Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships

Lv, Xue; Hu, Jingyang; Hu, Yiwen; Li, Yitian; Xu, Dongming; Ryder, Oliver A.; Irwin, David M.; Yu, Li

doi:10.1016/j.ympev.2020.107065

Cited by 7 publications

(8 citation statements)

References 117 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The current study revealed two dominant tree topologies for retrotransposon data: (Perissodactyla (Cetartiodactyla, Ferae)) [Cetartioferae hypothesis] and the exon sequence data: (Ferae (Cetartiodactyla, Perissodactyla)) [Euungulata hypothesis]. The sequence-based Euungulata clade was also previously supported by other sequence data (e.g., [18]). The retrotransposon-based Cetartioferae clade was indicated in the earlier presence/absence study of Doronina et al [36].…”

Section: Discussionsupporting

confidence: 81%

“…The second species helped reduce species-specific signals resulting from occasional instances of homoplasy [33]. As there is already strong evidence for the monophyly of Ferae (Carnivora + Pholidota) (e.g., [11,18,25,36,44]), we omitted pangolin from the initial computational screenings. However, we subsequently added sequence information of pangolins to the alignments.…”

Section: Screening For Phylogenetically Informative Retrotransposonsmentioning

confidence: 99%

“…Multiple large-scale sequence datasets have been applied to this problem, including protein-coding regions, introns, and ultra-conserved elements (UCEs) [15][16][17][18]. These studies have recovered well-supported but sometimes contradictory phylogenetic relationships even in cases where analyses of the same dataset were performed with different phylogenetic methods.…”

Section: Introductionmentioning

confidence: 99%

“…SVDquartets analysis of this dataset supported Fereuungulata and Euungulata. The most recent study of scrotiferan phylogeny [18] analysed four different phylogenomic data sets (proteins and their corresponding protein-coding sequences (4186 loci), introns (1210 loci), UCEs (1246 loci)) with both concatenation and summary coalescence methods. All of the analyses resulted in congruent results that support the monophyly of both Fereuungulata and Euungulata [18].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone

Doronina

Hughes

Moreno-Santillán

et al. 2022

Genes

View full text Add to dashboard Cite

Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest divergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto unsampled laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade.

show abstract

Section: Discussionsupporting

confidence: 81%

Section: Screening For Phylogenetically Informative Retrotransposonsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone

Doronina

Hughes

Moreno-Santillán

et al. 2022

Genes

View full text Add to dashboard Cite

show abstract

“…Contudo, existe um consenso científico de que longas sequências de DNA antigo (aDNA) de fósseis de mamíferos do Cenozoico poderão ajudar nessa empreitada crucial para a compreensão a respeito da evolução dos mamíferos (Lv et al, 2021). Logo, buscar elementos ósseos fossilizados com biocomponentes originais do grupo, principalmente de dados paleogenômicos, é uma tarefa valorosa.…”

Section: Laurasiatheriaunclassified

Exceptional preservation of nonmineralized biomaterials in Cenozoic fossils of the Mammalia clade

Gomes¹,

Machado²,

Alves³

2022

RSD

View full text Add to dashboard Cite

The members of the Mammalia class experienced high ecological, morphological and taxonomic diversification during the Cenozoic Era. With technological advances in molecular paleontology in recent decades, many claims for the exceptional preservation of nonmineralized biomaterials have been made for this clade. However, these data are scattered in the literature and have associated such reports with unique and rare events. This study presents a review of the literature published in the last six decades, aiming to investigate the frequency with which vestigial of nonmineralized biomaterials are found in Mammalia fossils. The results identified 79 published studies describing endogenous biocomponents in Metatheria and Theria members. Of these, protein fragments were more frequent in sedimentary deposits (33.3%), and ancient DNA sequences were more frequent in depositional environments more favorable to exceptional preservation (53.1%), such as ice and cave deposits. The data on organic material for mammalian fossils are geographically and taxonomically comprehensive, with the superordinates Laurasiatheria and Afrotheria presenting the largest number of reports. With the emergence and improvement of new techniques for the recovery of organic material, it is believed that paleomolecular information for fossil mammals should increase, in addition to broadening the understanding of taphonomic factors related to exceptional preservation.

show abstract