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1.
J Vet Med Educ ; 50(1): 1-14, 2023 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-35085060

RESUMO

Cultural competence in professional and research practice is important to effectively deliver animal and One Health services and programs. Veterinarians work with culturally and linguistically diverse teams, clients, and communities. Cultural perspectives on the significance and perceptions of animals and differences in consultation and engagement protocols and strategies can influence client-practitioner and researcher-community relationships, impacting animal health, welfare, and/or research outcomes. Curricula have been proposed to build cultural capacity in graduates, but these have not been reported in veterinary programs, and early attempts to integrate cultural competency into the University of Sydney veterinary curriculum lacked a formal structure and were ad hoc with respect to implementation. To address this, the authors introduced a broad curriculum framework into the University of Sydney veterinary program, which defines cultural competence, perceptions of animals, effective communication, and community engagement in a range of contexts. Cultural competency learning outcomes were described for units of study. These were contextually relevant and aligned to course learning outcomes and University of Sydney graduate qualities. Constructive alignment was achieved by linking learning outcomes to teaching and learning activities and assessment. The continuum of cultural competency underpinned mapping of cultural competency across the curriculum with staged, vertical integration of key principles. Additionally, action to engage staff, students, and stakeholders in a cultural competence agenda assisted in sustaining curriculum change. The result was integration of cultural competency across the curriculum aligning with recommendations from accrediting bodies and with best practice models in medicine, nursing, and allied health programs.


Assuntos
Competência Cultural , Educação em Veterinária , Animais , Competência Cultural/educação , Currículo , Aprendizagem
2.
Anal Biochem ; 602: 113781, 2020 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-32485163

RESUMO

MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. Understanding gene regulation in the saltwater crocodile in the context of relatively slow genomic change thus holds potential for the investigation of genomics, evolution, and adaptation. Utilizing eleven tissue types and sixteen small RNA libraries, we report 644 miRNAs in the saltwater crocodile with >78% of miRNAs being novel to crocodilians. We also identified potential targets for the miRNAs and analyzed the relationship of the miRNA repertoire to transposable elements (TEs). Results suggest an increased association of DNA transposons with miRNAs when compared to retrotransposons. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile. In addition, the data suggests a supporting role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.


Assuntos
Elementos de DNA Transponíveis/genética , MicroRNAs/genética , Jacarés e Crocodilos , Animais , Biblioteca Gênica , Salinidade
3.
Mol Biol Evol ; 35(5): 1238-1252, 2018 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-29688544

RESUMO

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10-9/bp/generation (95% CI 4.1 × 10-9-1.2 × 10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.


Assuntos
Distribuição Animal , Ornitorrinco/genética , Animais , Austrália , Feminino , Variação Genética , Endogamia , Masculino , Taxa de Mutação , Dinâmica Populacional , Sequenciamento Completo do Genoma
4.
Immunogenetics ; 70(6): 401-417, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29256177

RESUMO

The major histocompatibility complex (MHC) is a key genomic model region for understanding the evolution of gene families and the co-evolution between host and pathogen. To date, MHC studies have mostly focused on species from major vertebrate lineages. The evolution of MHC classical (Ia) and non-classical (Ib) genes in pigs has attracted interest because of their antigen presentation roles as part of the adaptive immune system. The pig family Suidae comprises over 18 extant species (mostly wild), but only the domestic pig has been extensively sequenced and annotated. To address this, we used a DNA-capture approach, with probes designed from the domestic pig genome, to generate MHC data for 11 wild species of pigs and their closest living family, Tayassuidae. The approach showed good efficiency for wild pigs (~80% reads mapped, ~87× coverage), compared to tayassuids (~12% reads mapped, ~4× coverage). We retrieved 145 MHC loci across both families. Phylogenetic analyses show that the class Ia and Ib genes underwent multiple duplications and diversifications before suids and tayassuids diverged from their common ancestor. The histocompatibility genes mostly form orthologous groups and there is genetic differentiation for most of these genes between Eurasian and sub-Saharan African wild pigs. Tests of selection showed that the peptide-binding region of class Ib genes was under positive selection. These findings contribute to better understanding of the evolutionary history of the MHC, specifically, the class I genes, and provide useful data for investigating the immune response of wild populations against pathogens.


Assuntos
Artiodáctilos/genética , Complexo Principal de Histocompatibilidade/genética , Suínos/genética , Animais , Sequência de Bases , Evolução Biológica , Hibridização Genômica Comparativa/métodos , Evolução Molecular , Genes MHC Classe I , Genoma , Filogenia , Análise de Sequência de DNA/métodos
5.
Mol Phylogenet Evol ; 112: 258-267, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28363818

RESUMO

The geographical range of extant peccaries extends from the southwestern United States through Central America and into northern Argentina. However, from the Miocene until the Pleistocene now-extinct peccary species inhabited the entirety of North America. Relationships among the living and extinct species have long been contentious. Similarly, how and when peccaries moved from North to South America is unclear. The North American flat-headed peccary (Platygonus compressus) became extinct at the end of the Pleistocene and is one of the most abundant subfossil taxa found in North America, yet despite this extensive fossil record its phylogenetic position has not been resolved. This study is the first to present DNA data from the flat-headed peccary and full mitochondrial genome sequences of all the extant peccary species. We performed a molecular phylogenetic analysis to determine the relationships among ancient and extant peccary species. Our results suggested that the flat-headed peccary is sister-taxon to a clade comprising the extant peccary species. Divergence date estimates from our molecular dating analyses suggest that if extant peccary diversification occurred in South America then their common ancestor must have dispersed from North America to South America well before the establishment of the Isthmus of Panama. We also investigated the genetic diversity of the flat-headed peccary by performing a preliminary population study on specimens from Sheriden Cave, Ohio. Flat-headed peccaries from Sheriden Cave appear to be genetically diverse and show no signature of population decline prior to extinction. Including additional extinct Pleistocene peccary species in future phylogenetic analyses will further clarify peccary evolution.


Assuntos
Artiodáctilos/genética , DNA Antigo/análise , Extinção Biológica , Animais , Teorema de Bayes , DNA Mitocondrial/genética , Evolução Molecular , Fósseis , Variação Genética , Genoma Mitocondrial , Geografia , Haplótipos/genética , América do Norte , Filogenia
6.
Proc Natl Acad Sci U S A ; 111(13): 4826-31, 2014 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-24639505

RESUMO

The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.


Assuntos
Migração Animal , Galinhas/genética , DNA/genética , Animais , Pareamento de Bases/genética , Teorema de Bayes , Genoma Mitocondrial/genética , Geografia , Haplótipos/genética , Humanos , Região de Controle de Locus Gênico/genética , Dados de Sequência Molecular , Oceano Pacífico , Filogenia , Polinésia , Fatores de Tempo
7.
Retrovirology ; 12: 26, 2015 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-25808580

RESUMO

BACKGROUND: Endogenous retroviruses (ERVs) are genetic elements with a retroviral origin that are integrated into vertebrate genomes. In felids (Mammalia, Carnivora, Felidae), ERVs have been described mostly in the domestic cat, and only rarely in wild species. To gain insight into the origins and evolutionary dynamics of endogenous retroviruses in felids, we have identified and characterized partial pro/pol ERV sequences from eight Neotropical wild cat species, belonging to three distinct lineages of Felidae. We also compared them with publicly available genomic sequences of Felis catus and Panthera tigris, as well as with representatives of other vertebrate groups, and performed phylogenetic and molecular dating analyses to investigate the pattern and timing of diversification of these retroviral elements. RESULTS: We identified a high diversity of ERVs in the sampled felids, with a predominance of Gammaretrovirus-related sequences, including class I ERVs. Our data indicate that the identified ERVs arose from at least eleven horizontal interordinal transmissions from other mammals. Furthermore, we estimated that the majority of the Gamma-like integrations took place during the diversification of modern felids. Finally, our phylogenetic analyses indicate the presence of a genetically divergent group of sequences whose position in our phylogenetic tree was difficult to establish confidently relative to known retroviruses, and another lineage identified as ERVs belonging to class II. CONCLUSIONS: Retroviruses have circulated in felids along with their evolution. The majority of the deep clades of ERVs exist since the primary divergence of felids' base and cluster with retroviruses of divergent mammalian lineages, suggesting horizontal interordinal transmission. Our findings highlight the importance of additional studies on the role of ERVs in the genome landscaping of other carnivore species.


Assuntos
Retrovirus Endógenos/classificação , Retrovirus Endógenos/isolamento & purificação , Felidae/virologia , Variação Genética , Infecções por Retroviridae/veterinária , Animais , Animais Selvagens , Análise por Conglomerados , Retrovirus Endógenos/genética , Evolução Molecular , Dados de Sequência Molecular , Filogenia , Infecções por Retroviridae/virologia , Análise de Sequência de DNA , Homologia de Sequência
8.
Virus Genes ; 50(2): 329-32, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25653017

RESUMO

Endogenous retroviruses (ERVs) are one of many families of transposable elements present in vertebrate genomes. We have examined the ERV complement of the freshwater crocodile (Crocodylus johnstoni) in order to investigate the diversity of ERVs present and possibility of ERV or retroviral activity in a diseased individual of this species. Amplification and sequencing of the highly conserved retroviral pro-pol domains revealed high levels of sequence variation in these ERVs. Phylogenetic analyses of these ERVs and those previously identified in other crocodilian species suggest that although many crocodilians share the same ERV lineages, the relative numbers of retroelement insertions from each of these lineages may vary greatly between species. The data generated in this study provide evidence for the presence of a unique and varied complement of ERVs in crocodilians. This study has also demonstrated the presence of species-specific evolution in ancient retroviral infections.


Assuntos
Jacarés e Crocodilos/virologia , Retrovirus Endógenos/genética , Retrovirus Endógenos/isolamento & purificação , Variação Genética , Infecções por Retroviridae/veterinária , Animais , Retrovirus Endógenos/classificação , Evolução Molecular , Dados de Sequência Molecular , Filogenia , Infecções por Retroviridae/virologia
9.
J Hered ; 106(4): 395-402, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25908666

RESUMO

Major histocompatibility complex (MHC) class II molecules have an important role in vertebrate adaptive immunity, being responsible for recognizing, binding, and presenting specific antigenic peptides to T lymphocytes. Here, we study the MHC class II DQB and DRB exon 2 genes of the Australian sea lion (Neophoca cinerea), an endangered pinniped species that experiences high pup mortality. Following characterization of N. cinerea DQB and DRB by molecular cloning, and evaluation of diversity in pups across 2 colonies using variant screening (n = 47), 3 DQB alleles and 10 DRB variants (including 1 pseudogene allele) were identified. The higher diversity at DRB relative to DQB is consistent with other studies in marine mammals. Despite overall lower MHC class II allelic diversity relative to some other pinniped species, we observed similar levels of nucleotide diversity and selection in N. cinerea. In addition, we provide support for recent divergence of MHC class II alleles. The characterization of MHC class II diversity in the Australian sea lion establishes a baseline for further investigation of associations with disease, including endemic hookworm infection, and contributes to the conservation management of this species.


Assuntos
Genes MHC da Classe II , Variação Genética , Leões-Marinhos/genética , Alelos , Sequência de Aminoácidos , Animais , Austrália , Espécies em Perigo de Extinção , Éxons , Cadeias beta de HLA-DQ/genética , Cadeias beta de HLA-DR/genética , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA
10.
Retrovirology ; 11: 71, 2014 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-25499090

RESUMO

BACKGROUND: Crocodilians are thought to be hosts to a diverse and divergent complement of endogenous retroviruses (ERVs) but a comprehensive investigation is yet to be performed. The recent sequencing of three crocodilian genomes provides an opportunity for a more detailed and accurate representation of the ERV diversity that is present in these species. Here we investigate the diversity, distribution and evolution of ERVs from the genomes of three key crocodilian species, and outline the key processes driving crocodilian ERV proliferation and evolution. RESULTS: ERVs and ERV related sequences make up less than 2% of crocodilian genomes. We recovered and described 45 ERV groups within the three crocodilian genomes, many of which are species specific. We have also revealed a new class of ERV, ERV4, which appears to be common to crocodilians and turtles, and currently has no characterised exogenous counterpart. For the first time, we formally describe the characteristics of this ERV class and its classification relative to other recognised ERV and retroviral classes. This class shares some sequence similarity and sequence characteristics with ERV3, although it is phylogenetically distinct from the other ERV classes. We have also identified two instances of gene capture by crocodilian ERVs, one of which, the capture of a host KIT-ligand mRNA has occurred without the loss of an ERV domain. CONCLUSIONS: This study indicates that crocodilian ERVs comprise a wide variety of lineages, many of which appear to reflect ancient infections. In particular, ERV4 appears to have a limited host range, with current data suggesting that it is confined to crocodilians and some lineages of turtles. Also of interest are two ERV groups that demonstrate evidence of host gene capture. This study provides a framework to facilitate further studies into non-mammalian vertebrates and highlights the need for further studies into such species.


Assuntos
Jacarés e Crocodilos/genética , Jacarés e Crocodilos/virologia , Retrovirus Endógenos/classificação , Retrovirus Endógenos/genética , Evolução Molecular , Variação Genética , Genoma , Animais , Análise por Conglomerados , Biologia Computacional , Filogenia , Recombinação Genética , Homologia de Sequência , Tartarugas/virologia
11.
Immunogenetics ; 66(1): 53-65, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24253731

RESUMO

The major histocompatibility complex (MHC) is a dynamic genomic region with an essential role in the adaptive immunity of jawed vertebrates. The evolution of the MHC has been dominated by gene duplication and gene loss, commonly known as the birth-and-death process. Evolutionary studies of the MHC have mostly focused on model species. However, the investigation of this region in non-avian reptiles is still in its infancy. To provide insights into the evolutionary mechanisms that have shaped the diversity of this region in the Order Crocodylia, we investigated MHC class I exon 3, intron 3, and exon 4 across 20 species of the families Alligatoridae and Crocodilidae. We generated 124 DNA sequences and identified 31 putative functional variants as well as 14 null variants. Phylogenetic analyses revealed three gene groups, all of which were present in Crocodilidae but only one in Alligatoridae. Within these groups, variants generally appear to cluster at the genus or family level rather than in species-specific groups. In addition, we found variation in gene copy number and some indication of interlocus recombination. These results suggest that MHC class I in Crocodylia underwent independent events of gene duplication, particularly in Crocodilidae. These findings enhance our understanding of MHC class I evolution and provide a preliminary framework for comparative studies of other non-avian reptiles as well as diversity assessment within Crocodylia.


Assuntos
Jacarés e Crocodilos/genética , Evolução Molecular , Genes MHC Classe I/genética , Variação Genética/genética , Jacarés e Crocodilos/classificação , Animais , Clonagem Molecular , DNA Complementar/genética , Filogenia , Reação em Cadeia da Polimerase , Recombinação Genética
12.
BMC Genet ; 14: 91, 2013 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-24063717

RESUMO

BACKGROUND: Norfolk Island has a population of feral chickens which could be the result of domestic stock introduced onto the island by British settlers in 1788. However, there is ongoing debate about their origins because multiple human arrivals to the island may have brought chickens with them. Here we investigate the genetic origins of these feral chickens by sequencing their mitochondrial control region. We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world. RESULTS: Eleven control region haplotypes were found among the Norfolk Island feral and Australian mainland domestic chickens. Six of the Norfolk Island haplotypes fall within haplogroup E, but given the worldwide distribution of this haplogroup, the putative European origin of these chickens requires further investigation. One haplotype common among Norfolk Island and Australian samples belonged to a subgroup of haplogroup D, which appears to be restricted to chickens from Indonesia, Vanuatu and Guam. CONCLUSIONS: Our data show that at least two mitochondrial DNA haplogroups (D and E) have contributed to the genetic make-up of Norfolk Island feral chickens. In addition, we have provided insights into the discrete geographical distribution and diversity of the chicken haplogroup D. In view of the worldwide interest in the characterisation of poultry resources, further assessment of chicken populations of Island Southeast Asia and the Pacific region is warranted.


Assuntos
Galinhas/genética , DNA Mitocondrial/química , Variação Genética , Mitocôndrias/genética , Animais , Austrália , Galinhas/classificação , DNA Mitocondrial/metabolismo , Genoma , Haplótipos , Melanesia , Filogenia , Análise de Sequência de DNA
13.
Immunogenetics ; 64(11): 825-38, 2012 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-22864956

RESUMO

Saltwater crocodiles are in high demand for the production of luxury fashion items. However, their susceptibility to disease incurs substantial losses and it is hoped to be able to genetically select these animals for disease resistance. So far, this has only been enabled by phenotypic selection. Investigating the major histocompatibility complex (MHC) could provide insight into the ability of an individual to respond to pathogens acting as a selective pressure on the host. Here, we assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 3 among 42 saltwater crocodiles from nine river basins in the Northern Territory, Australia. We generated 640 sequences using cloning and sequencing methods and identified 43 MHC variants among them. Phylogenetic analyses clustered these variants into two major clades, which may suggest two gene lineages. We found the number of variants within an individual varying between one and seven, indicating that there are at least four gene loci in this species. Selection detection analyses revealed an elevated ratio of nonsynonymous to synonymous substitutions (mean = 1.152 per codon), suggesting balancing selection. Population differentiation analyses revealed that the MHC did not show structuring among the river basins, and there were some shared variants among them. This may be a result of possible gene flow and/or similar selection pressures among populations. These findings provide background knowledge to identify potential MHC markers, which could be used for selecting genetically variable individuals for future disease associations. All MHC class I exon 3 sequences reported in this paper were submitted to the GenBank database with following accession numbers: HQ008785-HQ008789, HQ008791-HQ008798, HQ008808-HQ008815, HQ008824, HQ008826-HQ008830, HQ008835, HQ008839, HQ008842-HQ008850, and JX023536-JX023540.


Assuntos
Jacarés e Crocodilos/genética , Evolução Molecular , Genes MHC Classe I/genética , Polimorfismo Genético/genética , Seleção Genética/genética , Sequência de Aminoácidos , Animais , Dados de Sequência Molecular , Filogenia , Homologia de Sequência de Aminoácidos
15.
R Soc Open Sci ; 9(3): 210558, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-35308631

RESUMO

The Arabian oryx was the first species to be rescued from extinction in the wild by the concerted efforts of captive programmes in zoos and private collections around the world. Reintroduction efforts have used two main sources: the 'World Herd', established at the Phoenix Zoo, and private collections in Saudi Arabia. The breeding programme at the Al-Wusta Wildlife Reserve (WWR) in Oman has played a central role in the rescue of the oryx. Individuals from the 'World Herd' and the United Arab Emirates have been the main source for the WWR programme. However, no breeding strategies accounting for genetic diversity have been implemented. To address this, we investigated the diversity of the WWR population and historical samples using mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs). We found individuals at WWR contain 58% of the total mtDNA diversity observed globally. Inference of ancestry and spatial patterns of SNP variation shows the presence of three ancestral sources and three different groups of individuals. Similar levels of diversity and low inbreeding were observed between groups. We identified individuals and groups that could most effectively contribute to maximizing genetic diversity. Our results will be valuable to guide breeding and reintroduction programmes at WWR.

16.
Commun Biol ; 5(1): 1127, 2022 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-36329312

RESUMO

The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (FST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; FST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, FST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.


Assuntos
Ornitorrinco , Animais , Humanos , Ornitorrinco/genética , Rios , Ecologia , Movimento
17.
BMC Evol Biol ; 11: 139, 2011 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-21609472

RESUMO

BACKGROUND: Porcine endogenous retroviruses (PERVs) represent remnants of an exogenous form that have become integrated in the domestic pig (Sus scrofa) genome. Although they are usually inactive, the capacity of γ1 ERVs to infect human cells in vitro has raised concerns about xenotransplantation because the viruses could cross the species barrier to humans. Here we have analyzed the evolution of γ1 ERVs in ten species of Suidae (suids, pigs and hogs) from Eurasia and Africa using DNA sequences for their coding domains (gag, pro/pol and env genes). For comparison with γ1 PERVs, we have also analysed γ2 ERVs which in domestic pigs are known to be inactive and do not pose a risk to xenotransplantation. RESULTS: Phylogenetic analysis using Bayesian inference showed that γ1 and γ2 ERVs have distinctive evolutionary histories. Firstly, two different viral lineages of γ1 ERVs were found and a coevolutionary analysis demonstrated that they correspond broadly to their host phylogeny, one of Eurasian and another of African species, and show no evidence of horizontal transmission. γ2 ERVs, however, show a bush-like evolution, suggesting a rapid viral radiation from a single common ancestor with no correspondence between host and viral evolutionary trees. Furthermore, though γ1 ERV env genes do not possess frequent stop codons, γ2 env genes do. To understand whether γ1 suid ERVs may be still replicating, we have also evaluated their likely mechanism of proliferation by statistically testing internal to terminal branches using nonsynonymous versus synonymous substitution ratios. Our results suggest that γ1 ERVs are increasing in copy number by reinfection, which requires the translocation of the virus from one cell to another. CONCLUSIONS: Evidence of at least two viral subpopulations was observed in γ1 ERVs from Eurasian and African host species. These results should be taken into account in xenotransplantation since γ1 ERVs appear to be codiverging with their host and maintaining ongoing capacity to infect somatic and germ cells.


Assuntos
Gammaretrovirus/genética , Gammaretrovirus/fisiologia , Interações Hospedeiro-Patógeno , Suínos/virologia , África , Animais , Ásia , Teorema de Bayes , Europa (Continente) , Genes env , Genes gag , Genes pol , Dados de Sequência Molecular , Filogenia , Recombinação Genética
18.
Proc Natl Acad Sci U S A ; 105(30): 10308-13, 2008 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-18663216

RESUMO

European chickens were introduced into the American continents by the Spanish after their arrival in the 15th century. However, there is ongoing debate as to the presence of pre-Columbian chickens among Amerindians in South America, particularly in relation to Chilean breeds such as the Araucana and Passion Fowl. To understand the origin of these populations, we have generated partial mitochondrial DNA control region sequences from 41 native Chilean specimens and compared them with a previously generated database of approximately 1,000 domestic chicken sequences from across the world as well as published Chilean and Polynesian ancient DNA sequences. The modern Chilean sequences cluster closely with haplotypes predominantly distributed among European, Indian subcontinental, and Southeast Asian chickens, consistent with a European genetic origin. A published, apparently pre-Columbian, Chilean specimen and six pre-European Polynesian specimens also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing no support for a Polynesian introduction of chickens to South America. In contrast, sequences from two archaeological sites on Easter Island group with an uncommon haplogroup from Indonesia, Japan, and the Philippines [corrected] and may represent a genetic signature of an early Polynesian dispersal. Modeling of the potential marine carbon contribution to the Chilean archaeological specimen casts further doubt on claims for pre-Columbian chickens, and definitive proof will require further analyses of ancient DNA sequences and radiocarbon and stable isotope data from archaeological excavations within both Chile and Polynesia.


Assuntos
Galinhas/genética , DNA Mitocondrial/genética , Variação Genética , Filogenia , Animais , Ásia , Sequência de Bases , Chile , Análise por Conglomerados , Europa (Continente) , Haplótipos/genética , Dados de Sequência Molecular , Polimorfismo Genético , Polinésia , Análise de Sequência de DNA
19.
J Virol ; 83(19): 10305-8, 2009 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-19605486

RESUMO

Knowledge of endogenous retroviruses (ERVs) in crocodilians (Crocodylia) is limited, and their distribution among extant species is unclear. Here we analyzed the phylogenetic relationships of these retroelements in 20 species of crocodilians by studying the pro-pol gene. The results showed that crocodilian ERVs (CERVs) cluster into two major clades (CERV 1 and CERV 2). CERV 1 clustered as a sister group of the genus Gammaretrovirus, while CERV 2 clustered distantly with respect to all known ERVs. Interestingly, CERV 1 was found only in crocodiles (Crocodylidae). The data generated here could assist future studies aimed at identifying orthologous and paralogous ERVs among crocodilians.


Assuntos
Retrovirus Endógenos/genética , Retrovirus Endógenos/metabolismo , Algoritmos , Jacarés e Crocodilos , Aminoácidos/química , Animais , Análise por Conglomerados , Biologia Computacional/métodos , Evolução Molecular , Filogenia , Retroelementos
20.
Sci Rep ; 10(1): 20629, 2020 11 26.
Artigo em Inglês | MEDLINE | ID: mdl-33244111

RESUMO

The island of Madagascar, situated off the southeast coast of Africa, shows the first evidence of human presence ~ 10,000 years ago; however, other archaeological data indicates a settlement of the modern peoples of the island distinctly more recent, perhaps > 1500 years ago. Bushpigs of the genus Potamochoerus (family Suidae), are today widely distributed in Madagascar and presumed to have been introduced from Africa at some stage by human immigrants to the island. However, disparities about their origins in Madagascar have been presented in the literature, including the possibility of endemic subspecies, and few empirical data are available. Furthermore, the separation of bushpigs in Madagascar from their mainland relatives may have favoured the evolution of a different repertoire of immune genes first due to a founder effect and then as a response to distinct pathogens compared to their ancestors. Molecular analysis confirmed the species status of the bushpig in Madagascar as P. larvatus, likely introduced from the central region of southern Africa, with no genetic evidence for the recognition of eastern and western subspecies as suggested from previous cranial morphology examination. Investigation of the immunologically important SLA-DQB1 peptide-binding region showed a different immune repertoire of bushpigs in Madagascar compared to those on the African mainland, with seventeen exon-2 haplotypes unique to bushpigs in Madagascar (2/28 haplotypes shared). This suggests that the MHC diversity of the Madagascar populations may have enabled Malagasy bushpigs to adapt to new environments.


Assuntos
Suínos/genética , África Austral , Animais , Variação Genética/genética , Haplótipos , Humanos , Madagáscar , Filogenia
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