Immunological Distance Research Articles

Constrained evolution drives limited influenza diversity

H3N2 influenza A viruses have been widely circulating in human populations since the pandemic of 1968. A striking feature of the evolutionary development of this strain has been its 'canalized' nature, with narrow evolutionary trees dominated by long trunks with few branching, or bifurcation events and a consequent lack of standing diversity at any single point. This is puzzling, as one might expect that the strong human immune response against the virus would create an environment encouraging more diversity, not less. Previous models have used various assumptions in order to account for this finding. A new analysis published in BMC Biology suggests that this processive evolution down a single path can be recapitulated by a relatively simple model incorporating only two primary parameters - the mutation rate of the virus, and the immunological distance created by each mutation - so long as these parameters are within a particular narrow but biologically plausible range.See research article: http://www.biomedcentral.com/1741-7007/10/38

Phylogenetic relationships based on two mitochondrial genes and hybridization patterns in Anatidae

AbstractWe produced DNA sequence data from two mitochondrial genes (cytochrome b and the NADH dehydrogenase subunit 2) to reconstruct the phylogenetic relationships among 121 species of the Anseriformes (waterfowls including ducks, geese, swans, the magpie goose and screamers). Phylogenetic analyses converged into a congruent topology and defined several well‐supported clades. We calibrated a molecular clock and reconstructed ancestral biogeographical areas using Bayesian inference supporting an austral continental (Gondwanaland) origin of the waterfowls. Ducks, swans and geese might have diversified during the Miocene (23–5 Myr ago) reaching northern distributions in Holarctic and Afrotropical regions. The evolution of hybridization patterns in Anseriformes has been investigated using a cladistic analysis (morphology), which may underestimate or overestimate the phylogenetic divergence among species, or restricted only to ducks. Using a phylogenetic framework, genetic‐based distances and a Bayesian time calibration, our data support the hypothesis based on immunological distances of slow rate of appearance of reproductive incompatibilities in waterfowls compared with other vertebrates and the view that these birds may be like frogs in having lost their interspecific hybridization potential more slowly than mammals.

Modelling the relationship between antibody-dependent enhancement and immunological distance with application to dengue

When antibodies raised in response to a particular pathogen bind with immunologically similar pathogens it may facilitate infection through a phenomenon known as antibody-dependent enhancement (ADE). This process occurs between the four serotypes of dengue virus and, furthermore, secondary infection is a major risk factor in dengue hemorrhagic fever (DHF). Theory has suggested that ADE may be responsible for the large immunological distance between dengue serotypes. We investigate this hypothesis using an epidemic model for dengue in which immunological distance and the strength of immune cross-reaction are expressed separately. Cross-enhancement is considered in three alternative forms acting on susceptibility, transmission and mortality. Previous models have shown that transmission and mortality enhancement can lead to periodicity or chaos. We confirm this result for reasonable levels of susceptibility and transmission enhancement but not for mortality enhancement. We also show that when the two strains have identical basic reproductive numbers no form of enhancement leads to competitive exclusion. When the two strains have different basic reproductive numbers susceptibility or transmission enhancement allow strains with greater immunological similarity to stably coexist but mortality enhancement forces strains to be more distinct. All three forms of enhancement can be associated with DHF and we conclude that mortality enhancement must be dominant if ADE really is responsible for the immunological distance between dengue serotypes.

Why are dengue virus serotypes so distantly related? Enhancement and limiting serotype similarity between dengue virus strains.

Dengue virus, the causative agent of dengue fever, has four major serotypes characterized by large genetic and immunological distances. We propose that the unusually large distances between the serotypes can be explained in the light of a process of antibody-dependent enhancement (ADE) leading to increased mortality. Antibody-dependent enhancement results from a new infection with a particular serotype in an individual with acquired immunity to a different serotype. Classical dengue fever causes negligible mortality, but ADE leads to the risk of developing the significantly more dangerous dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS). A mathematical model is presented that describes the epidemiological dynamics of two serotypes of a pathogen where there is the possibility of co-infection and reinfection by a different serotype, along with increased mortality as a result of enhancement. We show that if there is no or slightly increased mortality after reinfection (enhancement), serotypes with a small immunological distance can stably coexist. This suggests that a cloud of serotypes with minor serological differences will constitute the viral population. By contrast, if enhancement is sufficiently great, a substantial immunological distance is necessary for two serotypes to stably coexist in the population. Therefore, high mortality owing to enhancement leads to an evolutionarily stable viral community comprising a set of distantly separated serotypes.

Morphological and pelage characteristics of wild living cats in Scotland: implications for defining the ‘wildcat’

AbstractThe indigenous wildcat, Felis silvestris Schreber, 1775, and the introduced domestic cat, F. catus L., have been sympatric in Britain for more than 2000 years. As a result of interbreeding, any distinction between these two forms has become obscured, although a range of morphological criteria (pelage patterns, body measurements, gut lengths, skull morphometrics) and genetic techniques (immunological distances, electrophoresis, DNA hybridization) have been used previously to distinguish between them.A sample of 333 wild‐living cats in Scotland was assessed for coloration and markings of pelage, standard body measurements and weights, and (for carcasses only) limb bone lengths, intestine lengths, and skull measurements. These cats were also classified as wildcat, hybrid, or domestic cat according to traditional pelage criteria.Multivariate analyses on these variables, for adult cats, failed to show any clearly distinct groups. When each of the variables was analysed separately, only the distribution of limb bone and intestine length measurements suggested the possibility that two groups might exist. Group 1 cats had short intestines and long limb bones. Group 2 consisted of cats with long intestines and short limb bones. Although the characteristics defining cats in Group 1 were similar to those traditionally associated with wildcats, they exhibited a much broader range of pelage and coloration than traditionally described.The groups exhibited a degree of geographical separation. The distribution of Group 1 cats was found to be related to certain environmental variables, namely mean annual temperature and land with poor potential for forestry and agriculture, suggesting that there may be a biological basis for the separation. The implications of these results on the identification and taxonomy of the wildcat are significant. The concept of the wildcat and the domestic cat as separate species can be challenged. The paper highlights the complexity and difficulties for conventional taxonomy when used as a means for distinguishing between a wild type and its domesticated form where there is interbreeding.

Determination of mycobacterial phylogeny on the basis of immunological relatedness of superoxide dismutases.

Sixteen strains of cultivable mycobacteria were grown in Sauton's medium, and Mycobacterium leprae was purified from armadillo liver. Cell extracts were prepared from log-phase growths of each of the cultivable mycobacterial strains. Superoxide dismutase (SOD) enzyme was purified from all cultivable mycobacterial strains included in the study, and antibodies against purified SOD enzyme were raised in rabbits. Immunological distances (ImDs) between these anti-SOD antibodies and SOD antigens were determined by a previously described immunoprecipitation method and by a recently developed enzyme-linked immunosorbent assay (ELISA) technique. The reciprocal ImDs among mycobacterial strains were constant, reproducible and consistent by these two methods. An evolutionary tree was constructed on the basis of estimated ImDs. Except for M. duvalii and M. terrae, slowly and rapidly growing mycobacterial species appeared to be separately grouped by this analysis. Rapid growers clustered into a group which is near that of some slow-growing mycobacteria. M. avium falls almost in the middle of the evolutionary tree and the position of M. leprae was found to be between those of M. avium and M. bovis BCG. Measurement of immunological relatedness of SODs provides an alternative system with which to study the taxonomical relatedness among mycobacteria.

Evolutionary relationships of cartilaginous fishes: an immunological study

An investigation of the phylogenetic relationships of a number of cartilaginous fish based on the use of the immunological properties of the iron‐binding serum protein, transferrin. is presented. Data on immunological distance and the rate of amino acid substitution are used to produce a dendrogram. The tree confirms the close relationships of the holocephalan species examined which are a sister group of other neoselachians. The tree also indicates that the squaloids and galeoids are separate groups and that Heterodontus belongs with the galeoids. It is also clear that the divergence between the squaloids, galeoids (including Heterodontus) and the Holocephali is an ancient one and that the rajids probably diverged from this basal stock rather than any more recent squaloid/squatinoid/galeoid grouping.

A multidisciplinary approach to the fine-systematics within Tisbe - an evaluation of morphological and molecular methods

Six species from the species-rich taxon Tisbe (Copepoda, Harpacticoida) were selected that could be reared in the laboratory as mass cultures. Phylogenetic relationships among these species were assessed by morphological studies of adults and larvae, DNA restriction site polymorphisms, allozymic, immunological distance, and lipid composition. Limits of scope and practicability of these analyses became apparent, as well as their potential and importance for future work in zoological systematics.

Geographic Variation of Serum Albumin in the Monotypic Snake Genus Diadophis (Colubridae: Xenodontinae)

-The ringneck snake, Diadophis punctatus (Colubridae [s.l.l Xenodontinae), is one of the most widespread snake species in North America. Thirteen subspecies currently are recognized based upon variation in several morphological characters. An antiserum prepared against the serum albumin of the eastern subspecies, D. p. edwardsii, revealed very high levels of variation in albumin across the range of this species. The immunological distances (direct estimates of amino acid differences) range from 0 to 25; this degree of albumin divergence typically is found between congeneric species in other vertebrates, including snakes, and indicates substantial genetic differentiation within D. punctatus. The primary division within this genus appears to separate eastern and western (including midwestern) subspecies and dates to approximately the Miocene. These data indicate that Diadophis may not be a monotypic genus, but instead contains at least two genetically distinct species. Molecular techniques have proven to be invaluable in detecting genetic variation between taxa having no obvious or consistent morphological differentiation (Highton, 1979; Donnellan and Aplin, 1989; Hedges and Thomas, 1991). Some workers have suggested that investigations of genetic variation at the species level is the province of isozyme, cytogenetic, and, most recently, DNA sequence data (Hillis and Moritz, 1990). However, estimates of amino acid sequence divergence between proteins obtained using the immunological technique of micro-complement fixation (MC'F) have helped to reveal a number of cryptic species (Maxson, 1978; Scanlan et al., 1980; Maha et al., 1983). Although MC'F primarily has been applied to problems of inter-specific and inter-generic lecular techniques have proven to be inluable in det cting genetic variation between a having no bvious or consistent morphoical dif erentiation (Highton, 1979; Donneland Aplin, 198 ; Hedges and Thomas, 1991). e workers have suggested that investigai ns of genetic vari t on at the species level is e province of isozyme, cytogenetic, and most cently, DNA sequence data (Hillis and Movariation, this technique has proven useful in intra-specific studies of geographic variation within widespread species (i.e., Plethodon glutinosus; Highton et al., 1989). Sequence divergence in serum albumin has been shown to increase in an approximately linear manner with time across a wide diversity of vertebrate taxa; an average of 10 amino acid substitutions between taxa accumulate every 6 million years (Maxson, 1992). This relationship indicates that data generated through MC'F can provide insights on divergence times between lineages. The xenodontine snake genus Diadophis (Baird and Girard, 1853), currently recognized as a monotypic species (punctatus), is one of the most widely distributed North American snakes, ranging from southern Canada into Mexico, and 105 This content downloaded from 157.55.39.177 on Fri, 18 Nov 2016 04:12:50 UTC All use subject to http://about.jstor.org/terms

Evolution in the Murinae (Rodentia) Assessed by Microcomplement Fixation of Albumin

The inter-relationship of 17 genera of Murinae rodents were studied using microcomplement fixation of albumin to measure immunological distances among taxa. The genera chosen represented six major clades and four monogeneric groups identified in earlier companion studies (an African group, a South-east Asian group, a New Guinean group, an Australasian group, an Acomys group, a Micromys group and Apodemus, Millardia, Mus and Phloeomys). When these companion studies are included 136 species and 67 genera were studied. Ten major clades were consistently supported by the data but apart from linking the South-east Asian and Australasian clades, the data do not resolve their inter-relationships. The Acomys-Uranomys-Lophouromys clade may be the sister-group to the rest of the Murinae. Otomys (Otomyinae) is considered to be a murine related to the African group of genera. Of the ten major clades identified, only one (Mus) occurs significantly in more than one primary biogeographic region. It is suggested that following an early period of relatively rapid dispersal from the place of origin, little further dispersal took place and subsequent evolution occurred within relatively confined geographic areas.

Evolution in Some South-East Asian Murinae (Rodentia), as Assessed by Microcomplement Fixation of Albumin, and Their Relationship to Australian Murines

The interrelationships of 16 genera and 49 species of predominantly South-east Asian murine rodents were studied by means of microcomplement fixation of albumin to measure immunological distances among taxa. The results are viewed as a hypothesis of the phylogenetic relationship of these taxa that can be tested by other data sets. Three main groupings are suggested: (1) Maxomys; (2) Leopoldomys, Niviventer and Tokudaia; and (3) Bandicota, Berylmys, Bullimus, Bunomys, Komodomys, Nesokia, Papagomys, Paruromys, Rattus, Stenomys, Sundamys and Taeromys. Within this latter group, Bunomys chrsogasta, Komodomys and Rattus timorensis group together, as do Bullimus, Rattus and Stenomys, and Bandicota with Nesokia. The Australian murines, represented by Mesembriomys, may be part of this South-east Asian radiation but, if so, arose early in its history. Biogeographically, the results support South-east Asia as being a centre of murine evolution with secondary foci in Sulawesi, New Guinea and Australia. There is some evidence to suggest that a relatively recent land bridge between Sulawesi, Flores and Timor may have existed.

Phylogenetic relationships and call structure in four African bufonid species

Four species of toads of the genus Bufo, comprising three species endemic to southern Africa and one closely-related species, were examined electrophoretically to infer their phylogenetic relationships. The evolution of advertisement call structure in these species is discussed in relation to this phylogeny. Bufo rangeri and B. gutturalis, two species with very different call structures, are sister taxa. Two pairs of species with very similar call structures, B. partialis and B. gutturalis, and B. rangeri and B. angusticeps, were only distantly related. Our resufts suggest that call parameters are poor characters to use in inferring phylogenies among congeneric species, probably because of selection for optimal audibility in different habitats, and because of the role that they play in premating isolation. The phylogeny derived from allozyme data agrees with evidence on albumin immunological distance, karyotype and morphology.

Evolution in New-Guinean Muridae (Rodentia) Assessed by Microcomplement Fixation of Albumin

The interrelationships of 19 genera and 28 species of New Guinean rodents representing 80% of the currently recognised New Guinean genera, were studied using microcomplement fixation of albumin to measure immunological distances among genera. The phylogenetic distinctiveness of Rattus and the closely related Stenomys from all other genera was confirmed. The remaining genera fall into three groups: (i) Lorentzimys; (ii) Anisomys, Coccymys, Chiruromys, Hyomys, Macruromys, Mallomys and Pogonomys; and (iii) Crossomys, Hydromys, Leptomys, Mayermys, Melomys, Neohydromys, Parahydromys, Pseudohydromys and Uromys. Solomys, from the Solomon islands, and Leggadina, Mesembriomys and Xeromys, from Australia, were shown to belong to this latter group. Groups (i) and (ii) are essentially endemic to New Guinea, while the third shares genera and species with Australia.

The sequence-immunology correlation revisited: Data for cetacean myoglobins and mammalian lysozymes

Quantitative microcomplement fixation tests employing rabbit antisera were done to compare immunologically 13 cetacean myoglobins and 15 mammalian lysozymes c of known amino acid sequence. In both cases there was a strong correlation between immunological distance (y) and percent sequence difference (x), as had been found for several other globular proteins. For myoglobin the relationship could be described by y = 10.5x and for lysozyme by y = 8.5x. The coefficients in both of these equations are appreciably higher than the values of 5.1-6.9 reported for three other vertebrate globular proteins (bird lysozyme c, mammalian ribonuclease, and mammalian serum albumin), and they imply that rabbit antisera to mammalian myoglobins and lysozymes are more sensitive to evolutionary substitutions. A strong inverse correlation (r = -0.95) was found when the slope of the line relating y to x for these five data sets was plotted against the percent sequence difference between the rabbit's own protein and the proteins immunized with. Specifically, the cetacean myoglobins on average differ in amino acid sequence from rabbit myoglobin by less than 13% and exhibit the steepest slope (10.5), while bird lysozyme sequences differ by nearly 40% from rabbit lysozyme and exhibit the shallowest slope (5.1).

Variations of molar morphology in the Spalax ehrenbergi superspecies: adaptive and phylogenetic significance

This study compares and contrasts variations of enamel fold pattern on the crowns of the molars of subterranean mole rats (Spalax) belonging to two superspecies, S. ehrenbergi and S. leucodon, and involving about 20 chromosomal species, distributed parapatrically and ranging on different soil types. The sample studied involved 397 skulls, subdivided as follows: 280 of S. ehrenbergi from Israel, representing the four chromosomal species 2n = 52, 54, 58 and 60; 59 of S. ehrenbergi from Egypt, Lebanon, Syria, Jordan and Turkey; 58 of S. leucodon from Turkey.In making the comparisons it was necessary to take into account the marked changes of molar pattern that take place as a result of wear.There is a reasonably good agreement between differences of molar pattern and genetic and immunological distances. The species in Israel and Egypt form a compact group, clearly differentiated from Turkish leucodon; ehrenbergi from Turkey and Syria are intermediate, in accordance with their geographical distribution.In Israel, differences associated with soil type are at about the same level as differences between species. Local populations show a higher level of diversity, and in a number of cases neighbouring populations differed significantly, sometimes over very short distances. Population differences within species are generally associated with differences of soil and vegetation, indicating the influence of natural selection. There are also differences across species boundaries, implying a phylogenetic (heritage) effect. The nature of the adaptive link between molar pattern and soil is unknown: possible factors are contamination of the food by soil, and toughness of the food which necessitates changes of enamel fold length to improve grinding efficiency.

A re-evaluation of the taxonomic status of the Moldavian steppe viper based on immunological investigations, with a discussion of the hypothesis of secondary intergradation between Vipera ursinii rakosiensis and Vipera (ursinii) renardi

AbstractThe taxonomic level and phylogenetic relationship of the Moldavian steppe viper was investigated using blood serum electrophoresis, immunological comparisons of blood serum albumin and morphological comparisons. The traditional hypothesis that the Moldavian steppe viper is a secondary intergradation between Vipera (ursinii) renardi and V. ursinii rakosiensis could not be verified. Although morphologically similar (but not identical) to these two taxa, it has a closer immunological distance to the Balkan mountain subspecies, V. u. macrops and V. u. graeca. Specific antisera against serum albumins of V. u. graeca, V. u. ursinii (wettsteini) and V. u. eriwanensis were available, and the three vipers to be tested: rakosiensis, renardi and the Moldavian steppe viper branch off from different stems: rakosiensis seems close to ursinii, V. (u.) renardi appears fairly close to eriwanensis, both of which share a common stem with the rakosiensis-ursinii lineage. The Moldavian steppe viper shows high distance to both ursinii and eriwanensis, but low distance to graeca. The electrophoretic pattern show great differences from all other geographic forms tested (seven). We conclude that the Moldavian steppe viper represents a separate subspecies: Vipera ursinii moldavica ssp.n.

Bootstrap approaches to estimating confidence intervals for molecular dissimilarities and resultant trees

Varied approaches to estimating confidence intervals for immunological and hybridization distances can be uniformly applied to any matrix of distances. One procedure bootstraps the pairwise dissimilarities between the distances of every pair of taxa to all others, creating a derived matrix of distances for which dispersions can be estimated. Another approach bootstraps the sample of differences between pairwise homologous branch lengths concerning each pair of taxa and between asymmetric halves of the matrix, to find a standard error of the dispersions. This allows comparison of the robustness of trees among different sources of data. DNA hybridization, transferrin immunology and protein immunodiffusion matrices all yield much the same result once standard deviations of dissimilarities are acknowledged: namely, unresolvable trichotomies among the human-chimp-gorilla clade and among this clade with orang and gibbon; conventional relationships among hominoids, cercopithecoids, ceboids and strepsirhines; and a polychotomy among anthropoids, strepsirhines, tarsiers, tupaiids and dermopterans.

Albumin evolution and phylogenetic relationships among Greek rodents of the families Arvicolidae and Muridae

The phylogenetic relationships of seven rodent species Microtus atticus, M. thomasi, M. epiroticus (family Arvicolidae) and Mus domesticus, Rattus norvegicus, Apodemus flavicollis and A. mystacinus (family Muridae) have been studied. In order to define these relationships we study the albumin evolution using the micro‐complement fixation test (MC'F). No phylogenetic (immunological) distance between M. atticus and M. thomasi was found, a fact which confirms from the biochemical point of view the opinion that the former taxon is a synonym of the latter one. A molecular time scale relating MC'F immunological distances and geological time was established based on the assumption of a rate of 100 amino acid substitutions per–20 million years. The time of divergence between M. epiroticus and M. thomasi was estimated to be 0.5–0.6 million years ago (Pleistocene). Such a recent divergence corroborates the opinion based on morphological and protein electrophoretic criteria according to which Terricola (formerly Pitymys) must be considered as a subgenus of the genus Microtus and not as a distinct genus Pitymys, as previously had been accepted. Apodemus flavicollis and A. mystacinus were separated about 0.65–0.8 million years ago (Pleistocene). The Rattus norvegicus lineage was separated–12.5 million years ago (end of Miocene), shortly before the Mus and Apodemus divergence. Our data indicate that the common ancestor of Arvicolidae and Muridae lived–25 million years ago (early Miocene). All these results are in agreement with paleontological and some recent DNA‐DNA hybridization and electrophoretic data.

Is survival of European wildcats Felis silvestris in Britain threatened by interbreeding with domestic cats?

The relationship of the domestic cat Felis catus in Britain to the European wildcat Felis silvestris remaining in northern Britain includes a significant overlap of the phenotypic features of introgressive hybrids. The status of wildcats as a separate endangered species requiring protection to remain viable in the wild required analysis of their genetic relationship to domestic cats. Despite the discovery of free-living cats with both phenotypic resemblance to F. silvestris and close genetic similarities to F. catus, as measured by nucleic acid probe analysis, albumin heterogeneity (immunological distance) and isoenzyme analysis, eight of 42 putative wildcats caught in remote areas of northern and western Scotland showed clear differences from F. catus in the genetic analyses used. These eight wildcats had pelages consistent with the wildcat; however, 15 of the remaining cats had pelages containing domestic cat characters and had either one or no wildcat genetic character. The results suggest that some genetically distinct European wildcats remain in Britain, and the efforts to prevent interbreeding with domestic cats may enhance their conservation.

Phylogeny and systematics of viperine snakes. III: resurrection of the genus Macrovipera (Reuss, 1927) as suggested by biochemical evidence

Abstract The phylogenetic relationships of the large Palaearctic vipers (Daboia sensu Obst, 1983) and Eristicophis were investigated using immunological comparisons of blood serum albumin and blood serum electrophoresis. The genus Echis was used for outgroup comparisons. Daboia was found to be polyphyletic. The name Daboia should be restricted to the type species russelli which was found to have the same immunological distance to the lebetina group as the monophyletic Pseudocerastes-Eristicophis group. The lebetina group was found to consist of the four species lebetina, schweizeri, mauritanica and deserti. For this group the generic name Macrovipera is revalidated. The taxa schweizeri and deserti are treated as full species. Vipera palaestinae was found to be the closest relative of the V. xanthina group. Nomenclatural history and distribution of the involved taxa is reviewed. Descriptions and diagnoses for the genus Macrovipera and the included species are given.