Evolution of metatherian and eutherian (mammalian) characters: a review based on cladistic methodology

Cladistic methodology is used to test the hypothesis that three major monophyletic groups exist among living mammals–the oviparous monotremes (Prototheria), and the viviparous marsupials (Metatheria) and placentals (Eutheria). Evaluation is made of the polarity (i.e. the direction of change in a primitive-to-derived sequence) of numerous characters which distinguish some or all of these groups, and of the usefulness of these characters in phylogenetic inference. An attempt is made to establish the state of these characters in the common Late Jurassic-Early Cretaceous therian ancestor of marsupials and placentals.
It is concluded that the most basic division of the Mammalia is the dichotomy into the subclasses Prototheria (including Monotremata, Multituberculata, Triconodonta, Docodonta) and Theria (including Metatheria, Eutheria, Pantotheria and Symmetrodonta). Two major groups exist among living viviparous mammals, the Metatheria and Eutheria; in a cladistic framework these are sister-groups. It is demonstrated that there is no special (sister-group) relationship between monotremes and marsupials, and there is no justification for placing them in a group Marsupionta.     

The allometry of avian basal metabolic rate: good predictions need good data

Basal metabolic rate (BMR) is often predicted by allometric interpolation, but such predictions are critically dependent on the quality of the data used to derive allometric equations relating BMR to body mass (Mb). An examination of the metabolic rates used to produce conventional and phylogenetically independent allometries for avian BMR in a recent analysis revealed that only 67 of 248 data unambiguously met the criteria for BMR and had sample sizes with n>/=3. The metabolic rates that represented BMR were significantly lower than those that did not meet the criteria for BMR or were measured under unspecified conditions. Moreover, our conventional allometric estimates of BMR (W; logBMR=-1.461+0.669logMb) using a more constrained data set that met the conditions that define BMR and had n>/=3 were 10%-12% lower than those obtained in the earlier analysis. The inclusion of data that do not represent BMR results in the overestimation of predicted BMR and can potentially lead to incorrect conclusions concerning metabolic adaptation. Our analyses using a data set that included only BMR with n>/=3 were consistent with the conclusion that BMR does not differ between passerine and nonpasserine birds after taking phylogeny into account. With an increased focus on data mining and synthetic analyses, our study suggests that a thorough knowledge of how data sets are generated and the underlying constraints on their interpretation is a necessary prerequisite for such exercises.     

Inference of higher-order relationships in the cycads from a large chloroplast data set

Theria includes Eutheria and its sister taxon Metatheria. Placentalia includes extant eutherians plus their most recent common ancestor. The oldest eutherian is from 125mya (million years ago). Molecular studies place this origin at about 130-185mya. Older dates cannot be refuted based on fossil evidence as earliest eutherian remains are scarce. Earliest superordinal clades (hence Placentalia) range from 64-104mya (median 84mya) based on molecules, similar to 85-90mya based on fossils. Superordinal clades Archonta, Ferungulata, Glires, and Paenungulata based on fossils are similar to molecularly based clades, except Afrotheria was not predicted by fossils. Both fossils and molecules recognize 16 of 18 extant placental orders. Fossils place the origins of orders around 65mya as do some molecular studies, but others suggest ordinal diversification as old as 100mya. Fossil evidence supports a Laurasian origin for Eutheria (and Metatheria) and Placentalia, although some molecular studies suggest a Gondwanan origin for both taxa.     

Marsupials and Eutherians reunited: genetic evidence for the Theria hypothesis of mammalian evolution

The three living monophyletic divisions of Class Mammalia are the Prototheria (monotremes), Metatheria (marsupials), and Eutheria (`placental' mammals). Determining the sister relationships among these three groups is the most fundamental question in mammalian evolution. Phylogenetic comparison of these mammals by either anatomy or mitochondrial DNA has resulted in two conflicting hypotheses, Theria and Marsupionta, and has fueled a ``genes versus morphology' controversy. We have cloned and analyzed a large nuclear gene, the mannose 6-phosphate/insulin-like growth factor II receptor (M6P/IGF2R), from representatives of all three mammalian groups, including platypus, echidna, opossum, wallaby, hedgehog, mouse, rat, rabbit, cow, pig, bat, tree shrew, colugo, ringtail lemur, and human. Statistical analysis of this nuclear gene unambiguously supports the morphology-based Theria hypothesis that excludes monotremes from a clade of marsupials and eutherians. The M6P/IGF2R was also able to resolve the finer structure of the eutherian mammalian family tree. In particular, our analyses support sister group relationships between lagomorphs and rodents, and between the primates and Dermoptera. Statistical support for the grouping of the hedgehog with Feruungulata and Chiroptera was also strong. Received: 8 December 2000 / Accepted: 01 February 2001     

Genome sizes in afrotheria, xenarthra, euarchontoglires, and laurasiatheria

Topical literature and Web site databases provide genome sizes for approximately 4,000 animal species, invertebrates and vertebrates, 330 of which are mammals. We provide the genome size for 67 mammalian species, including 51 never reported before. Knowledge of genome size facilitates sequencing projects. The data presented here encompassed 5 Metatheria (order Didelphimorphia) and 62 Eutheria: 15 Xenarthra, 24 Euarchontoglires (Rodentia), as well as 23 Laurasiatheria (22 Chiroptera and 1 species from Perissodactyla). Already available karyotypes supplement the haploid nuclear DNA contents of the respective species. Thus, we established the first comprehensive set of genome size measurements for 15 Xenarthra species (armadillos) and for 12 house-mouse species; each group was previously represented by only one species. The Xenarthra exhibited much larger genomes than the modal 3 pg DNA known for mammals. Within the genus Mus, genome sizes varied between 2.98 pg and 3.68 pg. The 22 bat species we measured support the low 2.63 pg modal value for Chiroptera. In general, the genomes of Euarchontoglires and Laurasiatheria were found being smaller than those of (Afrotheria and) Xenarthra. Interspecific variation in genome sizes is discussed with particular attention to repetitive elements, which probably promoted the adaptation of extant mammals to their environment.     

Evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs

It has been proposed that intron and genome sizes in birds are reduced in comparison with mammals because of the metabolic demands of flight. To test this hypothesis, we examined the sizes of 14 introns in a nonflying relative of birds, the American alligator (Alligator mississippiensis), and in 19 flighted and flightless birds in 12 taxonomic orders. Our results indicate that a substantial fraction (66%) of the reduction in intron size as well as in genome size had already occurred in nonflying archosaurs. Using phylogenetically independent contrasts, we found that the proposed inverse correlation of genome size and basal metabolic rate (BMR) is significant among amniotes and archosaurs, whereas intron and genome size variation within birds showed no significant correlation with BMR. We show statistically that the distribution of genome sizes in birds and mammals is underdispersed compared with the Brownian motion model and consistent with strong stabilizing selection; that genome size differences between vertebrate clades are overdispersed and punctuational; and that evolution of BMR and avian intron size is consistent with Brownian motion. These results suggest that the contrast between genome size/BMR and intron size/BMR correlations may be a consequence of different intensities of selection for these traits and that we should not expect changes in intron size to be significantly associated with metabolically costly behaviors such as flight.     

Molecular Clocks and the Timing of the Placental and Marsupial Radiations in Relation to the Cretaceous–Tertiary Boundary

Paleostratigraphic estimates of divergence time for nine independent cladogenic events within Mammalia, ranging from 14 to 130 million years, were regressed against Tamura–Nei-corrected 12S rRNA transversions. Relative rate-adjusted distances were also regressed against paleostratigraphic divergence times. The resulting equations were used to estimate interordinal divergence times within Eutheria and Metatheria for a data set that includes representatives of all orders in each infraclass. Without the adjustment for rate variation, divergence times range from 34 to 156 million years for placental orders, versus 32 to 86 million years for marsupial orders. With rate adjustments, the range of divergence estimates decreases to 53 to 133 million years for placentals versus 40 to 79 million years for marsupials. The effect of rate adjustments is most noticeable for carnivores and perissodactyls, where rates are slow, and proboscideans, where rates are fast. In agreement with studies based on nuclear genes, both unadjusted and rate-adjusted estimates of sequence divergence indicate that the majority of placental orders originated before the terminal Cretaceous extinction. Exceptions include the perissodactyl–carnivore split and cladogenesis among paenungulate orders. Most marsupial orders, in turn, may have originated in the early Tertiary although didelphimorphs, at least, appear to have split from other lineages in the late Cretaceous. Marsupial divergence times based on 12S rRNA data are in good agreement with estimates based on single-copy DNA hybridization and disagree with the suggestion of Hershkovitz (1992) that Dromiciops separated from other marsupials in the Jurassic.     

A HYPOTHESIS ON THE EVOLUTIONARY ORIGIN OF THE SQUAMOSAL BONE IN THE THERIAN MAMMALS

Theatheriansandthetherianshavebothinheritedthesquamosa1fromthecyno-dontidancestry,theprimitivepropertyofthesquamosa1intheatherianlineagehavebeenmaintainedfromthebeginning(theLateTriassic,Morganucodontids)totheend(Cretaceous,Triconodontids).Inthetherianlineage,thelowertherianshavethesamesquamosalastheatherians,however,thehighertherianshaveapeculiarsquamosal,so,thechangeofthepropertyofthesquamosaImaytakeplacelntheevolutionaryphasefromthelowertherianmammals(Symmetrodonta,Eupan-totheria,Multitu…     

N-3 polyunsaturated fatty acids impair lifespan but have no role for metabolism

Although generally considered as beneficial components of dietary fats, polyunsaturated fatty acids (PUFA) have been suspected to compromise maximum lifespan (MLSP) in mammals. Specifically, high amounts of phospholipid PUFAs are thought to impair lifespan due to an increase in the susceptibility of membranes to lipid peroxidation and its damaging effect on cellular molecules. Also, there is evidence from in vitro studies suggesting that highly unsaturated PUFAs elevate basal metabolic rate (BMR). Previous comparative studies in this context were based on small sample sizes, however, and, except for one study, failed to address possible confounding influences of body weight and taxonomic relations between species. Therefore, we determined phospholipid membrane composition in skeletal muscle from 42 mammalian species to test for a relation with published data on MLSP, and with literature data on BMR (30 species). Using statistical models that adjust for the effects of body weight and phylogeny, we found that among mammals, MLSP indeed decreases as the ratio of n-3 to n-6 PUFAs increases. In contrast to previous studies, we found, however, no relation between MLSP and either membrane unsaturation (i.e. PUFA content or number of double bonds) or to the very long-chain, highly unsaturated docosahexaenoic acid (DHA). Similarly, our data set gave no evidence for any notable relation between muscle phospholipid fatty acid composition and BMR, or MLSP and BMR in mammals. These results contradict the 'membrane pacemaker theory of aging', that is, the concept of a direct link between high amounts of membrane PUFAs, elevated BMR, and thus, impaired longevity.     

The linear allometric relationship between total metabolic energy per life span and body mass of mammals

The aim of this study is to establish and calculate the exact allometric relationship between the total metabolic energy per life span and the body mass in a wide range of mammals with about six orders of magnitude variation of the body mass of animals. The study shows that it exists a linear relationship between the total metabolic energy per life span PT(ls) (kJ) and the body mass M (kg) of 95 mammals (3 monotremes, Subclass Prototheria, 16 marsupialis (Subclass Theria, Infraclass Metatheria) and 76 placentals (Subclass Theria, Infraclass Eutheria)) from type: PT(ls)=A(ls)(+)M(1.0511), where P (kJ/day) is the basal rate of metabolism and T(ls) (days) is the mean life span of animals. The linear coefficient A(ls)(+)=7.158x10(5) kJ/kg is the total metabolic energy, exhausted during the life span per 1 kg body mass of the animals. The mean values of the total metabolic energy per life span, per unit body mass (A(ls)) for orders from Subclass Prototheria and Theria (Infraclass Metatheria) and orders Xenarthra, Pholidota, Soricomorpha, Rodentia (Infraclass Eutheria) varied negligible in interval (4.656-5.80)x10(5) kJ/kg. The coefficient A(ls) grows from (7.68-8.36)x10(5) kJ/kg in Lagomorpha and Artiodactyla (Eutheria) to (10.58-12.64)x10(5) kJ/kg in orders Carnivora, Pinnipeda and Chiroptera (Eutheria). A(ls) grows maximum to 18.5x10(5) kJ/kg in Primates. Thus, the values of coefficient A(ls) differ maximum four-fold in all orders. Across the all species the values of A(ls) are changes about one order of magnitude. Consequently, our survey shows that the changes of the body mass, basal metabolic rate and the life span of animals are three mutually related parameters, so that the product A(ls)=(PT(ls))/M remains relatively constant in comparison to 1 million fold difference in body mass and total metabolic energy per life span between mammals.     

COMPARATIVE PATTERNS OF CRANIOFACIAL DEVELOPMENT IN EUTHERIAN AND METATHERIAN MAMMALS

The sequence of differentiation of major elements of the skeletal, muscular and nervous systems of the head is examined in developmental series of five eutherian (placental) and four metatherian (marsupial) mammals. The analysis identifies the elements that are conserved across the Theria, those that are unique to the Metatheria and to the Eutheria, and those that are variable. It is shown that although there are slight shifts in the sequence of development within the somatic tissues of the head, the primary difference between marsupial and placental mammals involves the timing and rate of differentiation of structures of the central nervous system (CNS) relative to a specific subset of structures of the cranial skeleton and musculature. In eutherians, CNS morphogenesis is well underway before the somatic tissues of the head begin differentiation. In metatherians, CNS development is delayed considerably and certain elements of the skeletal and muscular systems are advanced. It is concluded that the developmental differences between marsupial and placental mammals are best explained by the interaction of several processes including neurogenesis as a potential rate-limiting step, the developmental requirements of somatic elements, and the extremely short period of organogenesis of marsupial mammals. Several other issues, including the way that these data may be applied to determine the primitive therian developmental condition, and the use of comparative developmental data to address basic questions on morphogenetic processes, are discussed.     

Relationships Among the Families and Orders of Marsupials and the Major Mammalian Lineages Based on Recombination Activating Gene-1

Controversies remain over the relationships among several of the marsupial families and between the three major extant lineages of mammals: Eutheria (placentals), Metatheria (marsupials), and Prototheria (monotremes). Two opposing hypotheses place the marsupials as either sister to the placental mammals (Theria hypothesis) or sister to the monotremes (Palimpsest or Marsupionta hypothesis). A nuclear gene that has proved useful for analyzing phylogenies of vertebrates is the recombination activation gene-1 (RAG1). RAG1 is a highly conserved gene in vertebrates and likely entered the genome by horizontal transfer early in the evolution of jawed vertebrates. Phylogenetic analyses were performed on RAG1 sequences from seven placentals, 28 marsupials, and all three living monotreme species. Phylogenetic analyses of RAG1 sequences support many of the traditional relationships among the marsupials and suggest a relationship between bandicoots (order Peramelina) and the marsupial mole (order Notoryctemorphia), two lineages whose position in the phylogenetic tree has been enigmatic. A sister relationship between South American shrew opossums (order Paucituberculata) and all other living marsupial orders is also suggested by RAG1. The relationship between the three major groups of mammals is consistent with the Theria hypothesis, with the monotremes as the sister group to a clade containing marsupials and placentals.     

Relationships of the dog-like marsupials, deltatheroidans and early tribosphenic mammals

A cladistic analysis of the major groups of early metatherian mammals shows that the Deltatheroida and South American dog-like Borhyaenoidea are closely related and are placed in a new supercohort Deltatheralia. while all other metatherians are placed in the supercohort Marsupialia. A reassessment of Early Cretaceous mammals with tribosphenic molars shows that metatherians and eutherians apparently evolved independently from a peramuran-like ancestor, and an entoconid. distinctly basined talonid and large protocone were acquired separately in each group. Consequently. the Tribosphenida ( sensu McKenna) is apparently paraphyletic. Aegialodontia are regarded as structurally ancestral to Metatheria but not Eutheria. The known fossil record supports the view that differentation of the stocks which gave rise to metatherians and eutherians apparently occurred in Late Jurassic or Early Cretaceous time.     

The evolution of body armor in mammals: plantigrade constraints of large body size

Predictions associated with opposing selection generating minimum variance in basal metabolic rate (BMR) in mammals at a constrained body mass (CBM; 358 g) were tested. The CBM is presumed to be associated with energetic constraints linked to predation and variable resources at intermediate sizes on a logarithmic mass scale. Opposing selection is thought to occur in response to energetic constraints associated with predation and unpredictable resources. As body size approaches and exceeds the CBM, mammals face increasing risks of predation and daily energy requirements. Fast running speeds may require high BMRs, but unpredictable and low resources may select for low BMRs, which also reduce foraging time and distances and thus predation risks. If these two selection forces oppose each other persistently, minimum BMR variance may result. However, extreme BMR outliers at and close to the CBM should be indicative of unbalanced selection and predator avoidance alternatives (escapers vs. defenders), and may therefore provide indirect support for opposing selection. It was confirmed that body armor in defenders evolves at and above the CBM, and armored mammals had significantly lower BMRs than their nonarmored counterparts. However, analyses comparing the BMR of escapers--the fastest nonarmored runners (Lagomorpha)--with similar-sized counterparts were inconclusive and were confounded by limb morphology associated with speed optimization. These analyses suggest that the risks and costs of predation and the speed limitations of the plantigrade foot may constrain the evolution of large body sizes in plantigrade mammals.     

Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia

Recent phylogenetic analyses of a large dataset for mammalian families (169 taxa, 26 loci) portray contrasting results. Supermatrix (concatenation) methods support a generally robust tree with only a few inconsistently resolved polytomies, whereas MP‐EST coalescence analysis of the same dataset yields a weakly supported tree that conflicts with many traditionally recognized clades. Here, we evaluate this discrepancy via improved coalescence analyses with reference to the rich history of phylogenetic studies on mammals. This integration clearly demonstrates that both supermatrix and coalescence analyses of just 26 loci yield a congruent, well‐supported phylogenetic hypothesis for Mammalia. Discrepancies between published studies are explained by implementation of overly simple DNA substitution models, inadequate tree‐search routines and limitations of the MP‐EST method. We develop a simple measure, partitioned coalescence support (PCS), which summarizes the distribution of support and conflict among gene trees for a given clade. Extremely high PCS scores for outlier gene trees at two nodes in the mammalian tree indicate a troubling bias in the MP‐EST method. We conclude that in this age of phylogenomics, a solid understanding of systematics fundamentals, choice of valid methodology and a broad knowledge of a clade's taxonomic history are still required to yield coherent phylogenetic inferences.     

Allometry of thermal variables in mammals: consequences of body size and phylogeny

A large number of analyses have examined how basal metabolic rate (BMR) is affected by body mass in mammals. By contrast, the critical ambient temperatures that define the thermo‐neutral zone (TNZ), in which BMR is measured, have received much less attention. We provide the first phylogenetic analyses on scaling of lower and upper critical temperatures and the breadth of the TNZ in 204 mammal species from diverse orders. The phylogenetic signal of thermal variables was strong for all variables analysed. Most allometric relationships between thermal variables and body mass were significant and regressions using phylogenetic analyses fitted the data better than conventional regressions. Allometric exponents for all mammals were 0.19 for the lower critical temperature (expressed as body temperature ‐ lower critical temperature), ?0.027 for the upper critical temperature, and 0.17 for the breadth of TNZ. The small exponents for the breadth of the TNZ compared to the large exponents for BMR suggest that BMR per se affects the influence of body mass on TNZ only marginally. However, the breadth of the TNZ is also related to the apparent thermal conductance and it is therefore possible that BMR at different body masses is a function of both the heat exchange in the TNZ and that encountered below and above the TNZ to permit effective homeothermic thermoregulation.     

Locomotor mode, maximum running speed, and basal metabolic rate in placental mammals

The locomotor performance (absolute maximum running speed [MRS]) of 120 mammals was analyzed for four different locomotor modes (plantigrade, digitigrade, unguligrade, and lagomorph-like) in terms of body size and basal metabolic rate (BMR). Analyses of conventional species data showed that the MRS of plantigrade and digitigrade mammals and lagomorphs increases with body mass, whereas that of unguligrade mammals decreases with body mass. These trends were confirmed in plantigrade mammals and lagomorphs using phylogenetically independent contrasts. Multiple regression analyses of MRS contrasts (dependent variable) as a function of body mass and BMR contrasts (predictor variables) revealed that BMR was a significant predictor of MRS in the complete data set, as well as in plantigrade and nonplantigrade mammals. However, there was severe multicollinearity in the nonplantigrade model that may influence the interpretation of these models. Although these data show mass-independent correlation between BMR and MRS, they are not necessarily indicative of a cause-effect relationship. However, the analyses do identify a negligible role of body size associated with MRS once phylogenetic and BMR effects are controlled, suggesting that the body size increase in large mammals over time (i.e., Cope's rule) can probably rule out MRS as a driving variable.     

Differences in mandibular disparity between extant and extinct species of metatherian and placental carnivore clades

There are a number of studies relating to skull morphology differences within the carnivoran clades of both placentals and metatherians. It is difficult to compare these studies because of differences in taxonomic sampling, for example some include fossil taxa while others include non‐carnivoran placentals. As a consequence, we studied mandible morphology in a broad range of both extant and extinct carnivorous species, including Carnivora, Marsupialia and Sparassodonta to test for differences between these clades. We used geometric morphometrics and two disparity indexes, the variance and Procrustes distances mean. When including fossil species, we found no significant differences for both disparities in some analyses, except after the exclusion of the sabretooth morphotype. This can be explained by the extreme morphology of this morphotype, which increases the variance and reduces the disparity effect of the other species in the analyses. Using Procrustes distances, we found significant differences in disparity distances between Carnivora and Metatheria for most of the analyses. We also found significant differences using the variance index in some analyses. The mandibular disparity in Carnivora is greater than in carnivorous metatherian mammals for most of the cases and this can be related with differences in evolutionary history and constraints of both groups. The pattern found in the mandible is similar to that found in the face of the skull but was not observed in the braincase, due to differences in skull function and mandible function.     

Postnatal long bone growth in terrestrial placental mammals: Allometry,life history,and organismal traits

The ontogenetic allometry of long bone proportions is poorly understood in Mammalia. It has previously been suggested that during mammalian ontogeny long bone proportions grow more slender (positive allometry; length ∝ circumference^>1.0), although this conclusion was based upon data from a few small‐bodied taxa. It remains unknown how ontogenetic long bone allometry varies across Mammalia in terms of both taxonomy and body size. We collected long bone length and circumference data for ontogenetic samples of 22 species of mammals spanning six major clades and three orders of magnitude in body mass. Using reduced major axis bivariate regressions to compare bone length to circumference, we found that isometry and positive allometry are the most widespread patterns of growth across mammals. Negative allometry (i.e., bones growing more robust during ontogeny) occurs in mammals but is largely restricted to cetartiodactyls. Using regression slope as a proxy for long bone allometry, we compared long bone allometry to life history and organismal traits. Neonatal body mass, adult body mass, and growth rate have a negative relationship with long bone allometry. At an adult mass of roughly 15–20 kg, long bone growth shifts from positive allometry to mainly isometry and negative allometry. There were no significant relationships between ontogenetic long bone allometry and either cursoriality or basal metabolic rate. J. Morphol. © 2012 Wiley Periodicals, Inc.     

Mammalian metabolism, longevity and parasite species richness

Basal metabolic rate (BMR) scales allometrically with body mass in mammals, but the reasons why some species have higher or lower metabolic rates than predicted from their body mass remain unclear. We tested the idea that parasite species richness may be a contributory factor by performing a comparative analysis on 23 species of mammals for which data were available on parasite species richness, BMR, body mass and two potentially confounding variables, i.e. host density and host longevity. Parasite species richness was positively correlated with BMR and negatively correlated with host longevity independent of body mass.