South American Lineage Research Articles

Migratory birds in southern Brazil are a source of multiple avian influenza virus subtypes.

BackgroundThere is insufficient knowledge about the relation of avian influenza virus (AIV) to migratory birds in South America. Accordingly, we studied samples obtained over a 4‐year period (2009‐2012) from wild birds at a major wintering site in southern Brazil.MethodsWe obtained 1212 oropharyngeal/cloacal samples from wild birds at Lagoa do Peixe National Park and screened them for influenza A virus by RT‐PCR amplification of the matrix gene. Virus isolates were subjected to genomic sequencing and antigenic characterization.ResultsForty‐eight samples of 1212 (3.96%) contained detectable influenza virus RNA. Partial viral sequences were obtained from 12 of these samples, showing the presence of H2N2 (1), H6Nx (1), H6N1 (8), H9N2 (1), and H12N5 (1) viruses. As H6 viruses predominated, we generated complete genomes from all 9 H6 viruses. Phylogenetic analyses showed that they were most similar to viruses of South American lineage. The H6N1 viruses caused no disease signs in infected ferrets and, despite genetic differences, were antigenically similar to North American isolates.ConclusionsLagoa do Peixe National Park is a source of multiple AIV subtypes, with the levels of influenza virus in birds being highest at the end of their wintering period in this region. H6N1 viruses were the predominant subtype identified. These viruses were more similar to viruses of South American lineage than to those of North American lineage.

Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages

Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing. The strains here sequenced are the first obtained in South America for the infectious bronchitis virus and provide new insights into the origin, spreading and evolution of viral variants. The complete genome of the GI-11 and GI-16 strains have 27,621 and 27,638 nucleotides, respectively, and possess the same genomic organization. Phylogenetic incongruence analysis reveals that both strains have a mosaic genome that arose by recombination between Euro Asiatic strains of the GI-16 lineage and ancestral South American GI-11 viruses. The recombination occurred in South America and produced two viral variants that have retained the full-length S1 sequences of the parental lineages but are extremely similar in the rest of their genomes. These recombinant virus have been extraordinary successful, persisting in the continent for several years with a notorious wide geographic distribution. Our findings reveal a singular viral dynamics and emphasize the importance of complete genomic characterization to understand the emergence and evolutionary history of viral variants.

Early and dynamic colonization of Central America drives speciation in Neotropical army ants.

The emergence of the Isthmus of Panama is one of the most important events in recent geological history, yet its timing and role in fundamental evolutionary processes remain controversial. While the formation of the isthmus was complete around 3million years ago (Ma), recent studies have suggested prior intercontinental biotic exchange. In particular, the possibility of early intermittent land bridges facilitating colonization constitutes a potential mechanism for speciation and colonization before full closure of the isthmus. To test this hypothesis, we employed genomic methods to study the biogeography of the army ant genus Eciton, a group of keystone arthropod predators in Neotropical rainforests. Army ant colonies are unable to disperse across water and are therefore ideally suited to study the biogeographic impact of land bridge formation. Using a reduced representation genome sequencing approach, we show that all strictly Central American lineages of Eciton diverged from their respective South American sister lineage between 4 and 7Ma, significantly prior to the complete closure of the isthmus. Furthermore, three of the lineage pairs form extensive and coincident secondary contact zones in Costa Rica and Nicaragua, with no evidence of gene flow. Such a discrete and repeated biogeographic pattern indicates at least two waves of army ant dispersal into Central America that were separated by significant genetic divergence times. Thus, by integrating phylogenomic, population genomic and geographic evidence, we show that early colonization of Central America across the emerging Isthmus of Panamá drove parallel speciation in Eciton army ants.

Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae.

BackgroundIn February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields.ResultsReinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae.ConclusionOur findings suggest that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-016-0309-7) contains supplementary material, which is available to authorized users.

Development of RT-qPCR assays for the specific identification of two major genotypes of avian infectious bronchitis virus

Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus (27.6kb) that causes one of the most persistent respiratory disease in poultry. The virus is classified in genotypes with different epidemiological relevance and clinical implications. The present study reports the development and validation of specific RT-qPCR assays for the detection of two major IBV genotypes: South America I (SAI) and Asia/South America II (A/SAII). The SAI genotype is an exclusive and widespread South American lineage while the A/SAII genotype is distributed in Asia, Europe and South America. Both identification assays employ TaqMan probes that hybridize with unique sequences in the spike glycoprotein gene. The assays successfully detected all the assessed strains belonging to both genotypes, showing high specificity and absence of cross-reactivity. Using serial dilutions of in vitro-transcribed RNA we obtained acceptable determination coefficients, PCR efficiencies and relatively small intra- and inter-assay variability. The assays demonstrated a wide dynamic range between 101–107 and 102–107 RNA copies/reaction for SAI and A/SAII strains, respectively. The possibility to characterize a large number of samples in a rapid, sensitive and reproducible way makes these techniques suitable tools for routine testing, IBV control, and epidemiological research in poultry.

The First Capybaras (Rodentia, Caviidae, Hydrochoerinae) Involved in the Great American Biotic Interchange

Abstract. The new combination Phugatherium dichroplax nov. comb. (Ahearn and Lance) is proposed for the North American species “Neochoerus” dichroplax Ahearn and Lance, and “N.” cordobai Carranza-Castaneda and Miller. Its age range is here expanded (late Early Blancan—latest Blancan; Piacenzian—Gelasian), being the youngest species of Phugatherium and thus extending the biochron of the genus into the early Pleistocene. This is the first mention of a Pliocene South American lineage of capybaras crossing the Panamanian bridge, implying the recognition of a third lineage of capybaras involved in the Great American Biotic Interchange. The proposed North American origin of the genus Neochoerus is discussed.

Phylodynamic analysis of avian infectious bronchitis virus in South America.

Infectious bronchitis virus (IBV) is a coronavirus of chickens that causes great economic losses to the global poultry industry. The present study focuses on South American IBVs and their genetic relationships with global strains. We obtained full-length sequences of the S1 coding region and N gene of IBV field isolates from Uruguay and Argentina, and performed Phylodynamic analysis to characterize the strains and estimate the time of the most recent common ancestor. We identified two major South American genotypes, which were here denoted South America I (SAI) and Asia/South America II (A/SAII). The SAI genotype is an exclusive South American lineage that emerged in the 1960s. The A/SAII genotype may have emerged in Asia in approximately 1995 before being introduced into South America. Both SAI and A/SAII genotype strains clearly differ from the Massachusetts strains that are included in the vaccine formulations being used in most South American countries.

Genetic diversity of Venezuelan alphaviruses and circulation of a Venezuelan equine encephalitis virus subtype IAB strain during an interepizootic period.

Several species of alphaviruses have been previously described in the Americas, some of which are associated with encephalitis and others are associated with arthralgia. Venezuelan equine encephalitis virus (VEEV) and eastern equine encephalitis virus (EEEV) are endemic to Venezuela, with the former being responsible for major outbreaks of severe and often fatal disease in animals and humans. The aim of this study was to analyze the genetic diversity of Venezuelan alphaviruses isolated during two decades (1973-1999) of surveillance in northern Venezuela. Phylogenetic analysis indicated the circulation of a VEEV subtype IAB strain 8 years after the last reported outbreak. Thirteen strains within two subclades of South American lineage III of EEEV were also found in Venezuela. Considerable genetic variability was observed among Venezuelan Una virus strains, which were widely distributed among the clades. The first Venezuelan Mayaro sequence was also characterized.

The diversification of the genusMonodelphisand the chronology of Didelphidae (Didelphimorphia)

To evaluate the monophyletic status of the genus Monodelphis, and its species complexes, we used a 9.3-kb multimarker alignment to build a phylogenetic tree based on the largest taxon sampling for this didelphid genus to date. Furthermore, using a Bayesian framework and six calibration points, we inferred the divergence times for the major Monodelphis lineages and their current geographical distribution to perform an ancestral state reconstruction for geographical areas. Our results indicate the monophyletic nature of Monodelphis and suggest ‘kunsi’ as a new species complex that includes Monodelphis kunsi and an undescribed species. Monodelphis is further subdivided into three clades showing a common vicariance pattern, with each major clade consisting of a northern South American lineage joined with an Atlantic Forest lineage. This geographic consistency suggests a vicariant event that might have been related to a warm period at the Oligocene/Miocene border, according to our time results. © 2015 The Linnean Society of London

Mitochondrial DNA analysis reveals hidden genetic diversity in captive populations of the threatened American crocodile (Crocodylus acutus) in Colombia.

Identification of units within species worthy of separate management consideration is an important area within conservation. Mitochondrial DNA (mtDNA) surveys can potentially contribute to this by identifying phylogenetic and population structure below the species level. The American crocodile (Crocodylus acutus) is broadly distributed throughout the Neotropics. Its numbers have been reduced severely with the species threatened throughout much of its distribution. In Colombia, the release of individuals from commercial captive populations has emerged as a possible conservation strategy that could contribute to species recovery. However, no studies have addressed levels of genetic differentiation or diversity within C. acutus in Colombia, thus complicating conservation and management decisions. Here, sequence variation was studied in mtDNA cytochrome b and cytochrome oxidase I gene sequences in three Colombian captive populations of C. acutus. Two distinct lineages were identified: C. acutus-I, corresponding to haplotypes from Colombia and closely related Central American haplotypes; and C. acutus-II, corresponding to all remaining haplotypes from Colombia. Comparison with findings from other studies indicates the presence of a single “northern” lineage (corresponding to C. acutus-I) distributed from North America (southern Florida), through Central America and into northern South America. The absence of C. acutus-II haplotypes from North and Central America indicates that the C. acutus-II lineage probably represents a separate South American lineage. There appears to be sufficient divergence between lineages to suggest that they could represent two distinct evolutionary units. We suggest that this differentiation needs to be recognized for conservation purposes because it clearly contributes to the overall genetic diversity of the species. All Colombian captive populations included in this study contained a mixture of representatives of both lineages. As such, we recommend against the use of captive-bred individuals for conservation strategies until further genetic information is available.

Re-establishment of the name Pombalia, and new combinations from the polyphyletic Hybanthus (Violaceae)

This paper introduces the re-establishment of Pombalia Vand., the earliest generic designation for the predominantly South American lineage of the polyphyletic Hybanthus Jacq. (Violaceae). Recent molecular-based phylogenies and ongoing morphological studies have resulted in the recognition of 41 species and one variety in this group, requiring their transfer to the currently monotypic Pombalia, as proposed here. The study also revealed the necessity to lectotypify 20 of the basionyms.

Optimizing Surveillance for South American Origin Influenza A Viruses Along the United States Gulf Coast Through Genomic Characterization of Isolates from Blue-winged Teal (Anas discors).

Relative to research focused on inter-continental viral exchange between Eurasia and North America, less attention has been directed towards understanding the redistribution of influenza A viruses (IAVs) by wild birds between North America and South America. In this study, we genomically characterized 45 viruses isolated from blue-winged teal (Anas discors) along the Texas and Louisiana Gulf Coast during March of 2012 and 2013, coincident with northward migration of this species from Neotropical wintering areas to breeding grounds in the United States and Canada. No evidence of South American lineage genes was detected in IAVs isolated from blue-winged teal supporting restricted viral gene flow between the United States and southern South America. However, it is plausible that blue-winged teal redistribute IAVs between North American breeding grounds and wintering areas throughout the Neotropics, including northern South America, and that viral gene flow is limited by geographical barriers further south (e.g., the Amazon Basin). Surveillance for the introduction of IAVs from Central America and northern South America into the United States may be further optimized through genomic characterization of viruses resulting from coordinated, concurrent sampling efforts targeting blue-winged teal and sympatric species throughout the Neotropics and along the United States Gulf Coast.

Phylogeny of Amazona barbadensis and the Yellow-headed Amazon complex (Aves: Psittacidae): a new look at South American parrot evolution.

The Yellow-shouldered Amazon (Amazona barbadensis) is the sole parrot of the genus Amazona that inhabits only dry forests. Its population has been dropping; therefore it has been the topic of many studies and conservation efforts. However, the phylogenetic relationship of this species to potential relatives classified within the Yellow-Headed Amazon (YHA) complex are still not clear. Therefore, we used more extensive data sets, including the newly sequenced mitochondrial genome of A. barbadensis, to conduct phylogenetic analyses. Various combinations of genes and many phylogenetic approaches showed that A. barbadensis clustered significantly with A. ochrocephala ochrocephala from Colombia and Venezuela, which created the Northern South American (NSA) lineage, clearly separated from two other lineages within the YHA complex, the Central (CA) and South American (SA). Tree topology tests and exclusion of rapidly evolving sites provided support for a NSA+SA grouping. We propose an evolutionary scenario for the YHA complex and its colonization of the American mainland. The NSA lineage likely represents the most ancestral lineage, which derived from Lesser Antillean Amazons and colonized the northern coast of Venezuela about a million years ago. Then, Central America was colonized through the Isthmus of Panama, which led to the emergence of the CA lineage. The southward expansion to South America and the origin of the SA lineage happened almost simultaneously. However, more intensive or prolonged gene flow or migrations have led to much weaker geographic differentiation of genetic markers in the SA than in the CA lineage.

Cyclestheria hislopi (Crustacea: Branchiopoda): A group of morphologically cryptic species with origins in the Cretaceous

Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hislopi represents a single circumtropic species. South American (French Guiana), Asian (India, Indonesia, Singapore) and several Australian populations were included in our investigation. Phylogenetic and genetic distance analyses revealed remarkable intercontinental genetic differentiation (uncorrected p-distances COI>13%, EF1α>3% and 28S>4%). Each continent was found to have at least one distinct Cyclestheria species, with Australia boasting four distinct main lineages which may be attributed to two to three species. The divergence of these species (constituting crown group Cyclestherida) was, on the basis of phylogenetic analyses of COI and EF1α combined with molecular clock estimates using several fossil branchiopod calibration points or a COI substitution rate of 1.4% per million years, dated to the Cretaceous. This was when the South American lineage split from the Asian–Australian lineage, with the latter diverging further in the Paleogene. Today’s circumtropic distribution of Cyclestheria may be best explained by a combination of Gondwana vicariance and later dispersal across Asia and Australia when the tectonic plates of the two continents drew closer in the early Miocene. The lack of morphological differentiation that has taken place in this taxon over such a long evolutionary period contrasts with the high level of differentiation and diversification observed in its sister taxon the Cladocera. Further insights into the evolution of Cyclestheria may help us to understand the evolutionary success of the Cladocera.

Phylogeny and colonization history of Pringlea antiscorbutica (Brassicaceae), an emblematic endemic from the South Indian Ocean Province

The origins and evolution of sub-Antarctic island floras are not well understood. In particular there is uncertainty about the ages of the contemporary floras and the ultimate origins of the lineages they contain. Pringlea R. Br. (Brassicaceae) is a monotypic genus endemic to four sub-Antarctic island groups in the southern Indian Ocean. Here we used sequences from both the chloroplast and nuclear genomes to examine the phylogenetic position of this enigmatic genus. Our analyses confirm that Pringlea falls within the tribe Thelypodieae and provide a preliminary view of its relationships within the group. Divergence time estimates and ancestral area reconstructions imply Pringlea diverged from a South American ancestor ∼5Myr ago. It remains unclear whether the ancestor of Pringlea dispersed directly to the South Indian Ocean Province (SIOP) or used Antarctica as a stepping-stone; what is clear, however, is that following arrival in the SIOP several additional long-distance dispersal events must be inferred to explain the current distribution of this species. Our analyses also suggest that although Pringlea is likely to have inherited cold tolerance from its closest relatives, the distinctive morphology of this species evolved only after it split from the South American lineage. More generally, our results lend support to the hypothesis that angiosperms persisted on the sub-Antarctic islands throughout the Pliocene and Pleistocene. Taken together with evidence from other sub-Antarctic island plant groups, they suggest the extant flora of sub-Antarctic is likely to have been assembled over a broad time period and from lineages with distinctive biogeographic histories.

The South American Gomphotheres (Mammalia, Proboscidea, Gomphotheriidae): Taxonomy, Phylogeny, and Biogeography

The taxonomic history of South American Gomphotheriidae is very complex and controversial. Three species are currently recognized: Amahuacatherium peruvium, Cuvieronius hyodon, and Notiomastodon platensis. The former is a late Miocene gomphothere whose validity has been questioned by several authors. The other two, C. hyodon and N. platensis, are Quaternary taxa in South America, and they have distinct biogeographic patterns: Andean and lowland distributions, respectively. South American gomphotheres became extinct at the end of the Pleistocene. We conducted a phylogenetic analysis of Proboscidea including the South American Quaternary gomphotheres, which resulted in two most parsimonious trees. Our results support a paraphyletic Gomphotheriidae and a monophyletic South American gomphothere lineage: C. hyodon and N. platensis. The late Miocene gomphothere record in Peru, Amahuacatherium peruvium, seems to be a crucial part of the biogeography and evolution of the South American gomphotheres.

Amplified Fragment Length Polymorphism Marker Diversity among High Yielding Perennial Alfalfa (Medicago sativa L.) Core Collection Accessions

Understanding the genetic structure of alfalfa (Medicago sativa L.) plant introductions, including the identification of divergent populations, may benefit their utilization in cultivar development programs. Two independent experiments (Exp. 1 and Exp. 2) were conducted to assess amplified fragment length polymorphism (AFLP) marker diversity among 18 high‐yielding alfalfa core collection accessions that were previously evaluated by diallel analysis for forage yield combining abilities and heterosis in southern New Mexico. Each experiment involved nine different M. sativa subsp. sativa populations and one control accession of M. sativa subsp. falcata (L.) Arcang. Both experiments indicated that the M. sativa subsp. sativa populations were genetically distinct from the M. sativa subsp. falcata accession. Genetic distances among the M. sativa subsp. sativa accessions were predominantly governed by the geographic distances of their historic origins in Exp. 1. In Exp. 2 such relationships were less obvious, perhaps because multiple accessions possessed South American and/or central Asian lineage. Genetic distances in both experiments were also influenced by the intersubspecific or intrasubspecific hybrid nature of some accessions. Multiple correspondence analysis of the AFLP data for the 18 accessions, in conjunction with yield performance and heterosis response of their diallel hybrids, indicated that most hybrids that exhibited positive heterosis and high yield possessed a genetically divergent accession as a parent.

Analytical Validation of a Real-Time Reverse Transcription Polymerase Chain Reaction Test for Pan-American Lineage H7 Subtype Avian Influenza Viruses

A real-time reverse transcription polymerase chain reaction test for the identification of the H7 subtype in North American avian influenza viruses AIV was first reported in 2002; however, recent (AIVs) surveillance efforts in wild birds and H7 outbreaks in poultry demonstrated that the 2002 test did not detect all H7 AIVs present in North and South America. Therefore, a new test, the 2008 Pan-American H7 test, was developed by using recently available H7 nucleotide sequences. The analytical specificity of the new assay was characterized with an RNA panel composed of 19 H7 viruses from around the world and RNA from all hemagglutinin subtypes except H16. Specificity for North and South American lineage H7 viruses was observed. Assay limits of detection were determined to be between 10(3) and 10(4) gene copies per reaction with in vitro transcribed RNA, and 10(0.0) and 10(0.8) 50% egg infectious doses per reaction. The 2008 Pan-American H7 test also was shown to perform similarly to the 2002 test with specimens from chickens experimentally exposed to A/Chicken/BritishColumbia/314514-2/04 H7N3 highly pathogenic AIV. Furthermore, the 2008 test was able to detect 100% (n = 27) of the H7 AI, V isolates recovered from North American wild birds in a 2006-2007 sample set, (none of which were detected by the 2002 H7 test).

Phylogeny and biogeography of Yellow‐headed and Blue‐fronted Parrots (Amazona ochrocephala and Amazona aestiva) with special reference to the South American taxa

The Yellow‐headed Parrot (Amazona ochrocephala) has a broad Neotropical distribution, ranging from Mexico to the Amazon Basin, and a history of complex taxonomy and controversial species limits. Recent molecular analyses have started to clarify the taxonomic arrangement of the complex, but have not included a representative geographical sampling from South America. These studies have shown that the Yellow‐headed complex can be divided into three main lineages, and seems to be paraphyletic, due to the inclusion of the Blue‐fronted Parrot (Amazona aestiva) that occurs in central South America. Here we present a phylogenetic analysis based on mitochondrial DNA sequences of 45 representatives of the Yellow‐headed complex from South and Central America, plus 13 Blue‐fronted individuals from different localities in South America. Our analyses recover the three primary lineages found previously in the Yellow‐headed complex, show that there is genetic structure in the South American lineage, which can be divided into two well‐supported, closely related clades, and demonstrate that Blue‐fronted samples are distributed in both clades. Differentiation of South American Blue‐fronted and Yellow‐headed Parrot populations does not correspond to the plumage differences used to distinguish the Blue‐fronted Parrot from the Yellow‐headed Parrot, nor to plumage differences used to distinguish among South American Yellow‐headed subspecies. This suggests that traditional taxonomy based on plumage characters needs revision, and that this may be an interesting example of ongoing divergence‐with‐gene‐flow related to the forest/open area ecotone in southern Amazonia.

The <I>Synammia</I> Enigma: Evidence for a Temperate Lineage of Polygrammoid Ferns (Polypodiaceae, Polypodiidae) in Southern South America

Abstract Evidence for a southern South American lineage of polygrammoid ferns was inferred from analyses using four cpDNA markers. The lineage corresponds to the genus Synammia, which has usually been treated as a synonym of the polyphyletic genus Polypodium. Seven specimens of two of the three recognized species were sampled to infer the phylogenetic relationships of this lineage to other polygrammoid ferns and the diversity within this lineage. All approaches found Synammia clearly separated from other polygrammoid ferns, but the exact relationships are still unclear. Model-based methods recovered Synammia as sister to a mainly Neotropical clade of polygrammoid ferns, but support for this hypothesis was provided only by Bayesian inference of phylogeny. The deletion of nearly the whole rps4-trnS IGS is a synapomorphy of Synammia. The lineage is separated from other extant polygrammoid ferns, but very low to zero sequence diversity was found among the seven samples of Synammia. The results strongly suppor...