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1.
Gene ; 747: 144684, 2020 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-32311412

RESUMO

PRMT8 is a neuron-specific protein arginine methyltransferase in vertebrates. From data mining, we found a novel prmt8e6+43 splicing variant with a 43-nucleotide (nt) extension at the 5' of exon 6 in chicken. RT-PCR analyses confirmed the existence of two splicing variants but also detected a third upper signal. The triplet pattern detected in chicken suggests that one strand from the prmt8e6+43 transcript and one strand from the regular splicing products form a heteroduplex with a bulb conformation and the two transcripts are of similar abundance. One short plus one faint upper heteroduplex signal detected in mouse and human indicate that the level of the variant is much less than the normal one in mammals. The relative expression of the normal and prmt8e6+43 variants in different species can be inferred from the reads of intron 5 that contains the 43-nt extension or not in the RNA-seq data of NCBI Gene database. The results of the analyses showed that the prmt8e6+43 variant is relatively abundant in birds but much less or even not detected in mammalian species. As conserved intron 5 sequences and evidences of alternative splicing (AS) are detected in elephant shark, a cartilaginous fish with the slowest-evolving genome, we propose that the prmt8e6+43 variant is present in the common ancestor of jawed vertebrates. The prmt8e6+43 variant includes a premature termination codon and thus should encode a truncated PRMT8 with deletion from the dimerization arm. Western blot analyses showed very weak low-molecular-weight signals in chicken, which might be the C-terminal truncated PRMT8. Why avian species maintain high RNA but not protein levels of the prmt8e6+43 variant and whether the evolutionary conserved sequence and AS might regulate PRMT8 expression require further investigation.


Assuntos
Processamento Alternativo/genética , Aves/genética , Variação Genética , Íntrons/genética , Proteína-Arginina N-Metiltransferases/genética , Sítios de Splice de RNA/genética , Vertebrados/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Galinhas/genética , Humanos , Camundongos , Nucleotídeos/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
2.
PLoS One ; 15(2): e0229415, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32109945

RESUMO

Avian adenoviruses (AdVs) are a very diverse group of pathogens causing diseases in poultry and wild birds. Wild birds, endangered by habitat loss and habitat fragmentation in the tropical forests, are recognised to play a role in the transmission of various AdVs. In this study, two novel, hitherto unknown AdVs were described from faecal samples of smooth-billed ani and tropical screech owl. The former was classified into genus Aviadenovirus, the latter into genus Atadenovirus, and both viruses most probably represent new AdV species as well. These results show that there is very limited information about the biodiversity of AdVs in tropical wild birds, though viruses might have a major effect on the population of their hosts or endanger even domesticated animals. Surveys like this provide new insights into the diversity, evolution, host variety, and distribution of avian AdVs.


Assuntos
Infecções por Adenoviridae/veterinária , Adenoviridae/genética , Adenoviridae/isolamento & purificação , Aves/virologia , DNA Viral/análise , Estrigiformes/virologia , Adenoviridae/classificação , Infecções por Adenoviridae/virologia , Animais , Aves/genética , DNA Viral/genética , Filogenia , Estrigiformes/genética
3.
Mol Genet Genomics ; 295(1): 31-46, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31414227

RESUMO

The buff-throated partridge (Tetraophasis szechenyii) is a hypoxia-tolerant bird living in an extremely inhospitable high-altitude environment, which has high ultraviolet (UV) radiation as well as a low oxygen supply when compared with low-altitude areas. To further understand the molecular genetic mechanisms of the high-altitude adaptation of the buff-throated partridges, we de novo assembled the complete genome of the buff-throated partridge. Comparative genomics revealed that positively selected hypoxia-related genes in the buff-throated partridge were distributed in the HIF-1 signaling pathway (map04066), response to hypoxia (GO:0001666), response to oxygen-containing compound (GO:1901700), ATP binding (GO:0005524), and angiogenesis (GO:0001525). Of these positively selected hypoxia-related genes, one positively selected gene (LONP1) had one buff-throated partridge-specific missense mutation which was classified as deleterious by PolyPhen-2. Moreover, positively selected genes in the buff-throated partridge were enriched in cellular response to DNA damage stimulus (corrected P value: 0.028006) and DNA repair (corrected P value: 0.044549), which was related to the increased exposure of the buff-throated partridge to UV radiation. Compared with other avian genomes, the buff-throated partridge showed expansion in genes associated with steroid hormone receptor activity and contractions in genes related to immune and olfactory perception. Furthermore, comparisons between the buff-throated partridge genome and red junglefowl genome revealed a conserved genome structure and provided strong evidence of the sibling relationship between Tetraophasis and Lophophorus. Our data and analysis contributed to the study of Phasianidae evolutionary history and provided new insights into the potential adaptation mechanisms to the high altitude employed by the buff-throated partridge.


Assuntos
Adaptação Fisiológica/genética , Aves/genética , Altitude , Animais , Evolução Biológica , Genoma/genética , Estudo de Associação Genômica Ampla/métodos , Hipóxia/genética , Masculino , Seleção Genética/genética
4.
PLoS One ; 14(12): e0226064, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31869373

RESUMO

Flight loss has evolved independently in numerous island bird lineages worldwide, and particularly in rails (Rallidae). The Aldabra white-throated rail (Dryolimnas [cuvieri] aldabranus) is the last surviving flightless bird in the western Indian Ocean, and the only living flightless subspecies within Dryolimnas cuvieri, which is otherwise volant across its extant range. Such a difference in flight capacity among populations of a single species is unusual, and could be due to rapid evolution of flight loss, or greater evolutionary divergence than can readily be detected by traditional taxonomic approaches. Here we used genetic and morphological analyses to investigate evolutionary trajectories of living and extinct Dryolimnas cuvieri subspecies. Our data places D. [c.] aldabranus among the most rapid documented avian flight loss cases (within an estimated maximum of 80,000-130,000 years). However, the unusual intraspecific variability in flight capacity within D. cuvieri is best explained by levels of genetic divergence, which exceed those documented between other volant taxa versus flightless close relatives, all of which have full species status. Our results also support consideration of Dryolimnas [cuvieri] aldabranus as sufficiently evolutionary distinct from D. c. cuvieri to warrant management as an evolutionary significant unit. Trait variability among closely related lineages should be considered when assessing conservation status, particularly for traits known to influence vulnerability to extinction (e.g. flightlessness).


Assuntos
Evolução Biológica , Aves/classificação , Animais , Aves/genética , Aves/fisiologia , Conservação dos Recursos Naturais , DNA/química , DNA/isolamento & purificação , DNA/metabolismo , Voo Animal , Variação Genética , Haplótipos , Oceano Índico , Ilhas , Filogenia , Análise de Sequência de DNA
5.
Biomed Res Int ; 2019: 2073919, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31886178

RESUMO

The islands of Sardinia, Crete, and Cyprus are hosting the last native insular griffon populations in the Mediterranean basin. Their states have been evaluated from "vulnerable" to "critically endangered". The sequence analysis of molecular markers, particularly the mtDNA D-loop region, provides useful information in studying the evolution of closely related taxa and the conservation of endangered species. Therefore, a study of D-loop region sequence was carried out to estimate the genetic diversity and phylogenetic relationship within and among these three populations. Among 84 griffon specimens (44 Sardinian, 33 Cretan, and 7 Cypriot), we detected four haplotypes including a novel haplotype (HPT-D) that was exclusively found in the Cretan population with a frequency of 6.1%. When considered as a unique population, haplotype diversity (Hd) and nucleotide diversity (π) were high at 0.474 and 0.00176, respectively. A similar level of Hd and π was found in Sardinian and Cretan populations, both showing three haplotypes. The different haplotype frequencies and exclusivity detected were in accordance with the limited matrilineal gene flow (FST = 0.07097), probably related to the species reluctance to fly over sea masses. The genetic variability we observe today would therefore be the result of an evolutionary process strongly influenced by isolation leading to the appearance of island variants which deserve to be protected. Furthermore, since nesting sites and food availability are essential elements for colony settlement, we may infer that the island's colonization began when the first domestic animals were transferred by humans during the Neolithic. In conclusion, our research presents a first contribution to the genetic characterization of the griffon vulture populations in the Mediterranean islands of Sardinia, Crete and Cyprus and lays the foundation for conservation and restocking programs.


Assuntos
Aves/genética , Conservação dos Recursos Naturais , Variação Genética/genética , Mitocôndrias/genética , Animais , DNA Mitocondrial/genética , Espécies em Perigo de Extinção , Genética Populacional , Haplótipos/genética , Humanos , Filogenia
6.
BMC Evol Biol ; 19(1): 189, 2019 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-31619159

RESUMO

BACKGROUND: Many living birds exhibit some nocturnal activity, but the genetic basis and evolutionary origins of their nocturnality remain unknown. RESULTS: Here, we used a molecular phyloecological approach to analyze the adaptive evolution of 33 phototransduction genes in diverse bird lineages. Our results suggest that functional enhancement of two night-vision genes, namely, GRK1 and SLC24A1, underlies the nocturnal adaption of living birds. Further analyses showed that the diel activity patterns of birds have remained relatively unchanged since their common ancestor, suggesting that the widespread nocturnal activity of many living birds may largely stem from their common ancestor rather than independent evolution. Despite this evolutionary conservation of diel activity patterns in birds, photoresponse recovery genes were found to be frequently subjected to positive selection in diverse bird lineages, suggesting that birds generally have evolved an increased capacity for motion detection. Moreover, we detected positive selection on both dim-light vision genes and bright-light vision genes in the class Aves, suggesting divergent evolution of the vision of birds from that of reptiles and that different bird lineages have evolved certain visual adaptions to their specific light conditions. CONCLUSIONS: This study suggests that the widespread nocturnality of extant birds has a deep evolutionary origin tracing back to their common ancestor.


Assuntos
Comportamento Animal/fisiologia , Aves/classificação , Filogenia , Animais , Aves/genética , Transdução de Sinal Luminoso/genética , Seleção Genética , Software
7.
Immunogenetics ; 71(8-9): 561-573, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31506710

RESUMO

The major histocompatibility complex (MHC) is critical to host-pathogen interactions. Class II MHC is a heterodimer, with α and ß subunits encoded by different genes. The peptide-binding groove is formed by the first domain of both subunits (α1 and ß1), but studies of class II variation or natural selection focus primarily on the ß subunit and II B genes. We explored MHC II A in Leach's storm-petrel, a seabird with two expressed, polymorphic II B genes. We found two II A genes, Ocle-DAA and Ocle-DBA, in contrast to the single II A gene in chicken and duck. In exon 2 which encodes the α1 domain, the storm-petrel II A genes differed strongly from each other but showed little within-gene polymorphism in 30 individuals: just one Ocle-DAA allele, and three Ocle-DBA alleles differing from each other by single non-synonymous substitutions. In a comparable sample, the two II B genes had nine markedly diverged alleles each. Differences between the α1 domains of Ocle-DAA and Ocle-DBA showed signatures of positive selection, but mainly at non-peptide-binding site (PBS) positions. In contrast, positive selection within and between the II B genes corresponded to putative PBS codons. Phylogenetic analysis of the conserved α2 domain did not reveal deep or well-supported lineages of II A genes in birds, in contrast to the pronounced differentiation of DQA, DPA, and DRA isotypes in mammals. This uncertain homology complicates efforts to compare levels of functional variation and modes of evolution of II A genes across taxa.


Assuntos
Proteínas Aviárias/genética , Aves/genética , Evolução Molecular , Antígenos de Histocompatibilidade Classe II/genética , Polimorfismo Genético , Sequência de Aminoácidos , Animais , Proteínas Aviárias/imunologia , Sequência de Bases , Aves/imunologia , Éxons , Feminino , Frequência do Gene , Antígenos de Histocompatibilidade Classe II/imunologia , Masculino , Filogenia , Homologia de Sequência
8.
Cytogenet Genome Res ; 159(1): 32-38, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31542782

RESUMO

Despite the variation observed in the diploid chromosome number of storks (Ciconiiformes, Ciconiidae), from 2n = 52 to 2n = 78, most reports have relied solely on analyses by conventional staining. As most species have similar macrochromosomes, some authors propose that karyotype evolution involves mainly fusions between microchromosomes, which are highly variable in species with different diploid numbers. In order to verify this hypothesis, in this study, the karyotypes of 2 species of storks from South America with different diploid numbers, the jabiru (Jabiru mycteria, 2n = 56) and the maguary stork (Ciconia maguary, 2n = 72), were analyzed by chromosome painting using whole chromosome probes from the macrochromosomes of Gallus gallus (GGA) and Leucopternis albicollis (LAL). The results revealed that J. mycteria and C. maguary share synteny within chromosome pairs 1-9 and Z. The syntenies to the macrochromosomes of G. gallus are conserved, except for GGA4, which is homologous to 2 different pairs, as in most species of birds. A fusion of GGA8 and GGA9 was observed in both species. Additionally, chromosomes corresponding to GGA4p and GGA6 are fused to other segments that did not hybridize to any of the macrochromosome probes used, suggesting that these segments correspond to microchromosomes. Hence, our data corroborate the proposed hypothesis that karyotype evolution is based on fusions involving microchromosomes. In view of the morphological constancy of the macrochromosome pairs in most Ciconiidae, we propose a putative ancestral karyotype for the family, including the GGA8/GGA9 fusion, and a diploid number of 2n = 78. The use of probes for microchromosome pairs should be the next step in identifying other synapomorphies that may help to clarify the phylogeny of this family.


Assuntos
Aves/genética , Coloração Cromossômica/veterinária , Cromossomos/genética , Variação Genética/genética , Cariótipo , Animais , Brasil , Diploide , Evolução Molecular , Feminino , Filogenia
9.
Virus Genes ; 55(6): 815-824, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31549291

RESUMO

Viruses are believed to be ubiquitous; however, the diversity of viruses is largely unknown because of the bias of previous research toward pathogenic viruses. Deep sequencing is a promising and unbiased approach to detect viruses from animal-derived materials. Although cranes are known to be infected by several viruses such as influenza A viruses, previous studies targeted limited species of viruses, and thus viruses that infect cranes have not been extensively studied. In this study, we collected crane fecal samples in the Izumi plain in Japan, which is an overwintering site for cranes, and performed metagenomic shotgun sequencing analyses. We detected aviadenovirus-like sequences in the fecal samples and tentatively named the discovered virus crane-associated adenovirus 1 (CrAdV-1). We determined that our sequence accounted for approximately three-fourths of the estimated CrAdV-1 genome size (33,245 bp). The GC content of CrAdV-1 genome is 34.1%, which is considerably lower than that of other aviadenoviruses. Phylogenetic analyses revealed that CrAdV-1 clusters with members of the genus Aviadenovirus, but is distantly related to the previously identified aviadenoviruses. The protein sequence divergence between the DNA polymerase of CrAdV-1 and those of other aviadenoviruses is 45.2-46.8%. Based on these results and the species demarcation for the family Adenoviridae, we propose that CrAdV-1 be classified as a new species in the genus Aviadenovirus. Results of this study contribute to a deeper understanding of the diversity and evolution of viruses and provide additional information on viruses that infect cranes, which might lead to protection of the endangered species of cranes.


Assuntos
Infecções por Adenoviridae/genética , Aviadenovirus/genética , Doenças das Aves/genética , Infecções por Adenoviridae/virologia , Animais , Aviadenovirus/isolamento & purificação , Doenças das Aves/virologia , Aves/genética , Aves/virologia , Fezes/virologia , Sequenciamento de Nucleotídeos em Larga Escala , Vírus da Influenza A/genética , Vírus da Influenza A/patogenicidade , Japão , Filogenia
10.
Physiol Biochem Zool ; 92(5): 481-495, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31393209

RESUMO

Hummingbirds are an emerging model for studies of the visual guidance of flight. However, basic properties of their visual systems, such as spatial and temporal visual resolution, have not been characterized. We measured both the spatial and temporal visual resolution of Anna's hummingbirds using behavioral experiments and anatomical estimates. Spatial visual resolution was determined behaviorally using the optocollic reflex and anatomically using peak retinal ganglion cell densities from retinal whole mounts and eye size. Anna's hummingbirds have a spatial visual resolution of 5-6 cycles per degree when measured behaviorally, which matches anatomical estimates (fovea: 6.26 ± 0.12 cycles per degree; area temporalis: 5.59 ± 0.15 cycles per degree; and whole eye average: 4.64 ± 0.08 ). To determine temporal visual resolution, we used an operant conditioning paradigm wherein hummingbirds were trained to use a flickering light to find a food reward. The limits of temporal visual resolution were estimated as 70-80 Hz. To compare Anna's hummingbirds with other bird species, we used a phylogenetically controlled analysis of previously published data on avian visual resolutions and body size. Our measurements for Anna's hummingbird vision fall close to and below predictions based on body size for spatial visual resolution and temporal visual resolution, respectively. These results indicate that the enhanced flight performance and foraging behaviors of hummingbirds do not require enhanced spatial or temporal visual resolution. This finding is important for interpreting flight control studies and contributes to a growing understanding of avian vision.


Assuntos
Aves/fisiologia , Fenômenos Fisiológicos Oculares , Processamento Espacial , Animais , Aves/genética , Masculino , Especificidade da Espécie , Fatores de Tempo , Gravação em Vídeo
11.
Virus Genes ; 55(6): 739-768, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31428925

RESUMO

Avian influenza viruses (AIVs) circulate globally, spilling over into domestic poultry and causing zoonotic infections in humans. Fortunately, AIVs are not yet capable of causing sustained human-to-human infection; however, AIVs are still a high risk as future pandemic strains, especially if they acquire further mutations that facilitate human infection and/or increase pathogenesis. Molecular characterization of sequencing data for known genetic markers associated with AIV adaptation, transmission, and antiviral resistance allows for fast, efficient assessment of AIV risk. Here we summarize and update the current knowledge on experimentally verified molecular markers involved in AIV pathogenicity, receptor binding, replicative capacity, and transmission in both poultry and mammals with a broad focus to include data available on other AIV subtypes outside of A/H5N1 and A/H7N9.


Assuntos
Marcadores Genéticos/genética , Influenza Aviária/genética , Influenza Humana/genética , Zoonoses/genética , Animais , Aves/genética , Aves/virologia , Farmacorresistência Viral/genética , Humanos , Virus da Influenza A Subtipo H5N1/genética , Virus da Influenza A Subtipo H5N1/patogenicidade , Subtipo H7N9 do Vírus da Influenza A/genética , Subtipo H7N9 do Vírus da Influenza A/patogenicidade , Influenza Aviária/epidemiologia , Influenza Aviária/virologia , Influenza Humana/virologia , Pandemias , Aves Domésticas/genética , Aves Domésticas/virologia , Zoonoses/virologia
12.
Environ Sci Pollut Res Int ; 26(30): 31086-31098, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31456147

RESUMO

With a length exceeding 210,000 km in Europe, railways are common linear features dissecting landscapes. However, the impact of railway networks on biodiversity is equivocal. In this study, we investigated the effect of railway embankments on bird diversity components in an agricultural landscape in southern Poland. Forty transects including 20 along railways and 20 as controls in open fields were established. Birds were counted twice in 2009, and environmental characteristics were estimated for each transect. Ordination techniques and generalized additive models were used to compare species composition, richness, abundance, conservation status, population trends and phylogenetic and functional diversity indices between railway and field transects. Species richness and phylogenetic diversity but not abundance nor functional diversity were higher along railway transects than along field transects. Diversity indices near railways, mostly species richness and phylogenetic diversity, were positively associated with bush cover, wet meadow cover, wetland cover and the slope of the railway but negatively associated with dry meadow cover and field cover. Our study shows that railway embankments may be beneficial for bird diversity but probably do not alter the functional properties of bird communities as much as open fields. Proper management of these linear habitats may increase their value for birds and contribute to long-term bird community persistence.


Assuntos
Biodiversidade , Aves , Ferrovias , Agricultura , Animais , Aves/genética , Ecossistema , Monitoramento Ambiental , Fazendas , Filogenia , Polônia
13.
PLoS One ; 14(7): e0217549, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31291248

RESUMO

The degree to which interspecific competition structures diverse communities is an oft-debated topic. An approach to answering this question is to examine spatial patterns of coexistence among putatively competing species. The degree to which interspecies competition predominates in a community can have important effects on our ability predict the response of that community to perturbations, most notably climate change, when shifting species' ranges may result in novel species assemblages. We present a study on the avifauna of the Eastern Himalayas. We hypothesize that in a community where competitive interactions predominate, there will be a relationship between pairwise altitudinal overlaps and morphological differences between species. Moreover, we hypothesize that both morphological traits and altitudinal traits depart from a Brownian motion evolution model, resulting in species trait covariances having a phylogenetic component. We find a significant relationship between morphological dissimilarity and altitudinal overlaps of species pairs. We also find that closely related species are significantly more altitudinally stratified than a null model would predict. However, as more distantly related species pairs are included in the analysis, this pattern disappears, indicating that competitive interactions predominate only in closely related species. This is further suggested by the fact that altitudinal ranges themselves are phylogenetically overdispersed at the genus level, as are morphological traits. This effect disappears when the entire phylogeny is examined, with morphology and altitude being phylogenetically underdispersed. Model fitting suggests that individual clades have evolved towards local clade-specific fitness peaks, while within-clade results show evidence of niche partitioning. We interpret these results as a tension between competition on shorter time scales and selection on longer time scales, where competition forces closely-related species away from fitness peaks in order to allow for niche separation and hence coexistence, suggesting that this effect is partially responsible for the recent diversification of Eastern Himalayan avifauna.


Assuntos
Evolução Biológica , Aves , Altitude , Animais , Biodiversidade , Aves/anatomia & histologia , Aves/genética , Aves/fisiologia , Mudança Climática , Comportamento Competitivo , Ecossistema , Filogenia
14.
Cytogenet Genome Res ; 158(3): 152-159, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31272100

RESUMO

Among birds, species with the ZZ/ZW sex determination system generally show significant differences in morphology and size between the Z and W chromosomes (with the W usually being smaller than the Z). In the present study, we report for the first time the karyotype of the spot-flanked gallinule (Gallinula melanops) by means of classical and molecular cytogenetics. The spot-flanked gallinule has 2n = 80 (11 pairs of macrochromosomes and 29 pairs of microchromosomes) with an unusual W chromosome that is larger than the Z. Besides being totally heterochromatic, it has a secondary constriction in its long arm corresponding to the nucleolar organizer region, as confirmed by both silver staining and mapping of 18S rDNA probes. This is an unprecedented fact among birds. Additionally, 18S rDNA sites were also observed in 6 microchromosomes, while 5S rDNA was found in just 1 microchromosomal pair. Seven out of the 11 used microsatellite sequences were found to be accumulated in microchromosomes, and 6 microsatellite sequences were found in the W chromosome. In addition to the involvement of heterochromatin and repetitive DNAs in the differentiation of the large W chromosome, the results also show an alternative scenario that highlights the plasticity that shapes the evolutionary history of bird sex chromosomes.


Assuntos
Aves/genética , Evolução Molecular , Sequências Repetitivas de Ácido Nucleico/genética , Cromossomos Sexuais/genética , Animais , Bandeamento Cromossômico , Mapeamento Cromossômico , Feminino , Cariótipo , Repetições de Microssatélites/genética , Região Organizadora do Nucléolo/genética
15.
Nat Commun ; 10(1): 3244, 2019 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-31324809

RESUMO

In crown group tetrapods, individual digits are homologized in relation to a pentadactyl ground plan. However, testing hypotheses of digit homology is challenging because it is unclear whether digits represent distinct and conserved gene regulatory states. Here we show dramatic evolutionary dynamism in the gene expression profiles of digits, challenging the notion that five digits have conserved developmental identities across amniotes. Transcriptomics shows diversity in the patterns of gene expression differentiation of digits, although the anterior-most digit of the pentadactyl limb has a unique, conserved expression profile. Further, we identify a core set of transcription factors that are differentially expressed among the digits of amniote limbs; their spatial expression domains, however, vary between species. In light of these results, we reevaluate the frame shift hypothesis of avian wing evolution and conclude only the identity of the anterior-most digit has shifted position, suggesting a 1,3,4 digit identity in the bird wing.


Assuntos
Proteínas Aviárias/genética , Aves/genética , Padronização Corporal/genética , Extremidades , Perfilação da Expressão Gênica/métodos , Asas de Animais/metabolismo , Animais , Aves/anatomia & histologia , Evolução Molecular , Humanos , Asas de Animais/anatomia & histologia
16.
Mol Biol Evol ; 36(10): 2358-2374, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31165149

RESUMO

Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, FST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a high mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with low density have the largest FST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into disconnected components. We illustrate our results using two example data sets-sky island birds of genus Sholicola and Indian tigers-identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity, and they can assist in designing strategies to alter population migration networks toward maximizing genetic variation in the context of conservation of endangered species.


Assuntos
Migração Animal , Genética Populacional/métodos , Animais , Aves/genética , Variação Genética , Tigres/genética
17.
BMC Genomics ; 20(1): 447, 2019 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-31159743

RESUMO

BACKGROUND: Under caged conditions, birds are affected more severely by environmental stressors such as dietary structure, activity space, human disturbances, and pathogens, which may be reflected in the gene expression in peripheral blood or other tissues. Elucidating the molecular mechanism of these stress responses will help improve animal welfare. RESULTS: In the present study, the blood transcriptomes of six male and five female caged magpies (Pica pica) were sequenced, and a total of ~ 100 Gb in clean reads were generated using the Illumina HiSeq 2000 sequencer. A total of 420,291 unigenes were identified after assembly, of which 179,316 were annotated in five databases, 7471 were assigned to 269 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 566 were assigned to the Clusters of Orthologous Groups (COG) functional classification "defense mechanisms". Analysis of differentially expressed genes (DEGs) showed that 2657 unigenes were differentially expressed between males and females (q < 0.1), and these DEGs were assigned to 45 KEGG pathways involving stress resistance, immunity, energy metabolism, reproduction, lifespan regulation, and diseases. Further analysis revealed that females might be more sensitive to stress through upregulation of c-Jun N-terminal kinases (JNKs) and 5'AMP-activated protein kinase (AMPK), and were also possibly more sensitive to dynamic changes in energy. Females expressed higher major histocompatibility complex (MHC) class II levels than males, enhancing resistance to pathogens, and the DEGs related to reproduction included MAPK, CaMK, CPEB, and Cdc25. The genes related to stress, energy, and immunity were also likely related to the regulation of longevity. The upregulated JNKs in females might prolong lifespan and relieve antioxidant stress. Females may also activate the AMPK pathway and implement dietary restrictions to prolong lifespan, whereas males may upregulate SIRT1 and CRAB to increase lifespan. CONCLUSIONS: Female magpies might be more sensitive to stress and dynamic changes in energy thus enhanced resistance to pathogens, and the genes related to stress, energy, and immunity were also possibly related to the regulation of longevity. Further confirmations with techniques such as RT-qPCR and western blot are necessary to validate the above arguments.


Assuntos
Proteínas Aviárias/genética , Aves/fisiologia , Perfilação da Expressão Gênica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Abrigo para Animais/estatística & dados numéricos , Estresse Fisiológico , Animais , Aves/genética , Feminino , Regulação da Expressão Gênica , Masculino
18.
Mol Biol Evol ; 36(10): 2340-2351, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31209473

RESUMO

Multiple sequence alignment (MSA) is ubiquitous in evolution and bioinformatics. MSAs are usually taken to be a known and fixed quantity on which to perform downstream analysis despite extensive evidence that MSA accuracy and uncertainty affect results. These errors are known to cause a wide range of problems for downstream evolutionary inference, ranging from false inference of positive selection to long branch attraction artifacts. The most popular approach to dealing with this problem is to remove (filter) specific columns in the MSA that are thought to be prone to error. Although popular, this approach has had mixed success and several studies have even suggested that filtering might be detrimental to phylogenetic studies. We present a graph-based clustering method to address MSA uncertainty and error in the software Divvier (available at https://github.com/simonwhelan/Divvier), which uses a probabilistic model to identify clusters of characters that have strong statistical evidence of shared homology. These clusters can then be used to either filter characters from the MSA (partial filtering) or represent each of the clusters in a new column (divvying). We validate Divvier through its performance on real and simulated benchmarks, finding Divvier substantially outperforms existing filtering software by retaining more true pairwise homologies calls and removing more false positive pairwise homologies. We also find that Divvier, in contrast to other filtering tools, can alleviate long branch attraction artifacts induced by MSA and reduces the variation in tree estimates caused by MSA uncertainty.


Assuntos
Alinhamento de Sequência/métodos , Homologia de Sequência , Animais , Aves/genética
19.
BMC Res Notes ; 12(1): 257, 2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31072404

RESUMO

OBJECTIVE: Use next-generation sequencing to develop microsatellite loci that will provide the variability necessary for studies of genetic diversity and population connectivity of two New World vulture species. RESULTS: We characterized 11 microsatellite loci for black vultures (Coragyps atratus) and 14 loci for turkey vultures (Cathartes aura). These microsatellite loci were grouped into 3 multiplex panels for each species. The number of alleles among black vulture samples ranged from 2 to 11, and 3 to 48 among turkey vulture samples.


Assuntos
Aves/genética , Repetições de Microssatélites/genética , Animais , Motivos de Nucleotídeos/genética , Reação em Cadeia da Polimerase
20.
PLoS One ; 14(5): e0214653, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31042737

RESUMO

Pacific martens (Martes caurina) are often associated with mature forests with complex structure for denning, resting, and efficient hunting. Nonetheless, a small isolated population of the Humboldt subspecies of Pacific martens (Martes caurina humboldtensis) occupies a narrow strip of young, coastal forest (< 70 years old) but not inland mature forest in the central Oregon Coast Range. We examined factors contributing to this unexpected distribution of martens by 1) analyzing marten diets using DNA metabarcoding to assess 90 scats, 2) using camera traps to assess differences in the relative abundances of prey, competitors, and predators across a coastal to inland gradient of vegetation types, and 3) quantifying differences in extent of fruit-producing shrubs and vegetation structure within vegetation types. Diets of martens were diverse (12, 10, and 3 species of birds, mammals, and amphibians respectively), and most fall and winter scats contained fruit. Voles, mice, and varied thrushes (Ixoreus naevius) were dominant prey items. Voles, mice, and most birds, but not varied thrushes, were more commonly observed in the coastal shrub-dominated forest than in inland forest. The coastal shrub-dominated forest had the highest diversity of vertebrates and potential prey overall. Bobcats (Lynx rufus), a key potential predator, were more commonly detected in inland forest. Of potential competitors, western spotted skunks (Spilogale gracilis) were more commonly detected in inland forest, with gray foxes (Urocyon cinereoargenteus) and raccoons (Procyon lotor) detected almost exclusively in coastal forests. Vegetation in coastal forests appears to provide, at least seasonally, more prey and fruit, and more overhead shrub cover compared with inland forest. Remaining plausible hypotheses for the restricted distribution of marten to coastal forests include increased prey, fruit, and overhead cover, and reduced predation risk from bobcats.


Assuntos
Anfíbios/classificação , Aves/classificação , Código de Barras de DNA Taxonômico/métodos , Mamíferos/classificação , Mustelidae/fisiologia , Anfíbios/genética , Animais , Aves/genética , Demografia , Dieta , Herbivoria , Mamíferos/genética , Comportamento Predatório , Gravação em Vídeo
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