Early history of mammals is elucidated with the ENCODE multiple species sequencing data

Understanding the early evolution of placental mammals is one of the most challenging issues in mammalian phylogeny. Here, we addressed this question by using the sequence data of the ENCODE consortium, which include 1% of mammalian genomes in 18 species belonging to all main mammalian lineages. Phylogenetic reconstructions based on an unprecedented amount of coding sequences taken from 218 genes resulted in a highly supported tree placing the root of Placentalia between Afrotheria and Exafroplacentalia (Afrotheria hypothesis). This topology was validated by the phylogenetic analysis of a new class of genomic phylogenetic markers, the conserved noncoding sequences. Applying the tests of alternative topologies on the coding sequence dataset resulted in the rejection of the Atlantogenata hypothesis (Xenarthra grouping with Afrotheria), while this test rejected the second alternative scenario, the Epitheria hypothesis (Xenarthra at the base), when using the noncoding sequence dataset. Thus, the two datasets support the Afrotheria hypothesis; however, none can reject both of the remaining topological alternatives.     

Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting

Extant xenarthrans (armadillos, anteaters and sloths) are among the most derived placental mammals ever evolved. South America was the cradle of their evolutionary history. During the Tertiary, xenarthrans experienced an extraordinary radiation, whereas South America remained isolated from other continents. The 13 living genera are relics of this earlier diversification and represent one of the four major clades of placental mammals. Sequences of the three independent protein-coding nuclear markers alpha2B adrenergic receptor (ADRA2B), breast cancer susceptibility (BRCA1), and von Willebrand Factor (VWF) were determined for 12 of the 13 living xenarthran genera. Comparative evolutionary dynamics of these nuclear exons using a likelihood framework revealed contrasting patterns of molecular evolution. All codon positions of BRCA1 were shown to evolve in a strikingly similar manner, and third codon positions appeared less saturated within placentals than those of ADRA2B and VWF. Maximum likelihood and Bayesian phylogenetic analyses of a 47 placental taxa data set rooted by three marsupial outgroups resolved the phylogeny of Xenarthra with some evidence for two radiation events in armadillos and provided a strongly supported picture of placental interordinal relationships. This topology was fully compatible with recent studies, dividing placentals into the Southern Hemisphere clades Afrotheria and Xenarthra and a monophyletic Northern Hemisphere clade (Boreoeutheria) composed of Laurasiatheria and Euarchontoglires. Partitioned likelihood statistical tests of the position of the root, under different character partition schemes, identified three almost equally likely hypotheses for early placental divergences: a basal Afrotheria, an Afrotheria + Xenarthra clade, or a basal Xenarthra (Epitheria hypothesis). We took advantage of the extensive sampling realized within Xenarthra to assess its impact on the location of the root on the placental tree. By resampling taxa within Xenarthra, the conservative Shimodaira-Hasegawa likelihood-based test of alternative topologies was shown to be sensitive to both character and taxon sampling.     

Molecular delineation of the Y-borne Sry gene in the Formosan pangolin (Manis pentadactyla pentadactyla) and its phylogenetic implications for Pholidota in extant mammals

The systematic status of Pholidota has been a matter of debate, particularly regarding the apparent inconsistency between morphological and molecular studies. The Sry gene, a master regulator of male sex determination in eutherian mammals, has not yet been used for phylogenetic analyses of extant mammals. The objective of the present study was to clone and characterize the complete gene (1300 base pairs; bp) and amino acid sequences (229 residues) of Sry from the Formosan pangolin (Manis pentadactyla pentadactyla), a member of Pholidota. The Sry amino acid identity between pangolin and other reported species ranged from 42.5% (mouse, Mus musculus) to 84.1% (European hare, Lepus europaeus). Sequence conservation was primarily in the high motility group (HMG) box (234 bp), whereas homology outside the HMG box was low. The cloned Sry was mapped to the pangolin Y chromosome by fluorescence in situ hybridization (FISH); this was confirmed to be the first Y-borne molecular marker identified in Pholidota. Based on Bayesian phylogenetic analysis for Sry HMG sequences from 36 representative taxa, including the Formosan pangolin, Pholidota was more closely related to Carnivora than to Xenarthra, consistent with the emerging molecular tree inferred from markers not located on the Y chromosome. In conclusion, this study characterized the gene structure of Sry of the Formosan pangolin and provided insights into the phylogenetic position of Pholidota.     

Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals

Vestigial structures occur at both the anatomical and molecular levels, but studies documenting the co-occurrence of morphological degeneration in the fossil record and molecular decay in the genome are rare. Here, we use morphology, the fossil record, and phylogenetics to predict the occurrence of “molecular fossils” of the enamelin (ENAM) gene in four different orders of placental mammals (Tubulidentata, Pholidota, Cetacea, Xenarthra) with toothless and/or enamelless taxa. Our results support the “molecular fossil” hypothesis and demonstrate the occurrence of frameshift mutations and/or stop codons in all toothless and enamelless taxa. We then use a novel method based on selection intensity estimates for codons (ω) to calculate the timing of iterated enamel loss in the fossil record of aardvarks and pangolins, and further show that the molecular evolutionary history of ENAM predicts the occurrence of enamel in basal representatives of Xenarthra (sloths, anteaters, armadillos) even though frameshift mutations are ubiquitous in ENAM sequences of living xenarthrans. The molecular decay of ENAM parallels the morphological degeneration of enamel in the fossil record of placental mammals and provides manifest evidence for the predictive power of Darwin''s theory.     

Mitogenomic relationships of placental mammals and molecular estimates of their divergences

Molecular analyses of the relationships of placental mammals have shown a progressive congruence between mitogenomic and nuclear phylogenies. Some inconsistencies have nevertheless persisted, notably with respect to basal divergences. The current study has aimed to extend the representation of groups, whose position in the placental tree has been difficult to establish in mitogenomic studies. Both ML (maximum likelihood) and Bayesian analyses identified four basal monophyletic groups, Afroplacentalia (=Afrotheria: Hyracoidea, Proboscidea, Sirenia, Tenrecidea, Tubulidentata, Macroscelidea, Chrysochloridea), Xenarthra, Archontoglires (Primates, Dermoptera, Scandentia, Lagomorpha, Rodentia) and Laurasiaplacentalia (Lipotyphla, Chiroptera, Pholidota, Carnivora, Perissodactyla, Artiodactyla, Cetacea). All analyses joined Archontoglires and Laurasiaplacentalia on a common branch (Boreoplacentalia), but the relationship between Afroplacentalia, Xenarthra and Boreoplacentalia was not conclusively resolved. The phylogenomic hypothesis with a sister group relationship between Notoplacentalia (Afroplacentalia/Xenarthra) and Boreoplacentalia served as the basis for estimating the times of placental divergences using paleontologically well-supported mammalian calibration points. These estimates placed the basal placental divergence between Boreoplacentalia and Notoplacentalia at approximately 102 MYA (million years ago). The current estimates of ordinal placental divergences are congruent with recent estimates based on nuclear data, but inconsistent with paleontological notions that have placed the origin of essentially all placental orders within an interval of 5-10 MY in the early Tertiary. Among less deep divergences the estimates placed the split between Gorilla and Pan/Homo at approximately 11.5 MYA and that between Pan and Homo at approximately 8 MYA. As a consequence of these estimates, which are in accord with recent progress in primate paleontology, the earliest divergences among recent humans become placed approximately 270,000 years ago, i.e. approximately 100,000 years earlier than the traditional age of "Mitochondrial Eve". Comparison between the two new mt genomes of Hylomys suillus (short-tailed gymnure) patently demonstrates the inconsistency that may exist between taxonomic designations and molecular difference, as the distance between these two supposedly conspecific genomes exceeds that of the three elephantid genera Elephas, Mammuthus and Loxodonta. In accordance with the progressive use of the term Placentalia for extant orders and extinct taxa falling within this group we forward new proposals for the names of some superordinal clades of placental mammals.     

The historical biogeography of Mammalia

Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar's endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.     

Lipotyphla limb myology comparison

Fore- and hindlimb muscles were dissected in four species of Lipotyphla: the western European hedgehog Erinaceus europaeus (Erinaceidae, Erinaceinae); the moonrat Echinosorex gymnura (Erinaceidae, Hylomyinae or Galericinae); the tailless tenrec Tenrec ecaudatus (Tenrecidae, Tenrecinae); and the common European white-toothed shrew Crocidura russula (Soricidae, Soricinae). This work completely reviews the limb musculature of these walking mammals. Twelve myological characters were evaluated in order to disclose phylogenetic relationships. The cladogram obtained supported previous ones based on cranial and dental characters. This study shows that myological characters are valuable in phylogenetic analyses.     

Genome Size: A Novel Genomic Signature in Support of Afrotheria

Molecular phylogenetic analyses suggest an emerging phylogeny for the extant Placentalia (eutherian) that radically departs from morphologically based constructions of the past. Placental mammals are partitioned into four supraordinal clades: Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires. Afrotheria form an endemic African clade that includes elephant shrews, golden moles, tenrecs, aardvarks, hyraxes, elephants, dugongs, and manatees. Datamining databases of genome size (GS) shows that till today just one afrotherian GS has been evaluated, that of the aardvark Orycteropus afer. We show that the GSs of six selected representatives across the Afrotheria supraordinal group are among the highest for the extant Placentalia, providing a novel genomic signature of this enigmatic group. The mean GS value of Afrotheria, 5.3 ± 0.7 pg, is the highest reported for the extant Placentalia. This should assist in planning new genome sequencing initiatives. [Reviewing Editor: Dmitri Petrov]     

Spiny Norman in the Garden of Eden? Dispersal and early biogeography of Placentalia

The persistent finding of clades endemic to the southern continents (Afrotheria and Xenarthra) near the base of the placental mammal tree has led molecular phylogeneticists to suggest an origin of Placentalia, the crown group of Eutheria, somewhere in the southern continents. Basal splits within the Placentalia have then been associated with vicariance due to the breakup of Gondwana. Southern-origin scenarios suffer from several problems. First, the place of origin of Placentalia cannot be reconstructed using phylogenetic reasoning without reference to outgroups. When available outgroups are considered, a Laurasian origin is most parsimonious. Second, a model of pure vicariance would require that basal placental splits occurred not with the breakup of Gondwana, but of Pangea in the Late Triassic—Early Jurassic. This event long preceded even the oldest molecular divergence estimates for the Placentalia and was coeval only with the earliest mammals in the fossil record. Third, a problem with the number of dispersal events that would be required emerges under different southern-origin scenarios. In considering the geographic distribution of the major placental clades at their first appearance (mostly Early Cenozoic), it becomes clear that a Laurasian center of origin would require fewer dispersal events. Southern-origin models would require at least twice the number of dispersal events in comparison with a model of Laurasian origins. This number of required dispersal events increases if extinct groups of placental mammals are also considered. Results are similar assuming a morphology-based phylogeny. These facts, along with earlier findings speaking against a major placental radiation deep in the Cretaceous without leaving fossil evidence, suggest an origin of Placentalia somewhere in Laurasia with few supraordinal splits occurring before the last 5–10 million years of the Cretaceous.     

Using Phylogenies to Study Convergence: The Case of the Ant-Eating Mammals

Identifying when homoplasy is due to convergence requires confidencein trees and precise analysis of potentially convergent characters.Some features of mammals that eat mostly ants and termites areused as examples of convergence; the most speciose assemblagesof these mammals are in the orders Xenarthra and Pholidota.My studies on cranial muscles in xenarthrans and pholidotansaim to 1) precisely describe the anatomy in ant-eating and non-ant-eatinglineages, 2) assess variation among ant-eating lineages, and3) compare the most derived conditions (in xenarthran anteatersand pholidotan pangolins). These data clarify the nature ofmorphological adaptation in ant-eating mammals, and when combinedwith accumulating phylogenetic studies, allow us to distinguishfeatures that have evolved convergently from those that arevariable but not correlated with diet. Interpreting the extremesimilarity in anteaters and pangolins remains problematic dueto lingering disagreement among phylogenetic hypotheses. Prevailingopinion favors interpretation of these similarities as convergent.     

A new phylogenetic marker,apolipoprotein B,provides compelling evidence for eutherian relationships

Higher-level relationships within, and the root of Placentalia, remain contentious issues. Resolution of the placental tree is important to the choice of mammalian genome projects and model organisms, as well as for understanding the biogeography of the eutherian radiation. We present phylogenetic analyses of 63 species representing all extant eutherian mammal orders for a new molecular phylogenetic marker, a 1.3kb portion of exon 26 of the apolipoprotein B (APOB) gene. In addition, we analyzed a multigene concatenation that included APOB sequences and a previously published data set (Murphy et al., 2001b) of three mitochondrial and 19 nuclear genes, resulting in an alignment of over 17kb for 42 placentals and two marsupials. Due to computational difficulties, previous maximum likelihood analyses of large, multigene concatenations for placental mammals have used quartet puzzling, less complex models of sequence evolution, or phylogenetic constraints to approximate a full maximum likelihood bootstrap. Here, we utilize a Unix load sharing facility to perform maximum likelihood bootstrap analyses for both the APOB and concatenated data sets with a GTR+Gamma+I model of sequence evolution, tree-bisection and reconnection branch-swapping, and no phylogenetic constraints. Maximum likelihood and Bayesian analyses of both data sets provide support for the superordinal clades Boreoeutheria, Euarchontoglires, Laurasiatheria, Xenarthra, Afrotheria, and Ostentoria (pangolins+carnivores), as well as for the monophyly of the orders Eulipotyphla, Primates, and Rodentia, all of which have recently been questioned. Both data sets recovered an association of Hippopotamidae and Cetacea within Cetartiodactyla, as well as hedgehog and shrew within Eulipotyphla. APOB showed strong support for an association of tarsier and Anthropoidea within Primates. Parsimony, maximum likelihood and Bayesian analyses with both data sets placed Afrotheria at the base of the placental radiation. Statistical tests that employed APOB to examine a priori hypotheses for the root of the placental tree rejected rooting on myomorphs and hedgehog, but did not discriminate between rooting at the base of Afrotheria, at the base of Xenarthra, or between Atlantogenata (Xenarthra+Afrotheria) and Boreoeutheria. An orthologous deletion of 363bp in the aligned APOB sequences proved phylogenetically informative for the grouping of the order Carnivora with the order Pholidota into the superordinal clade Ostentoria. A smaller deletion of 237-246bp was diagnostic of the superordinal clade Afrotheria.     

Mammalian superorders

The superordinal level can be used to great advantage in the taxonomy of mammals and other groups. Of the two cohorts of placental mammals, the Unguiculata is divided into six superorders: Archonta (Gregory's Archonta plus Lipotyphla), Glires, Ferae (including Delta-theridia and Carnivora), Paratheria (Edentata and Pholidota), Ganodonta, and an unnamed group for the Lagomorpha plus Anagalida. The cohort Ungulata is divided much as in Simpson (1945), with an additional superorder (Mutica) for the whales and with a superorder Amblypoda, separate from the Paenungulata, and corresponding to Romer's (1966) order of that name.     

Early Tertiary mammals from North Africa reinforce the molecular Afrotheria clade

The phylogenetic pattern and timing of the radiation of mammals, especially the geographical origins of major crown clades, are areas of controversy among molecular biologists, morphologists and palaeontologists. Molecular phylogeneticists have identified an Afrotheria clade, which includes several taxa as different as tenrecs (Tenrecidae), golden moles (Chrysochloridae), elephant-shrews (Macroscelididae), aardvarks (Tubulidentata) and paenungulates (elephants, sea cows and hyracoids). Molecular data also suggest a Cretaceous African origin for Afrotheria within Placentalia followed by a long period of endemic evolution on the Afro-Arabian continent after the mid-Cretaceous Gondwanan breakup (approx. 105-25 Myr ago). However, there was no morphological support for such a natural grouping so far. Here, we report new dental and postcranial evidence of Eocene stem hyrax and macroscelidid from North Africa that, for the first time, provides a congruent phylogenetic view with the molecular Afrotheria clade. These new fossils imply, however, substantial changes regarding the historical biogeography of afrotheres. Their long period of isolation in Africa, as assumed by molecular inferences, is now to be reconsidered inasmuch as Eocene paenungulates and elephant-shrews are here found to be related to some Early Tertiary Euramerican 'hyopsodontid condylarths' (archaic hoofed mammals). As a result, stem members of afrotherian clades are not strictly African but also include some Early Paleogene Holarctic mammals.     

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.     

Molecular Evidence for the Major Clades of Placental Mammals

Higher-level relationships among placental mammals, as well as the historical biogeography of this group against the backdrop of continental fragmentation and reassembly, remain poorly understood. Here, we analyze two independent molecular data sets that represent all placental orders. The first data set includes six genes (A2AB, IRBP, vWF, 12S rRNA, tRNA valine, 16S rRNA; total = 5.71 kb) for 26 placental taxa and two marsupials; the second data set includes 2.95 kb of exon 11 of the BRCA1 gene for 51 placental taxa and four marsupials. We also analyzed a concatenation of these data sets (8.66 kb) for 26 placentals and one marsupial. Unrooted and rooted analyses were performed with parsimony, distance methods, maximum likelihood, and a Bayesian approach. Unrooted analyses provide convincing support for a fundamental separation of placental orders into groups with southern and northern hemispheric origins according to the current fossil record. On rooted trees, one or both of these groups are monophyletic depending on the position of the root. Maximum likelihood and Bayesian analyses with the BRCA1 and combined 8.66 kb data sets provide strong support for the monophyly of the northern hemisphere group (Boreoeutheria). Boreoeutheria is divided into Laurasiatheria (Carnivora + Cetartiodactyla + Chiroptera + Eulipotyphla + Perissodactyla + Pholidota) and Euarchonta (Dermoptera + Primates + Scandentia) + Glires (Lagomorpha + Rodentia). The southern hemisphere group is either monophyletic or paraphyletic, depending on the method of analysis used. Within this group, Afrotheria (Proboscidea + Sirenia + Hyracoidea + Tubulidentata + Macroscelidea + Afrosoricida) is monophyletic. A unique nine base-pair deletion in exon 11 of the BRCA1 gene also supports Afrotheria monophyly. Given molecular dates that suggest that the southern hemisphere group and Boreoeutheria diverged in the Early Cretaceous, a single trans-hemispheric dispersal event may have been of fundamental importance in the early history of crown-group Eutheria. Parallel adaptive radiations have subsequently occurred in the four major groups: Laurasiatheria, Euarchonta + Glires, Afrotheria, and Xenarthra.     

Tarsals of the extinct insectivoran family Nyctitheriidae (Mammalia): evidence for archontan relationships

Astragali and calcanea from the English late Eocene, attributed to the extinct 'insectivoran' family Nyctitheriidae, are described for the first time. They contrast with those of the strict sense insectivorans, the Lipotyphla, in which order nyctitheres have usually been placed, and compare more closely with those of Scandentia (tree shrews) and the extinct Plesiadapiformes. Functional analysis demonstrates that inversion of the foot was possible between the astragalus and calcaneum of nyctitheres, allowing them to be interpreted as having had a tree-dwelling, probably scansorial, mode of life. These tarsal bones are compared with those of other placental mammals. Cladistic analysis of tarsal characters places nyctitheres as sister group to the Plesiadapiformes within the superorder Archonta, excluding Chiroptera (bats). An independent analysis of dental characters places them as sister group to the rest of the Archonta, but still excluding bats. Combining the dental and tarsal characters places nyctitheres as sister group to Plesiadapiformes and all modern groups of archontans except bats. A new osteological synapomorphy is proposed for the Archonta, which is thus considered to comprise Chiroptera, Deccanolestes , Nyctitheriidae, Plesiadapiformes, Dermoptera (including Mixodectidae), Scandentia and Primates. Insectivorans s.l . have long been at the centre of arguments on placental origins, although lipotyphlans are usually regarded as a monophyletic group, rather than paraphyletic stem placentals. Reidentification of an extinct lipotyphlan family as having archontan relationships raises the possibility of advances in other areas of insectivoran phylogeny when more postcranial elements become known. The early Oligocene extinction of nyctitheres may be causally related to the rise of insectivorous microchiropteran bats, which, because of their flying ability, would have been able to forage more widely.     

Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups

The phylogenetic positions of the 4 clades, Euarchontoglires, Laurasiatheria, Afrotheria, and Xenarthra, have been major issues in the recent discussion of basal relationships among placental mammals. However, despite considerable efforts these relationships, crucial to the understanding of eutherian evolution and biogeography, have remained essentially unresolved. Euarchontoglires and Laurasiatheria are generally joined into a common clade (Boreoeutheria), whereas the position of Afrotheria and Xenarthra relative to Boreoeutheria has been equivocal in spite of the use of comprehensive amounts of nuclear encoded sequences or the application of genome-level characters such as retroposons. The probable reason for this uncertainty is that the divergences took place long time ago and within a narrow temporal window, leaving only short common branches. With the aim of further examining basal eutherian relationships, we have collected conserved protein-coding sequences from 11 placental mammals, a marsupial and a bird, whose nuclear genomes have been largely sequenced. The length of the alignment of homologous sequences representing each individual species is 2,168,859 nt. This number of sites, representing 2840 protein-coding genes, exceeds by a considerable margin that of any previous study. The phylogenetic analysis joined Xenarthra and Afrotheria on a common branch, Atlantogenata. This topology was found to fit the data significantly better than the alternative trees.     

Extrinsic Snout Musculature in Afrotheria and Lipotyphla

As currently recognized, the mammalian order Lipotyphla contains six extant families: Chrysochloridae, Erinaceidae, Solenodontidae, Soricidae, Talpidae, and Tenrecidae. Although most mammalogists have accepted this taxon, the morphological support for Lipotyphla is relatively weak, and recent phylogenetic studies using molecular data have concluded that it is not monophyletic. Instead, these molecular studies place chrysochlorids and tenrecids in the proposed clade Afrotheria, together with aardvarks, elephants, elephant shrews, hyraxes, and sirenians. Despite strong molecular support, Afrotheria has received little or no morphological support. It was recently suggested that a mobile snout might be a morphological feature uniting afrotherians. To test this proposal, I dissected the extrinsic snout musculature in an assortment of lipotyphlan and afrotherian mammals. These muscles provide support for Lipotyphla but not for Afrotheria. The snout is moved by different muscles in different afrotherian taxa, suggesting that the mobile snout is not homologous across different afrotherian lineages. In contrast, lipotyphlans have a distinctive set of five snout muscles moving the snout tip that appears to be unique to these six families. In addition, in soricids and talpids, four of the five snout muscles originate posterior to the zygomatic arch, supporting sister-taxon status for these two lineages. Although the extrinsic snout musculature does not support Afrotheria as presently proposed, it is consistent with an Afrotheria that does not include chrysochlorids and tenrecids.     

Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews

For more than a century, living insectivore-like mammals have been viewed as little removed from the ancestral mammalian stock based on their retention of numerous primitive characteristics. This circumstance has made "insectivores" a group of special interest in the study of mammalian evolution. included hedgehogs, moles, shrews, solenodons, golden moles, tenrecs, flying lemurs, tree shrews, and elephant shrews in Insectivora. Subsequently, morphologists excluded flying lemurs, tree shrews, and elephant shrews from Insectivora and placed these taxa in the orders Dermoptera, Scandentia, and Macroscelidea, respectively. The remaining insectivores constitute Lipotyphla, which is monophyletic based on morphology. In contrast, molecular data suggest that lipotyphlans are polyphyletic, with golden moles and tenrecs placed in their own order (Afrosoricida) in the superordinal group Afrotheria. Studies based on nuclear genes support the monophyly of the remaining lipotyphlans (=Eulipotyphla) whereas mitochondrial genome studies dissociate hedgehogs from moles and place the former as the first offshoot on the placental tree. One shortcoming of previous molecular studies investigating lipotyphlan relationships is limited taxonomic sampling. Here, we evaluate lipotyphlan relationships using the largest and taxonomically most diverse data set yet assembled for Lipotyphla. Our results provide convincing support for both lipotyphlan diphyly and the monophyly of Eulipotyphla. More surprisingly, we find strong evidence for a sister-group relationship between shrews and hedgehogs to the exclusion of moles.     

A composite species-level phylogeny of the 'Insectivora' (Mammalia: Order Lipotyphla Haeckel, 1866)

The first MRP (matrix representation with parsimony) supertree phylogeny of the Lipotyphla is presented, covering all the families that were considered to make up the traditional mammalian order Insectivora. The phylogeny does not examine relationships within the shrew subfamily Crocidurinae, but all other taxa are considered at the species level, drawing upon 41 years of systematic literature and combining information from 47 published sources. The MRP technique is also critically discussed. This study will be of use to comparative biology studies of the Lipotyphla (or of mammals as a whole) and is a rigorous review of past systematic work, as well as clearly demonstrating our current level of knowledge. The supertree clearly details a strong imbalance in phylogenetic understanding across the taxon: a great deal is known about the hedgehogs and gymnures (Erinaceidae), the New World moles (Talpidae), Palaearctic species of Sorex (subgenus Sorex ) and the relationships between genera of red-toothed shrews (Soricinae). The supertree, however, clearly shows areas where our knowledge is conflicting or non-existent, and these gaps do not always correspond to obscure species: nothing is known about the systematics of Old World mole genera. Also very little is known about golden moles (Chrysochloridae) and the shrew-tenrec genus Microgale , some of the most threatened mammals on Earth.