Academic literature on the topic 'Phylogenetic analysis program (PAUP)'

Within the present study, it was conducted a genetic diversity analysis using ISSR markers for some apple genotypes grown in Ardahan region, Turkey. Total genomic DNA (gDNA) isolation from apple leaves was performed using commercial kits. Five ISSR primers were used to determine the genetic diversity among the genotypes studied. Polymerase Chain Reaction (PCR) was performed with all gDNA samples to produce bands to score. PCR products were run in agarose gel and visualized under UV light. Bands on the gels were scored as “1”, while no bands at the corresponding positions were scored as “0”, to generate the matrix file. Five ISSR primers produced a total of 35 bands, and 20 of them were polymorphic. The polymorphic bands rated approximately 57%. Phylogenetic relationships and genetic distances between the genotypes were calculated by using the PAUP [Phylogenetic Analysis Using Parsimony (and Other Methods)] program. According to the PAUP data, the closest genetic distance was 0.03704 between ‘Kaburga’ and ‘Japon Apple’ genotypes, while the furthest genetic distance was 0.48148 between ‘Karanfil Apple’ and ‘Sisli Uruset’. The phylogenetic analysis obtained using UPGMA algorithm produced a phylogenetic tree with two clades. The results suggest that ISSR markers are useful tools for determining genetic relationships among apple genotypes.

In this study, we performed a genetic diversity analysis using RAPD markers for some Vitex agnus-castus populations grown in Aydin, Turkey. Total genomic DNA isolation from the leaves of Vitex agnus-castus was performed using a commercial kit. Seven RAPD primers (OPA-02, OPA-05, OPA-13, OPA-15, OPA-16, OPA-18, OPA-20) were used to determine genetic diversity among populations. Polymerase Chain Reaction (PCR) was performed with all genomic DNA samples and primers. PCR products were run in agarose gel electrophoresis and visualized under UV light. The amplified products were scored as bands (1) and no bands (0) for all gel images and their matrix files were generated. A total of 36 characters were obtained from the primers. Phylogenetic relationships and genetic distances between the cultivars were calculated by using the PAUP* (Phylogenetic Analysis Using Parsimony and other methods) program. According to PAUP analysis, the closest genetic distances were between Çine pink flower and Çakmar purple flower, and Çakmar pink flower and Çakmar purple flower populations with a value of 0.05556; and the greatest genetic distance was between Çakmar pink flower and Köşk purple flower populations with a value of 0.36111. In the phylogenetic analysis obtained using UPGMA algorithms, the phylogenetic tree consisted of four groups. The results suggest that RAPD markers are useful tools for determining genetic relationships among Vitex agnus-castus genotypes.

In this study, genetic variation and phylogenetic analysis of 13 populations of 6 species belonging to Conringia genus spreading in Turkey were performed using RAPD markers. Genomic DNA isolation from the leaves of the Conringia plant samples was performed via using a commercial kit. Seven RAPD primers were used to identify the genetic diversity between the populations. Polymerase Chain Reaction (PCR) was performed using DNA samples and primers. PCR products were resolved using agarose gel electrophoresis and visualized under UV light. All gel images were analyzed, and the absence and presence of polymorphic bands were scored. The total of 34 DNA bands were detected by seven RAPD primers. PAUP 4.0b10 analysis program was used to calculate phylogenetic tree and genetic distances between the species. The phylogenetic tree was obtained using the UPGMA algorithm and it was composed of two clades. According to the PAUP analysis, the species having the closest distance between each other are C. planisiliqua (Ankara-Aya?) and C. planisiliqua (Ankara-Nall?han) with the value of 0.000 and those having the longest distance are C. grandiflora (Akseki ?ukurk?y) and C. orientalis (Elaz??-Baskil) with the value of 0.6000. The results suggest that the RAPD markers are useful tools to demonstrate the genetic relationships between populations of the Conringia species.

We have initiated a phylogenetic study using restriction fragment length polymorphisms to examine nuclear DNA variation in a number of Rosa species. Random genomic clones were isolated from the cultivar `Confection'. To generate these clones, genomic DNA was digested with the restriction enzymes Hind III and Eco RI and the resulting fragments cloned into a pUC8 plasmid and transformed into the E. coli bacterial strain JM83. Individual clones from the DNA library were screened for polymorphism by Southern hybridization methods. Those clones displaying polymorphisms were used in combination with one, two, or three restriction enzymes to identify different size restriction fragments. Each fragment was treated as a unit character and was used to generate a phylogenetic tree using the computer program “Phylogenetic Analysis Using Parsimony” (PAUP version 3.0). Results of the studies on the amount of genetic diversity and phylogenetic affinities of Rosa species among the different sections of the subgenus Rosa will be presented.

The cosmopolitan Phoma genus contains mainly phytopathogenic, opportunistic parasite, and saprophyte fungal species. Up to now the characterization of Phoma species and other taxa of Phoma has so far been determined on the basis of morphology on standardized media, and gene sequence analysis was only used as a confirmative or distinctive complement.In this study we have tried to study phylogenetic relationships by maximum likelihood method in the Phoma genus. We employed a part of the gene responsible for the synthesis of translation elongation factor 1 subunit alpha protein (tef1) containing both introns and exons, a part of the gene responsible for synthesis of tubulin protein and ITS region containing the internal transcribed spacer regions 1 and 2 and the 5.8S rDNA as potential genetic markers to infer phylogenetic relationships among different Phoma taxa. Twenty-four isolates of eleven different Phoma species were firstly characterised by morphologically, and then their tef1, tubulin and ITS sequences were sequenced and analysed by maximum likelihood method carried out by PAUP*4.0b program. According to constructed phylogenetic trees, the different Phoma taxons are well separated. However these trees do not support the traditional Phoma sections based on morphological characterization.The maximum likelihood analyses of all three sequences confirmed that the Phyllosticta sojicola species is clustered with the Phoma exigua var. exigua group and the Phoma sojicola is grouped with Phoma pinodella group. The experienced molecular evidences initiate the demand of reclassification of formerly mentioned soybean pathogens.

AbstractAn analysis is given of the relationships between the genera of the tribe Cylindroiulini. The situation at present is reviewed first. Various characters are described which are subsequently used in the construction of a cladogram. The result is the splitting of the genus Allajulus Koch into three genera, Allajulus, Cylindroiulus Verhoeff, and Kryphioiulus gen. n., this last genus being erected for occultus C. L. Koch. Use of a computer program, PAUP (phylogenetic analysis using parsimony), in general confirms these divisions. The nominal genera Micromastigoiulus Verhoeff, Dendroiulus Verhoeff, Solaenoiulus Schubart, Olisteroiulus Lohmander are synonymized with Cylindroiulus. The position of the Cylindroiulini within the family Julidae is also discussed and a preliminary phylogeny presented. A key to the genera and species of the tribe Cylindroiulini, omitting species in the genus Cylindroiulus, is given in an appendix.

The larvae of Antiporus blakeii (Clark), A. femoralis (Boheman), A. gilbertii (Clark), A. hollingsworthi Watts, A. jenniferae Watts, A. uncifer Sharp and A. willyamsi Watts are described with an emphasis on chaetotaxy of the head capsule, head appendages, legs, last abdominal segment and urogomphi. A parsimony analysis based on 17 informative larval characteristics was conducted using the program PAUP*. The 11 most parsimonious trees support a monophyletic origin of the genera Antiporus Sharp, Nebrioporus Régimbart, Scarodytes Gozis, and Stictotarsus Zimmermann. Unambiguous synapomorphies supporting this clade are the presence of natatory setae on the femur, tibia and tarsus and the presence of a very elongate urogomphomere 1. It is postulated that these features evolved as swimming devices. The genus Oreodytes Seidlitz is postulated to represent the sister-taxon of Antiporus + Nebrioporus + Stictotarsus + Scarodytes and this clade is characterised by the absence of the maxillary cardo and insertion of the primary seta MX1 on the maxillary stipes.

AbstractA cladistic analysis of the family Xyalidae has been carried out, with selected Monhysteridae and Sphaerolaimidae as presumptive outgroups. Forty nine characters, taken from published descriptions, were scored for 91 species from 33 genera. The way in which the characters were coded is illustrated by drawings and graphs. Phylogenetic analyses were conducted with the programs PAUP*4.0d65 and PAUP*4.0b2. Neighbour-joining and parsimony trees were constructed and the preferred consensus parsimony tree is presented. The tree has been divided into 15 groups for purposes of discussion. All eight species of Monhysteridae form a separate clade consistent with outgroup status, but the four species of Sphaerolaimidae are not separated from Xyalidae. Several of the Daptonema species, Pseudosteineria plus Steineria, and Rhynchonematinae form three well supported clades. Other groupings are much less well supported and are presumed to be paraphyletic. Many published descriptions do not include sufficient detail to allow relationships to be determined and suggestions are made as to data which should be included in future taxonomic descriptions of Xyalidae.

Armina is the most species-rich genus of the Arminidae family with over 50 nominal species. Material of the genus Armina from the western Atlantic and the eastern Pacific was revised. Six species have been documented from the western Atlantic; however, we have determined that only four of them are valid: Armina muelleri, A. wattla, A. juliana and A. elongata. Also, only three out of seven species previously registered in the eastern Pacific were recognized in the present study: A. californica, A. cordellensis and Armina sp., an unnamed species. The phylogenetic analysis of 13 taxa and 17 characters was performed using the program PAUP (Phylogenetic Analysis Using Parsimony). The Branch-and-Bound algorithm generated a 29-step tree with the following relations: (Histiomena convolvula, (Dermatobranchus sp., ((((A. californica , (A. maculata, A. muelleri)), ((A. loveni, A. neapolitana), A. wattla)), (A. cordellensis, (Armina sp., A. juliana))), (A. tigrina, A. elongata)))). The monophyletic evidence for Armina is discussed and compared to possible speciation processes similar to those found in other Opisthobranchia groups.

AbstractEighty characters of larvae and adults of 35 adephagan genera, 2 polyphagan genera, and 1 cupedid genus were analyzed using the cladistic computer programs PAUP and MacClade. The analysis resulted in 1961 equally parsimonious trees of 131 steps (minimum length cladogram). The monophyly of Adephaga and of all adephagan families is confirmed. A sistergroup relationship between Gyrinidae and the remaining Adephaga, a sistergroup relationship between Spanglerogyrus and Gyrininae, the monophyly of Dytiscoidea, a sistergroup relationship between Noteridae and the remaining Dytiscoidea, a sistergroup relationship between Hygrobiidae and Dytiscidae, the monophyly of Caraboidea (Rhysodidae and Carabidae), and the monophyly of Harpalinae sensu Crowson (1955) are in agreement with earlier phylogenetic hypotheses by Beutel & Roughley (1988) and Beutel (1992a, 1993, 1995). The sistergroup relationship between Haliplidae and Dytiscoidea and the monophyly of Geadephaga (Trachypachidae + Caraboidea) are in contrast to Beutel (1992a, 1993, 1995). The high number of equally parsimonius trees is largely due to an inconsistent distribution of character states in basal carabid taxa, i.e. reversals and convergencies. Further evidence is needed for a clarification of these systematic problems.

The morphology of the larvae, pupae and adults of Camptosomata (Cryptocephalinae and sister-group Lamprosomatinae) is reviewed, with special reference to the Australian fauna. Terminology for the larval structures is redefined and a special study is made of the adult female oviposition structures. The morphological data base is studied with the phylogenetic analysis program PAUP and the variation of characters and taxa examined further with the program MACCLADE. The morphological data and the phylogenetic analyses based on these data are applied to the redefinition of the Camptosomata and constituent taxa using a cladistic methodology. The Camptosomata are redefmed and their possible sister-groups discussed. The Camptosomata are shown to be a monophyletic group and to exclude both Megascelidini (a tribe ofEumolpinae) and Synetinae. The Camptosomata comprise two subfamilies, Lamprosomatinae and Cryptocephalinae. Four tribes of Cryptocephalinae are recognised and redefined. One of these, the Cryptocephalini, with a high proportion of Australian taxa, is divided into five subtribes of 1, 3, 3, 5 and 11 genera. The following nomenclatural changes are proposed (ignoring changes of rank): Platycolaspina subtribe nov., Coenobiina subtribe nov., Ditropidina subtribe nov. and synonymy of Monachina (a homonym) and Cryptocephalina. New genera or subgenera proposed are : Semelvillea (in Platycolaspina), Ditropidella (in Ditropidina)and M elatia (in Cryptocephalina), and the subgenera Aorocarpon and Cadnwides in Cadmus Erichson (Cryptocephalina). The following generic synonymy is proposed (senior synonym first) : Leasia Jacoby(= Agetinella Jacoby); Aprionota Maulik (= Cephalocryptus Gressitt, Pycnophthalma Maulik); Ditropidus Erichson (= Bucharis Baly, Elaphodes Suffrian, Euditropidus Lea, Pleonwrphus Chapuis, Polyachus Chapuis, Prasonotus Suffrian, Tappesia Baly); Scaphodius Chapuis (=Nyetra Baly); Cryptocephalus Geoffroy(= Jaxartiolus Jacobsen andBassareus Haldeman); Aporocera Saunders(= Chariderma Baly, Chloroplisma Saunders, Cyphodera Baly, Loxopleurus Suffrian, Melinobius Jacoby, Rhombosternus Suffrian, Schizosternus Chapuis). New combinations of genera in tribes and subtribes are Mylassa Stal reinstated as a valid genus in Pachybrachini, Platycolaspis Jacoby andLeasia Jacoby in Cryptocephalini (Platycolaspina) and Arnomus Sharp and Atenesus Weise in Platycolaspina. As a result of the above new generic synonymy, several new species combinations are made. The new genus Semelvillea ,with eight species, is mono graphed. Types of three-quarters of the described species of New Zealand and Australian Cryptocephalinae were examined and the following new species synonymy is made (senior synonym first): Chlamisus aterrimus (Lea)(= C. australis Bryant); Arnomus curtipes Broun (=A. impressus Broun, =A. viridicollis Broun); Arnomus signatus · Broun ( = A. fulvus Broun, =A. vicinus Broun); Ditropidus anthracinus Erichsen ( = D. punctivarius Lea); Ditropidus aurichalceus Suffiian (=D. oblongipennis Lea); Ditropidus carbonarius Baly (=D. subsimilis Lea); Ditropidus festivus (Suffrian) (=D. suffriani Chapuis); Ditropidus maculicollis Chapuis (=D. erythroderes (Lea), =D. niger (Lea), =D. maculicollis (Weise)); Ditropidus ornatus Baly (=D. alphabeticus Lea); Ditropidus pallidipennis Chapuis (=D. dolichognathus (Lea)); Ditropidus ruficollis Saunders (=D. elegantulus Baly, =D. rufipes Saunders); Ditropidus saundersi (Baly) (=D. multimaculatus (Lea)); Ditropidus variiceps Lea (=D. marginipennis Lea); Aporocera albogularis (Chapuis) (=A. coccineus (Chapuis), =A. delicatulus (Lea)); Aporocera apicalis Saunders(= A. bicolor Saunders); Aporocera argentata (Chapuis) (= A.fasciata (Weise)); Aporocera aurantiaca (Chapuis) (=A. monticola (Blackburn)); Aporocera australis (Saunders) (=A. erosa (Saunders), =A. larinus (Lea)); Aporocera cicatricosa (Chapuis) (=A. calomeloides (Lea)); Aporocera gibba (Chapuis) (=A.lugubris (Lea)); Aporocera iridipennis (Chapuis) (=A. decens (Weise)); Aporocera libertina (Suffrian) (=A. castor (Lea)); Aporocera nigrolineata (Chapuis) (=A. castigatus (Lea)); Aporocera parenthetica (Suffrian) (=A. melanopa (Lea)); Aporocera paupercula (Germar) (=A. rufescens (Boheman)); Aporocera ring ens (Chapuis) (=A. clypealis (Lea)); Aporocera tasmanica (Saunders) (=A. impressicollis (Boheman)); Aporocera viridipennis (Saunders)(= A. t-nigrum (Lea));Aporocera viridis (Saunders)(= A. aereus (Suffrian)); Aporocera analis (Chapuis) (= A.foveiventris (Lea)); Cadmus crucicollis (Boisduval) (=C. canaliculatus Chapuis, = C. rugosus Suffrian); Cadmus litigiosus Boheman (=C. vibrans Suffrian); Cadmus cariosus Chapuis (=C. minor (Blackburn)); Cadmus pauxillus Chapuis (=C. perlatus Lea); Cadmus braccatus (Klug) (=C. saundersi Baly); Cadmus breweri(Baly)(= C. duboulai Baly). Representation of Cryptocephalinae in Australia is shown to be as follows (number of genera in brackets) : Chlamisini (1), Clytrini (1), Pachybrachini (1, introduced), Platycolaspina (4), Coenobiina (1), Ditropidina (2) and Cryptocephalina (4). Larvae and adults of the genera and subgenera in Australia and the south-western Pacific are diagnosed and keys are provided for the identification of these taxa at both life stages. The entire Camptosomatan fauna of Australia and the south-western Pacific is catalogued.

Echinococcus vogeli (Rausch and Berstein, 1972) and Echinococcus oligarthra (Diesing, 1863) (Cestoda: Taeniidae) are the only two species known of Neotropical tapeworms, which cause Echinococcosis Polycystic (EP) and Echinococcosis Unicystic (EU), respectively, in humans and in wild rodents from Central and South America. This review applied a meta-analysis on published research about these diseases during the last decade (2010–2020) with the aim of finding out the new human cases reported on that decade on EP and EU. Several new human cases have been published in these 10 years, and important findings have been carried out on the phylogenetic taxonomy, on the genome of E. oligarthra, and on new molecular diagnostic techniques and imagenology applied upon this two neotropical echinococcosis, in particular in Argentina and Brazil. Finally, the life cycle of both Echinococcus species appears to be in a dynamic activity, apparently there is an expansion of both zoonotic diseases moving down to Southern zones of Argentina; therefore, a program of epidemiological surveillance on EP and EU is proposed to be carried out in those Patagonic regions.

<em>Abstract</em>.—A century ago, sea sturgeon (Atlantic sturgeon <em>Acipenser oxyrinchus</em> and European sturgeon <em>A. sturio</em>) were prevalent in the fish communities of all major German rivers, both in the North and the Baltic Sea drainages. Since then, population sizes have decreased rapidly due to overfishing, pollution, and hydropower construction. The last catches in the Baltic drainage occurred in the late 1960s. Only individual captures of sturgeon have been reported in the last 30 years, the most recent being in Lake Ladoga (Russia) in 1984 and off the coast of Estonia in 1996, approximately 25 years after the disappearance of the species from the fishery. Today, sturgeon are considered extinct in German waters. In 1996, the Federal Agency for Nature Conservation, in cooperation with the Society to Save the Sturgeon, started the pilot phase of a remediation program involving assessment of the prerequisites for remediation. The first juvenile European sturgeon were transferred to the Leibniz-Institute of Freshwater Ecology and Inland Fisheries under a scientific cooperation agreement with the Centre d’Étude du Machinisme Agricole, du Rural, des Eaux et Forêts in May 1996. With these specimens, an ex situ measure was initiated. In addition, phylogenetic and population genetic analyses of the species were carried out using mitochondrial DNA and microsatellites. These genetic analyses of recent and historical material have proven the existence of two different species in what was previously considered the Baltic or common sturgeon. The Atlantic sturgeon has been identified as endemic in the Baltic Sea and the European sturgeon in the North Sea. According to morphological evidence based on archaeological samples, the Atlantic sturgeon invaded the Baltic Sea approximately 2,000 years ago and has been the only sturgeon species there for the last few centuries. These results led to the separation of the remediation activities in North Sea and Baltic Sea tributaries. Broodstock development using the northernmost populations of the Atlantic sturgeon is currently being carried out. Subsequent reproduction for restocking requires a sufficiently large broodstock and a genetic breeding plan based on pedigree analysis. As a further prerequisite, an evaluation of the status of critical habitat for the early life stages of Atlantic sturgeon in the Oder River has been performed in collaboration with the Institute for Inland Fisheries of Poland. Alternative fisheries techniques, based on data for the bycatch of exotic sturgeon, are being developed to reduce the fishing pressure on juvenile sturgeon upon release.

Objectives 1. Establish diagnostic procedures to identify tolerant carrier birds based on a) Isolation of ALV-J from blood, b) Detection of group-specific antigen in cloacal swabs and egg albumen. Application of these procedures to broiler breeder flocks with the purpose of removing virus positive birds from the breeding program. 2. Survey the AL V-J infection status of foundation lines to estimate the feasibility of the eradication program 3. Investigate virus transmission through the embryonated egg (vertical) and between chicks in the early post-hatch period (horizontal). Establish a model for limiting horizontal spread by analyzing parameters operative in the hatchery and brooder house. 4. Compare the pathogenicity of AL V-J isolates for broiler chickens. 5. Determine whether AL V-J poses a human health hazard by examining its replication in mammalian and human cells. Revisions. The: eradication objective had to be terminated in the second year following the closing down of the Poultry Breeders Union (PBU) in Israel. This meant that their foundation flocks ceased to be available for selection. Instead, the following topics were investigated: a) Comparison of commercial breeding flocks with and without myeloid leukosis (matched controls) for viremia and serum antibody levels. b) Pathogenicity of Israeli isolates for turkey poults. c) Improvement of a diagnostic ELISA kit for measuring ALV-J antibodies Background. ALV-J, a novel subgroup of the avian leukosis virus family, was first isolated in 1988 from broiler breeders presenting myeloid leukosis (ML). The extent of its spread among commercial breeding flocks was not appreciated until the disease appeared in the USA in 1994 when it affected several major breeding companies almost simultaneously. In Israel, ML was diagnosed in 1996 and was traced to grandparent flocks imported in 1994-5, and by 1997-8, ML was present in one third of the commercial breeding flocks It was then realized that ALV-J transmission was following a similar pattern to that of other exogenous ALVs but because of its unusual genetic composition, the virus was able to establish an extended tolerant state in infected birds. Although losses from ML in affected flocks were somewhat higher than normal, both immunosuppression and depressed growth rates were encountered in affected broiler flocks and affected their profitability. Conclusions. As a result of the contraction in the number of international primary broiler breeders and exchange of male and female lines among them, ALV-J contamination of broiler breeder flocks affected the broiler industry worldwide within a short time span. The Israeli national breeding company (PBU) played out this scenario and presented us with an opportunity to apply existing information to contain the virus. This BARD project, based on the Israeli experience and with the aid of the ADOL collaborative effort, has managed to offer solutions for identifying and eliminating infected birds based on exhaustive virological and serological tests. The analysis of factors that determine the efficiency of horizontal transmission of virus in the hatchery resulted in the workable solution of raising young chicks in small groups through the brooder period. These results were made available to primary breeders as a strategy for reducing viral transmission. Based on phylogenetic analysis of selected Israeli ALV-J isolates, these could be divided into two groups that reflected the countries of origin of the grandparent stock. Implications. The availability of a simple and reliable means of screening day old chicks for vertical transmission is highly desirable in countries that rely on imported breeding stock for their broiler industry. The possibility that AL V-J may be transmitted to human consumers of broiler meat was discounted experimentally.

Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.