbou. ”

FOTO: Mark Bittman is 'n voedseljoernalis, voormalige rubriekskrywer van die New York Times, en skrywer van 'Animal, Vegetable, Junk: A History of Food, from Sustainable to Suicidal'. Foto deur Jim Henkens

Waar kom die verhaal vandaan van hierdie vroeë agrariese samelewings en die landbou wat oor die hele wêreld versprei het?

'Ek gaan terug na die vorming van landbou en die verantwoordelikheid daarvan om beskawings te vorm. ... Toe daar landbou was, het daar 'n oorskot begin word. En toe daar oorskot was, het daar mense geword wie se werk nie boere was nie. Tot op daardie tydstip was daar regtig niemand wie se werk niks met kos te doen het nie.

Maar sodra daar 'n oorskot was, het u priesters, bouers, rekenmeesters, skrifgeleerdes, politici, bestuurders, handelaars en al die dinge wat ons nou as beroepe of werk beskou. Dit is 'n groot verandering. En die feit dat u kos begin kweek het en wette en beskawing gemaak het, wat 10 000 jaar gelede begin het en miskien teen 2000 jaar gelede gekonsolideer is. Dit was 'n groot, groot sprong.

. Die volgende ding wat veral vir Noord -Amerikaners van belang is, is die 13de tot 16de eeu. En die maklikste manier om dit te verduidelik, dink ek, is om te begin deur te sê dat dit meer grond verg om mense wat van diereprodukte afhanklik is, te voed as om mense wat meer op vegetarisme gerig is, te voed.

Die hoër bevolkings van Asië word dus grootliks verklaar deur die feit dat daar meer kulture afhanklik was van plante in Asië as in Europa. Die tegnologie was net so gevorderd. Trouens, die Chinese vaar na Afrika, wat 'n baie langer reis is, lank voordat die Europeërs na Noord -Amerika gevaar het.

Maar op 'n manier het die druk van die bevolking, handel, kapitalisme en die nuwe ekonomie van die 15de, en veral die 16de eeue in Europa die saak werklik gedwing en die Europeërs gedwing om te gaan verken en nuwe lande te soek, vir die landbou en vir ander redes ook. Maar hoofsaaklik, of ten minste baie belangrik, landerye vir landbou. En u kan u net die verwondering van die Europeërs voorstel toe hulle Noord -Amerika begin verken en die grootte en rykdom van hierdie kontinent en die relatief klein bevolking van inheemse mense hier sien. En ongelukkig 'n inheemse volk wat kon oorwin word sodat die Europeërs kon oorneem.

Maar baie daarvan het ook oor landbou gegaan. Europeërs wat hul landbousisteme hierheen bring, hul grondeienaarskap hier, hul manier van grondverdeling en hul bereidwilligheid om grond van ander mense te steel en dood te maak as hulle dit moes doen. Dit was al die verhaal van die 15de en 16de eeu, en dit het voortgegaan. Soos ons weet, gaan dit nou voort, maar dit was veral die grondslag van hierdie land. ”

Waar sien ons die verhaal wat ons volgende neem, veral in die Verenigde State?

'Ek dink die belangrikste ding, een van die belangrikste dinge van die Verenigde State, het nou in die tydperk na die burgeroorlog gebeur. . In 1862, te midde van die burgeroorlog, is die Wet op Homestead die eerste keer uitgevaardig. ... Die hele land wes van die Appalachiërs is weggegee aan wit mans en spoorwegondernemings, wat natuurlik ook deur wit mans bestuur is. Maar grond is in relatief klein stukke weggegee - 160, 320 of 640 hektaar is basies weggegee aan die manne wat die Ooste wou verlaat of Europa wou verlaat en boere wou word. . Dit was 'n vroeë bepaler van welvaart in die Verenigde State. En grondbesit hou natuurlik verband met rykdom, en die feit dat grond van inheemse mense gesteel en meestal wit mans gegee is, was 'n geweldige oordrag van rykdom, en dit beïnvloed die manier waarop ons rykdom vandag in die Verenigde State definieer.

Dit is vanselfsprekend dat daar nooit herstel was vir die miljoene Afrikane wat teen hul wil hierheen gebring is en tot slaaf gemaak is nie. Daar is 'n paar beloftes gemaak om mans, oud-slawe, te bevry om grond aan hulle te gee. En Heropbou het ook baie belofte gehad om dit 'n meer gelyke land te maak. Maar daardie beloftes is verraai.

En ons het van 1860 tot nou gegaan sonder om aandag te skenk aan die vraag wie die grond laat boer. En wat ons in die tussenliggende tyd gesien het, is die konsolidasie van die grond wat deur die federale regering weggegee is, konsolidasie van grond wat deur blanke mans besit is, tot grootliks korporasies wat deur wit mans besit word.

As u vandag wil praat oor die aanpak van ongelykheid in die Verenigde State, moet u praat oor wie die grond boer, wie die grond besit en wat hulle doelwitte is om die grond te bewerk. Nou is ons op die plek waar u kan sien waarom ek dink voedsel so 'n bepalende faktor is vir wat in die samelewing gebeur.

Ons het nie eers die punt gekry om die openbare gesondheidskwessies wat rondom voedsel draai, of die regverdigheidskwessies of die toeganklikheidskwessies, te noem nie. Ons praat nog steeds oor grond en boerdery, en ons praat reeds oor die bepalende faktore van hoe ons land nou lyk. ”

Dus, selfs in die vroeëre tydperk in die Amerikaanse geskiedenis, het die feit dat die land deur hoofsaaklik wit mans beheer is, hierdie natuurlike voedselskeiding veroorsaak. En daar was verskillende maniere waarop voedsel versprei word, of hoe dit bemark word. Kan u dit meer as 'n springplank gebruik om oor sommige van hierdie ongelykhede te praat?

'Boerdery is omskep van 'n aktiwiteit waar mense voedsel vir hulself, hul bure, hul streke verbou het, na 'n aktiwiteit waar mense voedsel verbou om te stuur en elders te verkoop. En dit het vroeg begin gebeur. Die bou van die Erie -kanaal en die eerste spoorweë, en dit alles, het dit moontlik gemaak.

U sien hoe die landbougrond gaan van die verbouing van 'n verskeidenheid gewasse na ... En goedere -gewasse is sedert die Eerste Wêreldoorlog aangemoedig, ondersteun en selfs gesubsidieer deur die federale regering, maar veral in die Eerste Wêreldoorlog.

Die uiterste voorbeeld is dus die verbouing van mielies vir etanol. Minder ekstreme, maar nog steeds opregte voorbeelde, is die verbouing van voedsel, die verbouing van mielies om diere te voed, wat dan industrieel grootgemaak word. Of nog erger, na my mening, die verbouing van voedsel om te verander in hiper verwerkte voedsel, wat kwalik as voedsel kwalifiseer en watter. is 'n groot persentasie van ons bevolking vandag besig om te vergiftig of siek te word. En natuurlik is die persentasie van die bevolking wat die meeste vatbaar is vir die verkoop van gemorskos, mense met minder geld. ”

Kan u praat oor die groot produksie en verkoop van verwerkte suiker, en hoe die druk op die vetarm dieet groot gesondheidsprobleme veroorsaak het?

'In die 20ste eeu het voedsel net grootliks in voedselprodukte verander. Baie van die produkte waaraan ons as voedsel dink, is eintlik in die 20ste eeu uitgevind. Ek praat nie net van Twinkies nie, maar van bevrore etes en ingemaakte sop en 'n magdom ander dinge, tot op die punt dat 60% van ons kalorieë volgens die skatting nou in die vorm van ultra-verwerkte voedsel is. Met ultra verwerkte voedsel bedoel ek kos wat jy nie self kon maak nie. Kos gemaak van bestanddele wat in niemand se kombuis voorkom nie. Kos wat ons oumas nie sou herken nie.

Suiker is beslis 'n groot deel daarvan. En suiker is waarskynlik die grootste skuldige in die veroorsaak van dieetverwante chroniese siektes, wat die grootste moordenaar van ons land is, en ... veel groter as COVID. Maar hoogs verwerkte koolhidrate van alle soorte is sleg vir ons. En elke jaar is daar meer en meer voedselprodukte, voedselagtige stowwe, hoe u dit ook al wil noem, nie-identifiseerbare voedselagtige voorwerpe ... siektes styg.

… COVID het in 2020 ongeveer 300,000 Amerikaners doodgemaak. Ons erken dit as 'n krisis. Ons het dit, gegewe die perke van die administrasie, so goed moontlik hanteer, maar 1,5 tot 1,7 miljoen Amerikaners sterf aan dieetverwante chroniese siektes. Dit is die National Institutes of Health -nommer. En ons noem dit nie 'n krisis nie. Om een ​​of ander rede is ons bereid om daarmee saam te leef. En as ek 'n impak op die getal kan hê, op die manier waarop ons oor die getal dink en sê, het ons 'n dieetkrisis, waarvan die grondslag eintlik in die landbou is, omdat ons net kan eet wat ons produseer. En ons mense het geen beheer oor wat geproduseer, verwerk en verkoop word nie. Ons het baie min beheer oor ons dieet. Dit is wat moet verander. En dit is groot dinge. Dit is nie soos 'Koop by u boeremark' nie, hoewel dit 'n goeie idee is. Dit is asof ons fundamentele verandering nodig het in die manier waarop ons oor voedsel dink. ”

Ondersteun KCRW - u daaglikse reddingsboei.

KCRW staan ​​vas aan ons missie om ons gemeenskap te dien op alle moontlike maniere in hierdie moeilike tyd. Ons is hier om u plaaslike nuus, inligting oor openbare gesondheid, musiek vir u gees en kulturele verbintenis aan u te verskaf. Bly op die hoogte en meld u aan vir ons nuusbriewe. En as u in hierdie stadium ons pogings kan ondersteun, oorweeg dit om 'n skenking te maak.


Bespreking

TLC as 'n absolute meting wat verband hou met respiratoriese volume kan gebruik word om die kwessie van respiratoriese en energieke eise by moderne mense 44,45 en moontlik ook in fossielhominiene 9,35 aan te spreek.

Alhoewel TLC -waardes verkry word deur 'n eenvoudige tegniek by hospitaalvakke (soos in Bellemare se 44 studie), is dit meer uitdagend as ons die fossielrekord hanteer. Dit is omdat ons TLC slegs kan aflei uit veranderlikes gemeet in individuele elemente van die ribbekas, soos die ribbes en werwels. In hierdie verband is ons resultate baanbrekerswerk om aan te toon dat individuele ribgrootte (beoordeel in TVA_sml, TVC en CS) met TLC gekorreleer kan word. Ons spesifiseer ook dat, hoewel ons 3D -meting (CS) meer gekorreleer is met TLC as die tradisionele meting TVC vir ribbes 3-10, die tuberkel -ventrale boog (TVA_sml) nog meer insiggewend is oor TLC. Dit word moontlik veroorsaak deur die feit dat TVA inligting oor mediolaterale breedte en longomtrek opneem, terwyl TVC slegs die anteroposterior grootte opneem, wat ook CS moet beïnvloed. Daarbenewens spesifiseer ons dat die grootte van die sentraal -onderste ribbes meer gekorreleer is met TLC as die grootte van die boonste ribbes (fig. 1). Dit is in ooreenstemming met onlangse navorsing wat toon dat laer toraksgrootte meer gekorreleer is met funksionele grootte, verstaan ​​as die grootteverhoging van maksimum verstryking tot maksimum inspirasie 42.

Ons resultate vir Neanderthalers toon aan dat TLC absolute waardes bevat wat groter is as in hul ooreenstemmende menslike eweknieë (tabel 3). Kebara 2, 'n manlike Neanderthaler uit Israel, toon 'n gemiddelde waarde van 9,04 l TLC, wat statisties groter is as ons manlike menslike steekproef (gemiddelde = 7,20 l) en die van Bellemare et al. 44 (gemiddelde = 6,27 l). Ons ramings vir Tabun 1, 'n vroulike Neanderthaler uit Israel, het 'n gemiddelde waarde van 5,85 l opgelewer, wat statisties groter is as ons vroulike steekproef (gemiddelde = 4,85 l) en die gemiddelde van Bellemare et al. 44 (gemiddelde = 4,81 l). Daar moet op gelet word dat die manlike Kebara 2 TLC 54% groter was as die waarde vir die vroulike Tabun 1. Die feit dat hierdie persentasie in Neanderthalers effens groter is as in ons moderne menslike monster (ongeveer 48%, sien hierbo), kan die gevolg van verskille in liggaamsamestelling, omdat Kebara 'n groter maer massa het in vergelyking met Tabun 1 as ons manlike moderne mense in vergelyking met ons moderne wyfies (tabel 3). Die El Sidrón SD-1450-rib bied ook insig in die Neanderthaler-TLC, en aangesien dit statisties groter is as ons manlike monster, is dit waarskynlik dat dit aan 'n manlike persoon behoort het.

Dit is belangrik om daarop te let dat as ons probeer het om TLC -waardes van hierdie fossielmonsters te skat met behulp van ander veranderlikes (soos statuur) uit standaard menslike vergelykings, sou Tabun 1 TLC geraam word op 4.67 l, 4.50 l en 4.91 l met behulp van die formules van Crappo et al. 46, Roca et al. 47 en Quanjer et al. 48, onderskeidelik. As ons standaard menslike vergelykings gebruik het om die Kebara 2 TLC -waarde te skat, sou ons waardes van 6,18 l, 6,20 l en 6,36 l verkry het deur die formules van Quanjer et al. 48, Cordero et al. 49 en Neder et al. 50, onderskeidelik. Daarom bied beide Kebara 2 en Tabun 1 veel groter waardes van TLC met behulp van ons vergelykings as wanneer menslike standaardvergelykings gebruik word. Omdat verskillende vergelykings na gelang van die geslag gebruik word, het ons hierdie waarde nie bereken vir die El Sidrón Neanderthal- en ATD6 -hominiene nie, aangesien hulle nie bekend was nie.

Onlangse bewyse dui daarop dat die groot TLC wat in Neanderthalers waargeneem is in vergelyking met moderne mense, die gevolg was van groot ribbes in die sentrale -onderste toraks, tesame met 'n meer dorsale oriëntasie van die transversale prosesse in Neanderthalers in vergelyking met moderne mense, wat mediolaterale uitbreiding van die ribbes veroorsaak het 18 , 20. Hierdie morfologie van die ribbekas (Fig. 3), gekombineer met ons resultate van TLC vir Neanderthalers, stem ooreen met 'n groot suurstofinname om hul verwagte hoë DEE voorgestel deur vorige skrywers 9,35,51 voor te hou. Die groot DEE moet veroorsaak word vir hul groot brein (Fig. 3, Tabel 3) en hul groot maer liggaamsmassa (Tabel 3), maar alternatiewe verduidelikings, soos die moontlikheid dat Neanderthalers groot ingewande (lewer en urienstelsels) gehad het wat nodig is vir die verwerking van groot hoeveelhede vleis, kan ook gekoppel word aan hoë DEE 52.

a Thorax en longe se vorm in die vooraansig by moderne mense en Neanderthalers en hul verwante brein in die syaansig. Neanderthaler toraks en skedel behoort onderskeidelik aan Kebara 2 5 en Guattari Neanderthalers. Moderne menslike borskas en skedel behoort onderskeidelik aan gemiddeld vier moderne mense 82 en OI-2053. b Superimposisie in die vooraansig van die Neanderthaler en moderne menslike ribbes. c Superimposisie in die stertbeeld van die Neanderthaler en moderne menslike ribbes

Alhoewel daar ooreenstemming is oor die groot grootte van die Neanderthaler ribbekas 14,15,16,17,18,19,20, is dit nie so duidelik of hul ribbes groter was vir hul liggaamsmassa of hul statuur 35 nie. Skattings van die Shanidar 3 Neanderthaler respiratoriese gebied van rib 8 dui byvoorbeeld aan dat dit eweredig was aan sy liggaamsmassa, maar dat die respiratoriese gebied van die Kebara 2 rib 8 relatief groter was vir sy liggaamsmassa 35. In hierdie verband kan ons resultate daarop dui dat beide Kebara 2 en Tabun 1 'n groter TLC/M -verhouding bied as ons moderne menslike verwysingsmonsters, wat Churchill se 35 werk ondersteun. Die vraag of Neanderthalers groter TLC vir hul gestalte het in vergelyking met moderne mense, ons resultate ondersteun hierdie bewering aangesien TLC/S -waardes van Kebara 2 en Tabun 1 individue (gemiddeld) groter was as hul ooreenstemmende moderne menslike monsters. Die feit dat beide Neanderthalers groter TLC/M- en TLC/S -waardes aangebied het in vergelyking met ons moderne menslike monster, moet verband hou met hul groot DEE.

However, some caution must be taken in the interpretation of these results since TLC/M and TLC/S ratio are based on estimates of stature and lean body mass in Neanderthals 9,35,51,53 and this could introduce some error in the ratios. Even when including this potential error, it is clear that Neanderthals’ thoraces were larger for their stature (Fig. 2), which would be consistent with previous research on ribcage/body size ratios based on rib size/humerus length 15 . It is also important to recall that lean body mass estimates were calculated applying fat-free mass percentages to the total Neanderthal body mass, which were taken from modern Inuit individuals 51,54,55 . Therefore, it is possible that the percentages for Neanderthals were different than those of Inuits. In addition to differences in fat-free mass percentages, there may also be differences in other tissues, such as brown adipose tissue. Although the role of this tissue in environmental adaptation is speculative, it is the only human tissue dedicated exclusively to heat production 56 . Body composition in Neanderthals is not the focus of our work and should be addressed in future research.

Regarding the evolutionary origin of the large Neanderthal TLC, H. heidelbergensis (likely potential ancestors of Neanderthals) are also thought to have large thoraces, both in absolute terms and perhaps relative to their stature as well 6,57 . However, the lack of literature on fossil remains of the costal skeleton makes it difficult to address this issue. Lower Pleistocene hominins from the Gran Dolina site (Burgos, Spain) are hypothetical ancestors of H. heidelbergensis (and thus Neanderthals) and are also thought to have large thoraces because of their long clavicles 6,30 . Whether H. antecessor is actually a species itself or represents an European branch of H. erectus/ergaster 34 , recent Bayesian analyses 58,59 suggest that H. antecessor belongs to a basal clade of modern human and Neanderthals, alongside other early Homo species such as H. erectus, ergaster and the recently discovered species named as H. naledi 60 . Therefore, H. antecessor could be used as an approach to test whether large bodied early Homo species already presented a large TLC.

Our results of estimated TLC based on ribs 7 and 10 yielded values of 5.28 l and 8.70 l for ATD6 hominins, respectively, which were larger than our comparative sample of female and male modern humans, respectively. In this case, we are not certain that these ribs belonged to the same individual, so we hypothesize here that ATD6–39 (the larger value) could represent a male rib, whereas ATD6–89+206 (the smaller value) could represent a female rib. If this is confirmed, we would see in ATD6 hominins the same evolutionary trend that we see in Neanderthals, males and females being larger (on average) than our modern human comparative sample. However, some caution should be taken because of the uncertainty in the composition of the ATD6 sample 31 . The TLC/M ratio for these hominins could not be calculated since body mass values are not available in the current literature due to the fact that this fossil site did not yield any remains of lower limbs that were well enough preserved to provide evidence of body mass 30 . Regarding stature, ATD6 hominins presented an average stature of 172.5 cm, which was larger than the average for Neanderthals 6,30,57 . The TLC/S ratio for ATD6 hominins using rib 7 was larger than the female average and larger than the male average using rib 10. This would support the possibility that ribs ATD6–89+206 and ATD6–39 are female and male ribs, respectively. It would also support what we found in Neanderthals, that is, that the large TLC relative to stature was beginning to be evident in the Lower Pleistocene of Europe, even when considering that ATD6 hominins presented larger statures than Neanderthals 6,30 .

Therefore, according to the evidence of TLC, if we accept that H. antecessor was in the basal clade of both Neanderthals and modern humans, we suggest here that a large ribcage relative to stature is present in the whole European hominin lineage (represented here by ATD6 hominins and Neanderthals). However, whether it is also present in other European hypothetically intermediate species such as H. heidelbergensis must be addressed in future research. The large ribcage of the European hominin lineage could be linked to the wide trunks proposed by previous authors for those species 6 , which would show an evolutionary trend towards Neanderthals, based on relative stature reduction and relative thorax size increase.

Regarding the adaptive significance of this evolutionary trend, it should be noted that in the Lower and Middle Pleistocene there is a trend towards large body sizes across most of the mammal clade, with herbivores showing a larger size increase than carnivores 61,62,63,64,65 . In carnivores, this size increase could be important for facilitating hunting tasks, whereas in herbivores it could be important for avoiding being preyed upon by carnivores. This general ecological rule could also apply to hominins and perhaps underlie the large body mass of Lower and Middle Pleistocene hominins, partially explaining their wide trunks 9 . Besides this general explanation, other more specific ones have been proposed: the stout (“short but massive”) Neanderthal body could be explained by the eco-geographical rules of Allen and Bergmann 66,67 , which could cause the shortening of distal limbs and the widening of the trunk observed in Neanderthals 1,2,3,4,5,6,7,8,9 . However, recent studies on bioenergetics show that Neanderthals inhabiting the same climatic conditions as modern humans present larger DEE than modern humans. This could be the result of the cost of maintaining heavy and highly muscled bodies with large brains (Fig. 3, Table 3) along with the need to exert muscular force in the accomplishment of subsistence tasks 9,35,36,51 . This larger muscle mass would have provided them with a greater thermogenic capacity and also greater insulation against cold compared to modern humans, which could be understood as an exaptation 9,35 . Future studies should include more Neanderthal ribs and also other hominin species not included here, such as H. heidelbergensis of H. erectus, in order to expand the evolutionary framework.

Finally, even though physiological function must have been of evolutionary significance, caution should be used in assuming that an enlarged thorax was result of natural selection and was passed down as an adaptation to later European Pleistocene hominins. In particular, enhanced pulmonary function as modelled in modern human populations living at high altitudes shows that developmental processes have an important role in shaping the physiology of respiration and oxygen consumption 68,69,70,71,72 . Developmental factors also play an important role in determining thorax morphology. Here again, humans living at high altitudes from many different regions provide important data demonstrating this point, but the small sample sizes of hominin fossil assemblages make developmental factors difficult to test. The possibility that developmental processes contributed to the emergence of a large thorax and pulmonary capacity in early Pleistocene hominins of Europe and in later Neanderthals does not alter the results of this study.

Our work is, to our knowledge, the first successful attempt to estimate TLC in fossil hominins. We have found that Neanderthals presented around 20% larger lung capacities than modern humans, both absolutely and relative to their lean mass and stature. This could be caused by the large lean body mass of Neanderthals, coupled with their large brains and gut size (liver and urinary systems), contributing to their high DEE. Assuming that H. antecessor is in the basal clade of Neanderthals (which is still a heated debate), the trend towards large lung capacities could even be observed in the lower Pleistocene of ATD6. Finally, although we used a large sample of current Europeans to create a statistical model (controlled for stature and body mass) to calculate TLC in fossil hominins, future research should include broader samples from different modern humans populations. Those that present different limb proportions compared to Europeans and that could parallel Neanderthal body proportions (populations adapted to high altitudes and extreme low temperatures) are mostly necessary. In addition, future studies should make an effort to include early H. sapiens such as Cro-Magnon, Skhul or Abri Pataud.


Evolution Of Technology

By far the most interesting advancement in computers to me was the development of the “supercomper” called ATLAS. The University of Manchester developed ATLAS in the United Kingdom and it was officially authorized in 1962. This computer was unlike anything seen before it was ten times faster then any other computer built. There were many different changes in to the make the supercomputer so much faster and smarter. They changed their transistors from germanium to silicon.&hellip


CSIC reconstructs how Neanderthals grew, based on an El Sidrón child

How did Neanderthals grow? Does modern man develop in the same way as Homo neanderthalensis did? How does the size of the brain affect the development of the body? A study led by the Spanish National Research Council (CSIC) researcher, Antonio Rosas, has studied the fossil remains of a Neanderthal child's skeleton in order to establish whether there are differences between the growth of Neanderthals and that of sapiens.

According to the results of the article, which are published in Science, both species regulate their growth differently to adapt their energy consumption to their physical characteristics.

"Discerning the differences and similarities in growth patterns between Neanderthals and modern humans helps us better define our own history. Modern humans and Neanderthals emerged from a common recent ancestor, and this is manifested in a similar overall growth rate", explains CSIC researcher, Antonio Rosas, from Spain's National Natural Science Museum (MNCN). As fellow CSIC researcher Luis Ríos highlights, "Applying paediatric growth assessment methods, this Neanderthal child is no different to a modern-day child". The pattern of vertebral maturation and brain growth, as well as energy constraints during development, may have marked the anatomical shape of Neanderthals.

Neanderthals had a greater cranial capacity than today's humans. Neanderthal adults had an intracranial volume of 1,520 cubic centimetres, while that of modern adult man is 1,195 cubic centimetres. That of the Neanderthal child in the study had reached 1,330 cubic centimetres at the time of his death, in other words, 87.5% of the total reached at eight years of age. At that age, the development of a modern-day child's cranial capacity has already been fully completed.

"Developing a large brain involves significant energy expenditure and, consequently, this hinders the growth of other parts of the body. In sapiens, the development of the brain during childhood has a high energetic cost and, as a result, the development of the rest of the body slows down," Rosas explains.

Neanderthals and sapiens

The cost, in terms of energy, of anatomical growth of the modern brain is unusually high, especially during breastfeeding and during infancy, and this seems to require a slowing down of body growth. The growth and development of this juvenile Neanderthal matches the typical characteristics of human ontogeny, where there is a slow anatomical growth between weaning and puberty. This could compensate for the immense energy cost of developing such a large brain.

In fact, the skeleton and dentition of this Neanderthal present a physiology which is similar to that of a sapiens of the same age, except for the thorax area, which corresponds to a child between five and six years, in that it is less developed. "The growth of our Neanderthal child was not complete, probably due to energy saving", explains CSIC researcher Antonio Rosas.

The only divergent aspect in the growth of both species is the moment of maturation of the vertebral column. In all hominids, the cartilaginous joints of the middle thoracic vertebrae and the atlas are the last to fuse, but in this Neanderthal, fusion occurred about two years later than in modern humans.

"The delay of this fusion in the vertebral column may indicate that Neanderthals had a decoupling of certain aspects in the transition from infancy to the juvenile phase. Although the implications are unknown, this feature could be related to the characteristic enlarged shape of the Neanderthal torso, or slower brain growth", says Rosas.

The Neanderthal child

The protagonist of this study was 7.7 years old, weighed 26 kilos and measured 111 centimetres at the time of death. Although the genetic analyses failed to confirm the child's sex, the canine teeth and the sturdiness of the bones showed that it to be a male. 138 pieces, 30 of them teeth (including some milk teeth), and part of the skeleton- including some fragments of the skull from the individual- identified as El Sidrón J1, have recovered.

The researchers have been able to establish that our protagonist was right-handed and was already performing adult tasks, such as using his teeth as a third hand to handle skins and plant fibres. In addition, they know who his mother was, and that the child protagonist of this investigation had a younger brother in the group. Furthermore, this child was found to have suffered from enamel hypoplasia when he was two or three years old. Hypoplasia (white spots on the teeth, especially visible in the upper incisors), occurs when the teeth have less enamel than normal, the cause usually being malnutrition or disease.

Discovered in 1994, the El Sidrón cave, located in Piloña (in Asturias, northern Spain) has provided the best collection of Neanderthals that exists on the Iberian Peninsula. The team has recovered the remains of 13 individuals from the cave. The group consisted of seven adults (four women and three men), three teenagers and three younger children.

Previous studies have been carried out by a multidisciplinary team led by the paleoanthropologist Antonio Rosas (CSIC's National Museum of Natural Sciences), the geneticist Carles Lalueza-Fox (Institute of Evolutionary Biology, run by CSIC and the Pompeu Fabra University) and by the archaeologist Marco de la Rasilla (University of Oviedo).

Vrywaring: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.


Going with the gut

A teeming community of microbes thrives in the colon, all ultimately feeding on our leftovers. These tens of trillions of individual organisms (similar in number to all the human cells in the human body) belong to many different species. Our microbial communities vary enormously from person to person, but there’s a lot of what Carmody calls “redundancy in function”: different microbes can play the same roles. “At a functional level, we’re more similar than we would appear to be when we just look at the different bugs that are present,” she says.

There are about 150 times as many independent genes in our microbiome as we have in our own bodies, which gives our microbes a vast metabolic range—much bigger than ours. They can perform a whole bunch of functions that we can’t, says Carmody, such as breaking down materials we can’t digest, including cellulose. That functional range “has driven really profound, but very visible changes in biodiversity across animals that are linked to diet,” says Carmody. For example, unlike humans and most other primates, who carry our microbiomes at the rear end of our intestinal tracts, ruminants like cows and sheep that eat cellulose-rich grasses and shrubs but do not manufacture cellulose-digesting enzymes have evolved to keep theirs at the beginning, in four-chambered stomachs. This arrangement allows microbes to first break down the cellulose, which then makes the nutritional contents of the plant cell more available to the animal.

Although we lack cows’ stomachs, we too benefit from gut microbes that digest cellulose and other nutrients that resist digestion in the small intestine. They break these down into short-chain fatty acids, which we can absorb in our colons and use for energy. However, short-chain fatty acids provide fewer calories than the carbohydrates and proteins from which they are derived, because some of the energy goes to fuel the microbes themselves. “Microbes help us salvage energy from food that would otherwise go undigested. So under dietary conditions where fewer nutrients are absorbed in the small intestine and more make it into the colon, you’ve got greater energy return in the colon, but not greater energy return overall, because you’ve lost the ability to have first dibs on that food,” says Carmody.

When we change what we feed our microbes by changing what we eat, that will change the entire microbial ecosystem. “From the microbial communities’ perspective, on the raw diet the microbial community in the colon is seeing a large influx of starch. On the cooked diet, it’s not really seeing much starch come in at all,” says Carmody. “And so on the raw diet, competition will favor microbes that are very good at processing and metabolizing that starch, causing them to proliferate in number at the expense of those who can’t really take advantage of that starch.”


Neanderthals and sapiens

The cost, in terms of energy, of anatomical growth of the modern brain is unusually high, especially during breastfeeding and during infancy, and this seems to require a slowing down of body growth. The growth and development of this juvenile Neanderthal matches the typical characteristics of human ontogeny, where there is a slow anatomical growth between weaning and puberty. This could compensate for the immense energy cost of developing such a large brain.

In fact, the skeleton and dentition of this Neanderthal present a physiology which is similar to that of a sapiens of the same age, except for the thorax area, which corresponds to a child between five and six years, in that it is less developed. “The growth of our Neanderthal child was not complete, probably due to energy saving”, explains CSIC researcher Antonio Rosas.

The only divergent aspect in the growth of both species is the moment of maturation of the vertebral column. In all hominids, the cartilaginous joints of the middle thoracic vertebrae and the atlas are the last to fuse, but in this Neanderthal, fusion occurred about two years later than in modern humans.

“The delay of this fusion in the vertebral column may indicate that Neanderthals had a decoupling of certain aspects in the transition from infancy to the juvenile phase. Although the implications are unknown, this feature could be related to the characteristic enlarged shape of the Neanderthal torso, or slower brain growth”, says Rosas.


Materials and Methods

Materials.

Our sampling strategy aimed to collect dental calculus from a minimum of two independent populations, each consisting of at least five individuals, for each host genus and modern human lifestyle group (excepting Alouatta) (SI Appendix, Table S1 and Dataset S1). Dental calculus was sampled from twentieth-century skeletal remains of wild Alouatta (A. palliata), Gorilla (G. berengei beringei G. berengei graueri G. gorilla gorilla), en Pan (P. troglodytes schweinfurthii P. troglodytes ellioti P. troglodytes verus) and from archaeological Neanderthals and modern humans using established protocols (DOIs: 10.17504/protocols.io.7vrhn56 and 10.17504/protocols.io.7hphj5n). Although many present-day human dental plaque datasets are publicly available, they have been shown to not be directly comparable to dental calculus (23), and consequently we generated dental calculus data for present-day humans. The study of deidentified present-day dental calculus was approved by the Institutional Review Board for Human Research Participant Protection at the University of Oklahoma (IRB no. 4543). All samples were collected under informed consent during routine dental cleaning procedures by practicing dental odontologists. For additional sample context descriptions and additional ethical approval information, reference SI Appendix, section S2.1.

Laboratory Methods.

For all museum and field station samples, we performed DNA extraction in dedicated cleanroom facilities using a protocol optimized for the recovery of degraded and fragmentary DNA (86). Present-day calculus was extracted as previously described (23). For all samples, DNA was built into dual-indexed Illumina libraries (87) and shotgun sequenced. In addition, a subset of samples were separately subjected to UDG treatment (88), followed by deep sequencing. Negative controls were included in all extraction and library construction batches. Sequencing was performed on either Illumina NextSeq. 500 or HiSeq. 4000 platforms. For details, reference SI Appendix, section S2.2–S2.4 and protocols.io under DOI: 10.17504/protocols.io.bq7wmzpe.

Data Processing and Quality Filtering.

For detailed descriptions of preprocessing and analysis procedures, including code, reference SI Appendix and external data repository (GitHub repository: https://github.com/jfy133/Hominid_Calculus_Microbiome_Evolution Archive DOI: 10.5281/zenodo.3740493). Additional ancient (13) and present-day dental calculus (23) data from previous studies were downloaded from the Online Ancient Genome Repository (OAGR) (https://www.oagr.org.au/) and the European Bioinformatics Institute (EBI) European Nucleotide Archive (ENA) (https://www.ebi.ac.uk/ena/) databases, respectively. Comparative metagenomes from present-day modern human microbiome and environmental sources were additionally downloaded from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra/). Accession numbers and download instructions for all FASTQ files are provided in SI Appendix, section S3.1. The EAGER pipeline (89) was used to perform initial preprocessing of sequencing data to remove possible modern human DNA sequences that can interfere with taxonomic profiling (due to present-day modern human DNA contamination in microbial reference genomes). We used relaxed bwa aln (90) mapping parameters for aDNA (−n 0.01), and nonhuman reads from replicate samples and libraries were then concatenated per individual. Human-mapped sequences were then poly-G clipped prior to reporting of mapping statistics. Processing statistics are provided in SI Appendix, section S3.2.

Taxonomic Binning and Preservation Assessment.

For taxonomic binning, we used the aDNA-optimized high-throughput aligner MALT (27, 91) together with the NCBI nt database (October 2017 uploaded to Zenodo under DOI: 10.5281/zenodo.4382154) and a custom NCBI RefSeq database (containing bacteria, archaea, and Homo sapiens, October 2018, SI Appendix, section S3.3) and employed a relaxed percent identity parameter of 85% and a base tail cut off (“minimum support”) of 0.01%. Resulting RMA6 files were loaded into MEGAN6 CE (64) and prokaryotic Operational Taxonomic Unit (OTU) tables were exported (Dataset S2). A comparison of the two databases is provided in SI Appendix, section S3.3. Given the challenges of low preservation and contamination in ancient microbiome studies, we performed a multistep procedure to screen for and remove poorly preserved samples and contaminant OTUs from the non-UDG-treated dataset (SI Appendix, Fig. S2). We developed a visualization for the identification of calculus samples with weak oral microbiome signatures (SI Appendix, Fig. S3). This procedure involves comparing identified taxa to their previously reported isolation source(s), ranking these taxa from most to least abundant, and tracking the cumulative percentage of oral taxa along this rank (termed here as “decay”). Samples with a low percentage of oral taxa after an initial “burn-in” based on stabilization of curve fluctuation were removed from downstream analysis. Reference SI Appendix, section S3.4 for details. We compared this method to results obtained using SourceTracker (28)—which was performed on 16S-mapped reads filtered from shotgun data using EAGER (with comparative present-day modern human and environmental metagenomes as sources), followed by closed-reference clustering using QIIME (92)—and found concordance between the two methods (SI Appendix, Fig. S3). We next used the R package decontam (29) to statistically detect putative laboratory and environmental contaminants (as present in negative controls and a set of archaeological bone samples—SI Appendix, section S3.6), which were then removed prior to downstream analysis. To authenticate the remaining OTUs, we utilized the output of MaltExtract (93) in the MaltExtract-Interactive Plotting App (MEx-IPA) tool (DOI: 10.5281/zenodo.3380011), which we developed for rapid visualization of characteristic aDNA patterns, such as cytosine to thymine deamination, short fragment lengths, and edit distance from reference (SI Appendix, Fig. S4 and section S3.5). After mapping with EAGER to well-known oral taxa, we also validated DNA damage patterns using DamageProfiler (Fig. 1C) (94).

Microbial Compositional Analysis.

To remove low-abundance environmental contaminants or spurious hits, we selected a minimum abundance cutoff of 0.07% of alignments for genus-level and 0.04% of alignments for species-level identifications (SI Appendix, Figs. S7 and S8 and section 5.2). We normalized profiles through phylogenetic isometric-log-ratio transformation (95) of the abundance-filtered OTU tables and then performed PCoA on the resulting euclidean distances (SI Appendix Fig. S5 C en D en SI Appendix, section S4.1). To statistically verify host genus clusters, we used the adonis function from the R package vegan to perform PERMANOVA (35) analysis after controlling from unequal sample sizes (SI Appendix, section S4.2). After removal of poorly preserved samples, oral communities show distinct centroids for each host genus (bootstrapped PERMANOVA, ɑ = 0.05, P = 0.001, pseudo-F = 5.23, R 2 = 0.28) Alouatta was excluded due to small sample size. We performed bootstrapped hierarchical clustering (96) on the euclidean distances of centered log ratio–transformed OTU tables and visualized the results in the form of a heatmap (Fig. 3 and SI Appendix section S4.3). Sample and taxon clustering was performed with the McQuitty hierarchical clustering algorithm, and taxon blocks within the heatmap were selected by visual inspection. Bootstrap values of sample clusters were estimated through the R package pvclust (96). Species oxygen-tolerance metadata was obtained from the BacDive database (97) via the BacDiveR R package (DOI: 10.5281/zenodo.1308060). For validation of the observations made on the heatmaps, we also performed grouped indicator analysis (98) (SI Appendix, section S4.4). Clustering of human oral microbiomes by variables such as time, geography, and dietary subsistence was assessed using PCoA, PERMANOVA, and hierarchical clustering (SI Appendix, section S4).

Core Microbiome Analysis.

Using the contaminant-filtered OTU tables of well-preserved samples, we converted all taxa above the minimum support threshold to a presence/absence profile. Taxa were required to be present in at least half (50%) of the members of a population for it to be considered core to the population and to be present in at least two-thirds (66%) of populations to be considered core to a host group (SI Appendix, Fig. S9 reference SI Appendix, section S5.2 for parameter experimentation details). We then generated UpSet plots (99) to visualize the microbial intersections of each host group at both the species and genus levels (Fig. 2 A en B), and we also compared the results between both databases. Further discussion on the exclusion of the common soil genus Mycobacterium from core genera is provided in SI Appendix, section S5.2. Validation of results through smaller sample sizes was carried out by bootstrapping analysis, which was performed by randomly subsampling (with replacement) individuals from each host genus and rerunning the core calculation procedure to 1,000 replicates (SI Appendix, section S5.3). We created a diagram of the core human oral microbiome (Fig. 2C) based on published fluorescence in situ hybridization (FISH) images of human dental plaque (8, 100). For species/genera that were not analyzed in these publications, literature searches were performed to find evidence of their localization within plaque based on immunohistochemistry, immunofluorescence, or FISH (SI Appendix, sections S5.1 and S5.4). All members of the human core microbiome are shown, including those also shared with other African hominids and howler monkeys. For further details, reference SI Appendix, section S5.3.

Genomic Analysis.

We used EAGER to map (see below for more details) the deep-sequenced UDG-treated dataset and four samples from present-day individuals (Alouatta, 3 Gorilla, 3 Pan, 4 Neanderthal, 3 ancient modern human, 6 present-day modern human, 4 total: 23) against the reference genomes of Tannerella forsythia en Porphyromonas gingivalis (SI Appendix, section S5.5). We used bedtools (101) to calculate the breadth and depth coverage of a set of known virulence factors for these two taxa. To reduce the risk of spurious alignments (e.g., from cross mapping of conserved sequences), we filtered out genes that had a breadth of coverage less than 70% and/or that appeared to have strongly different coverage depths compared to the rest of the genome (reference SI Appendix, section S5.5 for more details). The resulting genes were visualized as a heatmap for comparison (SI Appendix, Fig. S9). We selected all species-level Streptococcus alignments from the shallow sequenced dataset minimum support filtered NCBI nt–MALT OTU tables and assigned them to one of eight species groups based on the literature (67) (reference SI Appendix, section S5.6 for group definitions). We then calculated the fraction of alignments for each species group over all taxonomic alignments for each sample (Fig. 5B). To further validate the results, we calculated a similar ratio but based on the mapping of the deep-sequenced dataset against a superreference of 166 Streptococcus genomes (see below). We identified abpA- and abpB-like gene coordinates from the superreference using panX (102), then extracted the number of reads mapping to these annotations and calculated the fraction of these reads over all Streptococcus superreference mapped reads. We then applied a Mann–Whitney U test to test the null hypothesis of no difference between the distributions of ratios of Homo and nonhuman primates, as well as compared these results to a distribution of P values of 100 randomly shuffled group assignments (reference SI Appendix, section S5.7 for more details). Reference sequences of abpA en abpB were extracted from Streptococcus genomes in RefSeq and indexed for mapping. All shallow sequencing dataset samples were mapped against all reference strains. For samples with a gene coverage of at least 40% at 1×, a consensus sequence was exported from the Integrative Genome Viewer (IGV) (103). An input file of the consensus sequences and references was generated in BEAUTi and used to run BEAST2 (104) for Bayesian skyline plot analysis. For details, reference SI Appendix, section S5.9.

Microbial Phylogenetics.

We first attempted a competitive-mapping strategy against genus-wide superreferences of identified core taxa (reference SI Appendix, sections S6.1 and S6.2), but this approach yielded only limited results (SI Appendix Fig. S10 and section S6.3). We then instead performed phylogenetic reconstruction by mapping the same dataset to a single representative genome for each genus, considered as representing a population of related taxa. To account for challenges with low-coverage ancient data, we called SNPs using MultiVCFAnalyzer and required each SNP call to have a minimum of 2× coverage and a support of ≥70% of reads (SI Appendix, section S6.5). The resulting FASTA alignments were loaded into R. Samples with fewer than 1,000 SNPs were removed, and pairwise distances were calculated based on the JC69 model (105). A bootstrapped neighbor-joining algorithm from the R package ape (106) was applied to the distance matrices with 100 replicates (SI Appendix, section S6.6). Trees were visualized with ggtree (107). Finally, we retained trees where the basal internal nodes had bootstrap supports of ≥70% (SI Appendix, Fig. S11). The same procedure was then applied to the shallow sequencing dataset with the additional samples described above in the main text (SI Appendix, Fig. S12). To test whether pre-14 ka individuals clustered with Neanderthals due to reference bias, we calculated the median number of positions that were shared between EMN001 and Neanderthals to a histogram of median pairwise comparisons between all modern human individuals (SI Appendix, section S6.6).

Functional and Metabolic Pathway Analysis.

We took two approaches to characterizing the functional profiles of the calculus metagenomes. First, we used HUMANn2 (63) [with MetaPhlAn2 (108) generated taxonomic profiles] to generate functional profiles based on the UniRef90 (109) and ChocoPhlAn (July 2018) (63) databases. Preservation was independently assessed for pathway abundance and Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog functional profiles, SI Appendix, section S7.1. We compared the functional profiles of well-preserved calculus between host groups using pathway abundance (n = 94) and gene families converted to KEGG orthologs (n = 109) using PCA (SI Appendix, Fig. S13). Orthologs with the strongest loadings were visualized with biplots (SI Appendix, Fig. S13 AC), and the species from which these orthologs were derived were determined (SI Appendix, Fig. S13 BD). The clustering of host genera in PCAs using only orthologs in specific pathways (carbohydrates, amino acids, lipids) was also explored (SI Appendix, Fig. S10 AC). For details, reference SI Appendix, section S7.1.4. Second, we used AADDER (included within MEGAN6 CE) (64) to profile the number of alignments to annotations present in the custom RefSeq database as aligned by MALT (see above). We then used MEGAN6 to export SEED category (110) profiles. Preservation was independently assessed for SEED protein functional profiles, reference SI Appendix, section S7.2. We compared the functional profiles of well-preserved calculus (n = 95) between host groups using proteins but not higher-level pathways (SI Appendix, Fig. S13). The proteins with the strongest loadings were visualized using biplots (SI Appendix, Fig. S13 EG), and the species from which these proteins were derived were determined (SI Appendix, Fig. S13 FH). The clustering of host genera in PCAs using only proteins in specific pathways (carbohydrates, amino acids, lipids) was also explored (SI Appendix, Fig. S14 DF). For details, reference SI Appendix, section S7.2.3.


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