the payara , hydrolycus scomberoides , is a species of dogtooth tetra .

this predatory fish is found in the amazon basin , where the tapajós river appears to the eastern limits of its range .

it was the first of four species to be described in the genus hydrolycus .

payara

payara foundation is the home for payara server’s and payara micro’s code and documentation .
payara foundation relies on the payara community for contributions to the payara server source code and documentation .
payara micro maven plugin has three goals ; payara - micro : bundle , payara - micro : start and payara - micro : stop .
to use payara micro is very easy . now payara micro is integrated with any ides by using payara micro maven plugin .
updated repository for payara dockerfiles . this repository is for the full profile of payara server .
payara server & payara micro docker images are available for you to download from the docker hub .
glassfish is a trademark of the eclipse foundation . payara is a trademark of the payara foundation .
you get exclusive access to extensively tested , fully supported binary builds of payara server and payara micro .
payara foundation is a uk not for profit organisation that organises the development and promotion of payara server .
previously , there is a problem that it ' s difficult to develop applications for payara micro without payara server because no ides support payara micro directly . now it has solved to use payara micro maven plugin .
payara server 5 development is coordinated by the payara foundation , a uk not - for - profit organisation .
you can now watch ondrej mihalyi , payara support engineer and steve millidge , payara ceo talks from . . .
you will benefit from payara’s partnership with azul , providing you with access to use zulu enterprise - fully - supported builds of openjdk - with payara server and payara micro .
you get exclusive access to monthly releases of payara server and payara micro including crucial fixes and patches via the features stream .
you can request specific fixes to be backported to the version of payara server and payara micro you use in production where possible .
multibytecode ( charset = cp 932 ) is included in domain . xml . · issue # 1827 · payara / payara · github
using payara support is also a vital form of contribution towards payara server development . our customers ' support subscriptions fund development and engineering effort of the payara server open source project - we would not be able to make the continuous improvements to payara server without their help ! to find out more about the payara support download our brochure here .
github - payara / payara : payara server is an open source middleware platform that supports reliable and secure deployments of java ee ( jakarta ee ) applications in any environment : on premise , in the cloud or hybrid .
payara 172 has various new features that are highly cloud - focused . a part of them , payara micro maven plugin is provided . it ' s a small but useful tools to develop applications running on payara micro .
© payara 2018 . all rights reserved . java & java ee are registered trademarks of oracle and / or its affiliates . glassfish is a registered trademark of eclipse foundation . payara and its logos are a trademark of payara foundation .
i’m very satisfied with the speediness and quality of replies from the payara’s support team .
our commercial support services give you 24 hour support for your production payara server environment .
the payara is featured in the first season of the animal planet show river monsters .
link to core documentation is broken + description looks outdated . - payara server · gitbook
payara ( cynodontidae et al . ) id and care guide 2 . 01 | urltoken
raise tickets for bugs , incidents or questions related to payara server or payara micro , including any general questions you may have about configuration , deployment , security , monitoring and troubleshooting .
goal payara - micro : start doesn ' t use uber jar in default . the goal supports various option of payara micro , thus it ' s not specified to uber jar .
if you want to know more information , see payara micro maven plugin ' s page .
the second is uber jar . we may run it either on cli directly or via the plugin ' s goals ; payara - micro : start and payara - micro : stop . the way to use the plugin can be integrated with any ides , so we ' re able to develop applications for payara micro easily even if we don ' t use payara server .
payara foundation is a not - for - profit with the mission to ensure the continued development and maintenance of payara server as open source software for the benefit of its community of users .
yes - payara will swim in schools of 6 or more in a very , very large space .
itac software is happy with the level of commercial support payara has provided to our company since 2015 . all tickets raised were fast resolved , we are certainly pleased with the payara developers ' team reaction time .
the payara is almost identical in appearance to its close relative the sabertooth characin hydrolycus armatus , but the payara is almost twice as large . the payara can also be distinguished from its cousin by a small circular dark spot on its gill cover , while the same marking on h . armatus is more of a bar shape .
we are a dedicated team of professionals devoted to open source , java , our customers , and the community . we are major contributors to the development and engineering effort of the payara server open source project and the payara foundation .
we are a dedicated team of professionals devoted to open source , java , our customers , and the community . we are major contributors to the development and engineering effort of the payara server open source project and the payara foundation .
1 unit = 1 payara server java virtual machine ( jvm ) , das or instance . 1 unit = 5 payara micro java virtual machines ( jvms ) . 1 unit = 6 cpu cores . cores can be physical or virtual .
we take glassfish , support it , add fixes , add enhancements and we release it as open source payara server .
there are also many types of frozen fishes that are very suitable for inclusion in the diet of tanked payara . since payara are more often sold as juveniles , common silversides work extremely well as a staple food fish due to their smaller size . of course , as the payara grow , their food will have to increase in size and quantity , too .
payara baits payara feed on a number of baitfish , and i imagine most fish found in their area that are small enough to get in their mouths would work . where to get the big payara they are only found in the amazon . venezuela has historically had the best fishery for big ones at uraima falls but that has become a much dicier destination due to safety concerns . columbia , peru , and bolivia all have good fisheries , and bolivia is where i caught the fish pictured . other payara resources these guys are the best in the business at putting people on payara : urltoken , urltoken
the support team replies are speedy and the payara engineers are always happy to go the extra mile to clarify a query .
see here for all versions of payara server including tar . gz format , web profile , embedded and multi - language .
we have added full jcache support , enhanced jbatch functionality , replaced shoal with hazelcast for session clustering and are driving development of payara micro . a completely new way of running war applications on top of an embedded glassfish core , payara micro is ideally suited to cloud and microservice architectures with elastic clustering and no installation . payara micro can run war applications simply , using :
we have to create a war file before run payara - micro : bundle . the goal assumes the war file exists .
irving , texas - - ( business wire ) - - exxon mobil corporation ( nyse : xom ) today announced it has discovered additional oil in the payara reservoir offshore guyana , increasing the total payara discovery to approximately 500 million oil - equivalent barrels .
payara server 5 is a patched , enhanced , and supported application server derived from glassfish server open source edition 5 . x .
the following example dockerfile will build an image that starts payara server and deploys myapplication . war when the docker container is started :
a hot fix is a patched module , or modules , of payara server which we can provide to you if an urgent solution is required . these personalized fixes enable you to get a rapid problem solution for your current version of payara server running in production .
the payara is a large , difficult fish to keep . the biggest concerns with the payara are lack of space and food , and providing pristine water that is highly oxygenated . even if these needs are met , payara mysteriously do not survive long in captivity . they often live only for 6 months to a year , with only a few reports of keeping them for up to 2 years .
the payara ' s diet mainly consist of smaller fish ; they impale other fish with their sharp teeth and consume them . in the
payara is a large fish species found in the amazon river basin and that is a popular fish among sport fishers . payara fishing allures a relatively large number of tourists to different fast moving waters in their natural habitats in brazil , bolivia , peru , ecuador and venezuela .
payara micro , compatible with eclipse microprofile , is perfect for microservice and cloud environments . this microservices - ready version of payara server enables you to run war files from the command line without any application server installation . it is small , less than 70mb in size , and incredibly simple to use . with its automatic and elastic clustering , payara micro is designed for running java ee applications in a modern virtualized infrastructure .
we received guidance through professional support on payara server clustering features as web session and ejb which contributed to a quick resolution of our issue .
payara server is a fully supported , developer - friendly , open source application server . payara server’s architecture is innovative , cloud - native and optimized for production deployments . the application server , compatible with eclipse microprofile , is built and supported by a team of devops engineers dedicated to the continued development and maintenance of the open source software and committed to optimizing payara server as the best option for production java ee applications .
you will receive full support for a growing number of payara integration components including maven plugins , cloud connectors , docker images and ide connectors .
the docker container specifies the default entry point , which starts the default domain domain1 in foreground so that payara server becomes the main process .
in default , this plugin uses payara micro 4 . 1 . 1 . 171 . unfortunately , this version cannot run on windows platform because of its bug . ( therefore payara micro 4 . 1 . 1 . 171 . 0 . 1 was released instead of it . )
payara can reach a length of 120 cm or 47 inch and a weight of 18 kg ( 40 pounds ) they are extremely aggressive predatory fish that is found in fast moving water and rapids . payara fish are capable of eating fish that are half their own body size .
the payara are mainly known as a game fish and are prized by fisherman for their fighting ability . this is a member of the cynodontidae family , which are called sabre toothed tiger fish , dogtooth characins , or dogteeth tetras . the hydrolycus genus consists of four species . collectively , they are called pirandirá or payara . its common names are vampire tetra , vampire characin , payara characin , and sabre toothed tiger fish .
feed your payara feeder fish and other live food . make sure to offer them a varied diet . you can often teach your payara to accept dead food such as frozen food and pieces of fish and it is sometimes possible to teach them to accept pellets although this isn’t always the case .
the payara ' s most noticeable feature is the two long fangs protruding from its lower jaw . these fangs can be 4 to 6 inches long .
payara fish usually hunts in open water rather then at the surface so sinking fish lures such as spoon and jigs are the best choice . make sure that you have enough line on your reel when fishing this fish since a payara easily can peel of up to 150 yards of line in the first few seconds of the fight . payara are usually fished on a catch and release basic since larger specimens today are becoming quite rare in many waters .
the default entry point starts the server in the domain1 domain . if you want to start it with a different domain , e . g . payaradomain , you may provide the domain name in the payara _ domain environment variable . the following would start payara server in payaradomain , without changing the entry point :
there are a lot of smaller payara and peixe - cachorro species present in the same areas and these usually makes better aquarium fish for the normal aquarist .
payara micro 172 or later , it shows urls and rest endpoints in the end of starting log . so we ' re able to obtain the paths definitely .
the payara developer support service has been relevant to us not only in terms of sorting out issues but it has also contributed to expand our knowledge about the server .
it best not too . that fish is a threat to other fish and even bigger fish . you can learn more info at payara , social behaviors . : )
payara fish is mainly suitable for public aquariums and is not suitable to be kept in private aquariums unless their demand for space and fast moving water can be meet and most aquarist are not capable of meeting the requirements . a payara requires a very large aquarium or a large pond . i would not recommend keeping them in aquarium tanks / ponds smaller then 500 gallons ( 2000 l ) due to their size and even then it might be impossible to keep more then one payara due to their aggressiveness . i can however vouch for the fact that a payara fish makes a fascinating addition to any aquarium large enough to house them even if i haven’t had the pleasure to keep one myself .
in order to deploy applications , you can mount the $ deploy _ dir ( / opt / payara41 / deployments ) folder as a docker volume to a directory , which contains your applications . the following will run payara server in the docker and will start applications that exist in the directory ~ / payara / apps on the local file - system :
it’s regularly confused with the payara , h . armatus , though that species grows considerably larger , is popular with sports anglers and unsuitable for all but the very largest home aquaria .
“payara - 2 confirms the second giant field discovered in guyana , ” said steve greenlee , president of exxonmobil exploration company . “payara , liza and the adjacent satellite discoveries at snoek and liza deep will provide the foundation for world class oil developments and deliver substantial benefits to guyana . we are committed to continue to evaluate the full potential of the stabroek block . ”
payara server is an open source middleware platform that supports reliable and secure deployments of java ee ( jakarta ee ) applications in any environment : on premise , in the cloud or hybrid .
this microservices - ready version of payara server is perfect for cloud environments . compatible with eclipse microprofile 1 . 2 , small ( < 70mb ) and incredibly simple to use , it enables you to run war files from the command line without any application server installation . with its automatic and elastic clustering , payara micro is designed for running java ee applications in a modern virtualized infrastructure .
the well was successfully drilled by exxonmobil affiliate esso exploration and production guyana limited and encountered 59 feet ( 18 meters ) of high - quality , oil - bearing sandstone in the payara field .
payara server is a patched , enhanced and supported application server derived from glassfish server open source edition 4 . x . visit urltoken for full 24 / 7 support and lots of free resources .
latest version of payara micro maven plugin is 1 . 0 . 0 - snapshot , thus it ' s not on maven central repository . at first we check out from github and build it .
payara are as earlier mentioned much appreciated sport fish due to the impressive fights they put up . payara fish is usually considered to be one of the fiercest struggling freshwater fishes , offering a larger fight then other popular fishes from the area such as peacock bass . they also add to the sport of catching them by jumping up and down out of the water in a similar way to salmon .
since version 172 , payara server supports running asadmin commands automatically after the domain is started , including the deploy command to deploy applications . this is the preferred way to deploy applications on docker container startup .
< build > < plugins > < ! - - snip - - > < plugin > < groupid > fish . payara . maven . plugins < / groupid > < artifactid > payara - micro - maven - plugin < / artifactid > < version > 1 . 0 . 0 - snapshot < / version > < / plugin > < ! - - snip - - > < / plugins > < / build >
when running the domain1 domain , payara server automatically deploys all deployable files in the directory specified by the $ autodeploy _ dir environment variable ( it refers to the autodeploy directory in the domain directory of domain1 ) .
because basically those are still young juvenile as an adult sabre tooth tetra can actually reach maximum length of 26 inches . there are also different variants of the fish and the most popular is the red tailed payara .
payara server 5 is a drop in replacement for glassfish server open source with the peace of mind of quarterly releases containing enhancements , bug fixes and patches including patches to dependent libraries , as required , including tyrus , eclipse link , jersey and others . our vision is to optimise payara server and make it the best server for production java applications with responsive 24 / 7 dedicated incident and software support from the best middleware engineers in the industry .
large catfishes should be excluded from a setup containing payara , as their nighttime forays will inadvertently freak out the payara and perhaps cause them to damage themselves by slamming into the tank’s glass , canopy , and decorations , as well as into other fishes . that having been said , though , i did see one nice display of h . armatus that contained several large pleco - type sucker - mouth catfish . needless to say , the tank was spotless !
our global team of specialist payara server support engineers delivers 24 / 7 production , development & migration support directly to our customers worldwide . when our customers need support – they get it straight from the engineers rather than an outsourced help desk employee .
payara are characins belonging to the subfamily cynodontinae , the root of which literally translates from latin into “dogtooth” in english . they are capable of exceeding 3 feet in total length and nearly 40 pounds in overall weight—now that’s a big , toothy tetra !
this runs goal payara - micro : bundle with goal install . so that we may do only one step ` mvn install ` to build an application and create uber jar . ( i think it ' s very useful , don ' t you ? )
payara generally do very poorly in aquariums that have bad water quality . on the whole , payara are very sensitive to water containing a high level of dissolved metabolites . i have found , through trial and error , that the best way to maintain proper water quality is to perform very large and very frequent water changes . never change a large percentage of water and clean the filter at the same time , however , as doing so will surely destroy too much of the beneficial bacteria colony , resulting in the aquarium becoming unbalanced . an unbalanced aquarium will have rising and falling levels of toxic compounds , such as ammonia , ammonium , and nitrites . payara that are exposed to these compounds will often break out in lesions , which quickly become infected and may lead to death .
if you do want to try and keep tankmates with payara , there are a few species that i have seen work . first are some of the larger barbs , like spanner or tinfoil barbs . silver dollars seem to work well , too . some folks have kept large peacock bass in with their payara , but i fear that the peacock bass are too aggressive when it comes to feeding time , thus i would hesitate to house them together . the same is true for other large cichlids , like wolf cichlids or oscars .
this microservices - ready version of payara server is perfect for cloud environments . compatible with eclipse microprofile 1 . 2 , small ( < 70mb ) and incredibly simple to use , it enables you to run war files from the command line without any application server installation .
the ph , hardness , and alkalinity of an aquarium containing payara are not nearly as critical , so long as extremes are avoided . a general ph of 7 ( neutral ) is good . hardness and alkalinity measuring in the “moderate” range is perfectly acceptable as well .
the enlarged canine teeth exhibited by payara enable them to trap their prey , thus allowing them to hold onto the fish until they can be positioned safely for ingestion , which occurs whole and head - first . only rarely are the eaten fishes actually punctured by the huge canines , but rather are held behind them before being swallowed . in aquariums , payara are more likely to just swallow the fish whole without employing this holding action ; perhaps in absence of a strong current , the need to hold their prey firmly is greatly reduced .
the support provided by payara has always been appropriate to the severity level of issues reported by bmw group . out - of - cycle patches were provided for more important issues which helped to fix problems in a short amount of time . regardless of where the root cause of the problem is located , either in payara server source code or application source code , the support team helped to find a solution and resolve the issue . bmw group has found that all major blocking issues have been resolved and newly found bugs are dealt with appropriately .
size information is wrong . hydrolycus scomb . is the smallest of the four payara species . h . armatus being the largest ( reaching 4’ + in the wild and 2’ + in aquariums ) . i have personally owned both species , and still own my hydrolycus armatus .
in the wild , payara are often seen in groups , but in captivity , they tend to become belligerent towards their own species when kept in small groups . they can be kept in a school of 6 or more in a very , very large space or singly .
this fish will not survive if it feels crowded , so even though other large fish , such as a pacu or large catfish , will probably be able to survive in the same tank , the payara will do better if kept in a single species , single specimen tank .
just a quick glance at their teeth should tell you that payara are obviously carnivorous by nature , and specifically they are considered piscivorous—that is , they eat fishes . in aquariums , and as with all types of predatory fishes , it is best to attempt to convert these predators to a diet of non - living foods . today we are blessed with a variety of various types of fresh and frozen foods like never before . i cannot stress enough the importance of converting payara to a diet of fresh smelt , mackerel , or other type of non - living food fish .
payara server installation is located in the / opt / payara41 directory . this directory is the default working directory of the docker image . the directory name is deliberately free of any versioning so that any scripts written to work with one version can be seamlessly migrated to the latest docker image .
payara are extremely difficult to keep . these large predacious fish are best cared for in public aquariums or by the most experienced fish keepers with the space , financial ability , and dedication to care for them . they sometimes refuse food in captivity , and once feeding , need a varied diet of fish .
i would like to thank paul reiss of acute angling for providing top - shelf information from first - hand knowledge of payara in their native waters , and i would like to extend a special thanks to the fine members of urltoken for their continued support and helpful knowledge about the predators covered in my column .
payara or vampire characin are not exactly rare , but smaller , aquarium - sized specimens are hard to find . when shipped from south america , they take up a lot of space , which makes shipping costs high . if you are lucky enough to find one for sale , the price will be high .
in his career as a producer and host of hunting and fishing shows for cable television , trevor gowdy has tangled with a wide range of trophy game fish , including 1 , 000 - pound hammerheads in the florida keys , giant stingrays off the coast of thailand and razor - toothed payara below venezuela’s uraima falls .
after you have converted your payara to feed on non - living whole fishes , the next step is to get them to consume a variety of other forms of seafood . i have used chopped squid , clam , and fish flesh with good success over the years . but i should also mention here that i primarily have kept the sister species h . scomberoides , which is a smaller , more aquarium - tolerant species of payara that should not be confused with the mighty h . armatus . regardless , the care of h . scomberoides is nearly identical to that of its bigger cousin—only with h . armatus everything must be much , much larger !
because payara server doesn ' t allow insecure remote admin connections ( outside of a docker container ) , the admin interface is secured by default ( in both the default domain1 as well as payaradomain ) , accessible using https on the host machine : https : / / localhost : 4848 the default user and password is admin .
tankmates are probably a no - no on a long - term basis . sure , while h . armatus is young it will be fine , as long as the tankmates cannot be swallowed and are not overly aggressive to the point that the payara stress out from their presence . i tend to err on the side of caution , however , and fear that tankmates will cause more harm than good with these fish—especially at the going rate for h . armatus these days ! don’t get me wrong , plenty of people keep payara with other fishes and have zero problems , i just prefer to maintain them in a single - species , single - specimen type of aquarium setup .
payara are carnivorous piscivores . they only eat live foods , and they love fish , preferably live ones . appropriate aquarium fare includes live foods such as feeder fish , earthworms , and river shrimps . these fish could probably be trained to eat whole dead fish , such as frozen silversides and lancefish , but this has not been confirmed .
payara are true giants in the fish world . known more as game fish than aquarium fish in their native waters , these fascinating creatures are a sight to behold in a large display aquarium . they grow to immense proportions and consume only meaty foods , but their care is easy so long as the basics are afforded to them . while volumes can be written about this interesting and exciting group of fishes , it simply cannot be done here . i invite you to visit one of the fine internet discussion forums advertised in this column for more information on these fishes and to speak to other hobbyists who are just as interested in learning all there is to know about the venerable payara .
as strategic members of the eclipse foundation , we invest our resources and expertise to improve , innovate and develop open source technologies . we are involved in shaping the future of the industry via our direct contribution to eclipse jakarta ee ( payara’s director , steve millidge , is a project management committee member ) , eclipse microprofile , eclipse ide and many other projects .
< build > < plugins > < ! - - snip - - > < plugin > < groupid > fish . payara . maven . plugins < / groupid > < artifactid > payara - micro - maven - plugin < / artifactid > < version > 1 . 0 . 0 - snapshot < / version > < executions > < execution > < goals > < goal > bundle < / goal > < / goals > < / execution > < / executions > < configuration > < payaraversion > 4 . 1 . 2 . 172 < / payaraversion > < useuberjar > true < / useuberjar > < / configuration > < / plugin > < ! - - snip - - > < / plugins > < / build >
payara are found in south america in the rio amazonas and its tributaries above the mouth of rio tapajós as well as in the orinoco river in venezuela . they inhabit clean , fast - flowing rivers where the water is turbulent , including rapids and at the bottom of waterfalls . they are often found in loose groups and feed on smaller fish , but the bulk of their diet consists of piranhas .
species . however , the payara are a migratory fish and begin reproduction with the onset of the rainy season . they move from lakes and river channels into the rising waters of large rivers , migrating long distances upstream for spawning and feeding . presumably , it would be difficult to impossible breed them in an aquarium and would require a very large tank . for a description of breeding characin fish , see
the ideal tank for payara is one that has minimal decorations , as these fish will often strike them while in pursuit of prey—especially if offered live fishes as feeders . the tank should have the sides and back painted black , or at least dark in color . this will bring out the fish’s best colors . payara tend to inhabit deeper waters , so they are not accustomed to overly bright light , which may stress them in the ultra - clear water of an aquarium . speaking of lighting , the tank’s illumination should be minimal and only afford the hobbyist to see sections of the tank clearly , which is generally referred to as “spotlighting . ” several very large enclosures that i have seen have utilized this illumination technique ; it is really effective , visually speaking , and the fish seem to do very well with it .
the payara can reach up to almost 4 feet ( 117 cm ) in length and weigh just over 39 pounds ( 17 . 8 kg ) in the wild . in captivity , it is unlikely to reach more than about 12 inches ( 75 cm ) . its body is an iridescent silver , and its fins are semi - transparent , tinged with black towards the outer portions , and sometimes spotted with white .
is a remarkable characin , but it is not your typical tetra . one look at the mouth of this fish and there will be no doubt that the payara is a vicious carnivore . this incredible fish has two large fangs on its lower jaw . these fangs can be 4 to 6 inches long . in fact , the two main lower teeth are so long that upper jaw has holes for them to fit into .
was described by cuvier in 1819 . the species is not listed on the iucn red list . other common names for this species are vampire tetra , vampire characin , vampire fish , cachorra , and chambira . the genus , which consists of four species , is collectively known as pirandirá or payara . as members of the cynodontidae family , they are known as sabre toothed tiger fish , dogtooth characin , or dogteeth tetra .
the payara ' s elongated body is streamlined and very powerful . it tapers towards the tail and has a large , fan - shaped caudal fin . the head is large with a prominent , upturned mouth full of needle - sharp teeth and two long fangs . the two main lower teeth are so long that the upper jaw has holes for them to fit into . these fangs can be 4 to 6 inches long !
a payara aquarium should be decorated with large rocks and large pieces of bogwood to create hiding places for these fishes . plants are not required since plants are unusual in the fast moving waters they normally live in , in the wild . the aquarium should be very well circulated and you can not create to much water movement for these fishes as long as they are provided with a few large rocks behind which to rest .
the group collectively known as payara contains several species , but i will only be covering the venerable hydrolycus armatus in this article . the largest of the clan , h . armatus is capable of growing to more than 3 feet in total length , thus making it a very highly sought - after food and game fish in its native waters of northern south america—specifically the rio orinoco drainage and the vast , winding rivers of the guyanas .
h . armatus is a powerful , sleek , and fast - moving species that is adept at living in several habitats across its native range . paul reiss , a well - known professional fisherman and the owner and operator of acute angling , reports that payara are most commonly found in extremely fast - flowing water . in aquariums , we have found that they do not necessarily need such strong current in order to thrive , but they do prefer water that has some degree of turbulence to it .
these fish often only survive for 6 months to a year , with just a few having been reported as living up to 2 years . their short lifespan may be a result of a large bio load , resulting in nitrogenous waste . an extremely large aquarium is necessary to support a school of payara , and as they mature , their habitat requirements change . juveniles may live in less turbulent water , but adults are found in fast - moving currents , like rapids and the base of waterfalls .
one of the most striking displays that i have ever seen was a very large aquarium in germany , probably somewhere in the range of 2000 or 3000 gallons . the tank contained a single h . armatus and several huge , fully mature river stingrays . it had a deep sandbed and dim lighting . the payara was like a ghost swimming in and out of the shadows . i remember being surprised to see how little current there was in the tank , but the fish were all very healthy and flawless in condition .
as strategic members of the eclipse foundation , the payara team is dedicated to helping shape the future of open source . our involvement allows us to support the sustainability of the community , participate in marketing programs , and have direct access to the governance of both the jakarta ee working group and the eclipse foundation . as active committers to the eclipse microprofile initiative we are also contributing to optimizing enterprise java for microservices architectures to help enterprises make their journey into the cloud , working closely with customers to shape jakarta ee to meet their future needs .
the payara , which is also sold as the saber tooth barracuda , vampire fish , vampire tetra , or saber tusk barracuda , is a popular species for large , aggressive aquariums . it can grow large enough to outgrow a lot of fish tanks , which presents a problem to the uneducated aquarist . it is recommended that they be fed live food , such as goldfish . they should be kept with fish that they cannot fit in their mouths , for example : siamese tigerfish , arowanas , gars , pacus , catfish , and pig - nosed turtle .
they are easily frightened so you must be careful not to make any quick movements when around their tank . payara have been known to fatally injure themselves by swimming into the sides of the aquarium when disturbed . it helps to cover the sides and back of the tank with either a dark aquarium background or paint them with a dark color . an overly bright light will also stress them out , so keep the lighting moderate and have some areas that are dim . a more subdued lighting coupled with a dark backdrop will bring out their best coloring too .
the payara is an extremely large predatory fish . because of their large adult size , and their propensity for schooling as juveniles , they need a very large aquarium . when first purchased as small juveniles , they may initially be kept in a large home aquarium . but eventually , be prepared to invest in a tank of 500 gallons or more with a better - than - average filter system . they require excellent water quality , and it must be well oxygenated . younger specimens may be fine with moderate water movement , but adults need strong , turbulent currents .
payara are fast and aggressive feeders . these fish usually swallow their prey whole but will sometimes chop them into smaller , bite - sized pieces . they get large , too , so if you want to keep one as a pet , be prepared to have a very high feeder - fish bill . in fact , it can grow to about twice the size of its almost identical looking relative , the sabertooth characin hydrolycus armatus . this fish can reach up to about 4 feet ( 117 cm ) in length and weigh up to 40 lbs ( 18 kg ) , though aquarium specimens are usually only reach a quarter of that size , around 12 inches .
the vampire tetra can be kept in a large aquarium , but it takes a lot of work by a very advanced hobbyist to accomplish this . they are occasionally available and will readily adapt to aquarium life , but they are most often short - lived . they often only survive for 6 months to a year in captivity , with just a few having been reported as living up to 2 years . their short lifespan is due , in part , to their diet and their need for a top quality environment . vampire characin need a varied diet , so just feeding them goldfish is inadequate . sometimes , payara refuse to feed . it seems that once they reach about 12 inches , they mysteriously die .
my first experiences with payara were some 20 years ago now ( i can’t believe i am even old enough to say that ! ) . anyway , i can remember cruising through the aisles of my favorite pet shops , and once in a while i would come across these big flashy silver fish with absolutely gargantuan teeth . i remember thinking they were such ugly and nasty critters , almost freakish - looking water wolves . who on earth would want such a thing in their tank ? granted , at the time i was into barbs and smaller “community” species , and big predatory fishes were simply not an option for my 20 - gallon aquarium . fast - forward to 2006 and my , how things have changed !
i would recommend attempting to train your payara off live food at an early age . i have had better luck with them learning this at a young age . it seems the older they get the more stubborn they get . the last batch i have obtained was a pack of 5 armatus at roughly the size of a quarter . they were actually to small to even eat rosies ( or tuffies ) so they were fed guppies up until about 2 inches . at that point they were switched to rosies . kept on rosies for about another 1 - 1 . 5 inches . i believe i made a mistake in how long i fed rosies . i believe you may have better luck getting them off live if you are to start feeding goldfish as soon as they are big enough to eat them . this will greatly increase your chances in getting them to go after krill as they are both orange in color , and the shape of freeze dried krill has more in common with goldfish then a rosie does .
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despite its fearsome appearance this species does not tend to attack similarly - sized fishes .
it will eat fishes it can fit into its mouth , but there ' s no need to feed it live food in captivity .
hydrolycus : from the greek hydro , meaning ‘water’ , and lykos , meaning ‘wolf’ .
scomberoides : from the greek skombros , meaning ‘tuna , mackerel’ , and the suffix - oides , meaning ‘similar to’ .
type locality is given simply as ‘brazil’ but this species is currently understood to be widespread in the central and upper amazon river system in brazil , bolivia , peru and ecuador , with the rio tapajós in brazil appearing to mark the downstream limit of its range .
this species is pelagic and adults tend to be associated with flowing stretches of main river channels and larger tributaries of both white and black water rivers .
reproduction occurs between november and april and adults perform long upstream migrations in order to do so .
the aquarium should ideally be designed to resemble a flowing stream or river with a substrate of variably - sized rocks , sand , fine gravel , and some larger water - worn boulders .
this can be further furnished with driftwood roots and branches if you wish but be sure to leave plenty of open swimming space .
while the majority of aquatic plants will fail to thrive in such surroundings hardy genera such as microsorum , bolbitis , or anubias spp . can be grown attached to the décor .
like many fishes that naturally inhabit running waters it’s intolerant to the accumulation of organic wastes and requires spotless water at all times in order to thrive .
it also does best if there is a high proportion of dissolved oxygen and moderate degree of water movement so external filter s , powerheads , airstones , etc . , should be employed as necessary .
as stable water conditions are obligatory for its well - being this fish should never be added to biologically - immature aquaria and weekly water changes of 30 - 50 % aquarium volume should be considered mandatory .
a tightly - fitting cover is essential as this species is a prodigious jumper , and it may also prove beneficial to cover the back and sides of the aquarium in order to reduce the chances of it swimming into the glass since it can be skittish , especially in confined surroundings .
newly - imported specimens often refuse to accept anything but live fishes but most can be weaned onto dead alternatives once recognised as edible .
like the vast majority of predatory fishes this species should not be fed mammalian or avian meat like beef heart or chicken , and similarly there is no benefit in the long - term use of ‘feeder’ fish such as livebearers or small goldfish which carry with them the risk of parasite or disease introduction and at any rate tend not have a high nutritional value unless properly conditioned beforehand .
best kept alone or with similarly - sized , non - aggressive fishes since it’s actually quite peaceful with those too large to be considered food .
it can also be maintained in a group in a suitably - sized aquarium but the purchase of at least three specimens is advisable .
juveniles tend to adopt a presumably cryptic , oblique , ‘head - down’ position and lurk among the décor whereas adults are fully pelagic .
this species may be referred to using a variety of names including ‘scomb’ , ‘sabre tooth tetra’ , ‘sabre tusk barracuda’ , ‘dog tooth characin , ‘vampire fish’ , ‘cachorra’ or ‘pirandirá’ ( the latter two names being used in brazil where they’re also applied to congeners ) .
it can be told apart from all congeners by the following combination of characters : serrations present on the exposed field of scales in specimens larger than 100 mm sl ; pelvic - fin base inserted laterally , distinctly above ventral profile of body ; a black spot at the base of the innermost pectoral - fin rays .
hydrolycus can be easily - separated from other genera in the family cynodontidae by the fact that the dorsal - fin origin is located distinctly anterior to a vertical through the anal - fin origin plus the dorsoventral enlargement of the mesethmoid spine is almost round in shape from a lateral view and enlarged in hydrolycus scomberoides , h . armatus and h . tatauaia .
it’s sometimes included in the putative subfamily cynodontinae alongside cynodon and rhaphiodon , these being separated from other characiformes by a series of derived features plus their oblique mouth shape and highly - developed dentary canine teeth .
the latter fit into a pair of corresponding openings in the upper jaw which allows the mouth to be closed completely .
cynodontinae contains two primary monophyletic lineages , one comprising the genus hydrolycus and the other a clade with cynodon and rhaphiodon spp . , with members sometimes referred to collectively as ‘dogtooth characins’ .
reis , r . e . , s . o . kullander and c . j . ferraris , jr . ( eds . ) , 2003 - edipucrs , porto alegre : i - xi + 1 - 729 check list of the freshwater fishes of south and central america . cloffsca .
toledo - piza , m . , 2000 - american museum novitates 3286 : 1 - 88 the neotropical fish subfamily cynodontinae ( teleostei : ostariophysi : characiformes ) : a phylogenetic study and a revision of cynodon and rhaphiodon .
toledo - piza , m . , n . a . menezes and g . m . dos santos , 1999 - ichthyological exploration of freshwaters 10 ( 3 ) : 255 - 280 revision of the neotropical fish genus hydrolycus ( ostariophysi : cynodontinae ) with the description of two new species .
how do you keep h . armatus ? surely it needs an absolutely enormous tank ?
yes , they require truly massive specifically designed tanks . i currently have my hydrolycus armatus in a 300gal custom tank . i will be building his next home 500gal aquarium this summer .
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alviniconcha is a genus of deep water sea snails , marine gastropod mollusks in the family provannidae .

these snails are part of the fauna of the hydrothermal vents in the indian and western pacific ocean .

these and another genus and species within the same family ( ifremeria nautilei ) are the only known currently existing animals whose nutrition is derived from an endosymbiotic relationship with proteobacteria : a member of bacteria from class epsilonproteobacteria occurs as an endosymbiont of the gills of alviniconcha hessleri .

alviniconcha

provannidae » alviniconcha hessleri , id : 118698 , shell detail « shell encyclopedia , conchology , inc .
one of them , alviniconcha strummeri , is named after joe strummer , the lead singer of the clash .
the other four new species are alviniconcha kojimai , a . boucheti , a . marisindica and a . adamantis .
the mitochondrial coi gene sequences from the alviniconcha gastropods are available at the ddbj under accession numbers ab235211 to ab235227 .
“the name also recognizes the surface of alviniconcha shells : the spiky periostracum resembles the fashion of punk rock bands . ”
species alviniconcha adamantis s . b . johnson , warén , tunnicliffe , van dover , wheat , schultz & vrijenhoek , 2014
species alviniconcha boucheti s . b . johnson , warén , tunnicliffe , van dover , wheat , schultz & vrijenhoek , 2014
species alviniconcha kojimai s . b . johnson , warén , tunnicliffe , van dover , wheat , schultz & vrijenhoek , 2014
species alviniconcha strummeri s . b . johnson , warén , tunnicliffe , van dover , wheat , schultz & vrijenhoek , 2014
this spiky mollusk is called alviniconcha strummeri , named after joe strummer , the late frontman for the clash . taylor & francis online hide caption
only strummeri have been named after a musician : the other alviniconcha species get their monikers from things like research facilities and gastropod experts . “the name highlights the ‘hardcore’ nature of alviniconcha snails , that inhabit the hottest , most acidic and most sulphidic microhabitats at indo - pacific hydrothermal vents , ” researchers wrote . “the name also recognises the surface of alviniconcha shells : the spiky periostracum resembles the fashion of punk rock bands . ”
coupling of the host and endosymbiont lineages of alviniconcha gastropods showed that , although alviniconcha sp . type 2 is associated with bacterial endosymbionts from two related ε - proteobacterial lineages , each of the other alviniconcha lineages harbors bacterial endosymbionts from one distinct lineage within either the γ - or ε - proteobacteria . these host - symbiont relationships in alviniconcha gastropods could potentially be used to motivate for the recognition each host lineage as a separate species . furthermore , since alviniconcha sp . types 1 and 2 harbor γ - and ε - proteobacterial endosymbionts , respectively , and , given that they appear to exclusively inhabit adjacent hydrothermal vents in the manus and north fiji basins , then the possibility that they occupy separate ecological niches should be explored further .
novel chemoautotrophic endosymbiosis between a member of the epsilonproteobacteria and the hydrothermal - vent gastropod alviniconcha aff . hessleri ( gastropoda : provannidae ) from the indian ocean
alviniconcha kojimai , a . adamantis , a . marisindica and a . boucheti ( clockwise ) . image credit : shannon b . johnson et al .
“the name highlights the ‘hardcore’ nature of alviniconcha snails that inhabit the hottest , most acidic and most sulfidic microhabitats at indo - pacific hydrothermal vents . ”
alviniconcha strummeri is known from hydrothermal vent localities at 1 , 850 m depth in the southern lau basin , especially at the tui malila vent site .
novel chemoautotrophic endosymbiosis between a member of the epsilonproteobacteria and the hydrothermal - vent gastropod alviniconcha aff . hessleri ( gastropoda : provannidae ) from the indian ocean †
alviniconcha strummeri , a new species of deep - sea snail named after joe strummer of the clash . image credit : shannon b . johnson et al .
the principle aim of the present study was to identify and clarify the host - endosymbiont lineages of the alviniconcha gastropods from the southwest pacific ocean . in addition , we attempted to determine the nature of the carbon metabolism and the trophic relationships between alviniconcha and their endosymbionts using bulk and compound - specific carbon isotopic analyses .
worms - world register of marine species - alviniconcha strummeri s . b . johnson , warén , tunnicliffe , van dover , wheat , schultz & vrijenhoek , 2014
the alviniconcha sp . from the lau basin harbors a γ - proteobacterial endosymbiont that is phylogenetically distinct from those found in other alviniconcha lineages ( fig . 2 ) . the γ - proteobacterial endosymbiont is closely related to the endosymbiont of the “scaly - footed” hydrothermal gastropod from the central indian ridge with which it shares a sequence identity of ca . 95 % .
a group of marine biologists headed by dr robert vrijenhoek from the monterey bay aquarium research institute has described five new species of deep water alviniconcha snails from the western pacific and the indian ocean .
wittenberg , j . b . , and j . l . stein . 1995 . hemoglobin in the symbiont - harboring gill of the marine gastropod alviniconcha hessleri . biological bulletin 188 : 5 - 7 .
a snail so hardcore it ' s named after a punk rocker inspired by the snails ' spiky shells and acid - loving nature , researchers named the new species alviniconcha strummeri , after clash frontman joe strummer .
since johnson had such success in calling the spiky , acid - loving mollusks punk - rock snails , she and her colleagues decided to name them alviniconcha strummeri , after the late joe strummer , frontman for the clash .
five new alviniconcha species were collected during several expeditions ( 1993 - 2008 ) to various segments of the north fiji , lau , manus and mariana back - arc basins , the mariana volcanic arc and the central indian ridge .
hairy things aren’t just for ye landlubbers . the deep - sea is home to several hairy critters including the hairy vent snail , alviniconcha . the hairy appearance are actually spines protruding from the periostracum , a thin organic layer that coats the mineralized shell of a snail . alviniconcha ‘s shell is very thin . it is this biologist’s opinion that the spines might help keep off fouling creatures , such as drilling limpets . but no one knows for sure quite yet .
a species of deep sea snail with the bold , spiky aesthetic of early clash fans has been named after joe strummer . alviniconcha strummeri are golf ball - sized invertebrates that live around 2 , 000 metres beneath the surface of the ocean .
shannon b . johnson et al . molecular taxonomy and naming of five cryptic species of alviniconcha snails ( gastropoda : abyssochrysoidea ) from hydrothermal vents . systematics and biodiversity , published online december 3 , 2014 ; doi : 10 . 1080 / 14772000 . 2014 . 970673
denis , f . , d . jollivet , and d . moraga . 1993 . genetic separation of two allopatric populations of hydrothermal snails alviniconcha spp . ( gastropoda ) from two south western pacific back - arc basins . biochemical systematics and ecology 21 : 431 - 440 .
to better understand the phylogenetic relationships among host lineages , the upstream region of the coi gene was amplified by pcr using primers lco1490 and hco2198 ( 5 ) for each of the five host lineages : a . hessleri ( smr - 93 - 10 in reference 12 ) , alviniconcha sp . type 1 ( mb - 96 - 16 in reference 14 ) , alviniconcha sp . type 2 ( fb - 90 - 7 in reference 12 ) , alviniconcha aff . hessleri ( the first specimen in reference 11 ) , and alviniconcha sp . from the lau basin ( fig . 1 ) . the primers coi - 7 ( 20 ) and coi - d ( 16 ) were used to amplify the coi fragment of ifremeria nautilei , a member of the provannidae from the north fiji ( haplotype f4 in reference 13 ) and the manus basins ( haplotype m1 in reference 13 ) . ifremeria was used as the outgroup for phylogenetic analysis . the conditions for pcr were 94°c for 60 s , followed by 30 to 40 cycles of 92°c for 40 s , 50°c for 60 s , and 72°c for 90 s .
kojima , s . , r . segawa , y . fijiwara , k . fujikura , s . ohta , and j . hashimoto . 2001 . phylogeny of hydrothermal - vent - endemic gastropods alviniconcha spp . from the western pacific revealed by mitochondrial dna sequences . biological bulletin 200 : 298 - 304 .
phylogenetic analysis also revealed that the sequence identities between the host lineage from the lau basin specimen and the four other host lineages ranged from 88 . 3 to 91 . 6 % , which is markedly lower than the identities among these lineages themselves , which ranged from 98 . 8 to 100 % . it is therefore proposed that the gastropod from the lau basin represent a new distinct lineage in the genus alviniconcha . the finding of marked genetic differentiation in the lau basin specimen is consistent with a previous study in which 20 enzymatic systems in alviniconcha gastropods from the lau and north fiji basins were analyzed ( 1 ) .
specimens of alviniconcha sp . type 1 from the pacmanus field d in the manus basin and the white lady site in the north fiji basin were found to harbor closely related γ - proteobacterial endosymbionts ( fig . 2 ) . similarly , the sequence identities among γ - proteobacterial endosymbionts within the manus and north fiji basins were greater than 99 . 3 and 97 . 8 % , respectively . sequence identities between specimens from the two basins were greater than 97 . 7 % . the endosymbionts of alviniconcha sp . type 1 were related to free - living thiomicrospira spp . with sequence identities of less than 90 % .
kojima , s . , k . fujikura , t . okutani , and j . hashimoto . 2003 . phylogenetic relationship of alviniconcha gastropods from the indian ocean to those from the pacific ocean ( mollusca : provannidae ) revealed by nucleotide sequence of mitochondrial dna . venus ( japan journal of malacology ) 63 : 65 - 68 .
in the present study , the symbiotic relationship in alviniconcha gastropods from the southwest pacific was defined more clearly by using molecular phylogenetic analyses and carbon isotopic characterizations . further ecological and anatomical studies of these uniquely evolved gastropod assemblages might increase our understanding of the gastropod - proteobacterial endosymbioses that have been discovered in hydrothermal vent ecosystems around the globe .
phylogenetic relationships among the five alviniconcha lineages known to date . the tree was constructed by using the mp method with two lineages of ifremeria nautilei used as outgroup taxa . numbers at the branch nodes represent bootstrap values ( 1 , 000 replicates ) obtained from the mp , nj , and the ml methods ; only values greater than 50 % are indicated .
distance tree of the members of the γ - and ε - proteobacteria , as well as the alviniconcha endosymbionts based on near - complete 16s rrna gene sequences ( 1 , 160 nucleotides ) . bootstrap values ( in percent values ) are based on 1 , 000 replicates ( nj and mp ) and are shown for branches with more than 50 % bootstrap support .
alviniconcha also has blue blood due the respiratory pigment hemocyanin and carries very enlarged gills . my measurements indicate that the dry weight of the gills can get up to 21 % of the total dry mass ( excluding shell ) . for comparison , the average intertidal intertidal snail has 4 - 7 % of its total body weight devoted to the gills . this makes sense since alviniconcha has a very reduced stomach and digestive tract . it gets most , if not all , of it’s nutrition from chemoautotrophic bacteria housed in its gills .
chemoautotrophic
means that the bacteria oxidize hydrogen sulfide as an energy source , normally a toxic chemical to most animal life . but these extreme snails can bring in the goods for their bacterial helpers and thrive en masse .
alviniconcha strummeri will now vie with amaurotoma zappa , named for frank , in the collections of malacologist music fans . those who are not simply interested in snails may also pursue exemplars of the isopod cirolana mercuryi , named from freddie , jaggermeryx naida , an extinct “long - legged pig” named after mick , and myrmekiaphila neilyoungi , a spider who is apparently looking for a heart of gold .
suzuki , y . , t . sasaki , m . suzuki , y . nogi , t . miwa , k . takai , k . h . nealson , and k . horikoshi . 2005 . novel chemoautotrophic endosymbiosis between a member of the epsilonproteobacteria and the hydrothermal - vent gastropod alviniconcha aff . hessleri ( gastropoda : provannidae ) from the indian ocean . applied and environmental microbiology 71 : 5440 - 5450 .
the alviniconcha gastropods that harbor γ - proteobacterial endosymbionts have biomass δ 13 c values ranging from −30 . 0 to −30 . 7 with fatty acids depleted of 13 c relative to the biomass by 5 . 3 to 7 . 7 ( table 2 ) ; these findings are consistent with the chemoautotrophy of the calvin - benson cycle and the subsequent synthesis of fatty acids from 13 c - depleted acetyl - coa ( 21 ) . as with alvinoconcha aff . hessleri , the biomass δ 13 c value of other alviniconcha gastropods that harbor ε - proteobacterial endosymbionts have values ranging from −10 . 3 to −13 . 4 with fatty acids enriched in 13 c relative to the biomass by 2 . 9 to 7 . 3 ( table 2 ) . since the 13 c enrichment of fatty acids relative to biomass is a characteristic of fatty acid synthesis from 13 c - enriched acetyl - coa produced through the rtca cycle , the observed isotope fractionation patterns are most likely to reflect the chemoautotrophy typical of the rtca cycle . although the carbon isotopic composition of hydrothermal co 2 from the sites and enzymatic activity of key enzymes involved in the two chemoautotrophic cycles were not examined in the present study , it seems likely that the γ - and ε - proteobacterial alviniconcha endosymbionts assayed in the present study are chemoautotrophs that convert co 2 into organic matter via the calvin - benson and rtca cycles , respectively .
suzuki , y . , s . kojima , t . sasaki , m . suzuki , t . utsumi , h . watanabe , h . urakawa , s . tsuchida , t . nunoura , h . hirayama , k . takai , k . h . nealson , and k . horikoshi . 2006 . host - symbiont relationships in hydrothermal vent gastropods of the genus alviniconcha from the southwest pacific . appl . environ . microbiol . 72 : 1388 - 1393 .
johnson , s . b . ; warén , a . ; tunnicliffe , v . ; dover , c . v . ; wheat , c . g . ; schultz , t . f . ; vrijenhoek , r . c . ( 2014 ) . molecular taxonomy and naming of five cryptic species of alviniconcha snails ( gastropoda : abyssochrysoidea ) from hydrothermal vents . systematics and biodiversity . 1 - 18 . , available online at urltoken [ details ] available for editors [ request ]
johnson , s . b . ; warén , a . ; tunnicliffe , v . ; dover , c . v . ; wheat , c . g . ; schultz , t . f . ; vrijenhoek , r . c . ( 2014 ) . molecular taxonomy and naming of five cryptic species of alviniconcha snails ( gastropoda : abyssochrysoidea ) from hydrothermal vents . systematics and biodiversity . 1 - 18 . , available online at urltoken page ( s ) : 13 , fig . 2 . 4 [ details ] available for editors [ request ]
johnson , s . b . ; warén , a . ; tunnicliffe , v . ; dover , c . v . ; wheat , c . g . ; schultz , t . f . ; vrijenhoek , r . c . ( 2014 ) . molecular taxonomy and naming of five cryptic species of alviniconcha snails ( gastropoda : abyssochrysoidea ) from hydrothermal vents . systematics and biodiversity . 1 - 18 . , available online at urltoken page ( s ) : 13 , fig . 2 . 5 [ details ] available for editors [ request ]
description alviniconcha hessleri was discovered and described almost 20 years ago ( 7 ) and is a mesogastropod in the family provannidae ( 14 ) . it is named both after the submersible alvin ( “alvin’s shell” ) and the preeminent deep - sea biologist , robert r . hessler . the snail is roughly spherical in shape and has a thin carbonate shell ( if allowed to air - dry , it will fall to pieces within weeks ! ) the protoconch is almost never visible and juvenile shells show considerable variation in sculpture ( 3 , 14 ) . the spiny appearance of this snail is part of the periostracum and can erode away in larger specimens . speaking of size , we have seen specimens up to 88mm in length , larger than a softball !
biogeography originally described from the mariana trough west of the philippines , these snails populate many of the back - arc basins in the western pacific , including the manus , north fiji , and lau back - arc basins . additionally , a . hessleri is reported from the central indian ridge . genetic data suggest there is 2 genetically distinct populations living hundreds of meters apart in the north fiji basin , the dominant genotype being most similar to populations from the manus basin ( 5 ) . populations from the lau basin are also genetically separated from those from the north fiji basin ( 1 ) . furthermore , populations from southwest pacific back - arc basins are distinct from those from the mariana trough are distinct from all of the western pacific back - arc basins ( 6 ) . the central indian ridge populations of alviniconcha are distinct from all other populations ( 4 , 13 ) , though most closely related to populations from the mariana trough ( 4 ) .
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corresponding author . mailing address : frontier research system for extremophiles , japan agency for marine - earth science and technology , 2 - 15 natsushima - cho , yokosuka 237 - 0061 , japan . phone : 81 - 468 - 67 - 9710 . fax : 81 - 468 - 67 - 9715 . e - mail :
shannon johnson , a researcher at the monterey bay aquarium research institute , found that when she talked to youngsters about sea snails , she communicated a little more effectively if she skipped the technical description and called them
punk - rock snails .
their entire shells are covered in spikes ,
johnson explains .
and then the spikes are actually all covered in fuzzy white bacteria .
these punk rock snails live thousands of feet underwater , crowded around the mouths of chimneys of hydrothermal vents — the kind of place that might survive the apocalyptic
nuclear error
in the clash album london calling .
they live in hot , acidic poison , basically , so they ' re pretty hardcore ,
she says .
not only was a he a punk - rock icon — he ' s kind of one of the originators of the punk movement — but he also was kind of an environmentalist ,
she says .
he started a foundation that was planting trees all over the world . he ' s a neat guy .
strummer is not the only big name with his own namesake animal . a wooly lemur from madagascar is named after john cleese — the avahi cleesei . a frog in the amazon that makes a shrill , bat - like call is named after ozzy osbourne .
the ramones each have their own trilobite , and there ' s a parasitic wasp named after shakira . the scientists who discovered the wasp say it causes the caterpillar it inhabits to wriggle and writhe , which reminds them of shakira ' s energetic dancing .
warén a . & bouchet p . ( 1993 ) new records , species , genera , and a new family of gastropods from hydrothermal vents and hydrocarbon seeps . zoologica scripta 22 : 1 - 90 . [ details ]
desbruyères , d . , m . segonzac & m . bright ( eds . ) . ( 2006 ) . handbook of deep - sea hydrothermal vent fauna . second edition denisia 18 : 1 - 544 . ( copepods 316 - 355 ) ( polychaeta 183 - 296 ) , available online at urltoken [ details ]
intergovernmental oceanographic commission ( ioc ) of unesco . the ocean biogeographic information system ( obis ) , available online at urltoken [ details ]
photo on left courtesy of c . fisher / ridge2000 . photo on the right from linda zelnio .
want to know more about this hairy little friend ? i wrote a detailed article on this snail for deep sea news over a year ago . - kaz
@ doppleganger : don’t forget to send it to carl zimmer for his science tattoo gallery too .
these deep - sea animals live in the hottest and most acidic waters near hydrothermal vents .
because these snails live in these extreme conditions , they have severely degraded shells ( size varies between 2 . 5 - 10 cm ) covered in spikes or have no shells at all .
“collections were conducted with the remotely operated vehicles ( rov ) jason ii and ropos , with the st212 trenching rov , and with the human - occupied vehicle shinkai 6500 , ” dr vrijenhoek and his colleagues wrote in a paper in the journal systematics and biodiversity .
“named in honor of joe strummer , the lead vocalist and guitarist from the clash , a british punk band , ” the scientists wrote .
a . kojimai is known from hydrothermal vent localities at 1 , 480 to 2 , 700 m depths in the manus , fiji and lau basins , in the western pacific . a . boucheti lives near hydrothermal vents at 1 , 300 to 2 , 700 m depths in the manus , fiji and lau basins , in the western pacific .
a . marisindica occurs at hydrothermal vents at 2 , 400 to 3 , 300 m depths on central indian ridge , in the indian ocean : kairei and edmunds vent fields . and a . adamantis lives near hydrothermal vents at 350 m depth on east diamante seamount .
juvenile australopithecus climbed trees , 3 . 32 - million - year - old foot fossil shows
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when you think of hydrothermal vents , what comes to mind first ? is it the gushing black smoke out of a chimney ? perhaps you envision the enormous tubeworms with their red velvety plumes sticking out of their white tubes . some may even be familiar with the dense swarms of blind shrimp . what may not come to mind are big hairy snails !
physiology a . hessleri has blue blood due to hemocyanin , but also contains hemoglobin in concentrations similar to chemoautotrophic bivalves from other hydrothermal vents ( 15 ) . the gill of this beast is enlarged and can get up to 21 % of the total soft - body mass ( dry weight , unpublished data ) . a normal snail’s gills from the intertidal may weigh around 4 - 7 % of the total soft - body weight .
desbruyères , d . , a . - m . alayse - danet , s . ohta , and scientific parties of biolau and starmer cruises . 1994 . deep - sea hydrothermal communities in southwestern pacific back - arc basins ( the north fiji and lau basins ) : composition , microdistribution and food web . marine geology 116 : 227 - 242 .
hasegawa , k . , k . fujikura , and t . okutani . 1997 . gastropod fauna associated with hydrothermal vents in the mariana back - arc basin : summary of the results of 1996 “shinkai 6500” dives . jamstec journal of deep sea research 13 : 69 - 83 .
kojima , s . , s . ohta , t . miura , y . fujiwara , and j . hashimoto . 2000 . molecular phylogeny study of chemosynthetic - based communities in the manus basin . jamstec journal of deep sea research 16 : 7 - 13 .
okutani , t . , and s . ohta . 1988 . a new gastropod mollusk associated with hydrothermal vents in the mariana back - arc basin , western pacific . venus ( japan journal of malacology ) 47 : 1 - 9 .
pranal , v . , a . fiala - medioni , and j . guezennec . 1997 . fatty acid characteristics in two symbiont - bearing mussels from deep - sea hydrothermal vents of the south - western pacific . journal of the marine biological association of the uk 77 : 473 - 492 .
stein , j . l . , s . c . cary , r . r . hessler , s . ohta , r . d . vetter , j . j . childress , and h . felbeck . 1988 . chemoautotrophic symbiosis in a hydrothermal vent gastropod . biological bulletin 174 : 373 - 378 .
urakawa , h . , n . dubilier , y . fujiwara , d . e . cunningham , s . kojima , and d . a . stahl . 2005 . hydrothermal vent gastropods from the same family ( provannidae ) harbour e - and g - proteobacterial endosymbionts . environmental microbiology 7 : 750 - 754 .
van dover , c . l . , s . e . humphris , d . fornari , c . m . cavanaugh , r . collier , s . k . goffredi , j . hashimoto , m . d . lilley , a . l . reysenbach , t . m . shank , k . l . von damm , a . banta , r . m . gallant , d . götz , d . green , j . hall , t . l . harmer , l . a . hurtado , p . johnson , z . p . mckiness , c . meredith , e . olson , i . l . pan , m . turnipseed , y . won , c . r . young iii , and r . c . vrijenhoek . 2001 . biogeography and ecological setting of indian ocean hydrothermal vents . science 294 : 818 - 823 .
warén , a . , and p . bouchet . 1993 . new records , species , genera , and a new family of gastropods from hydrothermal vents and hydrocarbon seeps . zoologica scripta 22 : 1 - 90 .
hairy crabs , hairy snails , … what’s next ? nice article , kevin . thanks ! i hope you do more .
yep , they have a thin operculum . i’m not sure how they keep from being predated , but a few observations from the field : 1 ) many of these snails are covered in white bacteria 2 ) when i crushed some snails incidentally , the crabs came pouring out of the woodwork toward the crushed snails .
so , it is unclear what the palatability of the snails are but it seems they were probably being eaten by the crabs . now , the reason why this certain crab may be highly associated with the snail in the first place is because it might be grazing the the bacteria off the snails shell . crabs are very opportunistic and if they sense an easy snack they might go for an injured snail . we don’t have much evidence to back up the claim , but just one of several things to consider .
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joe strummer doing his best snail impression . photograph : george rose / getty images
the strummer - indebted snails are one of five new species identified in a paper that was published in the journal systematics and biodiversity . “because they look like punk rockers in the 70s and 80s and have purple blood and live in such an extreme environment , we decided to name one new species after a punk rock icon , ” shannon johnson , a researcher at california’s monterey bay aquarium research institute , told the santa cruz sentinel ( via exclaim ) .
© 2018 guardian news and media limited or its affiliated companies . all rights reserved .
total dna was extracted from the head - food region of the specimens from the three back - arc basins by grinding , digestion with sodium dodecyl sulfate , and extraction with phenol and chloroform . the downstream region of the coi mitochondrial gene ( approximately 690 bp ) was amplified by the pcr using primers coi - b (
) . the pcr conditions were as follows : 94°c for 60 s followed by 30 to 40 cycles at 92°c for 40 s , 50°c for 60 s , and 72°c for 90 s . the nucleotide sequence of the amplified fragment was determined by using an abi3100 sequencer and a prism big dye terminator sequencing kit ( applied biosystems , inc . , foster city , ca ) with primers coi - b , tw - 2 (
phylogenetic relationships were estimated by the maximum - parsimony ( mp ) method using a multiple , equally parsimonious , heuristic search with tree bisection - reconnection and 1 , 000 random addition sequence replicates , the maximum - likelihood ( ml ) method of the paup * package ( version 4 . 0b10 ) ( 23 ) , and the neighbor - joining ( nj ) method ( 19 ) of the mega package ( version 2 . 19 [ 16 ] ) .
) , except that the endosymbiont dna was extracted from the dissected gill tissue by using a dneasy kit ( qiagen , valencia , ca ) in accordance with the manufacturer ' s instructions . endosymbiont 16s rrna gene sequences were amplified by pcr using la
) . the pcr conditions were 96°c for 120 s , followed by 27 to 30 cycles of 96°c for 20 s , 53°c for 45 s , and 72°c for 120 s . the amplified 16s rrna gene sequence products were cloned by using an original ta cloning kit ( invitrogen , carlsbad , ca ) before being sequenced with an abi 3100 sequencer and drhodamine sequencing kit according to the manufacturer ' s recommendations ( perkin - elmer / applied biosystems ) .
a single phylogenetic clone type ( phylotype ) was obtained from the clone type analysis . the partial sequence was extended and manually aligned by using the secondary structures with arb ( 18 ) . evolutionary analysis was performed by the nj and mp methods using paup ( 23 ) based on 1 , 160 nucleotide positions ( 64 to 1417 [ escherichia coli numbering ] ) , which have more than 50 % identity across the sequences analyzed .
the bacterial 16s rrna gene sequences from the gill endosymbionts are available at the ddbj under the accession numbers ab235228 to ab235239 .
) . the gastropod specimens were dissected into gill and mantle tissues , which were then lyophilized . the carbon isotopic compositions of the cultures and the acid - fumed gastropod tissues were analyzed by using a thermo electron delta
advantage mass spectrometer connected to an elemental analyzer ( ea1112 ) through a conflo iii interface . the measured isotopic composition was expressed as δ
c abundance ratio for the pee dee belemnite carbonate standard . the values of δ
) . briefly , approximately 20 mg of the gastropod tissue was incubated in 1 ml of anhydrous methanolic hydrochloric acid at 100°c for 3 h . the fatty acid methyl esters ( fames ) were then extracted with
- hexane . the identities of the fames were subsequently determined by comparison of their retention times and spectra to those of known fame standards by gas chromatography - mass spectrometry ( gcq ; shimadzu , tokyo , japan ) . the oven temperature was set to 140°c for 3 min before being increased to 250°c at a rate of 4°c / min with he at a constant flow of 1 . 1 ml / min through a db - 5ms column ( 30 m by 0 . 25 μm by 0 . 25 mm ; j & w scientific , folsom , ca ) . standard nomenclature was used for fatty acids , which were designated in an
the δ 13 c values of the fames were determined using the gc - carbon - isotope ratio ms using a thermo electron delta plus advantage mass spectrometer connected to a gas chromatograph ( agilent 6890 ; agilent , mountain view , ca ) through a gc / c / c / iii interface as described previously ( 22 ) . the oven temperature was set to 120°c for 3 min before being increased to 300°c at a rate of 4°c / min with he at a constant flow of 1 . 1 ml / min through an hp - 5 column ( 30 m by 0 . 25 μm by 0 . 25 mm ; agilent ) . the isotopic compositions of the fames were measured with an internal isotopic standard ( 19 : 0 , δ 13 c = −29 . 80 ) with a correction made for the additional carbon atom from the methanol - derivatizing reagent ( δ 13 c = −39 . 04 ) . the internal isotopic standard reduced measurement errors to within 1 for all isotopic analyses .
gastropods and their distribution in the south west pacific basins , a nucleotide sequence for the downstream region of the coi mitochondrial gene ( 696 bp ) was determined for a single specimen from the vai lili site in the lau basin , as well as several sites in the manus and north fiji basins . as summarized in table
sp . type 2 occurred in pacmanus field e and at the vienna woods site in the manus basin and in the starmer ii site in the north fiji basin . consequently , it appears that the distribution of
spp . types 1 and 2 within the fields and sites examined in the present study does not overlap . instead , despite the relatively close geographic proximity of
to determine the phylogenetic affiliations of gill endosymbionts , the host lineages of which were identified above , were analyzed based on their 16s rrna gene sequences . the examination of at least eight clones generated from a 16s rrna gene - sequence library from the gill filaments of each gastropod showed only one 16s rrna gene sequence . as shown in fig .
in this and previous studies , the phylogenetic relationships of host gastropods and their bacterial endosymbionts were conducted in conjunction with bulk and compound - specific carbon isotopic analyses at a global scale across five tectonic settings . analysis of fatty acid profiles of gastropod tissues revealed that the symbiont - free mantle tissue contained substantially more monosaturated c
) . this finding suggests that endosymbiont cells are consumed by , and incorporated into , the host gastropods .
we thank the captains and crews of the r / v yokosuka and natsushima and the shinkai 2000 and 6500 for their technical expertise . we also thank toshiyuki yamaguchi and yasunori kano for helpful discussions .
corresponding author . mailing address : extremobiosphere research center , japan agency for marine - earth science & technology , 2 - 15 natsushima - cho , yokosuka , kanagawa 237 - 0061 , japan . phone : 81 - 46 - 867 - 9710 . fax : 81 - 46 - 867 - 9715 . e - mail :
spp . ( gastropoda ) from two south western pacific back - arc basins .
desbruyeres , d . , a . - m . alayse , s . ohta , et al .
. deep - sea hydrothermal communities in southwestern pacific back - arc basins ( the north fiji and lau basins ) : composition , microdistribution , and food web .
folmer , o . , m . black , w . hoeh , r . a . lutz , and r . c . vrijenhoek .
. wide variation of chemical characteristics of submarine hydrothermal fluids due to due to secondary modification processes after high temperature water - rock interaction : a review , p .
hasegawa , t . , t . yamaguchi , s . kojima , and s . ohta .
hashimoto , j . , s . ohta , a . fialamedioni , j . - m . auzende , s . kojima , m . segonzac , y . fujiwara , j . c . hunt , k . gena , t . miura , t . kikuchi , t . yamaguchi , t . toda , h . chiba , s . tsuchida , j . ishibashi , k . henry , m . zbinden , a . pruski , a . inoue , h . kobayashi , j . - l . birrien , j . naka , t . yamanaka , c . laporte , k . nishimura , c . yeats , s . malagun , p . kia , m . oyaizu , and t . katayama .
. hydrothermal vent communities in the manus basin , papua new guinea : results of the bioaccess cruises ' 96 and ' 98 .
. fractionation of the isotopes of carbon and hydrogen in biosynthetic processes , p .
kojima , s . , k . fujikura , t . okutani , and j . hashimoto .
gastropods from the indian ocean to those from the pacific ocean ( provannidae : mollusca ) revealed by nucleotide sequences of mitochondrial dna .
kojima , s . , r . segawa , y . fujiwara , k . fujikura , s . ohta , and j . hashimoto .
kojima , s . , r . segawa , y . fujiwara , j . hashimoto , and s . ohta .
, between the north fiji basin and the manus basin revealed by nucleotide sequences of mitochondrial dna .
kojima , s . , r . segawa , j . hashimoto , and s . ohta .
. molecular phylogeny of vestimentiferans collected around japan revealed by the nucleotide sequences of mitochondrial dna .
kumar , s . , k . tamura , i . b . jacobsen , and m . nei .
. mega2 : molecular evolutionary genetics analysis software . arizona state university , tempe .
. john wiley & sons , inc . , new york , n . y .
ludwig , w . , o . strunk , r . westram , l . richter , h . meier , yadhukumar , a . buchner , t . lai , s . steppi , g . jobb , w . forster , i . brettske , s . gerber , a . w . ginhart , o . gross , s . grumann , s . hermann , r . jost , a . konig , t . liss , r . lussmann , m . may , b . nonhoff , b . reichel , r . strehlow , a . stamatakis , n . stuckmann , a . vilbig , m . lenke , t . ludwig , a . bode , and k . h . schleifer .
. the neighbor - joining method : a new method for reconstructing phylogenetic trees .
shimayama , t . , h . himeno , j . sasuga , s . yokobori , t . ueda , and k . watanabe .
suzuki , y . , t . sasaki , m . suzuki , k . h . nealson , and k . horikoshi .
suzuki , y . , t . sasaki , m . suzuki , y . nogi , t . miwa , k . takai , k . h . nealson , and k . horikoshi .
. paup * : phylogenetic analysis using parsimony ( * and other methods ) , version 4 . 0b10 . sinauer associates , sunderland , mass .
urakawa , h . , n . dubilier , y . fujiwara , d . e . cunningham , s . kojima , and d . a . stahl .
. hydrothermal vent gastropods from the same family ( provannidae ) harbour ε - and γ - proteobacterial endosymbionts .
. gastropoda and monoplacophora from hydrothermal vents and seeps ; new taxa and records .
the star system calculates the number of pieces that were handled by conchology , inc . in the last 15 years :
we want to point out that the star system is only very reliable for philippine shells only , as we handle very few foreign shells in general . as time goes , the system will become more and more performant .
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fiji . lau bassin . valufa ridge . site vailili . 23°13 ' s . 176°38 ' w . biolau expedition , taken by submarine , 1750 m . july 1989
© 1996 - 2018 guido t . poppe & philippe poppe - conchology , inc . ( 0 . 002 seconds . )
has blue blood due to hemocyanin , but also contains hemoglobin in concentrations similar to chemoautotrophic bivalves from other hydrothermal vents ( 15 ) . the gill of this beast is enlarged and can get up to 21 % of the total soft - body mass ( dry weight , unpublished data ) . a normal snail’s gills from the intertidal may weigh around 4 - 7 % of the total soft - body weight .
the digestive system is very reduced for the size of this snail . for instance , warén & bouchet ( 14 ) state , “the stomach is small , about 10mm3 in a specimen 45mm high and a shell volume of about 60 , 000 mm3 . a specimen of
living in the same environment , grazing the surface , has a stomach of 1 . 5mm3 at a shell of 75mm3 . this means that
has a stomach which is 100 times large in relation to the body volume . ” ( pg . 63 )
has separate sexes . they lay down flat , semi - transparent egg capsules on the rock which contains about 20 - 25 embryos ( 14 ) . larvae of
at north fiji and lau basins ( ( 2 ) , unpublished data ) . several copepods of the genus
commonly forms the center of a “bull’s eye” pattern we observe at the lau basin ( documented by warén & bouchet ( 14 ) for the north fiji basin ) , where is occupied the hottest part of the hydrothermal field with the highest concentrations of sulfide ( unpublished data ) . crabs of the genus
. my “pet hypothesis” is that the spines of the snail keep off fouling critters , perhaps those that might drill through its thin and fragile shell . still needs to be tested though…
originally described from the mariana trough west of the philippines , these snails populate many of the back - arc basins in the western pacific , including the manus , north fiji , and lau back - arc basins . additionally ,
is reported from the central indian ridge . genetic data suggest there is 2 genetically distinct populations living hundreds of meters apart in the north fiji basin , the dominant genotype being most similar to populations from the manus basin ( 5 ) . populations from the lau basin are also genetically separated from those from the north fiji basin ( 1 ) . furthermore , populations from southwest pacific back - arc basins are distinct from those from the mariana trough are distinct from all of the western pacific back - arc basins ( 6 ) . the central indian ridge populations of
are distinct from all other populations ( 4 , 13 ) , though most closely related to populations from the mariana trough ( 4 ) .
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“descriptions cannot be made full enough and accurate enough to satisfy later workers . each generation of taxonomists must see the actual specimens used by earlier generations , and i think the tendency now is , or should be , to make descriptions short , but of course explicit and carefully calculated , and to make specimens widely available . ”
the naming of organisms following standardized conventions is the basis for linking new information to existing knowledge . it is also the basis for biological classification , effective communication , and extrapolation of findings about organisms . the mere accession numbers of dna sequences ( or other strings of numbers lacking an agreed system of the numbers’ innate significance ) do not permit extrapolation of information about morphological traits , biogeographic ranges , or sharing of published knowledge across disciplines , all of which is possible with a widely used naming convention . most researchers are using the conventions of the linnaean system , with the fixed starting points being linnaeus’s treatments of plants and animals ( 1753 , 1758 ; persoon and fries for certain fungi and the names of lichens ) .
“the combined nucleotide sequences of the holotype strain . . . . the complete list of diagnostic d1 - d2 lsu , its ( iternal transcribed spacer ) / 5 . 8s and ssu gen - bank sequences which can be used as a genetic type for this species are reported in supplementary material . ” similarly for the other species
unspecified substitutions in nuclear its “ rhizoplaca polymorpha consists of specimens recovered within ‘clade ivc’ in leavitt et al . ( 2011a ) , which is supported as a lineage distinct from all other populations according to coalescent - based genetic analysis of multiple genetic loci . ”
“the least inclusive clade containing organisms with nuclear rrna its sequences with genbank accessions gq850318 , gq850355 gq850368 . . . ”
“with an its sequence ( genbank jq693160 ) that is distinct from other members of the gamsii / elongata clade , deviating in the its1 region from other species in the clade ; with a 94–97 % similarity . with a sister group relationship to a possibly polyphyletic clade containing mortierella sclerotiella ( basal ; genbank hq63031 , ex type ) , m . cogitans ( genbank hq630281 , ex type ) , and m . acrotona ( genbank hq630328 , ex type ) . ”
685 snails collected from 327 hosts , incl . type material , deposited in various collections
this species differs by ssu , lsu and its2 dna sequences ( jn636069 ) from all other species , listed in tables 1 and 2 . “note that these ribosomal dna sequences may vary within the species”
to date , two papers have discussed dna - based formal diagnoses ( cook et al . 2010 ; tripp and lendemer 2014 ) . both overlooked that the practice began 15 years ago ( westheide and hass - cordes 2001 ) , and they either focused on a hypothetical example ( ( cook et al . 2010 ) or examples from 2012 and 2013 ( tripp and lendemer 2014 ) . tripp and lendemer ( 2012 ) also raised a potential problem with one type of dna diagnosis , namely genetic distances , which i take up in the “discussion” section . no previous paper has surveyed the conceptual and factual history of dna - based formal naming , and the absence of a review of how taxonomists have incorsporated molecular characters into protologs has led to uncertainty and reinventing of the wheel ( cook et al . 2010 ; jörger and schrödl 2013 ) .
species are always delimited against already known species ( linnaeus 1753 , 1758 ; mayr 1992 ; naciri and linder 2015 ) . this holds true regardless of whether they are conceived as created ( linnaeus 1753 , 1758 ) or as the result of evolution ( mayr 1992 ) . huge numbers of “cryptic” species—a term only meaningful relative to the particular technology used for studying organisms—can be distinguished with genomic data , and taxonomists are facing the challenge of naming at least some of this organismal diversity as it may be relevant for their research interests . it is useful then to consider how earlier taxonomists facing large numbers of new species mastered the task .
the combination of the type method ( i . e . , name - bearing specimens deposited in one or more collections ) and the discrete nature of nucleotide characters ( substitutions or insertions / deletions of codons ) begs reconsideration of linnaeus’s focus of diagnosing species by features that distinguish them from their known closest relatives , instead of describing mixed sets of traits that vary at different hierarchical levels . here , i consider the ways in which taxonomists have incorporated dna characters directly into the publication of new species names , and i also review the history of dna - based formal naming . i conclude with recommendations about best practice dna - based diagnosis .
i compiled published molecular diagnoses through internet searches , surveying relevant journals and corresponding with colleagues . a molecular diagnosis involves the formal naming of a taxon by listing the dna or protein characters in which it differs from its closest relative ( s ) in the protolog , thus associating it with a binomial latinized name and the type material with its place of deposition . i checked that the molecular data indicated in the diagnosis were accessible in the cited database , usually the national center for biotechnology information ( ncbi : http : / / www . ncbi . nlm . urltoken , accessed 28 april 2016 ) .
my survey focused on species names . an example of a molecular diagnosis of a higher taxon is that of the family ambuchananiaceae seppelt & h . a . crum ex a . j . shaw , “fam . nov . plantae heterogeneae in morphologia , synapomorphis molecularibus in dna nuclei mitochondri et plasti unitae . type :
, p . 1523 ) . of course , this was before botanists abolished the latin requirement on 1 january 2012 . the baselines for bacterial names are
dna - based formal diagnoses of new species of eukaryotes ( mainly fungi , animals , and plants ) since 2000 ( based on data in table 1 ) . i am aware of only one molecular diagnosis published in 2015 ( irimia and gottschling 2016 ) .
the first to discuss how dna characters might be used in species diagnosis were don reynolds and john taylor ( 1991 ) who clarified that the exsisting rules of the international code of botanical nomenclature ( as it was then still called ) allowed dna - based species naming and that dna itself could serve as the type element . they provide two hypothetical examples of new fungal species names , one with a mix of dna and morphological type materials and the other with dna type material only , and call on herbaria to prepare for storing dna material as types . almost a quarter of a century has passed since this prescient article , but taxonomists are still feeling the need to defend the use of dna characters in protologs ( cook et al . 2010 ; jörger and schrödl 2013 ; tripp and lendemer 2014 ) , and the approach is only slowly becoming more common ( fig . 1 ) .
by november 2015 , 98 molecular diagnoses of species of acoelomorpha , alveolata , angiospermae , annelida , arachnida , arthropoda , ascomycota , chordata ( reptilia and pisces ) , fungi , lepidoptera , mollusca , and nematoda have been published ( table 1 ) . relatively few protologs refrain from also providing a morphological description ( brower 2010 ; molina et al . 2011 ; leavitt et al . 2013 ) .
this form of clade - based diagnosis ( “the least inclusive clade containing…” ) has been challenged by tripp and lendemer ( 2012 ) , who have requested the committee on the application of the code of nomenclature for algae , fungi , and plants to decide on the validity of this form , which in their view goes against the requirement in article 32 . 2 ( d ) that a diagnosis cannot describe properties such as purely aesthetic features , economic , medicinal or culinary usage , cultural significance , cultivation techniques , geographical origin , or geological age . this matter is currently unsolved , and i have not found examples from outside fungi and lichens of this form of diagnosis ( table 1 ) .
) . in most studies , dna diagnostic features serve to corroborate morphological differences . for example , diagnostic coi substitutions that agree with shell characters clearly diagnose species of parasitic snails , but “impoverished anatomical details [ alone ] do not allow identification” (
) , but fernández - triana and colleagues decided not to use dna barcoding traits as species diagnoses , instead using the form “sequences in bold : 2 , barcode compliant sequences : 2 . ”
between january 1935 and 2012 , botanists ( and mycologists ) had to write any diagnosis in latin ( table lists three such molecular diagnoses ) . since 2012 , however , a few plant species have been diagnosed with nucleotide substitutions described in english ( table 1 ) , and one study even provides both molecular and morphological diagnoses and molecular and morphological descriptions ( gonzález et al . 2013 ) .
a key advantage of molecular diagnoses is their utility for more precisely characterizing type material than is possible with morphological traits . the better a type collection ( including syntypes and paratypes ) is characterized , the more reliable the identification of future specimens . this does not mean that unidentified specimens in the future will need to be sequenced for identification . instead , identification may continue to rely on morphological matching of preserved specimens or , increasingly , of images using machine learning . having stringent diagnoses that specify dna differences among closely related species ( or subspecific taxa ) can facilitate identification in those cases where the correct identification of a specimen is crucial , for example , for parasites of crops or of animals , especially us , but also for specimens that are incomplete , poorly preserved , or immature , so that diagnostic features are missing . also , as pointed out by cook et al . ( 2010 ) , it is often quicker and cheaper to use diagnostic dna features than to rely on the traditional expert - centered paradigm of identification .