Recapitulating the evolution of Afrotheria: 57 genes and rare genomic changes (RGCs) consolidate their history

Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)

Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., the Paenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates. We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships and that despite strong support for a Proboscidea+Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea, Hyracoidea, and Sirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea, Hyracoidea, and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.

Ancestral chromosomal signatures of Paenungulata (Afroteria) reveal the karyotype of Amazonian manatee (Trichechus inunguis, Sirenia: Trichechidae) as the oldest among American manatees

BACKGROUND

Chromosomal painting in manatees has clarified questions about the rapid evolution of sirenians within the Paenungulata clade. Further cytogenetic studies in Afrotherian species may provide information about their evolutionary dynamics, revealing important insights into the ancestral karyotype in the clade representatives. The karyotype of Trichechus inunguis (TIN, Amazonian manatee) was investigated by chromosome painting, using probes from Trichechus manatus latirostris (TML, Florida manatee) to analyze the homeologies between these sirenians.

RESULTS

A high similarity was found between these species, with 31 homologous segments in TIN, nineteen of which are whole autosomes, besides the X and Y sex chromosomes. Four chromosomes from TML (4, 6, 8, and 9) resulted in two hybridization signals, totaling eight acrocentrics in the TIN karyotype. This study confirmed in TIN the chromosomal associations of Homo sapiens (HSA) shared in Afrotheria, such as the 5/21 synteny, and in the Paenungulata clade with the syntenies HSA 2/3, 8/22, and 18/19, in addition to the absence of HSA 4/8 common in eutherian ancestral karyotype (EAK).

CONCLUSIONS

TIN shares more conserved chromosomal signals with the Paenungulata Ancestral Karyotype (APK, 2n = 58) than Procavia capensis (Hyracoidea), Loxodonta africana (Proboscidea) and TML (Sirenia), where TML presents less conserved signals with APK, demonstrating that its karyotype is the most derived among the representatives of Paenungulata. The chromosomal changes that evolved from APK to the T. manatus and T. inunguis karyotypes (7 and 4 changes, respectively) are more substantial within the Trichechus genus compared to other paenungulates. Among these species, T. inunguis presents conserved traits of APK in the American manatee genus. Consequently, the karyotype of T. manatus is more derived than that of T. inunguis.

Species identity and behavior of cave-dwelling tree hyraxes of the Kenyan coast

We surveyed tree hyrax populations living in forests, limestone rocky formations, and caves in coastal Kenya to identify the species and estimate the threat-level populations are in. Tree hyrax vocalizations were recorded in three different habitats with passive acoustic monitoring (PAM) for a total of 84 h in January and February 2022. We also observed tree hyrax behavior with thermal imaging camera and photographed individuals. Tree hyraxes in coastal Kenya are vocally active throughout the night, with most calls emitted between 23.00 and 04.00. We identified four different calls: snort, hac, hac ping-pong, and wheeze. Their calling range is between 220 and 15,000 Hz. Calls of tree hyraxes from the coast of Kenya were compared with calls stored by the Oxford Brookes University's Nocturnal Primate Research Group and identified as eastern tree hyrax, previously recorded from Tanzania. Here, we present what are, to our knowledge, the first photographs of live D. validus from Kenya. These tree hyraxes live in social groups. Due to strong pressure from humans, conservation measures are necessary to prevent the extinction of these isolated D. validus populations in Kenya.

From Easy to Hopeless-Predicting the Difficulty of Phylogenetic Analyses

Phylogenetic analyzes under the Maximum-Likelihood (ML) model are time and resource intensive. To adequately capture the vastness of tree space, one needs to infer multiple independent trees. On some datasets, multiple tree inferences converge to similar tree topologies, on others to multiple, topologically highly distinct yet statistically indistinguishable topologies. At present, no method exists to quantify and predict this behavior. We introduce a method to quantify the degree of difficulty for analyzing a dataset and present Pythia, a Random Forest Regressor that accurately predicts this difficulty. Pythia predicts the degree of difficulty of analyzing a dataset prior to initiating ML-based tree inferences. Pythia can be used to increase user awareness with respect to the amount of signal and uncertainty to be expected in phylogenetic analyzes, and hence inform an appropriate (post-)analysis setup. Further, it can be used to select appropriate search algorithms for easy-, intermediate-, and hard-to-analyze datasets.

Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria)

Molecular phylogenetic studies that have included sirenians from the genera Trichechus, Dugong, and Hydrodamalis have resolved their interrelationships but have yielded divergence age estimates that are problematically discordant. The ages of these lineage splits have profound implications for how to interpret the sirenian fossil record-including clade membership, biogeographic patterns, and correlations with Earth history events. In an effort to address these issues, here we present a total evidence phylogenetic analysis of Sirenia that includes living and fossil species and applies Bayesian tip-dating methods to estimate their interrelationships and divergence times. In addition to extant sirenians, our dataset includes 56 fossil species from 106 dated localities and numerous afrotherian outgroup taxa. Genetic, morphological, temporal, and biogeographic data are assessed simultaneously to bring all available evidence to bear on sirenian phylogeny. The resulting time-tree is then used for Bayesian geocoordinates reconstruction analysis, which models ancestral geographic areas at splits throughout the phylogeny, thereby allowing us to infer the direction and timing of dispersals. Our results suggest that Pan-Sirenia arose in North Africa during the latest Paleocene and that the Eocene evolution of stem sirenians was primarily situated in the Tethyan realm. In the late Eocene, some lineages moved into more northern European latitudes, an area that became the source region for a key trans-Atlantic dispersal towards the Caribbean and northern-adjacent west Atlantic. This event led to the phylogenetic and biogeographic founding of crown Sirenia with the Dugongidae-Trichechidae split occurring at the Eocene-Oligocene boundary (~33.9 Ma), temporally coincident with the onset of dropping global sea levels and temperatures. This region became the nexus of sirenian diversification and supported taxonomically-rich dugongid communities until the earliest Pliocene. The Dugonginae-Hydrodamalinae split occurred near Florida during the early Miocene (~21.2 Ma) and was followed by a west-bound dispersal that gave rise to the Pacific hydrodamalines. The late middle Miocene (~12.2 Ma) split of Dugong from all other dugongines also occurred near Florida and our analyses suggest that the Indo-Pacific distribution of modern dugongs is the result of a trans-Pacific dispersal. From at least the early Miocene, trichechid evolution was based entirely in South America, presumably within the Pebas Wetlands System. We infer that the eventual establishment of Amazon drainage into the South Atlantic allowed the dispersal of Trichechus out of South America no earlier than the mid-Pliocene. Our analyses provide a new temporal and biogeographic framework for understanding major events in sirenian evolution and their possible relationships to oceanographic and climatic changes. These hypotheses can be further tested with the recovery and integration of new fossil evidence.

Patterns and tempo of PCSK9 pseudogenizations suggest an ancient divergence in mammalian cholesterol homeostasis mechanisms

Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a central role in cholesterol homeostasis in humans as a major regulator of LDLR levels. PCSK9 is an intriguing protease in that it does not act by proteolysis but by preventing LDLR recirculation from endosomes to the plasma membrane. This, and the inexistence of any other proteolytic substrate but itself could suggest that PCSK9 is an exquisite example of evolutionary fine-tuning. However, the gene has been lost in several mammalian species, and null alleles are present (albeit at low frequencies) in some human populations without apparently deleterious health effects, raising the possibility that the PCSK9 may have become dispensable in the mammalian lineage. To address this issue, we systematically recovered, assembled, corrected, annotated and analysed publicly available PCSK9 sequences for 420 eutherian species to determine the distribution, frequencies, mechanisms and timing of PCSK9 pseudogenization events, as well as the evolutionary pressures underlying the preservation or loss of the gene. We found a dramatic difference in the patterns of PCSK9 retention and loss between Euarchontoglires—where there is strong pressure for gene preservation—and Laurasiatheria, where multiple independent events have led to PCSK9 loss in most species. These results suggest that there is a fundamental difference in the regulation of cholesterol metabolism between Euarchontoglires and Laurasiatheria, which in turn has important implications for the use of Laurasiatheria species (e.g. pigs) as animal models of human cholesterol-related diseases.

A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers

BACKGROUND

Multiple alignments of mammalian genomes have been the basis of many comparative genomic studies aiming at annotating genes, detecting regions under evolutionary constraint, and studying genome evolution. A key factor that affects the power of comparative analyses is the number of species included in a genome alignment.

RESULTS

To utilize the increased number of sequenced genomes and to provide an accessible resource for genomic studies, we generated a mammalian genome alignment comprising 120 species. We used this alignment and the CESAR method to provide protein-coding gene annotations for 119 non-human mammals. Furthermore, we illustrate the utility of this alignment by 2 exemplary analyses. First, we quantified how variable ultraconserved elements (UCEs) are among placental mammals. Leveraging the high taxonomic coverage in our alignment, we estimate that UCEs contain on average 4.7%-15.6% variable alignment columns. Furthermore, we show that the center regions of UCEs are generally most constrained. Second, we identified enhancer sequences that are only conserved in placental mammals. We found that these enhancers are significantly associated with placenta-related genes, suggesting that some of these enhancers may be involved in the evolution of placental mammal-specific aspects of the placenta.

CONCLUSION

The 120-mammal alignment and all other data are available for analysis and visualization in a genome browser at https://genome-public.pks.mpg.de/and for download at https://bds.mpi-cbg.de/hillerlab/120MammalAlignment/.

Recurrent loss of HMGCS2 shows that ketogenesis is not essential for the evolution of large mammalian brains

Apart from glucose, fatty acid-derived ketone bodies provide metabolic energy for the brain during fasting and neonatal development. We investigated the evolution of HMGCS2, the key enzyme required for ketone body biosynthesis (ketogenesis). Unexpectedly, we found that three mammalian lineages, comprising cetaceans (dolphins and whales), elephants and mastodons, and Old World fruit bats have lost this gene. Remarkably, many of these species have exceptionally large brains and signs of intelligent behavior. While fruit bats are sensitive to starvation, cetaceans and elephants can still withstand periods of fasting. This suggests that alternative strategies to fuel large brains during fasting evolved repeatedly and reveals flexibility in mammalian energy metabolism. Furthermore, we show that HMGCS2 loss preceded brain size expansion in toothed whales and elephants. Thus, while ketogenesis was likely important for brain size expansion in modern humans, ketogenesis is not a universal precondition for the evolution of large mammalian brains.

Our brain requires a lot of energy to work properly. Sugars are usually the main type of fuel for the body, but when they run low – for example during a food shortage – fat, in the form of fatty acids, can be used instead. However, the brain cannot directly process these molecules; instead, fatty acids need to go through ketogenesis, a process that turns fat into ketone bodies, which the organ can then burn. Scientists believe that the ability to create ketone bodies was essential for us to evolve large brains. Yet, it is still unclear if all mammals can transform fatty acids into ketone bodies. One way to look into this question is to track whether other species have HMGCS2, the main enzyme that drives ketogenesis.

Jebb and Hiller examined the genomes of 70 different species of mammals for the gene that codes for HMGCS2. The comparisons revealed that cetaceans (whales, dolphins and porpoises), Old World fruit bats and the African savanna elephant have all independently lost their working version of HMGCS2. Yet, many members of these three groups have evolved brains that are large for their body size. The genetic analyses showed that dolphins and elephants developed big brains after the enzyme became inactive, challenging the idea that HMGCS2 – and by extension ketogenesis – is always required for the evolution of large brains.

These results may also be useful for conservation efforts. Many fruit bats across the world are severely threatened, and their lack of ketogenesis could explain why these animals are highly sensitive to starvation and quickly die when food becomes scarce.

Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals

Descent of testes from a position near the kidneys into the lower abdomen or into the scrotum is an important developmental process that occurs in all placental mammals, with the exception of five afrotherian lineages. Since soft-tissue structures like testes are not preserved in the fossil record and since key parts of the placental mammal phylogeny remain controversial, it has been debated whether testicular descent is the ancestral or derived condition in placental mammals. To resolve this debate, we used genomic data of 71 mammalian species and analyzed the evolution of two key genes (relaxin/insulin-like family peptide receptor 2 [RXFP2] and insulin-like 3 [INSL3]) that induce the development of the gubernaculum, the ligament that is crucial for testicular descent. We show that both RXFP2 and INSL3 are lost or nonfunctional exclusively in four afrotherians (tenrec, cape elephant shrew, cape golden mole, and manatee) that completely lack testicular descent. The presence of remnants of once functional orthologs of both genes in these afrotherian species shows that these gene losses happened after the split from the placental mammal ancestor. These “molecular vestiges” provide strong evidence that testicular descent is the ancestral condition, irrespective of persisting phylogenetic discrepancies. Furthermore, the absence of shared gene-inactivating mutations and our estimates that the loss of RXFP2 happened at different time points strongly suggest that testicular descent was lost independently in Afrotheria. Our results provide a molecular mechanism that explains the loss of testicular descent in afrotherians and, more generally, highlight how molecular vestiges can provide insights into the evolution of soft-tissue characters.

While fossils of whales with legs demonstrate that these species evolved from legged ancestors, the ancestral state of nonfossilizing soft-tissue structures can only be indirectly inferred. This difficulty is also confounded by uncertainties in the phylogenetic relationships between the animals concerned. A prime example is the case of testicular descent, a developmental process that determines the final position of testes, which occurs in most placental mammals but is absent from several afrotherian lineages. Here, we discovered that afrotherians possess remnants of genes known to be required for testicular descent. These “molecular vestiges” show that testicular descent was already present in the placental ancestor and was subsequently lost in Afrotheria. Our study highlights the potential of molecular vestiges in resolving contradictory ancestral states of soft-tissue characters.

Morphological Phylogenetics in the Genomic Age

Evolutionary trees underpin virtually all of biology, and the wealth of new genomic data has enabled us to reconstruct them with increasing detail and confidence. While phenotypic (typically morphological) traits are becoming less important in reconstructing evolutionary trees, they still serve vital and unique roles in phylogenetics, even for living taxa for which vast amounts of genetic information are available. Morphology remains a powerful independent source of evidence for testing molecular clades, and - through fossil phenotypes - the primary means for time-scaling phylogenies. Morphological phylogenetics is therefore vital for transforming undated molecular topologies into dated evolutionary trees. However, if morphology is to be employed to its full potential, biologists need to start scrutinising phenotypes in a more objective fashion, models of phenotypic evolution need to be improved, and approaches for analysing phenotypic traits and fossils together with genomic data need to be refined.

Evolution of mammalian diving capacity traced by myoglobin net surface charge

Extended breath-hold endurance enables the exploitation of the aquatic niche by numerous mammalian lineages and is accomplished by elevated body oxygen stores and adaptations that promote their economical use. However, little is known regarding the molecular and evolutionary underpinnings of the high muscle myoglobin concentration phenotype of divers. We used ancestral sequence reconstruction to trace the evolution of this oxygen-storing protein across a 130-species mammalian phylogeny and reveal an adaptive molecular signature of elevated myoglobin net surface charge in diving species that is mechanistically linked with maximal myoglobin concentration. This observation provides insights into the tempo and routes to enhanced dive capacity evolution within the ancestors of each major mammalian aquatic lineage and infers amphibious ancestries of echidnas, moles, hyraxes, and elephants, offering a fresh perspective on the evolution of this iconic respiratory pigment.

Brain volume of the newly-discovered species Rhynchocyon udzungwensis (Mammalia: Afrotheria: Macroscelidea): implications for encephalization in sengis

The Gray-faced Sengi (Rhynchocyon udzungwensis) is a newly-discovered species of sengi (elephant-shrew) and is the largest known extant representative of the order Macroscelidea. The discovery of R. udzungwensis provides an opportunity to investigate the scaling relationship between brain size and body size within Macroscelidea, and to compare this allometry among insectivorous species of Afrotheria and other eutherian insectivores. We performed a spin-echo magnetic resonance imaging (MRI) scan on a preserved adult specimen of R. udzungwensis using a 7-Tesla high-field MR imaging system. The brain was manually segmented and its volume was compiled into a dataset containing previously-published allometric data on 56 other species of insectivore-grade mammals including representatives of Afrotheria, Soricomorpha and Erinaceomorpha. Results of log-linear regression indicate that R. udzungwensis exhibits a brain size that is consistent with the allometric trend described by other members of its order. Inter-specific comparisons indicate that macroscelideans as a group have relatively large brains when compared with similarly-sized terrestrial mammals that also share a similar diet. This high degree of encephalization within sengis remains robust whether sengis are compared with closely-related insectivorous afrotheres, or with more-distantly-related insectivorous laurasiatheres.