Fern and lycophyte diversity in the Pacific Northwest: Patterns and predictors

Recent floristic efforts in the Pacific Northwest (PNW) have now made it possible to characterize the broad‐scale patterns of fern and lycophyte diversity across this large and geologically‐complex region of western North America. The physiography of the PNW has been developing for over 200 million years, but Pleistocene glaciation‐induced migrations and recolonizations have strongly influenced the assembly of the flora. With the high dispersal potential of fern and lycophyte spores, the distribution patterns of pteridophytes may be representative of habitat suitability more than dispersal constraints. Our objective was to describe the biodiversity of pteridophytes in the PNW, determine the spatial distribution of that biodiversity in terms of phylogenetic diversity, identify centers of regional endemism, explore the correlations between biodiversity and environmental variables, and infer possible influences of past glaciation on the pteridophyte flora. We obtained presence‐only distribution data from two online databases. A phylogenetic tree was constructed using chloroplast DNA sequence data from GenBank. We used the Biodiverse software package to estimate and map phylogenetic diversity and phylogenetic endemism across the PNW, and to identify those regions of the PNW where diversity was higher or lower than expected in comparison to randomization models. Environmental correlates of diversity were identified using principal components analysis with bioclimatic data from WorldClim.org, and we used Maxent to predict habitat suitability for species under past and future climate conditions. We found evidence for the influence of past glaciations and glacial refugia on the patterns of pteridophyte diversity, that moisture availability and cold temperatures are strongly correlated with patterns of genus richness, phylogenetic diversity, and phylogenetic endemism. We infer that the topographic complexity of the region may be driving the assembly of the pteridophyte flora indirectly by influencing climate and precipitation patterns.     

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.     

A guide to phylogenetic metrics for conservation,community ecology and macroecology

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub‐disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub‐disciplines hampers potential meta‐analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo‐diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo‐diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α‐diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.     

分子系统学在生物保护中的意义

本文综述了近年来分子系统学的原理和方法及其在生物多样性保护中的应用和发展。分子系统学方法可以很好地确定物种保护的基本单元——进化显著性单元,并可用于推测群体的发展状态,从而为物种的保护提供了一项新的具很强操作性的科学手段。     

中国石松类和蕨类植物的多样性与地理分布

物种编目及其科属系统排列是了解生物多样性的基础, 本文采用Flora of China使用的分类系统, 结合最新分子分类学研究成果以及近几年发表的新资料, 对中国石松类和蕨类植物多样性和地理分布数据进行了统计和分析。结果表明中国共有石松类和蕨类植物40科178属2,147种5个亚种118个变种, 其中特有种839个, 占总种数的39.08%。种数最多的5个科依次为鳞毛蕨科(505种, 含种下单位, 下同)、蹄盖蕨科(323种)、水龙骨科(280种)、凤尾蕨科(266种)和金星蕨科(209种); 种数最多的5个属依次为耳蕨属(Polystichum, 209种)、鳞毛蕨属(Dryopteris, 176种)、蹄盖蕨属(Athyrium, 137种)、双盖蕨属(Diplazium, 98种)和凤尾蕨属(Pteris, 97种)。在地理分布上, 种数排名前5的省份为云南(1,365种)、四川(875种)、贵州(838种)、广西(785种)和台湾(779种)。含中国特有石松类和蕨类植物的科属中, 排前3位的科分别为鳞毛蕨科(257种)、蹄盖蕨科(169种)和凤尾蕨科(113种); 排前3位的属为耳蕨属(140种)、蹄盖蕨属(82种)和鳞毛蕨属(61种)。     

Mammal diversity and taxonomy in Italy: implications for conservation

The paper attempts to describe Italian mammal diversity in an evolutionary context. With 122 species according latest researches, Italy holds the richest mammal assemblage among European countries. Specific taxa are often represented by clearly distinctive lineages and several of them appear restricted to the Italian peninsula. Poor knowledge of taxonomy and uncritical application of IUCN threat categories at the national level could produce a flawed set of conservation priorities, independently from the rigorous application of the proposed guidelines for national Red List assessments. Furthermore, classical conservation assessments and protective legislation only consider traditionally named taxa, often privileging insular taxa of artificial origin but neglecting most of the results of genetic and molecular studies on intraspecific variation. The aim of the present work is to outline the need to incorporate phylogenetic and biogeographic data in the assessment of conservation priorities among mammals in Italy, in order to maximise the national contribution to biodiversity conservation in Europe. To this end, distribution, threat status, intraspecific and supraspecific taxonomy of the native mammal fauna should be analysed in a global context. Phylogeographic patterns emerging from previous studies indicate the general inadequacy of continental European populations serving as sources for re-stocking or re-introductions operations in Italy and the other European peninsulas. Thus the importance of integrating international guidelines on reintroductions with a clear understanding of national biogeographical peculiarities is highlighted.     

Patterns of butterfly distribution in the Andaman islands: implications for conservation

Twenty-five islands of different sizes were rapidly surveyed in the Andaman islands for patterns of butterfly distribution and abundance. The surveys were conducted in the dry seasons of 1992 in the South Andaman islands, 1994 in the North Andaman islands and on both these years on the Little Andaman Island. Different habitat types were identified on each island and butterflies were sampled by the line transect method in each habitat type. Sixty-five species of butterflies were recorded from six families. Fifty-one species were less common and contributed to 25 % of the total count. Six species were very common. The overall distribution patterns of the species were nested. This suggests that small islands share their species with the larger islands but not vice versa. Many uncommon species were found exclusively on large islands. The presence of evergreen forest on islands significantly influenced the species encountered. Small and medium sized islands with evergreen forests had significantly more species than those without evergreen forests. Loss of primary forests due to logging and encroachment will result in the loss of many butterfly species. It is recommended that the large patches of primary evergreen forests be protected on a priority basis on large islands.     

A phylogenetic perspective on the evolutionary processes of floristic assemblages within a biodiversity hotspot in eastern Asia

Abstract How to maximize the conservation of biodiversity is critical for conservation planning, particularly given rapid habitat loss and global climatic change. The importance of preserving phylogenetic diversity has gained recognition due to its ability to identify some influences of evolutionary history on contemporary patterns of species assemblages that traditional taxonomic richness measures cannot identify. In this study, we evaluate the relationship between taxonomic richness and phylogenetic diversity of angiosperms at genus and species levels and explore the spatial pattern of the residuals of this relationship. We then incorporate data on historical biogeography to understand the process that shaped contemporary floristic assemblages in a global biodiversity hotspot, Yunnan Province, located in southwestern China. We identified a strong correlation between phylogenetic diversity residuals and the biogeographic affinity of the lineages in the extant Yunnan angiosperm flora. Phylogenetic diversity is well correlated with taxonomic richness at both genus and species levels between floras in Yunnan, where two diversity centers of phylogenetic diversity were identified (the northwestern center and the southern center). The northwestern center, with lower phylogenetic diversity than expected based on taxonomic richness, is rich in temperate‐affinity lineages and signifies an area of rapid speciation. The southern center, with higher phylogenetic diversity than predicted by taxonomic richness, contains a higher proportion of lineages with tropical affinity and seems to have experienced high immigration rates. Our results highlight that maximizing phylogenetic diversity with historical interpretation can provide valuable insights into the floristic assemblage of a region and better‐informed decisions can be made to ensure different stages of a region's evolutionary history are preserved.     

A systemic view of biodiversity and its conservation: processes, interrelationships, and human culture: presentation of a systemic view of biodiversity and its conservation that emphasizes complex interrelationships among subsystems and includes human culture

Historically, views and measurements of biodiversity have had a narrow focus, for instance, characterizing the attributes of observable patterns but affording less attention to processes. Here, we explore the question: how does a systems thinking view – one where the world is seen as elements and processes that connect and interact in dynamic ways to form a whole – affect the way we understand biodiversity and practice conservation? We answer this question by illustrating the systemic properties of biodiversity at multiple levels, and show that biodiversity is a collection of dynamic systems linking seemingly disparate biological and cultural components and requiring an understanding of the system as a whole. We conclude that systems thinking calls traditional views of species, ecosystem function, and human relationships with the rest of biodiversity into question. Finally, we suggest some of the ways in which this view can impact the science and practice of conservation, particularly through affecting our conservation targets and strategies.     

Coastal-marine discontinuities and synergisms: implications for biodiversity conservation

Coastal-marine biodiversity conservation must focus increasingly at the level of the land- and seascape. Five cases illustrate discontinuities and synergisms and how system changes may take place. For Caribbean coral reefs, the result of overfishing and disease has been a shrinkage in the entire system, the effects of which may cascade through the coastal seascape. For Beringia, patterns of benthic diversity are best understood in a manner that matches the multiscale, integrated dynamics of weather, ice, marine mammal feeding, and community structure. In the case of US East Coast estuaries, oyster reefs may be keystone elements, with important effects on functional diversity. Large-scale coastal systems depend upon the connectivity of fresh and marine waters in the coastal zone, having implications for the apparent stochasticity of coastal fisheries. And, for a coastal barrier-lagoon site, a state change may be described in terms of a combination of succession, the attainment of a quasi-equilibrium state, and disturbance. A profound problem for conservation is that there is very little information about the relationship between species diversity and ecological function. Coastal-marine biodiversity conservation is best addressed at the level of the land- and seascape.     

A synthetic phylogeny of freshwater crayfish: insights for conservation

Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world''s freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts.     

Patterns of ferns community assemblages in some Malaysian and Nigerian tropical forests

Research on fern ecology has gained attention in the last decade, yet there is a paucity of information on the comparison of ferns communities across continents. This study focused on comparing the ferns community assemblages in some tropical forests of Malaysia and Nigeria, thereby assessing the patterns of species richness (SR) and phylogenetic diversity (PD) in relation to the bioclimatic drivers across the continents. The diversity and taxonomic compositions of ferns were assessed using 180 plots of 10 m × 10 m in each country. The species richness and other diversity indices were determined using the combined forests data for each country and for the individual forests. Also, the phylogenetic diversity of the ferns was assessed using the genus‐based molecular sequences downloaded from the GeneBank. The patterns of the ferns SR and PD in the two countries as driven by some bioclimatic factors were evaluated using the regression analysis. The observed and rarefied–extrapolated fern species richness is significantly higher in Malaysian forests than in Nigerian forests. Also, the other diversity indices are significantly higher in Malaysian forests except for the Shannon index which showed no significant difference between the two biogeographic regions. There is a very low similarity (7.41%) in the taxonomic composition of ferns between the two biogeographic areas, although the similarity in composition increased with increasing taxonomic levels (species: 7.41%, genus: 12.77%, family: 70.96%). Terrestrial and epiphytic ferns are more dominant than the other life forms in the two countries. The precipitation variables drive the phylogenetic structure of ferns in Nigeria, whereas both precipitation and temperature variables drive the phylogenetic structure of ferns in Malaysia. This indicates that ferns assemblages in Nigeria and Malaysia are driven by both climatic variables. Besides, we also hypothesize that these observed differences could be due to other historical and evolutionary processes.     

Hierarchical partitioning of ant diversity: implications for conservation of biogeographical diversity in arid and semi‐arid areas

Aim The scale of observation is important in detecting the spatial variation of biological assemblages, which should be taken into consideration for an appropriate plan of biogeographical conservation. We investigated whether (1) World Wildlife Fund’s ecoregion units are the appropriate scale for conserving ant diversity in Iran, (2) each ecoregion represents a distinct ant community composition and (3) patterns of diversity partitioning differ among four ecoregions. Location Iran, a sampling transect along four arid and semi‐arid ecoregions. Methods We applied hierarchical partitioning to data collected from a nested sampling design including four hierarchical levels: ‘local’, ‘landscape’, ‘ecoregional’ and ‘whole‐region’. Observed alpha and beta diversity components were compared with values of null distributions. Hierarchical cluster analysis was applied to evaluate similarity of ant species composition among ecoregions. Results Partitioning of whole‐region species richness showed that 85% of the species richness was generated by beta diversity among ecoregions and landscapes. The highest value of diversity was generated by beta diversity among ecoregions. Unlike whole‐region partitioning, separate partitioning within each ecoregion revealed that beta component among localities contributed to species richness of each ecoregion. Ecoregions showed different patterns of diversity partitioning. The alpha component contributed largely to the total diversity of two ecoregions, but for two other ecoregions, beta component contributed more than alpha component. Cluster analysis identified four discrete ant species compositions; however, it split landscapes of one ecoregion into two distinct groups. Main conclusions Whole‐region diversity partitioning indicates that ecoregions represent the appropriate scale for conserving ant diversity and that each ecoregion has a distinct ant fauna. However, different conservation strategies should be considered for different ecoregions owing to the differing scales of variation within them. Boundaries of ecoregions remain a subject for further studies. The influence of climate change on ecoregional boundaries should be considered and should be predicted with respect to future conservation maps.     

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.     

Spatial phylogenetics of the native woody plant species in Hainan,China

To better identify biodiversity hotspots for conservation on Hainan Island, a tropical island in southern China, we assessed spatial variation in phylogenetic diversity and species richness using 18,976 georeferenced specimen records and a newly reconstructed molecular phylogeny of 957 native woody plants. Within this framework, we delineated bioregions based on vegetation composition and mapped areas of neoendemism and paleoendemism to identify areas of priority for conservation. Our results reveal that the southwest of Hainan is the most important hot spot for endemism and plant diversity followed by the southeast area. The distribution of endemic species showed a scattered, rather than clustered, pattern on the island. Based on phylogenetic range‐weighted turnover metrics, we delineated three major vegetational zones in Hainan. These largely correspond to natural secondary growth and managed forests (e.g., rubber and timber forests) in central Hainan, old‐growth forests and natural secondary growth forest at the margins of Hainan, and nature reserves on the island (e.g., Jianfeng and Diaoluo National Nature Reserves). Our study helps to elucidate potential botanical conservation priorities for Hainan within an evolutionary, phylogenetic framework.     

Spatial analysis of Tasmania’s native vegetation cover and potential implications for biodiversity conservation

Summary The landscape modification model proposed by McIntyre and Hobbs (1999) was used to assess the modification of Tasmania’s native vegetation and its potential implications for biodiversity conservation. The inclusion of new ‘substates’ in the model allowed the varying degrees of landscape variegation and fragmentation observed in Tasmania to be quantified. The mapped extent of Tasmania’s native vegetation is approximately 5.06 million ha or 74% of the land area. The extent of native vegetation varies across bioregions from a low of around 36% in the Tasmanian Northern Midlands bioregion to a high of 94% in the Tasmanian West bioregion. Overall, the Tasmanian landscape can be described as medium variegated as the State retains 76% cover of native vegetation, by area. Two of Tasmania’s nine bioregions are in an intact state, four are variegated, and three are fragmented. Seven of the State’s 48 catchments are in an intact state, 24 catchments are variegated, and 17 are fragmented. Tasmania was estimated to support 33 760 patches of native vegetation. Fewer than 3% of these patches exceed 50 ha in area. Small and medium patches occur predominantly on freehold land with grazing as a major land use, whereas large patches occur predominantly on crown land with conservation and production forestry as the major land uses. One feature of the State’s native vegetation is the large tract of native vegetation ecosystems in western Tasmania. Opportunities arise to sustain the resilience of these native ecosystems both by consolidating the formal protection of vegetation within catchments such as the Arthur and Pieman and by strengthening environmental management in adjacent areas. Bioregions and catchments where climate change may be of particular concern for biodiversity conservation and management include the Tasmanian Northern Midlands bioregion and Cam catchment in north‐western Tasmania. The maintenance and enhancement of patches of remnant vegetation in these areas will be challenging and appears likely to require strategic, multiscale and coordinated natural resource management over decades. Limiting the loss of native vegetation across the entire range of landscape states in Tasmania appears essential to mitigate the further decline of biodiversity.     

Microbial diversity: the importance of exploration and conservation

Microbial diversity is fundamental to maintenance and conservation of global genetic resources. As extreme environments are explored, the richness of microbial diversity is increasingly evident. Measures must be taken to estimate, record, and conserve microbial diversity, not only to sustain human health but also to enrich the human condition globally through wise use and conservation of genetic resources of the microbial world. Received 24 April 1996/ Accepted in revised form 07 January 1997     

Global pattern of phylogenetic species composition of shark and its conservation priority

The diversity of marine communities is in striking contrast with the diversity of terrestrial communities. In all oceans, species richness is low in tropical areas and high at latitudes between 20 and 40°. While species richness is a primary metric used in conservation and management strategies, it is important to take into account the complex phylogenetic patterns of species compositions within communities. We measured the phylogenetic skew and diversity of shark communities throughout the world. We found that shark communities in tropical seas were highly phylogenetically skewed, whereas temperate sea communities had phylogenetically diversified species compositions. Interestingly, although geographically distant from one another, tropical sea communities were all highly skewed toward requiem sharks (Carcharhinidae), hammerhead sharks (Sphyrnidae), and whale sharks (Rhincodon typus). Worldwide, the greatest phylogenetic evenness in terms of clades was found in the North Sea and coastal regions of countries in temperate zones, such as the United Kingdom, Ireland, southern Australia, and Chile. This study is the first to examine patterns of phylogenetic diversity of shark communities on a global scale. Our findings suggest that when establishing conservation activities, it is important to take full account of phylogenetic patterns of species composition and not solely use species richness as a target. Protecting areas of high phylogenetic diversity in sharks, which were identified in this study, could form a broader strategy for protecting other threatened marine species.     

Phylogenetic diversity,trait diversity and niches: species assembly of ferns along a tropical elevational gradient

Aim To analyse the structure of pteridophyte assemblages, based on phylogenetic relatedness and trait properties, along an elevational gradient. Ecological theory predicts that co‐occurring species may be: randomly selected from a regional pool; ecologically sorted so that they are functionally different hence resulting in reduced competition (overdispersion); or functionally similar as an adaptation to specific ecological conditions (clustering). Location Braulio Carrillo National Park and Cerro de la Muerte, Costa Rica, Central America. Methods We used an empirical dataset of the quantitative pattern of species occurrences and individual numbers of ferns within 156 plots along a tropical elevational gradient to test whether directed ecological sorting might cause deviations in patterns of trait and phylogenetic diversity. Mean pairwise distances of species based on phylogenetic and trait properties were compared with two different sets of null assemblages, one maintaining species frequency distributions (constrained) and one not (unconstrained). Results Applying different null models resulted in varying degrees of overdispersion and clustering, but overall patterns of deviation from random expectations remained the same. Contrary to theoretical predictions, phylogenetic and trait diversity were relatively independent from one another. Phylogenetic diversity showed no patterns along the elevational gradient, whereas trait diversity showed significant trends for epiphytes. Main conclusions Under stressful environmental conditions (drought at low elevations and frost at high elevations), epiphytic fern assemblages tended to be clustered with respect to trait characteristics, which suggests environmental filtering. Conversely, under less extreme environmental conditions (middle of the transect), the sorting was biased towards high differentiation (overdispersion), presumably because of interspecific competition and trait shifts among closely related species (character displacement).