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Abstract

A key step in understanding the distribution of biodiversity is the grouping of regions based on their shared elements. Historically, regionalization schemes have been largely species centric. Recently, there has been interest in incorporating phylogenetic information into regionalization schemes. Phylogenetic regionalization can provide novel insights into the mechanisms that generate, distribute, and maintain biodiversity. We argue that four processes (dispersal limitation, extinction, speciation, and niche conservatism) underlie the formation of species assemblages into phylogenetically distinct biogeographic units. We outline how it can be possible to distinguish among these processes, and identify centers of evolutionary radiation, museums of diversity, and extinction hotspots. We suggest that phylogenetic regionalization provides a rigorous and objective classification of regional diversity and enhances our knowledge of biodiversity patterns.

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... Cox, 2001;Holt et al., 2013;Kreft & Jetz, 2010;Smith, 1983;Wallace, 1876). Recent progress integrating evolutionary histories has permitted the rise of a new generation of regionalization maps (Daru et al., 2017(Daru et al., , 2020Holt et al., 2013). But for insects which represent an overwhelming component of biodiversity (Stork, 2018), similar efforts have been scant. ...
... Historically, the delineation of biogeographical regions has been based solely on taxonomic information, but in recent years, progress in phylogenetic methods (i.e. phylogenetic regionalization) has provided new opportunities to explore evolutionary relationships for entire assemblages and enhance the objectivity and repeatability of delineations (Daru et al., 2017;Holt et al., 2013;Ye et al., 2019). These techniques can identify historical connections between regions based on shared evolutionary history, which taxonomic delineations alone may not detect (Ye et al., 2019). ...
... For example, allopatric speciation events driven by geographical isolation can result in greater dissimilarity of species composition between two regions yet preserve a phylogenetic affinity between them (Daru et al., 2017). We thus expect the relationships between regions resulting from phylogenetic regionalization to differ from those of the taxonomic delineation, especially for geographically isolated species, and that these differences will help to reveal a more multilayered regional evolutionary history for the European ants. ...
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Abstract Aim Biogeographical regionalization is scant for most insect groups due to shortfalls in distribution and phylogenetic information, namely the Wallacean and Darwinian shortfalls respectively. Here, we focused on the European ants and compared new techniques to classical analyses based on regional lists and taxonomic methods. We asked the following: (1) Can grid-based regionalizations using novel distribution data improve biogeographical transitions? and (2) Can phylogenetic approaches reveal new insights regarding ant evolutionary history? Location Europe and Anatolia. Taxon Ants (Formicidae). Methods First, we developed a refined database integrating the occurrences of 747 ant species across 207 regions of Europe and Anatolia, based on newly expert-validated records derived from the existing Global Ant Biodiversity Informatics database. Using range estimates for these species derived from polygons and species distribution modelling, we produced species assemblages in 50 × 50 km grid cells. We calculated taxonomic and phylogenetic turnover of ant assemblages, then performed a hierarchical clustering procedure to delineate biogeographical structure. Results At both the regional list and grid assemblage levels, the Mediterranean has higher turnover and more biogeographical regions than northern Europe, both taxonomically and phylogenetically. Delineations based on grid assemblages detected more detailed biogeographical transitions, while those based on regional lists showed stronger insularity in biogeographical structure. The phylogenetic regionalization suggested a very similar spatial structure but varied affinities between assemblages in comparison to the taxonomic approach. Main Conclusions Here, we integrated expert-validated regional lists, species distribution modelling and a recent phylogeny to tackle Wallacean and Darwinian shortfalls for an important insect group by developing a next-generation map of biogeographical regionalization for European ants. The results of this study suggest strong constraints from geographical barriers and potential effects of climatic history on ant distributions and evolutionary history, and also provide baseline spatial information for future investigations of regional insect distributions.
... These geographic ranges of species distribution are determined by historical and current factors, and changes in these patterns over time might result from environmental filtering, geographic distance, or natural barriers, and is reflected in the phylogenetic affinities of species (Daru et al., 2017;Hortal et al., 2012). ...
... This geographic pattern might be favored by the climatic and environmental characteristics of the Chaco, which would act historically as a filter for species dispersion (Daru et al., 2017). ...
... This result is due to specialization in a single habitat component, allowing fossorial species to efficiently exploit underused parts of the available resource base (Greenville & Dickman, 2009). Another explanation could be that the limited dispersal capacity of fossorial species makes them geographically restricted, resulting in evolutionary and geographically distant phyloregions (Daru et al., 2017). Furthermore, species distribution and range limits are determined by biotic and abiotic factors, movement, population dynamics, and intraspecific variability, which are related to the physiological tolerances of species (Gouveia, Hortal, et al., 2014). ...
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Macroecological studies describe large-scale diversity patterns through analyses of species distribution patterns and allows us to elucidate how species differing in ecology, physical requirements, and life histories are distributed in a multidimensional space. These patterns of distributions can be explained by vegetation, and climatic factors, and are determined by historical and current factors. The continuous accumulation of information on the distribution patterns of species is essential to understand the history and evolution of the biota. In this study, we aimed to identify functional and evolutionary drivers that explain the geographic patterns of vertical stratification. We compiled morphological, ecological, and distribution data of 140 species of Chacoan snakes and constructed null models to map their geographic pattern. We used a range of environmental variables to assess which drivers are influencing these biogeographic patterns. Lastly, we used evolutionary data to build the first map of the phylogenetic regions of Chacoan snakes. We found a latitudinal pattern, with a marked verticality in the snake assemblies in the Chaco. Verticality and long-tailed species richness increased in areas with high stratified habitats and stable temperature. Fossoriality is driven mainly by soil conditions, especially soils with fewer sand particles and less stratified habitat. Phylogenetic regions in the Chaco showed a marked latitudinal pattern, like that observed in the geographic pattern of verticality. The distribution pattern of Chacoan snakes also reflects their evolutionary history, with a marked phylogenetic regionalization.
... We use standard clustering algorithms, which in a geographic context have been termed regionalization approaches (Kreft and Jetz, 2010;Linder et al., 2012;Vilhena and Antonelli, 2015;Daru et al., 2017), to delimit clusters. Several authors have used biogeographic regionalization methods on a relatively similar (Linder et al., 2012;Fayolle et al., 2018;Aleman et al., 2020) or even larger scales (e.g., Kreft and Jetz, 2010;Holt et al., 2013;Vilhena and Antonelli, 2015;Ficetola et al., 2017) and argued that the results are comparable to biomes (Vilhena and Antonelli, 2015;Aleman et al., 2020). ...
... Our approach differs from classical and modern approaches that fall under the umbrella of "biogeographical regionalization" or "bioregionalization" (e.g., Kreft and Jetz, 2010;Linder et al., 2012;Holt et al., 2013;Vilhena and Antonelli, 2015;Daru et al., 2016Daru et al., , 2017Edler et al., 2017;Ficetola et al., 2017). Most such analyses are essentially focused on understanding the signature of historical (i.e., geographic barriers) processes in explaining the spatial distribution of specific "groups" of organisms across geographically confined areas, rather than delimiting biomes that are applicable across the tree of life. ...
... Most such analyses are essentially focused on understanding the signature of historical (i.e., geographic barriers) processes in explaining the spatial distribution of specific "groups" of organisms across geographically confined areas, rather than delimiting biomes that are applicable across the tree of life. Those that do include broader ranges of taxa still rely only on floristic (e.g., Linder et al., 2012) or phylogenetic (e.g., Daru et al., 2017) data to classify the "bioregions, " rather than attempting to integrate floristic, functional, and phylogenetic data. The resulting areas are more akin to "biogeographic regions" (sensu Wallace, 1876;Holt et al., 2013) than "biomes." ...
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While we have largely improved our understanding on what biomes are and their utility in global change ecology, conservation planning, and evolutionary biology is clear, there is no consensus on how biomes should be delimited or mapped. Existing methods emphasize different aspects of biomes, with different strengths and limitations. We introduce a novel approach to biome delimitation and mapping, based upon combining individual regionalizations derived from floristic, functional, and phylogenetic data linked to environmentally trained species distribution models. We define “core Biomes” as areas where independent regionalizations agree and “transition zones” as those whose biome identity is not corroborated by all analyses. We apply this approach to delimiting the neglected Caatinga seasonally dry tropical forest biome in northeast Brazil. We delimit the “core Caatinga” as a smaller and more climatically limited area than previous definitions, and argue it represents a floristically, functionally, and phylogenetically coherent unit within the driest parts of northeast Brazil. “Caatinga transition zones” represent a large and biologically important area, highlighting that ecological and evolutionary processes work across environmental gradients and that biomes are not categorical variables. We discuss the differences among individual regionalizations in an ecological and evolutionary context and the potential limitations and utility of individual and combined biome delimitations. Our integrated ecological and evolutionary definition of the Caatinga and associated transition zones are argued to best describe and map biologically meaningful biomes.
... Multiple factors have promoted the regionalization of faunas (Daru et al., 2017). First, physical barriers (e.g., sea or mountains) limit species dispersal and prevent the mixture of assemblages (e.g., Australia with the rest of the world). ...
... Still, many biogeographical boundaries cross continents, and some do not coincide with clear and visible physical barriers ( Figure 1; Supporting Information Figure S1). Second, differences in eco-physiological requirements may cause environmental filtering and a high faunistic turnover in areas representing sharp climatic transitions (Buckley & Jetz, 2008;Daru et al., 2017;Melo et al., 2009;White et al., 2019). For instance, high turnover of bird communities has been observed in regions representing the transition from tropical to temperate climates (White et al., 2019). ...
... Third, tectonic movements have strongly modified the configuration of continents and determined biogeographical differences between regions due to limited dispersal (Lomolino et al., 2010). Finally, past climatic changes during the Pleistocene led to species extinctions and species range shifts that might still be visible in some present-day patterns of species ranges, richness, and endemism (Daru et al., 2017;Nogués-Bravo et al., 2010;Sandel et al., 2011). The complex nature of bioregions further challenges the identification of the driving factors. ...
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Aim Worldwide distribution patterns of living animals are structured in multiple zoogeographical regions, characterized by faunas with homogeneous composition that are separated by sharp boundaries. These zoogeographical regions can differ depending on the considered animal group, probably because they have distinct characteristics such as dispersal, metabolism, or evolutionary history, and thus divergent responses to major biogeographical drivers, such as tectonic movements, abrupt climate transitions and orographic barriers. Here, we tested if the drivers of biogeographical boundaries are different between vertebrate classes with strongly divergent traits and evolutionary history. Location Global. Time period Present. Major taxa studied Amphibians, birds and mammals. Methods We focused on terrestrial biogeographical boundaries, considering multiple potential drivers: spatial heterogeneity of present-day climate, altitudinal variation, long-term tectonic movements and past climate change (temperature). We used spatially explicit regression models and geographically weighted regressions to select and quantify the factors explaining the position of the biogeographical boundaries between vertebrate classes. Results For mammals, tectonic movements, abrupt climatic transitions and orographic barriers jointly determined extant biogeographical boundaries, with tectonic movements being the most important. For birds, abrupt climatic transitions played the strongest role, while the effect of orographic barriers was weak. For amphibians, biogeographical boundaries mostly corresponded to areas with abrupt climatic transitions. The strongest transitions of amphibian faunas occur in areas with abrupt shifts of temperature and precipitation regimes. Main conclusions Our analyses confirmed that different drivers have jointly shaped the global vertebrate biogeographical regions, and highlight that taxa with different features show heterogeneous responses across the globe. Eco-physiological constraints likely increase the importance of spatial heterogeneity of climate, while dispersal limitations magnify the relevance of physical barriers (mountain chains and long-term tectonic instability). Integrating among-taxa heterogeneity into analyses thus provides a more complete view of how different processes determine biodiversity variation across the globe.
... Phylogenetic turnover may highlight breaks in lineage distribution among sites, which is shown to be correlated with the borders of biogeographical regions (e.g. ecoregions, domains) (Daru et al., 2017). Although biogeographical regionalization is the classification of biotas and areas into distinct entities, it reflects processes that shape biotas, such as vicariance, dispersal and niche filtering (Daru et al., 2018;Vilhena & Antonelli, 2015), often correlating with climatic breaks, orographic barriers and tectonic history (Ficetola et al., 2017). ...
... Higher phylogenetic turnover is also expected with increasing elevation, due to greater isolation and habitat heterogeneity in highlands, and along extreme and ancient environmental gradients (Bryant et al., 2008), whereas lowlands may facilitate faunal interchange , resulting in low phylogenetic turnover. If both the degree of phylogenetic turnover over evolutionary history and the responses to geography and environment are similar among taxa, the result is a common pattern of phylogenetic regionalization of the biota (Daru et al., 2017). ...
... Finally, ground characteristics can be critical to driving connectivity among sites for both groups due to habitat preferences of distinct taxa, from fossorial organisms (several reptile taxa) to rock-outcrop specialists-breeding sites for several amphibian species and also preferred habitat for saxicolous reptiles (Vitt, 1993). Thus, if local habitat influences connectivity and isolation among regions for long periods, this may result in contrasting rates of phylogenetic turnover (Daru et al., 2017) between reptiles and amphibians. ...
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Aim Cross‐taxonomic congruence in biodiversity patterns is key to understanding the main drivers of community structure, for biogeographical regionalization and to guide conservation. We aim to map the patterns of phylogenetic turnover and disentangle the geographical and environmental factors that drive the phylogenetic composition of distinct faunal assemblages. Location The Cerrado savannas of South America. Taxa Reptiles and amphibians. Methods We measured the proportion of phylogenetic branches shared among sites (i.e. phylogenetic turnover) using presence‐absence matrices for all species in the Cerrado and for endemics only, including only well‐sampled localities from previously compiled inventories. We then tested whether phylogenetic turnover is different from null expectations based on taxonomic turnover. We used generalized dissimilarity modelling (GDM) to test whether geography, topography, soil or climate best explain phylogenetic turnover. Finally, we mapped the observed and the GDM‐predicted clustering of phylogenetic turnover to assess geographical congruence between reptiles and amphibians. Results For all reptiles, geographical distance is the most important factor explaining phylogenetic turnover, whereas for endemic reptiles and amphibians, in general, a set of climatic variables and relief roughness are more important. We did not find any significant correlation between the phylogenetic turnover of reptiles and amphibians, as evidenced by non‐congruent phylogenetic clustering and by different responses to geographical and environmental gradients. Main conclusions The different relationships of phylogenetic turnover of reptiles and amphibians to geographical and environmental distances have ultimately shaped the phylogenetic regionalization of these two groups. This incongruence indicates the differential importance of niche filtering, dispersal limitation and the influence of neighbouring biomes in the regionalization of different groups of organisms. Therefore, diversity patterns of one group should ideally not be used as a surrogate to map general patterns or to understand the drivers of diversity of other co‐occurring groups. Thus, conservation efforts need to be designed and implemented for each organismal group.
... Additionally, if both annual and perennial components of plant communities are dispersal-limited, then we would expect a significant correlation of taxonomic and phylogenetic spatial turnover with geographic distance among communities (Daru et al., 2017). If annuals and perennials developed specific adaptations to cope with water limitations, then a significant correlation between turnover and climatic dissimilarity among communities would be expected (Daru et al., 2017;Fine and Kembel, 2011). ...
... Additionally, if both annual and perennial components of plant communities are dispersal-limited, then we would expect a significant correlation of taxonomic and phylogenetic spatial turnover with geographic distance among communities (Daru et al., 2017). If annuals and perennials developed specific adaptations to cope with water limitations, then a significant correlation between turnover and climatic dissimilarity among communities would be expected (Daru et al., 2017;Fine and Kembel, 2011). However, to our knowledge, no study has been undertaken to investigate the response of both annual and perennial species to the same aridity gradient. ...
... Both climatic and topo-edaphic variables explained more variance in the taxonomic and phylogenetic turnover of annuals and perennials than spatial variables, reinforcing our view of adaptation to local factors. Alternatively, niche conservatism of recently diversified lineages in the Mediterranean basin may also be an essential process underlying these patterns through slow evolution of niches that keeps species in their area of origin, regardless of their dispersal capacity (Daru et al., 2017). ...
Article
Aridity is a critical driver of the diversity and composition of plant communities. However, how aridity influences the phylogenetic structure of functional groups (i.e. annual and perennial species) is far less understood than its effects on species richness. As perennials have to endure stressful conditions during the summer drought, as opposed to annuals that avoid it, they may be subjected to stronger environmental filtering. In contrast, annuals may be more susceptible to interannual climatic variability. Here we studied the phylogenetic structure of the annual and perennial components of understorey plant communities, along a regional aridity gradient in Mediterranean drylands. Specifically, we asked: (1) How do species richness (S) and phylogenetic structure (PS) of annuals and perennials in plant communities respond to aridity? (2) What is the contribution of other climatic and topo-edaphic variables in predicting S and PS for both components? (3) How does the taxonomic and phylogenetic turnover of annuals and perennials vary with spatial and environmental distances? We assessed annuals’ and perennials’ species richness, the phylogenetic structure at deep and shallow phylogenetic levels, and taxonomic and phylogenetic turnover along spatial and environmental distances. We found no relationship between annuals’ richness and aridity, whereas perennials’ richness showed a unimodal pattern. The phylogenetic structure of annuals and perennials showed contrasting responses to aridity and negatively correlated with topo-edaphic variables. We found phylogenetic clustering at intermediate-to-higher aridity levels for annuals, and at lower aridity levels for perennials. Both taxonomic and phylogenetic turnover in annuals and perennials correlated with the environmental distance rather than with spatial distance between communities, suggesting adaptation to local factors. Overall, our results show a decoupling in the response of the phylogenetic structure of annual and perennial components of plant communities to aridity in Mediterranean drylands. Our findings have significant implications for land management strategies under climate change.
... The association of species assemblages into distinct phylogenetically delimited biogeographic units can capture historical processes, such as diversification, niche conservatism, dispersal and extinction that have operated over millions of years (Crisp & Cook, 2012;Daru et al., 2017;Guo et al., 2012;Wu et al., 2016). Recently, phylogenetic information for plants has begun to be incorporated into regionalization schemes, which has shown how such evolutionary data can provide new insights into the spatial structure of biodiversity, and reveal hidden evolutionary affinities between vegetation types (Daru et al., 2016(Daru et al., , 2017Segovia et al., 2020). ...
... The association of species assemblages into distinct phylogenetically delimited biogeographic units can capture historical processes, such as diversification, niche conservatism, dispersal and extinction that have operated over millions of years (Crisp & Cook, 2012;Daru et al., 2017;Guo et al., 2012;Wu et al., 2016). Recently, phylogenetic information for plants has begun to be incorporated into regionalization schemes, which has shown how such evolutionary data can provide new insights into the spatial structure of biodiversity, and reveal hidden evolutionary affinities between vegetation types (Daru et al., 2016(Daru et al., , 2017Segovia et al., 2020). The means by which vegetation types are grouped into compositional units has major implications for conservation, landscape management and projected ecosystem change, and the implementation of a phylogenetic perspective may provide additional information beyond traditional hotspot approaches. ...
... The means by which vegetation types are grouped into compositional units has major implications for conservation, landscape management and projected ecosystem change, and the implementation of a phylogenetic perspective may provide additional information beyond traditional hotspot approaches. As suggested by Daru et al. (2017), more evolutionarily distinct phyloregions, or phylogenetically delimited groups of assemblages, might deserve greater conservation priority since they may encompass more rare and distinct biodiversity. Thus, by grouping species assemblages into biogeographic units using information on their shared evolutionary histories (Holt et al., 2013), we can gain insight into the evolutionary and ecological processes shaping species geographical distributions, which can in turn serve as a tool to help guide conservation projects on the basis of evolutionary heritage. ...
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Abstract Aim We used a phylogenetic approach to group assemblages of woody plant into major vegetation units in the Atlantic Forest, thus for the first time incorporating information on species evolutionary relationships into a bioregionalization of this critical hotspot. A phylogenetic regionalization will provide a spatially explicit framework for answering many basic and applied questions in biogeography, ecology and conservation. Location Atlantic Forest. Taxon Angiosperms Methods Our data set comprises 614 genera and 116 families, spread over 1,755 assemblages. To place assemblages in a multivariate evolutionary composition space, we used a phylogenetically informed ordination analysis, and to determine what the main phylogenetic groups of assemblages were, we used K‐means clustering based on phylogenetic dissimilarity of assemblages. To quantify how well environmental variables distinguish the phylogenetic groups found, we implemented classification tree approaches. Then, to explore the evolutionary turnover between the phylogenetic groups, we calculated phylogenetic beta diversity. Finally, we determined the lineages that are most strongly associated with individual phylogenetic groups using an indicator analysis for lineages. Results Our analyses suggest that there are seven principal groups, in terms of evolutionary lineage composition, in the Atlantic Forest. The greatest turnover of phylogenetic lineage composition separates tropical evergreen rain forest and semideciduous assemblages from subtropical and highland assemblages. The mixed subtropical forest showed the lowest phylogenetic compositional similarity values with other groups. Tropical rain forest had the highest number of significant indicator lineages, and the highest values of the indicator statistic for lineages. Main conclusions We found that the most pronounced evolutionary division separates southern and highland tree assemblages from those occurring under more tropical climates and at lower elevations. Our phylogenetic analyses point to an environmentally driven compositional division, likely based on the regular occurrence of freezing versus non‐freezing temperatures. Precipitation and edaphic regimes that assemblages experience had less definitive effects on their evolutionary lineage composition.
... However, more classical bioregional schemes were delineated based on taxonomical similarity across geographical space (e.g. Birks 1976;Moreno-Saiz et al. 2013), which is unlikely to have adequately captured species' evolutionary affinities and, thus, may have underrated the importance of historical factors (Daru et al. 2017). Nevertheless, the recent incorporation of phylogenetic information in bioregionalization exercises could help overcoming this potential flaw (Holt et al. 2013;Daru et al. 2017), which may be particularly relevant for lineages with long and complex evolutionary histories, such as ferns (Rothfels et al. 2015;Testo and Sundue 2016;Lehtonen et al. 2017). ...
... Birks 1976;Moreno-Saiz et al. 2013), which is unlikely to have adequately captured species' evolutionary affinities and, thus, may have underrated the importance of historical factors (Daru et al. 2017). Nevertheless, the recent incorporation of phylogenetic information in bioregionalization exercises could help overcoming this potential flaw (Holt et al. 2013;Daru et al. 2017), which may be particularly relevant for lineages with long and complex evolutionary histories, such as ferns (Rothfels et al. 2015;Testo and Sundue 2016;Lehtonen et al. 2017). ...
... Nevertheless, phylogenetic bioregionalization poses the advantage of being much less sensitive to different taxonomic treatments than earlier bioregionalization exercises that were based exclusively on taxonomic dissimilarity. For example, apomictic Dryopteris affinis taxa are very closely related in the phylogeny, thus contributing very little to phylogenetic beta diversity despite they may notably increase taxonomic dissimilarity among bioregions (Daru et al. 2017). ...
Article
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Biogeographic regions have been extensively used as reference units in macroecological studies and to prioritize biodiversity conservation efforts. However, classical bioregionalizations were delineated based on taxonomical similarity across space, and thus the importance of historical factors may have been underrated. This limitation may be particularly relevant for lineages with long and complex evolutionary histories, such as ferns. Here, we drew on an exhaustive distribution dataset including all fern species and subspecies of Europe (661 grid-cells of c. 110 × 110 km each), as well as a nearly complete molecular phylogeny to define fern phyloregions based on their phylogenetic relatedness. Also, we quantified the degree of specificity of individual phylogenetic clades to the phyloregions using a new index of geographical confinement based on phylogenetic diversity. Six distinct phyloregions were identified, with a primary divide between north-eastern and south-western Europe. Both phylogenetic beta diversity and clade specificity were overall low, supporting the idea that dispersal limitation is not a major driver of fern distribution. Yet, the phylogenetic specificity analysis revealed that ancient fern lineages show preference for northern latitudes, which explained the northeast to southwest split of the territory. More than 40 years after the only bioregionalization analysis for the European fern flora, our study provides a fresh regional delineation that takes into account the evolutionary history of the group. In addition to classical bioregionalization approaches, our phylogenetic specificity index allowed us to elucidate the identity of the clades that ultimately shaped the bioregions, which might otherwise had remained obscure.
... However, more classical bioregional schemes were delineated based on taxonomical similarity across geographical space (e.g. Birks 1976;Moreno-Saiz et al. 2013), which is unlikely to have adequately captured species' evolutionary affinities and, thus, may have underrated the importance of historical factors (Daru et al. 2017). Nevertheless, the recent incorporation of phylogenetic information in bioregionalization exercises could help overcoming this potential flaw (Holt et al. 2013;Daru et al. 2017), which may be particularly relevant for lineages with long and complex evolutionary histories, such as ferns (Rothfels et al. 2015;Testo and Sundue 2016;Lehtonen et al. 2017). ...
... Birks 1976;Moreno-Saiz et al. 2013), which is unlikely to have adequately captured species' evolutionary affinities and, thus, may have underrated the importance of historical factors (Daru et al. 2017). Nevertheless, the recent incorporation of phylogenetic information in bioregionalization exercises could help overcoming this potential flaw (Holt et al. 2013;Daru et al. 2017), which may be particularly relevant for lineages with long and complex evolutionary histories, such as ferns (Rothfels et al. 2015;Testo and Sundue 2016;Lehtonen et al. 2017). ...
... Nevertheless, phylogenetic bioregionalization poses the advantage of being much less sensitive to different taxonomic treatments than earlier bioregionalization exercises that were based exclusively on taxonomic dissimilarity. For example, apomictic Dryopteris affinis taxa are very closely related in the phylogeny, thus contributing very little to phylogenetic beta diversity despite they may notably increase taxonomic dissimilarity among bioregions (Daru et al. 2017). ...
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Climate change is a major driver of biodiversity decline with pervasive effects in biodiversity hotspots, where many endemic and threatened species thrive. However, the biological drivers of extinction susceptibility remain largely elusive, which hampers the implementation of effective conservation policies. Here, we advocate for the use of phylogenies as a complementary tool to inform policy makers. If we assume that the traits that determine extinction susceptibility are somewhat evolutionarily conserved, identifying the clades that accumulate a disproportionate amount of threatened species may help to mitigate potential increases in extinction risk among currently unthreatened species in these clades, even if the underlying biological drivers are unknown. We focused on the complete endemic angiosperm flora of a Mediterranean hotpot (Iberian Peninsula) to examine phylogenetic patterns in extinction risk expressed as IUCN categories (Least Concern “LC”, Near Threatened “NT”, Vulnerable “VU”, Endangered “EN” and Critically Endangered “CR”) using alpha and beta diversity metrics, comparative methods and a “hot node” approach. Phylogenetic diversity was significantly low for EN species and marginally significant for NT and CR, while LC and VU categories showed random pattern. Phylogenetic beta diversity (PBD) between IUCN categories was intermediate (0.40 – 0.61) and predominantly due to the “true” turnover component of PBD. Phylogenetic turnover was significantly low between NT – VU and VU – EN, suggesting that closely related species tend to show different threat status. In contrast, the comparisons involving the CR category sit toward the higher tail of the distribution, indicating a somewhat higher degree of clade specificity for CR species. In line with these patterns, phylogenetic signal in extinction risk was rather low (lambda = 0.23). Several of the “hot” clades that accumulated a significantly high number of species with the same threat status were specific to certain IUCN categories, yet few of them were observed across the categories. Most notably, the Caryophyllales stood out as the main threat-accumulating lineage, particularly within the Plumbaginaceae. All in all, our results indicate that few phylogenetic clades concentrate a great fraction of the extinction-risk gradient in the endemic flora of the western Mediterranean, and monitoring programs should pay particular attention to these extinction-prone lineages.
... Thirdly, we hypothesise that there will be low phylobeta diversity at deep phylogenetic levels across restingas, indicating unrestricted colonisation by distantly related lineages (i.e. plant families, such as Myrtaceae and Fabaceae) with extensive geographic ranges along the AFD (Daru et al., 2017). We also hypothesise that there will be high phylobeta diversity at shallow phylogenetic levels due to: (i) the lack of time for plant species to disperse out of their local assemblages; and (ii) niche conservatism of these more derived lineages that colonised restingas from neighbouring ecosystems: through slow evolution of niches, species tend to remain in their area of origin, regardless of their dispersal capacity (Daru et al., 2017). ...
... plant families, such as Myrtaceae and Fabaceae) with extensive geographic ranges along the AFD (Daru et al., 2017). We also hypothesise that there will be high phylobeta diversity at shallow phylogenetic levels due to: (i) the lack of time for plant species to disperse out of their local assemblages; and (ii) niche conservatism of these more derived lineages that colonised restingas from neighbouring ecosystems: through slow evolution of niches, species tend to remain in their area of origin, regardless of their dispersal capacity (Daru et al., 2017). ...
... We suggest two main processes for these patterns, namely dispersal limitation and niche conservatism, also discussed in other studies (e.g. Daru et al., 2017). Geographic distances are important to phylobeta diversity as a surrogate for connectivity or isolation between assemblages. ...
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Question How do ecological and evolutionary processes affect the phylogenetic alpha and beta diversity of angiosperm tree assemblages in an evolutionarily young coastal environment? Location Coastal vegetation of the Brazilian Atlantic forest domain (restingas), spanning 20º of latitude. Methods We calculated phylogenetic alpha and beta diversity at deep and shallow levels for angiosperm tree species in 136 circular sites of 10 km diameter (hereafter assemblages). The metrics we used for alpha diversity were the mean pairwise distance (MPD) and mean nearest taxon distance (MNTD), and mean pairwise distance separating species in two assemblages (Dpw) and mean nearest taxon distance separating species in two assemblages (Dnn) for beta diversity. We then investigated the relationship between phylogenetic diversity, historical (Quaternary) and current climatic variables, and edaphic conditions along the latitudinal gradient. Results We found that MPD increased with precipitation and latitude. MNTD increased with modern‐day temperature, historical temperature instability and precipitation, and it was higher in more fertile and less saline soils. Dpw did not correlate either with geographic or environmental distances between assemblages. However, Dnn was strongly correlated with both geographic and environmental distances between assemblages. Conclusions The increase in MPD with precipitation and latitude suggests the presence of old Gondwanan lineages colonising restingas from refugia at higher latitudes. The increase in MNTD with modern‐day temperature, historical temperature instability, precipitation, and being higher in more fertile and less saline soils indicates that the distance between phylogenetic closest relatives tends to increase in assemblages less affected by environmental filtering. Low Dpw suggests the presence of widespread lineages across restingas, whereas high Dnn may indicate niche conservatism and dispersal limitation of more derived lineages. Our results offer insights into how ecological and evolutionary processes act to shape current patterns of biodiversity in geologically young environments.
... D iscrete differences between the fauna and flora in different regions of the world have led biologists to delineate a nested hierarchy of biogeographic regions [1][2][3][4] . Starting with metrics of species turnover across space (beta diversity), Holt et al. 2 identified 20 zoogeographic regions within which species are on average relatively closely related to each other, more so than between regions. ...
... These probabilistic models are used extensively in population genetics 14 and Natural Language Processing 15 and have also been applied in ecology 16 . By contrast, previous approaches to partitioning global diversity have used hard clustering techniques where by a locality can only belong to one realm [2][3][4]17 . In the Grade of Membership model, the species present at each location consist of a proportional mix of all biotas. ...
... To infer species motifs, as in previous studies of realms [2][3][4]17 , we start with an N × G data matrix of 0s and 1s denoting the absence and presence 18 of all terrestrial breeding bird species (g = 1, 2, …, G, here G = 9518) resolved to 1°× 1°across the globe (n = 1, 2,…, N; here n = 17,441), respectively. We fix the number of motifs (K) a priori and estimate (1) the probability of membership of the gth species in the kth motif (θ kg ) and (2) the proportional contribution of the kth motif to the nth map cell (ω nk , Supplementary Fig. 1 illustrates the general method). ...
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Many models to explain the differences in the flora and fauna of tropical and temperate regions assume that whole clades are restricted to the tropics. We develop methods to assess the extent to which biotas are geographically discrete, and find that transition zones between regions occupied by tropical-associated or temperate-associated biotas are often narrow, suggesting a role for freezing temperatures in partitioning global biotas. Across the steepest tropical-temperate gradient in the world, that of the Himalaya, bird communities below and above the freezing line are largely populated by different tropical and temperate biotas with links to India and Southeast Asia, or to China respectively. The importance of the freezing line is retained when clades rather than species are considered, reflecting confinement of different clades to one or another climate zone. The reality of the sharp tropical-temperate boundary adds credence to the argument that exceptional species richness in the tropics reflects species accumulation over time, with limited transgressions of species and clades into the temperate.
... For example, patterns phylogenetic regionalization may result from the clustering of species in their ancestral biome or following a long-distance dispersal event, and changes in landforms may limit (e.g. a mountain range) or promote (e.g. a land bridge) dispersal (Daru et al., 2017). The field of phylogenetic biogeography, founded in the 1960s with the emergence of cladistics (Hennig, 1965) and its application to biogeography (Brundin, 1965), aims to uncover the most likely pathways of speciation, extinction, and dispersal that lineages have taken to arrive at their current locations, given their phylogenetic relationships (Ronquist & Sanmartín, 2011). ...
... The field of phylogenetic biogeography, founded in the 1960s with the emergence of cladistics (Hennig, 1965) and its application to biogeography (Brundin, 1965), aims to uncover the most likely pathways of speciation, extinction, and dispersal that lineages have taken to arrive at their current locations, given their phylogenetic relationships (Ronquist & Sanmartín, 2011). Understanding these pathways can also enable tests of hypotheses about the mechanisms behind the patterns, such as the contribution of mountain uplift to the radiation of new species or the role of glaciation or climate change in causing extinction (Daru et al., 2017;Ronquist & Sanmartín, 2011;Sanmartín, 2012). ...
Thesis
Global change is putting unprecedented pressure on plants to adapt or migrate to avoid extinction. Studying the past responses of plants to environmental change can shed light on the potential evolutionary outcomes and sensitivity of species to future environmental change. These processes are especially relevant to highly diverse, evolutionarily rich, and ecologically vulnerable alpine ecosystems. My PhD aims to narrow the uncertainty about how plant lineages with a range of lowland and alpine species will be impacted by global change by studying the historical biogeography, trait and species diversification, and ecological strategies of alpine species in a phylogenetic framework. Chapter 1 reviews current knowledge about the relative roles of migration and adaptation in plant responses to climate change and how historical biogeographical and evolutionary modeling provide novel insights to these questions. Chapter 2 applies recent developments in sequencing methods to construct a new, near-complete phylogeny of a diverse species radiation, New Zealand Veronica, also addressing questions about how to resolve difficulties in reconstructing phylogenetic relationships in recent, rapid radiations such as Veronica. This group serves as an important case study for further evolutionary questions about the relationships between habitat, species diversity, and environmental change. Chapter 3 estimates the contributions of in situ cladogenesis (i.e., the formation of new species) and colonization from lowland habitat in generating mountain diversity in Veronica. Further, the chapter explores the importance of niche adaptation and divergence in contributing to cladogenesis, and presents a general, conceptual model to understand how mountain diversity accumulates. Chapter 4 compares the potential range and niche change required for plant species to respond to future climate change relative to the change undergone since the mid-Holocene. It also determines which niche traits can predict “winners” and “losers” under climate change. Chapter 5 discusses the main findings of the thesis and ends with proposed avenues for future research.
... The field of phylogenetics holds promise beyond simply providing clustering methods. Phylogenetics can actually provide units for biogeographic analysis, replacing taxa with clades across levels of depth in the phylogenetic tree, and thus has become integral in understanding the distribution of biodiversity patterns (Daru et al., 2017). Wallace originally envisioned a scheme based on the relationships between species, not only distributional data (Holt et al., 2013). ...
... Wallace originally envisioned a scheme based on the relationships between species, not only distributional data (Holt et al., 2013). Phylogenetic trees provide important information about the evolutionary relationships between species, allowing for schemata to be derived fulfilling Wallace's original vision (Holt et al., 2013;Daru et al., 2017). In the past, regions were delineated based on species distributions and the presence (or absence) of characteristic genera (Wallace, 1876;Rueda et al. 2013). ...
Chapter
Regionalization is the discipline that groups geographic areas of the world into regions based on predetermined criteria. While these may be abiotic criteria (e.g., climate), in biogeography the term (more specifically referred to as bioregionalization), has essentially come to mean that regions are defined on the basis of distribution patterns in living organisms. Most often this has been done using species of tetrapod vertebrates and vascular plants, with other studies considering other taxa, or shared branch lengths in the phylogenies for these groups. This process was initially performed intuitively, but currently, this is achieved using increasingly sophisticated algorithms. The results for approaches using different methods and looking at different taxa tend to converge towards common global schemata which can be explained using past and present climate, plate tectonics, and the evolution of life on Earth. Preserving distinctive assemblages of living organisms, as illustrated in regionalisation exercises, is increasingly viewed as one important facet of biodiversity conservation.
... We subsequently estimated PE and PD SES (see the Supplementary Material for more details on this metric) for each grid cell using functions from the 'phyloregion' 1.0.4 [94][95][96] and the 'PhyloMeasures' 2.1 [97] R packages, respectively. Afterwards, following [11,98], we located the biodiversity hotspots for all taxonomic and phylogenetic biodiversity metrics that correspond to the highest 1% values (L1) for each of these metrics. ...
... We identified these biodiversity hotspots using functions from the 'phyloregion' 1.0.4 [94][95][96] R package. Biodiversity hotspots are herein and hereafter defined as regional biodiversity hotspots (i.e., hotspots within global biodiversity hotspots [99]). ...
Article
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Sparsely vegetated habitats of cliffs and screes act as refugia for many regional and local endemic specialized plant taxa most of which have evolved precisely for that type of habitat. The interplay between taxonomic, phylogenetic, and functional plant diversity on rock and scree habitats of extreme environmental conditions, enlightens the relations of plant communities and ecosystems and facilitates management planning for the conservation of biodiversity and ecosystem services. The identification of biodiversity patterns and hotspots (taxonomic, phylogenetic, and functional) contributes to the integration of the ecosystem services (ES) approach for the mapping and assessment of ecosystems and their services (MAES) implementation in Greece and the creation of thematic maps based on the MAES reporting format. The overlap among the protected areas’ network revealed that almost all areas of cliffs and screes of medium, high, and very high taxonomic and phylogenetic plant endemism are included in the Natura 2000 area network. The results of this study provide the baseline information for ES assessments at sparsely vegetated land of cliffs and screes. Our results contribute to the implementation of certain indicators of the national set of MAES indicators in Greece such as (a) floristic diversity and (b) microrefugia of endemic diversity and support of decision-making.
... A high dispersal rate will cause fewer species to be confined to a specific area, leading to a lower concentration of endemic species 49 . Conversely, the phylogenetic composition of communities including species with poor dispersal abilities will cause the aggregation of close relatives, leading to increased phylogenetic endemism 52 . ...
... However, insights into more complex evolutionary processes such as dispersal, speciation and extinction shaping biodiversity patterns are captured at larger continental to global extents (e.g. ref. 52 ). We integrated our results across variations of tree topologies and branch lengths for both birds and amphibians by repeating the phylogenetic endemism calculation for each 100 trees from the posterior distribution and taking the median across grid cells for further analysis. ...
Article
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Areas of endemism are important in biogeography because they capture facets of biodiversity not represented elsewhere. However, the scales at which they are relevant to research and conservation are poorly analysed. Here, we calculate weighted endemism (WE) and phylogenetic endemism (PE) separately for all birds and amphibians across the globe. We show that scale dependence is widespread for both indices and manifests across grain sizes, spatial extents and taxonomic treatments. Variations in taxonomic opinions—whether species are treated by systematic ‘lumping’ or ‘splitting’—can profoundly affect the allocation of WE hotspots. Global patterns of PE can provide insights into complex evolutionary processes but this congruence is lost at the continental to country extents. These findings are explained by environmental heterogeneity at coarser grains, and to a far lesser extent at finer resolutions. Regardless of scale, we find widespread deficits of protection for endemism hotspots. Our study presents a framework for assessing areas for conservation that are robust to assumptions on taxonomy, spatial grain and extent.
... In such circumstances, dispersal or immigration can contribute to more shared species and lower the opportunity for lineage differentiation or speciation, resulting in increased community similarity (Olden & Rooney, 2006). Consequently, the current patterns of beta diversity and faunistic differentiation are proposed to be shaped by a combination of environmental filtering, historical differences and biotic interactions (Alahuhta et al., 2017;Daru, Elliott, Park, & Davies, 2017). ...
... One method is to infer historical biotic changes by estimating beta diversity patterns along phylogenetic time-scales (e.g., Cowma, Parravicini, Kulbicki, & Floeter, 2017;Mazel et al., 2017); another method uses fossil collections (e.g., Graham et al., 1996;Xing et al., 2015). The former method, which is based on molecular phylogenetic data, provides a transparent taxonomic assignment and successive time slices of changes in beta diversity (Mazel et al., 2017), shedding light on biodiversity changes in deep time (Daru et al., 2017). However, this approach is not without problems (Marshall, 2017), considering past extinctions and the potential for geographical range shifts (Silvestro et al., 2016). ...
Article
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Aim Historical changes in community structure underlie modern spatial diversity patterns, but few empirical studies have focused on the variation in the community composition of fossil assemblages at large spatio‐temporal scales. We investigated how the spatial differentiation of mammal communities changed in China throughout the Cenozoic in response to tectonic uplift and palaeoclimatic changes and explore the timing of the emergence of the modern spatially structured faunas. Location China. Time period Cenozoic (from 65 Ma to the present). Major taxa studied Terrestrial mammals. Methods We used a compiled database of the distributions of fossils and extant mammals to compare the multiple‐site beta diversity among families and genera within six time intervals of the Cenozoic using Sørensen dissimilarity (βsor) and Simpson dissimilarity (βsim). To investigate the timing of the emergence of the modern spatially structured faunas, we applied hierarchical clustering and non‐metric multidimensional scaling ordination based on pairwise βsim among seven zoogeographical regions for each time slice. Results The multiple‐site beta diversity at the family level displayed hump‐shaped changes during the Cenozoic, and it peaked in the Eocene and gradually decreased towards the present. However, the genus‐level multiple‐site beta diversity remained rather constant throughout the Cenozoic. Pronounced variations in the relationships among the zoogeographical regions were revealed in both the cluster analyses and the ordinations. The modern spatial structure of mammal faunas at the family level was broadly similar to those observed in the Pliocene and Pleistocene. Main conclusions The spatial differentiation of mammal faunas in China dates back to the Eocene and pre‐dates the formation of modern topography and climate. Throughout the Cenozoic, the spatial structure of mammal faunas was reorganized by an interplay of the uplift of the Tibetan Plateau, the emergence of the monsoon system and global macroevolutionary processes. The modern relationships among zoogeographical regions at the family level were established in the Pleistocene.
... This computes all pairwise dissimilarities between the accessions in a cluster and accessions in another cluster and considers the largest value of these dissimilarities as a distance between the two clusters. To assess the optimal number of clusters, we used the elbow method 71 , which plots the total within-cluster sum of squares (WSS) against the number of clusters to show the 'elbow' where the WSS rate of decrease slows and indicates diminishing returns with more clusters 72 . ...
Article
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Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity. Multiple population genetic analyses indicate the presence of four genetic clusters and show that the most genetically differentiated cluster contains accessions imported from Southeast Asia (mainly those from Thailand). We find that genetic structure was strongly associated with three traits: trunk circumference, fruit blush colour and intensity in M. indica. This suggests that the history of these accessions could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype can improve the accuracy of genomic selection, which can assist the future development of new cultivars.
... Climate change, particularly during the Pleistocene, was an important factor affecting species richness, endemism, distribution, population persistence and the threat of extinction in many animal lineages (Daru et al., 2017;Nogués-Bravo et al., 2010;Sandel et al., 2011). More recently, climate change, along with changes in species interactions in response to anthropogenic habitat conversion, has resulted in local population extinctions, as well as species shifts in biogeography, population size, patterns of gene flow and subpopulation isolation (Chen et al., 2011;Lenoir & Svenning, 2015;Parmesan & Yohe, 2003). ...
Article
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Aim Determining the mechanisms by which climate change and human activities affect patterns of ecological specialization in different genetic units of the same species is crucial for developing local or regionally‐based conservation solutions. This study uses species distribution models and genetic analysis to (1) identify the evidence of intraspecific differences in the population size and distribution of the three extant lineages (Sichuan/Gansu (SG), Qinling (QL) and Shennongjia (SNJ)) of Sichuan snub‐nosed monkeys and (2) determine why some lineages have lower population numbers, a smaller geographical distribution, and are more threatened with extinction. Location China. Methods We used n‐dimensional hypervolume modelling and genotype‐environment association (GEA) models to compare the climatic niches of three snub‐nosed monkey lineages, SDMs to reconstruct the historical, current and future distributions of each lineage and SMC++ to calculate their effective population sizes. Results We found evidence of: (1) climatic niche differentiation among the SG, QL and SNJ lineages of Sichuan snub‐nosed monkeys; (2) geographical isolation combined with a decrease in population size during the LGM resulted in ecological specialization among these three lineages; and (3) a decline in climatic suitability and anthropogenically driven land conversion, combined with small population size and a narrow distributional range, indicates that the SNJ lineage is at a greater risk of extinction than the SG and QL lineages. Main conclusions We demonstrate that during the LGM a reduction in habitat suitability driven by climate change, in concert with decreasing population size, resulted in the geographical isolation of the three Sichuan snub‐nosed monkey subpopulations, leading to lineage differences in ecological specialization. GEA models and hypervolume models demonstrated that the three lineages occupy different ecological niches. Based on lineage‐level models, the SNJ and QL lineages should be the immediate focus of conservation efforts due to their small effective population size and expected future reductions in available suitable habitats. The modelling approach used here is robust and can be applied effectively to examine the biogeography, recent evolutionary history and effective population size of other endangered animal taxa.
... Dispersal rates also have important influences on PE. While higher dispersal rates reduce the concentration of endemic species, poor dispersal ability increases endemism (Daru et al., 2017). ...
Article
Mapping biodiversity patterns across taxa and environments is crucial to address the evolutionary and ecological dimensions of species distribution, suggesting areas of particular importance for conservation purposes. Within Cactaceae, spatial diversity patterns are poorly explored, as are the abiotic factors that may predict these patterns. We gathered geographic and genetic data from 921 cactus species by exploring both the occurrence and genetic databases, which are tightly associated with drylands, to evaluate diversity patterns, such as phylogenetic diversity and endemism, paleo-, neo-, and superendemism, and the environmental predictor variables of such patterns in a global analysis. Hotspot areas of cacti diversity are scattered along the Neotropical and Nearctic regions, mainly in the desertic portion of Mesoamerica, Caribbean Island, and the dry diagonal of South America. The geomorphological features of these regions may create a complexity of areas that work as locally buffered zones over time, which triggers local events of diversification and speciation. Desert and dryland/dry forest areas comprise paleo- and superendemism and may act as both museums and cradles of species, displaying great importance for conservation. Past climates, topography, soil features, and solar irradiance seem to be the main predictors of distinct endemism types. The hotspot areas that encompass a major part of the endemism cells are outside or poorly covered by formal protection units. The current legally protected areas are not able to conserve the evolutionary diversity of cacti. Given the rapid anthropogenic disturbance, efforts must be reinforced to monitor biodiversity and the environment and to define/plan current and new protected areas.
... In Figure 2, dominant plant species such as Ficus virens, Morus alba and Broussonetia papyrifera are aggregated into four groups. The reason for this may be related to the dispersal limits the species assemblages into phylogenetic units [53]. So, besides the many propagules plants still have further evolved "edible" propagules, including males and females, to adapt to the disturbed riparian habitat. ...
Article
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Riparian zones possesses unique ecological position with biota differing from aquatic body and terrestrial lands, and plant–animal coevolution through a propagule-dispersal process may be the main factor for the framework of riparian vegetation was proposed. In the current study, the riparian forests and avifauna along with three subtropical mountainous riparian belts of Chongqing, China, were investigated, and multivariate analysis technique was adopted to examine the associations among the plants’ and birds’ species. The results show that: (1) the forest species’ composition and vertical layers are dominated by native catkins of Moraceae species, which have the reproductive traits with small and numerous propagules facilitating by frugivorous bird species, revealing an evolutionary trend different from the one in the terrestrial plant climax communities in the subtropical evergreen broad-leaved forests. The traits may provide a biological base for the plant–bird coevolution; (2) there are significant associations of plant–bird species clusters, i.e., four plant–bird coevolution groups (PBs) were divided out according to the plant species’ dominance and growth form relating to the fruit-dispersing birds’ abundance; (3) the correlation intensity within a PB ranks as PB I > II > IV > III, indicating the PB I is the leading type of coevolution mainly shaped by the dominant plant species of Moraceae; (4) the PB correlation may be a key node between patterns vs. process of a riparian ecosystem responsible for the riparian native vegetation, or even the ecosystem health. Our results contribute understanding the plant–animal coevolution interpreting the forests’ structures in riparian environments. The results may also be used by urban planner and managers to simulate the patterns for restoring a more stable riparian biota, a better functioning ecosystem in subtropical zone.
... We used functions from the "phyloregion" 1.0.4 R package [96][97][98] to locate the L1 hotspots. L1 hotspots, as herein outlined, come under the regional hotspots, according to [99]. ...
Article
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he ongoing climate change has already left its imprint on species distributions, with rare, endemic species being more threatened. These changes are more prominent in regional biodiversity hotspots, such as Greece, which is already facing the short term impacts of human induced climate change. Greek flora hosts numerous endemic medicinal and aromatic plant taxa (MAPs), which are economically important and provide integral ecosystem services. The genus Nepeta is one of the largest Lamiaceae genera, containing several MAPs, yet, despite its taxonomical and economical significance, it remains vastly understudied in Greece. We explore the effects of climate change on the range of the Greek endemic Nepeta MAPs, via a species distribution models (SDMs) approach in an ensemble modeling framework, using soil, topographical and bioclimatic variables as predictors in three different time steps. By doing so, we attempt to estimate the current and future extinction risk of these taxa and to locate their current and future species richness hotspots in Greece. The taxa analyzed are expected to experience severe range retractions, with minor intraspecific variation across all time steps (p > 0.05), driven mainly by soil- and aridity-related variables. The extinction risk status of only one taxon is predicted to worsen in the future, while all other taxa will remain threatened. Current species richness hotspots are mainly located in southern Greece and are projected to shift both altitudinally and latitudinally over time (p < 0.01).
... We used functions from [123] and the 'phyloregion' 1.0.4 R package [124][125][126] to estimate CWE and locate the L1 hotspots, respectively. L1 hotspots as herein outlined, come under the regional hotspots according to [127]. ...
Article
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Pollinators’ climate change impact assessments focus mainly on mainland regions. Thus, we are unaware how island species might fare in a rapidly changing world. This is even more pressing in the Mediterranean Basin, a global biodiversity hotspot. In Greece, a regional pollinator hotspot, climate change research is in its infancy and the insect Wallacean shortfall still remains unaddressed. In a species distribution modelling framework, we used the most comprehensive occurrence database for bees in Greece to locate the bee species richness hotspots in the Aegean, and investigated whether these might shift in the future due to climate change and assessed the Natura 2000 protected areas network effectiveness. Range contractions are anticipated for most taxa, becoming more prominent over time. Species richness hotspots are currently located in the NE Aegean and in highly disturbed sites. They will shift both altitudinally and latitudinally in the future. A small proportion of these hotspots are currently included in the Natura 2000 protected areas network and this proportion is projected to decrease in the coming decades. There is likely an extinction debt present in the Aegean bee communities that could result to pollination network collapse. There is a substantial conservation gap in Greece regarding bees and a critical re-assessment of the established Greek protected areas network is needed, focusing on areas identified as bee diversity hotspots over time.
... Although the global bioregionalization based on taxonomic data (Leroy et al., 2019) is so far the most comprehensive assessment for freshwater organisms, future analytical improvements can be provided and data included to evaluate whether these results are consistent with other freshwater organisms (Holt et al., 2013). Determining the drivers of biogeographical boundaries can also shed light on the processes related to the evolution and dispersal of freshwater organisms over time (Daru et al., 2017;Ficetola et al., 2017). Yet, prior to human intervention, no species of freshwater fish naturally occurred in all these biogeographic regions and only few species occurred in more than one region (Leroy et al., 2019;Rahel, 2007). ...
Chapter
Defining the number and geographical borders of regions containing similar organisms and high levels of endemism can shed light on the evolution and distribution of life on Earth. We provide an historical overview of studies delineating the global biogeographical regions of freshwater organisms, mainly focusing on fish, to understand whether aquatic and terrestrial organisms share similar distribution patterns. Then, we provide a geographical and biological description giving special attention to major biogeographical fish patterns and taxa present in each of the considered regions.
... For instance, the development of macroecology (Brown, 1995) conducted extensive research on ecological processes that determine large geographic scales patterns of distribution; while phylogeography (Avise, 2000) investigated the population-level geographic distribution of genealogical lineages. Additionally, the huge accumulation of DNA sequences and published phylogenies permitted the incorporation of phylogenetic information into community ecology and biogeographic regionalization (Daru et al., 2017;Graham et al., 2018) integrating seamlessly ecology, phylogeny, and biogeography. ...
Chapter
Biogeographic transition zones involve the passage from one biogeographic unit to another one at a variety of spatial and temporal scales. Environmental conditions and ecological factors allow their mixture and the co-occurrence but also constrain their distribution further into one another. The deconstruction of biota into biogeographical affinities allow detecting a gradual pattern of variation across transition zone and to map sites of highest compositional heterogeneity. Biogeographic transition zones represent areas of great interest because they synthesize evolutionary and ecological principles shaping biological distribution and differentiation.
... In Figure 2a, dominant plant species such as Ficus virens, Morus alba and Broussonetia papyrifera are aggregated into four groups. The reason for this may be related to the dispersal limits the species assemblages into phylogenetic units (Daru et al. (2017). So, besides the many propagules plants still have further evolved "edible" propagules, including males and females, to adapt to the disturbed riparian habitat. ...
Preprint
Full-text available
Riparian zone possesses ecological position with biota differing from aquatic body and terrestrial lands, and plant-animal coevolution may be the main factor for the framework of riparian vegetation. In the current study, the riparian plant community patterns along the subtropical mountainous riparian belts of Chongqing, China, was proposed to be regulated by co-evolving with the avifauna through propagule-dispersal process. The results show that: 1) the forests’ species composition and vertical layers are dominated by native catkins of Moraceae species with adapting traits of small and numerous propagules to frugivorous bird species, revealing an evolutionary trend different from the one in the terrestrial plant climax communities in the subtropics, and which forms a biological base for the plant-bird co-evolution; 2) there are significant associations of plant-bird species clusters, i.e., four plant-bird co-evolution groups (PBs) were divided out according to the plant species’ dominance and growth form relating to the fruit-dispersing birds’ abundance; 3) the correlation intensity within PB ranks as PBⅠ>Ⅱ>Ⅳ>Ⅲ, indicating the PBⅠis the leading type of co-evolution mainly shaped by the dominant plant species; 4) the PB correlation may be a key node between patterns vs. process of a riparian ecosystem responsible for the native vegetation, or even the ecosystem health. The results theoretically contribute new evidence to plant-animal co-evolution interpreting the forests’ characters in riparian environments, and urban planner and managers may simulate the native forests for restoring a more stable riparian biota, a better functioning ecosystem in subtropical zone.
... L1 SR and CWE hotspots are herein delineated as the cells belonging to the 1% quantile for each metric [111] and were located via the 'phyloregion' 1.0.4 R package [112][113][114]. The biodiversity hotspots as defined here refer to regional biodiversity hotspots [115]. ...
Article
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Human-induced climate- and land-use change have been affecting biogeographical and biodiversity patterns for the past two centuries all over the globe, resulting in increased extinction and biotic homogenization rates. High mountain ecosystems are more sensitive to these changes, which have led to physiological and phenological shifts, as well as to ecosystem processes’ deformation. Glacial relicts, such as arctic-alpine taxa, are sensitive indicators of the effects of global warming and their rear-edge populations could include warm-adapted genotypes that might prove—conservation-wise—useful in an era of unprecedented climate regimes. Despite the ongoing thermophilization in European and Mediterranean summits, it still remains unknown how past and future climate-change might affect the distributional patterns of the glacial relict, arctic-alpine taxa occurring in Greece, their European southernmost distributional limit. Using species distribution models, we investigated the impacts of past and future climate changes on the arctic-alpine taxa occurring in Greece and identified the areas comprising arctic-alpine biodiversity hotspots in Greece. Most of these species will be faced with severe range reductions in the near future, despite their innate resilience to a multitude of threats, while the species richness hotspots will experience both altitudinal and latitudinal shifts. Being long-lived perennials means that there might be an extinction-debt present in these taxa, and a prolonged stability phase could be masking the deleterious effects of climate change on them. Several ex situ conservation measures (e.g., seed collection, population augmentation) should be taken to preserve the southernmost populations of these rare arctic-alpine taxa and a better understanding of their population genetics is urgently needed.
... We identified these biodiversity hotspots using functions from the 'phyloregion' 1.0.4 R package (Daru et al., 2017;Daru et al., 2020a;Daru et al., 2020b). ...
Article
Full-text available
Climate change is predicted to dramatically affect mountain biodiversity and especially mountain pollination systems due to the mutual dependence between plants and pollinators. In this work, we investigate climate change effects on pollinator distribution and diversity along the altitudinal gradient of Mt. Olympus, a biodiversity hotspot. We used a species distribution modelling framework and predicted species richness hotspots, potential distribution and altitude change for 114 pollinator species, comprising bees, butterflies, and hoverflies along the altitudinal gradient (327–2596 m a.s.l.). We projected potential loss of suitable habitat and upward shift for most pollinator groups, with the exception of bumblebees and hoverflies which were predicted to descend. Pollinator extinctions were not forecasted; instead, we observed a pronounced species-specific response to climate change. Species richness hotspots will be relocated to higher altitudes and to the north-eastern mountain side. Projections for substantial but not detrimental climate change effects on pollinator fauna may be due to species differential resilience to climate change along with the existence of microrefugia on Mt. Olympus. Divergent response to global warming by bumblebees and hoverflies is probably due to species distribution modelling limitations, resulting in exclusion of the rarest species. We conclude that the predicted climate change impact stresses for the need of urgent conservation measures, including the expansion of the protection status over the whole mountain.
... A biogeographical regionalization is typically seen as a hierarchical system that classifies geographic areas according to their shared biotic composition. These hierarchical relations implicitly represent a shared evolutionary history among areas (Daru et al., 2017). Thus, biogeographical regionalization is the underlying framework for many basic and applied issues in ecology, evolution, and conservation (Kreft & Jetz, 2010;Wen et al., 2013;Morrone, 2018). ...
Article
Full-text available
Existing global regionalisation schemes for plants consider the compositional affinities among biotas, but these have not explicitly considered phylogenetic information. Here, we present for the first time, a phytogeographical delineation of the global vascular flora based on species-level evolutionary relationships. We analysed 8,738,520 geographical occurrence records for vascular plants together with a time‐calibrated phylogeny including 67,420 species. We constructed a global phylogenetic regionalisation by estimating species composition and phylogenetic beta diversity among 200×200 km grid cells across the world. We identified de novo 16 phytogeographical units that are deeply split into two clusters: Laurasian and Gondwanan. Our regionalisation broadly matches previous schemes, but also highlights the separation of the Gondwanan region into an Holotropical cluster and an Australian-Neozealandic-Patagonian cluster. In contrast, no clear split among Laurasian and Gondwanan biotas was retrieved when omitting phylogenetic information. The integration of phylogenetic and geographical information provides new insights into the delineation of phytogeographical areas and their historical relationships, enabling the identification of three large, clearly differentiated biotas, here referred to as kingdoms: Holarctic, Holotropical, and Austral. Our results provide further evidence for delineating transition zones and show a clear latitudinal pattern of increasing evolutionary distinctiveness towards the poles.
... The relative contribution of a species to PD can also be used to represent evolutionary distinctiveness (ED), which reflects the degree of phylogenetic isolation/uniqueness for a particular species (Isaac et al., 2007;Pavoine et al., 2005;Redding and Mooers, 2006). When ED is combined with extinction risk derived from the International Union for Conservation of Nature (IUCN) Red List, the Evolutionary Distinctiveness and Global Endangerment (EDGE) index can be used to prioritize species for conservation not only based on their likelihood of extinction, but also on their irreplaceability (Daru et al., 2020(Daru et al., , 2017Isaac et al., 2007;Redding and Mooers, 2006). Each of these metrics is informative for a specific facet of biodiversity and when integrated within a unified framework across multiple taxonomic groups, can provide a more robust and comprehensive characterization of evolutionary history and biodiversity patterns that can be used to design more effective conservation initiatives (González-Orozco et al., 2015;Posadas et al., 2001). ...
Article
Full-text available
Malaysia is recognized as a megadiverse country and biodiversity hotspot which necessitates sufficient levels of habitat protection and effective conservation management. However, conservation planning in Malaysia has hitherto relied largely on species distribution data without taking into account the rich evolutionary history of taxa. This represents the first study that integrates spatial and evolutionary approaches to identify important centers of diversity, endemism, and bioregionalization that can be earmarked for conservation priorities in Peninsular Malaysia. Using georeferenced species occurrences, comprehensive phylogenies, and threat assessments of frogs and lizards, we employed a spatial phylogenetics framework that incorporates various diversity metrics including weighted endemism, phylogenetic diversity, phylogenetic endemism, and evolutionary distinctiveness and global endangerment. Ten areas of high conservation value were identified via the intersection of these metrics—northern Perlis, Langkawi Geopark, southern Bintang range, Cameron Highlands, Fraser’s Hill, Benom-Krau complex, Selangor-Genting complex, Endau-Rompin National Park, Seribuat Archipelago (Tioman and Pemanggil Islands), and southern Johor. Of these, Cameron Highlands requires the highest conservation priority based on the high numbers of endangered and evolutionary distinct species coupled with severe environmental degradation and inadequately protected areas. Other areas, especially in the northwestern (states of Kedah and Penang) and northeastern regions (states of Kelantan) were not only identified as areas of high conservation value but also areas of biogeographic importance. Taken together, frogs and lizards demonstrate distinct east-west and north-south patterns of bioregionalization that are largely modulated by mountain ranges.
... A biogeographical regionalization is typically seen as a hierarchical system that classifies geographic areas according to their shared biotic composition. These hierarchical relations implicitly represent a shared evolutionary history among areas (Daru et al., 2017). Thus, biogeographical regionalization is the underlying framework for many basic and applied issues in ecology, evolution, and conservation (Kreft & Jetz, 2010;Wen et al., 2013;Morrone, 2018). ...
Preprint
Existing global regionalisation schemes for plants consider the compositional affinities among biotas, but these have not considered phylogenetic information explicitly. Incorporating phylogenetic information may substantially advance our understanding of the relationships among regions and the synopsis of biogeographical schemes, because phylogeny captures information on the evolutionary history of taxa. Here, we present the first phytogeographical delineation of the global vascular flora based on the evolutionary relationships of species. We analysed 8,738,520 geographical occurrence records for vascular plant species together with a time-calibrated phylogenetic tree including 67,420 species. We estimated species composition within 200 × 200 km grid cells across the world, and used a metric of phylogenetic beta diversity to generate a phylogenetic delineation of floristic regions. We contrasted these results with a regionalisation generated using a taxonomic beta diversity metric. We identified 16 phylogenetically distinct phytogeographical units, deeply split into two main clusters that broadly correspond to the Laurasia-Gondwana separation. Our regionalisation broadly matches currently recognized phytogeographical classifications, but also highlights that the Gondwanan area is split into a large Holotropical cluster and an Australian-NeoZelandic-Patagonian cluster. In turn, we found that the northernmost and southernmost units have the most evolutionarily distinct vascular plant assemblages. In contrast, taxonomic dissimilarity returned a regionalisation composed of 23 units with a high degree of shared taxa between Laurasian and Gondwanan areas, with no clear split among their biotas. The integration of phylogenetic information provided new insights into the historical relationships among phytogeographical units, enabling the identification of three large, clearly differentiated biotas, here referred to as kingdoms: Holarctic, Holotropical, and Austral. Our regionalization scheme provides further evidence for delineating transition zones between the Holarctic and Holotropical kingdoms. The latitudinal patterns of evolutionary distinctiveness of vascular plant assemblages are consistent with recent evidence of higher and more recent diversification of flowering plants outside tropical regions.
... Factors selecting for favourable combinations of traits are generally scale-dependent (Garnier et al., 2016). At continental scales, trait pools are defined by the interplay of macroclimate and evolutionary history (Moncrieff et al., 2016;Mucina, 2019), with the latter constrained by the long-term isolation of major land forms (Chaboureau et al., 2014) and by the phylogenetic origin of species occurring in a biogeographic realm (Holt et al., 2013;Daru et al., 2017;Daru et al., 2018). At the scale of local plant communities, trait pools are further constrained by biotic and abiotic filters that select species assemblages with favourable trait syndromes (Lavorel et al., 1997;Zobel, 2016;Mucina, 2019). ...
Article
Questions What are the functional trade‐offs of vascular plant species in global alpine ecosystems? How is functional variation related to vegetation zones, climatic groups and biogeographic realms? What is the relative contribution of macroclimate and evolutionary history in shaping the functional variation of alpine plant communities? Location Global. Methods We compiled a data set of alpine vegetation with 5,532 geo‐referenced plots, 1,933 species and six plant functional traits. We used principal component analysis to quantify functional trade‐offs among species and trait probability density to assess the functional dissimilarity of alpine vegetation in different vegetation zones, climatic groups and biogeographic realms. We used multiple regression on distance matrices to model community functional dissimilarity against environmental and phylogenetic dissimilarity, controlling for geographic distance. Results The first two PCA axes explained 66% of the species’ functional variation and were related to the leaf and stem economic spectra, respectively. Trait probability density was largely independent of vegetation zone and macroclimate but differed across biogeographic realms. The same pattern emerged for both species pool and community levels. The effects of environmental and phylogenetic dissimilarities on community functional dissimilarity had similar magnitude, while the effect of geographic distance was negligible. Conclusions Plant species in alpine areas reflect the global variation of plant function, but with a predominant role of resource use strategies. Current macroclimate exerts a limited effect on alpine vegetation, mostly acting at the community level in combination with evolutionary history. Global alpine vegetation is functionally unrelated to the vegetation zones in which it is embedded, exhibiting strong functional convergence across regions.
... Providing a spatial dimension for biodiversity, distribution data are central to many applications in ecology, evolution and conservation (Franklin et al., 2013;Keppel et al., 2015;Daru et al., 2017). Several sources of occurrence data are available, and each has its challenges and limitations (Meyer et al., 2016;König et al., 2019). ...
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Aims Trees dominate the biomass in many ecosystems and are essential for ecosystem functioning and human well‐being. They are also one of the best studied functional groups of plants, with vast amounts of biodiversity data available in scattered sources. We here aim to illustrate that an efficient integration of this data could produce a more holistic understanding of vegetation. Methods To assess the extent of potential data integration, we use key databases of plant biodiversity to 1) obtain a list of tree species and their distributions, 2) identify coverage and gaps of different aspects of tree biodiversity data, and 3) discuss large‐scale patterns of tree biodiversity in relation to vegetation. Results Our global list of trees included 58,044 species. Taxonomic coverage varies in three key databases, with data on the distribution, functional traits, and molecular sequences for about 84%, 45% and 44% of all tree species, which is > 10% greater than for plants overall. For 28% of all tree species, data are available in all three databases. However, less data are digitally accessible about the demography, ecological interactions, and socio‐economic role of tree species. Integrating and imputing existing tree biodiversity data, mobilization of non‐digitized resources and targeted data collection, especially in tropical countries, could help closing some of the remaining data gaps. Conclusions Due to their key ecosystem roles and having large amounts of accessible data, trees are a good model group for understanding vegetation patterns. Indeed, tree biodiversity data are already beginning to elucidate the community dynamics, functional diversity, evolutionary history and ecological interactions of vegetation, with great potential for future applications. An interoperable and openly accessible framework linking various databases would greatly benefit future macroecological studies, and should be linked to a platform that makes information readily accessible to end users in biodiversity conservation and management.
... We defined CWE, SR and ER diversity hotspots as the 1%, 5% and 10% of cells (i.e., the 99%, 95% and 90% percentile; L1, L2 and L3 diversity hotspots, respectively) that had the highest score for each of these indices. In a similar manner, we defined CWE diversity coldspots for the 1%, 5% and 10% percentile, using functions from the "phyloregion" [47,150,151] R package. Biodiversity hotspots are herein and hereafter defined as regional biodiversity hotspots (i.e., hotspots within global biodiversity hotspots [40]). ...
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Biodiversity hotspots (BH) cover a small fraction of the Earth’s surface, yet host numerous endemics. Human-induced biodiversity loss has been increasing worldwide, despite attempts to halt the extinction crisis. There is thus an urgent need to efficiently allocate the available conservation funds in an optimised conservation prioritization scheme. Identifying BH and endemism centres (EC) is therefore a valuable tool in conservation prioritization and planning. Even though Greece is one of the most plant species-rich European countries, few studies have dealt with the identification of BH or EC and none has ever incorporated phylogenetic information or extended to the national scale. Consequently, we are unaware of the extent that Special Areas of Conservation (SAC) of the Natura 2000 network efficiently protect Greek plant diversity. Here, we located for the first time at a national scale and in a phylogenetic framework, the areas serving as BH and EC, and assessed the effectiveness of the Greek SAC in safeguarding them. BH and EC are mainly located near mountainous areas, and in areas supposedly floristically impoverished, such as the central Aegean islands. A critical re-assessment of the Greek SAC might be needed to minimize the extinction risk of the Greek endemics, by focusing the conservation efforts also on the BH and EC that fall outside the established Greek SAC.
... This phylogeny included all species in our analysis, but provided only an approximate degree of relatedness based on taxonomic hierarchy at family level; many relationships, especially within genera, were unresolved. This is problematic because recent theoretical and empirical studies have shown that a lack of resolution in a community phylogeny may mask significant patterns by reducing statistical power (Schaefer et al., 2011;Daru et al., 2017) or suggest significant phylogenetic patterns that are not supported by more completely resolved phylogenies . ...
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Non-random collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. We determined spatial, temporal, trait, phylogenetic, and collector biases in ∼5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England (NE). We identified numerous shared and unique biases among these regions. Shared biases included specimens i) collected close to roads and herbaria; ii) collected more frequently during spring; iii) of threatened species collected less frequently; and iv) of close relatives collected in similar numbers. Regional differences included i) over-representation of graminoids in SA and AU and of annuals in AU; and ii) peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by a few individuals. These mega-collectors, and their associated preferences and idiosyncrasies, may have shaped patterns of collection bias via ‘founder effects’. Studies using herbarium collections should account for sampling biases and future collecting efforts should avoid compounding these biases.
... These differences would result in incongruent biogeographical patterns across different taxonomic lineages over space or time 7,14 . Furthermore, present-day zoogeographical regions were structured by a combination of multiple speciations, extinctions and dispersal processes at several time periods 21,22 . Thus, biogeographical meta-analysis 16,22 and community-level analyses 5,23 , which integrate individual taxon histories into shared biotic area histories, were more promising to clarify the processes shaping biogeographical regions over time 19,24 . ...
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The Tibetan Plateau (TP) and surrounding regions have one of the most complex biotas on Earth. However, the evolutionary history of these regions in deep time is poorly understood. Here, we quantify the temporal changes in beta dissimilarities among zoogeographical regions during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278 extinct mammal genera. We identify ten present-day zoogeographical regions and find that they underwent a striking change over time. Specifically, the fauna on the TP was close to the Oriental realm in deep time but became more similar to the Palearctic realms more recently. The present-day zoogeographical regions generally emerged during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate that geological events such as the Indo-Asian Collision, the TP uplift, and the aridification of the Asian interior underpinned the evolutionary history of the zoogeographical regions surrounding the TP over different time periods.
... These indicated that the enclaves appearing in our map were produced by assemblages whose species composition were markedly distinct from the species composition prevailing in the surrounding sub- Veloso et al., 1991). The existence of enclaves is commonly attributed to the existence of island-like environmental conditions like mountain tops with climates colder than those prevailing in the surrounding subregions (Cantidio & Souza, 2019;Silva & Souza, 2018a or historical biogeographical processes like assemblages that are relicts of communities with wider distribution in the past (Cantidio & Souza, 2019;Daru, Elliott, Park, & Davies, 2017;Jeske-Pieruschka & Behling, 2012). An example is our subregion 13, whose enclaves within subregion 12 corresponded to Cerrado savanna and open-canopy forest patches within central and eastern Amazon (Magnusson, Lima, Albernaz, Sanaiotti, & Guillaumet, 2008). ...
Article
The Amazon forest covers 7.5 million Km2 in nine countries, hosts 25% of the global biodiversity and is a major contributor to the biogeochemical and climatic functioning of the Earth system. Despite its global importance, a regionalization of the Amazon tree flora is still lacking. Clear and data‐driven delimitation of subregions is important for macroecological studies, to the identification of metacommunities, and is a requisite for conservation planning. We aimed at identifying and mapping plant species subregions and investigated their relationships with environmental, historical, and human correlates. We provide the first woody plant regionalization of the entire Amazon forest using a data‐driven approach based on assemblage composition patterns. We compiled data on woody species composition from 301 assemblages based on species occurrences. We then used unconstrained ordination, interpolation and clustering techniques to identify and map discrete woody subregions. Hierarchical clustering analysis was conducted in order to investigate the relationships between the identified subregions. We used multinomial logistic regression model and deviance partitioning to investigate the influence of environmental, historical, and human factors on subregions distribution. We identified 13 woody subregions in the entire Amazon forest. The hierarchical subregion classification showed a broad Andean‐Cratonic east‐west division. Variation in subregions were explained jointly by human factors and spatial structure followed by environmental factors and spatial structure combined. Synthesis. Our woody plant subregions differed from WWF ecoregions and physiognomic‐based maps, highlighting the importance of basing regionalizations on taxon‐specific groups and confirming that vegetation maps should not be used as proxies to plant diversity subregions. Our findings also confirm the need for multiple and extensive protected areas in the Amazon forest. The relevance of current climate factors in our study alerts to a profound impact that climate change could have on the spatial organization of the Amazon flora.
... Ecology is as important as biogeographic history in determining the distribution pattern of species diversity at the global scale (Wiens and Donoghue 2004). Ecologists focus on using climatic niche conservatism and regional climate to clarify species' geographic ranges and the accumulation of species within regions (Wiens and Donoghue 2004;Pyron et al. 2015;Daru et al. 2017;Saupe et al. 2018), whereas historical biogeographers tend to use geological connections among regions (Leprieur et al. 2016). However, there is a lack of empirical studies that clarify the linkages between ecology and biogeographic history. ...
Article
Biological migrations between India and Southeast (SE) Asia provide an ideal system for exploring the effects of geology and climate on species ranges. Geologists have confirmed that the direct collision between India and Eurasia occurred in the Early Eocene, but most migrations occurred between the Indian subcontinent and SE Asia rather than the former and the southern margin of Eurasia. To explain this seemingly paradoxical disconnect between the routes of plate movement and biological migration, we studied the evolutionary history of the tropical spider family Ochyroceratidae based on 101 globally distributed species. We infer a robust dated phylogeny using both transcriptomic data and a dataset of classical markers and relate these to biogeographic and climatic analyses. Our results indicate that the monophyly of Ochyroceratidae is strongly supported, and the divergence times suggest a Cretaceous Gondwanan origin of the family. Reconstructed biogeographic histories support a dispersal event from the Indian subcontinent to islands of SE Asia 55-38 million years ago. Climatic analyses and the fossil record reveal that ochyroceratids are characterized by a high degree of tropical niche conservatism, and that the ancestor of the Indian and SE Asian clades originated in very warm, wet environments. Early Eocene tropical, perhumid climates in India and SE Asia may have facilitated ochyroceratid migration, whereas the dry or seasonal climate extending from the eastern coast of China to Central Asia may have acted as a barrier, preventing dispersal. Our analyses suggest that climate plays a more important role than geology in biological migration from the Indian subcontinent to SE Asia, providing new insights into the Indian-Asian biogeographic link.
... In phylogenetic community ecology, two important quantities to estimate are relatedness among species within a community (i.e., phylogenetic alpha diversity) and relatedness among species between communities (i.e., phylogenetic beta diversity). The measurement of alpha and beta diversity indices can inform us whether or not a given community has greater phylogenetic diversity or more distinct phylogenetic components than other communities (e.g., Daru, Elliott, Park, & Davies, 2017;Kembel et al., 2010). Poor phylogenetic signal, however, may lead to erroneous inferences about phylogenetic relatedness among species within a community or among communities. ...
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Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). In this proof-of-concept study, we leveraged this resource by developing and applying a phylogenomic strategy to seek candidate plastid markers suitable for phylogenetic community analysis. We ranked the core genes of 107 published plastid genomes based on various sequence-derived properties and their tree distance to plastid genome phylogenies. The resulting ranking revealed that the most widely used marker, rbcL, is not necessarily the optimal marker, while other promising markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of them, rpoC1, in a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for investigating the biodiversity and community ecology of the red algae.
... Additionally, phylogenetic trees have been used to detect the turnover of phylogenetic patterns, which reflects the relative importance of evolutionary and ecological factors in shaping current diversity patterns across broad spatial scales (Graham and Fine, 2008). Several studies have inferred biogeographical regionalization incorporating phylogenies at different geographical scales and within different taxa (Holt et al., 2013;Kubota et al., 2014;Hattab et al. 2015;Jønsson and Holt, 2015;Li et al., 2015;Daru et al., 2016Daru et al., , 2017aDaru et al., , 2017bSlik et al., 2018). Phylogeny-based regionalizations have also provided rigorous and objective classifications of biota, and enhanced our knowledge of biodiversity (Holt et al., 2013). ...
Article
Biogeographical regionalization schemes have traditionally been constructed based on taxonomic endemism of families, genera, and/or species, and rarely incorporated the phylogenetic relationships between taxa. However, phylogenetic relationships are important for understanding historical connections within and among biogeographical regions. Phylogeny-based delineation of biota is a burgeoning and fruitful field that is expected to provide novel insights into the conservation of regional diversity and the evolutionary history of biota. Using the Chinese flora as an example, we compared regionalization schemes that were based on: (1) taxonomic endemism, (2) taxonomic dissimilarity, and (3) phylogenetic dissimilarity. Our results revealed general consistency among different regionalization schemes and demonstrated that the phylogenetic dissimilarity approach is preferable for biogeographical regionalization studies. Using the phylogenetic dissimilarity approach, we identified five phytogeographical regions within China: the Paleotropic, Holarctic, East Asiatic, Tethyan, and Qinghai–Tibet Plateau Regions. The relationship of these regions was inferred to be: (Paleotropic, ((East Asiatic + Holarctic) + (Tethyan + Qinghai–Tibet Plateau)).
... Although there was low spatial congruence among three evolutionary diversity metrics for the different taxonomic groups, we found that the three types of diversity overlap in some areas in the tropics (South America, Africa and Southeast Asia). These areas reflect a complex biogeographical history of speciation, extinction and dispersal (Chown & Gaston, 2000;Daru, Elliott, Park, & Davies, 2017;Rosenzweig, 1995). The general lack of spatial overlap suggests that one diversity metric cannot be used reliably as a surrogate for others. ...
Article
Aim A common approach for prioritizing conservation is to identify concentrations (hotspots) of biodiversity. Such hotspots have traditionally been designated on the basis of species‐level metrics (e.g., species richness, endemism and extinction vulnerability). These approaches do not consider phylogenetics explicitly, although phylogenetic relationships reflect the ecological, evolutionary and biogeographical processes by which biodiversity is generated, distributed and maintained. The aim of this study was to identify hotspots of phylogenetic diversity and compare these with hotspots based on species‐level metrics and with the existing protected areas network. Location Global. Time period Contemporary. Major taxa studied Terrestrial vertebrates (mammals, birds and amphibians) and angiosperms. Methods We used comprehensive phylogenies and distribution maps of terrestrial birds, mammals, amphibians and angiosperms to identify areas with high concentrations of phylogenetic diversity, phylogenetic endemism, and evolutionary distinctiveness and global endangerment. We compared the locations of these areas with those included within the current network of protected areas and concentrations of species‐level indices: species richness, species endemism and species threat. Results We found spatial incongruence among the three evolutionary diversity metrics in each taxonomic group. Spatial patterns of diversity and endemism also differed among taxonomic groups, with some differences between vertebrates and angiosperms. Complementarity analyses of phylogenetic diversity identified the minimal area that encapsulates the full branch lengths for each taxonomic group. The current network of protected areas and species‐level hotspots largely does not overlap with areas of high phylodiversity. Main conclusion Overall, < 10% of hotspot areas were designated as protected areas. Patterns of diversity, endemism and vulnerability differ among taxonomic groups.
... The distribution areas of plants are unique, but some species show a high level of spatial similarity which can be exploited for the definition of 'biogeographical coincidence' underpinning concepts such as the geoelement (Meusel et al., 1965) and phytochorion (Takhtajan, 1986), including floristic kingdoms, regions and the like. These biogeographical realms/regions (also called phytochoria or zoochoria) are based on distributional data and/or shared evolutionary history (e.g. in terms of phylogenetic origin; Holt et al., 2013;Daru et al., 2017Daru et al., , 2018. Plant species also co-occur in habitats where they assemble into plant communities; these also occupy space (have distribution area). ...
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Biome is and remains a key community ecological and biogeographical concept and as such profited from overall progress of community ecology which was punctuated by two major innovations: shifting focus from pure pattern description to understanding functionality, changing approach from observational to explanatory and, most importantly, from descriptive to predictive. The functional focus enabled development of mechanistic and function‐focused predictive and retrodictive modelling; it also shaped the current understanding of the concept of biome as a dynamic biological entity having many faces, deep roots in evolutionary past, and undergoing changes. The evolution of the biome concept was punctuated by three synthetic steps: The First Synthesis formulated a solid body of theory explaining ecological and biogeographical meaning of zonality and collated our knowledge on drivers of vegetation patterns at large spatial scales. The Second Synthesis translated this knowledge into effective mechanistic modelling tools, developing further linking ecosystem functionality and biogeography. The Third Synthesis (still in progress) is seeking common grounds between large‐scale ecological and biogeographic phenomena, using tools of macroecology and macroevolutionary research. This article is protected by copyright. All rights reserved.
... One of the basic assumptions underlying community phylogenetics is that closely related species should be more ecologically similar (i.e., niche conservatism), and thus should be "filtered" into similar environments, although evidence for this assumption is mixed (Cavender-Bares, Ackerly, Baum, & Bazzaz, 2004;Cavender-Bares et al., 2009;Graham et al., 2009;Vamosi et al., 2009). If the assumption of niche conservatism holds, we might predict that PhBD indices would be more sensitive to detecting environmental turnover and thus boundaries between communities (Graham & Fine, 2008;Daru, Elliott, Park, & Davies, 2017). Here, we contrast the performance of traditional beta diversity approaches (BD), based on variation in species composition among sampled plots, to approaches that include phylogenetic information (PhBD) in describing differences among plant assemblages using vegetation data collected across the boreal forest-tundra ecotone. ...
Article
Question Ecologists have long been interested in the delineation and description of plant communities but have only recently included phylogenetic data into these analyses. Here, we assess whether species‐based dissimilarities (beta diversity – BD) and more recent phylogenetic beta diversity (PhBD) measures are correlated with dissimilarities among sites based on abiotic variables. Additionally, we examine if BD and PhBD measures aggregate sites into clusters that reflect their environmental attributes. Assuming phylogenetic conservatism in abiotic niche preferences, we predict PhBD dissimilarity matrices will correlate to those based on abiotic site variables, and that clusters determined by PhBD will more closely match to assemblages clustered by abiotic environment than will clusters determined by species BD. Location Mount Irony, Labrador in the Eastern Canadian subarctic. Methods We combine vascular plant co‐occurrence data collected from an elevation gradient on Mount Irony with information on phylogenetic relatedness to compare site dissimilarities based on abiotic variables with those estimated on measures of BD and PhBD. We also examine whether clusters based on BD and PhBD resemble clusters based on abiotic variables, and investigate whether similarly clustered sites are composed of species with similar evolutionary histories. Results We found significant correlations among the dissimilarity matrices and ordinations for the abiotic variables, BD and PhBD; however, neither BD nor PhBD aggregated assemblages into clusters that reflected their environmental differences. Further, we found no evidence that species within clusters were any more closely related than expected by chance. We observed similar patterns when communities were defined by all vascular plants and only angiosperms. Conclusions The correlations among site dissimilarities based on abiotic variables, BD and PhBD suggest environmental filtering; however, sites clustered by BD and PhBD did not resemble those clustered by abiotic variables, indicating that the added value of phylogenetic data for local scale analyses might be limited. This article is protected by copyright. All rights reserved.
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Background and Aims The Atlantic Forest biodiversity hotspot is a complex mosaic of habitat types. However, the diversity of the rainforest at the core of this complex has received far more attention than that of its marginal habitats, such as cloud forest, semideciduous forest or restinga. Here, we investigate broad-scale angiosperm tree diversity patterns along elevation gradients in the Southeast Atlantic Forest and test if the diversity of marginal habitats is shaped from the neighbouring rainforest, as commonly thought. Methods We calculated phylogenetic indices that capture basal (mean pairwise phylogenetic distance - MPD) and terminal (mean nearest taxon distance - MNTD) phylogenetic variation, phylogenetic endemism (PE) and taxonomic and phylogenetic beta diversity (BD and PBD) for 2074 angiosperm tree species distributed in 108 circular sites of 10 km diameter across four habitat types including rainforest, cloud forest, semideciduous forest and coastal vegetation known as restinga. We then related these metrics to elevation and environmental variables. Key Results Communities in wetter and colder forests show basal phylogenetic overdispersion and short phylogenetic distances towards the tips, respectively. In contrast, communities associated with water deficit and salinity show basal phylogenetic clustering and no phylogenetic structure toward the tips. Unexpectedly, rainforest shows low PE given its species richness, whereas cloud and semideciduous forests show unusually high PE. BD and PBD between most habitat types are driven by the turnover of species and lineages, except for restinga. Conclusions Our results contradict the idea that all marginal habitat types of the Atlantic Forest are subsets of the rainforest. We show that marginal habitat types have different evolutionary histories and may act as “equilibrium zones for biodiversity” in the Atlantic Forest, generating new species or conserving others. Overall, our results add evolutionary insights that reinforce the urgency of encompassing all habitat types in the Atlantic Forest concept.
Article
At the macroscale, climate strongly correlates with species richness gradients, resulting from differences in in‐situ diversification and dispersal. One historical explanation for the pattern is that regions spanning temperate climates contain few species because past disturbances have generated high extinction rates, and species from tropical regions are unable to easily colonize temperate regions. We test these postulates for Himalayan plants, which span subtropical to temperate climates over steep elevational gradients. Himalaya. Present day. Angiosperms. We use a comprehensive survey of 31 floras to document the elevational and geographical distributions of native Himalayan plants, augmented by field studies of trees in both the east and west Himalaya. We use grade of membership models to cluster species according to locations shared and phylogenetic analysis to evaluate diversification rates. Species fall into four cohesive biotas, organized by climate. Points of turnover between biotas occur where the mean minimum temperature of the coldest month is approximately 0 °C (2,000–2,500 m), and at the point of occasional annual freezing (1,000–1,500 m); these boundaries run the length of the Himalaya. The patterns are retained when we consider whole clades rather than species. All plants (and the subsets trees, herbs and shrubs) belonging to the biota above the 2,000–2,500 m line have higher recent speciation rates than those lower down. We attribute the high rate of recent speciation in temperate climates to high rates of turnover, creating ecological and geographical opportunity. The high elevation biota has few species, but spans the largest area, implying species numbers are far from any carrying capacity, at least with respect to accumulation of allopatric forms. This study thus links climatic restrictions of clades to differences in diversification rates, and by inference species numbers.
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Identifying structure underlying high-dimensional data is a common challenge across scientific disciplines. We revisit correspondence analysis (CA), a classical method revealing such structures, from a network perspective. We present the poorly-known equivalence of CA to spectral clustering and graph-embedding techniques. We point out a number of complementary interpretations of CA results, other than its traditional interpretation as an ordination technique. These interpretations relate to the structure of the underlying networks. We then discuss an empirical example drawn from ecology, where we apply CA to the global distribution of Carnivora species to show how both the clustering and ordination interpretation can be used to find gradients in clustered data. In the second empirical example, we revisit the economic complexity index as an application of correspondence analysis, and use the different interpretations of the method to shed new light on the empirical results within this literature.
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Uncertainties from sampling biases present challenges to ecologists and evolutionary biologists in understanding species sensitivity to anthropogenic climate change. Here, we synthesize possible impediments that can constrain research to assess present and future seagrass response from climate change. First, our knowledge of seagrass occurrence information is prevalent with biases, gaps and uncertainties that can influence inferences on species response to global change. Second, research on seagrass diversity has been focused on species-level metrics that can be measured with data from the present – but rarely accounting for the shared phylogenetic relationships and evolutionary distinctiveness of species despite species evolved and diversified from shared ancestors. Third, compared to the mass production of species occurrence records, computational tools that can analyze these datasets in a reasonable amount of time are almost non-existent or do not scale well in terms of computer time and memory. These impediments mean that scientists must work with incomplete information and often unrepresentative data to predict how seagrass diversity might change in the future. We discuss these shortfalls and provide a framework for overcoming the impediments and diminishing the knowledge gaps they generate.
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Understanding how the world’s biodiversity is organized and how it changes across geographic regions is critical to predicting the effects of global change ¹ . Ecologists have long documented that the world’s terrestrial fauna is organized hierarchically in large regions - or realms - and continental scale subregions 2–6 , with boundaries shaped by geographic and climatic factors 2,7 . However, little is known about how global biodiversity is assembled below the continental level and the factors, including the potential role of human impacts, triggering faunistic differences as the biogeographical scale becomes smaller. Here we show that the hierarchical organization of global zoogeographical regions extends coherently below the region level to reach a local scale, and that multiple determinants act across varying spatial and temporal scales. Among these determinants, anthropogenic land use during the Late Holocene stands out showing a footprint across biogeographical scales and explaining 22% of the faunistic differences among the larger bioregions. The Late Holocene coincided with the development of large cities and substantial transformation of ecosystems into agricultural land 8,9 . Our results show that past human activity has played a role in the global organization of present-day animal assemblages, leaving a detectable signal that warns us about significant time-lag effects of human-mediated impacts on biodiversity.
Article
Biogeographical regionalization is the classification of regions in terms of their biotas and is key to our understanding of the ecological and historical drivers affecting species distribution in macroecological or large‐scale conservation studies. However, despite the mass production of species distributions and phylogenetic data, statistical and computational infrastructure to successfully incorporate, manipulate and analyze such massive amounts of data had not been fully developed. Here, we present phyloregion, a statistical package for the analysis of biogeographic regionalization and macroecology in the R computing environment, tailored for mega phylogenies and macroecological datasets of ever‐increasing size and complexity. Compared to available packages, phyloregion is several times faster and allocates less memory than other packages for analysis of alpha diversity (including phylogenetic diversity, phylogenetic endemism, and evolutionary distinctiveness and global endangerment) and beta diversity (including cluster analysis, determining optimal number of clusters, and evolutionary distinctiveness of regions). We demonstrate the scalability of the package to large datasets with comprehensive phylogenies and global distribution maps of squamate reptiles (amphisbaenians, lizards, and snakes), and show that different phyloregions differ strongly in evolutionary distinctiveness across scales. Visualization tools allow graphical exploration of the generated patterns of biogeographical regionalization and macroecology in geographic space. Ultimately, phyloregion will facilitate rapid biogeographic analyses that will accommodate the ongoing mass‐production of species occurrence records and phylogenetic datasets at any scale and for any taxonomic group into completely reproducible R workflows.
Article
Aim Focussing on pairs of sister species across three genera of scincid lizards, we use genomic evidence to test for larger‐scale, late‐Pleistocene changes in distributions of lizards in the Australian arid zone (AZ) than in the adjacent monsoonal tropics (MT). Location Northern and central Australia. Taxon Scincidae: Squamata. Methods We sequenced ~2000 nuclear exons and one mitochondrial gene across the distributions of species with primarily MT or AZ distributions from three genera of lizards. Using phylogenetic analysis and population structure analyses we identified major phylogeographic lineages and then compared the spatial scale of structuring and tested for recent demographic expansions. Results Two genera in particular, Proablepharus and Morethia, showed deeper and more geographically localized phylogeographic diversity in the MT than the AZ. In the MT, localized diversity was prevalent in the relatively mesic regions. By contrast, the AZ was characterized by widespread and often genetically uniform lineages and a higher proportion of these had signals of recent population expansion. Main conclusions Consistent with other recent, but mostly less genetically extensive studies, our results point to deeper and more localized diversity in MT compared to AZ. In turn, this suggests higher local persistence in more mesic and topographically diverse biome through the late Quaternary climate fluctuations. For the AZ, geographically extensive range expansions have likely contributed to the low spatial turnover of this exceptionally rich lizard fauna.
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Phylogenetic turnover quantifies the evolutionary distance among species assemblages and is central to understanding the main drivers shaping biodiversity. It is affected both by geographic and environmental distance between sites. Therefore, analyzing phylogenetic turnover in environmental space requires removing the effect of geographic distance. Here, we apply a novel approach by deciphering phylogenetic turnover of European tetrapods in environmental space after removing geographic land distance effects. We demonstrate that phylogenetic turnover is strongly structured in environmental space, particularly in ectothermic tetrapods, and is well explained by macroecological characteristics such as niche size, species richness and relative phylogenetic diversity. In ectotherms, rather recent evolutionary processes were important in structuring phylogenetic turnover along environmental gradients. In contrast, early evolutionary processes had already shaped the current structure of phylogenetic turnover in endotherms. Our approach enables the disentangling of the idiosyncrasies of evolutionary processes such as the degree of niche conservatism and diversification rates in structuring biodiversity.
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Traditional attempts to delineate floristic regions typically focus on species distributions, often ignoring the rich context that phylogenetic relationships can provide. In this study, we explore how phylogenetic relatedness, taxonomic composition, and regional phylogenetic structure change across a global biodiversity hotspot region, Yunnan, located in southwestern China. We propose a system of floristic regions within Yunnan by combining data on the distributions and phylogenetic relationships of 1,983 genera of native seed plants. We identified eight distinct floristic regions in Yunnan, which were grouped into two larger northern and southern geographical units. Phylogenetic relatedness was well correlated with taxonomic composition between floras in Yunnan. Across the Yunnan region we examined, the central Yunnan region shows the lowest level of spatial turnover in phylogenetic relationships and taxonomic composition of the floristic assemblages. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region, in which four areas show higher phylogenetic turnover than expected given the underlying taxonomic composition between sites. Our results show that the integration of phylogenetic information can provide valuable insight in floristic assessments, and help us to better understand the structure of a global biodiversity hotspot.
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Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion - often attributed to negative biotic interactions - are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure. © 2014 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.
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Compared to species turnover, patterns of phylogenetic turnover provide extra information about the spatial structure of biodiversity, for example providing more informative comparisons between the biota of sites which share no species. To harness this information for broad-scale spatial analysis, we present phylo-GDM, a technique for interpolating the spatial structure of phylogenetic turnover between sampled locations in relation to environment, based on generalised dissimilarity modelling (GDM). Using a database of over 150 000 location records for 114 myobatrachid frog species in Australia, linked to a species-level phylogeny inferred from 2467 base pairs of mitochondrial DNA, we calculated species and phylogenetic turnover between pairs of sites. We show how phylogenetic turnover extended the range of informative comparison of compositional turnover to more biologically and environmentally dissimilar sites. We generated GDM models which predict species and phylogenetic turnover across Australia, and tested the fit of models for different ages within the phylogeny to find the phylogenetic tree depth at which the relationship to current day environment is greatest. We also incorporated explanatory variables based on biogeographic patterns, to represent broad-scale turnover resulting from divergent evolutionary histories. We found that while the predictive power of our models was lower for full phylogenetic turnover than for species turnover, models based on the more recent components of the phylogeny (closer to the tips) outperformed species models and full phylogenetic models. Phylo-GDM has considerable potential as a method for incorporating phylogenetic relationships into biodiversity analyses in ways not previously possible. Because phylogenies do not require named taxa, phylo-GDM may also provide a means of including lineages with poorly resolved taxonomy (e.g. from metagenomic sequencing) into biodiversity planning and phylogeographic analysis.
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Understanding spatial patterns of biodiversity is critical for conservation planning, particularly given rapid habitat loss and human-induced climatic change. Diversity and endemism are typically assessed by comparing species ranges across regions. However, investigation of patterns of species diversity alone misses out on the full richness of patterns that can be inferred using a phylogenetic approach. Here, using Australian Acacia as an example, we show that the application of phylogenetic methods, particularly two new measures, relative phylogenetic diversity and relative phylogenetic endemism, greatly enhances our knowledge of biodiversity across both space and time. We found that areas of high species richness and species endemism are not necessarily areas of high phylogenetic diversity or phylogenetic endemism. We propose a new method called categorical analysis of neo- and paleo-endemism (CANAPE) that allows, for the first time, a clear, quantitative distinction between centres of neo- and paleo-endemism, useful to the conservation decision-making process.
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The conservation and sustainable use of marine resources is a highlighted goal in a growing number of national and international policy agendas. Unfortunately, efforts to assess progress, as well as to strategically plan and prioritize new marine conservation measures, have been hampered by the lack of a detailed and comprehensive biogeographic system to classify the oceans. Here we report on a new global system for coast and shelf areas – the Marine Ecoregions of the World (MEOW) – a nested system of 12 realms, 62 provinces and 232 ecoregions. This system provides considerably better spatial resolution than previous global systems, while preserving many common elements, and can be cross-referenced to many regional biogeographic classifications. The designation of terrestrial ecoregions has revolutionized priority setting and planning for land conservation; we anticipate similar benefits from the creation of a coherent and credible marine system.
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Significance The diversity of living things generally peaks in the tropics and declines toward the poles. This “latitudinal gradient” is Earth’s most prevalent biogeographic pattern, but biologists do not agree about its cause. Here, we use geographic and evolutionary data for over 12,500 species of woody flowering plants to test the “tropical conservatism hypothesis,” which attributes the phenomenal diversity of tropical environments to their large extent over the past 55 million years (My) and the evolutionary conservatism of environmental tolerances. As predicted, we find that transitions between tropical and temperate environments are quite rare over the evolutionary history and that most temperate lineages originated as Earth cooled over the past 34 My. Thus, the correlation between diversity and climate reflects plants’ evolutionary history.
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We investigate patterns of phylogenetic diversity in relation to species diversity for European birds, mammals and amphibians, to evaluate their congruence and highlight areas of particular evolutionary history. We estimate the extent to which the European network of protected areas (PAs) network retains interesting evolutionary history areas for the three groups separately and simultaneously. Europe. Phylogenetic (QEPD) and species diversity (SD) were estimated using the Rao's quadratic entropy at 10' resolution. We determined the regional relationship between QEPD and SD for each taxa with a spatial regression model and used the tails of the residuals (QERES) distribution to identify areas of higher and lower QEPD than predicted. Spatial congruence of biodiversity between groups was assessed with Pearson's correlation. A simple classification scheme allowed building a convergence map where a convergent pixel equalled to a QERES value of the same sign for the 3 groups. This convergence map was overlaid to the current PAs network to estimate the level of protection in convergent pixels and compared it to a null expectation built on 1000 randomization of PAs over the landscape. QERES patterns across vertebrates show a strong spatial mismatch highlighting different evolutionary histories. Convergent areas represent only 2.7% of the Western Palearctic, with only 8.4% of these areas being covered by the current PAs network while a random distribution would retain 10.4% of them. QERES are unequally represented within PAs: areas with higher QEPD than predicted are better covered than expected, while low QEPD areas are undersampled. Patterns of diversity strongly diverge between groups of vertebrates in Europe. Although Europe has the world's most extensive PAs network, evolutionary history of terrestrial vertebrates is unequally protected. The challenge is now to reconcile effective conservation planning with a contemporary view of biodiversity integrating multiple facets.
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Kreft and Jetz’s critique of our recent update of Wallace’s zoogeographical regions disregards the extensive sensitivity analyses we undertook, which demonstrate the robustness of our results to the choice of phylogenetic data and clustering algorithm. Their suggested distinction between “transition zones” and biogeographic regions is worthy of further investigation but is thus far unsubstantiated.
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Holt et al. (Report, 4 January 2013, p. 74) propose substantial modifications of Wallace’s long-standing zoogeographic regions based on clustering of a pairwise similarity matrix of vertebrate assemblages. We worry about their compromised use of phylogenies and show that a fundamental point of their analysis—i.e., the delineation of new realms—is only weakly supported by their results and conceptually flawed.
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Ecologists have generally agreed that beta diversity is a key component of global patterns of species richness. Incorporating phylogenetic information into the study of beta diversity allows researchers to identify the degree to which the shared evolutionary histories of species explain ecological patterns observed today. For example, phylogenetic analyses can determine whether closely related species tend to occupy similar positions along broad climatic gradients and whether this explains the compositional turnover along these gradients. Despite the promise of phylogenetic beta diversity analyses, few continental-scale investigations exist. Here, we quantify the phylogenetic beta diversity and taxonomic beta diversity of the angiosperm flora across North America. We relate these metrics to one another and to geographical and environmental distances to uncover the phylogenetic signal underlying species compositional turnover.
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A fundamental problem in ecological research is to explain large-scale gradients in species richness1,2. Although many causative agents for this phenomenon have been suggested, the species richness-energy hypothesis has received the strongest empirical support3-6: this hypothesis states that higher energy availability provides a broader resource base, permitting more species to coexist. Here we show that the species richness-energy hypothesis applies to North American mammals only over a limited geographical area in which climatic energy levels are low (Alaska and most of Canada), rather than on a continental scale as had previously been accepted6. In relatively high-energy regions of North America, corresponding to most of the continental United States and southern Canada, we find that mammal species richness is best predicted by topographic heterogeneity and local variation in energy availability. Our results contradict previous studies of large-scale richness patterns that dismissed the importance of habitat heterogeneity2,7-9, and have implications for climate change research.
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The mangrove biome stands out as a distinct forest type at the interface between terrestrial, estuarine, and near-shore marine ecosystems. However, mangrove species are increasingly threatened and experiencing range contraction across the globe that requires urgent conservation action. Here, we assess the spatial distribution of mangrove species richness and evolutionary diversity, and evaluate potential predictors of global declines and risk of extinction. We found that human pressure, measured as the number of different uses associated with mangroves, correlated strongly, but negatively, with extinction probability, whereas species ages were the best predictor of global decline, explaining 15% of variation in extinction risk. Although the majority of mangrove species are categorised by the IUCN as Least Concern, our finding that the more threatened species also tend to be those that are more evolutionarily unique is of concern because their extinction would result in a greater loss of phylogenetic diversity. Finally, we identified biogeographic regions that are relatively species-poor but rich in evolutionary history, and suggest these regions deserve greater conservation priority. Our study provides phylogenetic information that is important for developing a unified management plan for mangrove ecosystems worldwide.
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Species distribution models (SDMs) trained on presence-only data are frequently used in ecological research and conservation planning. However, users of SDM software are faced with a variety of options, and it is not always obvious how selecting one option over another will affect model performance. Working with MaxEnt software and with tree fern presence data from New Zealand, we assessed whether (a) choosing to correct for geographical sampling bias and (b) using complex environmental response curves have strong effects on goodness of fit. SDMs were trained on tree fern data, obtained from an online biodiversity data portal, with two sources that differed in size and geographical sampling bias: a small, widely-distributed set of herbarium specimens and a large, spatially clustered set of ecological survey records. We attempted to correct for geographical sampling bias by incorporating sampling bias grids in the SDMs, created from all georeferenced vascular plants in the datasets, and explored model complexity issues by fitting a wide variety of environmental response curves (known as "feature types" in MaxEnt). In each case, goodness of fit was assessed by comparing predicted range maps with tree fern presences and absences using an independent national dataset to validate the SDMs. We found that correcting for geographical sampling bias led to major improvements in goodness of fit, but did not entirely resolve the problem: predictions made with clustered ecological data were inferior to those made with the herbarium dataset, even after sampling bias correction. We also found that the choice of feature type had negligible effects on predictive performance, indicating that simple feature types may be sufficient once sampling bias is accounted for. Our study emphasizes the importance of reducing geographical sampling bias, where possible, in datasets used to train SDMs, and the effectiveness and essentialness of sampling bias correction within MaxEnt.