Mammal extinctions and the increasing isolation of humans on the tree of life

Global conservation status of the jawed vertebrate Tree of Life

Human-driven extinction threatens entire lineages across the Tree of Life. Here we assess the conservation status of jawed vertebrate evolutionary history, using three policy-relevant approaches. First, we calculate an index of threat to overall evolutionary history, showing that we expect to lose 86-150 billion years (11-19%) of jawed vertebrate evolutionary history over the next 50-500 years. Second, we rank jawed vertebrate species by their EDGE scores to identify the highest priorities for species-focused conservation of evolutionary history, finding that chondrichthyans, ray-finned fish and testudines rank highest of all jawed vertebrates. Third, we assess the conservation status of jawed vertebrate families. We found that species within monotypic families are more likely to be threatened and more likely to be in decline than other species. We provide a baseline for the status of families at risk of extinction to catalyse conservation action. This work continues a trend of highlighting neglected groups-such as testudines, crocodylians, amphibians and chondrichthyans-as conservation priorities from a phylogenetic perspective.

Biodiversity and Economy but Not Social Factors Predict Human Population Dynamics in South Africa

The ongoing exponential growth of human population poses a risk to sustainable development goals (SDGs). Unless we understand the drivers of this growth and inform policy development accordingly, SDGs would remain a dream. One of the old theories of population growth known as the Malthusian theory predicts that resource availability drives population growth until a certain time when population growth outrun resource availability, leading to all sort of crises summarized as Malthusian crisis. Although the link between economic growth and population has been widely investigated while testing the theory, little is known about environmental and social factors potentially driving population growth. Here, because of various crises of our time recalling the Malthusian crisis, we revisited the theory by fitting structural equation models to environmental, social and economic data collected over 30-year period in South Africa. None of the social variables tested predicts population growth. Instead, we found that biodiversity (species protection index) correlates positively with population growth. Biodiversity provides various resources through ecosystem goods and services to human, thus supporting population growth as predicted in the Malthusian theory. However, we also found that this population growth may lead to conservation conflict as we found that biodiversity habitat (wetland area) correlates negatively with population growth, thus raising the compromising effect of population growth on life on earth. What’s more, we found a significant link between economic growth measured as GDP and population growth, further supporting the Malthusian prediction. Overall, our study re-affirms the value of biodiversity to human and suggests that the Malthusian theory should continuously be tested with predictors other than economic.

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.

The ghost of hosts past: impacts of host extinction on parasite specificity

A growing body of research is focused on the extinction of parasite species in response to host endangerment and declines. Beyond the loss of parasite species richness, host extinction can impact apparent parasite host specificity, as measured by host richness or the phylogenetic distances among hosts. Such impacts on the distribution of parasites across the host phylogeny can have knock-on effects that may reshape the adaptation of both hosts and parasites, ultimately shifting the evolutionary landscape underlying the potential for emergence and the evolution of virulence across hosts. Here, we examine how the reshaping of host phylogenies through extinction may impact the host specificity of parasites, and offer examples from historical extinctions, present-day endangerment, and future projections of biodiversity loss. We suggest that an improved understanding of the impact of host extinction on contemporary host-parasite interactions may shed light on core aspects of disease ecology, including comparative studies of host specificity, virulence evolution in multi-host parasite systems, and future trajectories for host and parasite biodiversity. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.

Looming extinctions due to invasive species: Irreversible loss of ecological strategy and evolutionary history

Biological invasions are one of the main drivers of biodiversity decline worldwide. However, many associated extinctions are yet to occur, meaning that the ecological debt caused by invasive species could be considerable for biodiversity. We explore extinction scenarios due to invasive species and investigate whether paying off the current extinction debt will shift the global composition of mammals and birds in terms of ecological strategy and evolutionary history. Current studies mostly focus on the number of species potentially at risk due to invasions without taking into account species characteristics in terms of ecological or phylogenetic properties. We found that 11% of phylogenetic diversity worldwide is represented by invasive-threatened species. Furthermore, 14% of worldwide trait diversity is hosted by invasive-threatened mammals and 40% by invasive-threatened birds, with Neotropical and Oceanian realms being primary risk hotspots. Projected extinctions of invasive-threatened species result in a smaller reduction in ecological strategy space and evolutionary history than expected under randomized extinction scenarios. This can be explained by the strong pattern in the clustering of ecological profiles and families impacted by invasive alien species (IAS). However, our results confirm that IAS are likely to cause the selective loss of species with unique evolutionary and ecological profiles. Our results also suggest a global shift in species composition away from those with large body mass, which mostly feed in the lower foraging strata and have an herbivorous diet (mammals). Our findings demonstrate the potential impact of biological invasions on phylogenetic and trait dimensions of diversity, especially in the Oceanian realm. We therefore call for a more systematic integration of all facets of diversity when investigating the consequences of biological invasions in future studies. This would help to establish spatial prioritizations regarding IAS threats worldwide and anticipate the consequences of losing specific ecological profiles in the invaded community.

Spaceship Earth Revisited: The Co-Benefits of Overcoming Biological Extinction of Experience at the Level of Person, Place and Planet

Extensive research underscores that we interpret the world through metaphors; moreover, common metaphors are a useful means to enhance the pursuit of personal and collective goals. In the context of planetary health—defined as the interdependent vitality of all natural and anthropogenic ecosystems (social, political and otherwise)—one enduring metaphor can be found in the concept of “Spaceship Earth”. Although not without criticism, the term “Spaceship Earth” has been useful to highlight both resource limitations and the beauty and fragility of delicate ecosystems that sustain life. Rene Dubos, who helped popularize the term, underscored the need for an exposome perspective, one that examines the total accumulated environmental exposures (both detrimental and beneficial) that predict the biological responses of the “total organism to the total environment” over time. In other words, how large-scale environmental changes affect us all personally, albeit in individualized ways. This commentary focuses the ways in which microbes, as an essential part of all ecosystems, provide a vital link between personal and planetary systems, and mediate the biopsychosocial aspects of our individualized experience—and thus health—over our life course journey. A more fine-grained understanding of these dynamics and our power to change them, personally and collectively, lies at the core of restoring “ecosystems balance” for person, place and planet. In particular, restoring human connectedness to the natural world, sense of community and shared purpose must occur in tandem with technological solutions, and will enhance individual empowerment for personal well-being, as well as our collective potential to overcome our grand challenges. Such knowledge can help shape the use of metaphor and re-imagine solutions and novel ways for restoration or rewilding of ecosystems, and the values, behaviors and attitudes to light the path toward exiting the Anthropocene.

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.