No Evidence for a Second Evolutionary Stratum during the Early Evolution of Mammalian Sex Chromosomes

Mammalian sex chromosomes originated from a pair of autosomes, and homologous genes on the sex chromosomes (gametologs) differentiated through recombination arrest between the chromosomes. It was hypothesized that this differentiation in eutherians took place in a stepwise fashion and left a footprint on the X chromosome termed “evolutionary strata.” The evolutionary stratum hypothesis claims that strata 1 and 2 (which correspond to the first two steps of chromosomal differentiation) were generated in the stem lineage of Theria or before the divergence between eutherians and marsupials. However, this prediction relied solely on the molecular clock hypothesis between pairs of human gametologs, and molecular evolution of marsupial sex chromosomal genes has not yet been investigated. In this study, we analyzed the following 7 pairs of marsupial gametologs, together with their eutherian orthologs that reside in stratum 1 or 2: SOX3/SRY, RBMX/Y, RPS4X/Y, HSFX/Y, XKRX/Y, SMCX/Y (KDM5C/D, JARID1C/D), and UBE1X/Y (UBA1/UBA1Y). Phylogenetic analyses and estimated divergence time of these gametologs reveal that they all differentiated at the same time in the therian ancestor. We have also provided strong evidence for gene conversion that occurred in the 3′ region of the eutherian stratum 2 genes (SMCX/Y and UBE1X/Y). The results of the present study show that (1) there is no compelling evidence for the second stratum in the stem lineage of Theria; (2) gene conversion, which may have occurred between SMCX/Y and UBE1X/Y in the eutherian lineage, potentially accounts for their apparently lower degree of overall divergence.     

Resolving the relationships of Paleocene placental mammals

The ‘Age of Mammals’ began in the Paleocene epoch, the 10 million year interval immediately following the Cretaceous–Palaeogene mass extinction. The apparently rapid shift in mammalian ecomorphs from small, largely insectivorous forms to many small‐to‐large‐bodied, diverse taxa has driven a hypothesis that the end‐Cretaceous heralded an adaptive radiation in placental mammal evolution. However, the affinities of most Paleocene mammals have remained unresolved, despite significant advances in understanding the relationships of the extant orders, hindering efforts to reconstruct robustly the origin and early evolution of placental mammals. Here we present the largest cladistic analysis of Paleocene placentals to date, from a data matrix including 177 taxa (130 of which are Palaeogene) and 680 morphological characters. We improve the resolution of the relationships of several enigmatic Paleocene clades, including families of ‘condylarths’. Protungulatum is resolved as a stem eutherian, meaning that no crown‐placental mammal unambiguously pre‐dates the Cretaceous–Palaeogene boundary. Our results support an Atlantogenata–Boreoeutheria split at the root of crown Placentalia, the presence of phenacodontids as closest relatives of Perissodactyla, the validity of Euungulata, and the placement of Arctocyonidae close to Carnivora. Periptychidae and Pantodonta are resolved as sister taxa, Leptictida and Cimolestidae are found to be stem eutherians, and Hyopsodontidae is highly polyphyletic. The inclusion of Paleocene taxa in a placental phylogeny alters interpretations of relationships and key events in mammalian evolutionary history. Paleocene mammals are an essential source of data for understanding fully the biotic dynamics associated with the end‐Cretaceous mass extinction. The relationships presented here mark a critical first step towards accurate reconstruction of this important interval in the evolution of the modern fauna.     

New basal eutherian mammal from the Early Cretaceous Jehol biota,Liaoning, China

A new genus and species of eutherian mammal, Acristatherium yanensis gen. et sp. nov., is described from the Early Cretaceous Jehol biota, China. The new taxon is based on a partial skull that is preserved in three dimensions from the Lujiatun bed of the Yixian Formation and dated 123.2±1.0 Ma. Its right upper and lower dentitions are nearly complete and it has a dental formula 4.1.5.3/3.1.5.3. The new mammal reveals several craniodental characteristics of Early Cretaceous eutherians previously unknown in fossil records of therians, such as a possible vestige of the septomaxilla. The craniodental features of the new taxon are compared with those of relevant Early Cretaceous eutherians and therians. Phylogenetic analyses based on a data matrix containing 70 taxa and 408 characters place A. yanensis as the most basal eutherian in the selected group. The morphological differences between Acristatherium and Eomaia indicate that eutherians already had a significant degree of generic diversification ca 125 Ma.     

Monophyly or polyphyly of the order Rodentia: Possible conflict between morphological and molecular interpretations

Recent analyses of amino acid sequence data from selected proteins inCavia, Rattus, Homo, Bos, Sus, and a few additional rodents and other eutherians suggested that Rodentia is not a monophyletic taxon and thatCavia and other hystricognaths may have branched off earlier than the separation between Muroidea and Primates during mammalian evolution. Because this hypothesis of polyphyly is contrary to the otherwise unanimous recognition of rodent monophyly, we have reevaluated the morphological and developmental evidence from the cranium, dentition, postcranial skeleton, and fetal membranes for the taxa Hystricognathi, Muroidea, other Rodentia, Primates, Artiodactyla, and Lagomorpha, as well as for the eutherian morphotype. Our character analyses provide strong corroboration for the traditional hypothesis of rodent monophyly and lend additional support to the suggestion that Lagomorpha is the sister taxon of Rodentia. Our survey of published molecular data furnishes little or no support for the proposed hypothesis of rodent polyphyly. We conclude that this hypothesis is the result of poor sampling of sequence data from rodents and other eutherians, rather than any inherent difficulties in the use of molecular evidence for the assessment of mammalian evolution. The available molecular data suggest thatCavia differs considerably from other hystricognaths in many proteins, but the reasons for this remain to be investigated.     

The nocturnal bottleneck and the evolution of activity patterns in mammals

In 1942, Walls described the concept of a ‘nocturnal bottleneck’ in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail.     

In silico identification of opossum cytokine genes suggests the complexity of the marsupial immune system rivals that of eutherian mammals

Background

Cytokines are small proteins that regulate immunity in vertebrate species. Marsupial and eutherian mammals last shared a common ancestor more than 180 million years ago, so it is not surprising that attempts to isolate many key marsupial cytokines using traditional laboratory techniques have been unsuccessful. This paucity of molecular data has led some authors to suggest that the marsupial immune system is 'primitive' and not on par with the sophisticated immune system of eutherian (placental) mammals.

Results

The sequencing of the first marsupial genome has allowed us to identify highly divergent immune genes. We used gene prediction methods that incorporate the identification of gene location using BLAST, SYNTENY + BLAST and HMMER to identify 23 key marsupial immune genes, including IFN-γ, IL-2, IL-4, IL-6, IL-12 and IL-13, in the genome of the grey short-tailed opossum (Monodelphis domestica). Many of these genes were not predicted in the publicly available automated annotations.

Conclusion

The power of this approach was demonstrated by the identification of orthologous cytokines between marsupials and eutherians that share only 30% identity at the amino acid level. Furthermore, the presence of key immunological genes suggests that marsupials do indeed possess a sophisticated immune system, whose function may parallel that of eutherian mammals.     

Cretaceous Therian Tarsals and the Metatherian-Eutherian Dichotomy

Diverse metatherian and eutherian tarsal remains from the Late Cretaceous (middle-late Turonian) Bissekty Formation, Kyzylkum Desert, Uzbekistan (ca 90 MYA) are described. Their functional and taxonomic properties, along with those of other tarsal evidence, led to a reassessment of polarity hypotheses of therian, metatherian, and eutherian cruropedal attributes, and the consequences of this for phylogeny of taxa. There are calcaneal remains of several types of marsupials, and a single astragalus that probably belongs to one of these. This represents greater taxonomic diversity than the dental record suggests. Exceptionally large and distally extending peroneal processes, and small and steeply angled calcaneocuboid articulations facing mediodistally, as seen in the Early Cretaceous Sinodelphys and other Cretaceous and Paleogene taxa, attest not only to the metatherian status of these specimens, but also to the retention of many ancestral therian features, even more so than in both the Tiupampa and Itaboraí marsupials of the South American Paleocene (both the calcanea and the astragalus suggest therian traits that are decidedly unlike those of symmetrodonts). Calcanea allocated to the deltatherioid species at Bissekty testify unequivocally to their metatherian affinity. The morphology of the best represented sample of eutherian calcanea from Bissekty, presumably of a number of zhelestid species, appears to be more derived than that of the Late Cretaceous/Paleocene Protungulatum in having a much more reduced peroneal process and a calcaneocuboid articulation that faces distally, oriented nearly at a 90° angle to the long axis of the calcaneus. In fact, this distally facing facet, common in later eutherians (except for lineages in the Paleogene record, and various Carnivora), may not be diagnostic of either the protoeutherian, or even of the protoplacentalian, in spite of its presence in Eomaia. Many putatively “basal” lineages have derived characters, hence such outgroups should not be considered the unequivocal repositories of only ancestral character states.     

A new Early Cretaceous eutherian mammal from the Sasayama Group,Hyogo, Japan

We here describe a new Early Cretaceous (early Albian) eutherian mammal, Sasayamamylos kawaii gen. et sp. nov., from the ‘Lower Formation’ of the Sasayama Group, Hyogo Prefecture, Japan. Sasayamamylos kawaii is characterized by a robust dentary, a distinct angle on the ventral margin of the dentary at the posterior end of the mandibular symphysis, a lower dental formula of 3–4 : 1 : 4 : 3, a robust lower canine, a non-molariform lower ultimate premolar, and a secondarily reduced entoconid on the molars. To date, S. kawaii is the earliest known eutherian mammal possessing only four premolars, which demonstrates that the reduction in the premolar count in eutherians started in the late Early Cretaceous. The occurrence of S. kawaii implies that the relatively rapid diversification of eutherians in the mid-Cretaceous had already started by the early Albian.     

Identification of tammar wallaby SIRH12, derived from a marsupial-specific retrotransposition event

In humans and mice, there are 11 genes derived from sushi-ichi related retrotransposons, some of which are known to play essential roles in placental development. Interestingly, this family of retrotransposons was thought to exist only in eutherian mammals, indicating their significant contributions to the eutherian evolution, but at least one, PEG10, is conserved between marsupials and eutherians. Here we report a novel sushi-ichi retrotransposon-derived gene, SIRH12, in the tammar wallaby, an Australian marsupial species of the kangaroo family. SIRH12 encodes a protein highly homologous to the sushi-ichi retrotransposon Gag protein in the tammar wallaby, while SIRH12 in the South American short-tailed grey opossum is a pseudogene degenerated by accumulation of multiple nonsense mutations. This suggests that SIRH12 retrotransposition occurred only in the marsupial lineage but acquired and retained some as yet unidentified novel function, at least in the lineage of the tammar wallaby.     

Identification of a Novel PNMA-MS1 Gene in Marsupials Suggests the LTR Retrotransposon-Derived PNMA Genes Evolved Differently in Marsupials and Eutherians

Two major gene families derived from Ty3/Gypsy long terminal repeat (LTR) retrotransposons were recently identified in mammals. The sushi-ichi retrotransposon homologue (SIRH) family comprises 12 genes: 11 in eutherians including Peg10 and Peg11/Rtl1 that have essential roles in the eutherian placenta and 1 that is marsupial specific. Fifteen and 12 genes were reported in the second gene family, para-neoplastic antigen MA (PNMA), in humans and mice, respectively, although their biological functions and evolutionary history remain largely unknown. Here, we identified two novel candidate PNMA genes, PNMA-MS1 and -MS2 in marsupials. Like all eutherian-specific PNMA genes, they exhibit the highest homology to a Gypsy12_DR (DR, Danio rerio) Gag protein. PNMA-MS1 is conserved in both Australian and South American marsupial species, the tammar wallaby and grey short-tailed opossum. However, no PNMA-MS1 orthologue was found in eutherians, monotremes or non-mammalian vertebrates. PNMA-MS1 was expressed in the ovary, mammary gland and brain during development and growth in the tammar, suggesting that PNMA-MS1 may have acquired a marsupial-specific function. However, PNMA-MS2 seems to be a pseudogene. The absence of marsupial orthologues of eutherian PNMA genes suggests that the retrotransposition events of the Gypsy12_DR-related retrotransposons that gave rise to the PNMA family occurred after the divergence of marsupials and eutherians.     

Exploring the impact of fossil constraints on the divergence time estimates of derived liverworts

In this study, we evaluate the impact of fossil assignments and different models of calibration on divergence time estimates carried out as Bayesian analyses. Estimated ages from preceding studies and liverwort inclusions from Baltic amber are used as constraints on a molecular phylogeny of Cephaloziineae (Jungermanniopsida) obtained from sequences of two chloroplast coding regions: rbcL and psbA. In total, the comparison of 12 different analyses demonstrates that an increased reliability of the chronograms is linked to the number of fossils assigned and to the accuracy of their assignments. Inclusion of fossil constraints leads to older ages of most crown groups, but has no influence on lineage through time plots suggesting a nearly constant accumulation of diversity since the origin of Cephaloziineae in the early to Middle Jurassic. Our results provide a note of caution regarding the interpretation of chronograms derived from DNA sequence variation of extant species based on a single calibration point and/or low accuracy of the assignment of fossils to nodes in the phylogeny.     

Multigene Molecular Phylogeny and Biogeographic Diversification of the Earth Tongue Fungi in the Genera Cudonia and Spathularia (Rhytismatales,Ascomycota)

The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the “earth tongue fungi” in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America.     

Mammalian Faunal Succession in the Cretaceous of the Kyzylkum Desert

Both metatherians and eutherians are known from the Early Cretaceous (Barremian, 125 mya; million years ago) of China, while eutherian-dominated mammalian faunas appeared in Asia at least by the earliest Late Cretaceous (Cenomanian, 95 mya). The approximately 99–93 my old (Cenomanian) Sheikhdzheili l.f. from western Uzbekistan is a small sample of only eutherians, including three zhelestids and a possible zalambdalestoid. The much better-known 90 my old (Turonian) Bissekty l.f. at Dzharakuduk in the central Uzbekistan includes 15 named and unnamed species, based on ongoing analyses. Of these, 12 are eutherians represented by at least the three groups—asioryctitheres, zalambdalestids, and zhelestids—plus an eutherian of uncertain position—Paranyctoides. Zalambdalestids and zhelestids have been argued to be related to the origin of the placental gliriforms (Euarchontoglires) and ferungulates (Laurasiatheria), respectively. Although there are four previously recognized metatherians, we believe three are referable to the deltatheroid Sulestes karakshi and the fourth, Sailestes quadrans, may belong to Paranyctoides. There is one multituberculate and one symmetrodont in the Bissekty l.f. While comparably aged (Turonian) localities in North America have somewhat similar non-therians, they have more metatherians and no eutherians. The next younger localities (early Campanian, ∼80 mya) in North America have both a zhelestid and Paranyctoides, suggesting dispersal of eutherians from Asia. At Dzharakuduk, the approximately 85 my old (late Turonian/Coniacian) Aitym l.f. is much less well known than the Bissekty l.f., but yields nearly identical taxa, with two non-therians, one metatherian, and six eutherians.     

Megalictis,the Bone-Crushing Giant Mustelid (Carnivora,Mustelidae, Oligobuninae) from the Early Miocene of North America

We describe cranial and mandibular remains of three undescribed individuals of the giant mustelid Megalictis ferox Matthew, 1907 from the latest Arikareean (Ar4), Early Miocene mammal fauna of Nebraska, and Wyoming (USA) housed at the American Museum of Natural History (New York, USA). Our phylogenetic hypothesis indicates that Ar4 specimens assigned to M. ferox constitute a monophyletic group. We assign three additional species previously referred to Paroligobunis to Megalictis: M. simplicidens, M. frazieri, and “M.” petersoni. The node containing these four species of Megalictis and Oligobunis forms the Oligobuninae. We test the hypothesis that Oligobuninae (Megalictis and Oligobunis) is a stem mustelid taxon. Our results indicate that the Oligobuninae form the sister clade to the crown extant mustelids. Based on the cranium, M. ferox is a jaguar-size mustelid and the largest terrestrial mustelid known to have existed. This new material also sheds light on a new ecomorphological interpretation of M. ferox as a bone-crushing durophage (similar to hyenas), rather than a cat-like hypercarnivore, as had been previously described. The relative large size of M. ferox, together with a stout rostrum and mandible made it one of the more powerful predators of the Early Miocene of the Great Plains of North America.     

Forelimb Kinematics of Rats Using XROMM,with Implications for Small Eutherians and Their Fossil Relatives

The earliest eutherian mammals were small-bodied locomotor generalists with a forelimb morphology that strongly resembles that of extant rats. Understanding the kinematics of the humerus, radius, and ulna of extant rats can inform and constrain hypotheses concerning typical posture and mobility in early eutherian forelimbs. The locomotion of Rattus norvegicus has been extensively studied, but the three-dimensional kinematics of the bones themselves remains under-explored. Here, for the first time, we use markerless XROMM (Scientific Rotoscoping) to explore the three-dimensional long bone movements in Rattus norvegicus during a normal, symmetrical gait (walking). Our data show a basic kinematic profile that agrees with previous studies on rats and other small therians: rats maintain a crouched forelimb posture throughout the step cycle, and the ulna is confined to flexion/extension in a parasagittal plane. However, our three-dimensional data illuminate long-axis rotation (LAR) movements for both the humerus and the radius for the first time. Medial LAR of the humerus throughout stance maintains an adducted elbow with a caudally-facing olecranon process, which in turn maintains a cranially-directed manus orientation (pronation). The radius also shows significant LAR correlated with manus pronation and supination. Moreover, we report that elbow flexion and manus orientation are correlated in R. norvegicus: as the elbow angle becomes more acute, manus supination increases. Our data also suggest that manus pronation and orientation in R. norvegicus rely on a divided system of labor between the ulna and radius. Given that the radius follows the flexion and extension trajectory of the ulna, it must rotate at the elbow (on the capitulum) so that during the stance phase its distal end lies medial to ulna, ensuring that the manus remains pronated while the forelimb is supporting the body. We suggest that forelimb posture and kinematics in Juramaia, Eomaia, and other basal eutherians were grossly similar to those of rats, and that humerus and radius LAR may have always played a significant role in forelimb and manus posture in small eutherian mammals.     

A Molecular Phylogeny of Plesiorycteropus Reassigns the Extinct Mammalian Order ‘Bibymalagasia’

Madagascar is well known for its diverse fauna and flora, being home to many species not found anywhere else in the world. However, its biodiversity in the recent past included a range of extinct enigmatic fauna, such as elephant birds, giant lemurs and dwarfed hippopotami. The ‘Malagasy aardvark’ (Plesiorycteropus) has remained one of Madagascar’s least well-understood extinct species since its discovery in the 19^th century. Initially considered a close relative of the aardvark (Orycteropus) within the order Tubulidentata, more recent morphological analyses challenged this placement on the grounds that the identifiably derived traits supporting this allocation were adaptations to digging rather than shared ancestry. Because the skeletal evidence showed many morphological traits diagnostic of different eutherian mammal orders, they could not be used to resolve its closest relatives. As a result, the genus was tentatively assigned its own taxonomic order ‘Bibymalagasia’, yet how this order relates to other eutherian mammal orders remains unclear despite numerous morphological investigations. This research presents the first known molecular sequence data for Plesiorycteropus, obtained from the bone protein collagen (I), which places the ‘Malagasy aardvark’ as more closely related to tenrecs than aardvarks. More specifically, Plesiorycteropus was recovered within the order Tenrecoidea (golden moles and tenrecs) within Afrotheria, suggesting that the taxonomic order ‘Bibymalagasia’ is obsolete. This research highlights the potential for collagen sequencing in investigating the phylogeny of extinct species as a viable alternative to ancient DNA (aDNA) sequencing, particularly in cases where aDNA cannot be recovered.     

Increasing the data size to accurately reconstruct the phylogenetic relationships between nine subgroups of the Drosophila melanogaster species group (Drosophilidae, Diptera)

Previous phylogenetic analyses of the melanogaster species group have led to conflicting hypotheses concerning their relationship; therefore the addition of new sequence data is necessary to discover the phylogeny of this species group. Here we present new data derived from 17 genes and representing 48 species to reconstruct the phylogeny of the melanogaster group. A variety of statistical tests, as well as maximum likelihood mapping analysis, were performed to estimate data quality, suggesting that all genes had a high degree of contribution to resolve the phylogeny.Individual locus was analyzed using maximum likelihood (ML), and the concatenated dataset (12,988 bp) were analyzed using partitioned maximum likelihood (ML) and Bayesian analyses. Separated analysis produced various phylogenetic relationships, however, phylogenetic topologies from ML and Bayesian analysis based on concatenated dataset, at the subgroup level, were completely identical to each other with high levels of support. Our results recovered three major clades: the ananassae subgroup, followed by the montium subgroup, the melanogaster subgroup and the oriental subgroups form the third monophyletic clade, in which melanogaster (takahashii, suzukii) forms one subclade and ficusphila [eugracilis (elegans, rhopaloa)] forms another. However, more data are necessary to determine the phylogenetic position of Drosophila lucipennis which proved difficult to place.