Phylogenetic Relationship and Molecular Divergence Dating Using SRY Gene Polymorphism about Four Ladoum Sheep Lineages in Senegal

Animal genetic resources are playing a vital role in livestock production and are essential to food security. The present study aims to contribute to a better understanding genetic local sheep breeds and to elucidate the phylogenetic relationships through the evolution of the SRY gene in four different lineages of Ladoum sheep raised in Senegal. After a brief analysis of genetic diversity, the phylogenetic relationships and molecular dating were inferred through haplotype networks and four phylogenetic reconstruction methods. The different haplotype networks are constructed with NETWORK ver. 5.0.0.0 using the Median-Joining method. Phylogenetic trees were reconstructed using neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference. The robustness of the nodes in phylogenetic trees of the three first methods was assessed by 1000 bootstraps. For Bayesian inference, the posterior probability distribution of the trees was estimated by 4 MCMC chains. 5,000,000 generations were performed for each of the chains by sampling the different parameters every 1000 generations. Results show a low polymorphism. Haplotypic diversity is much higher than the average nucleotide divergence between all pairs of haplotypes. The majority and central haplotype indicates a close relationship between “Batling” and “Tyson” individuals. “Birahim” lineage is very distinct from the rest. Phylogenetic trees confirm two genetically separate clades between “Birahim” and the other lineages. The period of divergence between “Birahim” lineage versus the common ancestor of the other three lineages was 2504 years ago. The polyphyly revealed in “Birahim” lindicates that this lineage does not contain the common ancestor of all individuals who compose it. It could therefore be derived from two or more sheep breeds with a common ancestor, Ovis aries. The monophyletic clade appears to be a group including a common ancestor and all of its genetic descendants. This group, bringing together the other three lineages, is in the process of being structured into sub-lineages. This study is the first to show that there are only two genetic lines within ladoum sheep in Senegal.

A preliminary analysis of phylogenetic relationships of Arundinaria and related genera based on nucleotide sequences of nrDNA （ITS region） and cpDNA （trnL-F intergenic spacer）

Phylogenetic relationships of Arundinaria and related genera (Pleioblastus, Pseudosasa, Oligostachyum, Bashania, Clavinodum, etc.) were assessed by analyzing the sequences of the nrDNA internal transcribed spacer (ITS) and the cpDNA trnL-F intergenic spacer (IGS). Comparison with trnL-F IGS sequence, the ITS region provided the higher number of parsimony informative characters, and the interspecific variation of the ITS sequence was higher than that of the trnL-F IGS sequence.The tree obtained by combining both sets of data showed that the species sampled in Arundinaria and the related genera were monophyletic and divided into two clades. The relationships and positioning of all the taxa surveryed (including A. oleosa, A. hsienchuensis, A. chino, A. amara, A. yixingensis, A. amabilis, A. fortunei, A. pygmaea, A. gramineus, A. fargesii, A. faberi, A. hupehense, Pseudosasa japonica cv. Tsutsumiana, P. japonica and Brachystachyum densiflorum) were also discussed. The results from the sequences were broadly consistent with morphological characters, appearing all these taxa sampled belong to the genus of Arundinaria. The topologies of the trees generated from individual data and the combined data were similar.

Phylogenetic Relationships in Genus Arachis Based on SSR and AFLP Markers

Fourteen wild species of different sections in the genus Arachis and 24 accessions of the AABB allotetraploid A. hypogaea （cultivated peanut） from several countries which belong to different botanical varieties, were analyzed by SSR and AFLP marker systems. The assay-units per system needed to distinguish among all the tested accessions were at least five for SSR or two for AFLP. The genetic distance detected by the SSR markers ranged from 0.09 to 0.95, and the mean was 0.73; and the genetic distance detected by the AFLP markers ranged from 0.01 to 0.79 with an average of 0.42. All the tested peanut SSR primer pairs were multilocus ones, and the amplified fragments per SSR marker in each peanut genome ranged from 2 to 15 with the mean of 4.77. The peanut cultivars were closely related to each other, and shared a large numbers of SSR and AFLP fragments. In contrast, the species in the genus Arachis shared few fragments. The results indicated that the cultivated peanut （A. hypogaea L.） varieties could be partitioned into two main groups and four subgroups at the molecular level, and that A. duranensis is one of the wild ancestors of A. hypogaea. The lowest genetic variation was detected between A. cardenasii and A. batizocoi, and the highest was detected between A. pintoi and the species in the section Arachis. The relationships among the botanical varieties in the cultivated peanut （A. hypogaea L.） and among wild species accessions in section Arachis and those in other sections in the genus Arachis were discussed.

Phylogenetic Relationships of Sorghum and Related Species Inferred from Sequence Analysis of the nrDNA ITS Region

Analysis of phylogenetic and evolution in six species of Sorghum was based on internal transcribed spacer （ITS） sequences in nuclear ribosomal DNA. Results showed that the length of the ITS regions among the six species ranged from 588 to 589 bp and the contents of G＋C in ITS （ITS1 ＋5.8S＋ITS2） regions ranged from 60.27 to 61.05%; the length of ITS1 ranged from 207 to 208 bp and the contents of G ＋ C in the ITS 1 regions ranged from 53.91 to 61.54%. The length of the 5.8S rDNA and ITS2 regions in the six species was 164 and 217 bp respectively, and the contents of G ＋ C ranged from 56.10 to 58.54% in the 5.8S rDNA region and 66.36 to 67,28% in the ITS2 region. Among regions of ITS, ITS1, ITS2, and 5.8S, the best sequence for genetic relationship analysis in the six species was the ITS region. On the basis of the Jaccard coefficient and phylogentic tree, S. sp. was more related to S, propinguum than to other species. This was consistent with the fact that S. sp. is derived from S. propinguum. From the phylogenetic tree based on ITS1, S. halepense, silk sorghum and S. sudanense, are identical in the ITS 1 sequence, whereas the phylogenetic tree based one shows that S. sudanense has a closer genetic association with S. almum rather than with S. halepense and silk sorghum.

Phylogenetic relationships among five species of Armeniaca Scop. (Rosaceae) using microsatellites (SSRs) and capillary electrophoresis

The genus Armeniaca Scop. is well known for its popular cultivated edible fruit trees such as Armeniaca vul- garis Lam. and ornamental flowers such as A. mume Sieb. Another species, A. cathayana Fu et al., one of six important dry fruits （kernel-using apricot）, is cultivated for its edible seeds in North China. In the present study, DNA from 70 individuals of A rmeniaca, including 38 of A. cathayana, 18 ofA. vulgaris, 12 ofA. sibirica, 1 ofA. dasycarpa and 1 of A. mume, was extracted and analyzed using microsatellites and capillary electrophoresis. For 20 polymorphic loci selected, 339 alleles and 140.7 effective alleles were detected. The number of alleles per locus ranged from 8 to 28, with an average of 16.95 alleles per locus. The observed heterozygosity （Ho） and the expected heterozygosity （He） ranged from 0.427 to 0.971 and from 0.737 to 0.912, respectively. The polymorphism information content varied from 0.708 to0.905, with an average of 0.827. Based on the genetic similarity among 70 individuals, a UPGMA was used to establish the phylogenetic relationships. The taxonomic positions among five species were clearly revealed, and A. cathayana was more closely related to A. vulgaris than to A. sibirica. The results will provide a scientific basis for research on the taxonomy, germplasm resources and breeding ofArmeniaca, especially for A. cathayana.

Investigation of Phylogenetic Relationship among Three Species of Channa Based on ITS Sequence Analysis

[ Objective ] This study aimed to analyze genetic variation of ribosomal ITS region sequences in Channa argus, C moculata and C. asiatica, and to in- vestigate the phylogenetic relationship among Charma species based on ITS sequences. [ Method] ITS sequences of three Channa species were amplified by PCR, cloned and assembled to obtain the full length of ITS sequences. [ Result] The full length of ITS sequences of C. argus, C. maculata and C. asiatica was 902, 927, and 902/903 bp, respectively. ITS sequences of C. argus, C. maculata and C. asiatica exhibited higher G ＋ C （72%） than A ＋ T. Interspecific nucleotide differences were significantly greater than intraspecific differences of these three Channa species. Thus, these remarkably differential ITS fragments could be used to identify C. argus, C. maculata and C. asiatica. Phylogenetic tree constructed by Neighbor-joining and Maximum Likehood methods showed that C. argus shared the lowest genetic distance with C. maculata and the highest genetic distance with C. asiatica. [ Conclusion] This study provided reference for classification, i- dentification, phylogenetic analysis and interspecific hybridization of Channa species.

Studies on Phylogenetic Relationship of Sheep Population in East and South of Central Asia

This paper was based on the Hu sheep in China, after collecting the same data about 9 Asia sheep populations and 5 European sheep (breeds in Japan) populations. It clustered 15 populations in terms of the gene frequency of 10 loci and 33 allele in blood enzyme and other protein variations. The result of Hierarchy Clustering showed that the sheep populations in the East and South of Central Asia could be classified into three genetic groups: Mongolia sheep, South Asia sheep and European sheep, and the Hu sheep belonged to Mongolia sheep.

Evaluation of the effect of genetic diversity and phylogenetic relationships on different strains of Staphylococcus aureus in clinical specimens

Introduction:Staphylococcus aureus is one of the main pathogens in humans.Also,this bacterium can be colonized in the nose.The spa gene is present in all strains of Staphylococcus aureus(S.aureus)and can be used to identify species and toxins such as Panton-Valentine Leukocidin(PVL)that can affect a wide range of skin,soft tissue,and necrotizing pneumonia.Arthritis and life-threatening infections.This study aimed to investigate the effect of genetic diversity and phylogenetic relationships on different strains of Staphylococcus aureus in clinical specimens.Methods:This review study was conducted in 2021 by searching for keywords such as genetic diversity,phylogenetics,and Staphylococcus aureus in reputable databases such as pub med and google scholar.Finally,30 articles were found,of which 30 articles were used out of 26 articles.Results:In general,23%and 18%of health care workers and patients were carriers,respectively.The incidence of methicillin-resistant Staphylococcus aureus(MRSA)is higher in the relevant population.The molecular types of MRSA isolates indicate that the most common virulence gene is Hla,and the most common type of SCCmec is SCCmec type III.Conclusion:Sites with high risk of Staphylococcus aureus should be highly protected,and relevant personnel should be paid attention and health management.

Phylogenetic analysis of 48 gene families revealing relationships between Hagfishes, Lampreys, and Gnathostomata

It has become clear that the extant vertebrates are divided into three major groups, that is, hagfishes, lampreys, and jawed vertebrates. Morphological and molecular studies, however, have resulted in conflicting views with regard to their interrelationships. To clarify the phylogenetic relationships between them, 48 orthologous protein-coding gene families were analyzed. Even as the analysis of 34 nuclear gene families supported the monophyly of cyclostomes, the analysis of 14 mitochondrial gene families suggested a closer relationship between lampreys and gnathostomes compared to hagfishes. Lampreys were sister group of gnathostomes. The results of this study supported the cyclostomes. Choice of outgroup, tree-making methods, and software may affect the phylogenetic prediction, which may have caused much debate over the subject. Development of new methods for tackling such problems is still necessary.

Phylogenetic and morphometric relationships between two species of genus Auxis from the South China Sea and Java Sea

This study was aimed at examining the phylogenetic and morphometric relationship of frigate tuna（Auxis thazard） and bullet tuna（Auxis rochei） using mt DNA D-loop（control） region sequences and truss measurements,respectively. Maximum-likelihood（ML） tree and median-joining network showed that haplotypes from Auxis populations grouped separately. Discriminant function analyses and non-metric multidimensional scaling of morphometric data showed that bullet and frigate tuna were differed mainly with respect to truss measurements on the anterior region, suggesting adaptation to different diets available in different environments. Historic demographic analyses of sequence data showed that both bullet and frigate tuna had not undergone a significant sudden population expansion recently. Non-significant value of Tajimas＇ s D and Fu＇s F_S were indicated an effective large and stable population size for longer period of both species in South China Sea and Java Sea species. This study gives first report on the complementary relationship between morphometric and genetic analysis in stock discrimination of genus Auxis.

Molecular phylogenetic relationship of Epinephelus based on sequences of mtDNA Cty b

The mtDNA Cyt b gene was sequenced partially for Variola louti of Serranidae,Epinephelinae and seven endemic species of groupers—Epinephelus awoara,E.brunneus,E.coioides,E.longispinis,E.sexfasciatus,E.spilotoceps and E.tauvina in China.The seven endemic species and other seven foreign species of groupers—E.aeneus,E.caninus,E.drummondhayi,E.haifensis,E.labriformis,E.marginatus and E.multinotatus from the GenBank were combined and analysed as ingroup,while Variola louti was used as outgroup.We compared the 420 bp sequences of Cyt b among the 15 species and constructed two types of molecular phylogenetic trees with maximum parsimony method(MP)and neighbor-joining method(NJ)respectively.The results were as follows:(1)As to the base composition of mtDNA Cyt b sequence(402 bp)of 14 species of Epinephelus,the content of(A+T)was 53.6%,higher than that of(G+C)(46.4%).The transition/transversion ratio was 4.78 with no mutation saturation.(2)The cluster relationships between E.awoara and E.sexfasciatus,E.coioides and E.tauvina,E.longispinis and E.spilotoceps were consistent with phenotypes in taxonomy.(3)In the phylogenetic tree,the species in the Atlantic Ocean were associated closely with those in the Pacific Ocean,which suggested that the Cyt b sequences of Epinephelus were highly conserved.This may be attributed to the coordinate evolution.(4)In wel1-bred mating or heredity management,mating Epinephelus of the same branch should be avoided.It is likely to be an effective way to mate the species of the Atlantic Ocean with those of the Pacific Ocean to improve the inheritance species.

The complete mitochondrial genome of Parachiloglanis hodgarti and its phylogenetic position within Sisoridae

The complete mitogenome of Parachiloglanis hodgarti was sequenced and characterized,which is the first mitogenome of the genus Parachiloglanis within Sisoridae.The mitogenome is 16511-bp long and included 13 protein-coding genes,22 transfer RNAs,two ribosomal RNAs,and one control region.The genome composition was A+T biased(58.64%)and exhibited a positive AT-skew(0.095)and a negative GC-skew(-0.283).Compared with other Sisoridae fishes,the characteristics of nucleotide skews,codon usage,and amino acid usage of the P.hodgarti mitogenome are more similar to those of non-Glyptosternoid fishes.Furthermore,the phylogenetic trees show that Sisoridae fishes fall into four major clades and P.hodgarti(CladeⅠ)is basal to the Sisoridae family,forming a sister clade to the Glyptosternoids(CladeⅣ).The topological structures constructed in this study raised doubts over the traditional classification system.These results will help better understand the feature s of the P.hodgarti mitogenome and provide a reference for further phylogenetic research on Sisoridae species.

New record of the feather star Palaeocomatella hiwia(Echinodermata:Crinoidea:Comatulida)from Zhenbei Seamount in South China Sea:new insights into the taxonomic position of Palaeocomatella

One specimen belonging to the family Comatellinae was collected from the Zhenbei Seamount(332.5–478.2 m)in the South China Sea in July 2022.Based on the morphological characters,the specimen was identified as Palaeocomatella hiwia McKnight,1977.It is first recorded from China Sea and redescribed in detail.This specimen differs from the original description from New Zealand for never showing syzygy at br4+5 or br5+6 on interior and br1+2 on exterior arms.However,it is much conform to the redescription to specimens from Indonesia,with only differences in position of the second syzygy and distalmost pinnule comb.Specimen is deposited in the Institute of Oceanology,Chinese Academy of Sciences.Phylogenetic analyses based on the mitochondrial c oxidase subunit I(COI)and 16S rRNA genes indicated that P.hiwia was nested within the tribe Phanogeniini and clustered with Aphanocomaster pulcher.Furthermore,P.hiwia showed same morphological features in terms of mouth placement,comb location,and number of comb teeth rows as other genera of Phanogeniini.Therefore,we suggest that the genus Palaeocomatella should be put in the tribe Phanogeniini.

Origin and phylogenetic analysis of Tibetan Mastiff based on the mitochondrial DNA sequence

At present, the Tibetan Mastiff is the oldest and most ferocious dog in the world. However, the origin of the Tibetan Mastiff and its phylogenetic relationship with other large breed dogs such as Saint Bernard are unclear. In this study, the primers were designed accord- ing to the mitochondrial genome sequence of the domestic dog, and the 2,525 bp mitochondrial sequence, containing the whole sequence of Cytochrome b, tRNA-Thr, tRNA-Pro, and control region of the Tibetan Mastiff, was obtained. Using grey wolves and coyotes as out- groups, the Tibetan Mastiff and 12 breeds of domestic dogs were analyzed in phylogenesis. Tibetan Mastiff, domestic dog breeds, and grey wolves were clustered into a group and coyotes were clustered in a group separately. This indicated that the Tibetan Mastiff and the other domestic dogs originated from the grey wolf, and the Tibetan Mastiff belonged to Carnivora, Canidae, Canis, Canis lupus, Canis lupus familiaris on the animal taxonomy. In domestic dogs, the middle and small breed dogs were clustered at first; German Sheepdog, Swedish Elkhound, and Black Russian Terrier were clustered into one group, and the Tibetan Mastiff, Old English Sheepdog, Leonberger, and Saint Bernard were clustered in another group. This confirmed the viewpoint that many of the famous large breed dogs worldwide such as Saint Bernard possibly had the blood lineage of the Tibetan Mastiff, based on the molecular data. According to the substitution rate, we concluded that the approximate divergence time between Tibetan Mastiff and grey wolf was 58,000 years before the present （YBP）, and the approximate divergence time between other domestic dogs and grey wolf was 42,000 YBP, demonstrating that the time of origin of the Tibetan Mastiff was earlier than that of the other domestic dogs.

The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

The complete mitochondrial genome （16,837 bp） from the Keeled box turtle （Pyxidea mouhotii） was determined. The genome content, gene order, and base composition conformed to the consensus vertebrate type mtDNA. However, a remarkable feature was found in this molecule： a large number of （ATTATATC） n direct tandem repeats followed by （TA） n microsatellite at the 3＇ end of the control region （D-loop）, which might be useful as molecular markers for studying population genetics and helpful for species identification and conservation. Besides, to review phylogenetic relationships among major turtle lineages, maximum-likelihood （ML） and Bayesian （BI） analyses were conducted based on concatenated sequences of 13 protein-coding genes from 16 taxa. The resultant ML and BI analyses showed homological topologies, which only differed on the exact placement of Platysternon. Nevertheless, the results strongly supported that 1） Pyxidea mouhotii and Cuora aurocapitata formed a monophyletic clade, whereas Cyclemys atripons was not closer to the Pyxidea-Cuora than to Chinemys reevesii, suggesting that Cyclemys and the Cuora group （containing Pyxidea） may have originated from two ancestors; 2） the Geoemydidae with Testudinidae was a sister group rather than with the Emydidae.

Phylogenetic Analysis on SLG and SRK Genes in Brassica and Raphanus

S-locus genes were cloned from three Brassica napus and three B. campestris lines by using PCR walking and homologuesequence methods. A phylogenetic gene tree was constructed based on the six cloned genes and fifty-one previouslyreported SLG/SRK genes of Brassica and Raphanus. The SLGs from R. sativus were dispersed in the phylogenetic treeintermingling with SLG/SRKs from B. oleracea, B. napus and B. campestris. The SLG/SRK genes of classⅡclusteredindependently in one group. The SLG/SRK genes of classⅠshowed to be more divergent than classⅡgenes. Theseresults suggested that the divergence of classⅠand classⅡ should have occurred before the differentiation of thegenera Brassica and Raphanus. In addition, SLG and SRK of the same S haplotypes belonged to the same class. Itsuggested that class-Ⅰ and class-Ⅱ group divergence occurred first, and then SLG and SRK diverged. The three SC SRKgenes from B. napus and B. campestris were grouped into one cluster, displaying difference from the SC SLG of B.oleracea. These three SC SRK genes were close to SI SRK of SI1300, SI271 and guanyou in phylogenetic relationships.These results indicated that SC and SI genes diverged more recently. It is not clear yet whether the differentiation of SCand SI genes was earlier than the differentiation of Brassica and Raphanus. Studies based on more genes are necessaryfor a comprehensive elucidation of the phylogenetic relationships in Brassicaceae.

Assessment of Genetic Relationship of Foxtail Millet with Its Wild Ancestor and Close Relatives by ISSR Markers

Inter simple sequence repeat（ISSR） analysis was applied to samples of foxtail millet and its wild ancestor and other close relatives of the genus Setaria in order to detect domestication-related geographical structure and phylogenetic relationship of those species.Eighty-one accessions of nine Setaria species that originated from different regions were used in this study.Fourteen out of the 27 ISSR primers screened amplified successfully and a total of 156 markers were scored for all the accessions,with a high level of polymorphism being detected.The dendrogram based on UPGMA cluster analysis showed clear geographic structure among foxtail millet and its wild ancestor green foxtail,which implies that northern China is the domestication center for both the Chinese and European foxtail millet landraces used in this study.This result did not support the hypothesis that China and Europe are independent domestication centers for foxtail millet proposed by several previous studies based on morphological and isozyme data.The dendrogram also clearly classified the Setaria sample used into two groups,a viridis and a pumila groups.The viridis group was composed of S.viridis,S.italica,S.faberii,S.verticillata,S.leucopila,and S.queenslandica,and the pumila group consisted of S.parviflora and S.pumila,which is consistent with the recently proposed hypothesis of multiple origin of Setaria species.The phylogenetic relationships among different species are discussed.

Karyomorphology of three species in Dipentodon(Dipentodontaceae),Perrottetia(Celastraceae),and Tapiscia(Tapisciaceae) of the order Huerteales and their phylogenetic implications

Abstract The karyomorphology of three species in Dipentodon （Dipentodontaceae）, Perrottetia （Celastraceae）, and Tapiscia （Tapisciaceae）, namely Dipentodon sinicus, Perrottetia racemosa, and Tapiscia sinensis, was investigated in the present study. Recent molecular research has discovered close relationships among these three genera, which has led to the establishment of the order Huerteales with Perrottetia being placed in Dipentodontaceae. Herein we report the chromosome numbers of D. sinicus and P. racemosa for the first time, and present their karyotype formulas as 2n = 34 = 22 sm ＋ 12 st （D. sinicus）, 2n = 20 = 11 m ＋ 9 sm （P. racemosa）, and 2n = 30 = 22 m（2SAT） ＋ 8sm （T. sinensis）. Asymmetry of their karyotypes is categorized to be Type 3B in D. sinicus, Type 2A in P. racemosa, and Type 2A in T. sinensis. Each of the species shows special cytological features. Compared with Perrottetia, Dipentodon has a different basic chromosome number, a higher karyotype asymmetry, and different karyomorphology of its interphase nuclei, mitotic prophase, and metaphase. Thus, on the basis of these results, we have reservations regarding the suggestion of placing Dipentodon and Perrottetia together in the family Dipentodontaceae.

Phylogenetic, evolutionary, and biogeographic origin of the genus Sheathia (Batrachospermales, Rhodophyta)

The genus Sheathia consists of over 20 species primarily distributed in Asia,Europe,Oceania,North America,and Africa.However,the origin and evolution of this genus remain unclear.Two gametophyte stage specimens(SAS18052 and SAS18523)and two“Chantransia”stage specimens(YTS19161 and YTS19017)were collected from Shanxi and Henan Provinces in China,respectively.Based on morphological data,isolates YTS19161 and YTS19017 were similar to Audouinella pygmaea,whereas the morphological characteristics of SAS18052 and SAS18523 were in good agreement with the circumscription description of S.longipedicellata.Molecular sequences of rbc L,COI-5P,and psb A were used to investigate the phylogenetic,evolutionary,and biogeographic origin of the genus Sheathia.The three molecular markers supported that the two gametophyte stage specimens belong to S.longipedicellata,while the isolates YTS19161 and YTS19017 were the“Chantransia”of S.longipedicellata.Ancestral area reconstruction and divergence time estimation speculated that Sheathia originated in North America,a portion of the Pangaea at approximately 328.07-184.73 million years ago(Ma).Our relaxed molecular clock analysis suggests that the Florideophyceae diverged approximately 741.04(894.36-631.70)Ma.The major divergences in this class involved the emergence of Nemaliophycidae[ca.662.01(779.83-580.51)Ma],and the split of orders Batrachospermales and Thoreales[ca.456.10(552.80-367.88)Ma].

Sequence Comparison of MHCClassⅡβ(Exon 2)and Phylogenetic Relation-ship Between Poultry and Mammalian

A fragment spanning over exon 2 and intron 2 of major histocompatibility complex B-LB Ⅱ genes was amplified using PCR, cloned and sequenced in 13 individuals from eight Chinese indigenous chicken breeds and one introduced breed. Another 41 sequences of MHC class Ⅱ β from ten vertebrate species were cited from the NCBI GenBank. Thirteen new B-LB Ⅱ alleles were found in the chicken breeds sampled. Alignment of the exon 2 sequences revealed 91.1-97.8% similarity to each other within the chickens sampled, and the chickens shared 84.1-87.0% homology to Phasianus colchicus, 78.5-81.5% similarity to Coturnix japonica. The sequences in poultry showed 62.6-68.1% identity to HLA-DRB1, 50-61.5% similarity to DQB (HLA-, SLA- and H2-BB), 53.7-60% to HLA-DPB and 53.3-57.8% similarity to HLA-DOB. The frequency of nonsynonymous substitutions of nucleotide was higher than that of synonymous substitutions, and the frequencies of nonsynonymous and synonymous substitutions in poultry B-LB Ⅱ genes were lower than those observed in mammalian DRB1 and DQB1 genes. The deduced amino acid sequences of MHC class Ⅱ β1 domain exhibited extreme difference in conversed region and variable region patterns among the various species, but the two conserved cysteines forming disulfide-bond were shown consistent in poultry with that in mammalian species; and the carbohydrate attachment site was found more conserved in chicken, Homo sapiens, Bos taurus, Ovis aries and Capra hircus than in Sus scrofa and rodent animals. Compared with exon 2 of DQB1 genes of Homo sapiens, ruminant species and Sus scrofa, the differentia that the deletion of six nucleotides at position195 to 200 of exon 2 of DQB1 genes, and insertion of three nucleotides at position 247 to 249 of the exon 2 existed in rodent species were found, which led to the absence of three AA residues at position 65, 66, and 67 within β1 domain of DQB1 chain, and the insertion of one AA residue at position 85. The difference of the deletion of six nucleotides at position 72 to 77 of exon 2 of DPB1 genes was observed with Homo sapiens DQB1, which caused absence of three AA residues at position 24, 25, and 26 of β1 domain of DPB1 chain. The phylogenetic tree revealed that the B-LB Ⅱ sequences from poultry are not orthologous to the class Ⅱ MHC β-chain genes of mammalian species. The tree indicated that genetic evolutionary relationship of chickens with Phasianus colchicus was much closer than with Coturnix japonica, and the DQB and DPB clusters are more tightly related to each other than to the remaining clusters.