New insights on intercontinental origins of paternal lineages in Northeast Brazil

Schaan, Ana Paula; Gusmão, Leonor; Jannuzzi, Juliana; Modesto, Antônio André Conde; Amador, Marcos Antônio Trindade; Marques, Diego; Rabenhorst, Sílvia Helena Barem; Montenegro, Raquel Carvalho; Lopes, Thayson Rodrigues; Pinto, Giovanny R.; Santos, Sidney Emanuel Batista dos; Costa, Lorenna; Silbiger, Vivian Nogueira; Ribeiro-dos-Santos, Ândrea

doi:10.1186/s12862-020-1579-9

Cited by 6 publications

(4 citation statements)

References 53 publications

(70 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Phylogenetic inference using subsampled data sets was performed using IQ-TREE 1.6.3 ( Nguyen et al 2015 ) under the LG+F + G model, and node support was estimated using 1,000 replicates of ultrafast bootstrap (UFBoot; Hoang et al 2018 ). Characterizing the performance of these data sets is complicated by the fact that the underlying phylogenies are unknown (in fact some of the trees used here have already been challenged to some degree; see Meusemann et al 2020 ; Szucsich et al 2020 ; Tihelka et al 2020) . Although large phylogenomic data sets generally produce fully resolved and supported topologies, model violations can favor incorrect trees ( Delsuc et al 2005 ; KapLi et al 2021) .…”

Section: Resultsmentioning

confidence: 99%

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Koch

2021

Molecular Biology and Evolution

View full text Add to dashboard Cite

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale datasets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods, or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different datasets. Here, I calculate multiple gene properties for a range of phylogenomic datasets spanning animal, fungal and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared to alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties, and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.

show abstract

Section: Resultsmentioning

confidence: 99%

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Koch

2021

Molecular Biology and Evolution

View full text Add to dashboard Cite

show abstract

“…Although Eurasian ancestry prevails in most admixed populations from Latin America [ 13 , 14 , 29 , 39 , 45 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 ], the studied sample of the current population of Tierra del Fuego is among those reported with the highest proportions ( Figure 2 ).…”

Section: Resultsmentioning

confidence: 98%

“… Paternal ancestry estimates on different South American populations [ 13 , 14 , 29 , 39 , 45 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 ]. …”

Section: Figurementioning

confidence: 99%

Tierra Del Fuego: What Is Left from the Precolonial Male Lineages?

Rodrigues

Velázquez

Ribeiro³

et al. 2022

Genes

View full text Add to dashboard Cite

Similar to other South American regions, Tierra del Fuego has an admixed population characterized by distinct ancestors: Native Americans who first occupied the continent, European settlers who arrived from the late 15th century onwards, and Sub-Saharan Africans who were brought to the Americas for slave labor. To disclose the paternal lineages in the current population from Tierra del Fuego, 196 unrelated males were genotyped for 23 Y-STRs and 52 Y-SNPs. Haplotype and haplogroup diversities were high, indicating the absence of strong founder or drift events. A high frequency of Eurasian haplogroups was detected (94.4%), followed by Native American (5.1%) and African (0.5%) ones. The haplogroup R was the most abundant (48.5%), with the sub-haplogroup R-S116* taking up a quarter of the total dataset. Comparative analyses with other Latin American populations showed similarities with other admixed populations from Argentina. Regarding Eurasian populations, Tierra del Fuego presented similarities with Italian and Iberian populations. In an in-depth analysis of the haplogroup R-M269 and its subtypes, Tierra del Fuego displayed a close proximity to the Iberian Peninsula. The results from this study are in line with the historical records and reflect the severe demographic change led mainly by male newcomers with paternal European origin.

show abstract

“…Proportions of maternal and paternal ancestries in admixed South American populations were retrieved from the literature [21,34,56,57,59,61,63,[70][71][72][73][74][75][76][77][78][79][80][81][82][83][84][85][86][87][88][89] and represented in a bar chart, together with those obtained for Paraguay.…”

Section: Discussionmentioning

confidence: 99%

The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture

Simão¹,

Ribeiro²,

Vullo³

et al. 2021

Genes

Self Cite

View full text Add to dashboard Cite

Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.

show abstract

New insights on intercontinental origins of paternal lineages in Northeast Brazil

Cited by 6 publications

References 53 publications

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Tierra Del Fuego: What Is Left from the Precolonial Male Lineages?

The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture

Contact Info

Product

Resources

About