From the Cover: Protein sequence signatures support the African clade of mammals

Abstract

DNA sequence evidence supports a superordinal clade of mammals that comprises elephants, sea cows, hyraxes, aardvarks, elephant shrews, golden moles, and tenrecs, which all have their origins in Africa, and therefore are dubbed Afrotheria. Morphologically, this appears an unlikely assemblage, which challenges-by including golden moles and tenrecs-the monophyly of the order Lipotyphla (Insectivora). We here identify in three proteins unique combinations of apomorphous amino acid replacements that support this clade. The statistical support for such ''sequence signatures'' as unambiguous synapomorphic evidence for the naturalness of the Afrotherian clade is reported. Using likelihood, combinatorial, and Bayesian methods we show that the posterior probability of the mammalian tree containing the Afrotherian clade is effectively 1.0, based on conservative assumptions. Presenting sequence data for another African insectivore, the otter shrew Micropotamogale lamottei, we demonstrate that such signatures are diagnostic for including newly investigated species in the Afrotheria. Sequence signatures provide ''protein-morphological'' synapomorphies that may aid in visualizing monophyletic groupings.

Comparative Anatomy of the Bony Labyrinth (Inner Ear) of Placental Mammals

“…Although some morphological data support a sistergroup relationship between Hyracoidea and Perissodactyla [101], [127]–[128], the majority of morphological [33], [102], [104]–[105], [129]–[130] and molecular data [66], [98], [109]–[110], [112]–[113], [130] support a pairing of Hyracoidea and Tethytheria within the group Paenungulata. The results of most phylogenetic analyses recover a sistergroup relationship between Hyracoidea and a monophyletic Tethytheria, but the results of a few recent analyses, including the supertree used here [66], support a closer relationship between Hyracoidea and Sirenia, rendering Tethytheria paraphyletic.…”

“…A close relationship between Xenarthra and Pholidota (pangolins) within a group called Edentata has been proposed based on morphology (as recently as the mid-1980’s [33]), but such anatomical similarities, which include adaptations for a fossorial lifestyle and a reduction in teeth, are considered homoplastic in light of more recent phylogenetic analyses and evolutionary discussions [66], [139]. Further, nearly all molecular analyses group Pholidota with other placental clades separate from Xenarthra [66], [68], [98], [108], [112]–[113], [121]–[122], [140]–[141]. At least one exception is a study using protein sequences that recovered a sistergroup relationship between Xenarthra and Pholidota [142].…”

Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses

“…The superordinal clades Euarchontoglires, Laurasiatheria and Afrotheria are highly supported, and within these clades most bootstrap percentages and posterior probabilities are also high. Afrotheria is now generally accepted as a natural group since molecular studies unanimously support its monophyly, using various methods [ 1 , 4 , 27 - 29 ]. In contrast, until now only few morphological synapomorphies, notably placental morphology [ 30 ], an increase in number of thoracolumbar vertebrae [ 31 ], and testicondy [ 32 ], appear to support this grouping.…”

Signatures of conserved and unique molecular features in Afrotheria

“…The Afrotheria superorder represents a diverse group of mammals that differ distinctively from each other 1 . It contains the six orders of the elephants (Order Proboscidea), sea cows (Sirenia), hyraxes (Hyracoidea), aardvark (Tubulidentata), elephant shrews (Macroscelidea), golden moles and tenrecs (Afrosoricida).…”

“…Protein-centric analysis involving Afrotherian species have mainly focused on understanding species phylogeny 1 . Detailed comparative studies involving the distribution of various functional and structural domains within the Afrotheria could help to recognize protein domains that are specifically amplified or occur in distinct combinations.…”