Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation

The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies.However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China. We conducted a spatial phylogenetic analysis of the Chinese angiosperm flora at the generic level to identify centers of neo-and pale...     

Phylogenetic relationships between two rare acacias and their common, widespread relatives in south-western Australia

Knowledge of phylogenetic relationships betweentaxa is particularly valuable for conservationmanagement of threatened taxa in anevolutionarily diverse flora such as that foundin the south-west of Western Australia. Acacia sciophanes and A. lobulata aretwo threatened species that have restricteddistributions at the edge of the range of theirwidespread relatives, A. anfractuosa andA. verricula respectively. The phylogenyof these species pairs was investigated usingRFLP analysis of cpDNA. Both restricted specieswere shown to be phylogenetically distinct.Acacia sciophanes and A. anfractuosaare sister species and display the characteristics of a relatively recent evolutionary lineage. In comparison A. lobulata shows significant divergence from A. verricula and is not closely related to the species group in which A. verricula is placed. Acacia lobulataappears to represent an ancient lineage and ismost likely a relictual species. Acaciaverricula also has characteristics of a moreancient evolutionary lineage than A.sciophanes and A. anfractuosa. Ifpriority setting processes based onphylogenetic principles were to be applied tothese species A. lobulata would have thegreater biodiversity value for conservationmanagement.     

A molecular phylogenetic analysis of the bloodroot and kangaroo paw family, Haemodoraceae: taxonomic, biogeographic and conservation implications

A phylogenetic analysis of plastid DNA sequences from the trn L-F region corroborates the hypothesis that Haemodoraceae, a small monocotyledonous family centred in southwestern Australia, are monophyletic with relationships to Philydraceae, Pontederiaceae and Comme–linaceae. It also supports the long-standing recognition of two subfamilies. In Conostylidoideae Tribonanthes falls in an isolated position, thus supporting its segregation as a recently recognized monogeneric tribe. Tribal status for Phlebocarya is not supported as this taxon is unexpectedly placed in Conostylideae as sister to Conostylis–Blancoa. Macropidia falls as sister to Anigozanthos . The DNA tree permits continued recognition of Macropidia and Blancoa as distinct genera, contrary to a recent morphological cladistic analysis. Haemodoroideae fall into two clades: ( Dilatris(Lachnanthes+Haemodorum )) and ( Xiphidium(Schiekia+Wachendofia )). It is unlikely that Haemodoraceae are of Gondwanan origin, and the phylogenetic pattern indicates a largely relictual distribution with a recent radiation in Western Australia.     

云南被子植物菊类分支的系统发育多样性及其分布格局

全球气候变化与人为活动等因素导致的生物多样性丧失,引起了全球各界对生物多样性保护的高度关注。传统生物多样性保护主要对物种、特有种、受威胁物种的种类组成及其分布模式开展研究,忽视了进化历史在生物多样性保护中的作用。云南是全球生物多样性热点地区的交汇区,生物多样性的保护历来受到广泛关注,为了更好地探讨云南生物多样性的保护措施,该研究以云南被子植物菊类分支物种为研究对象,基于物种间的演化关系,结合其地理分布,从进化历史的角度探讨物种、特有种、受威胁物种的种类组成及系统发育组成的分布格局,并整合自然保护地的空间分布,识别生物多样性的重点保护区域。结果表明：云南被子植物菊类分支的物种、特有种及受威胁物种的物种密度与系统发育多样性均显著正相关;通过零模型分析发现,由南向北标准化系统发育多样性逐渐降低;云南南部、东南部、西北部是云南被子植物菊类分支的重点保护区域,加强这些区域的保护,将最大化地保护生物多样性的进化历史和进化潜能。由此可见,融合进化历史信息的植物多样性格局分析不仅有助于更加深入地理解植物多样性的形成与演变,也为生物多样性保护策略的制定提供更多的思路。     

The importance of an evolutionary perspective in conservation policy planning

Prioritization of taxa for conservation must rest on a foundation of correctly identified species boundaries, enhanced by an understanding of evolutionary history and phylogenetic relationships. Therefore, we can incorporate both evolutionary and ecological processes into efforts to sustain biodiversity. In this issue of Molecular Ecology, Malaney & Cook ( 2013 ) highlight the critical value of an evolutionary biogeographical approach, combining multilocus phylogeography with climatic niche modelling to infer phylogenetically weighted conservation priorities for evolutionary lineages of jumping mice across North America. Remarkably, they find that the Preble's meadow jumping mouse (Zapus hudsonius preblei), long debated as a threatened taxon, in fact represents the southern terminus of a relatively uniform lineage that expanded well into Alaska during the Holocene. By contrast, some other relictual and phylogenetically divergent taxa of jumping mice likely warrant greater conservation priority. This study highlights the value of integrative approaches that place current taxonomy in a broader evolutionary context to identify taxa for conservation assessment, but also highlights the challenges in maintaining potential for adaptive responses to environmental change.     

Towards integrated conservation of Australian endangered plants—the Western Australian model

Four percent of the Australian flora is rare and endangered with over 100 taxa presumed extinct. Western Australia contains a large proportion of the endangered flora of Australia with 238 taxa in a critical state of conservation and 70 species presumed extinct. Kings Park and Botanic Garden in south-west Australia is responsible for developing specialized collections of rare and endangered indigenous flora. Macro-and micropropagation procedures are used including conventional cutting and seed propagation, grafting and in thein vitro programme whole seeds (asymbiotic and symbiotic germination), excised seed embryos, shoot apices and inflorescence sections. Wherever possible explants are collected from major provenances of the species and a wide cross section of a species population. Although many of the rare flora of Western Australia are now in theex situ collection maintained by Kings Park and Botanic Garden attempts are being made to develop slow growth storage forin vitro cultures and cryostorage. Trial recovery programmes have commenced with a number of species including the rare and endangered Purdie's donkey orchid (Diuris purdiei). Results of these recovery programmes will guide future efforts in conserving and recovering rare Australian species.     

A comparative study of the distribution of genus size in twenty angiosperm floras

The biodiversity of floras has until recently been measured solely in terms of their species number or species density, with little regard to the breadth of phylogenetic diversity represented by the species. The latter is partly a function of the size of the flora, and partly of the pattern of distribution of the species into higher taxa. To determine whether floras differ in this respect, this study compares the frequency distribution of genus size in 20 island and regional floras. Certain floras (Cape Region, S.W. Australia, New Zealand, Hawaii) are found to have high concentrations of genera containing many species. Others are notably lacking in large genera (Java, Jamaica, Nepal, Niger), though this group tend to be family-rich. In floras with high endemism (Cape, New Zealand, Fiji, Jamaica, Hawaii), the level of endemism is consistently higher in larger genera. Possible reasons for the observed differences between floras are geographic and temporal isolation, level of habitat diversity, climatic history, volcanic, orogenic and tectonic events. Clusters of large genera may indicate recent speciation, possibly following the last glaciation. Genus size may be an important consideration when limited conservation resources have to be targetted to retain the maximum phylogenetic diversity in a threatened flora.     

Where are the survivors? Tracking relictual populations of endangered frogs in Costa Rica

Aim We used abiotic environmental variables and historical locality records to infer distributions of endangered anuran species of Costa Rica to promote efficient strategies for future amphibian surveys. Location Costa Rica. Methods We used a Maximum Entropy Algorithm (Maxent) to predict potential distribution maps for 17 species of endangered anurans and create a consensus map of species richness. We compared the environmental conditions from localities where relictual amphibian populations were recently rediscovered with the conditions across their historical range to evaluate the possibility that these relictual populations might occur in specific climatic conditions that could explain their persistence. We used a multicriteria analysis considering the following factors: the intersection zones between the consensus map, conservation areas, potential Batrachochytrium dendrobatidis (Bd) distribution, collecting effort and areas within the precipitation range at which reappearances had occurred to locate sites for future surveys. Results The resulting predictions suggest that suitable areas for the highest number of species occur between 1300 and 2500 m.a.s.l and are concentrated along the Pacific slopes of the Cordillera de Talamanca and Cordillera Volcánica Central. Around 45% of the high potential richness area is under protection. Relictual populations of declined species seem to persist mainly in highly humid localities (2500–3500 mm of mean annual precipitation). Around 240 km² has an ideal environment for the rediscovery of relictual populations. The multicriteria analysis showed that around 0.5% of the Costa Rican territory should be surveyed exhaustively for frogs. Main conclusions Many of the potential refugia we identified here have not been surveyed since 2000, the areas identified by the best model predictions correspond well with the localities of the relictual populations recently reported. We suggest future surveys of missing amphibian species should focus on these areas. The discovery of populations of endangered species can be used to propose conservation areas.     

Unravelling the evolutionary origins of biogeographic assemblages

Aim

Floristic and faunal diversity fall within species assemblages that can be grouped into distinct biomes or ecoregions. Understanding the origins of such biogeographic assemblages helps illuminate the processes shaping present‐day diversity patterns and identifies regions with unique or distinct histories. While the fossil record is often sparse, dated phylogenies can provide a window into the evolutionary past of these regions. Here, we present a novel phylogenetic approach to investigate the evolutionary origins of present‐day biogeographic assemblages and highlight their conservation value.

Location

Southern Africa.

Methods

We evaluate the evolutionary turnover separating species clusters in space at different time slices to determine the phylogenetic depth at which the signal for their present‐day structure emerges. We suggest present‐day assemblages with distinct evolutionary histories might represent important units for conservation. We apply our method to the vegetation of southern Africa using a dated phylogeny of the woody flora of the region and explore how the evolutionary history of vegetation types compares to common conservation currencies, including species richness, endemism and threat.

Results

We show the differentiation of most present‐day vegetation types can be traced back to evolutionary splits in the Miocene. The woody flora of the Fynbos is the most evolutionarily distinct, and thus has deeper evolutionary roots, whereas the Savanna and Miombo Woodland show close phylogenetic affinities and likely represent a more recent separation. However, evolutionarily distinct phyloregions do not necessarily capture the most unique phylogenetic diversity, nor are they the most species‐rich or threatened.

Main conclusions

Our approach complements analyses of the fossil record and serves as a link to the history of diversification, migration and extinction of lineages within biogeographic assemblages that is separate from patterns of species richness and endemism. Our analysis reveals how phyloregions capture conservation value not represented by traditional biodiversity metrics.

     

Habitat resources, remnant vegetation condition and area determine distribution patterns and abundance of butterflies and day-flying moths in a fragmented urban landscape, south-west Western Australia

The creation of cities, towns and farms following European settlement of Australia has fragmented the original vegetation. Many native species that were previously widespread are now found only within isolated remnants of their original habitat. These relictual populations are at increased risk of decline and local extinction, so identifying the factors that determine their persistence is important for ongoing management and conservation. I compared the effects of site area, connectivity, vegetation condition and habitat resources on the presence, abundance and total number of species of butterflies and day-flying moths within 46 urban fragments of remnant vegetation in south-west Western Australia. Site area and vegetation condition were the dominant determinants of species presence: large sites with more undisturbed vegetation favoured 16 of 20 native species and only one (Geitoneura minyas) benefited from disturbance. Another nine species that were not sufficiently widespread or abundant to enable individual analysis were collectively more prevalent in larger sites. Resource quality and quantity dominated the patterns of site occupancy, consistent with habitat resources, not metapopulation effects, determining current distribution patterns. The total number of species at each site reflected the collective responses of the individual species: increasing with area and declining with vegetation disturbance. The effects of area and vegetation condition were not simply additive: disturbance had a far greater impact on small remnants. Restoration or maintenance of high vegetation condition will be essential to maintain regional species diversity and to prevent local extinctions of butterflies and day-flying moths, especially in small remnants.     

Bird pollination in South Western Australia: A checklist

At least 560 species of flowering plants distributed in 64 genera and 16 families native to Southern Western Australia are pollinated by birds. This represents 15% of the total flora, and indicates adaptation to bird pollination is a major evolutionary force in this region.     

Spatial patterns of phylogenetic diversity

Ecologists and conservation biologists have historically used species-area and distance-decay relationships as tools to predict the spatial distribution of biodiversity and the impact of habitat loss on biodiversity. These tools treat each species as evolutionarily equivalent, yet the importance of species' evolutionary history in their ecology and conservation is becoming increasingly evident. Here, we provide theoretical predictions for phylogenetic analogues of the species-area and distance-decay relationships. We use a random model of community assembly and a spatially explicit flora dataset collected in four Mediterranean-type regions to provide theoretical predictions for the increase in phylogenetic diversity - the total phylogenetic branch-length separating a set of species - with increasing area and the decay in phylogenetic similarity with geographic separation. These developments may ultimately provide insights into the evolution and assembly of biological communities, and guide the selection of protected areas.     

Independent colonization and extensive cryptic speciation of freshwater amphipods in the isolated groundwater springs of Australia's Great Artesian Basin

The groundwater-dependent springs of the Great Artesian Basin (GAB) in arid inland Australia represent a unique and threatened ecosystem. These incredibly isolated springs support a diverse array of endemic flora and fauna. One of the common faunal groups in the GAB springs is the freshwater amphipods of the family Chiltoniidae. The morphological conservatism and taxonomic uncertainty associated with these amphipods has ensured their true biodiversity, phylogeographical history and evolutionary affinities have remained unknown. We have used mitochondrial DNA and allozyme data to unravel a complicated history of isolation, extinction and dispersal among spring amphipod populations across the GAB. The results provide evidence for multiple independent colonizations in the GAB springs, particularly within the Lake Eyre group of springs. The inclusion of a group of Western Australian (WA) stygobitic amphipods from populations up to 1500 km away found surprising evidence for a shared evolutionary history between stygobitic and GAB spring amphipods. Approximate dating of the diversity found between major clades suggests the majority of lineages originated in the late Miocene, around the time of the aridification of inland Australia. The large number of independent lineages and the close connection between GAB spring and WA stygobitic amphipods suggest that a significantly rich amphipod fauna existed in the much wetter environment that once existed in inland Australia. The results also provide evidence for a gross underestimation of the species diversity within the springs, with 12 putative species identified, a conclusion with significant implications for the ongoing conservation of the GAB springs.     

Measuring genome conservation across taxa: divided strains and united kingdoms

Species evolutionary relationships have traditionally been defined by sequence similarities of phylogenetic marker molecules, recently followed by whole-genome phylogenies based on gene order, average ortholog similarity or gene content. Here, we introduce genome conservation--a novel metric of evolutionary distances between species that simultaneously takes into account, both gene content and sequence similarity at the whole-genome level. Genome conservation represents a robust distance measure, as demonstrated by accurate phylogenetic reconstructions. The genome conservation matrix for all presently sequenced organisms exhibits a remarkable ability to define evolutionary relationships across all taxonomic ranges. An assessment of taxonomic ranks with genome conservation shows that certain ranks are inadequately described and raises the possibility for a more precise and quantitative taxonomy in the future. All phylogenetic reconstructions are available at the genome phylogeny server: .     

Phylogenetic properties of Tertiary relict flora in the east Asian continental islands: imprint of climatic niche conservatism and in situ diversification

Understanding biodiversity patterns on islands has long been a central aim in ecology and conservation biology. Island‐specific biogeographical processes play substantial roles in the formation of endemic biota. Here, we examined how climate niche conservatism and geohistorical factors are interactively associated with in situ diversification of Tertiary relict flora in the east Asian continental islands. We generated two novel datasets for species distribution and phylogeny that included all of the known vascular plant species in Japan (5575). Then we tested phylogenetic signal of climatic tolerance, in terms of absolute minimum temperature and water balance, and explored environmental predictors of phylogenetic structure (evolutionary derivedness and clustering) of species assemblages. Although phylogenetic signal of climatic tolerance was significant across the phylogeny of most species, the strength of climatic niche conservatism differed among ferns, gymnosperms, angiosperm trees, and angiosperm herbs. For angiosperm trees, cold temperatures acted as environmental filters that generated phylogenetic derivedness/clustering of species assemblages. For fern and angiosperm herb species, however, phylogenetic properties were not associated with climatic harshness. These contrasting patterns among groups reflected climate niche evolution in vascular plants with different growth forms and traits; for example, diversification of angiosperm trees (but not fern and herb) occurred in response to historical climatic cooling. More importantly, geographical constraints contributed to evolutionary radiation that resulted from isolation by distance from the continent or by elevation. Quaternary climate change was also associated with clade‐specific radiation in refugial habitats. The degree to which geographical, geological, and palaeoclimatic variables explain the phylogenetic structure underscores the importance of isolation‐ and habitat‐stability‐related geohistorical processes in driving in situ diversification despite climatic niche conservatism. We propose that the highly endemic flora of the east Asian islands resulted from the interplay of idiosyncratic regional factors, and ecological and evolutionary processes, such as climate niche assembly and adaptive/nonadaptive radiation.     

Australian Assassins, Part I: A review of the Assassin Spiders (Araneae, Archaeidae) of mid-eastern Australia

The Assassin Spiders of the family Archaeidae are an ancient and iconic lineage of basal araneomorph spiders, characterised by a specialised araneophagic ecology and unique, 'pelican-like' cephalic morphology. Found throughout the rainforests, wet sclerophyll forests and mesic heathlands of south-western, south-eastern and north-eastern Australia, the genus Austrarchaea Forster & Platnick, 1984 includes a diverse assemblage of relictual, largely short-range endemic species. With recent dedicated field surveys and significant advances in our understanding of archaeid biology and ecology, numerous new species of assassin spiders have been discovered in the montane sub-tropical and warm-temperate closed forests of mid-eastern Australia, including several rare or enigmatic taxa and species of conservation concern. This fauna is revised and 17 new species are described from south-eastern Queensland and eastern New South Wales: Austrarchaea alanisp. n., Austrarchaea aleenaesp. n., Austrarchaea binfordaesp. n., Austrarchaea christopherisp. n., Austrarchaea clyneaesp. n., Austrarchaea cunninghamisp. n., Austrarchaea dianneaesp. n., Austrarchaea harmsisp. n., Austrarchaea helenaesp. n., Austrarchaea judyaesp. n., Austrarchaea mascordisp. n., Austrarchaea mcguiganaesp. n., Austrarchaea milledgeisp. n., Austrarchaea monteithisp. n., Austrarchaea platnickorumsp. n., Austrarchaea ravenisp. n. and Austrarchaea smithaesp. n. Adult specimens of the type species, Austrarchaea nodosa (Forster, 1956) are redescribed from the Lamington Plateau, south-eastern Queensland, and distinguished from the sympatric species Austrarchaea dianneaesp. n. A key to species and a molecular phylogenetic analysis of COI and COII mtDNA sequences complement the species-level taxonomy, with maps, habitat photos, natural history information and conservation assessments provided for all species.     

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.     

Phylogeny,extinction and conservation: embracing uncertainties in a time of urgency

Evolutionary studies have played a fundamental role in our understanding of life, but until recently, they had only a relatively modest involvement in addressing conservation issues. The main goal of the present discussion meeting issue is to offer a platform to present the available methods allowing the integration of phylogenetic and extinction risk data in conservation planning. Here, we identify the main knowledge gaps in biodiversity science, which include incomplete sampling, reconstruction biases in phylogenetic analyses, partly known species distribution ranges, and the difficulty in producing conservation assessments for all known species, not to mention that much of the effective biological diversity remains to be discovered. Given the impact that human activities have on biodiversity and the urgency with which we need to address these issues, imperfect assumptions need to be sanctioned and surrogates used in the race to salvage as much as possible of our natural and evolutionary heritage. We discuss some aspects of the uncertainties found in biodiversity science, such as the ideal surrogates for biodiversity, the gaps in our knowledge and the numerous available phylogenetic diversity-based methods. We also introduce a series of cases studies that demonstrate how evolutionary biology can effectively contribute to biodiversity conservation science.     

Partnering conservation actions. <Emphasis Type="Italic">Inter situ</Emphasis> solutions to recover threatened species in South West Western Australia

South West Western Australia has a rich endemic flora of global significance. The threats facing this floral diversity are increasing in type, severity and scale, demonstrated by the rising numbers of species threatened with extinction. In particular, the root-rot pathogen Phytophthora cinnamomi is causing widespread destruction, threatening the survival of many of the region’s unique plants. In situ conservation of wild plants is considered the most essential component of a flora conservation program, but the ability to conserve some species adequately is often unachievable in the short term and urgent management intervention is required to prevent extinction. We present data on the status and management of wild populations of four threatened species from the region, including an ex situ program, and describe our efforts to bridge the gap between these two components. Such inter situ conservation recovery work enables monitoring of biological attributes, research into reproductive biology and collection of genetic material for further ex situ conservation, and provides the source of material for future restoration of wild populations.     

Contrasting patterns of phylogenetic diversity across climatic zones of Western Ghats: A biodiversity hotspot in peninsular India

This study attempts to understand the biogeographic history of the Western Ghats forests by investigating decoupling between phylogenetic and taxonomic diversity. We specifically test whether the deciduous forests have been recently established, whether the southern region was a refuge, and whether the deciduous and evergreen forest species have disparate evolutionary histories. We used species composition data from 23 forest types along the Western Ghats for all woody angiosperms above 10‐cm diameter at breast height. Forests were broadly grouped as either evergreen or deciduous. Mean phylogenetic distances corrected for species richness and mean phylogenetic beta diversity corrected for shared species were assessed using z‐scores from null distributions. Null distributions were generated by randomizing the species relationships on the phylogeny. We found that all evergreen forests showed a greater phylogenetic diversity as compared with null expectations. Deciduous forests showed the inverse pattern. Within the evergreen belt, there was a decreasing phylogenetic diversity from south to north, as predicted by the southern refuge hypothesis. The phylogenetic beta diversity across evergreen–deciduous forests was lesser than the null expectation, whereas it was much higher across forests within the evergreen belt. This study provides the first phylogenetic evidence for the antiquity of evergreen forests as well as the southern refuge hypothesis in the Western Ghats. The deciduous forests species have shared evolutionary histories with the evergreen forest species, suggesting multiple shifts between evergreen and deciduous states through the lineages. Conversely, the evergreen species exhibited a disparate evolutionary history across these forests, possibly owing to sharper ecological or climatic gradients.