The Andean Ibis (Theristicus branickii) in South America: potential distribution, presence in protected areas and anthropic threats

The avifauna of South America is one of the most widely studied groups of vertebrates. However, certain species, such as the Andean Ibis (Theristicus branickii), have received limited attention regarding their ecological patterns, biology, current distribution, and environmental requirements. This study analyzed observation data from the Global Biodiversity Information Facility (GBIF) on the Andean Ibis in four countries to identify and understand critical variables that determine the species' presence, assess the proportion of its habitat within protected areas and identify possible threats to the species. Additionally, this study considered environmental and ecological variables to model ecological niches using the maximum entropy approach in MaxEnt to map the suitable habitat of the species. The findings revealed the extent of suitable Andean Ibis habitats in Ecuador, Peru, Bolivia and Chile. The variables that most determined the presence of the species were: altitude (36.57%), distance to lakes (23.29%) and ecological isothermality (13.34%). The distribution area of the Andean Ibis totaled 300,095.00 km2, spanning both sides of the Andean mountains range. Human activities have left a significant impact on the Andean Ibis habitat, with 48% of this area impacted by the human footprint and only 10% of the territory falling within protected areas designated by the respective countries. The results of this study show that the Andean Ibis presents characteristics of a specialist species due to its adaptation to the climate conditions of the plateau and highlands, including low temperatures, herbaceous vegetation and the presence of water bodies. The species is distributed in disconnected Andean landscape areas, whose functionality could be compromised by increased human activities. Complementary studies will be necessary to understand the ecological role and effectiveness of protected areas for conserving the species.

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.

Functional compensation of mouse duplicates by their paralogs expressed in the same tissues

Analyses in a number of organisms have shown that duplicated genes are less likely to be essential than singletons. This implies that genes can often compensate for the loss of their paralogs. However, it is unclear why the loss of some duplicates can be compensated by their paralogs, whereas the loss of other duplicates cannot. Surprisingly, initial analyses in mice did not detect differences in the essentiality of duplicates and singletons. Only subsequent analyses, using larger gene knockout datasets and controlling for a number of confounding factors, did detect significant differences. Previous studies have not taken into account the tissues in which duplicates are expressed. We hypothesized that in complex organisms, in order for a gene's loss to be compensated by one or more of its paralogs, such paralogs need to be expressed in at least the same set of tissues as the lost gene. To test our hypothesis, we classified mouse duplicates into two categories based on the expression patterns of their paralogs: "compensable duplicates" (those with paralogs expressed in all the tissues in which the gene is expressed) and "non-compensable duplicates" (those whose paralogs are not expressed in all the tissues where the gene is expressed). In agreement with our hypothesis, the essentiality of non-compensable duplicates is similar to that of singletons, whereas compensable duplicates exhibit a substantially lower essentiality. Our results imply that duplicates can often compensate for the loss of their paralogs, but only if they are expressed in the same tissues. Indeed, the compensation ability is more dependent on expression patterns than on protein sequence similarity. The existence of these two kinds of duplicates with different essentialities, which has been overlooked by prior studies, may have hindered the detection of differences between singletons and duplicates.

Myxosporea (Myxozoa, Cnidaria) Lack DNA Cytosine Methylation

DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known instances of secondary loss in animals. Myxozoans are a group of microscopic, obligate endoparasitic cnidarians that have lost many genes over the course of their evolution from free-living ancestors. Here, we investigated the evolution of the key enzymes involved in DNA cytosine methylation in 29 cnidarians and found that these enzymes were lost in an ancestor of Myxosporea (the most speciose class of Myxozoa). Additionally, using whole-genome bisulfite sequencing, we confirmed that the genomes of two distant species of myxosporeans, Ceratonova shasta and Henneguya salminicola, completely lack DNA cytosine methylation. Our results add a notable and novel taxonomic group, the Myxosporea, to the very short list of animal taxa lacking DNA cytosine methylation, further illuminating the complex evolutionary history of this epigenetic regulatory mechanism.

Mycoplasma agassizii, an opportunistic pathogen of tortoises, shows very little genetic variation across the Mojave and Sonoran Deserts

Mycoplasma agassizii is a common cause of upper respiratory tract disease in Mojave desert tortoises (Gopherus agassizii). So far, only two strains of this bacterium have been sequenced, and very little is known about its patterns of genetic diversity. Understanding genetic variability of this pathogen is essential to implement conservation programs for their threatened, long-lived hosts. We used next generation sequencing to explore the genomic diversity of 86 cultured samples of M. agassizii collected from mostly healthy Mojave and Sonoran desert tortoises in 2011 and 2012. All samples with enough sequencing coverage exhibited a higher similarity to M. agassizii strain PS6^T (collected in Las Vegas Valley, Nevada) than to strain 723 (collected in Sanibel Island, Florida). All eight genomes with a sequencing coverage over 2x were subjected to multiple analyses to detect single-nucleotide polymorphisms (SNPs). Strikingly, even though we detected 1373 SNPs between strains PS6^T and 723, we did not detect any SNP between PS6^T and our eight samples. Our whole genome analyses reveal that M. agassizii strain PS6^T may be present across a wide geographic extent in healthy Mojave and Sonoran desert tortoises.

The Local South American Chicken Populations Are a Melting-Pot of Genomic Diversity

Chicken have a considerable impact in South American rural household economy as a source of animal protein (eggs and meat) and a major role in cultural traditions (e.g., cockfighting, religious ceremonies, folklore). A large number of phenotypes and its heterogeneity are due to the multitude of environments (from arid to tropical rain forest and high altitude) and agricultural systems (highly industrialized to subsistence agriculture). This heterogeneity also represents the successive introduction of domestic chicken into this continent, which some consider predating Columbus’ arrival to South America. In this study, we have used next-generation restriction site-associated DNA sequencing to scan for genome-wide variation across 145 South American chickens representing local populations from six countries of South America (Colombia, Brazil, Ecuador, Peru, Bolivia, and Chile). After quality control, the genotypes of 122,801 single nucleotide polymorphisms (SNPs) were used to assess the genomic diversity and interpopulation genetic relationship between those populations and their potential sources. The estimated population genetic diversity displayed that the gamefowl has the least diverse population (θπ = 0.86; θS = 0.70). This population is also the most divergent (F_ST = 0.11) among the South American populations. The allele-sharing analysis and the admixture analysis revealed that the current diversity displayed by these populations resulted from multiple admixture events with a strong influence of the modern commercial egg-layer chicken (ranging between 44% and 79%). It also revealed an unknown genetic component that is mostly present in the Easter Island population that is also present in local chicken populations from the South American Pacific fringe.

On the origins and genetic diversity of South American chickens: one step closer

Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens.