Vertebrates, Overview

Carl Gans , Christopher J. Bell , in Encyclopedia of Biodiversity (Second Edition), 2001

Tetrapoda

Tetrapoda is divers as the nigh recent common antecedent of Amphibia and Amniota, and all of that ancestor'due south descendants. Tetrapoda is diagnosed by the presence of differentiated fingers and toes and past a bony joint formed between the occipital condyles of the skull and the anterior vertebral elements.

Extant amphibians share three morphological characteristics: (1) loss of several skull bones constitute in extinct amphibian groups; (2) short or absent-minded ribs; (3) pedicellate dentition (an upper tooth crown resting on a lower pedicel). The relationships among the three major extant amphibian groups are not well supported, but combined analyses of morphological and molecular information favor a sister taxon human relationship between Anura (frogs and toads) and Caudata (salamanders). Batrachia is defined as the nearly recent common ancestor of Anura and Caudata, and all of its descendants. In this arrangement, Batrachia and Gymnophiona (the caecilians) are sister taxa (Figure one; come across too Cannatella and Hillis, 1993).

There are approximately 165 species of living caecilians. All extant caecilians are limbless, and their distribution encompasses tropical and subtropical regions of Cardinal and Southward America, Africa, India, and Southeast Asia. Well-nigh caecilians are fossorial, spending the bulk of their life underground. One Southward American group (Typhlonectes) is secondarily aquatic. The otic capsules, exoccipital, basioccipital, and parasphenoid ossifications of the braincase are fused into a solid unit (the os basale). Caecilians possess a pair of sensory organs called tentacles that are unique among vertebrates. The tentacles are protrusible organs, commonly situated between the external naris and the orbit, and probably function in chemoreception. Although the orbits of caecilians are often covered with skin (and sometimes bone), the optics are photoreceptive in most species that have been examined. In some caecilians, the heart is closely associated with the tentacle and in at to the lowest degree one species, they eye is protruded from the skull during protrusion of the tentacle (Nussbaum, 1992). The derived groups of caecilians fuse many elements of the skull and lack a tail. The fossil tape of caecilians is notably poor just extends back at least equally far as the Cretaceous. The Jurassic Eocaecilia shares many characteristics with extant caecilians (including the reported presence of a tentacular foramen) simply retains limbs and other anatomical features non seen in extant forms (Jenkins and Walsh, 1993).

There are approximately 415 described species of extant salamanders, the majority of which are found in the Northern Hemisphere. A pregnant radiations of tropical South American salamanders extends equally far due south every bit southern Brazil and Bolivia. Caudates share a number of morphological features of the skeleton, including the loss of the quadratojugal ossification and the presence of intravertebral spinal foramina in the atlas vertebra. Most salamanders also accept a reduced number of basic in the pectoral girdle relative to extinct amphibian groups and frogs (caecilians lack a pectoral girdle), and they have an anteriorly projecting process on the atlas (the first vertebra), the tuberculum interglenoideum, which forms accessory articulations between the skull and the vertebral cavalcade. Members of one large assemblage of caudates (the Plethodontidae) lack lungs, and this status is also found in one gymnophionan. The early history of salamanders is poorly known, but fossils belonging to Caudata (as defined above) are known from the Mesozoic. Stem-group salamanders (outside of Caudata equally defined in a higher place, only on the evolutionary stem leading to modern salamanders) are reported from the Jurassic. A recent review of Mesozoic taxa was provided past Evans and Milner (1996).

There are more than 4100 described species of extant anurans, distributed on all the major continental land-masses except Antarctica. Skeletal features shared by frogs include the fusion of forearm bones (radius and ulna), fusion of the lower leg bones (tibia and fibula), elongation of the ankle basic, reduced number of trunk vertebrae (ten or fewer amidst extant frogs), and presence of a urostyle (a rodlike, posterior bony extension of the vertebral cavalcade). Many of these skeletal features are associated with jumping ability and evolved equally early every bit the early Jurassic (Shubin and Jenkins, 1995). The fossil record of the group is extensive (see recent review by Sanchiz, 1998) and at least two stalk-group frogs are now know from the early Triassic (Evans and Borsuk-Bialynicka, 1998).

Many amphibians take a larval phase followed by metamorphosis into the adult form. Metamorphosis was defined by Duellman and Trueb (1986, p. 173) as "a serial of sharp postembryonic changes involving structural, physiological, biochemical, and behavioral transformations." The transformations that take place in frogs are the most dramatic of whatever within the Tetrapoda. The majority of frog species take a larval stage in the life bike (following hatching from an egg and preceding development of the mature adult body form) known as a tadpole. The tadpole has a more or less oval-shaped body with a tail; there is no distinct head region, but the oral cavity includes a beak and a number of rows of chitinous toothlike structures. During metamorphosis many morphological and physiological changes accept place that completely transform the animal'south appearance and the style information technology interacts with its environment (east.g., the tail is resorbed, limbs grow, the axial and appendicular skeleton is dramatically transformed, the digestive tract shortens, gills disappear, and respiration function is transferred to lungs). Many frogs show variants of direct development.

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The Evolution of Consciousness in Animals

R.V. Rial , ... S. Esteban , in Consciousness Transitions, 2007

3.3.1 The evolution of land vertebrates

Looking at the vertebrate evolutionary tree, the land vertebrates evolved from the primitive tetrapod stock, existence the coelacant ( Latimeria) a living instance of such torso. Tetrapoda gave origin to amphibians and also to amniotes. Iii main groups of amniota are recognized; (1) anapsids (turtles), (2) diapsids, which comprises tecodonts (birds and crocodiles) and lepidosauria (lizards, snakes and sphenodonts) and (3) synapsids, from which mammals were developed (Laurin and Reisz, 1995). In the search of vertebrate consciousness, we should expect backwards, from witting humans to their ancestors. Indeed, consciousness leaves no fossil remnants and therefore the study must be limited to the extant representatives of those earlier groups. Nobody tin warrant the bodily groups to be equivalent to those from which they appeared. In fact, extant reptiles, for instance, could be as different from their ancestors equally current mammals are from their predecessors; all extant animals take evolved during the aforementioned amount of time and the assumption that reptiles would have remained stable during a fourth dimension in which mammals suffered progressive changes is unsupported. However, there is a continuity betwixt the brains of current fish, amphibians, reptiles, mammals and birds, which could give evolutionary value to comparative studies (Butler and Hodos, 1996).

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Cladistics☆

I.J. Kitching , ... D.M. Williams , in Reference Module in Life Sciences, 2017

Groups

Cladistics recognizes just monophyletic groups of organisms, which are those based on synapomorphies. Monophyletic groups are the but groups that can be confining past objective boundaries, defined by characters. In evolutionary terms, monophyletic groups comprise the near contempo common ancestor and all of its descendants. In Fig. 2, Amniota, Tetrapoda, Osteichthyes, and Gnathostomata are all monophyletic. Two other types of "groups" are sometimes referred to but these are not groups in the same sense as monophyletic groups. Paraphyletic "groups" are based on symplesiomorphy; in evolutionary terms, their members are linked by common ancestry but one or more of the descendants of the well-nigh recent common ancestor are excluded. In Fig. 2, Pisces (fishes) is a paraphyletic assemblage. Many taxa traditionally regarded as ancestral, such every bit fishes, reptiles, and light-green algae, are paraphyletic. Polyphyletic "groups" are based on homoplasy, that is, characters that are considered convergently derived and that cannot be inferred to accept been nowadays in the most contempo common ancestor of the included taxa. In Fig. two, an assemblage comprising the dogfish and the turkey (maybe based on the observation that both lay eggs surrounded by a shell, although no ane would claim such a homology) would exist a polyphyletic grouping.

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The Evolution of The Nervous Systems in Nonmammalian Vertebrates

A.K. Balanoff , Yard.S. Bever , in Evolution of Nervous Systems (2d Edition), 2017

1.ten.1.ane Crown, Stem, and the Heuristic Potential of Fossil Endocasts

Considered against the backdrop of Life'southward more than four billion year history (Bong et al., 2015), the extant biota provides us with a rather impoverished view of taxonomic, and probably, process variety. At the same time, we rely heavily on living species both for our understanding of detailed biological functions and every bit a framework for establishing broad, macroevolutionary patterns. Nosotros tend to perceive extant forms equally islands of either actuated or potential insight floating in a rather murky sea of extinction. These islands are not floating freely, of course, but are instead tethered to each other within the historical edifice of the evolutionary process. The logical framework provided by this edifice is what gives us hope that we may meaningfully clarify the deep biological history which extinction has muddled. The involved model of inference, and the beneficial role that fossils play inside that model, is mayhap best demonstrated using an explicit crown-stem distinction (Fig. one).

Figure 1. Tree depicting the phylogenetic concept of crown and stem as it applies to birds. The concept is critical because crown clades define the inferential framework lying at the heart of all comparative biological science and within which fossils (including fossil endocasts) play a cardinal function (meet text). The extant sister taxon to the avian crown clade (Aves) is the crown clade Crocodilia, and together Crocodilia and Aves ascertain crown-clade Archosauria. The avian stem lineage includes all those extinct forms (including pterosaurs and all nonavian dinosaurs) that are more closely related to Aves than Crocodilia. The crown-stem stardom is a nested concept, so that, for example, stem-group birds are also crown-clade archosaurs.

A crown clade is a monophyletic group whose definition is drawn from the bequeathed difference of ii lineages, both of which retain at least some extant members (Hennig, 1966; Budd and Jensen, 2000; Gauthier and De Queiroz, 2001). The crown clade of mammals (Mammalia; Rowe, 1987), for case, is defined as the about recent common ancestor of monotremes and therians and all of that ancestor'due south descendants. The extant sister taxon to crown mammals is the crown clade of reptiles (Reptilia; Gauthier et al., 1988), which is divers based on the ancestral split between the lineages that would eventually produce the modern radiations of turtles, lepidosaurs (modern lizards, snakes, and tuatara), crocodilians, and birds. The near exclusive clade that includes both Mammalia and Reptilia is the crown clade of amniotes (Amniota; Gauthier et al., 1988). More than inclusive crown clades in our own ancestral line as chordates include (Fig. 2; run across also Rowe, 2004): Tetrapoda (Amniota   +   Amphibia), Choanata [Tetrapoda   +   Dipnoi (lungfish)], Sarcopterygii [Choanata   +   Actinistia (coelacanths)], Osteichthyes [Sarcopterygii   +   Actinopterygians (ray-finned fish)], Gnathostomata [Osteichthyes   +   Chondrichthyes (sharks and rays)], Vertebrata [Gnathostomata   +   Cyclostomata (lampreys and hagfish)], Euchordata [Vertebrata   +   Cephalochordata (lancelets or amphioxus)], and Chordata [Euchordata   +   Urochordata (tunicates or sea squirts)].

Effigy 2. Phylogenetic relationships of the major euchordate crown clades discussed in this chapter. For an expanded discussion of the tree topology, see Rowe (2004) and Benton et al. (2015).

All crown clades, from the most inclusive to the virtually exclusive, are separated from each other by some expanse of evolutionary fourth dimension, which is circumscribed by their collective stalk lineages (Fig. 1). These stalk lineages are somewhat of an evolutionary black box because, by definition, they lack any modern representatives (outside of the crown clade). Our agreement of the evolutionary transformations that populate these stems is based largely on a combination of: (i) the empirical observations that we make on the extant taxa inside the associated crown clades—observations that we cannot brand straight on stem taxa and (2) phylogenetically justified inferences (Farris, 1983; Bryant and Russell, 1992; De Queiroz and Gauthier, 1992; Witmer, 1995). This model is rich in explanatory ability and forms the basis of all comparative biology, including all the biomedical enquiry that is grounded in the study of model organisms. The trouble is that as these phylogenetic stems come to stand for more and more time and are inhabited by an increasing number of evolutionary transformations, the model itself grows less and less heuristically powerful. In other words, as the stems lengthen, the explanatory power of the inferential model tends to diminish.

Recognizing the inverse tendencies of this human relationship is important, peculiarly when we consider the incredible spans of evolutionary time represented by some stem lineages—including many of those attracting great interest from comparative neuroscientists. The phylogenetic stalk of our ain human being crown clade, for example, is currently estimated at approximately half dozen   one thousand thousand years (Dos Reis et al., 2012; Benton et al., 2015), whereas that of crown Mammalia is approximately 150   1000000 years (O'Leary et al., 2013; Luo et al., 2015), and that of crown-group birds (Aves; Gauthier, 1986) exceeds 150   meg years (Prum et al., 2015). The stems associated with the crown clades informing the earliest history of the vertebrate brain (ie, cephalochordates, cyclostomes, chondrichthyans) may exceed 200   million years (Kuraku and Kuratani, 2006; Chen et al., 2012; Hedges et al., 2015).

The inherent difficulty of inferring details beyond such long stalk lineages can be eased through an effective utilization of the fossil tape. Fossils, and merely fossils, afford windows (in the form of semaphoronts; Hennig, 1966) into these otherwise empirically opaque histories. Fossils tin enlighten, either directly or indirectly, the nature and timing of evolutionary transformations and thus assistance to "break upward" long phylogenetic stems (Fig. i). The most obvious beneficiary of integrating vertebrate fossils into comparative studies is our understanding of transformations within the more readily fossilized bony skeleton. The skeleton enjoys, still, at least some class of correlative relationship with most other anatomical systems, including the brain (see the following section). Establishing the strength of these correlations is disquisitional to maximizing the explanatory potential of fossils for macroevolutionary patterns.

The crown-stem stardom is a nested concept wherein every individual fossil falls along a single phylogenetic stem, but at the same time, is nested within a series of more inclusive crown clades. Ardipithecus is a fossil form on the stem of the homo crown clade (White et al., 2009) but one that is nested within the crown clades of Catarrhini, Primates, Placentalia, Theria, Mammalia, and then forth. Archaeopteryx is a stem bird that lies relatively nigh, but still outside, the radiation of crown-clade avians (Gauthier, 1986; Turner et al., 2012), but Archaeopteryx is a crown-clade archosaur, reptile, and amniote. Fossils, similar extant forms, limited a combination of archaic (plesiomorphic) and derived (apomorphic) morphologies, non all of which are going to reflect the ancestral phenotype of their most closely related crown clade. A well-supported understanding of a fossil'south phylogenetic position is crucial to maximizing its potential for informing the bequeathed series of stem transformations (accrual of apomorphies along the stem), which make its associated crown clade unique compared to those of other lineages. Fifty-fifty when this position enjoys widespread consensus, however, the inferential role of the fossil tin can exist dislocated when the employed terminology and taxonomy mean dissimilar things to different researchers.

Paleontologists and neuroscientists often employ "crown" and "stem" in ways that differ significantly from the usage advocated here. Paleontologists are known to utilize these terms to wholly extinct groups, especially when these lineages include a subclade that is especially distinct morphologically (eg, crown and stem sauropterygians; Rieppel, 1994). Neuroscientists often describe extant groups lying exterior some clade of interest as "stalk." For case, Corfield et al. (2015) recently referred to turtles equally stem reptiles in a study whose focus was the neuroanatomy of crown-clade birds. It is not that these usages are wrong—the meanings intended by their authors may be effectively conveyed, peculiarly within their respective research communities. Different usages, however, exercise misfile the inferential roles of crown and stem and thus hinder meaningful integration of what are complementary datasets.

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Tetrapod Relationships and Evolutionary Systematics

Laurie J. Vitt , Janalee P. Caldwell , in Herpetology (Fourth Edition), 2014

Rules and Exercise

The International Code of Zoological Nomenclature is a legal document for the practise of classification, specifically for the selection and assignment of names to animals from species through family groups. Unlike our civil law, there are no enforcement officers. Enforcement occurs through the biological customs's credence of a scholar's nomenclatural decisions. If the rules and recommendations are followed, the scholar'south decisions are accustomed; if the rules are non followed, the decisions are invalid and not accustomed by the customs. Where an estimation of the Lawmaking is unclear or a scholar'southward conclusion uncertain relative to the Code, the thing is presented to the International Commission for Zoological Classification (a panel of systematic zoologists), which, like the U.S. Supreme Courtroom, provides an interpretation of the Lawmaking and selects or rejects the decision, thereby establishing a precedent for similar cases in the future.

The Code has six major tenets:

1.

All animals extant or extinct are classified identically, using the aforementioned rules, classificatory hierarchies, and names where applicable. This exercise avoids dual and conflicting terminology for living species that may have a fossil record. Further, extant and fossil taxa share evolutionary histories and are properly classified together.

2.

Although the Lawmaking applies only to the naming of taxa at the family-group rank and below, all classificatory ranks have Latinized formal names. All except the specific and subspecific epithets are capitalized when used formally; these latter 2 are never capitalized. For instance, the major rank or category names (phylum, class, order, family, genus, species) for the green iguana of Cardinal America are Chordata, Vertebrata, Tetrapoda, Iguanidae, Iguana iguana. The names may derive from any language, although the word must be transliterated into the Roman alphabet and converted to a Latin course.

3.

To ensure that a proper name volition be associated correctly with a taxon, a type is designated—type genus for a family, type species for a genus, and a type specimen for a species. Such a designation permits other systematists to confirm that what they are calling taxon X matches what the original author recognized as taxon X. Comparison of specimens to the type is critical in determining the specific identity of a population. Although the designation of a single specimen to represent a species is typological, a single specimen as the name-bearer unequivocally links a detail name to a single population of animals. Of these three levels of types, but the blazon of the species is an actual specimen; however, this specimen serves conceptually and physically to delimit the genus and family unit. A family unit is linked to a single genus by the designation of a type genus, which in turn is linked to a unmarried species past a type species, and hence to the type specimen of a detail species. The characterization at each level thus includes traits possessed or potentially possessed by the type specimen. An instance of such a nomenclatural chain follows: Xantusia Baird, 1859 is the type genus of the family Xantusiidae Baird, 1859; Xantusia vigilis Baird, 1859 is the type species of Xantusia; and three specimens, USNM 3063 (in the U.s. National Museum of Natural History) are syntypes of Xantusia vigilis. Several kinds of types are recognized by the Code. The holotype is the single specimen designated equally the name-bearer in the original description of the new species or subspecies, or the single specimen on which a taxon was based when no type was designated. In many nineteenth-century descriptions, several specimens were designated every bit a type series; these specimens were syntypes. Often syntypic series contain individuals of more than one species, and sometimes to avoid defoliation, a unmarried specimen, a lectotype, is selected from the syntypic series. Partially considering of this kind of problem, more recent Codes do not approve the designation of syntypes. If the holotype or syntypes are lost or destroyed, a new specimen, a neotype, can be designated as the proper name-bearer for the species. Other types (paratypes, topotypes, etc.) are used in taxonomic publications; nevertheless, they have no official status under the Code.

4.

Simply ane name may exist used for each species. Still normally, a species has been recognized and described independently by unlike authors at different times. These multiple names for the same beast are known as synonyms and arise because different life history stages, geographically afar populations, or males and females were described separately, or because an author is unaware of some other author'southward publication. Whatever the reason, the utilize of multiple names for the same animal would cause confusion; hence but one name is correct. Systematists take selected the simplest way to make up one's mind which of many names is correct, namely by using the oldest name that was published in concordance with rules of the Code. The concept of the first published proper name beingness the correct name is known every bit the Principle of Priority. The oldest proper noun is the primary (senior) synonym, and all names published subsequently are secondary (inferior) synonyms (Table 1.four). Although uncomplicated in concept, the implementation of the Principle may not promote stability, especially so when the oldest name of a common species has been unknown for many decades and then is rediscovered. Should viridisquamosa Lacépéde, 1788 replace the widely used kempii Garman, 1880 for the widely known Kemp'southward ridley sea turtle Lepidochelys kempii? No. The goal of the Code is to promote stability of taxonomic names, and then the Lawmaking has a 50-yr dominion that allows commonly used and widely known secondary synonyms to be conserved and the primary synonym suppressed. The difficulty with deviating from priority is deciding when a proper name is usually used and widely known—the extremes are easy to recognize, but the centre ground is broad. In these circumstances, the instance must be decided by the international commission. In deciding whether one proper noun should replace another name, a researcher determines whether a name is "bachelor" prior to deciding which of the names is "valid." The concept of availability depends upon a taxonomic description of a new name obeying all the tenets of the Code in force at the time of the clarification. Some basic tenets are equally follows: published subsequent to 1758 (tenth edition of Systema Naturae), a binomial proper noun for a species-group taxon, name in Roman alphabet, appearing in a permissible publication, and description differentiates the new taxon from existing ones. If the presentation of a new proper noun meets these criteria and others, the name is bachelor. Failure to run across even ane of the criteria, such every bit publication in a mimeographed (not printed) newsletter, prevents the name from condign available. Even if available, a name may non be valid. Only a unmarried name is valid, no matter how many other names are bachelor. Usually, the valid name is the primary synonym. The valid name is the merely one that should exist used in scientific publications.

TABLE 1.iv. Abbreviated Synonymies of the European Viperine Serpent ( Natrix maura ) and the Cosmopolitian Green Seaturtle ( Chelonia mydas )

Natrix maura (Linnaeus)
1758 Coluber maurus Linnaeus, Syst. Nat., ed. 10, ane:219. Type locality, Algeria. [original clarification; primary synonym]
1802 Coluber viperinus Sonnini and Latreille, Hist. nat. Rept. four:47, fig. 4. Type locality, France. [description of French population, considered to be distinct from Algerian population]
1824 Natrix cherseoides Wagler in Spix, Serp. brasil. Spec. nov. :29, fig. 1. Blazon locality, Brazil. [geographically mislabeled specimen mistaken as a new species]
1840 Coluber terstriatus Duméril in Bonaparte, Mem. Accad. Sci. Torino, Sci. fis. mat. (2) ane:437. Blazon locality, Yugoslavia. Nomen nudum. [=naked name; proper noun proposed without a description and so terstriatus is non available]
1840 Natrix viperina var. bilineata Bonaparte, Op. cit. (2) one:437. Blazon locality, Yugoslavia. Non Coluber bilineata Bibron and Bory 1833, non Tropidonotus viperinus var. bilineata Jan 1863, non Tropidonus natrix var. bilineata January 1864. [recognition of a distinct population of viperina; potential homonyms listed to avert confusion of Bonaparte's clarification with other description using bilineata as a species epithet]
1929 Natrix maura, Lindholm, Zool. Anz. 81:81. [outset appearance of current usage]
Chelonia mydas (Linneaus)
1758 Testudo mydas Linnaeus, Syst. Nat., ed. ten, one:197. Blazon locality, Ascent Island. [original clarification; principal synonym]
1782 Testudo macropus Wallbaum, Chelonogr. :112. Type locality, not stated. Nomen nudum.
1788 Testudo marina vulgaris Lacédè, Hist. nat. Quadrup. ovip. 1: Synops. method., 54. Substitute name for Testudo mydas Linnaeus.
1798 T. mydas small-scale Suckow, Anfangsg. theor. Naturg. Thiere. 3, Amphibien :xxx. Type locality, not stated. Nomen oblitum, nomen dubium. [forgotten proper name, not used for many years then rediscovered; name of uncertain attribution, tentatively assign to mydas]
1812 Chelonia mydas, Schweigger, Königsber. Curvation. Naturgesch. Math. 1:291. [present usage but many variants appeared after this]
1868 Chelonia agassizii Bocourt, Ann. Sci. nat., Paris 10:122. Blazon locality, Guatemala. [clarification of Pacific Guatemalan population as distinct species]
1962 Chelonia mydas carrinegra Caldwell, Los Angeles Co. Mus. Contrib. Sci. (61): 4. Type locality, Baja California. [description of Baja population equally a subspecies]

Note: The full general format of each synonym is: original date of publication; proper noun as originally proposed; author; abbreviation of publication; volume number and showtime folio of description; and type locality. Explanations of the synonyms are presented in brackets.

Source: Modified from Mertens and Wermuth, 1960, and Catalogue of American Amphibians and Reptiles, respectively.

5.

Just as for a species, simply one name is valid for each genus or family unit. Further, a taxonomic proper noun may be used only in one case for an beast taxon. A homonym (the same name for different animals) creates confusion and is also eliminated by the Principle of Priority. The oldest name is the senior homonym and the valid 1. The same names (identical spelling) published subsequently are junior homonyms and invalid names. Two types of homonyms are possible. Master homonyms are the aforementioned names published for the same taxon, for case Natrix viperina bilineata Bonaparte, 1840 and Tropidonotus viperina bilineata Jan, 1863. Secondary homonyms are the same names for unlike taxa, for example the insect family unit Caeciliidae Kolbe, 1880 and the amphibian family Caeciliidae Gray, 1825.

six.

When a revised Lawmaking is approved and published, its rules immediately replace those of the previous edition. This action could be confusing if the new Code differed profoundly from the preceding i, but well-nigh rules remain largely unchanged. Such stasis is non surprising, for the major goal of the code is to establish and maintain a stable nomenclature. Rules tested past long use and found functional are not discarded. Those with ambiguities are modified to clarify the meaning. When a dominion requires major alteration and the replacement rule results in an entirely different action, a qualifying statement is added so actions correctly executed nether previous rules remain valid. For case, the commencement edition of the Lawmaking required that a family-group proper name be replaced if the generic name on which it was based was a secondary synonym; the second and third editions do not require such a replacement; thus, the latter ii editions allow the retention of the replacement proper name proposed prior to 1960 if the replacement has won general acceptance past the systematic community. Such exceptions promote nomenclature stability.

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HBV evolution and genetic variability: Impact on prevention, treatment and development of antivirals

Dieter Glebe , ... Stefan Seitz , in Antiviral Research, 2021

ii.2 Reconstructing the origin and evolutionary history of hepadnaviruses

Nackednaviruses represented the ideal outgroup to safely root the phylogenetic tree of hepatitis B viruses for the very first fourth dimension, while the inclusion of an avian EVE of known age (eAHBV-FRY) enabled time-calibrating this phylogeny. These analyses advise that both virus families separated from a common antecedent in the Silurian near 430 mya concomitant with the divergence of ray-finned fishes (Actinopterygii) and lobe-finned fishes (Sarcopterygii), the latter ones including all terrestrial vertebrates (Tetrapoda). The envelope protein gene in the hepadnaviral lineage emerged de novo in a rather short window of time between 380 and 360 mya, concomitant with the rise of the first tetrapods ( Fig. two).

Fig. 2

Fig. 2. Hepadnavirus phylogeny basing on a multiple sequence alignment of conserved Politico regions and rooted using thirteen nackednaviruses as outgroup. The BEAST tool was used to reconstruct this Bayesian tree under the LG + G4+I substitution model, a relaxed molecular clock with log-normally distributed rates and a Yule speciation prior. Size of the circles at internal branching points is proportional to the posterior probability of a separate, which ranges from 0.43 to one.0. The unit of the scale bar is boilerplate number of substitutions per site. Major evolutionary innovations are marked by red arrows.

Since then, these viruses coevolved in intimate association with their corresponding host lineages. On the deep evolutionary scale, virus-host cospeciation appears to boss, although some successful host jumps beyond vertebrate classes occurred. The gain of the envelope poly peptide factor represents a cardinal transition in viral lifestyle. Nosotros assume that it was directly involved in the development of the hepatotropism, which in turn might have resulted in narrowing the host tropism limiting cross-species transmission.

Afterwards, several contained "innovations" appeared in the distinct branches of the viral family. In the lineage leading to avi- and herpetohepadnaviruses, the C ORFs became elongated due to several insertions (Fig. 2). The largest C protein to date is found in the skink hepatitis B virus (SkHBV) and comprises 335 aa (vs. 183 aa in man HBV). In a mutual antecedent of ortho- and metahepadnaviruses, the latter infecting fishes, the a-determinant emerged. This insertion into the Due south ORF constitutes the major immunogenic ectodomain on the viral particle surface, confronting which the anti-HBs response is directed (see also Fig. 5). Finally, the Ten ORF originated in the ancestry unique to orthohepadnaviruses (Fig. 2; see also Fig. iC and D).

The potent association of hepadnaviruses with their hosts over geologic eras suggests that the rate of viral macroevolution approximates that of their hosts. This synchronicity stays in sharp contrast to much faster rates of viral molecular development observed within infected individuals (Tedder et al., 2013). In line with the latter are findings from a written report on intra- and inter-host evolution in a family of chronic HBV carriers across three generations covering a 100-twelvemonth period of virus diversification (Lin et al., 2015). The viral evolutionary rate within each family unit member during the years of chronic infection was institute to be significantly faster than that betwixt the carriers in the vertical (female parent-to-baby) transmission bondage. Importantly, the authors observed an accumulation of not-synonymous substitutions at immune epitopes of structural genes in the viral quasispecies within each individual. To explicate the difference in substitution rates within and between hosts, the authors hence proposed the viral mutant spectrum to switch betwixt colonization and adaptation. ''Colonizers'' are thought to represent optimally replicating viruses that are in advantage early afterwards transmission into an immunologically naive host, particularly in newborns or immune-compromised persons. ''Adaptors'', on the other side, diversify under pressure of the host immune system during the late inflammatory phase of chronic infection at the price of replicative fitness. The fast intra-host evolutionary rates are hence attributed to the deviation of the ''adaptors,'' whereas the back-selection toward ''colonizers'' succeeding each transmission consequence is thought to be responsible for the slow viral macroevolution.

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