A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence

<p>Abstract</p> <p>Background</p> <p>The placental mammalian clade Afrotheria is now supported by diverse forms of genomic data, but interordinal relationships within, and morphological support for, the group remains elusive. As a means for addressing these outstanding problems, competing hypotheses of afrotherian interordinal relationships were tested through simultaneous parsimony analysis of a large data set (> 4,590 parsimony informative characters) containing genomic data (> 17 kb of nucleotide data, chromosomal associations, and retroposons) and 400 morphological characters scored across 16 extant and 35 extinct afrotherians.</p> <p>Results</p> <p>Parsimony analysis of extant taxa alone recovered the interordinal topology (Afrosoricida, ((Macroscelidea, Tubulidentata), (Hyracoidea, (Proboscidea, Sirenia)))). Analysis following addition of extinct taxa instead supported Afroinsectivora (Afrosoricida + Macroscelidea) and Pseudoungulata (Tubulidentata + Paenungulata), as well as Tethytheria (Proboscidea + Sirenia). This latter topology is, however, sensitive to taxon deletion and different placements of the placental root, and numerous alternative interordinal arrangements within Afrotheria could not be statistically rejected. Relationships among extinct stem members of each afrotherian clade were more stable, but one alleged stem macroscelidean (<it>Herodotius</it>) never grouped with that clade and instead consistently joined pseudoungulates or paenungulates. When character transformations were optimized onto a less resolved afrotherian tree that reflects uncertainty about the group's interordinal phylogeny, a total of 21 morphological features were identified as possible synapomorphies of crown Afrotheria, 9 of which optimized unambiguously across all character treatments and optimization methods.</p> <p>Conclusion</p> <p>Instability in afrotherian interordinal phylogeny presumably reflects rapid divergences during two pulses of cladogenesis – the first in the Late Cretaceous, at and just after the origin of crown Afrotheria, and the second in the early Cenozoic, with the origin of crown Paenungulata. Morphological evidence for divergences during these two pulses either never existed or has largely been "erased" by subsequent evolution along long ordinal branches. There may, nevertheless, be more morphological character support for crown Afrotheria than is currently assumed; the features identified here as possible afrotherian synapomorphies can be further scrutinized through future phylogenetic analyses with broader taxon sampling, as well as recovery of primitive fossil afrotherians from the Afro-Arabian landmass, where the group is likely to have first diversified.</p

Early anthropoid femora reveal divergent adaptive trajectories in catarrhine hind-limb evolution

The divergence of crown catarrhines—i.e., the split of cercopithecoids (Old World monkeys) from hominoids (apes and humans)—is a poorly understood phase in our shared evolutionary history with other primates. The two groups differ in the anatomy of the hip joint, a pattern that has been linked to their locomotor strategies: relatively restricted motion in cercopithecoids vs. more eclectic movements in hominoids. Here we take advantage of the first well-preserved proximal femur of the early Oligocene stem catarrhine Aegyptopithecus to investigate the evolution of this anatomical region using 3D morphometric and phylogenetically-informed evolutionary analyses. Our analyses reveal that cercopithecoids and hominoids have undergone divergent evolutionary transformations of the proximal femur from a similar ancestral morphology that is not seen in any living anthropoid, but is preserved in Aegyptopithecus, stem platyrrhines, and stem cercopithecoids. These results highlight the relevance of fossil evidence for illuminating key adaptive shifts in primate evolution

Evolution and Allometry of Calcaneal Elongation in Living and Extinct Primates

Specialized acrobatic leaping has been recognized as a key adaptive trait tied to the origin and subsequent radiation of euprimates based on its observed frequency in extant primates and inferred frequency in extinct early euprimates. Hypothesized skeletal correlates include elongated tarsal elements, which would be expected to aid leaping by allowing for increased rates and durations of propulsive acceleration at takeoff. Alternatively, authors of a recent study argued that pronounced distal calcaneal elongation of euprimates (compared to other mammalian taxa) was related primarily to specialized pedal grasping. Testing for correlations between calcaneal elongation and leaping versus grasping is complicated by body size differences and associated allometric affects. We re-assess allometric constraints on, and the functional significance of, calcaneal elongation using phylogenetic comparative methods, and present an evolutionary hypothesis for the evolution of calcaneal elongation in primates using a Bayesian approach to ancestral state reconstruction (ASR). Results show that among all primates, logged ratios of distal calcaneal length to total calcaneal length are inversely correlated with logged body mass proxies derived from the area of the calcaneal facet for the cuboid. Results from phylogenetic ANOVA on residuals from this allometric line suggest that deviations are explained by degree of leaping specialization in prosimians, but not anthropoids. Results from ASR suggest that non-allometric increases in calcaneal elongation began in the primate stem lineage and continued independently in haplorhines and strepsirrhines. Anthropoid and lorisid lineages show stasis and decreasing elongation, respectively. Initial increases in calcaneal elongation in primate evolution may be related to either development of hallucal-grasping or a combination of grasping and more specialized leaping behaviors. As has been previously suggested, subsequent increases in calcaneal elongation are likely adaptations for more effective acrobatic leaping, highlighting the importance of this behavior in early euprimate evolution

Evolution of the primate vomeronasal system: fossil evidence from the Fayum

Extant primates vary dramatically in the presence and development of the vomeronasal system (VNS), which largely detects social pheromones and anti-predator chemosignals. While the strepsirrhine VNS resembles most mammals, haplorhines either have derived VNS traits with ambiguous effects on vomeronasal function, or have lost the system entirely. While a reduced reliance on vomeronasal olfaction in haplorhines is inferred, few studies have addressed VNS variation in extinct primates to examine the timing and context of the loss of this system. We have previously identified an osteological correlate of the vomeronasal organ, the vomeronasal groove (VNG), which allows us to implement a paleontological approach toward understanding primate VNS evolution. We investigated cranial material of fossil primates for the presence or absence of a VNG using microCT scans. The VNG was present in a broad temporal and taxonomic range of primate fossils, including plesiadapiforms, adapiforms, omomyoids, crown platyrrhines, stem anthropoids, and stem catarrhines. Notably the VNG persists as a relatively small gutter in the stem catarrhine Aegyptopithecus zeuxis, but is absent in advanced stem catarrhine Saadanius hijazensis, and the Miocene cercopithecoid Victoriapithecus. We estimate that VNG loss occurred between 30-28ma, based on our sample. These dates complement estimates for the accelerated rate of deleterious mutations, and loss of function, in the TRPC2 pheromone transduction gene in catarrhines between 40-25ma. Further exploration of the VNG in fossil primates will lead to a more thorough understanding of past sensory environments and their ultimate effects on sensory specializations of extant lineages.First author draf

Palaeontological evidence for an Oligocene divergence between Old World monkeys and apes

Apes and Old World monkeys are prominent components of modern African and Asian ecosystems, yet the earliest phases of their evolutionary history have remained largely undocumented(1). The absence of crown catarrhine fossils older than similar to 20 million years (Myr) has stood in stark contrast to molecular divergence estimates of similar to 25-30 Myr for the split between Cercopithecoidea (Old World monkeys) and Hominoidea (apes), implying long ghost lineages for both clades(2-4). Here we describe the oldest known fossil 'ape', represented by a partial mandible preserving dental features that place it with 'nyanzapithecine' stem hominoids. Additionally, we report the oldest stem member of the Old World monkey clade, represented by a lower third molar. Both specimens were recovered from a precisely dated 25.2-Myr-old stratum in the Rukwa Rift, a segment of the western branch of the East African Rift in Tanzania. These finds extend the fossil record of apes and Old World monkey swell into the Oligocene epoch of Africa, suggesting a possible link between diversification of crown catarrhines and changes in the African landscape brought about by previously unrecognized tectonic activity(5) in the East African rift system

Craniodental Morphology and Systematics of a New Family of Hystricognathous Rodents (Gaudeamuridae) from the Late Eocene and Early Oligocene of Egypt

BACKGROUND: Gaudeamus is an enigmatic hystricognathous rodent that was, until recently, known solely from fragmentary material from early Oligocene sites in Egypt, Oman, and Libya. Gaudeamus' molars are similar to those of the extant cane rat Thryonomys, and multiple authorities have aligned Gaudeamus with Thryonomys to the exclusion of other living and extinct African hystricognaths; recent phylogenetic analyses have, however, also suggested affinities with South American caviomorphs or Old World porcupines (Hystricidae). METHODOLOGY/PRINCIPAL FINDINGS: Here we describe the oldest known remains of Gaudeamus, including largely complete but crushed crania and complete upper and lower dentitions. Unlike younger Gaudeamus species, the primitive species described here have relatively complex occlusal patterns, and retain a number of plesiomorphic features. Unconstrained parsimony analysis nests Gaudeamus and Hystrix within the South American caviomorph radiation, implying what we consider to be an implausible back-dispersal across the Atlantic Ocean to account for Gaudeamus' presence in the late Eocene of Africa. An analysis that was constrained to recover the biogeographically more plausible hypothesis of caviomorph monophyly does not place Gaudeamus as a stem caviomorph, but rather as a sister taxon of hystricids. CONCLUSIONS/SIGNIFICANCE: We place Gaudeamus species in a new family, Gaudeamuridae, and consider it likely that the group originated, diversified, and then went extinct over a geologically brief period of time during the latest Eocene and early Oligocene in Afro-Arabia. Gaudeamurids are the only known crown hystricognaths from Afro-Arabia that are likely to be aligned with non-phiomorph members of that clade, and as such provide additional support for an Afro-Arabian origin of advanced stem and basal crown members of Hystricognathi

IL4I1 Is a Metabolic Immune Checkpoint that Activates the AHR and Promotes Tumor Progression

Immune checkpoint blockade therapy induces the AHR-activating enzyme IL4I1, which promotes tumor progression, through its effects on tumor cell motility and adaptive immunity

A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence-3

<p><b>Copyright information:</b></p><p>Taken from "A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence"</p><p>http://www.biomedcentral.com/1471-2148/7/224</p><p>BMC Evolutionary Biology 2007;7():224-224.</p><p>Published online 13 Nov 2007</p><p>PMCID:PMC2248600.</p><p></p>I = 0.50, RI = 0.44, RCI = 0.28) and with some morphological characters ordered and scaled (1 MPT, TL = 18689.54, CI = 0.50, RI = 0.44, RCI = 0.28). Branches depicted with dashes break down in the strict consensus of all 13 trees. Values above and below branches are bootstrap support (1000 replicates) from analysis of the matrix with some multistate characters ordered and scaled (above) and with all multistate characters unordered (below). Herodotiine taxa (alleged stem macroscelideans) are in bold face; asterisks identify "wild card" taxa whose variable positions given different character treatments lead to decreased resolution in the strict consensus tree