Loss Of Phylogenetic Diversity Research Articles

Climate change impact assessments on the Andean genus Menonvillea (Brassicaceae) reveal uneven vulnerability among major phylogenetic and biogeographic groups

Climate change impact on species can be heterogeneous depending on their environments, exposure, and intrinsic characteristics. Likewise, global warming may have an uneven effect on lineages, depending on whether phylogenetic conservatism or divergence of ecological niches predominates during clade diversification, imposing a higher risk to species groups from certain regions, habitats and lineages. This study evaluates the impact of future climate change on Menonvillea, a genus with 24 species distributed along the Andes and contiguous regions of the Southern Cone. The impact on the main phylogenetic, ecological and biogeographic groups is evaluated, also analyzing the effect on its richness and phylogenetic diversity. Results show a strongly negative impact on most species of the genus. However, the greatest pressure seems to be recovered for high Andean species, mainly from the southern portion of the Southern Andes (between 34°S–53S°), and mostly included in Menonvillea sect. Cuneata. Richness appears to be more impacted in high Andean regions, and the loss of phylogenetic diversity is greater than expected at random. These results highlight the strong negative impact that climate change can induce on lineages distributed in the Andean-Patagonian region, and that show patterns of phylogenetic niche conservatism.

Methods for Estimating Personal Disease Risk and Phylogenetic Diversity of Hematopoietic Stem Cells.

An individual's chronological age does not always correspond to the health of different tissues in their body, especially in cases of disease. Therefore, estimating and contrasting the physiological age of tissues with an individual's chronological age may be a useful tool to diagnose disease and its progression. In this study, we present novel metrics to quantify the loss of phylogenetic diversity in hematopoietic stem cells (HSCs), which are precursors to most blood cell types and are associated with many blood-related diseases. These metrics showed an excellent correspondence with an age-related increase in blood cancer incidence, enabling a model to estimate the phylogeny-derived age (phyloAge) of HSCs present in an individual. The HSC phyloAge was generally older than the chronological age of patients suffering from myeloproliferative neoplasms (MPNs). We present a model that relates excess HSC aging with increased MPN risk. It predicted an over 200 times greater risk based on the HSC phylogenies of the youngest MPN patients analyzed. Our new metrics are designed to be robust to sampling biases and do not rely on prior knowledge of driver mutations or physiological assessments. Consequently, they complement conventional biomarker-based methods to estimate physiological age and disease risk.

Extinction risk patterns in a biodiversity hotspot—The case of Thesium (Santalaceae) in the Greater Cape Floristic Region

AbstractEcologically specialized plants are expected to be at greater risk of extinction than generalists due to climate change. Such risk is greatest in biodiversity hotspots such as the Greater Cape Floristic Region (GCFR), which accommodates both ecological specialists and generalists. Thesium L., a genus with the highest number of species in Santalaceae and the most diverse in Africa, offers an appropriate system for evaluating both the correlates of range extent and specialization and the relative extinction risks associated with both. We hypothesized that range size, ecological specialization, and consequent climatically modulated extinction risks are all phylogenetically structured, such that climate change will precipitate a disproportionate loss of phylogenetic diversity in the GCFR Thesium. Past and future species distribution ranges were predicted using MaxEnt models based on present‐day occurrences and environmental conditions. Of the 101 Thesium species modeled, 70% have had large range sizes during the Last Glacial Maximum (LGM), 50% currently have a large range size, and future conditions are predicted to allow 40% to obtain large range sizes. Between the LGM and the present, 17% of species are thought to have undergone a contraction of available range space in the present time whereas 37% are expected to expand their ranges into the future, while 51% of species will experience range contractions. Of the 65 species currently ranked as Least Concern in the South African Red List, 24% will likely shift into higher extinction risk categories. Interestingly, 8.5% of ecological specialists, although having experienced a range reduction from the LGM to the present, are predicted to persist in the face of future climate change. However, the range extent, ecological specialization, and extinction risk are phylogenetically random and therefore should have a negligible impact on the phylogenetic diversity of the GCFR Thesium.

Six decades of museum collections reveal disruption of native ant assemblages by introduced species

There is a looming environmental crisis characterized by widespread declines in global biodiversity,1,2,3,4,5,6 coupled with the establishment of introduced species at accelerated rates.7,8,9,10,11,12,13,14 We quantified how multi-species invasions affect litter ant communities in natural ecosystems by leveraging museum records and contemporary collections to assemble a large (18,990 occurrences, 6,483 sampled local communities, and 177 species) 54-year (1965-2019) dataset for the entire state of Florida, USA. Nine of ten species that decreased most strongly in relative abundance ("losers") were native, while nine of the top ten "winners" were introduced species. These changes led to shifts in the composition of rare and common species: in 1965, only two of the ten most common ants were introduced, whereas by 2019, six of ten were introduced species. Native losers included seed dispersers and specialist predators, suggesting a potential loss of ecosystem function through time, despite no obvious loss of phylogenetic diversity. We also examined the role of species-level traits as predictors of invasion success. Introduced species were more likely to be polygynous than native species. The tendency to form supercolonies, where workers from separate nests integrate, also differed between native and introduced species and was correlated with the degree to which species increased in their rank abundances over 50 years. In Florida, introduced ants now account for 30% of occurrence records, and up to 70% in southern Florida. If current trends continue, introduced species will account for over half of occurrence records in all Florida's litter ant communities within the next 50 years.

Phylogenetic patterns of rarity and vulnerability in the flora of a temperate mountain range

Species rarity has puzzled ecologists for decades owing to its theoretical fundamentals and practical implications. The main concern that rarity raises from a conservation standpoint is that rare species tend to have higher extinction risk. Understanding the underlying phylogenetic patterns of rarity can shed light on the evolutionary processes yielding rarity, contribute to forecasting potential vulnerable species or lineages, and assess the consequences of the loss of rare species. Here, we apply Rabinowitz's rarity classification scheme and explore phylogenetic patterns in the flora of the Pyrenees, a temperate mountain range. We first categorized species according to their geographic range (endemicity and regional geographic range), habitat specialization and local abundance. Then we analyzed the phylogenetic signal of each rarity type, along with the phylogenetic association between species according to their rarity, and decomposed the variation of rarity among taxonomic levels to better understand its diversification through time. Finally, we estimated the expected loss of phylogenetic diversity (PD) in the regional flora if rare species go extinct. All rarity types showed a certain degree of phylogenetic signal, with endemics, species of limited regional geographic range and habitat specialists forming groups of phylogenetically close species. The decomposition of variation supported these results, as the rarity types with the strongest signal had more variation explained by higher taxonomic levels. The loss of these groups of species had different consequences based on the type of rarity, with the disappearance of habitat specialists having the strongest, negative effect on PD. Our results show a general pattern of phylogenetic association in rarity among the flora of the Pyrenees, which leads to increased vulnerability along certain branches of the Tree of Life. Phylogenetic patterns should be taken into account in conservation planning to effectively protect all facets of biodiversity.

The homogenization of avian morphological and phylogenetic diversity under the global extinction crisis

Biodiversity is facing a global extinction crisis that will reduce ecological trait diversity, evolutionary history, and ultimately ecosystem functioning and services.1-4 A key challenge is understanding how species losses will impact morphological and phylogenetic diversity at global scales.5,6 Here, we test whether the loss of species threatened with extinction according to the International Union for Conservation of Nature (IUCN) leads to morphological and phylogenetic homogenization7,8 across both the whole avian class and within each biome and ecoregion globally. We use a comprehensive set of continuous morphological traits extracted from museum collections of 8,455 bird species, including geometric morphometric beak shape data,9 and sequentially remove species from those at most to least threat of extinction. We find evidence of morphological, but not phylogenetic, homogenization across the avian class, with species becoming more alike in terms of their morphology. We find that most biome and ecoregions are expected to lose morphological diversity at a greater rate than predicted by species loss alone, with the most imperiled regions found in East Asia and the Himalayan uplands and foothills. Only a small proportion of assemblages are threatened with phylogenetic homogenization, in particular parts of Indochina. Species extinctions will lead to a major loss of avian ecological strategies, but not a comparable loss of phylogenetic diversity. As the decline of species with unique traits and their replacement with more widespread generalist species continues, the protection of assemblages at most risk of morphological and phylogenetic homogenization should be a key conservation priority.

Relative Importance of Ecological, Evolutionary and Anthropogenic Pressures on Extinction Risk in Chinese Angiosperm Genera

China has many threatened plant species, which are exposed to environmental degradation and other anthropogenic pressures. We assessed support for potential extinction pathways in Chinese angiosperm genera and quantified possible threats to phylogenetic diversity. We compiled a database and phylogeny for 27,409 Chinese angiosperm species in 2,453 genera. For each genus, we used the International Union for Conservation of Nature (IUCN) Red List classifications to quantify extinction risk and calculated predictors corresponding to their ecological, evolutionary characteristics and exposure to human pressures. We first tested for phylogenetic clustering in extinction risk among genera and then tested support for direct and indirect causal pathways involving our predictors using piecewise structural equation models. Finally, we quantified the potential loss of phylogenetic diversity under different extinction scenarios. We found that extinction risk is non-randomly distributed among Chinese angiosperm genera, with the proportion of threatened species higher in range-limited and species-rich taxa. Habitat loss had a significant positive effect on threatened species richness. Phylogenetic diversity loss under scenarios: the decreasing habitat loss and relative extinction rate were high. Thus, genera would suffer from high extinction risk, if species in these genera occupy similar niches and overlapping ranges. While diversification or speciation via niche divergence might increase range-limited species vulnerable to stochastic extinction, this could reduce extinction risk of the whole clade by expanding its range and climatic niche tolerance. Endemic genera with higher extinction rates, less climatic niche divergence, and lower range segregation are especially vulnerable to anthropogenic disturbances.

Loss of phylogenetic diversity under landscape change

Habitat alteration and destruction are primary drivers of biodiversity loss. However, the evolutionary dimensions of biodiversity loss remain largely unexplored in many systems. For example, little is known about how habitat alteration/loss can lead to phylogenetic deconstruction of ecological assemblages at the local level. That is, while species loss is evident, are some lineages favored over others? Using a long-term dataset of a globally, ecologically important guild of invertebrate consumers, stream leaf “shredders,” we created a phylogenetic tree of the taxa in the regional species pool, calculated mean phylogenetic distinctiveness for >1000 communities spanning >10 year period, and related species richness, phylogenetic diversity, and distinctiveness to watershed-scale impervious cover. Using a combination of changepoint and compositional analyses, we learned that increasing impervious cover produced marked reductions in all three measures of diversity. These results aid in understanding both phylogenetic diversity and mean assemblage phylogenetic distinctiveness. Our findings indicate that, not only are species lost when there is an increase in watershed urbanization, as other studies have demonstrated, but that those lost are members of more distinct lineages relative to the community as a whole..

Functional diversity of Himalayan bat communities declines at high elevation without the loss of phylogenetic diversity

Species richness exhibits well-known patterns across elevational gradients in various taxa, but represents only one aspect of quantifying biodiversity patterns. Functional and phylogenetic diversity have received much less attention, particularly for vertebrate taxa. There is still a limited understanding of how functional, phylogenetic and taxonomic diversity change in concert across large gradients of elevation. Here, we focused on the Himalaya—representing the largest elevational gradients in the world—to investigate the patterns of taxonomic, functional and phylogenetic diversity in a bat assemblage. Combining field data on species occurrence, relative abundance, and functional traits with measures of phylogenetic diversity, we found that bat species richness and functional diversity declined at high elevation but phylogenetic diversity remained unchanged. At the lowest elevation, we observed low functional dispersion despite high species and functional richness, suggesting a niche packing mechanism. The decline in functional richness, dispersion, and divergence at the highest elevation is consistent with patterns observed due to environmental filtering. These patterns are driven by the absence of rhinolophid bats, four congeners with extreme trait values. Our data, some of the first on mammals from the Himalayan region, suggest that in bat assemblages with relatively high species diversity, phylogenetic diversity may not be a substitute to measure functional diversity.

Urbanization is associated to a loss of phylogenetic diversity of birds in a medium size city on the Andes of Colombia, South America

ABSTRACT Accelerated rates of urbanization negatively impact natural habitats and biodiversity. Studies of the effects of urbanization on fauna have emphasized taxonomic diversity, but this does not necessarily reflect effects on the evolutionary history of assemblages. Here, we study how urbanization influences phylogenetic diversity (PD) of bird assemblages in a small–medium city in the Central Andes of Colombia. Between 2016 and 2017, we performed bird surveys in 76 urban cells and 23 rural cells around the city. Then, we measured habitat characteristics (e.g. anthropogenic noise level, impervious and forested area) in sampled cells. PD of birds was between 1.37–1.42 MY higher in the rural than in the urban habitat. Within the urban habitat, the PD of birds reduces as impervious area and noise levels increase, while in the urban cells with most forested areas reach the highest PD values. Most of these differences and relationships disappear when we performed similar analysis controlling for differences in species richness. A low turnover of PD between assemblages of birds recorded inside Armenia and its less urbanized surroundings suggest green areas in the study area could mitigate the effects of urbanization in native fauna, and ameliorate connectivity between urban cells.

Phylogeny‐based conservation priorities for Australian freshwater fishes

AbstractConservation scientists are increasingly interested in the question of how extinction prunes the tree of life. This question is particularly important for Australian freshwater fishes because there is a broad mix of ∼300 old and young species, many of which are severely threatened. We used a complete species‐level phylogeny of Australian freshwater fishes to examine phylogenetic nonrandomness of extinction risk. We computed the potential loss of phylogenetic diversity by simulating extinction across the tree under a pattern weighted based on International Union for Conservation of Nature extinction risk category and compared this loss to projected diversity loss under a random null model of extinction. Finally, we calculated EDGE (evolutionary distinctiveness, global endangerment) scores for 251 freshwater and 60 brackish species and compiled a list of high‐priority species for conservation actions based on their extinction risk and evolutionary uniqueness. Extinction risk was not random and was clustered in both diversity cradles (recently diversifying, species‐rich clades, such as Galaxiidae and Percichthyidae) and museums (older, species‐poor groups, such as freshwater chondrichthyans). Clustered extinction made little difference to the average expected loss of phylogenetic diversity. However, the upper bound of loss was higher under a selective model of extinction, particularly when the counts of species lost were low. Thus, the loss of highly threatened species would diminish the tree of life more than a null model of randomly distributed extinction. High priority species included both widely recognized and charismatic ones, such as the Queensland lungfish (Neoceratodus forsteri), river sharks, and freshwater sawfishes, and lesser‐known species that receive less public attention, including the salamanderfish (Lepidogalaxias salamandroides), cave gudgeons, and many galaxiids, rainbowfishes, and pygmy perches.

Decoupled erosion of amphibians’ phylogenetic and functional diversity due to extinction

AbstractAimIt has been argued that the loss of phylogenetic diversity (PD) from species extinctions will result in concomitant loss of functional diversity (FD). As a result, species extinction undermines not only unique evolutionary history, but also ecosystem function and stability. Using data from > 6,000 amphibian species globally, we assess the potential erosion of PD and FD as a result of extinction.LocationGlobal.Time periodFrom the present day to the next 100 years.Major taxa studiedAmphibians (Anura, Caudata and Gymnophiona).MethodsWe simulated future biogeographical patterns of extinction based on International Union for Conservation of Nature (IUCN) threat status, and estimated the loss of PD and FD accordingly. We used null models to determine the extent to which extinctions may result in disproportional losses of PD and FD relative to random extinction. Using spatial regressions, we tested whether the loss of PD can predict the loss of FD.ResultsAlthough spatial patterns of current amphibian PD and FD were similar, extinctions did not retain this similarity. The magnitude of such a decoupling varied widely in space, with most of the global assemblages losing more FD than PD.Main conclusionThis study challenges the assumption that extinctions should yield comparable loss of PD and FD. Species may not be equivalent in the amount of unique evolutionary history and ecological functions that would be lost if they become extinct. Designing conservation strategies based on a single dimension of biodiversity has the danger of leading to misinformed outcomes.

Climate drives loss of phylogenetic diversity in a grassland community

While climate change has already profoundly influenced biodiversity through local extinctions, range shifts, and altered interactions, its effects on the evolutionary history contained within sets of coexisting species-or phylogenetic community diversity-have yet to be documented. Phylogenetic community diversity may be a proxy for the diversity of functional strategies that can help sustain ecological systems in the face of disturbances. Under climatic warming, phylogenetic diversity may be especially vulnerable to decline in plant communities in warm, water-limited regions, as intensified water stress eliminates drought-intolerant species that may be relicts of past wetter climates and may be distantly related to coexisting species. Here, we document a 19-y decline of phylogenetic diversity in a grassland community as moisture became less abundant and predictable at a critical time of the year. This decline was strongest in native forbs, particularly those with high specific leaf area, a trait indicating drought sensitivity. This decline occurred at the small spatial scale where species interact, but the larger regional community has so far been buffered against loss of phylogenetic diversity by its high levels of physical and biotic heterogeneity.

Plant evolutionary assembly along elevational belts at Mt. Kilimanjaro: Using phylogenetics to asses biodiversity threats under climate change

Accumulating evidence suggests that species sensitivity to climatic change is strongly related to their ecological niches, which are somewhat evolutionary conserved. Insofar as this is true, climate change-driven extinctions may be non-random with respect to phylogeny, and entire branches of the tree of life might be lost. In mountainous regions, where macroecological conditions change abruptly with elevation, evolutionarily lineages may show deep phylogenetic turnover along elevational belts, and such “layering” of the phylogeny may lead to disproportionate losses of phylogenetic diversity. Here, we explored phylogenetic alpha and beta diversity patterns of plant assemblages among six elevational belts at Kilimanjaro (i.e. savanna woodland, lower montane forest, middle-montane Ocotea forest, upper-montane Podocarpus forest, Erica subalpine bushland and Helichrysum alpine scrubland). Specifically, we aimed at determining the degree of elevational turnover of plant evolutionary lineages as a diagnostic tool to assess phylogenetic diversity threats owing to shifting environmental conditions. We found relatively deep phylogenetic discontinuities that roughly matched the main modern vegetation types in East Africa, this is, subalpine-alpine vegetation, montane forests and savannas lowlands. However, the upper-montane Podocarpus forest was phylogenetically closer to subalpine-alpine vegetation than to middle (Ocotea) and lower montane forests, despite all these forest belts constituted a floristically integrated unit. Phylogenetic diversity followed a hump-shape relationship with elevation, with significantly high values in lower montane forest and lower than expected scores in savanna, subalpine and alpine belts. Overall, the phylogenetic layering of Kilimanjaro flora reported here suggests that a disproportionate amount of phylogenetic diversity in mountainous regions might be at risk, although the generality of this pattern is yet to be confirmed. In the particular case of Kilimanjaro, human population growth represents a pervasive threat to montane forest, and particularly to the phylogenetically singular remnants of lower montane forest. Besides, climate-change induced fires in the subalpine belt are causing over-riding shrinkage of the upper-montane Podocarpus forest from the timberline. Should these continuing pressures of global change persist, the montane forests of Kilimanjaro may experience substantial shrinking within the next decades, trapped between the “hammer and the anvil” of climate and land-use change.

Non‐random loss of phylogenetically distinct rare species degrades phylogenetic diversity in semi‐natural grasslands

Abstract Although biodiversity loss is a critically important topic, our understanding of how both land abandonment and land‐use intensification in semi‐natural grasslands alters the community diversity and assembly mechanisms is very limited. Large‐scale economic drivers of land‐use change might inadvertently result in the loss of vulnerable species and reduce ecosystem service provisioning. In this study, we assessed non‐random community change by examining patterns of low‐abundance species loss, and community assembly in semi‐natural grasslands due to land abandonment and intensification in southwest Japan. We analysed relationships between evolutionary distinctiveness and abundance for each species. In addition, we used metrics of species and phylogenetic diversity and phylogenetic structure to assess patterns of non‐random biodiversity loss due to both abandoned and intensified land‐use. We demonstrated that low‐abundance species were more evolutionarily distinct compared to high‐abundance (i.e. dominant) species. Furthermore, land‐use intensification resulted in further declines in low‐abundance species, whereas land abandonment resulted in declines in all species, regardless of their initial abundance. We found that both forms of land‐use change (abandonment and intensification) resulted in non‐random patterns of community change, with traditional land‐use maintaining the highest biodiversity and land‐use change coinciding with decreased species and phylogenetic diversity measures. Intensified land‐use caused phylogenetic community structure to be more closely related than expected by chance, whereas the metrics of how distant species are from one another on average based on phylogenetic tree (i.e. mean pairwise phylogenetic distance) did not change from land abandonment. Synthesis and applications. We show that the loss of phylogenetic diversity, and especially of low‐abundance species with high value of phylogenetic distinctiveness, resulted in non‐random community disassembly. Our results argue that in order to maintain biodiversity in these semi‐natural grasslands, traditional management practices should be encouraged over intensification and simple abandonment. Government agencies should adopt policies or provide incentives that encourage the maintenance of traditional practices in rural Japan, and elsewhere where the combination of land consolidation and abandonment are important conservation issues.

Species splitting increases estimates of evolutionary history at risk

Changes in species concepts and the rapid advances in DNA-based taxonomy and phylogeny of the past decades have led to increasing splits of single species into several new species. The consequences of such splits include the delineation of post-split species that may have restricted ranges and potentially increased extinction risks. Species splitting also leads to a re-evaluation of phylogenetic trees, with post-split trees having more species, but species that are less evolutionarily distinctive compared to pre-split trees. Such changes in extinction risks and distinctiveness may influence strategies for the conservation of phylogenetic diversity (PD). In this study, we evaluated the effect of splitting a species into two sister species on two widely used measures to evaluate PD at risk: (i) the expected loss of phylogenetic diversity associated with a set of species and, (ii) for each species, the gain in the expected phylogenetic diversity if the species is saved from extinction. We developed theoretical predictions and then explored these in a real-world case study of species splitting in the Rhinocerotidae family. Species splitting increases both of our measures related to PD at risk, implying underestimation of PD at risk when valid species splitting is not recognised. This bias may lead to suboptimal conservation decisions: the subset of species or sites given priority for conservation may be different from the subset that actually deserves priority conservation attention. We discuss how our findings can be applied to more complex studies and the perspectives this highlights for accommodating new taxonomic knowledge in conservation strategies.

Terrestrial Vertebrate Biodiversity Loss under Future Global Land Use Change Scenarios

Efficient forward-looking mitigation measures are needed to halt the global biodiversity decline. These require spatially explicit scenarios of expected changes in multiple indicators of biodiversity under future socio-economic and environmental conditions. Here, we link six future (2050 and 2100) global gridded maps (0.25° × 0.25° resolution) available from the land use harmonization (LUH) database, representing alternative concentration pathways (RCP) and shared socio-economic pathways (SSPs), with the countryside species–area relationship model to project the future land use change driven rates of species extinctions and phylogenetic diversity loss (in million years) for mammals, birds, and amphibians in each of the 804 terrestrial ecoregions and 176 countries and compare them with the current (1900–2015) and past (850–1900) rates of biodiversity loss. Future land-use changes are projected to commit an additional 209–818 endemic species and 1190–4402 million years of evolutionary history to extinction by 2100 depending upon the scenario. These estimates are driven by land use change only and would likely be higher once the direct effects of climate change on species are included. Among the three taxa, highest diversity loss is projected for amphibians. We found that the most aggressive climate mitigation scenario (RCP2.6 SSP-1), representing a world shifting towards a radically more sustainable path, including increasing crop yields, reduced meat production, and reduced tropical deforestation coupled with high trade, projects the lowest land use change driven global biodiversity loss. The results show that hotspots of future biodiversity loss differ depending upon the scenario, taxon, and metric considered. Future extinctions could potentially be reduced if habitat preservation is incorporated into national development plans, especially for biodiverse, low-income countries such as Indonesia, Madagascar, Tanzania, Philippines, and The Democratic Republic of Congo that are otherwise projected to suffer a high number of land use change driven extinctions under all scenarios.

Ranked Tree Shapes, Nonrandom Extinctions, and the Loss of Phylogenetic Diversity.

Phylogenetic diversity (PD) is a measure of the evolutionary legacy of a group of species, which can be used to define conservation priorities. It has been shown that an important loss of species diversity can sometimes lead to a much less important loss of PD, depending on the topology of the species tree and on the distribution of its branch lengths. However, the rate of decrease of PD strongly depends on the relative depths of the nodes in the tree and on the order in which species become extinct. We introduce a new, sampling-consistent, three-parameter model generating random trees with covarying topology, clades relative depths, and clades relative extinction risks. This model can be seen as an extension to Aldous' one parameter splitting model ($\beta$, which controls for tree balance) with two additional parameters: a new parameter $\alpha$ quantifying the relation between age and richness of subclades, and a parameter $\eta$ quantifying the relation between relative abundance and richness of subclades, taken herein as a proxy for overall extinction risk. We show on simulated phylogenies that loss of PD depends on the combined effect of all three parameters, $\beta$, $\alpha,$ and $\eta$. In particular, PD may decrease as fast as species diversity when high extinction risks are clustered within small, old clades, corresponding to a parameter range that we term the "danger zone" ($\beta<-1$ or $\alpha<0$; $\eta>1$). Besides, when high extinction risks are clustered within large clades, the loss of PD can be higher in trees that are more balanced ($\beta>0$), in contrast to the predictions of earlier studies based on simpler models. We propose a Monte-Carlo algorithm, tested on simulated data, to infer all three parameters. Applying it to a real data set comprising 120 bird clades (class Aves) with known range sizes, we show that parameter estimates precisely fall close to the danger zone: the combination of their ranking tree shape and nonrandom extinctions risks makes them prone to a sudden collapse of PD.

Predicting the impacts of co-extinctions on phylogenetic diversity in mutualistic networks

An important bias in the estimations of threatened evolutionary history is that extinctions are considered as independent events. However, the extinction of a given species may affect the vulnerability of its partners and cause extinction cascades. Co-extinctions are likely not random in the tree of life and may cause the loss of large amounts of unique evolutionary history. Here, we propose a method to assess the consequences of co-extinctions for the loss of evolutionary history and to identify conservation priorities. We advise considering both the complexity of the interaction networks and the phylogenetic complementarities of extinction risks among species. Using this approach, we demonstrated how co-extinction events can prune the tree of life using various species loss scenarios. As a case study, we identified pollinators for which extinctions would greatly impact plant phylogenetic diversity within local pollination networks from Europe. We also identified species features that may result in the highest losses of phylogenetic diversity. Our approach highlights the consequences of co-extinctions on the loss of evolutionary history and may help address various conservation issues related to co-extinctions and their impacts on biodiversity.

Projecting global land use‐driven evolutionary history loss

AbstractAimRecent studies have mapped the global hotspots hosting high phylogenetic diversity (PD), but not the regions where this diversity is under threat due to human land use. This is because, to date, it is not clear how much PD is lost as species of a given taxon go extinct. The aim of this study was to identify the global regions projected to suffer the highest PD loss due to human land use in the near future.LocationGlobal.MethodsWe demonstrate a novel approach combining countryside species–area relationship, species‐specific evolutionary distinctiveness (ED) scores and a newly derived strong linear relationship between the cumulative ED loss and PD loss through pruning simulations on global evolutionary trees of mammals, birds, and amphibians under random species loss, to project global land use‐driven phylogenetic diversity loss in 804 terrestrial ecoregions and 175 countries. We also allocate the total projected PD loss to different land use types (agriculture, forestry, grazing or urbanization) in each region to pinpoint the major drivers.ResultsFor the three taxa combined, we project a total loss of 9,472 million years (MY) of evolutionary history due to all land uses in all countries: 1,541 MY of mammal PD is at stake, 3,336 MY of bird PD and 4,595 MY of amphibian PD. Agriculture is responsible for loss of 1,579 MY; pasture 1990 MY, forestry 5,381 and urbanization 522. Land use in Indonesia, Colombia, India, Papua New Guinea, Madagascar and Philippines is projected to cause the most loss of PD.Main conclusionsThrough the integrated approach, we can now project PD loss associated with species extinctions under alternative land conversion scenarios in a region. Overall, the results on hotspots and land use drivers may inform individual nations in designing regional strategies to achieve the international biodiversity and sustainability targets.