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15.3: Klades van Amfibieë - Biologie

15.3: Klades van Amfibieë - Biologie


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Amfibieë bestaan ​​uit 'n geskatte 6 770 bestaande spesies wat tropiese en gematigde streke regoor die wêreld bewoon. Amfibieë kan in drie klades verdeel word: Urodela (“sterts”), die salamanders; Anura ("stertloses"), die paddas; en Apoda (“beenloses”), die caecilians.

Urodela: Salamanders

Salamanders is amfibieë wat tot die orde Urodela behoort. Lewende salamanders (Figuur 1) sluit ongeveer 620 spesies in, waarvan sommige akwaties is, ander terrestriële, en sommige wat net as volwassenes op land leef. Volwasse salamanders het gewoonlik 'n algemene vierpotige liggaamsplan met vier ledemate en 'n stert. Hulle beweeg deur hul liggame van kant tot kant te buig, wat laterale golwing genoem word, op 'n visagtige manier terwyl hulle hul arms en bene voor en agter "loop". Daar word gedink dat hul gang soortgelyk is aan dié wat deur vroeë viervoetiges gebruik word. Asemhaling verskil tussen verskillende spesies. Die meerderheid salamanders is longloos, en asemhaling vind deur die vel of deur uitwendige kieue plaas. Sommige aardse salamanders het primitiewe longe; 'n paar spesies het beide kieue en longe.

Anders as paddas maak feitlik alle salamanders staat op interne bevrugting van die eiers. Die enigste manlike amfibieë wat kopulerende strukture besit, is die caecilians, so bevrugting onder salamanders behels tipies 'n uitgebreide en dikwels langdurige hofmakery. So 'n hofmakery laat die suksesvolle oordrag van sperm van manlik na vroulik via 'n spermatofoor toe. Ontwikkeling in baie van die mees ontwikkelde salamanders, wat ten volle terrestrisch is, vind plaas tydens 'n lang eierstadium, met die eiers wat deur die moeder bewaak word. Gedurende hierdie tyd word die kieuwlarfstadium slegs binne die eierkapsule aangetref, met die kieue wat geresorbeer word, en metamorfose word voltooi, voordat dit uitbroei. Broeikas lyk dus soos klein volwassenes.

Sien riviermonsters: vis met arms en hande? om 'n video oor 'n buitengewoon groot salamanderspesie te sien.

Anura: Paddas

Paddas is amfibieë wat tot die orde Anura behoort (Figuur 2a). Anurane is een van die mees diverse groepe gewerwelde diere, met ongeveer 5 965 spesies wat op al die vastelande behalwe Antarktika voorkom. Anurane het 'n liggaamsplan wat meer gespesialiseerd is vir beweging. Volwasse paddas gebruik hul agterste ledemate om op land te spring. Paddas het 'n aantal modifikasies wat hulle toelaat om roofdiere te vermy, insluitend vel wat as kamoeflering optree. Baie spesies paddas en salamanders stel ook verdedigende chemikalieë vry uit kliere in die vel wat giftig is vir roofdiere.

Padda-eiers word uitwendig bevrug, en soos ander amfibieë, lê paddas gewoonlik hul eiers in klam omgewings. ’n Vogtige omgewing word vereis aangesien eiers nie ’n dop het nie en dus vinnig in droë omgewings dehidreer. Paddas toon 'n groot verskeidenheid van ouerlike gedrag, met sommige spesies wat baie eiers lê en min ouerlike sorg toon, tot spesies wat eiers en paddavissies op hul agterpote of rug dra. Die lewensiklus van paddas, soos ander amfibieë, bestaan ​​uit twee afsonderlike stadiums: die larfstadium gevolg deur metamorfose tot 'n volwasse stadium. Die larfstadium van 'n padda, die padda vis, is dikwels 'n filtervoedende herbivoor. Paddavissies het gewoonlik kieue, 'n sylynstelsel, langvinsterte en 'n gebrek aan ledemate. Aan die einde van die paddavisse stadium ondergaan paddas metamorfose in die volwasse vorm (Figuur 2b). Gedurende hierdie stadium verdwyn die kieue, stert en sylynstelsel, en vier ledemate ontwikkel. Die kake word groter en is geskik vir vleisetende voeding, en die spysverteringstelsel verander in die tipiese kort derm van 'n roofdier. 'n Oortrom en lugasemende longe ontwikkel ook. Hierdie veranderinge tydens metamorfose laat die larwes in die volwasse stadium land toe beweeg.

Apoda: Caecilians

'n Geskatte 185 spesies bestaan ​​uit caecilians (Figuur 3), 'n groep amfibieë wat tot die orde Apoda behoort. Alhoewel hulle gewerwelde diere is, lei 'n volledige gebrek aan ledemate tot hul ooreenkoms met erdwurms in voorkoms.

Hulle is aangepas vir 'n grondgrawende of akwatiese leefstyl, en hulle is byna blind. Hierdie diere word in die trope van Suid-Amerika, Afrika en Suider-Asië aangetref. Hulle het vestigiale ledemate, 'n bewys dat hulle uit 'n voorouer met bene ontwikkel het.


Opsomming

Sedert die begin van die geskiedenis was amfibieë deel van die menslike kultuur. Wes-Europeërs het vure gebou vir kook en warmte en groot stompe bygevoeg soos nodig. Wat af en toe na vore gekom het, was verstommend: groot swart diere (wat skuiling in die stompe gevind het) met vier pote en 'n stert, gitswart met opvallende heldergeel kolle. Hierdie vuursalamanders is op verskillende maniere gedink om die produk van die vuur self te wees, of, soos Aristoteles berig het, in staat om vuur te blus. Daar word gesê dat Plinius die Ouderling hierdie idee getoets het deur 'n salamander in vlamme te gooi - die salamander het gesterf! — nietemin het die assosiasie met vuur voortgeduur. Plinius het ander fantastiese aansprake voortgesit, wat versprei het, selfs Leonardo da Vinci het tot die legende bygedra, en mites uit verskillende streke het saamgesmelt - op 'n stadium is beweer dat asbes salamanderwol was. Salamanders is groot magte toegeskryf. 'n enkele salamander stroomop is gedink om voldoende te wees om 'n leër dood te maak. Koning Francis I. van Frankryk het 'n salamander as sy embleem gekies - 'n kragtige simbool, gebore uit vuur, gevul met gif, immuun teen brand, en selfs in staat om vlamme te blus. Voor die ontstaan ​​van groot stede en woonbuurte het mense grootgeword omring deur die natuur. Salamanders en salamanders, paddas en paddas was alles deel van normale menslike ervaring. Mites soos dié rondom die vuursalamanders was alledaags. Shakespeare se hekse gebrou met 'n oog van newt en stert van padda. As kind het ons paddavissies grootgemaak en is ons geleer om te sidder oor die verskyning van 'n tiersalamander in 'n wortelkelder. Oor die algemeen word amfibieë as goedaardig en onskadelik beskou, selfs nuttig as wesens wat skadelike insekte verslind en as 'n alternatiewe voedselbron dien. Dit het dus in die 1980's vir die meeste bioloë en die breë publiek as 'n skok gekom dat amfibieë regoor die wêreld besig was om agteruit te gaan en dat hulle 'n groter risiko loop om as 'n takson uit te sterf as enige ander gewerwelde groep. 'n Studie van elke amfibiese spesie wat in 2004 bekend was, het getoon dat ongeveer 40% 'n hoë risiko van uitsterwing het, en teen 2008 is die afname van amfibieë gesien as 'n bewys van 'n naderende sesde massa-uitsterwing.


Oor Amfibieë

Mark Wilson / Getty Images

Amfibieë is uniek in hul vermoë om beide op land en in water te lewe. Daar is vandag ongeveer 6 200 spesies amfibieë op aarde. Amfibieë het sekere eienskappe wat hulle van reptiele en ander diere skei:

  • Hulle word in water gebore en metamorfoseer (verander) dan in volwassenes wat op land kan lewe.
  • Amfibieë kan asemhaal en water deur hul dun vel absorbeer.
  • Hulle het baie verskillende maniere om voort te plant: sommige lê eiers, sommige dra lewendige jong, sommige dra hul eiers, terwyl ander weer hul kleintjies laat om vir hulself te sorg.

Resultate en bespreking

K-mer tot laagste gemeenskaplike voorouer databasis

Die kern van Kraken is 'n databasis wat rekords bevat wat bestaan ​​uit 'n k-mer en die LCA van alle organismes wie se genome dit bevat k-meer. Hierdie databasis, gebou met behulp van 'n gebruiker-gespesifiseerde biblioteek van genome, laat 'n vinnige opsoek na die mees spesifieke nodus in die taksonomiese boom wat geassosieer word met 'n gegewe k-meer. Reekse word geklassifiseer deur die databasis vir elkeen te bevraagteken k-mer in 'n volgorde, en gebruik dan die resulterende stel LCA-taksa om 'n gepaste etiket vir die volgorde te bepaal (Figuur 1 en Materiale en metodes). Reekse wat geen k-mers in die databasis word ongeklassifiseer gelaat deur Kraken. Kraken bou standaard die databasis met k = 31, maar hierdie waarde kan deur die gebruiker verander word.

Die Kraken volgorde klassifikasie algoritme. Om 'n volgorde te klassifiseer, elk k-mer in die volgorde word gekarteer na die laagste gemeenskaplike voorouer (LCA) van die genome wat dit bevat k-mer in 'n databasis. Die taksa wat met die volgorde geassosieer word k-mers, sowel as die taksa se voorouers, vorm 'n gesnoeide subboom van die algemene taksonomieboom, wat vir klassifikasie gebruik word. In die klassifikasieboom het elke nodus 'n gewig gelyk aan die aantal k-mere in die volgorde wat met die nodus se takson geassosieer word. Elke wortel-tot-blaar (RTL)-pad in die klassifikasieboom word aangeteken deur alle gewigte in die pad by te voeg, en die maksimum RTL-pad in die klassifikasieboom is die klassifikasiepad (nodes in geel uitgelig). Die blaar van hierdie klassifikasiepad (die oranje, mees linkse blaar in die klassifikasieboom) is die klassifikasie wat vir die navraagvolgorde gebruik word.

Gesimuleerde metagenoom data

Alhoewel ware metagenomiese leeswerk die mees realistiese toets van prestasie kan bied, sal sulke data ons nie toelaat om klassifikasie akkuraatheid te assesseer nie, want die ware spesies in metagenomiese datastelle vandag is meestal onbekend. Ons het eerder twee gesimuleerde metagenome gebruik wat geskep is deur werklike volgordes te kombineer wat verkry is uit projekte wat geïsoleerde mikrobiese genome opvolg. Toe ons hierdie gesimuleerde metagenome geskep het, het ons data gebruik wat deur die Illumina HiSeq- en MiSeq-volgordebepalingsplatforms in volgorde geplaas is, en daarom noem ons dit onderskeidelik die HiSeq- en MiSeq-metagenome (sien Materiale en metodes). Hierdie metagenome is gekonstrueer om klassifikasiespoed en genusvlakakkuraatheid te meet vir data gegenereer deur huidige en wyd gebruikte volgordebepalingsplatforms.

Benewens die twee gesimuleerde metagenome wat saamgestel is met volgordes van geïsoleerde genome, het ons 'n derde metagenomiese monster geskep wat 'n baie wyer reeks van die opeenvolgende filogenie dek. Hierdie monster, met gesimuleerde bakteriële en argeale lees (genoem simBA-5), is geskep met 'n foutkoers vyf keer hoër as wat verwag sou word, om Kraken se werkverrigting te evalueer op data wat baie foute bevat of sterk verskille van Kraken se genomiese biblioteek het (sien Materiale en metodes).

Klassifikasie akkuraatheid

Klassifiseerders neem oor die algemeen een van twee strategieë aan: PhymmBL en NBC klassifiseer byvoorbeeld alle reekse so akkuraat as moontlik, terwyl Kraken en Megablast sommige reekse ongeklassifiseer laat as daar onvoldoende bewyse bestaan. Omdat PhymmBL en NBC alles etiketteer, sal hulle geneig wees om meer vals positiewe te produseer as metodes soos Kraken. Op sy beurt kan 'n mens verwag dat 'n selektiewe klassifiseerder hoër akkuraatheid sal hê teen 'n sekere koste vir sensitiwiteit. Uniek onder metagenomika-klassifiseerders, PhymmBL verskaf vertroue tellings vir sy klassifikasies, wat gebruik kan word om lae-vertroue voorspellings weg te gooi en akkuraatheid te verbeter. Deur 'n ondergrens van 0.65 vir genusvlak-vertroue te gebruik, het ons 'n selektiewe klassifiseerder geskep gebaseer op PhymmBL se voorspellings wat ons as PhymmBL65 aandui.

Om Kraken se akkuraatheid met hierdie van ander klassifikasiemetodes te vergelyk, het ons 10 000 rye van elk van ons gesimuleerde metagenome geklassifiseer en genusvlak-sensitiwiteit en akkuraatheid gemeet (Figuur 2 en Tabel 1). Hier verwys sensitiwiteit na die proporsie rye wat aan die korrekte genus toegewys is. Presisie, ook bekend as positiewe voorspellingswaarde, verwys na die proporsie korrekte klassifikasies uit die totale aantal klassifikasies wat gepoog is. Kraken se sensitiwiteit en akkuraatheid is baie na aan dié van Megablast. Vir al drie metagenome was Kraken se sensitiwiteit binne 2,5 persentasiepunte van Megablast s'n. Die gebruik van presiese 31-basis-passings blyk egter 'n hoër akkuraatheid vir Kraken te lewer, aangesien die akkuraatheid die hoogste van alle klassifiseerders vir elk van die drie metagenome was. Soos verwag kan word, kon die nie-selektiewe klassifiseerders effens hoër sensitiwiteit bereik as die selektiewe klassifiseerders, maar ten koste van 'n aansienlik laer presisie, ongeveer 80% teenoor naby aan 100% vir Kraken.

Klassifikasie akkuraatheid en spoed vergelyking van klassifikasie programme vir drie gesimuleerde metagenome. Vir elke metagenoom word genus-presisie en -sensitiwiteit vir vyf klassifiseerders gewys, en spoed word vir vyf programme gewys (PhymmBL65 is bloot 'n vertroue-gefiltreerde weergawe van PhymmBL se resultate, en MetaPhlAn klassifiseer slegs 'n subset van lees wat na een van sy merkergene gekoppel is , aangesien dit 'n oorvloed skatting program is). Getoonde resultate is vir: (a) die HiSeq-metagenoom, bestaande uit HiSeq-lesings (gemiddelde lengte μ = 92 bp) in gelyke verhouding van tien bakteriese volgordebepalingsprojekte (b) die MiSeq metagenoom, bestaande uit MiSeq lees (μ = 156 bp) in gelyke verhouding van tien bakteriese projekte en (c) die simBA-5-metagenoom, bestaande uit gesimuleerde 100-bp-lesings met 'n hoë foutkoers van 1 967 bakteriese en argaeale taksa. Let daarop dat die horisontale asse in alle spoedgrafieke 'n logaritmiese skaal het.

Ons let ook op die onlangse publikasie van 'n metode, LMAT [12], wat a k-mer-indekseringskema soortgelyk aan Kraken s'n, maar verskil andersins in sy klassifikasiestrategie. LMAT kan nie maklik afgelaai en uitgevoer word op ons gesimuleerde data nie (sien Addisionele lêer 1: Nota 1), so ons het Kraken eerder op 'n datastel wat vir LMAT se gepubliseerde resultate gebruik word, laat loop. Vir daardie data (die PhymmBL-stel) het Kraken LMAT se akkuraatheid oorskry in beide die identifisering van leesoorsprong en die identifisering van die teenwoordigheid van spesies in die monster. Albei metodes het in wese perfekte (byna 100%) presisie gehad, maar Kraken het die spesie van 89% van die lesings korrek gemerk terwyl LMAT dit net vir 74% van die leeswerk gedoen het. Soos ons egter opmerk, bied daardie datastel nie 'n goeie basis vir vergelyking nie, want die lesings word sonder foute gesimuleer vanaf genome wat in beide Kraken en LMAT se databasisse ingesluit is.

Klassifikasie spoed

As gevolg van die baie groot grootte van metagenomiese datastelle vandag, is klassifikasiespoed krities belangrik, soos gedemonstreer deur die opkoms van vinnige oorvloed skattingsprogramme soos MetaPhlAn. Om klassifikasiespoed te evalueer, het ons elke klassifiseerder, sowel as MetaPhlAn, teen elk van die drie metagenome gehardloop wat ons gebruik het om akkuraatheid te toets (Figuur 2).

Kraken geklassifiseer lees baie vinniger as enige ander klassifiseerder, met prestasie wat wissel van 150 tot 240 keer vinniger as die naaste mededinger. Kraken het data verwerk teen 'n tempo van meer as 1,5 miljoen lesings per minuut (rpm) vir die HiSeq-metagenoom, meer as 1,3 miljoen rpm vir die simBA-5-metagenoom en meer as 890 000 rpm vir die MiSeq-metagenoom. Die volgende vinnigste klassifiseerder, Megablast, het spoed van 7 143 rpm vir die HiSeq-metagenoom gehad, 4 511 rpm vir die simBA-5-metagenoom en 2 830 rpm vir die MiSeq-metagenoom. Vir al drie metagenome, PhymmBL geklassifiseer teen 'n tempo van <100 rpm en NBC by <10 rpm. Kraken is ook meer as drie keer so vinnig as MetaPhlAn (wat slegs 'n subset van leeswerk klassifiseer), wat spoed van onderskeidelik 445 000 rpm, 371 000 rpm en 276 000 rpm gehad het vir die HiSeq-, simBA-5- en MiSeq-metagenome. Hierdie resultate word in Figuur 2 getoon. Soos verwag, word alle gereedskap verwerk hoe langer MiSeq lees (gemiddelde lengte μ = 156 bp) stadiger as die simBA-5 (μ = 100 bp) of HiSeq (μ = 92 bp) lees. Ons het ook 'n spoedvergelyking met LMAT uitgevoer deur een van die werklike monsters wat in LMAT se gepubliseerde resultate op hierdie monster bespreek is, te gebruik Kraken was 38.82 keer vinniger as LMAT en 7.55 keer vinniger as 'n weergawe van LMAT wat 'n kleiner databasis gebruik (Bykomende lêer 1: Nota 1) .

Ander variante van Kraken

Om maksimum spoed te verkry, moet Kraken bladsyfoute vermy (gevalle waar data van 'n hardeskyf na fisiese geheue gebring moet word), daarom is dit belangrik dat Kraken op 'n rekenaar met genoeg RAM loop om die hele databasis te hou. Alhoewel Kraken se verstekdatabasis 70 GB RAM benodig, het ons ook 'n metode ontwikkel om te verwyder k-mers van die databasis, wat die geheuevereistes dramaties verminder. Ons noem hierdie weergawe van Kraken, wat 'n kleiner databasis, MiniKraken, gebruik. Vir ons resultate hier het ons 'n 4 GB databasis gebruik. In vergelyking met Kraken, is die vermoë van MiniKraken om spesies uit kort leeswerk te herken laer, met sensitiwiteit vir ons werklike volgorde metagenome wat ongeveer 11% daal (Figuur 3 en Tabel 1). Op die hoë-fout simBA-5 metagenoom was MiniKraken se sensitiwiteit meer as 25 persentasiepunte laer as Kraken s'n, wat aandui dat hoë foutkoerse vir kort leeswerk aansienlike verlies in sensitiwiteit kan veroorsaak. Vir al drie metagenome was MiniKraken egter meer presies as Kraken.

Klassifikasie akkuraatheid en spoed vergelyking van variante van Kraken vir drie gesimuleerde metagenome. Vir elke metagenoom word genus akkuraatheid en sensitiwiteit vir vyf klassifiseerders getoon, en spoed word vir Kraken getoon, saam met 'n verminderde geheue weergawe van Kraken (MiniKraken), vinnige uitvoering weergawes van beide (Kraken-Q en MiniKraken-Q), en Kraken loop met 'n databasis wat konsep- en voltooide mikrobiese genome van GenBank (Kraken-GB) bevat. Getoonde resultate is vir dieselfde metagenome wat in Figuur 2 gebruik word. Let daarop dat die skale van die asse verskil van Figuur 2, aangesien die akkuraatheid en spoed van Kraken (en sy variante) dié van die ander klassifiseerders wat gebruik is, oorskry. (a) HiSeq metagenoom. (b) MiSeq metagenoom. (c) simBA-5 metagenoom.

MiniKraken se hoë akkuraatheid demonstreer dat ons in baie gevalle nie almal hoef te ondersoek nie k-mers in 'n volgorde om die korrekte klassifikasie te kry. Om hierdie idee tot sy uiterste te neem, het ons 'n 'vinnige werking'-modus vir Kraken (en MiniKraken) ontwikkel, waar in plaas daarvan om navrae te doen oor alle k-mers in 'n volgorde teen ons databasis, stop ons eerder by die eerste k-mer wat in die databasis bestaan, en gebruik die LCA wat daarmee geassosieer word k-mer om die volgorde te klassifiseer. Hierdie operasiemodus (aangedui deur -Q by die klassifiseerdernaam te voeg) laat Kraken toe om tiene of honderde oor te slaan k-mer navrae per reeks, wat sy klassifikasiespoed aansienlik verhoog met slegs 'n klein daling in akkuraatheid (Figuur 3 en Tabel 1). Omdat 'n databasis wat minder bevat k-mers vereis meer navrae van 'n reeks om 'n treffer te vind, MiniKraken-Q is stadiger as Kraken-Q, selfs wanneer MiniKraken vinniger as Kraken is.

Ons het ook 'n variant Kraken-databasis geskep wat GenBank se konsep- en voltooide genome vir bakterieë en archaea bevat, wat ons Kraken-GB noem. Die gewone weergawe van Kraken bevat slegs RefSeq volledige genome, waarvan daar 2 256 is, terwyl Kraken-GB 8 517 genome bevat. Ons hipotese was dat Kraken-GB 'n hoër sensitiwiteit as standaard Kraken vir ons metagenome sou hê, op grond van sy groter databasis. Kraken-GB het 'n baie hoër sensitiwiteit vir die HiSeq- en MiSeq-metagenome in vergelyking met Kraken (Figuur 3 en Tabel 1), hoofsaaklik as gevolg van die teenwoordigheid van twee genome in hierdie gesimuleerde metagenomiese monsters wat naasbestaandes slegs in Kraken-GB se databasis het (Materials). en metodes).

Alhoewel Kraken-GB wel 'n hoër sensitiwiteit as Kraken het, maak dit soms verrassende foute, wat ons ontdek het is veroorsaak deur kontaminant- en adaptervolgordes in die samestelling van sommige konsepgenome. Hierdie kontaminantvolgordes kom van ander bakterieë, virusse of selfs menslike genome, en dit lei tot verkeerde etikette k-mers in die databasis. Ons het probeer om dit uit Kraken-GB te verwyder (Materiale en metodes), maar sommige kontaminante kan steeds deur enige filters glip. Dus gebruik die verstekweergawe van Kraken vir eers slegs volledige RefSeq-genome.

Klade uitsluiting eksperimente

'n Belangrike doelwit van metagenomika is die ontdekking van nuwe organismes, en die behoorlike klassifikasie van nuwe organismes is 'n uitdaging vir enige klassifiseerder. Alhoewel 'n klassifiseerder onmoontlik nie 'n nuwe spesie die regte spesie-etiket kan gee nie, kan dit moontlik die korrekte genus identifiseer. Om die teenwoordigheid van nuwe organismes te simuleer, het ons die simBA-5-metagenoom herontleed nadat ons eers organismes uit die Kraken-databasis verwyder het wat aan dieselfde klade behoort het. Dit wil sê, ons het vir elke lees databasistreffers vir die spesie van die lees se oorsprong uitgemasker en Kraken se akkuraatheid by die hoër geledere (bv. genus en familie) geëvalueer. Ons het hierdie maskerings- en evalueringsproses vir klades van oorsprong tot by die filumrang voortgesit. Hierdie prosedure benader hoe Kraken die metagenomiese lees sal klassifiseer as daardie klade nie in die databasis teenwoordig was nie.

Tabel 2 bevat die resultate van hierdie analise. Kraken het hoë rangvlak-presisie getoon in alle gevalle waar 'n klade uitgesluit is, met rangvlak-presisie wat op of bo 93% gebly het vir alle pare van gemete en uitgesluit rangorde. Sensitiwiteit was egter dramaties laer: op sy beste kon Kraken ongeveer 33% van lesings klassifiseer wanneer hul spesie nog nooit voorheen gesien is nie. Dit is nie verbasend nie in die lig van Kraken se vertroue op presiese wedstryde van relatief lank k-mers: rye wat van verskillende genera afkomstig is, deel selde lang presiese passings. Nietemin, die hoë akkuraatheid in hierdie eksperiment dui daarop dat wanneer Kraken met nuwe organismes aangebied word, dit waarskynlik hulle behoorlik op hoër vlakke sal klassifiseer of glad nie sal klassifiseer nie.

Menslike mikrobioomprojekdata

Ons het Kraken gebruik om lesings te klassifiseer van drie speekselmonsters wat as deel van die Menslike Mikrobioomprojek ingesamel is. Omdat hierdie monsters van mense verkry is, het ons 'n Kraken-databasis geskep wat bakteriese, virale en menslike genome bevat om hierdie leesstukke te klassifiseer. Deur die drie monsters saam te kombineer, rapporteer ons die taksonomiese verspreiding van die geklassifiseerde leesstukke (Figuur 4). 'n Ontleding van die geklassifiseerde lesings van die gekombineerde monsters toon dat 'n meerderheid van daardie leeswerk in een van drie genera geklassifiseer is: Streptokokke (30%), Haemophilus (17%) en Prevotella (13%). Streptococcus mitis[13], Haemophilus parainfluenzae[14] en Prevotella melaninogenica[15], die volopste spesies (volgens gelees telling) van elk van hierdie drie genera, is almal bekend om geassosieer te word met menslike speeksel. Ons het ook die klassifikasie op elke monster afsonderlik uitgevoer (Bykomende lêer 1: Figure S1, S2, S3).

Taksonomiese verspreiding van speekselmikrobioomlese geklassifiseer deur Kraken. Sekwensies van speekselmonsters wat van drie individue versamel is, is deur Kraken geklassifiseer. Die verspreiding van daardie leesstukke wat deur Kraken geklassifiseer is, word getoon.

Opmerklik is dat 68,2% van die leesstukke nie deur Kraken geklassifiseer is nie. Om vas te stel waarom hierdie lesings nie deur Kraken geklassifiseer is nie, het ons 'n ewekansige geselekteerde subset van 2,500 van hierdie ongeklassifiseerde leeswerk in lyn gebring met die RefSeq bakteriese genome met behulp van BLASTN. Slegs 11% (275) van die subset van ongeklassifiseerde leesstukke het 'n BLASTN-belyning gehad met E-waarde ≤ 10 −5 en identiteit ≥90%. Dit dui daarop dat die oorgrote meerderheid van die leesstukke wat nie deur Kraken geklassifiseer is nie, aansienlik verskil het van enige bekende spesie, en dus eenvoudig onmoontlik om te identifiseer.


Evolusie en biogeografie van paddas en salamanders, afgelei van fossiele, morfologie en molekules

Moderne amfibieë, geklassifiseer in die Lissamphibia, is die enigste nie-amniote tetrapods wat vandag leef. Hulle bestaan ​​uit drie morfologies afsonderlike groepe: die stertlose paddas en paddas (Anura), die ledemaatlose caecilians (Gymnophiona), en die stertsalamanders en salamanders (Urodela). Met 205 spesies is die caecilians hoogs gespesialiseerde wurmagtige vorms wat 'n fossiele leefstyl leef, met 'n relatief smal verspreiding in die tropiese reënwoude van Suid-Amerika, Afrika en Asië (Duellman en Trueb, 1994 Amphibiaweb, 2015). Salamanders, met 683 spesies, kom wydverspreid in Noord-Amerika, Asië en Europa voor, met 'n paar pletodontiede wat na Sentraal- en Suid-Amerika strek (Duellman en Trueb, 1994 Amphibiaweb, 2015). Paddas is die mees diverse amfibiese groepe, met 6644 spesies wat oor alle vastelande versprei is, behalwe Antarktika (Duellman en Trueb, 1994 Amphibiaweb, 2015). Beide paddas en salamanders ontwikkel 'n wye verskeidenheid lewensstyle, wat wissel van land-, water-, fossiel- tot aboreal-leefstyle (Duellman en Trueb, 1994). Tydens ontogenie ondergaan amfibiese larwes gewoonlik 'n drastiese post-embrioniese verskuiwing na 'n volwasse vorm, 'n term wat bekend staan ​​as metamorfose. By salamanders kom 'n ander ontwikkelingsweg - neotenie - ook voor, waarin die larwemorfologie in seksueel volwasse volwassenes behoue ​​bly (Duellman en Trueb, 1994 Rose, 2003). As gevolg van die uiteenlopende leefstyle en ontwikkelingsweë, word paddas en salamanders dikwels as modelstelsels in baie velde van biologie gebruik (bv. evo-devo).
Oor 'n eeu, maar veral in die afgelope twee dekades, is 'n rykdom padda- en salamanderfossiele ontdek uit die Mesosoïkum en Senosoïkum van Oos-Asië (bv. Noble, 1924 Young, 1936 Borsuk-Bialynicka, 1978 Gao, 1986 Dong en Wang , 1998 Gao en Shubin, 2001, 2003, 2012 Gao en Wang, 2001 Gao en Chen, 2004 Wang en Rose, 2005 Wang en Evans, 2006b Zhang et al., 2009 Chen et al., 2016 hierdie studie). Sommige van hierdie fossiele verteenwoordig die vroegste lede van baie kroonklades, insluitend die vroegste kroonsalamanders uit die Middel Jurassic (

165 Ma, Gao en Shubin, 2003), die vroegste salamandroid uit die Laat Jurassic, die vroegste sireneed uit die Laat Jurassic (hierdie studie), en die vroegste spadefoot-paddas uit die laat Paleocence (Chen et al., 2016). Ander fossiele bevat ook belangrike anatomiese, tydelike en geografiese inligting om hul evolusie te verstaan. Ongelukkig bly die belangrikheid van baie van hierdie fossiele duister in 'n filogenetiese konteks. Byvoorbeeld, 'n vroeë-middel Oligoseen Mongoolse graafpootpadda Macropelobates osborni (Noble, 1924) is buite die huidige verspreiding van graafpootpaddas ontdek, maar sy filogenetiese posisie en die implikasie daarvan op graafpootpadda se biogeografie bly nie goed verstaan ​​nie.
'n Groot rede vir die swak begrip van hierdie fossiele kan toegeskryf word aan 'n neiging van tweespalt tussen morfologiese en molekulêre filogenieë op amfibieë. Terwyl morfoloë en paleontoloë soms 'n relatief klein morfologiese datastel gebruik om verwantskappe te rekonstrueer (bv. Gao en Shubin, 2012 Henrici, 2013), word grootskaalse filogenieë byna altyd uitgevoer met molekulêre data met slegs lewende taksa (bv. Roelants en Bossuyt, 2005). Pyron en Wiens, 2011). Baie min studies oor amfibiese filogenie het morfologiese en molekulêre data saam gekombineer, en nog minder het ook fossiele gekombineer. As gevolg hiervan bly die posisies van baie belangrike fossiele onduidelik, en die evolusionêre scenario's wat slegs van lewende spesies afgelei word, kan soms nie met fossielbewyse ooreenstem nie.
In hierdie tesis volg ek 'n totaalbewysbenadering om die evolusie van amfibieë, veral paddas en salamanders, te verstaan. Ek sal inligting van fossiele, morfologie en molekules saam inkorporeer om die verwantskappe te rekonstrueer. In vergelyking met studies met elke individuele datastelle, inkorporeer hierdie benadering alle beskikbare data in 'n enkele analise, met 'n doel om robuuste en kongruente resultate te bereik wat verdere besprekings oor karakterevolusie en biogeografiese rekonstruksie moontlik maak. Die insluiting van fossiele direk in die gekombineerde analise verskaf die tydsdimensie wat onafhanklik is van molekulêre data (Norell, 1992). Die anatomiese kombinasie van fossiele kan tussenvorme verteenwoordig wat help om die "langtak"-probleme wat deur hoogs gespesialiseerde moderne taksa veroorsaak word, op te los. Die morfologiese datastel, ten spyte van sy baie kleiner grootte met molekulêre data, is die enigste skakel tussen fossiele en moderne taksa. Die insluiting van sleutel morfologiese karakters in beide die rekonstruksie van filogenetiese hipoteses en die ondersoek van karakterevolusie lewer konsekwente resultate wat bespreking oor die homologie/homoplasie van 'n sekere karakter sonder dubbelsinnigheid toelaat. Die molekulêre volgorde data verskaf oorweldigend groot data oor moderne taksa vir filogenetiese rekonstruksies in vergelyking met morfologiese data, wat help om 'n robuuste hipotese te bereik. Alhoewel fossiele geen molekulêre data bevat nie, het die insluiting van molekulêre volgordedata in die gekombineerde analise wel 'n effek op die posisies van fossieltaksa. Deur die verwantskap "raamwerk" van moderne taksa te verander, verskil die karakteroptimering van fossiele en ander taksa van 'n gekombineerde analise ook in vergelyking met resultate van slegs morfologie-analise, en verander dus die posisies van fossiele. In die volgende vyf hoofstukke sal ek 'n aantal fossiel-amfibiespesies beskryf, drie gekombineerde filogenieë rekonstrueer en die resultate gebruik vir besprekings oor karakterevolusie en biogeografie.
In Hoofstuk 1 en Hoofstuk 2 fokus ek op 'n paddaklade genaamd spadepoot-paddas (Anura: Pelobatoidea). In Hoofstuk 1 verskaf ek beskrywings oor drie belangrike fossiele spadepoot-paddas uit die Senosoïkum van Oos-Asië en Noord-Amerika: Macropelobates osborni van die vroeë-middel Oligoseen van Mongolië, Prospea holoserisca van die jongste Paleoseen van Mongolië, en Scaphiopus skinneri van die middel Oligoseen van die Verenigde State. In Hoofstuk 2 doen ek 'n gekombineerde filogenetiese analise van argeobatrachiese paddas, en bespreek die evolusie van die benerige graaf en die historiese biogeografie van graafpootpaddas gebaseer op die resultate van die filogenie.
In Hoofstuk 3 beskryf ek 'n nuwe fossielpadda uit die Vroeë Kryt van Binne-Mongolië, China. Die unieke morfologie van die nuwe fossiel verskil van vorige Vroeë Kryt paddas uit die Jehol Biota van China. Resultate van die gekombineerde ontleding toon dat die nuwe padda 'n basale lid van die Pipanura verteenwoordig. Vergelykings tussen die Vroeë Kryt paddas uit China, Spanje en Brasilië toon 'n hoë diversiteit van spesies tesame met 'n hoë mate van endemisme tydens die Vroeë Kryt. Ek bespreek in die filogenetiese konteks hoe vroeë paddas geleidelik hul postkraniale liggaamsplan bereik met 'n verkorte vertebrale kolom, verlies van ribbes en gespesialiseerde bekkenstreke.
In Hoofstuk 4 gee ek 'n kort oorsig van Mesosoïese fossielsalamanders van Noord-China, en beskryf 'n nuwe fossiel uit die Laat Jura van die Liaoning-provinsie, China. Ek voer 'n gekombineerde filogenie van hoër-vlak verhoudings van salamanders. Die nuwe fossiel, ten spyte van sy algemene voorkoms, verteenwoordig 'n basale lid van die hoogs gespesialiseerde palingagtige neoteniese familie Sirenidae op die kladogram. Ek bespreek karakterevolusies in die Sirenidae, en hoe die neoteniese ontwikkelingspad in vroeë salamanders ontwikkel het.
In Hoofstuk 5 doen ek 'n gekombineerde filogenetiese analise van die salamander suborde Cryptobranchoidea, bestaande uit die neoteniese reuse salamanders (Cryptobranchidae) en die metamorfe Asiatiese salamanders (Hynobiidae). Die nuwe morfologiese matriks sluit nuwe karakters in wat voorheen minder gemonster is in die hinobranchiale streek. Die monofilie van die Hynobiidae word deur die nuwe ontleding bevestig, en vier ondubbelsinnige sinapomorfies word vir die klade gevind. 'n S-DIVA biogeografiese rekonstruksie word uitgevoer om die verspreidingspatrone van die Hynobiidae te bespreek.


Apoda: Caecilians

'n Geskatte 185 spesies bestaan ​​uit caecilians, 'n groep amfibieë wat tot die orde Apoda behoort. Alhoewel hulle gewerwelde diere is, lei 'n volledige gebrek aan ledemate tot hul ooreenkoms met erdwurms in voorkoms. Hulle is aangepas vir 'n grondgrawende of akwatiese leefstyl, en hulle is byna blind. These animals are found in the tropics of South America, Africa, and Southern Asia. They have vestigial limbs, evidence that they evolved from a legged ancestor.

Evolution Connection

The Paleozoic Era and the Evolution of Vertebrates The climate and geography of Earth was vastly different during the Paleozoic Era, when vertebrates arose, as compared to today. The Paleozoic spanned from approximately 542 to 251 million years ago. The landmasses on Earth were very different from those of today. Laurentia and Gondwana were continents located near the equator that subsumed much of the current day landmasses in a different configuration (Figure). At this time, sea levels were very high, probably at a level that hasn’t been reached since. As the Paleozoic progressed, glaciations created a cool global climate, but conditions warmed near the end of the first half of the Paleozoic. During the latter half of the Paleozoic, the landmasses began moving together, with the initial formation of a large northern block called Laurasia. This contained parts of what is now North America, along with Greenland, parts of Europe, and Siberia. Eventually, a single supercontinent, called Pangaea, was formed, starting in the latter third of the Paleozoic. Glaciations then began to affect Pangaea’s climate, affecting the distribution of vertebrate life.

During the Paleozoic Era, around 550 million years ago, the continent Gondwana formed. Both Gondwana and the continent Laurentia were located near the equator.

During the early Paleozoic, the amount of carbon dioxide in the atmosphere was much greater than it is today. This may have begun to change later, as land plants became more common. As the roots of land plants began to infiltrate rock and soil began to form, carbon dioxide was drawn out of the atmosphere and became trapped in the rock. This reduced the levels of carbon dioxide and increased the levels of oxygen in the atmosphere, so that by the end of the Paleozoic, atmospheric conditions were similar to those of today.

As plants became more common through the latter half of the Paleozoic, microclimates began to emerge and ecosystems began to change. As plants and ecosystems continued to grow and become more complex, vertebrates moved from the water to land. The presence of shoreline vegetation may have contributed to the movement of vertebrates onto land. One hypothesis suggests that the fins of aquatic vertebrates were used to maneuver through this vegetation, providing a precursor to the movement of fins on land and the development of limbs. The late Paleozoic was a time of diversification of vertebrates, as amniotes emerged and became two different lines that gave rise, on one hand, to mammals, and, on the other hand, to reptiles and birds. Many marine vertebrates became extinct near the end of the Devonian period, which ended about 360 million years ago, and both marine and terrestrial vertebrates were decimated by a mass extinction in the early Permian period about 250 million years ago.

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Background & Summary

Organisms’ life forms and ecological strategies (simply referred to as ‘traits’) reflect the outcome of continuous evolutionary pressures by biotic and abiotic factors 1,2 . Traits strongly determine the species’ ability to persist in a variety of environments, including interactions with other species 2–5 . At evolutionary time scales, the expression of new traits may create opportunities for phylogenetic lineages to explore novel niches, escape from predation or competition, and hence promote speciation by adaptive radiation 6–8 . At the ecological scale, traits are especially relevant in the study of community assembly where species coexistence is determined by different processes that influence trait composition of the community (e.g., coexisting species share more or less similar traits than expected by chance) 4,9,10 . Furthermore, species traits are linked to ecosystem functions and services necessary for human well-being (e.g., burrowing behavior alters soil properties, body size is associated with animal nutrient transport capacity, and feeding habits control food web structure) 11–14 . However, recent biodiversity loss due to anthropogenic causes raise questions about the ability of ecosystems to continue providing these benefits 15 . Therefore, understanding the mechanisms influencing patterns in trait diversity (or functional diversity), including human disturbance, is increasingly needed in face of rapid global changes 16,17 .

The last decade experienced a surge in the availability of natural history trait (i.e., morphological, ecological and reproduction traits) databases with broad taxonomic coverage 18–22 allowing unprecedented broad scale approaches in ecology and evolution 23–26 . Such data are still scarce for many amphibian species 27–29 . Amphibians are among the most diverse vertebrate groups on Earth, with more than 7,400 species and dozens of new species described every year 30 . They are abundant in many terrestrial and freshwater ecosystems, where they perform important ecosystem functions 31,32 . They are also the most threatened vertebrate group worldwide, with many species on the edge of extinction 33,34 . As such, it is urgent to improve our knowledge on amphibian traits in order to assess and predict their response to environmental changes and create conservation strategies that guarantee their survival.

In this context, we introduce AmphiBIO, an extensive database containing natural history traits for 6,775 amphibian species globally. AmphiBIO releases information on error-checked and referenced traits related to ecology, morphology and reproduction features of amphibians. Trait information was assembled from more than 1,500 literature sources, including peer-reviewed papers, existing life history databases, and other aggregated sources, in order to stimulate more comprehensive research in ecology, evolution, and conservation of amphibians. To enhance data quality, we implemented a protocol in which incorporated data were double-checked for potential errors. By making this data available to the scientific community we aim to advance the sharing of biological data and support a more integrative trait-based evolutionary and ecological science.


Skrywer inligting

Affiliations

Centro de Ciencias de la Atmosfera, Universidad Nacional Autónoma de México, CDMX, Mexico

Julián A. Velasco, Francisco Estrada, Oscar Calderón-Bustamante, Carolina Ureta & Carlos Gay

Institute for Environmental Studies, VU Amsterdam, Amsterdam, the Netherlands

Programa de Investigación en Cambio Climático, Universidad Nacional Autónoma de México, CDMX, Mexico

Environnements et Paléoenvironnements Océaniques et Continentaux, CNRS, Université de Bordeaux, Pessac, France

Cátedra Consejo Nacional de Ciencia y Tecnología, CDMX, Mexico

ESPACE-DEV, Univ Montpellier, IRD, Univ Guyane, Univ Reunion, Univ Antilles, Univ Avignon, Maison de la Télédétection, Montpellier, Cedex, France

The Climate Data Factory, Paris, France

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Bydraes

J.A.V. and F.E. contributed equally to the conceptual design J.A.V., F.E., O.C.B., D.S., D.D., and C.U. analyzed data. J.A.V. and F.E. wrote the paper and D.S., O.C.B., C.G., and C.U. contributed to it. All authors discussed the results and commented on the manuscript.

Corresponding author


152 Amphibians

Aan die einde van hierdie afdeling sal jy die volgende kan doen:

  • Describe the important difference between the life cycle of amphibians and the life cycles of other vertebrates
  • Distinguish between the characteristics of Urodela, Anura, and Apoda
  • Describe the evolutionary history of amphibians

Amphibians are vertebrate tetrapods (“four limbs”), and include frogs, salamanders, and caecilians. The term “amphibian” loosely translates from the Greek as “dual life,” which is a reference to the metamorphosis that many frogs and salamanders undergo and the unique mix of aquatic and terrestrial phases that are required in their life cycle. In fact, they cannot stray far from water because their reproduction is intimately tied to aqueous environments. Amphibians evolved during the Devonian period and were the earliest terrestrial tetrapods. They represent an evolutionary transition from water to land that occurred over many millions of years. Thus, the Amphibia are the only living true vertebrates that have made a transition from water to land in both their ontogeny (life development) and phylogeny (evolution). They have not changed much in morphology over the past 350 million years!

Watch this series of five Animal Planet videos on tetrapod evolution:

    1: The evolution from fish to earliest tetrapod

Characteristics of Amphibians

As tetrapods, most amphibians are characterized by four well-developed limbs. In some species of salamanders, hindlimbs are reduced or absent, but all caecilians are (secondarily) limbless. An important characteristic of extant amphibians is a moist, permeable skin that is achieved via mucus glands. Most water is taken in across the skin rather than by drinking. The skin is also one of three respiratory surfaces used by amphibians. The other two are the lungs and the buccal (mouth) cavity. Air is taken first into the mouth through the nostrils, and then pushed by positive pressure into the lungs by elevating the throat and closing the nostrils.

All extant adult amphibians are carnivorous, and some terrestrial amphibians have a sticky tongue used to capture prey. Amphibians also have multiple small teeth at the edge of the jaws. In salamanders and caecilians, teeth are present in both jaws, sometimes in multiple rows. In frogs and toads, teeth are seen only in the upper jaw. Additional teeth, called vomerine teeth , may be found in the roof of the mouth. Amphibian teeth are pedicellate, which means that the root and crown are calcified, separated by a zone of noncalcified tissue.

Amphibians have image-forming eyes and color vision. Ears are best developed in frogs and toads, which vocalize to communicate. Frogs use separate regions of the inner ear for detecting higher and lower sounds: the papilla amphibiorum, which is sensitive to frequencies below 10,000 hertz and unique to amphibians, and the papilla basilaris, which is sensitive to higher frequencies, including mating calls, transmitted from the eardrum through the stapes bone. Amphibians also have an extra bone in the ear, the operculum, which transmits low-frequency vibrations from the forelimbs and shoulders to the inner ear, and may be used for the detection of seismic signals.

Evolution of Amphibians

The fossil record provides evidence of the first tetrapods: now-extinct amphibian species dating to nearly 400 million years ago. Evolution of tetrapods from lobe-finned freshwater fishes (similar to coelacanths and lungfish) represented a significant change in body plan from one suited to organisms that respired and swam in water, to organisms that breathed air and moved onto land these changes occurred over a span of 50 million years during the Devonian period.

Aquatic tetrapods of the Devonian period include Ichthyostega en Acanthostega. Both were aquatic, and may have had both gills and lungs. They also had four limbs, with the skeletal structure of limbs found in present-day tetrapods, including amphibians. However, the limbs could not be pulled in under the body and would not have supported their bodies well out of water. They probably lived in shallow freshwater environments, and may have taken brief terrestrial excursions, much like “walking” catfish do today in Florida. In Ichthyostega, the forelimbs were more developed than the hind limbs, so it might have dragged itself along when it ventured onto land. What preceded Acanthostega en Ichthyostega?

In 2006, researchers published news of their discovery of a fossil of a “tetrapod-like fish,” Tiktaalik roseae, which seems to be a morphologically “intermediate form” between sarcopterygian fishes having feet-like fins and early tetrapods having true limbs ((Figure)). Tiktaalik likely lived in a shallow water environment about 375 million years ago. 1 Tiktaalik also had gills and lungs, but the loss of some gill elements gave it a neck, which would have allowed its head to move sideways for feeding. The eyes were on top of the head. It had fins, but the attachment of the fin bones to the shoulder suggested they might be weight-bearing. Tiktaalik preceded Acanthostega en Ichthyostega, with their four limbs, by about 10 million years and is considered to be a true intermediate clade between fish and amphibians.


The early tetrapods that moved onto land had access to new nutrient sources and relatively few predators. This led to the widespread distribution of tetrapods during the early Carboniferous period, a period sometimes called the “age of the amphibians.”

Modern Amphibians

Amphibia comprises an estimated 6,770 extant species that inhabit tropical and temperate regions around the world. All living species are classified in the subclass Lissamphibia (“smooth-amphibian”), which is divided into three clades: Urodela (“tailed”), the salamanders Anura (“tail-less”), the frogs and Apoda (“legless ones”), the caecilians.

Urodela: Salamanders

Salamanders are amphibians that belong to the order Urodela (or Caudata). These animals are probably the most similar to ancestral amphibians. Living salamanders ((Figure)) include approximately 620 species, some of which are aquatic, others terrestrial, and some that live on land only as adults. Most adult salamanders have a generalized tetrapod body plan with four limbs and a tail. The placement of their legs makes it difficult to lift their bodies off the ground and they move by bending their bodies from side to side, called lateral undulation, in a fish-like manner while “walking” their arms and legs fore-and-aft. It is thought that their gait is similar to that used by early tetrapods. The majority of salamanders are lungless, and respiration occurs through the skin or through external gills in aquatic species. Sommige landsalamanders het primitiewe longe, 'n paar spesies het beide kieue en longe. The giant Japanese salamander, the largest living amphibian, has additional folds in its skin that enlarge its respiratory surface.

Most salamanders reproduce using an unusual process of internal fertilization of the eggs. Mating between salamanders typically involves an elaborate and often prolonged courtship. Such a courtship ends in the deposition of sperm by the males in a packet called a spermatophore , which is subsequently picked up by the female, thus ultimately fertilization is internal. All salamanders except one, the fire salamander, are oviparous. Aquatic salamanders lay their eggs in water, where they develop into legless larvae called efts. Terrestrial salamanders lay their eggs in damp nests, where the eggs are guarded by their mothers. These embryos go through the larval stage and complete metamorphosis before hatching into tiny adult forms. One aquatic salamander, the Mexican axolotl, never leaves the larval stage, becoming sexually mature without metamorphosis.


View River Monsters: Fish With Arms and Hands? to see a video about an unusually large salamander species.

Anura: Frogs

Frogs ((Figure)) are amphibians that belong to the order Anura or Salientia (“jumpers”). Anurans are among the most diverse groups of vertebrates, with approximately 5,965 species that occur on all of the continents except Antarctica. Anurans, ranging from the minute New Guinea frog at 7 mm to the huge goliath frog at 32 cm from tropical Africa, have a body plan that is more specialized for movement. Adult frogs use their hind limbs and their arrow-like endoskeleton to jump accurately to capture prey on land. Tree frogs have hands adapted for grasping branches as they climb. In tropical areas, “flying frogs” can glide from perch to perch on the extended webs of their feet. Frogs have a number of modifications that allow them to avoid predators, including skin that acts as camouflage. Many species of frogs and salamanders also release defensive chemicals that are poisonous to predators from glands in the skin. Frogs with more toxic skins have bright warning (aposematic) coloration.


Frog eggs are fertilized externally, and like other amphibians, frogs generally lay their eggs in moist environments. Although amphibian eggs are protected by a thick jelly layer, they would still dehydrate quickly in a dry environment. Frogs demonstrate a great diversity of parental behaviors, with some species laying many eggs and exhibiting little parental care, to species that carry eggs and tadpoles on their hind legs or embedded in their backs. The males of Darwin’s frog carry tadpoles in their vocal sac. Many tree frogs lay their eggs off the ground in a folded leaf located over water so that the tadpoles can drop into the water as they hatch.

The life cycle of most frogs, as other amphibians, consists of two distinct stages: the larval stage followed by metamorphosis to an adult stage. However, the eggs of frogs in the genus Eleutherodactylus develop directly into little froglets, guarded by a parent. The larval stage of a frog, the tadpole, is often a filter-feeding herbivore. Tadpoles usually have gills, a lateral line system, longfinned tails, and lack limbs. At the end of the tadpole stage, frogs undergo metamorphosis into the adult form ((Figure)). During this stage, the gills, tail, and lateral line system disappear, and four limbs develop. The jaws become larger and are suited for carnivorous feeding, and the digestive system transforms into the typical short gut of a predator. 'n Oortrom en lugasemende longe ontwikkel ook. These changes during metamorphosis allow the larvae to move onto land in the adult stage.


Apoda: Caecilians

An estimated 185 species comprise the caecilians , a group of amphibians that belong to the order Apoda. They have no limbs, although they evolved from a legged vertebrate ancestor. The complete lack of limbs makes them resemble earthworms. This resemblance is enhanced by folds of skin that look like the segments of an earthworm. However, unlike earthworms, they have teeth in both jaws, and feed on a variety of small organisms found in soil, including earthworms! Caecilians are adapted for a burrowing or aquatic lifestyle, and they are nearly blind, with their tiny eyes sometimes covered by skin. Although they have a single lung, they also depend on cutaneous respiration. These animals are found in the tropics of South America, Africa, and Southern Asia. In the caecelians, the only amphibians in which the males have copulatory structures, fertilization is internal. Some caecilians are oviparous, but most bear live young. In these cases, the females help nourish their young with tissue from their oviduct before birth and from their skin after birth.

The Paleozoic Era and the Evolution of Vertebrates When the vertebrates arose during the Paleozoic Era (542 to 251 MYA), the climate and geography of Earth was vastly different. The distribution of landmasses on Earth were also very different from that of today. Near the equator were two large supercontinents, Laurentia and Gondwana , which included most of today’s continents, but in a radically different configuration ((Figure)). At this time, sea levels were very high, probably at a level that hasn’t been reached since. As the Paleozoic progressed, glaciations created a cool global climate, but conditions warmed near the end of the first half of the Paleozoic. During the latter half of the Paleozoic, the landmasses began moving together, with the initial formation of a large northern block called Laurasia , which contained parts of what is now North America, along with Greenland, parts of Europe, and Siberia. Eventually, a single supercontinent, called Pangaea , was formed, starting in the latter third of the Paleozoic. Glaciations then began to affect Pangaea’s climate and the distribution of vertebrate life.


During the early Paleozoic, the amount of carbon dioxide in the atmosphere was much greater than it is today. This may have begun to change later, as land plants became more common. As the roots of land plants began to infiltrate rock and soil began to form, carbon dioxide was drawn out of the atmosphere and became trapped in the rock. This reduced the levels of carbon dioxide and increased the levels of oxygen in the atmosphere, so that by the end of the Paleozoic, atmospheric conditions were similar to those of today.

As plants became more common through the latter half of the Paleozoic, microclimates began to emerge and ecosystems began to change. As plants and ecosystems continued to grow and become more complex, vertebrates moved from the water to land. The presence of shoreline vegetation may have contributed to the movement of vertebrates onto land. One hypothesis suggests that the fins of aquatic vertebrates were used to maneuver through this vegetation, providing a precursor to the movement of fins on land and the further development of limbs. The late Paleozoic was a time of diversification of vertebrates, as amniotes emerged and became two different lines that gave rise, on one hand, to synapsids and mammals, and, on the other hand, to the codonts, reptiles, dinosaurs, and birds. Many marine vertebrates became extinct near the end of the Devonian period, which ended about 360 million years ago, and both marine and terrestrial vertebrates were decimated by a mass extinction in the early Permian period about 250 million years ago.

Afdeling Opsomming

As vierpotiges word die meeste amfibieë gekenmerk deur vier goed ontwikkelde ledemate, hoewel sommige spesies salamanders en alle caeciliane ledemate is. The most important characteristic of extant amphibians is a moist, permeable skin used for cutaneous respiration, although lungs are found in the adults of many species.

All amphibians are carnivores and possess many small teeth. The fossil record provides evidence of amphibian species, now extinct, that arose over 400 million years ago as the first tetrapods. Living Amphibia can be divided into three classes: salamanders (Urodela), frogs (Anura), and caecilians (Apoda). In the majority of amphibians, development occurs in two distinct stages: a gilled aquatic larval stage that metamorphoses into an adult stage, acquiring lungs and legs, and losing the tail in Anurans. A few species in all three clades bypass a free-living larval stage. Various levels of parental care are seen in the amphibians.


'Dead clades walking': Fossil record provides new insights into mass extinctions

Mass extinctions are known as times of global upheaval, causing rapid losses in biodiversity that wipe out entire animal groups. Some of the doomed groups linger on before going extinct, and a team of scientists found these "dead clades walking" (DCW) are more common and long-lasting than expected.

"Dead clades walking are a pattern in the fossil record where some animal groups make it past the extinction event, but they also can't succeed in the aftermath," said Benjamin Barnes, a doctoral student in geosciences at Penn State. "It paints the pictures of a group consigned to an eventual extinction."

The scientists found 70 of the 134 orders of ancient sea-dwelling invertebrates they examined could be identified as DCW in a new statistical analysis of the fossil record.

"What really fascinated us was that over half of all the orders we looked at have this phenomenon and that it can look like many different things," said Barnes, who led a group of graduate students and a postdoctoral researcher on the study. "In some cases, you have a group that has a sudden drop in diversity and lasts for a few more million years before disappearing from the record. But we also found many orders straggled along sometimes for tens or hundreds of millions of years."

The findings, published in the journal Verrigtinge van die Nasionale Akademie van Wetenskappe, challenge the view of extinction as a sudden disappearance and suggest that the full impact of mass extinctions lag behind the events themselves longer than previously expected, the scientists said.

"I think it raises questions about how the so-called kill mechanism operates," Barnes said. "We think of mass extinctions as being these selective forces that cause large groups of animals to go extinct, but our results really show there are a lot of instances where it's not so sudden. It raises questions about why that's such a long delay."

Paleontologist David Jablonski first coined the term DCW more than 20 years ago, and since then it has been associated almost exclusively with mass extinctions. Using a wealth of new fossil record data made available over the last two decades, the study found DCW are also common around smaller, more localized background extinction stages, the scientists said.

"Our results suggest that rather than representing a rare, brief fossil pattern in the wake of mass extinction events, DCWs are actually a really diverse phenomenon and that there might be a lot of drivers that produce this pattern in the fossil record," Barnes said. "These DCWs may represent a major macroevolutionary pattern."

The scientists used a statistical technique called a Bayesian change point algorithm to analyze fossil records from the Paleobiology Database, a public record of paleontological data maintained by international scientists.

The method allowed the researchers to search time series data for significant points where the data deviated from the pattern. They were able to identify negative jagged shifts in diversity and rule out that the organism went extinct immediately but instead persisted.

"So you might be looking in the fossil record and you'll find tons of a type of brachiopod," Barnes said. "Each order has a handful of families and dozens of genera within those families. Then you might see a drop in diversity, and the majority of those genera disappear and perhaps there's only one family that continues to survive."

Those survivors can continue in their niche for millions of years, even into the present. But their lack of diversity makes them more susceptible to future environmental challenges or extinction events, the scientists said.

"I think these findings cause you to reexamine how you measure success," Barnes said. "It's quite possible for an animal group not to produce new families and new genera at a rate like it did before, but if it continues to survive for many millions of years, that's still some form of success. I think it raises a lot of questions about what it means to be successful as a fossil organism and what ultimately are the controls of origination."


Kyk die video: Vroege Vogels - Tuin vol amfibieën en reptielen (September 2022).