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关键词：
protein evolution;epistasis;evolution of protein structure-function;Meta II stability;Cetacea;spectral tuning;Orcinus orca
DOI：
doi:10.5061/dryad.5k0s6
摘要：
Like many aquatic vertebrates, whales have blue-shifting spectral tuning substitutions in the dim-light visual pigment, rhodopsin, that are thought to increase photosensitivity in underwater environments. We have discovered that known spectral tuning substitutions also have surprising epistatic effects on another function of rhodopsin, the kinetic rates associated with light-activated intermediates. By using absorbance spectroscopy and fluorescence-based retinal release assays on heterologously expressed rhodopsin, we assessed both spectral and kinetic differences between cetaceans (killer whale) and terrestrial outgroups (hippo, bovine). Mutation experiments revealed that killer whale rhodopsin is unusually resilient to pleiotropic effects on retinal release from key blue-shifting substitutions (D83N and A292S), largely due to a surprisingly specific epistatic interaction between D83N and the background residue, S299. Ancestral sequence reconstruction indicated that S299 is an ancestral residue that predates the evolution of blue-shifting substitutions at the origins of Cetacea. Based on these results, we hypothesize that intramolecular epistasis helped to conserve rhodopsin's kinetic properties while enabling blue-shifting spectral tuning substitutions as cetaceans adapted to aquatic environments. Trade-offs between different aspects of molecular function are rarely considered in protein evolution, but in cetacean and other vertebrate rhodopsins, may underlie multiple evolutionary scenarios for the selection of specific amino acid substitutions.
负责人：
关键词：
GBIF
biodiversity
species occurrences
DOI：
doi:10.15468/dl.jlwmuk
摘要：
A dataset containing 571 species occurrences available in GBIF matching the query: TaxonKey: Orcinus orca (Linnaeus, 1758) Geometry: POLYGON((-145.72
负责人：
关键词：
GBIF
biodiversity
species occurrences
DOI：
doi:10.15468/dl.amf1uj
摘要：
A dataset containing 2546 species occurrences available in GBIF matching the query: TaxonKey: Orcinus orca (Linnaeus, 1758). The dataset includes
负责人：
关键词：
GBIF
biodiversity
species occurrences
DOI：
doi:10.15468/dl.tlpzbe
摘要：
A dataset containing 2546 species occurrences available in GBIF matching the query: TaxonKey: Orcinus orca (Linnaeus, 1758). The dataset includes
负责人：
关键词：
GBIF
biodiversity
species occurrences
DOI：
doi:10.15468/dl.ybfy4t
摘要：
A dataset containing 2545 species occurrences available in GBIF matching the query: TaxonKey: Orcinus orca (Linnaeus, 1758). The dataset includes
负责人：
关键词：
Notropis jemezanus;Meda fulgida;Cyprinella callistia;Ichthyomyzon castaneus;Noturus elegans;Hybopsis winchelli;Clinostomus funduloides;Ptychocheilus grandis;Macrhybopsis australis;Oncorhynchus nerka;Cottus perplexus;Etheostoma serrifer;Lepidomeda mollispinis;Etheostoma fricksium;Etheostoma asprigene;Relictus solitarius;Apeltes quadracus;Cottus aleuticus;Fundulus dispar;Percina palmaris;Noturus crypticus;Pungitius pungitius;Xyrauchen texanus;Percina sipsi;Cyprinella callisema;Notropis rubellus;Notropis cummingsae;Centrarchus macropterus;Etheostoma kanawhae;Cottus confusus;Cottus beldingii;Esox niger;Cyprinodon salinus;Menidia beryllina;Erimonax monachus;Notropis boops;Noturus flavipinnis;Catostomus warnerensis;Cyprinella labrosa;Pomoxis annularis;Micropterus punctulatus;Forbesichthys agassizii;Oregonichthys kalawatseti;Cyprinella gibbsi;Cottus rhotheus;Luxilus cerasinus;Eleotris amblyopsis;Notropis texanus;Notropis alborus;Pteronotropis grandipinnis;Moxostoma pappillosum;Etheostoma nuchale;Lepisosteus platostomus;Macrhybopsis aestivalis;Ictalurus furcatus;Ctenogobius fasciatus;Fundulus julisia;Notropis spectrunculus;Poecilia formosa;Cottus tallapoosae;Fundulus euryzonus;Oncorhynchus clarkii;Etheostoma microlepidum;Macrhybopsis hyostoma;Aplodinotus grunniens;Ameiurus melas;Notropis baileyi;Percina maculata;Rhinichthys falcatus;Ictalurus lupus;Lota lota;Cyprinella chloristia;Percina jenkinsi;Phoxinus erythrogaster;Lepisosteus platyrhincus;Sander canadensis;Gila ditaenia;Percina pantherina;Catostomus latipinnis;Etheostoma vulneratum;Scaphirhynchus albus;Cichlasoma cyanoguttatum;Notropis nubilus;Etheostoma ditrema;Semotilus atromaculatus;Catostomus columbianus;Catostomus snyderi;Lythrurus snelsoni;Noturus leptacanthus;Awaous banana;Etheostoma okaloosae;Umbra limi;Thaleichthys pacificus;Rhinichthys obtusus;Gila robusta;Hybognathus hankinsoni;Etheostoma tippecanoe;Notropis scabriceps;Etheostoma boschungi;Notropis altipinnis;Etheostoma rafinesquei;Etheostoma chuckwachatte;Mugil cephalus;Rhinichthys cataractae;Luxilus albeolus;Cottus greenei;Etheostoma kantuckeense;Oncorhynchus gorbuscha;Campostoma ornatum;Catostomus discobolus;Prosopium abyssicola;Hiodon tergisus;Speoplatyrhinus poulsoni;Etheostoma nigripinne;Noturus lachneri;Noturus nocturnus;Catostomus utawana;Chologaster cornuta;Gila intermedia;Notropis percobromus;Lepomis gulosus;Etheostoma lepidum;Etheostoma exile;Notropis girardi;Etheostoma whipplei;Perca flavescens;Notropis procne;Notropis suttkusi;Etheostoma maculatum;Lepomis microlophus;Etheostoma colorosum;Morone chrysops;Gila orcuttii;Moxostoma duquesnei;Noturus funebris;Cottus caeruleomentum;Lythrurus roseipinnis;Etheostoma lawrencei;Cottus tenuis;Eremichthys acros;Thoburnia hamiltoni;Etheostoma gracile;Leptolucania ommata;Lampetra richardsoni;Lythrurus lirus;Cyprinella spiloptera;Phoxinus tennesseensis;Lepomis cyanellus;Cottus gulosus;Percina roanoka;Cottus marginatus;Cyprinodon bovinus;Etheostoma grahami;Percina gymnocephala;Coregonus reighardi;Etheostoma olivaceum;Atractosteus spatula;Coregonus nigripinnis;Etheostoma sagitta;Notropis ammophilus;Fundulus albolineatus;Lampetra similis;Lepomis symmetricus;Cottus hypselurus;Oncorhynchus mykiss;Hysterocarpus traskii;Moxostoma rupiscartes;Fundulus luciae;Alosa aestivalis;Deltistes luxatus;Etheostoma obeyense;Cyprinella trichroistia;Scaphirhynchus suttkusi;Leptocottus armatus;Carpiodes cyprinus;Etheostoma swannanoa;Hybognathus hayi;Notropis ozarcanus;Osmerus mordax;Notropis anogenus;Gambusia senilis;Dormitator maculatus;Coregonus nipigon;Etheostoma punctulatum;Rhinichthys evermanni;Salvelinus namaycush;Noturus flavater;Syngnathus scovelli;Percina sciera;Moxostoma poecilurum;Lampetra appendix;Moxostoma anisurum;Percina shumardi;Fundulus rubrifrons;Chasmistes cujus;Cottus cognatus;Cyprinella camura;Nocomis effusus;Cyprinodon nevadensis;Etheostoma chlorobranchium;Cycleptus elongatus;Lythrurus fumeus;Etheostoma caeruleum;Gila crassicauda;Cottus bendirei;Notropis shumardi;Percina rex;Richardsonius egregius;Trogloglanis pattersoni;Richardsonius balteatus;Percina macrolepida;Notropis hudsonius;Notropis sabinae;Ictiobus bubalus;Cyprinella callitaenia;Ptychocheilus umpquae;Etheostoma tecumsehi;Notropis bairdi;Gila purpurea;Rhinichthys deaconi;Spirinchus thaleichthys;Gila atraria;Lampetra folletti;Astyanax mexicanus;Catostomus microps;Notropis harperi;Ammocrypta beanii;Ambloplites cavifrons;Fundulus sciadicus;Lepisosteus oculatus;Moxostoma ariommum;Pylodictis olivaris;Etheostoma marmorpinnum;Gila nigra;Luxilus pilsbryi;Cyprinodon pecosensis;Thoburnia rhothoeca;Lucania goodei;Microgadus tomcod;Etheostoma tetrazonum;Notropis maculatus;Catostomus occidentalis;Notropis buccatus;Notropis chiliticus;Etheostoma fusiforme;Esox masquinongy;Catostomus rimiculus;Polyodon spathula;Coregonus kiyi;Percina macrocephala;Prosopium coulterii;Lepisosteus osseus;North America;Nocomis leptocephalus;Gila elegans;Empetrichthys merriami;Lepomis punctatus;Etheostoma cinereum;Typhlichthys subterraneus;Noturus trautmani;Oncorhynchus tshawytscha;Percina nasuta;Cyprinodon rubrofluviatilis;Ammocrypta vivax;Thymallus arcticus;Fundulus notatus;Elassoma okatie;Chasmistes muriei;Etheostoma etnieri;Lythrurus alegnotus;Ctenogobius pseudofasciatus;Percina copelandi;Erimystax x-punctatus;Notropis potteri;Lampetra minima;Pteronotropis signipinnis;Petromyzon marinus;Phenacobius catostomus;Esox americanus;Poecilia latipinna;Clinostomus elongatus;Moapa coriacea;Amblyopsis spelaea;Ammocrypta meridiana;Jordanella floridae;Alosa mediocris;Etheostoma olmstedi;Oncorhynchus keta;Etheostoma sellare;Moxostoma breviceps;Notropis petersoni;Cycleptus meridionalis;Micropterus notius;Notropis perpallidus;Salvelinus malma;Cyprinella venusta;Dorosoma cepedianum;Ameiurus nebulosus;Notropis chlorocephalus;Prosopium cylindraceum;Lythrurus fasciolaris;Semotilus thoreauianus;Hybognathus argyritis;Percina fulvitaenia;Crenichthys nevadae;Dasyatis sabina;Etheostoma tallapoosae;Etheostoma uniporum;Percina squamata;Pteronotropis merlini;Cottus chattahoochee;Cyprinodon elegans;Dionda episcopa;Ambloplites constellatus;Notropis semperasper;Etheostoma cragini;Etheostoma blennius;Cyprinella zanema;Percina phoxocephala;Rhinichthys umatilla;Notropis candidus;Notropis chihuahua;Etheostoma chienense;Pogonichthys ciscoides;Noturus eleutherus;Lepomis macrochirus;Etheostoma rubrum;Pimephales vigilax;Etheostoma mariae;Cyprinodon eremus;Hybognathus placitus;Cottus carolinae;Cottus girardi;Cyprinella nivea;Ichthyomyzon fossor;Campostoma pauciradii;Notropis rafinesquei;Percina suttkusi;Notropis orca;Moxostoma robustum;Cottus bairdii;Labidesthes sicculus;Luxilus coccogenis;Fundulus rathbuni;Etheostoma trisella;Percina nigrofasciata;Percina smithvanizi;Hybognathus nuchalis;Etheostoma wapiti;Pogonichthys macrolepidotus;Iotichthys phlegethontis;Notropis longirostris;Salvelinus fontinalis;Scaphirhynchus platorynchus;Lepidomeda copei;Alosa chrysochloris;Myoxocephalus quadricornis;Cyprinodon tularosa;Dorosoma petenense;Notropis bifrenatus;Chasmistes liorus;Percina crassa;Cyprinella galactura;Morone mississippiensis;Lepomis humilis;Etheostoma pyrrhogaster;Lampetra hubbsi;Percina burtoni;Coregonus johannae;Hybognathus regius;Notropis heterolepis;Plagopterus argentissimus;Gila alvordensis;Phenacobius mirabilis;Mylocheilus caurinus;Satan eurystomus;Alosa sapidissima;Notropis hypsilepis;Alosa pseudoharengus;Notropis amabilis;Etheostoma chermocki;Lepomis marginatus;Notropis scepticus;Luxilus cardinalis;Ameiurus catus;Etheostoma virgatum;Notropis uranoscopus;Percina caprodes;Etheostoma stigmaeum;Hybopsis amnis;Acipenser brevirostrum;Notropis mekistocholas;Etheostoma brevispinum;Cyprinodon arcuatus;regionalization;Etheostoma collis;Notropis albizonatus;Oregonichthys crameri;Cottus paulus;Etheostoma bellum;Ameiurus platycephalus;Etheostoma artesiae;Cymatogaster aggregata;Etheostoma nianguae;faunal similarity;Lepidomeda vittata;Paralichthys lethostigma;Anchoa mitchilli;Novumbra hubbsi;Prosopium spilonotus;Catostomus clarkii;Cyprinodon diabolis;Hybopsis lineapunctata;Alosa alabamae;Prosopium gemmifer;Cyprinella formosa;Fundulus jenkinsi;Ptychocheilus lucius;Notropis buchanani;Pteronotropis welaka;Elassoma alabamae;Pteronotropis hypselopterus;Notropis edwardraneyi;Fundulus diaphanus;Fundulus waccamensis;Crystallaria asprella;Cyprinodon radiosus;Etheostoma jordani;Menidia extensa;Phenacobius crassilabrum;Etheostoma moorei;Lepomis miniatus;Coregonus clupeaformis;Notropis wickliffi;Gila bicolor;Notropis telescopus;Pomoxis nigromaculatus;Moxostoma collapsum;Luxilus zonistius;Rhinichthys atratulus;Crystallaria cincotta;Etheostoma raneyi;Phenacobius uranops;Gambusia holbrooki;Noturus gilberti;Etheostoma lynceum;Notropis micropteryx;Etheostoma rupestre;Notropis photogenis;Noturus stigmosus;Acipenser oxyrinchus;Microphis brachyurus;Carpiodes carpio;Erimyzon tenuis;Enneacanthus chaetodon;Gasterosteus aculeatus;Rhinichthys osculus;Aphredoderus sayanus;Etheostoma smithi;Notropis blennius;Etheostoma proeliare;Etheostoma zonifer;Etheostoma swaini;Etheostoma longimanum;Margariscus margarita;Mylopharodon conocephalus;Rhinichthys cobitis;Phenacobius teretulus;Notropis amoenus;Noturus gladiator;Moxostoma lacerum;Amia calva;Lampetra ayresii;Cottus pitensis;Prosopium williamsoni;Thoburnia atripinnis;Fundulus chrysotus;primary-freshwater fishes;Moxostoma congestum;Percina cymatotaenia;Acipenser medirostris;Chasmistes brevirostris;Hybopsis amblops;Percina brevicauda;Etheostoma brevirostrum;Ichthyomyzon greeleyi;Ammocrypta bifascia;continental-freshwater fishes;Lucania parva;Etheostoma rufilineatum;Coregonus hoyi;Catostomus ardens;Lepomis megalotis;Hemitremia flammea;Etheostoma barrenense;Hypentelium nigricans;Lythrurus umbratilis;Dionda nigrotaeniata;Etheostoma douglasi;Salmo salar;Etheostoma jessiae;Noturus stanauli;Poeciliopsis occidentalis;Dionda diaboli;Gila seminuda;Etheostoma squamiceps;Noturus flavus;Etheostoma aquali;Gila boraxobius;Notropis amplamala;Notropis chalybaeus;Percina vigil;Archoplites interruptus;Etheostoma crossopterum;Luxilus chrysocephalus;Notropis simus;Campostoma oligolepis;Pimephales promelas;Campostoma anomalum;Cyprinella whipplei;Hybopsis hypsinotus;Pteronotropis euryzonus;Etheostoma euzonum;Pararhinichthys bowersi;Lythrurus atrapiculus;Etheostoma sitikuense;Erimyzon sucetta;Acipenser transmontanus;Noturus placidus;Salvelinus alpinus;Macrhybopsis tetranema;Etheostoma parvipinne;Notropis rupestris;Cottus leiopomus;Lythrurus matutinus;Nocomis biguttatus;Oncorhynchus kisutch;Micropterus salmoides;Moxostoma macrolepidotum;Salvelinus agassizii;Cottus asperrimus;Gambusia nobilis;Catostomus catostomus;Etheostoma acuticeps;Lythrurus ardens;Percina kathae;Erimystax insignis;Etheostoma juliae;Gila pandora;Etheostoma zonale;Etheostoma neopterum;Hypentelium roanokense;Notropis leuciodus;Etheostoma nigrum;Etheostoma chlorosoma;Myoxocephalus thompsonii;Gambusia gaigei;Etheostoma camurum;Fundulus grandis;Etheostoma derivativum;Percopsis omiscomaycus;Menidia audens;Platygobio gracilis;Hiodon alosoides;Catostomus bernardini;Notropis oxyrhynchus;fish biogeography;Moxostoma austrinum;Percina nevisense;Noturus maydeni;Micropterus treculii;Nocomis platyrhynchus;Notropis volucellus;Etheostoma simoterum;Percina carbonaria;Noturus phaeus;Empetrichthys latos;Noturus albater;Percina stictogaster;Etheostoma cervus;Moxostoma cervinum;Lepidomeda aliciae;Ammocrypta pellucida;Catostomus fumeiventris;Percina aurantiaca;Luxilus cornutus;Fundulus stellifer;Fundulus kansae;Ammocrypta clara;Cottus klamathensis;Cyprinodon macularius;Hypentelium etowanum;Etheostoma osburni;Etheostoma spectabile;Etheostoma variatum;Etheostoma flabellare;Gobiomorus dormitor;Morone saxatilis;Fundulus lineolatus;Phoxinus cumberlandensis;Agosia chrysogaster;Micropterus dolomieu;Pteronotropis stonei;Agonostomus monticola;Notropis chrosomus;Etheostoma corona;Percina uranidea;Etheostoma microperca;Strongylura marina;Trinectes maculatus;Notropis stramineus;Semotilus corporalis;Esox lucius;Semotilus lumbee;Hybopsis rubrifrons;Etheostoma duryi;Gila nigrescens;Notropis xaenocephalus;Noturus gyrinus;Etheostoma pallididorsum;Fundulus nottii;Etheostoma kennicotti;Ameiurus natalis;Noturus fasciatus;Etheostoma hopkinsi;Gambusia geiseri;Acipenser fulvescens;Phoxinus eos;Etheostoma luteovinctum;Etheostoma sanguifluum;Heterandria formosa;Fundulus escambiae;Notropis atrocaudalis;Notropis atherinoides;Etheostoma podostemone;Etheostoma fragi;Catostomus tahoensis;Cyprinella caerulea;Cyprinella leedsi;Morone americana;Notropis ortenburgeri;Elassoma evergladei;Etheostoma etowahae;Etheostoma coosae;peripheral-freshwater fishes;Notropis dorsalis;Percina kusha;Fundulus cingulatus;Catostomus commersonii;Notropis melanostomus;Gambusia affinis;Catostomus insignis;Fundulus zebrinus;Cottus echinatus;Couesius plumbeus;Noturus exilis;Dionda argentosa;Micropterus coosae;Lampetra lethophaga;Ambloplites ariommus;Coregonus artedi;Oncorhynchus gilae;Catostomus platyrhynchus;Elassoma zonatum;Noturus miurus;Lampetra tridentata;Etheostoma barbouri;Percina aurolineata;Coregonus zenithicus;Macrhybopsis gelida;Percopsis transmontana;Etheostoma histrio;Amblyopsis rosae;Percina lenticula;Ichthyomyzon gagei;Moxostoma carinatum;Gambusia amistadensis;Ariopsis felis;Etheostoma davisoni;Etheostoma edwini;Cyprinella proserpina;Enneacanthus obesus;Cottus baileyi;Notropis buccula;Moxostoma erythrurum;Etheostoma scotti;Gila coerulea;Percina williamsi;Notropis cahabae;Ameiurus brunneus;Exoglossum maxillingua;Elassoma gilberti;Phoxinus oreas;Macrhybopsis meeki;Nocomis raneyi;Etheostoma forbesi;Erimystax cahni;Cyprinella analostana;Etheostoma lachneri;Lythrurus bellus;Noturus munitus;Ambloplites rupestris;Lepomis auritus;Pimephales tenellus;Coregonus hubbsi;Noturus insignis;Notropis lutipinnis;Noturus taylori;Hybognathus amarus;Percina tanasi;Ictalurus punctatus;Gambusia heterochir;Notropis asperifrons;Cyprinodon variegatus;Cottus princeps;Gila cypha;Lavinia symmetricus;Ichthyomyzon bdellium;Etheostoma bison;Etheostoma fonticola;Etheostoma inscriptum;Gambusia clarkhubbsi;Noturus hildebrandi;Opsopoeodus emiliae;Etheostoma tuscumbia;Etheostoma flavum;Macrhybopsis storeriana;Etheostoma thalassinum;Cyprinella pyrrhomelas;Sander vitreus;Etheostoma gutselli;Gambusia speciosa;Notropis greenei;Etheostoma akatulo;Etheostoma striatulum;Exoglossum laurae;Moxostoma pisolabrum;Umbra pygmaea;Cyprinella lepida;Notropis topeka;Minytrema melanops;Nocomis micropogon;Etheostoma ramseyi;Etheostoma denoncourti;Nocomis asper;Notropis rubricroceus;Catostomus macrocheilus;Ameiurus serracanthus;Lepidomeda albivallis;Etheostoma lemniscatum;Notropis stilbius;Anguilla rostrata;Ictiobus niger;Cyprinella lutrensis;Dionda serena;Fundulus catenatus;Percina notogramma;Erimyzon oblongus;Gambusia georgei;Etheostoma radiosum;Catostomus plebeius;Erimystax harryi;Elassoma boehlkei;Culaea inconstans;Erimystax dissimilis;Lepomis gibbosus;Luxilus zonatus;Notropis ariommus;Lepidomeda altivelis;Fundulus olivaceus;Percina evides;Pteronotropis hubbsi;Notropis heterodon;Etheostoma baileyi;Acrocheilus alutaceus;Pteronotropis metallicus;Ichthyomyzon unicuspis;Cottus extensus;Percina antesella;Phoxinus neogaeus;Pimephales notatus;Percina oxyrhynchus;Lampetra aepyptera;Hypomesus transpacificus;Cyprinella xaenura;Cottus asper;Etheostoma meadiae;Ptychocheilus oregonensis;Noturus baileyi;Noturus furiosus;Enneacanthus gloriosus;Salvelinus confluentus;Notemigonus crysoleucas;Orthodon microlepidotus;Percina peltata;Catostomus santaanae;Etheostoma zonistium;Ictiobus cyprinellus;Cyprinodon eximius;Carpiodes velifer;Etheostoma blennioides
DOI：
doi:10.5061/dryad.49n4k
摘要：
Although the conterminous USA has a long history of ichthyological exploration, the description of biogeographical provinces has been ad hoc. In this study we quantitatively determined fish faunal provinces and interpreted them in the context of the geological history of North America. We also evaluated influences of major river basin occupancy and contemporary environmental factors on provincial patterns. Our data set comprised 794 native fishes, which we used to generate a presence and absence matrix for U.S. Geological Survey (USGS) four-digit hydrologic units. Three nested data sets were analysed separately: primary freshwater families, continental freshwater families (including primary and secondary families) and all freshwater families (including primary, secondary and peripheral families). We used clustering analysis to delimit faunal breaks and one-way analysis of similarity (ANOSIM) to determine significance among clusters (i.e. provinces). We used an indicator-species analysis to identify species that contributed most to province delineations and a similarity-percentage (SIMPER) analysis to describe the relative influence of representatives from each category (i.e. primary, secondary, peripheral) on provincial boundaries. Lastly, we used a parsimony redundancy analysis to determine the roles of historical (i.e. major river basin) and contemporary environmental factors in shaping provinces. Analysis of the nested data sets revealed lessening provincial structure with inclusion of more families. There were 10 primary freshwater provinces, 9 continental freshwater provinces and 7 all freshwater provinces. Major basin occupancy, but not contemporary environmental factors, explained substantial variance in faunal similarities among provinces. However, provincial boundaries did not conform strictly to modern river basins, but reflected river-drainage connections of the Quaternary. Provinces represent broad-scale patterns of endemism and provide a starting point for future studies. Relative malleability of province boundaries in the continental interior highlights this region as biogeographically diverse and dynamic. Interior-core provinces of this region (Central Gulf Coastal Plains, Northern Interior) have not been recognized previously and warrant further study.
