A species-level phylogeny of all extant and late Quaternary extinct mammals using a novel heuristic-hierarchical Bayesian approach

Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes

Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.

The evolution of same-sex sexual behaviour in mammals

Same-sex sexual behaviour has attracted the attention of many scientists working in disparate areas, from sociology and psychology to behavioural and evolutionary biology. Since it does not contribute directly to reproduction, same-sex sexual behaviour is considered an evolutionary conundrum. Here, using phylogenetic analyses, we explore the evolution of same-sex sexual behaviour in mammals. According to currently available data, this behaviour is not randomly distributed across mammal lineages, but tends to be particularly prevalent in some clades, especially primates. Ancestral reconstruction suggests that same-sex sexual behaviour may have evolved multiple times, with its appearance being a recent phenomenon in most mammalian lineages. Our phylogenetically informed analyses testing for associations between same-sex sexual behaviour and other species characteristics suggest that it may play an adaptive role in maintaining social relationships and mitigating conflict.

Marsupial position on life-history continua and the potential contribution of life-history traits to population growth

Previous studies have suggested that mammal life history varies along the fast-slow continuum and that, in eutherians, this continuum is linked to variation in the potential contribution of survival and reproduction to population growth rate (λ). Fast eutherians mature early, have large litters and short lifespans, and exhibit high potential contribution of age at first reproduction and fertility to λ, while slow eutherians show high potential contribution of survival to λ. However, marsupials have typically been overlooked in comparative tests of mammalian life-history evolution. Here, we tested whether the eutherian life-history pattern extends to marsupials, and show that marsupial life-history trade-offs are organized along two major axes: (i) the reproductive output and dispersion axis, and (ii) the fast-slow continuum, with an additional association between adult survival and body mass. Life-history traits that potentially drive changes in λ are similar in eutherians and marsupials with slow life histories, but differ in fast marsupials; age at first reproduction is the most important trait contributing to λ and fertility contributes little. Marsupials have slower life histories than eutherians, and differences between these clades may derive from their contrasting reproductive modes; marsupials have slower development, growth and metabolism than eutherians of equivalent size.

What is a mammalian omnivore? Insights into terrestrial mammalian diet diversity, body mass and evolution

Mammalian omnivores are a broad group of species that are often treated uniformly in ecological studies. Here, we incorporate omnivorous dietary differences to investigate previously found mammalian macroevolutionary and macroecological trends. We investigate the frequency with which vertebrate prey, invertebrate prey, fibrous plant material and non-fibrous plant material co-occur in the diets of terrestrial mammals. We quantify the body size distributions and phylogenetic signal of different omnivorous diets and use multistate reversible jump Markov chain Monte Carlo methods to assess the transition rates between diets on the mammalian phylogenetic tree. We find omnivores that consume all four food types are relatively rare, as most omnivores consume only invertebrate prey and non-fibrous plants. In addition, omnivores that only consume invertebrate prey, many of which are from Rodentia, are on average smaller than omnivores that incorporate vertebrate prey. Our transition models have high rates from invertivorous omnivory to herbivory, and from vertivory to prey mixing and ultimately invertivory. We suggest prey type is an important aspect of omnivore macroevolution and macroecology, as it is correlated with body mass, evolutionary history and diet-related evolutionary transition rates. Future work should avoid lumping omnivores into one category given the ecological variety of omnivore diets and their strong evolutionary influence.

The EDGE2 protocol: Advancing the prioritisation of Evolutionarily Distinct and Globally Endangered species for practical conservation action

The conservation of evolutionary history has been linked to increased benefits for humanity and can be captured by phylogenetic diversity (PD). The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to prioritise threatened species for practical conservation that embody large amounts of evolutionary history. While there have been important research advances since 2007, they have not been adopted in practice because of a lack of consensus in the conservation community. Here, building from an interdisciplinary workshop to update the existing EDGE approach, we present an "EDGE2" protocol that draws on a decade of research and innovation to develop an improved, consistent methodology for prioritising species conservation efforts. Key advances include methods for dealing with uncertainty and accounting for the extinction risk of closely related species. We describe EDGE2 in terms of distinct components to facilitate future revisions to its constituent parts without needing to reconsider the whole. We illustrate EDGE2 by applying it to the world's mammals. As we approach a crossroads for global biodiversity policy, this Consensus View shows how collaboration between academic and applied conservation biologists can guide effective and practical priority-setting to conserve biodiversity.

Thermal adaptation of pelage in desert rodents balances cooling and insulation

Phenotypic convergence across distantly related taxa can be driven by similar selective pressures from the environment or intrinsic constraints. The roles of these processes on physiological strategies, such as homeothermy, are poorly understood. We studied the evolution of thermal properties of mammalian pelage in a diverse community of rodents inhabiting the Mojave Desert, USA. We used a heat flux device to measure the thermal insulation of museum specimens and determined whether thermal properties were associated with habitat preferences while assessing phylogenetic dependence. Species that prefer arid habitats exhibited lower conductivity and thinner pelage relative to species with other habitat preferences. Despite being thinner, the pelage of arid species exhibited comparable insulation to the pelage of the other species due to its lower conductivity. Thus, arid species have insulative pelage while simultaneously benefitting from thin pelage that promotes convective cooling. We found no evidence of intrinsic constraints or phylogenetic dependence, indicating pelage readily evolves to environmental pressures. Thermoregulatory simulations demonstrated that arid specialists reduced energetic costs required for homeothermy by 14.5% by evolving lower conductivity, providing support for adaptive evolution of pelage. Our study indicates that selection for lower energetic requirements of homeothermy has shaped evolution of pelage thermal properties.

Teeth, prenatal growth rates, and the evolution of human-like pregnancy in later Homo

Evidence of how gestational parameters evolved is essential to understanding this fundamental stage of human life. Until now, these data seemed elusive given the skeletal bias of the fossil record. We demonstrate that dentition provides a window into the life of neonates. Teeth begin to form in utero and are intimately associated with gestational development. We measured the molar dentition for 608 catarrhine primates and collected data on prenatal growth rate (PGR) and endocranial volume (ECV) for 19 primate genera from the literature. We found that PGR and ECV are highly correlated (R² = 0.93, P < 0.001). Additionally, we demonstrated that molar proportions are significantly correlated with PGR (P = 0.004) and log-transformed ECV (P = 0.001). From these correlations, we developed two methods for reconstructing PGR in the fossil record, one using ECV and one using molar proportions. Dental proportions reconstruct hominid ECV (R² = 0.81, P < 0.001), a result that can be extrapolated to PGR. As teeth dominate fossil assemblages, our findings greatly expand our ability to investigate life history in the fossil record. Fossil ECVs and dental measurements from 13 hominid species both support significantly increasing PGR throughout the terminal Miocene and Plio-Pleistocene, reflecting known evolutionary changes. Together with pelvic and endocranial morphology, reconstructed PGRs indicate the need for increasing maternal energetics during pregnancy over the last 6 million years, reaching a human-like PGR (i.e., more similar to humans than to other extant apes) and ECV in later Homo less than 1 million years ago.

Phylogenetic and functional clustering illustrate the roles of adaptive radiation and dispersal filtering in jointly shaping late-Quaternary mammal assemblages on oceanic islands

Islands frequently harbour unique assemblages of species, yet their ecological roles and differences are largely ignored in island biogeography studies. Here, we examine eco-evolutionary processes structuring mammal assemblages on oceanic islands worldwide, including all extant and extinct late-Quaternary mammal species. We find island mammal assemblages tend to be phylogenetically clustered (share more recent evolutionary histories), with clustering increasing with island area and isolation. We also observe that mammal assemblages often tend to be functionally clustered (share similar traits), but the strength of clustering is weak and generally independent from island area or isolation. These findings indicate the important roles of in situ speciation and dispersal filtering in shaping island mammal assemblages under pre-anthropogenic conditions, notably through adaptive radiation of a few clades (e.g. bats, with generally high dispersal abilities). Our study demonstrates that considering the functional and phylogenetic axes of diversity can better reveal the eco-evolutionary processes of island community assembly.

Evolution of the bovid cranium: morphological diversification under allometric constraint

The role of environmental selection in generating novel morphology is often taken for granted, and morphology is generally assumed to be adaptive. Bovids (antelopes and relatives) are widely differentiated in their dietary and climatic preferences, and presumably their cranial morphologies are the result of adaptation to different environmental pressures. In order to test these ideas, we performed 3D geometric morphometric analyses on 141 crania representing 96 bovid species in order to assess the influence of both extrinsic (e.g. diet, habitat) and intrinsic (size, modularity) factors on cranial shape. Surprisingly, we find that bovid crania are highly clumped in morphospace, with a large number of ecologically disparate species occupying a very similar range of morphology clustered around the mean shape. Differences in shape among dietary, habitat, and net primary productivity categories are largely non-significant, but we found a strong interaction between size and diet in explaining shape. We furthermore found no evidence for modularity having played a role in the generation of cranial differences across the bovid tree. Rather, the distribution of bovid cranial morphospace appears to be mainly the result of constraints imposed by a deeply conserved size-shape allometry, and dietary diversification the result of adaptation of existing allometric pathways.

A cross-species framework to identify vocal learning abilities in mammals

Vocal production learning (VPL) is the experience-driven ability to produce novel vocal signals through imitation or modification of existing vocalizations. A parallel strand of research investigates acoustic allometry, namely how information about body size is conveyed by acoustic signals. Recently, we proposed that deviation from acoustic allometry principles as a result of sexual selection may have been an intermediate step towards the evolution of vocal learning abilities in mammals. Adopting a more hypothesis-neutral stance, here we perform phylogenetic regressions and other analyses further testing a potential link between VPL and being an allometric outlier. We find that multiple species belonging to VPL clades deviate from allometric scaling but in the opposite direction to that expected from size exaggeration mechanisms. In other words, our correlational approach finds an association between VPL and being an allometric outlier. However, the direction of this association, contra our original hypothesis, may indicate that VPL did not necessarily emerge via sexual selection for size exaggeration: VPL clades show higher vocalization frequencies than expected. In addition, our approach allows us to identify species with potential for VPL abilities: we hypothesize that those outliers from acoustic allometry lying above the regression line may be VPL species. Our results may help better understand the cross-species diversity, variability and aetiology of VPL, which among other things is a key underpinning of speech in our species. This article is part of the theme issue 'Voice modulation: from origin and mechanism to social impact (Part II)'.

Identifying co-phylogenetic hotspots for zoonotic disease

The incidence of zoonotic diseases is increasing worldwide, which makes identifying parasites likely to become zoonotic and hosts likely to harbour zoonotic parasites a critical concern. Prior work indicates that there is a higher risk of zoonotic spillover accruing from closely related hosts and from hosts that are infected with a high phylogenetic diversity of parasites. This suggests that host and parasite evolutionary history may be important drivers of spillover, but identifying whether host-parasite associations are more strongly structured by the host, parasite or both requires co-phylogenetic analyses that combine host-parasite association data with host and parasite phylogenies. Here, we use host-parasite datasets containing associations between helminth taxa and free-range mammals in combination with phylogenetic models to explore whether host, parasite, or both host and parasite evolutionary history influences host-parasite associations. We find that host phylogenetic history is most important for driving patterns of helminth-mammal association, indicating that zoonoses are most likely to come from a host's close relatives. More broadly, our results suggest that co-phylogenetic analyses across broad taxonomic scales can provide a novel perspective for surveying potential emerging infectious diseases. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Killing conspecific adults in mammals

Mammals kill both conspecific infants and adults. Whereas infanticide has been profusely studied, the killing of non-infants (adulticide) has seldom attracted the attention of researchers. Mammals kill conspecific adults by at least four, non-exclusive reasons: during intrasexual aggression for mating opportunities, to defend valuable resources, to protect their progeny and to prey upon conspecifics. In this study, we test which reason is most likely to explain male and female adulticide in mammals. For this, we recorded the presence of adulticide, the ecological and behavioural traits, and the phylogenetic relationship for more than 1000 species. Adulticide has been recorded in over 350 species from the most important Mammalian clades. Male adulticide was phylogenetically correlated with the presence of size dimorphism and intrasexually selected weapons. Female adulticide was phylogenetically associated with the occurrence of infanticide. These results indicate that the evolutionary pathways underlying the evolution of adulticide differ between sexes in mammals. Whereas males commit adulticide to increase breeding opportunities and to compete with other males for mating, females commit adulticide mainly to defend offspring from infanticidal conspecifics.

Quantifying the link between craniodental morphology and diet in the Soricidae using geometric morphometrics

Dietary adaptations have often been associated with heightened taxonomic diversity. Yet, one of the most species-rich mammalian families, the Soricidae, is often considered to be ecologically and morphologically relatively homogenous. Here, we use geometric morphometrics to capture skull and dentary morphology in a broad sample of shrew species and test the hypothesis that morphological variation among shrew species reflects adaptations to food hardness. Our analyses demonstrate that morphology is associated with dietary ecology. Species that consume hard food items are larger and have specific morphological adaptions including an anteroposteriorly expanded parietal, an anteroposteriorly short and dorsoventrally tall rostrum, a mediolaterally wide palate, buccolingually wide cheek teeth, a large coronoid process and a dorsoventrally short jaw joint. The masseter muscle does not appear to play an important role in the strong bite force of shrews and the dentary is a better indicator of ecology than the skull. Our phylogenetic flexible discriminant function analysis suggests that the evolutionary history of shrews has shaped their morphology, canalizing dietary adaptations and enabling functional equivalence whereby different morphologies achieve similar dietary performances. Our work makes possible future studies of niche partitioning among sympatric species as well as the investigation of the diet of extinct soricids.

The evolution of mammalian brain size

Relative brain size has long been considered a reflection of cognitive capacities and has played a fundamental role in developing core theories in the life sciences. Yet, the notion that relative brain size validly represents selection on brain size relies on the untested assumptions that brain-body allometry is restrained to a stable scaling relationship across species and that any deviation from this slope is due to selection on brain size. Using the largest fossil and extant dataset yet assembled, we find that shifts in allometric slope underpin major transitions in mammalian evolution and are often primarily characterized by marked changes in body size. Our results reveal that the largest-brained mammals achieved large relative brain sizes by highly divergent paths. These findings prompt a reevaluation of the traditional paradigm of relative brain size and open new opportunities to improve our understanding of the genetic and developmental mechanisms that influence brain size.

The evolution of critical thermal limits of life on Earth

Understanding how species’ thermal limits have evolved across the tree of life is central to predicting species’ responses to climate change. Here, using experimentally-derived estimates of thermal tolerance limits for over 2000 terrestrial and aquatic species, we show that most of the variation in thermal tolerance can be attributed to a combination of adaptation to current climatic extremes, and the existence of evolutionary ‘attractors’ that reflect either boundaries or optima in thermal tolerance limits. Our results also reveal deep-time climate legacies in ectotherms, whereby orders that originated in cold paleoclimates have presently lower cold tolerance limits than those with warm thermal ancestry. Conversely, heat tolerance appears unrelated to climate ancestry. Cold tolerance has evolved more quickly than heat tolerance in endotherms and ectotherms. If the past tempo of evolution for upper thermal limits continues, adaptive responses in thermal limits will have limited potential to rescue the large majority of species given the unprecedented rate of contemporary climate change.

Historical climate adaptation can give insight into the potential for adaptation to contemporary changing climates. Here Bennett et al. investigate thermal tolerance evolution across much of the tree of life and find different effects of ancestral climate on the subsequent evolution of ectotherms vs. endotherms.

Functional traits of the world's late Quaternary large-bodied avian and mammalian herbivores

Prehistoric and recent extinctions of large-bodied terrestrial herbivores had significant and lasting impacts on Earth's ecosystems due to the loss of their distinct trait combinations. The world's surviving large-bodied avian and mammalian herbivores remain among the most threatened taxa. As such, a greater understanding of the ecological impacts of large herbivore losses is increasingly important. However, comprehensive and ecologically-relevant trait datasets for extinct and extant herbivores are lacking. Here, we present HerbiTraits, a comprehensive functional trait dataset for all late Quaternary terrestrial avian and mammalian herbivores ≥10 kg (545 species). HerbiTraits includes key traits that influence how herbivores interact with ecosystems, namely body mass, diet, fermentation type, habitat use, and limb morphology. Trait data were compiled from 557 sources and comprise the best available knowledge on late Quaternary large-bodied herbivores. HerbiTraits provides a tool for the analysis of herbivore functional diversity both past and present and its effects on Earth's ecosystems.

Effects of land use, habitat characteristics, and small mammal community composition on Leptospira prevalence in northeast Madagascar

Human activities can increase or decrease risks of acquiring a zoonotic disease, notably by affecting the composition and abundance of hosts. This study investigated the links between land use and infectious disease risk in northeast Madagascar, where human subsistence activities and population growth are encroaching on native habitats and the associated biota. We collected new data on pathogenic Leptospira, which are bacteria maintained in small mammal reservoirs. Transmission can occur through close contact, but most frequently through indirect contact with water contaminated by the urine of infected hosts. The probability of infection and prevalence was compared across a gradient of natural moist evergreen forest, nearby forest fragments, flooded rice and other types of agricultural fields, and in homes in a rural village. Using these data, we tested specific hypotheses for how land use alters ecological communities and influences disease transmission. The relative abundance and proportion of exotic species was highest in the anthropogenic habitats, while the relative abundance of native species was highest in the forested habitats. Prevalence of Leptospira was significantly higher in introduced compared to endemic species. Lastly, the probability of infection with Leptospira was highest in introduced small mammal species, and lower in forest fragments compared to other habitat types. Our results highlight how human land use affects the small mammal community composition and in turn disease dynamics. Introduced species likely transmit Leptospira to native species where they co-occur, and may displace the Leptospira species naturally occurring in Madagascar. The frequent spatial overlap of people and introduced species likely also has consequences for public health.

Many neglected tropical diseases have reservoirs in wildlife. The effects of human activities on wildlife include changes in species abundance, community composition, and the transmission dynamics of parasites. Introduced species, especially black rats (Rattus rattus) are known to transmit zoonotic diseases among wildlife species and people. Leptospira, a water-borne bacterium that infects wildlife and people, is an important pathogen in the tropics, and in Madagascar, multiple strains and hosts have been identified. We tested how land use gradients in a forest-frontier agricultural system affect the composition of small mammal communities, and in turn the prevalence of Leptospira. We investigated 11 species of small mammals, including native rodents and tenrecs, as well as introduced rodents and shrews, in old growth forest, forest fragments, agricultural fields, and in a village. Leptospira prevalence and infection risk were highest in introduced species compared to native species and lower in forest fragments. The results highlight how the introduction of non-native species affects the variation in disease prevalence in small mammals, with potential consequences for spill-over to people.

Historical climatic instability predicts the inverse latitudinal pattern in speciation rate of modern mammalian biota

Evolutionary rate explanations for latitudinal diversity gradients predict faster speciation and diversification rates in richer, older and more stable tropical regions (climatic stability hypothesis). Numerous modern lineages have emerged in high latitudes, however, suggesting that climatic oscillations can drive population divergence, at least among extratropical species (glacial refugia hypothesis). This conflicting evidence suggests that geographical patterns of evolutionary rates are more complicated than previously thought. Here, we reconstructed the complex evolutionary dynamics of a comprehensive data set of modern mammals, both terrestrial and marine. We performed global and regional regression analyses to investigate how climatic instability could have indirectly influenced contemporary diversity gradients through its effects on evolutionary rates. In particular, we explored global and regional patterns of the relationships between species richness and assemblage-level evolutionary rates and between evolutionary rates and climatic instability. We found an inverse relationship between evolutionary rates and species richness, especially in the terrestrial domain. Additionally, climatic instability was strongly associated with the highest evolutionary rates at high terrestrial latitudes, supporting the glacial refugia hypothesis there. At low latitudes, evolutionary rates were unrelated to climatic stability. The inverse relationship between evolutionary rates and the modern latitudinal diversity gradient casts doubt on the idea that higher evolutionary rates in the tropics underlie the current diversity patterns of modern mammals. Alternatively, the longer time spans for diversity to accumulate in the older and more stable tropics (and not high diversification rates) may explain the latitudinal diversity gradient.

Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation

The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.

Investigating Biotic Interactions in Deep Time

Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.

Herbivores at the highest risk of extinction among mammals, birds, and reptiles

As a result of their extensive home ranges and slow population growth rates, predators have often been perceived to suffer higher risks of extinction than other trophic groups. Our study challenges this extinction-risk paradigm by quantitatively comparing patterns of extinction risk across different trophic groups of mammals, birds, and reptiles. We found that trophic level and body size were significant factors that influenced extinction risk in all taxa. At multiple spatial and temporal scales, herbivores, especially herbivorous reptiles and large-bodied herbivores, consistently have the highest proportions of threatened species. This observed elevated extinction risk for herbivores is ecologically consequential, given the important roles that herbivores are known to play in controlling ecosystem function.

Climate Change and Thermoregulatory Consequences of Activity Time in Mammals

Activity times structure the thermal environments experienced by organisms. In mammals, species shift from being nocturnal to diurnal and vice versa, but the thermal consequences of variable activity patterns remain largely unexplored. Here we used theoretical thermoregulatory polygons bounded by estimates of basal metabolic rates (BMR), maximum metabolic rates (MMR), and thermal conductance (C) in small mammals to explore the metabolic consequences of exposure to global-scale daytime and nighttime temperatures. Model predictions indicated higher metabolic scope for activity for nocturnal species at low latitudes and that reduced minimum C and larger body size increased the geographic range in which nocturnality was advantageous. Consistent with predictions, within rodents nocturnal species have low C. However, nocturnal mammals tend to be smaller than diurnal species, likely reflecting the importance of additional factors driving body size. Projections of warming impacts on small mammals suggest that diurnal species could lose habitable space globally. Conversely, warming could lift cool temperature constraints on nocturnal species and increase habitable space, suggesting that a shift toward nocturnal niches might be favored in a warming world. Taken together, these findings demonstrate the importance of energetic considerations for endotherms in managing global change impacts on nocturnal and diurnal species.

Evolutionary history and past climate change shape the distribution of genetic diversity in terrestrial mammals

Knowledge of global patterns of biodiversity, ranging from intraspecific genetic diversity (GD) to taxonomic and phylogenetic diversity, is essential for identifying and conserving the processes that shape the distribution of life. Yet, global patterns of GD and its drivers remain elusive. Here we assess existing biodiversity theories to explain and predict the global distribution of GD in terrestrial mammal assemblages. We find a strong positive covariation between GD and interspecific diversity, with evolutionary time, reflected in phylogenetic diversity, being the best predictor of GD. Moreover, we reveal the negative effect of past rapid climate change and the positive effect of inter-annual precipitation variability in shaping GD. Our models, explaining almost half of the variation in GD globally, uncover the importance of deep evolutionary history and past climate stability in accumulating and maintaining intraspecific diversity, and constitute a crucial step towards reducing the Wallacean shortfall for an important dimension of biodiversity.

The drivers of genetic diversity (GD) are poorly understood at the global scale. Here the authors show, for terrestrial mammals, that within-species GD covaries with phylogenetic diversity and is higher in locations with more stable past climates. They also interpolate GD for data-poor locations such as the tropics.

Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past

Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here, we develop a robust probabilistic approach for estimating diversity through time curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia-a species-poor group of old frog clades often found in temperate regions-formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade-clade competitive effects or the effect of species richness on phenotypic divergence.

Palm fruit colours are linked to the broad-scale distribution and diversification of primate colour vision systems

A long-standing hypothesis in ecology and evolution is that trichromatic colour vision (the ability to distinguish red from green) in frugivorous primates has evolved as an adaptation to detect conspicuous (reddish) fruits. This could provide a competitive advantage over dichromatic frugivores which cannot distinguish reddish colours from a background of green foliage. Here, we test whether the origin, distribution and diversity of trichromatic primates is positively associated with the availability of conspicuous palm fruits, i.e. keystone fruit resources for tropical frugivores. We combine global data of colour vision, distribution and phylogenetic data for more than 400 primate species with fruit colour data for more than 1700 palm species, and reveal that species richness of trichromatic primates increases with the proportion of palm species that have conspicuous fruits, especially in subtropical African forests. By contrast, species richness of trichromats in Asia and the Americas is not positively associated with conspicuous palm fruit colours. Macroevolutionary analyses further indicate rapid and synchronous radiations of trichromats and conspicuous palms on the African mainland starting 10 Ma. These results suggest that the distribution and diversification of African trichromatic primates is strongly linked to the relative availability of conspicuous (versus non-conspicuous) palm fruits, and that interactions between primates and palms are related to the coevolutionary dynamics of primate colour vision systems and palm fruit colours.

Geographically divergent evolutionary and ecological legacies shape mammal biodiversity in the global tropics and subtropics

Studies of the factors governing global patterns of biodiversity are key to predicting community responses to ongoing and future abiotic and biotic changes. Although most research has focused on present-day climate, a growing body of evidence indicates that modern ecological communities may be significantly shaped by paleoclimatic change and past anthropogenic factors. However, the generality of this pattern is unknown, as global analyses are lacking. Here we quantify the phylogenetic and functional trait structure of 515 tropical and subtropical large mammal communities and predict their structure from past and present climatic and anthropogenic factors. We find that the effects of Quaternary paleoclimatic change are strongest in the Afrotropics, with communities in the Indomalayan realm showing mixed effects of modern climate and paleoclimate. Malagasy communities are poorly predicted by any single factor, likely due to the atypical history of the island compared with continental regions. Neotropical communities are mainly codetermined by modern climate and prehistoric and historical human impacts. Overall, our results indicate that the factors governing tropical and subtropical mammalian biodiversity are complex, with the importance of past and present factors varying based on the divergent histories of the world's biogeographic realms and their native biotas. Consideration of the evolutionary and ecological legacies of both the recent and ancient past are key to understanding the forces shaping global patterns of present-day biodiversity and its response to ongoing and future abiotic and biotic changes in the 21st century.

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.

Adaptation, phylogeny, and covariance in milk macronutrient composition

Background

Milk is a complicated chemical mixture often studied through macronutrient concentrations of fat, protein, and sugar. There is a long-standing natural history tradition describing interspecific diversity in these concentrations. However, recent work has shown little influence of ecological or life history variables on them, aside from maternal diet effects, along with a strong phylogenetic signal.

Methods

I used multivariate phylogenetic comparative methods to revisit the ecological and life history correlates of milk macronutrient composition and elaborate on the nature of the phylogenetic signal using the phylogenetic mixed model. I also identified clades with distinctive milks through nonparametric tests (KSI) and PhylogeneticEM evolutionary modeling.

Results

In addition to the previously reported diet effects, I found increasingly aquatic mammals have milk that this is lower in sugar and higher in fat. Phylogenteic heritabilities for each concentration were high and phylogenetic correlations were moderate to strong indicating coevolution among the concentrations. Primates and pinnipeds had the most outstanding milks according to KSI and PhylogeneticEM, with perissodactyls and marsupials as other noteworthy clades with distinct selection regimes.

Discussion

Mammalian milks are diverse but often characteristic of certain higher taxa. This complicates identifying the ecological and life history correlates of milk composition using common phylogenetic comparative methods because those traits are also conservative and clade-specific. Novel methods, careful assessment of data quality and hypotheses, and a “phylogenetic natural history” perspective provide alternatives to these traditional tools.

Intraspecific male combat behaviour predicts morphology of cervical vertebrae in ruminant mammals

Cranial weapons of all shapes and sizes are common throughout the animal kingdom and are frequently accompanied by the evolution of additional traits that enhance the use of those weapons. Bovids (cattle, sheep, goats, antelope) and cervids (deer) within the mammal clade Ruminantia are particularly well known for their distinct and varied cranial appendages in the form of horns and antlers, which are used as weapons in intraspecific combat between males for access to mates. Combat in these species takes many forms, including head-on collisions (ramming); stabbing an opponent's head or body with horn tips (stabbing); rearing and clashing downwards with horns (fencing); or interlocking antlers or horns while vigorously pushing and twisting (wrestling). Some aspects of weapon and skull morphology have been linked to combat behaviours in bovid and cervid species, but the contribution of postcranial structures that support these weapons, such as the neck, has not been explored. To investigate the role of the neck in intraspecific combat, we quantified biomechanically relevant linear variables of the cervical vertebrae (C1-C7) from males and females of 55 ruminant species. We then used phylogenetic generalized least-squares regression to assess differences among species that display primarily ramming, stabbing, fencing and wrestling combat styles. In males, we found that wrestlers have longer vertebral centra and longer neural spines than rammers, stabbers or fencers, while rammers have shorter and wider centra and taller neural spine lever arms. These results suggest a supportive role for the cervical vertebrae in resisting forces generated by male-male combat in ruminant mammals and indicate that evolutionary forces influencing cranial weapons also play a role in shaping the supporting anatomical structures.

From low to high latitudes: changes in fatty acid desaturation in mammalian fat tissue suggest a thermoregulatory role

Background

Most fatty acids (FAs) making up the adipose tissue in mammals have a dietary origin and suffer little modification when they are stored. However, we propose that some of those FAs, specifically those that can be synthesised or modified by mammals, are also being influenced by thermal forces and used as part of the mechanism to regulate core body temperature. As FA desaturation increases, adipose tissues can reach colder temperatures without solidifying. The ability to cool the superficial fat tissues helps create a thermal gradient, which contributes to body heat loss reduction. Therefore, it is expected that animals exposed to colder environments will possess adipose tissues with higher proportions of desaturated FAs. Here, through a model selection approach that accounts for phylogeny, we investigate how the variation in FA desaturation in 54 mammalian species relates to the thermal proxies: latitude, physical environment (terrestrial, semi-aquatic and fully-aquatic) and hair density.

Results

The interaction between the environment (terrestrial, semi- or fully-aquatic) and the latitude in which the animals lived explained best the variation of FA desaturation in mammals. Aquatic mammals had higher FA desaturation compared to terrestrial mammals. Semi-aquatic mammals had significantly higher levels of desaturated FAs when living in higher latitudes whereas terrestrial and fully-aquatic mammals did not. To account for dietary influence, a double bond index was calculated including all FAs, and revealed no correlation with latitude in any of the groups.

Conclusions

We propose that FA modification is an important component of the thermoregulatory strategy, particularly in semi-aquatic mammals. Potentially this is because, like terrestrial mammals, they experience the greatest air temperature variations across latitudes, but they lack a thick fur coat and rely primarily on their blubber. Unlike fully-aquatic mammals, extremely thick blubber is not ideal for semi-aquatic mammals, as this is detrimental to their manoeuvrability on land. Therefore, the adipose tissue in semi-aquatic mammals plays a more important role in keeping warm, and the modification of FAs becomes crucial to withstand cold temperatures and maintain a pliable blubber.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1473-5) contains supplementary material, which is available to authorized users.

Evidence of strong stabilizing effects on the evolution of boreoeutherian (Mammalia) dental proportions

The dentition is an extremely important organ in mammals with variation in timing and sequence of eruption, crown morphology, and tooth size enabling a range of behavioral, dietary, and functional adaptations across the class. Within this suite of variable mammalian dental phenotypes, relative sizes of teeth reflect variation in the underlying genetic and developmental mechanisms. Two ratios of postcanine tooth lengths capture the relative size of premolars to molars (premolar-molar module, PMM), and among the three molars (molar module component, MMC), and are known to be heritable, independent of body size, and to vary significantly across primates. Here, we explore how these dental traits vary across mammals more broadly, focusing on terrestrial taxa in the clade of Boreoeutheria (Euarchontoglires and Laurasiatheria). We measured the postcanine teeth of N = 1,523 boreoeutherian mammals spanning six orders, 14 families, 36 genera, and 49 species to test hypotheses about associations between dental proportions and phylogenetic relatedness, diet, and life history in mammals. Boreoeutherian postcanine dental proportions sampled in this study carry conserved phylogenetic signal and are not associated with variation in diet. The incorporation of paleontological data provides further evidence that dental proportions may be slower to change than is dietary specialization. These results have implications for our understanding of dental variation and dietary adaptation in mammals.

Global synergies and trade-offs between multiple dimensions of biodiversity and ecosystem services

Ensuring the persistence of biodiversity and ecosystem services represents a global challenge that need to be addressed with high urgency. Global priority areas can only be identified by means of an integrated prioritization approach that would not only preserve species numbers and ecosystem services, but also the evolutionary and functional components of diversity. In this study we combine global datasets on the distribution of mammals and birds with species traits and phylogenetic data and we identify conservation priorities for taxonomic, functional and phylogenetic diversity, as well as for three ecosystem services, including potential for carbon sequestration, pollination potential and groundwater recharge. We show that, when priority areas are identified based only on individual, e.g. functional diversity, or any combination of the three biodiversity components, these areas do not allow a sufficient protection of the three ecosystem services. However, an integrated approach whereby prioritization is based on all biodiversity components and ecosystem services would allow to identify areas that maximize protection of all ecosystem services with a minimal loss in biodiversity coverage. Our results highlight the need for an integrated conservation planning framework in order to optimally allocate resources and achieve the long-term preservation of the multiple dimensions of biodiversity and ecosystems services.

Wing morphology predicts geographic range size in vespertilionid bats

Why some species are widespread across continents while others are confined geographically remains an open question in ecology and biogeography. Previous research has attempted to explain interspecific variation in geographic range size based on differences in dispersal ability. However, the relationship between dispersal ability and geographic range size remains uncertain, particularly in mammals. The goal of this study is to test whether geographic range size can be predicted by dispersal capacity among vespertilionid bats within a phylogenetic comparative framework. We integrated a large dataset on range area, longitudinal extent, wing morphology (a proxy for dispersal ability), migratory habit, and biogeographic realm across 126 vespertilionid bat species. We used phylogenetic regressions to disentangle the associations between these predictor factors and species range size while controlling for the effects of migration and biogeographic realm. Our analyses revealed that bat species with higher wing loading exhibit larger distribution ranges than those with lower wing loading, and that the size of geographic ranges was associated with wing aspect ratio in bats. These results highlight the relationship between wing morphology and range size in flying mammals, and suggest a role of dispersal capacity in shaping species’ geographic distributions.

The ecomorphology of southern African rodent incisors: Potential applications to the hominin fossil record

The taxonomic identification of mammalian fauna within fossil assemblages is a well-established component of paleoenvironmental reconstructions. However, many fragmentary specimens recovered from fossil sites are often disregarded as they can be difficult to identify with the precision required for taxonomic methods. For this reason, the large numbers of isolated rodent incisors that are often recovered from hominin fossil bearing sites are generally regarded as offering little interpretive value. Ecomorphological analysis, often referred to as a “taxon-free” method, can potentially circumvent this problem by focusing on the adaptive, rather than the taxonomic significance of rodent incisor morphology. Here, we determine if the morphology of the upper incisors of modern southern African rodents reflects dietary behavior using discriminant function analysis. Our model suggests that a strong ecomorphological signal exists in our modern sample and we apply these results to two samples of isolated incisors from the hominin fossil bearing sites, Sterkfontein and Swartkrans.

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.

Phylogeny matters: revisiting 'a comparison of bats and rodents as reservoirs of zoonotic viruses'

Diseases emerging from wildlife have been the source of many major human outbreaks. Predicting key sources of these outbreaks requires an understanding of the factors that explain pathogen diversity in reservoir species. Comparative methods are powerful tools for understanding variation in pathogen diversity and rely on correcting for phylogenetic relatedness among reservoir species. We reanalysed a previously published dataset, examining the relative effects of species' traits on patterns of viral diversity in bats and rodents. We expanded on prior work by using more highly resolved phylogenies for bats and rodents and incorporating a phylogenetically controlled principal components analysis. For rodents, sympatry and torpor use were important predictors of viral richness and, as previously reported, phylogeny had minimal impact in models. For bats, in contrast to prior work, we find that phylogeny does have an effect in models. Patterns of viral diversity in bats were related to geographical distribution (i.e. latitude and range size) and life history (i.e. lifespan, body size and birthing frequency). However, the effects of these predictors were marginal relative to citation count, emphasizing that the ability to accurately assess reservoir status largely depends on sampling effort and highlighting the need for additional data in future comparative studies.

Metabolic asymmetry and the global diversity of marine predators

Species richness of marine mammals and birds is highest in cold, temperate seas—a conspicuous exception to the general latitudinal gradient of decreasing diversity from the tropics to the poles. We compiled a comprehensive dataset for 998 species of sharks, fish, reptiles, mammals, and birds to identify and quantify inverse latitudinal gradients in diversity, and derived a theory to explain these patterns. We found that richness, phylogenetic diversity, and abundance of marine predators diverge systematically with thermoregulatory strategy and water temperature, reflecting metabolic differences between endotherms and ectotherms that drive trophic and competitive interactions. Spatial patterns of foraging support theoretical predictions, with total prey consumption by mammals increasing by a factor of 80 from the equator to the poles after controlling for productivity.

Evolutionary and ecological success is decoupled in mammals

AIM

To identify which factors distinguish ecologically successful mammalian clades (i.e., clades with a large combined range size) from less successful ones.

LOCATION

Global.

METHODS

We estimated the total range sizes for each individual mammalian subfamily and used phylogenetic regressions to identify the relative importance of factors related to colonization ability (body size and niche width) and adaptability (rate of evolution of body size and rate of evolution of climatic preference) in determining these ranges. We then estimated the importance of the same factors on the variation in diversification rate within mammals.

RESULTS

We found strong support for a link between total range size and traits related to colonization ability. In particular, we found larger total range sizes among clades containing larger bodied species and clades with wider climatic niche width, while we did not find support for any predictors related to adaptability being linked to total range size. We also found that traits related to increased range size were associated with reduced diversification rate.

MAIN CONCLUSIONS

Range size for mammalian clades is mainly predicted by colonization ability, suggesting that most clades are limited by dispersal rather than their ability to adapt to new environments. The most ecologically successful (i.e., most widespread) mammalian clades tend to possess traits that reduce geographical isolation among populations, but the same traits tend to decrease diversification rates. Our results unveil a decoupling between evolutionary and ecological success in mammals.

Evolutionary history predicts the response of tree species to forest loss: A case study in peninsular Spain

Evolutionary history can explain species resemblance to a large extent. Thus, if closely related species share combinations of traits that modulate their response to environmental changes, then phylogeny could predict species sensitivity to novel stressors such as increased levels of deforestation. To test this hypothesis, we used 66,949 plots (25-m-radius) of the Spanish National Forest Inventory and modelled the relationships between local (plot-level) stem density of 61 Holarctic tree species and forest canopy cover measured at local and landscape scales (concentric circles centred on the plots with radiuses of 1.6, 3.2 and 6.4 km, respectively). Then, we used the output model equations to estimate the probability of occurrence of the species as a function of forest canopy cover (i.e. response to forest loss), and quantified the phylogenetic signal in their responses using a molecular phylogeny. Most species showed a lower probability of occurrence when forest canopy cover in the plots (local scale) was low. However, the probability of occurrence of many species increased when forest canopy cover decreased across landscape scales. We detected a strong phylogenetic signal in species response to forest loss at local and small landscape (1.6 km) scales. However, phylogenetic signal was weak and non-significant at intermediate (3.2 km) and large (6.4 km) landscape scales. Our results suggest that phylogenetic information could be used to prioritize forested areas for conservation, since evolutionary history may largely determine species response to forest loss. As such, phylogenetically diverse forests might ensure contrasted responses to deforestation, and thus less abrupt reductions in the abundances of the constituent species.

Inferring Evolutionary Process From Neuroanatomical Data

Brain evolution has interested neuroanatomists for over a century. These interests often fall on how free the brain is to evolve independently of the body, how free brain regions are to evolve independently of each other, and how different environmental and ecological factors affect the brain over evolutionary time. But despite major advances in phylogenetic methods, comparative neuroanatomists have tended to limit their macroevolutionary toolbox to regression-based analyses and ignored the scope of evolutionary process-based models at their disposal. This Review summarizes the history of comparative neuroanatomy and highlights the pitfalls of the methodologies traditionally used. It provides an overview of evolutionary process-based modeling approaches for investigating univariate and multivariate data, as well as more sophisticated methods that incorporate hypotheses about biotic and abiotic pressures that may drive brain evolution. The benefits of evolutionary process-based models, and shortcomings of regression-based ones, are illustrated with widely used neuroanatomical data. Ultimately, the intent of this Review is to be a guide for subsuming macroevolutionary methods not typically used in comparative neuroanatomy, in order to improve our understanding of how the brain evolves.

Prioritizing phylogenetic diversity captures functional diversity unreliably

In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have assumed that maximizing phylogenetic diversity (PD) should indirectly capture FD, a hypothesis that we name the “phylogenetic gambit”. Here, we empirically test this gambit using data on ecologically relevant traits from >15,000 vertebrate species. Specifically, we estimate a measure of surrogacy of PD for FD. We find that maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain obscures the fact that in over one-third of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky conservation strategy.

An ongoing conservation question is if we can maintain functional diversity by optimizing for preservation of phylogenetic diversity. Here, Mazel et al. show that functional diversity increases with phylogenetic diversity in some clades but not others, and thus could be a risky conservation strategy.

Phylogenetic signal in tooth wear dietary niche proxies

In the absence of independent observational data, ecologists and paleoecologists use proxies for the Eltonian niches of species (i.e., the resource or dietary axes of the niche). Some dietary proxies exploit the fact that mammalian teeth experience wear during mastication, due to both tooth-on-tooth and food-on-tooth interactions. The distribution and types of wear detectible at micro- and macroscales are highly correlated with the resource preferences of individuals and, in turn, species. Because methods that quantify the distribution of tooth wear (i.e., analytical tooth wear methods) do so by direct observation of facets and marks on the teeth of individual animals, dietary inferences derived from them are thought to be independent of the clade to which individuals belong. However, an assumption of clade or phylogenetic independence when making species-level dietary inferences may be misleading if phylogenetic niche conservatism is widespread among mammals. Herein, we test for phylogenetic signal in data from numerous analytical tooth wear studies, incorporating macrowear (i.e., mesowear) and microwear (i.e., low-magnification microwear and dental microwear texture analysis). Using two measures of phylogenetic signal, heritability (H2) and Pagel's λ, we find that analytical tooth wear data are not independent of phylogeny and failing to account for such nonindependence leads to overestimation of discriminability among species with different dietary preferences. We suggest that morphological traits inherited from ancestral clades (e.g., tooth shape) influence the ways in which the teeth wear during mastication and constrain the foods individuals of a species can effectively exploit. We do not suggest that tooth wear is simply phylogeny in disguise; the tooth wear of individuals and species likely varies within some range that is set by morphological constraints. We therefore recommend the use of phylogenetic comparative methods in studies of mammalian tooth wear, whenever possible.