This content will become publicly available on April 28, 2024
- NSF-PAR ID:
- 10421105
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Date Published:
- Journal Name:
- Science
- Volume:
- 380
- Issue:
- 6643
- ISSN:
- 0036-8075
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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With the dawn of the Paleogene, the mammalian survivors of the Cretaceous–Paleogene mass extinction, 66 million years ago, found themselves in an emptied landscape. Within a million years of the bolide impact, placental mammals reached a diversity and abundance never seen during the Age of Dinosaurs. The North American ‘condylarths’ were amongst the first mammals to diversify during the early Paleogene and are often considered the ancestral ‘stock’ from which other euungulate groups evolved. Amongst these, Phenacodontidae are often regarded to lie at the base of the perissodactyl family tree, but their phylogenetic position, and that of other ‘condylarths’, remain contentious. Tetraclaenodon, a medium-sized herbivorous phenacodontid from the Torrejonian (~64 to ~62 Ma) of North America is generally recognized as the oldest member of Phenacodontidae, and thus is instrumental for untangling the evolutionary relationships of ‘condylarths’ and perissodactyls. Here we present new information on Tetraclaenodon based on a description of new and previously known fossil material from the San Juan Basin of New Mexico, U.S.A., which we studied using high-resolution computed tomography (CT) scanning. From CT scans of the cranium, we segmented the brain endocast, which is relatively small and smooth (lissencephalic), similar to that of other Paleocene mammals. The petrosal lobules, which are involved in eye movement coordination, are small. The semi-circular canals associated with balance, provide an agility score of 3 indicating that Tetraclaenodon was probably moderately agile, similar to the extant raccoon dog or the aardwolf. A multivariate analysis of tarsal measurements for a sample of Paleocene and extant mammals, which informs locomotor style, indicates that Tetraclaenodon was most suited to terrestrial locomotion. This is in line with anatomical and myological features of the limbs of Tetraclaenodon and other phenacodontids, early perissodactyls and extant mammals. These findings contradict previous studies that designated Tetraclaenodon as a scansorial mammal, capable of habitually climbing trees. Our results shed light on the locomotory adaptations of Tetraclaenodon in comparison to more cursorial phenacodontids and perissodactyls, such as Phenacodus and Hyrachyus. The earliest member of the perissodactyl stem lineage apparently lacked the more cursorial adaptations of their relatives in the late Paleocene and onwards.more » « less
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With the dawn of the Paleogene, the mammalian survivors of the Cretaceous–Paleogene mass extinction, 66 million years ago, found themselves in an emptied landscape. Within a million years of the bolide impact, placental mammals reached a diversity and abundance never seen during the Age of Dinosaurs. The North American ‘condylarths’ were amongst the first mammals to diversify during the early Paleogene and are often considered the ancestral ‘stock’ from which other euungulate groups evolved. Amongst these, Phenacodontidae are often regarded to lie at the base of the perissodactyl family tree, but their phylogenetic position, and that of other ‘condylarths’, remain contentious. Tetraclaenodon, a medium-sized herbivorous phenacodontid from the Torrejonian (~64 to ~62 Ma) of North America is generally recognized as the oldest member of Phenacodontidae, and thus is instrumental for untangling the evolutionary relationships of ‘condylarths’ and perissodactyls. Here we present new information on Tetraclaenodon based on a description of new and previously known fossil material from the San Juan Basin of New Mexico, U.S.A., which we studied using high-resolution computed tomography (CT) scanning. From CT scans of the cranium, we segmented the brain endocast, which is relatively small and smooth (lissencephalic), similar to that of other Paleocene mammals. The petrosal lobules, which are involved in eye movement coordination, are small. The semi-circular canals associated with balance, provide an agility score of 3 indicating that Tetraclaenodon was probably moderately agile, similar to the extant raccoon dog or the aardwolf. A multivariate analysis of tarsal measurements for a sample of Paleocene and extant mammals, which informs locomotor style, indicates that Tetraclaenodon was most suited to terrestrial locomotion. This is in line with anatomical and myological features of the limbs of Tetraclaenodon and other phenacodontids, early perissodactyls and extant mammals. These findings contradict previous studies that designated Tetraclaenodon as a scansorial mammal, capable of habitually climbing trees. Our results shed light on the locomotory adaptations of Tetraclaenodon in comparison to more cursorial phenacodontids and perissodactyls, such as Phenacodus and Hyrachyus. The earliest member of the perissodactyl stem lineage apparently lacked the more cursorial adaptations of their relatives in the late Paleocene and onwards.more » « less
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Abstract The end‐Cretaceous mass extinction allowed placental mammals to diversify ecologically and taxonomically as they filled ecological niches once occupied by non‐avian dinosaurs and more basal mammals. Little is known, however, about how the neurosensory systems of mammals changed after the extinction, and what role these systems played in mammalian diversification. We here use high‐resolution computed tomography (
CT ) scanning to describe the endocranial and inner ear endocasts of two species,Chriacus pelvidens andChriacus baldwini , which belong to a cluster of ‘archaic’ placental mammals called ‘arctocyonid condylarths’ that thrived during theca . 10 million years after the extinction (the Paleocene Epoch), but whose relationships to extant placentals are poorly understood. The endocasts provide new insight into the paleobiology of the long‐mysterious ‘arctocyonids’, and suggest thatChriacus was an animal with anencephalization quotient (EQ) range of 0.12–0.41, which probably relied more on its sense of smell than vision, because the olfactory bulbs are proportionally large but the neocortex and petrosal lobules are less developed. Agility scores, estimated from the dimensions of the semicircular canals of the inner ear, indicate thatChriacus was slow to moderately agile, and its hearing capabilities, estimated from cochlear dimensions, suggest similarities with the extant aardvark.Chriacus shares many brain features with other Paleocene mammals, such as a small lissencephalic brain, large olfactory bulbs and small petrosal lobules, which are likely plesiomorphic for Placentalia. The inner ear ofChriacus also shares derived characteristics of the elliptical and spherical recesses with extinct species that belong to Euungulata, the extant placental group that includes artiodactyls and perissodactyls. This lends key evidence to the hypothesized close relationship betweenChriacus and the extant ungulate groups, and demonstrates that neurosensory features can provide important insight into both the paleobiology and relationships of early placental mammals. -
Abstract In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
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Abstract Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.]