Bayesian Prediction of Multivariate Ecology from Phenotypic Data Yields New Insights into the Diets of Extant and Extinct Taxa

AbstractMorphology often reflects ecology, enabling the prediction of ecological roles for taxa that lack direct observations, such as fossils. In comparative analyses, ecological traits, like diet, are often treated as categorical, which may aid prediction and simplify analyses but ignores the multivariate nature of ecological niches. Furthermore, methods for quantifying and predicting multivariate ecology remain rare. Here, we ranked the relative importance of 13 food items for a sample of 88 extant carnivoran mammals and then used Bayesian multilevel modeling to assess whether those rankings could be predicted from dental morphology and body size. Traditional diet categories fail to capture the true multivariate nature of carnivoran diets, but Bayesian regression models derived from living taxa have good predictive accuracy for importance ranks. Using our models to predict the importance of individual food items, the multivariate dietary niche, and the nearest extant analogs for a set of data-deficient extant and extinct carnivoran species confirms long-standing ideas for some taxa but yields new insights into the fundamental dietary niches of others. Our approach provides a promising alternative to traditional dietary classifications. Importantly, this approach need not be limited to diet but serves as a general framework for predicting multivariate ecology from phenotypic traits.

The dynamic adaptive landscape of cetacean body size

Adaptive landscapes are central to evolutionary theory, forming a conceptual bridge between micro- and macroevolution.^1,2,3,4 Evolution by natural selection across an adaptive landscape should drive lineages toward fitness peaks, shaping the distribution of phenotypic variation within and among clades over evolutionary timescales.⁵ The location and breadth of these peaks in phenotypic space can also evolve,⁴ but whether phylogenetic comparative methods can detect such patterns has largely remained unexplored.⁶ Here, we characterize the global and local adaptive landscape for total body length in cetaceans (whales, dolphins, and relatives), a trait that spans 5 orders of magnitude, across their ∼53 million year evolutionary history. Using phylogenetic comparative methods, we analyze shifts in long-term mean body length⁷ and directional changes in average trait values⁸ for 345 living and fossil cetacean taxa. Remarkably, we find that the global macroevolutionary adaptive landscape of cetacean body length is relatively flat, with very few peak shifts occurring after cetaceans entered the oceans. Local peaks are more numerous and manifest as trends along branches linked to specific adaptations. These results contrast with previous studies using only extant taxa,⁹ highlighting the vital role of fossil data for understanding macroevolution.^10,11,12 Our results indicate that adaptive peaks are dynamic and are associated with subzones of local adaptations, creating moving targets for species adaptation. In addition, we identify limits in our ability to detect some evolutionary patterns and processes and suggest that multiple approaches are required to characterize complex hierarchical patterns of adaptation in deep time.

Topographically distinct adaptive landscapes for teeth, skeletons, and size explain the adaptive radiation of Carnivora (Mammalia)

Models of adaptive radiation were originally developed to explain the early, rapid appearance of distinct modes of life within diversifying clades. Phylogenetic tests of this hypothesis have yielded limited support for temporally declining rates of phenotypic evolution across diverse clades, but the concept of an adaptive landscape that links form to fitness, while also crucial to these models, has received more limited attention. Using methods that assess the temporal accumulation of morphological variation and estimate the topography of the underlying adaptive landscape, I found evidence of an early partitioning of mandibulo-dental morphological variation in Carnivora (Mammalia) that occurs on an adaptive landscape with multiple peaks, consistent with classic ideas about adaptive radiation. Although strong support for this mode of adaptive radiation is present in traits related to diet, its signal is not present in body mass data or for traits related to locomotor behavior and substrate use. These findings suggest that adaptive radiations may occur along some axes of ecomorphological variation without leaving a signal in others and that their dynamics are more complex than simple univariate tests might suggest.

Extant species fail to estimate ancestral geographical ranges at older nodes in primate phylogeny

A clade's evolutionary history is shaped, in part, by geographical range expansion, sweepstakes dispersal and local extinction. A rigorous understanding of historical biogeography may therefore yield insights into macroevolutionary dynamics such as adaptive radiation. Modern historical biogeographic analyses typically fit statistical models to molecular phylogenies, but it remains unclear whether extant species provide sufficient signal or if well-sampled phylogenies of extinct and extant taxa are necessary to produce meaningful estimates of past ranges. We investigated the historical biogeography of Primates and their euarchontan relatives using a novel meta-analytical phylogeny of over 900 extant (n= 419) and extinct (n = 483) species spanning their entire evolutionary history. Ancestral range estimates for young nodes were largely congruent with those derived from molecular phylogeny. However, node age exerts a significant effect on ancestral range estimate congruence, and the probability of congruent inference dropped below 0.5 for nodes older than the late Eocene, corresponding to the origins of higher-level clades. Discordance was not observed in analyses of extinct taxa alone. Fossils are essential for robust ancestral range inference and biogeographic analyses of extant clades originating in the deep past should be viewed with scepticism without them.

Evolutionary history of quadrupedal walking gaits shows mammalian release from locomotor constraint

Vertebrates employ an impressive range of strategies for coordinating their limb movements while walking. Although this gait variation has been quantified and hypotheses for its origins tested in select tetrapod lineages, a comprehensive understanding of gait evolution in a macroevolutionary context is currently lacking. We used freely available internet videos to nearly double the number of species with quantitative gait data, and used phylogenetic comparative methods to test key hypotheses about symmetrical gait origin and evolution. We find strong support for an ancestral lateral-sequence diagonal-couplet gait in quadrupedal gnathostomes, and this mode is remarkably conserved throughout tetrapod phylogeny. Evolutionary rate analyses show that mammals overcame this ancestral constraint, resulting in a greater range of phase values than any other tetrapod lineage. Diagonal-sequence diagonal-couplet gaits are significantly associated with arboreality in mammals, though this relationship is not recovered for other tetrapod lineages. Notably, the lateral-sequence lateral-couplet gait, unique to mammals among extant tetrapods, is not associated with any traditional explanations. The complex drivers of gait diversification in mammals remain unclear, but our analyses suggest that their success was due, in part, to release from a locomotor constraint that has probably persisted in other extant tetrapod lineages for over 375 Myr.

Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades

Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs, and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with a steep diversification drop (PyRate) or without one (BAMM), and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic datasets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to yield potentially unreliable inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations, and suggest how the latter may be mitigated.

A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.

Disparities in the analysis of morphological disparity

Analyses of morphological disparity have been used to characterize and investigate the evolution of variation in the anatomy, function and ecology of organisms since the 1980s. While a diversity of methods have been employed, it is unclear whether they provide equivalent insights. Here, we review the most commonly used approaches for characterizing and analysing morphological disparity, all of which have associated limitations that, if ignored, can lead to misinterpretation. We propose best practice guidelines for disparity analyses, while noting that there can be no 'one-size-fits-all' approach. The available tools should always be used in the context of a specific biological question that will determine data and method selection at every stage of the analysis.

Palaeoproteomics resolves sloth relationships

The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.

Shared extremes by ectotherms and endotherms: Body elongation in mustelids is associated with small size and reduced limbs

An elongate body with reduced or absent limbs has evolved independently in many ectothermic vertebrate lineages. While much effort has been spent examining the morphological pathways to elongation in these clades, quantitative investigations into the evolution of elongation in endothermic clades are lacking. We quantified body shape in 61 musteloid mammals (red panda, skunks, raccoons, and weasels) using the head-body elongation ratio. We also examined the morphological changes that may underlie the evolution toward more extreme body plans. We found that a mustelid clade comprised of the subfamilies Helictidinae, Guloninae, Ictonychinae, Mustelinae, and Lutrinae exhibited an evolutionary transition toward more elongate bodies. Furthermore, we discovered that elongation of the body is associated with the evolution of other key traits such as a reduction in body size and a reduction in forelimb length but not hindlimb length. This relationship between body elongation and forelimb length has not previously been quantitatively established for mammals but is consistent with trends exhibited by ectothermic vertebrates and suggests a common pattern of trait covariance associated with body shape evolution. This study provides the framework for documenting body shapes across a wider range of mammalian clades to better understand the morphological changes influencing shape disparity across all vertebrates.

Are increases in skeletal muscle mass accompanied by changes to resting metabolic rate in rugby athletes over a pre-season training period?

Optimising dietary energy intake is essential for effective sports nutrition practice in rugby athletes. Effective dietary energy prescription requires careful consideration of athletes' daily energy expenditure with the accurate prediction of resting metabolic rate (RMR) important due to its influence on total energy expenditure and in turn, energy balance. This study aimed to (a) measure rugby athletes RMR and (b) report the change in RMR in developing elite rugby players over a rugby preseason subsequent to changes in body composition and (c) explore the accurate prediction of RMR in rugby athletes. Eighteen developing elite rugby union athletes (age 20.2 ± 1.7 years, body mass 101.2 ± 14.5 kg, stature 184.0 ± 8.4 cm) had RMR (indirect calorimetry) and body composition (dual energy x-ray absorptiometry) measured at the start and end of a rugby preseason ∼14 weeks later. There was no statistically significant difference in RMR over the preseason period (baseline 2389 ± 263 kcal·day^-1 post 2373 ± 270 kcal·day^-1) despite a significant increase in lean mass of +2.0 ± 1.6 kg (P < 0.01) and non-significant loss of fat mass. The change in RMR was non-significant and non-meaningful; thus, this study contradicts the commonly held anecdotal perception that an increase in skeletal muscle mass will result in a significant increase in metabolic rate and daily energy needs. Conventional prediction equations generally under-estimated rugby athletes' measured RMR, and may be problematic for identifying low energy availability, and thus updated population-specific prediction equations may be warranted to inform practice.

Lineage Diversity and Size Disparity in Musteloidea: Testing Patterns of Adaptive Radiation Using Molecular and Fossil-Based Methods

Adaptive radiation is hypothesized to be a primary mechanism that drives the remarkable species diversity and morphological disparity across the Tree of Life. Tests for adaptive radiation in extant taxa are traditionally estimated from calibrated molecular phylogenies with little input from extinct taxa. With 85 putative species in 33 genera and over 400 described extinct species, the carnivoran superfamily Musteloidea is a prime candidate to investigate patterns of adaptive radiation using both extant- and fossil-based macroevolutionary methods. The species diversity and equally impressive ecological and phenotypic diversity found across Musteloidea is often attributed to two adaptive radiations coinciding with two major climate events, the Eocene-Oligocene transition and the Mid-Miocene Climate Transition. Here, we compiled a novel time-scaled phylogeny for 88% of extant musteloids and used it as a framework for testing the predictions of adaptive radiation hypotheses with respect to rates of lineage diversification and phenotypic evolution. Contrary to expectations, we found no evidence for rapid bursts of lineage diversification at the origin of Musteloidea, and further analyses of lineage diversification rates using molecular and fossil-based methods did not find associations between rates of lineage diversification and the Eocene-Oligocene transition or Mid-Miocene Climate Transition as previously hypothesized. Rather, we found support for decoupled diversification dynamics driven by increased clade carrying capacity in the branches leading to a subclade of elongate mustelids. Supporting decoupled diversification dynamics between the subclade of elongate mustelids and the ancestral musteloid regime is our finding of increased rates of body length evolution, but not body mass evolution, within the decoupled mustelid subclade. The lack of correspondence in rates of body mass and length evolution suggest that phenotypic evolutionary rates under a single morphological metric, even one as influential as mass, may not capture the evolution of diversity in clades that exhibit elongate body shapes. The discordance in evolutionary rates between body length and body mass along with evidence of decoupled diversification dynamics suggests that body elongation might be an innovation for the exploitation of novel Mid-Miocene resources, resulting in the radiation of some musteloids.

Independent evolution of baleen whale gigantism linked to Plio-Pleistocene ocean dynamics

Vertebrates have evolved to gigantic sizes repeatedly over the past 250 Myr, reaching their extreme in today's baleen whales (Mysticeti). Hypotheses for the evolution of exceptionally large size in mysticetes range from niche partitioning to predator avoidance, but there has been no quantitative examination of body size evolutionary dynamics in this clade and it remains unclear when, why or how gigantism evolved. By fitting phylogenetic macroevolutionary models to a dataset consisting of living and extinct species, we show that mysticetes underwent a clade-wide shift in their mode of body size evolution during the Plio-Pleistocene. This transition, from Brownian motion-like dynamics to a trended random walk towards larger size, is temporally linked to the onset of seasonally intensified upwelling along coastal ecosystems. High prey densities resulting from wind-driven upwelling, rather than abundant resources alone, are the primary determinant of efficient foraging in extant mysticetes and Late Pliocene changes in ocean dynamics may have provided an ecological pathway to gigantism in multiple independent lineages.

Evolutionary Relationships among Extinct and Extant Sloths: The Evidence of Mitogenomes and Retroviruses

Macroevolutionary trends exhibited by retroviruses are complex and not entirely understood. The sloth endogenized foamy-like retrovirus (SloEFV), which demonstrates incongruence in virus–host evolution among extant sloths (Order Folivora), has not been investigated heretofore in any extinct sloth lineages and its premodern history within folivorans is therefore unknown. Determining retroviral coevolutionary trends requires a robust phylogeny of the viral host, but the highly reduced modern sloth fauna (6 species in 2 genera) does not adequately represent what was once a highly diversified clade (∼100 genera) of placental mammals. At present, the amount of molecular data available for extinct sloth taxa is limited, and analytical results based on these data tend to conflict with phylogenetic inferences made on the basis of morphological studies. To augment the molecular data set, we applied hybridization capture and next-generation Illumina sequencing to two extinct and three extant sloth species to retrieve full mitochondrial genomes (mitogenomes) from the hosts and the polymerase gene of SloEFV. The results produced a fully resolved and well-supported phylogeny that supports dividing crown families into two major clades: 1) The three-toed sloth, Bradypus, and Nothrotheriidae and 2) Megalonychidae, including the two-toed sloth, Choloepus, and Mylodontidae. Our calibrated time tree indicates that the Miocene epoch (23.5 Ma), particularly its earlier part, was an important interval for folivoran diversification. Both extant and extinct sloths demonstrate multiple complex invasions of SloEFV into the ancestral sloth germline followed by subsequent introgressions across different sloth lineages. Thus, sloth mitogenome and SloEFV evolution occurred separately and in parallel among sloths.

Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology

Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M. tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and “New World monk seals” (Hawaiian and Caribbean) is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals (Monachus and Neomonachus) represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

SUMMARY

Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0, a complete overhaul of the popular R package geiger. We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types.

AVAILABILITY AND IMPLEMENTATION

 This R package is available on the CRAN repository http://cran.r-project.org/web/packages/geiger/. All source code is also available on github http://github.com/mwpennell/geiger-v2. geiger v2.0 depends on the ape package.

CONTACT

mwpennell@gmail.com

SUPPLEMENTARY INFORMATION

 Supplementary data are available at Bioinformatics online.

Himalayan fossils of the oldest known pantherine establish ancient origin of big cats

Pantherine felids ('big cats') include the largest living cats, apex predators in their respective ecosystems. They are also the earliest diverging living cat lineage, and thus are important for understanding the evolution of all subsequent felid groups. Although the oldest pantherine fossils occur in Africa, molecular phylogenies point to Asia as their region of origin. This paradox cannot be reconciled using current knowledge, mainly because early big cat fossils are exceedingly rare and fragmentary. Here, we report the discovery of a fossil pantherine from the Tibetan Himalaya, with an age of Late Miocene-Early Pliocene, replacing African records as the oldest pantherine. A 'total evidence' phylogenetic analysis of pantherines indicates that the new cat is closely related to the snow leopard and exhibits intermediate characteristics on the evolutionary line to the largest cats. Historical biogeographic models provide robust support for the Asian origin of pantherines. The combined analyses indicate that 75% of the divergence events in the pantherine lineage extended back to the Miocene, up to 7 Myr earlier than previously estimated. The deeper evolutionary origin of big cats revealed by the new fossils and analyses indicate a close association between Tibetan Plateau uplift and diversification of the earliest living cats.

Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution

A central prediction of much theory on adaptive radiations is that traits should evolve rapidly during the early stages of a clade's history and subsequently slowdown in rate as niches become saturated--a so-called "Early Burst." Although a common pattern in the fossil record, evidence for early bursts of trait evolution in phylogenetic comparative data has been equivocal at best. We show here that this may not necessarily be due to the absence of this pattern in nature. Rather, commonly used methods to infer its presence perform poorly when when the strength of the burst--the rate at which phenotypic evolution declines--is small, and when some morphological convergence is present within the clade. We present two modifications to existing comparative methods that allow greater power to detect early bursts in simulated datasets. First, we develop posterior predictive simulation approaches and show that they outperform maximum likelihood approaches at identifying early bursts at moderate strength. Second, we use a robust regression procedure that allows for the identification and down-weighting of convergent taxa, leading to moderate increases in method performance. We demonstrate the utility and power of these approach by investigating the evolution of body size in cetaceans. Model fitting using maximum likelihood is equivocal with regards the mode of cetacean body size evolution. However, posterior predictive simulation combined with a robust node height test return low support for Brownian motion or rate shift models, but not the early burst model. While the jury is still out on whether early bursts are actually common in nature, our approach will hopefully facilitate more robust testing of this hypothesis. We advocate the adoption of similar posterior predictive approaches to improve the fit and to assess the adequacy of macroevolutionary models in general.

Clade age and species richness are decoupled across the eukaryotic tree of life

Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fundamental expectation in macroevolutionary studies is simply that species richness in extant clades should be correlated with clade age: all things being equal, older clades will have had more time for diversity to accumulate than younger clades. Here, we test the relationship between stem clade age and species richness across 1,397 major clades of multicellular eukaryotes that collectively account for more than 1.2 million described species. We find no evidence that clade age predicts species richness at this scale. We demonstrate that this decoupling of age and richness is unlikely to result from variation in net diversification rates among clades. At the largest phylogenetic scales, contemporary patterns of species richness are inconsistent with unbounded diversity increase through time. These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms.

Species richness varies by many orders of magnitude across the evolutionary "tree of life." Some groups, like beetles and flowering plants, contain nearly incomprehensible species diversity, but the overwhelming majority of groups contain far fewer species. Many processes presumably contribute to this variation in diversity, but the most general explanatory variable is the evolutionary age of each group: older groups will simply have had more time for diversity to accumulate than younger groups. We tested whether evolutionary age explains differences in species richness by compiling diversity and age estimates for nearly 1,400 groups of multicellular organisms. Surprisingly, we find no evidence that old groups have more species than young groups. This result appears to hold across the entire tree of life, for taxa as diverse as ferns, fungi, and flies. We demonstrate that this pattern is highly unlikely under simple but widely used evolutionary models that allow diversity to increase through time without bounds. Paleontologists have long contended that diversity-dependent processes have regulated species richness through time, and our results suggest that such processes have left a footprint on the living biota that can even be seen without data from the fossil record.

The evolution of island gigantism and body size variation in tortoises and turtles

Extant chelonians (turtles and tortoises) span almost four orders of magnitude of body size, including the startling examples of gigantism seen in the tortoises of the Galapagos and Seychelles islands. However, the evolutionary determinants of size diversity in chelonians are poorly understood. We present a comparative analysis of body size evolution in turtles and tortoises within a phylogenetic framework. Our results reveal a pronounced relationship between habitat and optimal body size in chelonians. We found strong evidence for separate, larger optimal body sizes for sea turtles and island tortoises, the latter showing support for the rule of island gigantism in non-mammalian amniotes. Optimal sizes for freshwater and mainland terrestrial turtles are similar and smaller, although the range of body size variation in these forms is qualitatively greater. The greater number of potential niches in freshwater and terrestrial environments may mean that body size relationships are more complicated in these habitats.

Aquatic adaptations in the nose of carnivorans: evidence from the turbinates

Inside the mammalian nose lies a labyrinth of bony plates covered in epithelium collectively known as turbinates. Respiratory turbinates lie anteriorly and aid in heat and water conservation, while more posterior olfactory turbinates function in olfaction. Previous observations on a few carnivorans revealed that aquatic species have relatively large, complex respiratory turbinates and greatly reduced olfactory turbinates compared with terrestrial species. Body heat is lost more quickly in water than air and increased respiratory surface area likely evolved to minimize heat loss. At the same time, olfactory surface area probably diminished due to a decreased reliance on olfaction when foraging under water. To explore how widespread these adaptations are, we documented scaling of respiratory and olfactory turbinate surface area with body size in a variety of terrestrial, freshwater, and marine carnivorans, including pinnipeds, mustelids, ursids, and procyonids. Surface areas were estimated from high-resolution CT scans of dry skulls, a novel approach that enabled a greater sampling of taxa than is practical with fresh heads. Total turbinate, respiratory, and olfactory surface areas correlate well with body size (r(2) ≥0.7), and are relatively smaller in larger species. Relative to body mass or skull length, aquatic species have significantly less olfactory surface area than terrestrial species. Furthermore, the ratio of olfactory to respiratory surface area is associated with habitat. Using phylogenetic comparative methods, we found strong support for convergence on 1:3 proportions in aquatic taxa and near the inverse in terrestrial taxa, indicating that aquatic mustelids and pinnipeds independently acquired similar proportions of olfactory to respiratory turbinates. Constraints on turbinate surface area in the nasal chamber may result in a trade-off between respiratory and olfactory function in aquatic mammals.

Biomechanical consequences of rapid evolution in the polar bear lineage

The polar bear is the only living ursid with a fully carnivorous diet. Despite a number of well-documented craniodental adaptations for a diet of seal flesh and blubber, molecular and paleontological data indicate that this morphologically distinct species evolved less than a million years ago from the omnivorous brown bear. To better understand the evolution of this dietary specialization, we used phylogenetic tests to estimate the rate of morphological specialization in polar bears. We then used finite element analysis (FEA) to compare the limits of feeding performance in the polar bear skull to that of the phylogenetically and geographically close brown bear. Results indicate that extremely rapid evolution of semi-aquatic adaptations and dietary specialization in the polar bear lineage produced a cranial morphology that is weaker than that of brown bears and less suited to processing tough omnivorous or herbivorous diets. Our results suggest that continuation of current climate trends could affect polar bears by not only eliminating their primary food source, but also through competition with northward advancing, generalized brown populations for resources that they are ill-equipped to utilize.

Diversity versus disparity and the radiation of modern cetaceans

Modern whales are frequently described as an adaptive radiation spurred by either the evolution of various key innovations (such as baleen or echolocation) or ecological opportunity following the demise of archaic whales. Recent analyses of diversification rate shifts on molecular phylogenies raise doubts about this interpretation since they find no evidence of increased speciation rates during the early evolution of modern taxa. However, one of the central predictions of ecological adaptive radiation is rapid phenotypic diversification, and the tempo of phenotypic evolution has yet to be quantified in cetaceans. Using a time-calibrated molecular phylogeny of extant cetaceans and a morphological dataset on size, we find evidence that cetacean lineages partitioned size niches early in the evolutionary history of neocetes and that changes in cetacean size are consistent with shifts in dietary strategy. We conclude that the signature of adaptive radiations may be retained within morphological traits even after equilibrium diversity has been reached and high extinction or fluctuations in net diversification have erased any signature of an early burst of diversification in the structure of the phylogeny.

Allometry and performance: the evolution of skull form and function in felids

Allometric patterns of skull-shape variation can have significant impacts on cranial mechanics and feeding performance, but have received little attention in previous studies. Here, we examine the impacts of allometric skull-shape variation on feeding capabilities in the cat family (Felidae) with linear morphometrics and finite element analysis. Our results reveal that relative bite force diminishes slightly with increasing skull size, and that the skulls of the smallest species undergo the least strain during biting. However, larger felids are able to produce greater gapes for a given angle of jaw opening, and they have overall stronger skulls. The two large felids in this study achieved increased cranial strength by increasing skull bone volume relative to surface area. Allometry of skull geometry in large felids reflects a trade-off between the need to increase gape to access larger prey while maintaining the ability to resist unpredictable loading when taking large, struggling prey.

Multigene phylogeny of the Mustelidae: resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation

BACKGROUND

Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is a central concept in evolutionary biology and characterizes the evolutionary histories of many groups of organisms. One such group is the Mustelidae, the most species-rich family within the mammalian order Carnivora, encompassing 59 species classified into 22 genera. Extant mustelids display extensive ecomorphological diversity, with different lineages having evolved into an array of adaptive zones, from fossorial badgers to semi-aquatic otters. Mustelids are also widely distributed, with multiple genera found on different continents. As with other groups that have undergone adaptive radiation, resolving the phylogenetic history of mustelids presents a number of challenges because ecomorphological convergence may potentially confound morphologically based phylogenetic inferences, and because adaptive radiations often include one or more periods of rapid cladogenesis that require a large amount of data to resolve.

RESULTS

We constructed a nearly complete generic-level phylogeny of the Mustelidae using a data matrix comprising 22 gene segments (approximately 12,000 base pairs) analyzed with maximum parsimony, maximum likelihood and Bayesian inference methods. We show that mustelids are consistently resolved with high nodal support into four major clades and three monotypic lineages. Using Bayesian dating techniques, we provide evidence that mustelids underwent two bursts of diversification that coincide with major paleoenvironmental and biotic changes that occurred during the Neogene and correspond with similar bursts of cladogenesis in other vertebrate groups. Biogeographical analyses indicate that most of the extant diversity of mustelids originated in Eurasia and mustelids have colonized Africa, North America and South America on multiple occasions.

CONCLUSION

Combined with information from the fossil record, our phylogenetic and dating analyses suggest that mustelid diversification may have been spurred by a combination of faunal turnover events and diversification at lower trophic levels, ultimately caused by climatically driven environmental changes. Our biogeographic analyses show Eurasia as the center of origin of mustelid diversity and that mustelids in Africa, North America and South America have been assembled over time largely via dispersal, which has important implications for understanding the ecology of mustelid communities.

Validation of a skinfold based index for tracking proportional changes in lean mass

BACKGROUND

The lean mass index (LMI) is a new empirical measure that tracks within-subject proportional changes in body mass adjusted for changes in skinfold thickness.

OBJECTIVE

To compare the ability of the LMI and other skinfold derived measures of lean mass to monitor changes in lean mass.

METHODS

20 elite rugby union players undertook full anthropometric profiles on two occasions 10 weeks apart to calculate the LMI and five skinfold based measures of lean mass. Hydrodensitometry, deuterium dilution, and dual energy x ray absorptiometry provided a criterion choice, four compartment (4C) measure of lean mass for validation purposes. Regression based measures of validity, derived for within-subject proportional changes through log transformation, included correlation coefficients and standard errors of the estimate.

RESULTS

The correlation between change scores for the LMI and 4C lean mass was moderate (0.37, 90% confidence interval -0.01 to 0.66) and similar to the correlations for the other practical measures of lean mass (range 0.26 to 0.42). Standard errors of the estimate for the practical measures were in the range of 2.8-2.9%. The LMI correctly identified the direction of change in 4C lean mass for 14 of the 20 athletes, compared with 11 to 13 for the other practical measures of lean mass.

CONCLUSIONS

The LMI is probably as good as other skinfold based measures for tracking lean mass and is theoretically more appropriate. Given the impracticality of the 4C criterion measure for routine field use, the LMI may offer a convenient alternative for monitoring physique changes, provided its utility is established under various conditions.

Physique traits of lightweight rowers and their relationship to competitive success

OBJECTIVES

Physique traits and their relationship to competitive success were assessed amongst lightweight rowers competing at the 2003 Australian Rowing Championships.

METHODS

Full anthropometric profiles were collected from 107 lightweight rowers (n = 65 males, n = 45 females) competing in the Under 23 and Open age categories. Performance assessments were obtained for 66 of these rowers based on results in the single sculls events. The relationship between physique traits and competitive success was then determined.

RESULTS

Lower body fat (heat time estimate -8.4 s kg(-1), p<0.01), greater total body mass (heat time estimate -4.4 s kg(-1), p = 0.03), and muscle mass (heat time estimate -10.2 s kg(-1), p<0.01) were associated with faster 2000 m heat times.

CONCLUSIONS

The more successful lightweight rowers were those who had lower body fat and greater total muscle mass.

Live high:train low increases muscle buffer capacity and submaximal cycling efficiency

This study investigated whether hypoxic exposure increased muscle buffer capacity (beta(m)) and mechanical efficiency during exercise in male athletes. A control (CON, n=7) and a live high:train low group (LHTL, n=6) trained at near sea level (600 m), with the LHTL group sleeping for 23 nights in simulated moderate altitude (3000 m). Whole body oxygen consumption (VO2) was measured under normoxia before, during and after 23 nights of sleeping in hypoxia, during cycle ergometry comprising 4 x 4-min submaximal stages, 2-min at 5.6 +/- 0.4 W kg(-1), and 2-min 'all-out' to determine total work and VO(2peak). A vastus lateralis muscle biopsy was taken at rest and after a standardized 2-min 5.6 +/- 0.4 W kg(-1) bout, before and after LHTL, and analysed for beta(m) and metabolites. After LHTL, beta(m) was increased (18%, P < 0.05). Although work was maintained, VO(2peak) fell after LHTL (7%, P < 0.05). Submaximal VO2 was reduced (4.4%, P < 0.05) and efficiency improved (0.8%, P < 0.05) after LHTL probably because of a shift in fuel utilization. This is the first study to show that hypoxic exposure, per se, increases muscle buffer capacity. Further, reduced VO2 during normoxic exercise after LHTL suggests that improved exercise efficiency is a fundamental adaptation to LHTL.

Beta-hydroxy-beta-methylbutyrate (HMB) supplementation and the promotion of muscle growth and strength

Beta-hydroxy beta-methylbutyrate (HMB), a metabolite of the essential amino acid leucine, is one of the latest dietary supplements promoted to enhance gains in strength and lean body mass associated with resistance training. Unlike anabolic hormones that induce muscle hypertrophy by increasing muscle protein synthesis, HMB is claimed to influence strength and lean body mass by acting as an anticatabolic agent, minimising protein breakdown and damage to cells that may occur with intense exercise. Research on HMB has recently tested this hypothesis, under the assumption that it may be the active compound associated with the anticatabolic effects of leucine and its metabolites. While much of the available literature is preliminary in nature and not without methodological concern, there is support for the claims made regarding HMB supplementation, at least in young, previously untrained individuals. A mechanism by which this may occur is unknown, but research undertaken to date suggests there may be a reduction in skeletal muscle damage, although this has not been assessed directly. The response of resistance trained and older individuals to HMB administration is less clear. While the results of research conducted to date appear encouraging, caution must be taken when interpreting outcomes as most manuscripts are presented in abstract form only, not having to withstand the rigors of peer review. Of the literature reviewed relating to HMB administration during resistance training, only 2 papers are full manuscripts appearing in peer reviewed journals. The remaining 8 papers are published as abstracts only, making it difficult to critically review the research. There is clearly a need for more tightly controlled, longer duration studies to verify if HMB enhances strength and muscular hypertrophy development associated with resistance training across a range of groups, including resistance trained individuals.

Beta-hydroxy beta-methylbutyrate (HMB) supplementation does not influence the urinary testosterone: epitestosterone ratio in healthy males

Six healthy, recreationally active, males undertook two weeks supplementation with beta-Hydroxy beta-Methylbutyrate (HMB). Supplementation was in capsule form with 3 g consumed each day in three even doses of 1 g at main meals. Mid stream urine samples were collected prior to, as well as, after one and two weeks of supplementation and subsequently analysed for testosterone and epitestosterone. The testosterone: epitestosterone ratio was not affected by 2 weeks of HMB supplementation (mean +/- SD baseline 1.02 +/- 0.68; week one 0.98 +/- 0.61; week two 0.92 +/- 0.62). Our results support the claim that supplementation with HMB at the doses recommended will not influence the urinary testosterone: epitestosterone ratio and thus not breach doping policies of the International Olympic Committee for exogenous testosterone or precursor administration.

Pancreatic enhancement and pulse sequence analysis using low-dose mangafodipir trisodium

OBJECTIVE

The purpose of this study was to evaluate pancreatic enhancement with low-dose mangafodipir trisodium (5 mumol/kg) using three different T1-weighted pulse sequences.

SUBJECTS AND METHODS

Fifteen patients, six of whom had proven focal pancreatic tumors, underwent T1-weighted gradient-recalled echo imaging, spin-echo imaging, and fat-suppressed spin-echo imaging before and 30 min after injection of 5 mumol/kg of mangafodipir trisodium. Region-of-interest measurements were obtained in the pancreas before and after contrast enhancement. Signal-to-noise ratios were calculated in all 15 patients. Contrast-to-noise ratios were calculated in the six patients with pancreatic tumors.

RESULTS

The signal-to-noise ratios of the pancreas increased after injection of mangafodipir trisodium on all three T1-weighted pulse sequences (p < .001). Enhanced fat-suppressed sequences (29 +/- 7.7) and gradient-recalled echo sequences (29 +/- 9.6) had the highest signal-to-noise ratios. Contrast-to-noise ratios between normal pancreatic tissue and pancreatic tumor also increased after contrast administration (p < .05) and were highest on the fat-suppressed (-9.6 +/- 4.0) pulse sequence.

CONCLUSION

Mangafodipir trisodium produced marked pancreatic enhancement at a dose of 5 mumol/kg for all three T1-weighted pulse sequences. The enhanced T1-weighted spin-echo fat-suppressed sequence showed the highest signal-to-noise and contrast-to-noise ratios.

MR imaging of pelvic lymph nodes in primary pelvic carcinoma with ultrasmall superparamagnetic iron oxide (Combidex): preliminary observations

The potential of ultrasmall superparamagnetic iron oxide (Combidex)-enhanced MRI of pelvic lymph nodes in patients with primary pelvic carcinoma is evaluated. Fifteen histologically classified lymph nodes in six patients with known primary pelvic cancer (four prostate; one rectum; one uterus) were evaluated with T2-weighted fast spin-echo (FSE) and T2*-weighted gradient-echo (GRE) MRI at 1.5T 12 to 48 hours after intravenous administration of Combidex at a dose of 1.7 mg Fe/kg. Quantitative image evaluation was performed by comparing signal intensity of individual nodes on pre- and postcontrast images. All patients proceeded to pelvic lymph-node biopsy or surgical dissection, where six were found to be benign and nine were malignant. Of the 15 lymph nodes, four nodes showed a decrease in signal intensity. Of these, three, in which signal loss was homogenous were benign, and one, in which the signal-intensity decrease was heterogeneous, was malignant (micrometastases). No signal change was noted in 11 of 15 lymph nodes of which three were benign (inflammatory) and eight were malignant. Combidex is a promising MR contrast agent for evaluating pelvic lymph nodes. Our preliminary observations suggest that the agent is most useful for classifying normal lymph nodes.

Mn-DPDP enhanced MR imaging of the liver: analysis of pulse sequence performance

AIM

To compare liver enhancement and lesion-liver contrast on T1-weighted (T1W) gradient recalled echo (GRE), spin-echo (SE) and fat-suppressed SE (FS-SE) pulse sequences at Manganese-DPDP (Mn-DPDP) enhanced magnetic resonance (MR) imaging of the liver. PATIENTS AND METHODS. Twenty-one patients with known liver lesions were administered 5 mumol/kg of Mn-DPDP. TIW GRE (78/2.3/80 degrees), SE and F-SE (300/12) images were obtained before and 15 min after Mn-DPDP. Signal/noise ratio (SNR) and lesion-liver contrast/noise ratio (CNR) were calculated for each pulse sequence.

RESULTS

Liver SNR (n = 21) and lesion-liver CNR (n = 10) increased significantly after Mn-DPDP on all three pulse sequences (P < 0.0001). Liver SNR was highest on the FS-SE and GRE pulse sequences (FS-SE = 43.8, GRE = 38.4, SE = 29.2). Lesion-liver CNR was highest on the FS-SE pulse sequence (FS-SE = -29.3, SE = -23.2, GRE = -19.8), which was significantly higher than the GRE pulse sequence (P < 0.05).

CONCLUSION

The T1-weighted fat-suppressed SE (FS-SE) pulse sequence provides highest liver enhancement and lesion-liver contrast and is recommended for Mn-DPDP enhanced MR imaging.