Museums and cradles of diversity are geographically coincident for narrowly distributed Neotropical snakes

Factors driving the spatial configuration of centres of endemism have long been a topic of broad interest and debate. Due to different eco-evolutionary processes, these highly biodiverse areas may harbour different amounts of ancient and recently diverged organisms (paleo- and neo-endemism, respectively). Patterns of endemism still need to be measured at distinct phylogenetic levels for most clades and, consequently, little is known about the distribution, the age and the causes of such patterns. Here we tested for the presence of centres with high phylogenetic endemism (PE) in the highly diverse Neotropical snakes, testing the age of these patterns (paleo- or neo-endemism), and the presence of PE centres with distinct phylogenetic composition. We then tested whether PE is predicted by topography, by climate (seasonality, stability, buffering and relictualness), or biome size. We found that most areas of high PE for Neotropical snakes present a combination of both ancient and recently diverged diversity, which is distributed mostly in the Caribbean region, Central America, the Andes, the Atlantic Forest and on scattered highlands in central Brazil. Turnover of lineages is higher across Central America, resulting in more phylogenetically distinct PE centres compared to South America, which presents a more phylogenetically uniform snake fauna. Finally, we found that elevational range (topographic roughness) is the main predictor of PE, especially for paleo-endemism, whereas low paleo-endemism levels coincide with areas of high climatic seasonality. Our study highlights the importance of mountain systems to both ancient and recent narrowly distributed diversity. Mountains are both museums and cradles of snake diversity in the Neotropics, which has important implications for conservation in this region.     

Congruent spatial patterns of species richness and phylogenetic diversity in karst flora: Case study of Primulina (Gesneriaceae)

The karst landform in southern China is renowned for its high levels of species diversity and endemism. Globally, karst ecosystems are under threat from unsustainable anthropogenic disturbance and climate changes and are among the most threatened ecosystems worldwide. In this study, we used the typical karst endemic genus in southern China, Primulina Hance, as a model to identify areas within the karst landform with high diversity and to investigate congruence between phylogenetic and species‐based measures of diversity. Using phylogenetic information and species distribution data, we measured geographical patterns of diversity with four metrics: species richness (SR), corrected weighted endemism (CWE), phylogenetic diversity (PD), and phylogenetic endemism (PE). Our results revealed a high spatial congruence among SR, PD, and PE, with hotspot areas identified in the Nanling Mountains (i.e., north Guangdong and northeast Guangxi) and southeast Yungui Plateau (i.e., north and southwest Guangxi), whereas the hotspots of CWE are comparatively uniform throughout the geographic extent. The categorical analysis of neo‐ and paleoendemism identified a pattern of mixed neo‐ and paleoendemism in numerous grid cells, suggesting that karst areas in southern China have acted as both “museums” and “cradles” of plant evolution. Conservation gap analysis of hotspots revealed that the majority of prioritized hotspots (>90%) of the genus are outside of protected areas, therefore indicating the limited effectiveness of national nature reserves for the karst flora. Overall, our results suggest that the karst flora merits more conservation attention and SR can be an effective surrogate to capture PD in conservation planning.     

Contrasting patterns of diversification in a bird family (Aves: Gruiformes: Rallidae) are revealed by analysis of geospatial distribution of species and phylogenetic diversity

Geospatial patterns in the distribution of regional biodiversity reflect the composite processes that underpin evolution: speciation, dispersal and extinction. The spatial distribution and phylogeny of a globally widespread and species rich bird family (Rallidae) were used to help assess the role of large‐scale biogeographical processes in diversity and diversification. Here, we examine how different geostatistical diversity metrics enhance our understanding of species distribution by linking occurrence records of rail species to corresponding species level phylogeny. Tropical regions and temperate zones contained a large proportion of rail species richness and phylogenetic diversity whilst small islands in Australian, Oceanian and Oriental regions held the highest weighted and phylogenetic endemism. Our results suggest that habitat connectivity and dispersal were important ecological features in rail evolution and distribution. Spatial isolation was a significant driver of diversification where islands in Oceania were centres of neo‐endemism with recent multiple and independent speciation events and could be considered as nurseries of biodiversity. Palaeo‐endemism was mostly associated with older stable regions, so despite extensive long distance range shifting these areas retain their own ancient and distinct character. Madagascar was the major area of palaeo‐endemism associated with the oldest rail lineages and could be considered a museum of rail diversity. This implies a mixture of processes determine the current distribution and diversity of rail clades with some areas dominated by recent ‘in situ’ speciation while others harbour old diversity with ecological traits that have stood the test of time.     

Patterns in the diversity and endemism of extant Eocene age lineages across southern Africa

Southern Africa boasts a wealth of endemic fauna and flora, comprising both massive recent radiations such as those characteristic of the Cape flora, and solitary ancient species such as the peculiar desert gymnosperm Welwitschia. This study was undertaken to identify ancient biological lineages (tetrapod and vascular plant lineages of Eocene age or older) endemic to southern Africa, and to map their distribution across the region. Twenty‐seven (17 plant and ten animal) lineages were identified, and distribution maps were generated for each of them across 74 operational geographic units, which were then combined into total endemism and corrected weighted endemism per unit area. Total endemism peaked along South Africa's coast and Great Escarpment, but in the case of weighted endemism high values were also recorded along other portions of the Great Escarpment further north. A review of the lineages sister to southern African ancient endemic lineages showed that these are often globally widespread, and many of them differ substantially from the southern African ancient lineages in terms of morphology and ecology. The mechanisms of ancient lineage survival in the region are discussed, and their importance for conservation in southern Africa is emphasised.     

基于系统发育的黄土高原地区木本植物多样性及特有性格局

黄土高原地区植被类型多样, 森林、草原和荒漠在此交汇并逐渐过渡。由于水热条件限制和人类活动加剧, 该地区生态环境脆弱, 生物多样性保护面临的形势日益严峻, 因此获取该区域物种多样性的空间分布格局并阐明其影响因素成为该地区生物多样性保护的首要任务。本研究首先结合标本采集记录与环境因子, 利用物种分布模型获取了293种木本植物的潜在分布区, 分析了物种丰富度和物种加权特有性的空间格局。其次, 引入系统发育信息, 分析系统发育多样性和系统发育特有性的空间格局, 并进一步利用环境因子对上述格局分别进行解释。最后, 对黄土高原地区的特有中心性质和显著性进行分析。结果表明, 生物多样性热点地区均出现在黄土高原南部水热条件较好的地区, 即秦岭和中条山一带。本区域的生物多样性空间格局由年平均降水量和最冷月最低温主导, 符合植物区系交汇带的特点。特有中心集中在南部地区和青海省, 由南向北分别是古特有中心和混合特有中心, 不存在单独的新特有中心。黄土高原地区木本植物起源较为古老, 生物多样性格局的形成以来源于热带或亚热带的物种扩散为主, 物种的分化不占主导地位。上述结果表明了将植物的进化历史纳入生物多样性保护的重要性。     

Spatial phylogenetics of the North American flora

North America is a large continent with extensive climatic, geological, soil, and biological diversity. As biota faces threat from habitat destruction and climate change, making a quantitative assessment of biodiversity becomes critically important. Rapid digitization of plant specimen records and accumulation of DNA sequence data enable a much‐needed broad synthesis of species occurrences with phylogenetic data. In this study, the first such synthesis of a flora from such a large and diverse part of the world is attempted, all seed plants from the North American continent (here defined to include Canada, United States, and Mexico), with a focus on examining phylogenetic diversity and endemism. We collected digitized plant specimen records and chose a coarse grain for analysis, recognizing that this grain is currently necessary for reasonable completeness per sampling unit. We found that raw richness and endemism patterns largely support previous hypotheses of biodiversity hotspots. The application of phylogenetic metrics and a randomization test revealed novel results, including a significant phylogenetic clustering across the continent, a striking east–west geographical difference in the distribution of branch lengths, and the discovery of centers of neo‐ and paleoendemism in Mexico, the southwestern USA, and the southeastern USA. Finally, our examination of phylogenetic beta diversity provides a new approach to compare centers of endemism. We discuss the empirical challenges of working at the continental scale and the need for more sampling across large parts of the continent, for both DNA data for terminal taxa and spatial data for poorly understood regions, to confirm and extend these results.     

Phylogenetic diversity,functional trait diversity and extinction: avoiding tipping points and worst-case losses

The phylogenetic diversity measure, (‘PD’), measures the relative feature diversity of different subsets of taxa from a phylogeny. At the level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of lineages and features include those integrating probabilities of extinction, providing estimates of expected PD. This approach has known advantages over the evolutionarily distinct and globally endangered (EDGE) methods. Expected PD methods also have limitations. An alternative notion of expected diversity, expected functional trait diversity, relies on an alternative non-phylogenetic model and allows inferences of diversity at the level of functional traits. Expected PD also faces challenges in helping to address phylogenetic tipping points and worst-case PD losses. Expected PD may not choose conservation options that best avoid worst-case losses of long branches from the tree of life. We can expand the range of useful calculations based on expected PD, including methods for identifying phylogenetic key biodiversity areas.     

The spatial structure of phylogenetic and functional diversity in the United States and Canada: An example using the sedge family (Cyperaceae)

Systematically quantifying diversity across landscapes is necessary to understand how clade history and ecological heterogeneity contribute to the origin, distribution, and maintenance of biodiversity. Here, we chart the spatial structure of diversity among all species in the sedge family (Cyperaceae) throughout the USA and Canada. We first identify areas of remarkable species richness, phylogenetic diversity, and functional trait diversity, and highlight regions of conservation priority. We then test predictions about the spatial structure of this diversity based on the historical biogeography of the family. Incorporating a phylogeny, over 400 000 herbarium records, and a database of functional traits mined from online floras, we find that species richness and functional trait diversity peak in the Northeastern USA, while phylogenetic diversity peaks along the Gulf of Mexico. Floristic turnover among assemblages increases significantly with distance, but phylogenetic turnover is twice as rapid along latitudinal gradients as along longitudinal gradients. These patterns reflect the expected distribution of Cyperaceae, which originated in the tropics but radiated in temperate regions. We identify assemblages with an abundance of rare, range‐restricted lineages, and assemblages composed of species generally lacking from diverse regions. We argue that both of these metrics are useful for developing targeted conservation strategies. We use the data generated here to establish future research priorities, including the testing of a series of hypotheses regarding the distribution of chromosome numbers, photosynthetic pathways, and resource partitioning in sedges.     

Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation

The value of biodiversity lies in its option value for the future, the greater the complement of contemporary biodiversity conserved today, the greater the possibilities for future biodiversity because of the diverse genetic resource needed to ensure continued evolution in a changing and uncertain world. From this perspective, biodiversity option value can be equated with richness in the different features expressed by species. An individual species of greater value is one contributing more novel features to a given subset. The feature diversity of species and communities is difficult to estimate directly, but can be predicted by the phylogenetic relationships among the species. The ‘Phylogenetic Diversity’ measure (PD) (Faith, 1992a) estimates the relative feature diversity of any nominated set of species by the sum of the lengths of all those branches spanned by the set. These branch lengths reflect patristic or path‐length distances. This study first reviews and expands on some of the properties of PD, and develops simple modifications of the measure (δnPD and enPD) to enable capture of both the phylogenetic relatedness of species and their abundances in each sample. Then the application of PD, δnPD and enPD to a wide range of conservation and resource management issues is demonstrated using avian case studies. Supertree construction procedures (matrix representation using parsimony analysis; average consensus) were used to combine the extensive DNA‐DNA hybridization tree of Sibley & Ahlquist (1990) with numerous, recently published phylogenetic reconstructions to derive a phylogenetic tree for the global avian fauna. Using this supertree as a systematic framework, the utility of PD was demonstrated in four case studies: (i) state of the environment reporting, with changes in avian faunas resulting from extinctions quantified as indicators of the state of biodiversity at Global, New Zealand and Waikato region scales, and changes in available habitat quantified as indicators of pressures on biodiversity in the Waikato region; (ii) setting priorities for threatened species management, with PD as a measure of option value integrated with information on survivorship expectations to develop a ranking among threatened New Zealand forest bird species; (iii) monitoring biotic response to management, with data from 5‐minute counts used to analyse changes in forest bird communities under three management regimes in New Zealand; and (iv) selection of indicator species, with PD used to objectively identify subsets of species in the Global, New Zealand and Waikato avian faunas that comprise a high proportion of the option value in those faunas.     

Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history

We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation. PE has a number of desirable properties not combined in previous approaches. It assesses endemism consistently, independent of taxonomic status or level, and independent of previously defined political or biological regions. The results can be directly compared between areas because they are based on equivalent spatial units. PE builds on previous phylogenetic analyses of endemism, but provides a more general solution for mapping endemism of lineages. We illustrate the broad applicability of PE using examples of Australian organisms having contrasting life histories: pea-flowered shrubs of the genus Daviesia (Fabaceae) and the Australian species of the Australo-Papuan tree frog radiation within the family Hylidae.     

Identifying hotspots of endemic woody seed plant diversity in China

Aim This study aimed to detect distribution patterns and identify diversity hotspots for Chinese endemic woody seed plant species (CEWSPS). Location China. Methods Presence of 6885 CEWSPS throughout China was mapped by taking the Chinese administrative county as the basic spatial analysis unit. The diversity was measured with five indices: endemic richness (ER), weighted endemism (WE), phylogenetic diversity (PD), phylogenetic endemism (PE) and biogeographically weighted evolutionary distinctiveness (BED). Three levels of area (i.e. 1, 5 and 10% of China’s total land area) were used to identify hotspots, but the 5% level was preferred when both the total area of the hotspots identified and the diversity of CEWSPS reached by the hotspots were considered. Results Distribution patterns of CEWSPS calculated with the five indices are consistent with each other over the national extent. However, the hotspots do not show a high degree of consistency among the results derived from the five indices. Those identified with ER and PD are very similar, and so are those with WE and BED. In total, 20 hotspots covering 7.9% of China’s total land area were identified, among which 11 were identified with all the five indices, including the Hengduan Mountains, Xishuangbanna Region, Hainan Island, and eight mountainous areas located in east Chongqing and west Hubei, in east Yunnan and west Guangxi, in north Guangxi, south‐east Guizhou and south‐west Hunan, in north Guangdong and south Hunan, in south‐east Tibet, and in south‐east Hubei and north‐west Jiangxi. Taiwan Island was also identified as a major hotspot with WE, PE and BED. Main conclusions Hotspots of CEWSPS were identified with five indices considering both distributional and phylogenetic information. They cover most of the key areas of biodiversity defined by previous researchers using other approaches. This further verifies the importance of these areas for China’s biodiversity conservation.     

Patterns of species diversity and endemism in comparable temperate brown algal floras

Brown algal species diversity is compared in 100 km sections of the coastlines of four warm temperate regions: southern Australia, California, southwestern Africa, north-central Chile. The highest diversity (over 140 species per section) is found in southern Australia. California has a reasonable diversity (around 70 species per section), and both southern Australia and California have high regional endemism. Sections of north-central Chile and southwestern Africa have similar patterns, with low diversity (< 30 species per 100 km section), low endemism, few or no fucoids, and up to 25% of the brown algal flora are environmentally tolerant species of Scytosiphonales. Species turnover between contiguous sections of coast is generally related to relative change in temperature regime. Thus the high diversity of southern Australia is due to high species diversity within the 100 km sections, with little turnover, except for a rapid reduction in eastern Victoria likely to be related to lack of rocky substatum. It is hypothesized that low diversity and endemism in Chile and southwestern Africa can be explained by the occurrence of major environmental perturbations (upwelling and El Nino effects) in these regions, producing variable inter-annual temperature conditions that select out tolerant species from the local floras.     

Spatial patterns of phylogenetic diversity and endemism in the Western Ghats,India: A case study using ancient predatory arthropods

The Western Ghats (WG) mountain chain in peninsular India is a global biodiversity hotspot, one in which patterns of phylogenetic diversity and endemism remain to be documented across taxa. We used a well‐characterized community of ancient soil predatory arthropods from the WG to understand diversity gradients, identify hotspots of endemism and conservation importance, and highlight poorly studied areas with unique biodiversity. We compiled an occurrence dataset for 19 species of scolopendrid centipedes, which was used to predict areas of habitat suitability using bioclimatic and geomorphological variables in Maxent. We used predicted distributions and a time‐calibrated species phylogeny to calculate taxonomic and phylogenetic indices of diversity, endemism, and turnover. We observed a decreasing latitudinal gradient in taxonomic and phylogenetic diversity in the WG, which supports expectations from the latitudinal diversity gradient. The southern WG had the highest phylogenetic diversity and endemism, and was represented by lineages with long branch lengths as observed from relative phylogenetic diversity/endemism. These results indicate the persistence of lineages over evolutionary time in the southern WG and are consistent with predictions from the southern WG refuge hypothesis. The northern WG, despite having low phylogenetic diversity, had high values of phylogenetic endemism represented by distinct lineages as inferred from relative phylogenetic endemism. The distinct endemic lineages in this subregion might be adapted to life in lateritic plateaus characterized by poor soil conditions and high seasonality. Sites across an important biogeographic break, the Palghat Gap, broadly grouped separately in comparisons of species turnover along the WG. The southern WG and Nilgiris, adjoining the Palghat Gap, harbor unique centipede communities, where the causal role of climate or dispersal barriers in shaping diversity remains to be investigated. Our results highlight the need to use phylogeny and distribution data while assessing diversity and endemism patterns in the WG.     

Geographic patterns and environmental correlates of taxonomic and phylogenetic diversity of aquatic plants in China

Studies on large-scale geographic patterns of aquatic plant diversity can promote research on the generality of macroecological patterns in different ecosystems. Here, we compiled a checklist of 889 aquatic angiosperms in China, including 738 helophytes (emergent and marshy plants) and 151 hydrophytes (submerged, free-floating, and floating-leaved plants). We explore the geographic patterns and environmental correlates of aquatic plant diversity based on six metrics including species richness (SR), weighted endemism (WE), phylogenetic diversity (PD), phylogenetic endemism (PE), the standardized effect size of phylogenetic diversity (PDses), and the standardized effect size of mean phylogenetic distance (MPDses). Our results show that the diversity of aquatic plants in China is extremely uneven, with high diversity in southeastern China and low diversity in northwestern China, and the geographic patterns of taxonomic and PD are generally consistent. The pattern of helophytes differs from that of hydrophytes. Notably, the wavy-shaped pattern of aquatic plant diversity (especially SR and PD for hydrophytes) across the latitude observed in this study is not consistent with those previously observed for aquatic plants in other continents. Climatic variables and water environmental variables are the main drivers of aquatic plant diversity in China; however, the effects of individual variables differ between helophytes and hydrophytes. Water environmental variables have a greater impact on PDses and MPDses of hydrophytes than those of helophytes. Overall, our work provides insight into understanding the large-scale patterns of aquatic plant diversity and is a critical addition to previous studies on the macroecological pattern of terrestrial organisms.     

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

Although it is generally recognized that global biodiversity is declining, few studies have examined long‐term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5‐year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.     

Incorporating phylogenetic information for the definition of floristic districts in hyperdiverse Amazon forests: Implications for conservation

Using complementary metrics to evaluate phylogenetic diversity can facilitate the delimitation of floristic units and conservation priority areas. In this study, we describe the spatial patterns of phylogenetic alpha and beta diversity, phylogenetic endemism, and evolutionary distinctiveness of the hyperdiverse Ecuador Amazon forests and define priority areas for conservation. We established a network of 62 one‐hectare plots in terra firme forests of Ecuadorian Amazon. In these plots, we tagged, collected, and identified every single adult tree with dbh ≥10 cm. These data were combined with a regional community phylogenetic tree to calculate different phylogenetic diversity (PD) metrics in order to create spatial models. We used Loess regression to estimate the spatial variation of taxonomic and phylogenetic beta diversity as well as phylogenetic endemism and evolutionary distinctiveness. We found evidence for the definition of three floristic districts in the Ecuadorian Amazon, supported by both taxonomic and phylogenetic diversity data. Areas with high levels of phylogenetic endemism and evolutionary distinctiveness in Ecuadorian Amazon forests are unprotected. Furthermore, these areas are severely threatened by proposed plans of oil and mining extraction at large scales and should be prioritized in conservation planning for this region.