Comparative phylogeography and the identification of genetically divergent areas for conservation

Genetic diversity is recognized as a fundamental component of biodiversity and its protection is incorporated in several conventions and policies. However, neither the concepts nor the methods for assessing conservation value of the spatial distribution of genetic diversity have been resolved. Comparative phylogeography can identify suites of species that have a common history of vicariance. In this study we explore the strengths and limitations of Faith's measure of 'Phylogenetic Diversity' (PD) as a method for predicting from multiple intraspecific phylogeographies the underlying feature diversity represented by combinations of areas. An advantage of the PD approach is that information on the spatial distribution of genetic diversity can be combined across species and expressed in a form that allows direct comparison with patterns of species distributions. It also seeks to estimate the same parameter, feature diversity, regardless of the level of biological organization. We extend the PD approach by using Venn diagrams to identify the components of PD, including those unique to or shared among areas and those which represent homoplasy on an area tree or which are shared across all areas. PD estimation should be complemented by analysis of these components and inspection of the contributing phylogeographies. We illustrate the application of the approach using mtDNA phylogeographies from vertebrates resident in the wet tropical rainforests of north-east Queensland and compare the results to biodiversity assessments based on the distribution of endemic vertebrate species. The genetic vs. species approaches produce different assessments of conservation value, perhaps reflecting differences in the temporal and spatial scale of the determining processes. The two approaches should be seen as complementary and, in this case, conservation planning should incorporate information on both dimensions of biodiversity.     

Biodiversity in the Gulf of Guinea: an overview

Patterns of species-richness and endemism in the Gulf of Guinea reflect the region's biogeographic history. Bioko is a continental-shelf island that was recently connected to the African mainland, whereas Príncipe, São Tomé and Annobón are truly oceanic and have never been connected with each other or with the mainland. As a result, Bioko supports a much more diverse flora and fauna but with relatively low levels of endemism at the species level, whereas the oceanic islands are relatively depauperate because of their isolation but rich in endemic taxa. Species endemism is 0–3% on Bioko for angiosperms, bats, birds, reptiles and amphibians, compared with much higher values on Principe for these same taxa of 8% (plants) to 100% (amphibians), on São Tomé between 14% (plants) and 100% (amphibians), and on Annobón 0% (bats) to 71% (reptiles). On a global scale, for their size both Príncipe and São Tomé support unusually high numbers of single-island endemic species of birds, reptiles and amphibia. For its tiny size, Annobón is also notable for its endemic birds and reptiles. Among terrestrial molluscs the rates of endemism are in general higher than for plants and vertebrates, from ca 50% on Bioko to ca 80% on the oceanic islands. In contrast and as might be expected, only Bioko supports a rich freshwater fish fauna and it contains many endemic taxa, whereas the oceanic islands support only a few salt-tolerant species. The Gulf of Guinea islands are also important for their marine organisms, amongst which coral reef fish and marginellid molluscs show high levels of endemism, though they are not especially species-rich. The Gulf of Guinea islands are of great interest to conservationists and evolutionary biologists. Each island, of greatly differing size and degree of isolation, has acquired its unique sub-set of plants and animals separately from the neighbouring mainland, followed by adaptive radiations in situ. For this reason the conservation value of the archipelago as a whole is greater than the sum of the biodiversity contained in its individual islands. Conservation initiatives in the Gulf of Guinea should therefore ensure that representative terrestrial, freshwater and marine habitats and groups of organisms are targeted in a co-ordinated manner among the islands.     

Distribution and conservation status of primates in Bioko island,Equatorial Guinea

Ten species of non-human primates are indigenous to Bioko; half of these are endangered and between five and eight are endemic subspecies. Recent data on their status and distribution have been lacking. In 1986, a ten-week survey of the island was carried out to determine the distribution and status of the primates and the natural vegetation, and to evaluate the effects of man on them. This paper presents the results of that survey, gives an update of conservation achievements since 1986, and highlights current concerns. Between 1974 and 1986 it is probable that numbers of all Bioko primates rose as a result of an increase in habitat and of reduced hunting. At the time of the survey there was considerably more natural, undisturbed, vegetation remaining in Bioko tran expected. Much of this vegetation occurs within two large blocks that are of outstanding importance to the conservation of species in tropical Africa, particularly of plants and primates.     

Diversity and endemism of angiosperms in the Gulf of Guinea islands

The richness of flowering plants (1666 native taxa) and the originality of the flora of the islands of the Gulf of Guinea are remarkable. The flora of Bioko shows the highest diversity in terms of families, genera and species of angiosperms but, due to its proximity to the mainland, the level of endemism is relatively low. The number of endemics in the four islands has suffered a decrease in the last years, due to taxonomic changes. Currently, 176 endemic taxa of angiosperms are recognized. Most of the endemic taxa are under-collected and information is lacking on their biology and distribution, hence the need for inventory work on the flora of the islands. A measure of the similarity between the floras of the islands can be given by determination of genera in common. The results are comparable to those obtained with Exell and Wild's quotient of affinity and show a great similarity between neighbouring islands. The presence of afromontane elements and several palaeoendemics in the mountain rain forest of the islands is notable and makes the study of its flora a priority for research.     

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.     

The role of zoological parks in biodiversity conservation in the Gulf of Guinea islands

Modern zoological institutions are devoting more of their resources to research, education and conservation than they have in the past. Many zoos recently have become increasingly involved in external or field (in situ) projects, with a view to conserving species and their habitats where they occur naturally. An opportunity to practice in situ conservation exists on Bioko, the largest and biologically the most diverse of the Gulf of Guinea islands. Although urgent political and economic problems confront Equatorial Guinea, of which Bioko is part, external aid will be needed if the infrastructure is to be developed to protect and maintain two important nature reserves on the island. Several initiatives are suggested for the involvement of zoos in this process.     

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.     

Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai‐Tibetan plateau

Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Pleistocene for the Qinghai‐Tibetan (Tibetan) plateau, a region where glaciation was not synchronous with the North Hemisphere ice sheet maxima, remains poorly understood. Here, we compared the phylogeographical patterns of five avian species on the Qinghai‐Tibetan plateau by three mitochondrial DNA fragments: the Tibetan snow finch (Montifringilla adamsi), the Blanford’s snow finch (Pyrgilauda blanfordi), the horned lark (Eremophila alpestris), the twite (Carduelis flavirostris) and the black redstart (Phoenicurus ochruros). Our results revealed the three species mostly distributed on the platform region of the plateau that experienced population expansion following the retreat of the extensive glaciation period (0.5–0.175 Ma). These results are at odds with the results from avian species of Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023–0.018 Ma). A single refugium was identified in a restricted semi‐continuous area around the eastern margin of the plateau, instead of multiple independent refugia for European and North American species. For the other two species distributed on the edges of the plateau (the twite and black redstart), populations were maintained at stable levels. Edge areas are located on the eastern margin, which might have had little or no ice cover during the glaciation period. Thus, milder climate may have mitigated demographic stresses for edge species relative to the extremes experienced by platform counterparts, the present‐day ranges of which were heavily ice covered during the glaciation period. Finally, various behavioural and ecological characteristics, including dispersal capacities, habitat preference and altitude specificity along with evolutionary history might have helped to shape different phylogeographical structures appearing in these five species.     

Comparative avian biodiversity of five mountains in northern Cameroon and Bioko

Larison, B., Smith, T.B., Fotso, R. & McNiven, D. 2000. Comparative avian biodiversity of five mountains in northem Cameroon and Bioko. Ostrich 71 (1 & 2): 269–276.

Endemism among birds is widespread in the montane forests of western Cameroon and the Gulf of Guinea. The region includes some of the rarest and most threatened species in Africa. We conducted avian surveys of four previously unsurveyed montane sites in northern Cameroon, including Mt. Ngang-Ha, Hoséré Vokré, Tchabal Gandaba, and Tchabal Mbabo, as well as the northern slope of Caldera de Luba on the island of Bioko, Equatorial Guinea. We report here on avian species richness and relative abundance, and evaluate the conservation potential of each site based on avifaunal richness. The montane forest on both Tchabal Mbabo and Caldera de Luba is extensive, while on the other mountains, the vegetation is not characteristic of montane forest, and consists primarily of small gallery forests embedded in savanna. Tchabal Mbabo and Caldera de Luba had the greatest species richness and abundance of montane birds, while Tchabal Gandaba had the greatest overall avian species richness and abundance. Few montane species were noted on Mt. Ngang-Ha and Hosere Vokre, and avian abundance was quite low on both mountains. Of the mountains surveyed, Tchabal Mbabo and Caldera de Luba exhibit the greatest potential for conservation based on extent of montane forest, and montane species richness and abundance.     

Bats of the Gulf of Guinea islands: faunal composition and origins

The present study compares the bat faunas of the islands of the Gulf of Guinea. Species composition. endemism and hypothetical origins are discussed. All families present in the mainland region are found in Bioko, a typical landbridge island. Foliage gleaning guild species (Nycteridae) show limited colonization abilities. This is also true of the family Rhinolophidae, but not for the closely related family Hipposideridae. The majority of the oceanic island species are African bats which show a widespread distribution and, therefore, have a high ecological plasticity. The continental relatives of the two endemic species Myonycteris brachycephala and Chaerephon tomensis are restricted to relatively small forested areas. Bioko's bat fauna is the result of the recent isolation from a formerly land-connected community. The oceanic bat faunas originated from the establishment of incomers from other areas. Nevertheless, extinction appears in both vicariant and dispersal processes, as an important factor in modelling the current bat communities of the Gulf of Guinea islands.     

Diversity and status of sea turtle species in the Gulf of Guinea islands

In West Africa, the Gulf of Guinea islands are important nesting places for four sea turtle species. The Green turtle (Chelonia mydas), the Hawksbill (Eretmochelys imbricata), the Olive Ridley (Lepidochelys olivacea) and the Leatherback (Dermochelys coriacea) turtles nest on Bioko's southern beaches. The Green, Hawksbill and Leatherback turtles breed on Príncipe and São Tomé. The Leatherback turtle nests, at least, on Annobón. The Leatherback turtle is reported on the four islands for the first time, and the Olive Ridley turtle for Bioko. Bioko is probably the most important island in terms of number of species and nesting individuals; the Green turtle being the most abundant species. However, the nesting places are at present restricted to barely 20 km along the coastline. On Príncipe and São Tomé, the most common species is the Hawksbill turtle. Sea turtle nesting populations are being severely depleted on the four islands. The main causes of cverexploitation are the meat and egg trade on Bioko and the Hawksbill shell-craft trade on São Tomé and Príncipe.     

Phylogenetic diversity of Sri Lankan freshwater crabs and its implications for conservation

As part of a Global Biodiversity Hotspot, the conservation of Sri Lanka's endemic biodiversity warrants special attention. With 51 species (50 of them endemic) occurring in the island, the biodiversity of freshwater crabs is unusually high for such a small area (65 600 km²). Freshwater crabs have successfully colonized most moist habitats and all climatic and elevational zones in Sri Lanka. We assessed the biodiversity of these crabs in relation to the different elevational zones (lowland, upland and highland) based on both species richness and phylogenetic diversity. Three different lineages appear to have radiated simultaneously, each within a specific elevational zone, with little interchange thereafter. The lowland and upland zones show a higher species richness than the highland zone while – unexpectedly – phylogenetic diversity is highest in the lowland zone, illustrating the importance of considering both these measures in conservation planning. The diversity indices for the species in the various IUCN Red List categories in each of the three zones suggest that risk of extinction may be related to elevational zone. Our results also show that overall more than 50% of Sri Lanka's freshwater crab species (including several as yet undescribed ones), or approximately 72 million years of evolutionary history, are threatened with extinction.     

Comparative phylogeography of five widespread tree species: Insights into the history of western Amazonia

Various historical processes have been put forth as drivers of patterns in the spatial distribution of Amazonian trees and their population genetic variation. We tested whether five widespread tree species show congruent phylogeographic breaks and similar patterns of demographic expansion, which could be related to proposed Pleistocene refugia or the presence of geological arches in western Amazonia. We sampled Otoba parvifolia/glycycarpa (Myristicaceae), Clarisia biflora, Poulsenia armata, Ficus insipida (all Moraceae), and Jacaratia digitata (Caricaceae) across the western Amazon Basin. Plastid DNA (trnH–psbA; 674 individuals from 34 populations) and nuclear ribosomal internal transcribed spacers (ITS; 214 individuals from 30 populations) were sequenced to assess genetic diversity, genetic differentiation, population genetic structure, and demographic patterns. Overall genetic diversity for both markers varied among species, with higher values in populations of shade‐tolerant species than in pioneer species. Spatial analysis of molecular variance (SAMOVA) identified three genetically differentiated groups for the plastid marker for each species, but the areas of genetic differentiation were not concordant among species. Fewer SAMOVA groups were found for ITS, with no detectable genetic differentiation among populations in pioneers. The lack of spatially congruent phylogeographic breaks across species suggests no common biogeographic history of these Amazonian tree species. The idiosyncratic phylogeographic patterns of species could be due instead to species‐specific responses to geological and climatic changes. Population genetic patterns were similar among species with similar biological features, indicating that the ecological characteristics of species impact large‐scale phylogeography.     

Variable phylogeographic histories of five forest birds with populations in Upper and Lower Guinea: implications for taxonomy and evolutionary conservation

This study evaluates phylogeographic structure in selected forest bird species distributed on either side of the Dahomey Gap in West Africa to extend analyses of avian diversification across the Guineo-Congolean forest. Mitochondrial DNA sequence data were collected for five species, including four with a break in distribution across the Dahomey Gap and one with a more continuous distribution. Data for the five focal species were included in a single analysis along with appropriate outgroup taxa, allowing estimates of divergence time on a common timescale. Both phylogeographic patterns and estimated divergence times were highly variable. In two cases (Green Hylia Hylia prasina and Yellow-whiskered Greenbul Eurillas latirostris), samples from east and west of the Dahomey Gap belong to divergent mitochondrial lineages, but with substantially older divergence in Eurillas (～4.1 MY). In Western Bluebill Spermophaga haematina, relatively divergent eastern and western lineages (～1.1 MY) were sampled in the same locality in eastern Ghana, suggesting east to west gene flow across the gap following earlier vicariance. In Forest Robin Stiphrornis erythrothorax, birds sampled within Ghana were from two highly divergent lineages (～1.9 MY), one of which is more closely related to birds from Cameroon and Equatorial Guinea, such that divergence across the Dahomey Gap was comparatively recent (～0.36 MY). For both Hylia and Stiphrornis, we corroborate recent studies documenting multiple divergent lineages within each genus, some of which may represent distinct species. Consistent with previous studies, our analysis shows that the Dahomey Gap can be a significant barrier to gene flow for species restricted to forest habitats. At the same time, individual species exhibit a broad range of divergence times and phylogeographic histories of variable complexity. We discuss the taxonomic implications of our results for each focal species.     

Endemicity of Afromontane grasshopper assemblages: implications for grassland conservation

The Drakensberg escarpment in southern Africa is extensively afforested with pine plantations. The Afromontane grasslands in this area have large numbers of endemic plant taxa, but very little is known of their invertebrate fauna. We report on the microgeographical and broad‐scale geographical characteristics of grasshoppers and their allies (Orthoptera) at the Groenvaly grassland fragmentation experiment site, South Africa. Pre‐fragmentation sampling indicates that control sites and experimental fragments were comparable at the start of the experiment. Of the surveyed species (total 31 species) 25% are endemic to this grassland with another 33% occurring more widely in montane grasslands of south‐eastern South Africa. The level of orthopteran endemicity is therefore similar to that of plants, emphasizing the conservation importance of this threatened habitat. There was a significant inverse relation between the degree of stenotopy of a species within the study site and its geographical range in southern Africa, with implications for interpreting the conservation importance of taxonomically and geographically unknown taxa such as the beetles (Coleoptera) in the Afromontane grassland. This information on endemicity of the Afromontane Orthoptera indicates that these grasslands harbour a diverse endemic fauna representing a significant part of southern African biodiversity.     

Biodiversity conservation in the Gulf of Guinea islands: taking stock and preparing action

This paper introduces an Action Statement on biodiversity conservation in the four Gulf of Guinea islands arising from a workshop held in Jersey in 1993. The current state of the main habitats on all the islands, pressures acting upon them, existing institutions and actions taken so far are reviewed. The 24-point Action Statement was produced as a framework for future international initiatives in biodiversity research and conservation in this part of Africa. Attention is drawn to the progress made by the governments of the region in legislation and institutional support. The workshop recommended the establishment of a regional programme of research and conservation in conjunction with the Governments of Equatorial Guinea and of São Tomé and Príncipe.     

报春花属的保育遗传学及亲缘地理学研究进展

现存物种的分布格局、遗传结构是当前因素和历史因素共同作用的结果。人类的过度开发、全球变暖等当前因素造成的生境片段化是目前许多报春花属植物濒危的一大原因。该文总结了近年来报春花属内的保育遗传学研究进展,期望以此为更好地保护报春花属植物提供一定的理论基础。应用亲缘地理学研究方法可以弥补古生物学难以研究报春花植物历史成因的不足,因此也总结该方法在报春花属内的研究进展,并初步整理不同地区间的报春花属植物的分化式样,同时期望这些研究成果能为为研究报春花属植物在应对全球气候变化的响应机制方面提供一些参考。     

The biogeography of land snails in the islands of the Gulf of Guinea

Data on land snail diversity in the Gulf of Guinea islands is presented and the biogeography of the Gulf of Guinea fauna is discussed with reference to island snail faunas in the other areas of the world. Although the land snail faunas of the four islands clearly have west and central African affinities, speciation events following rare colonizations have led to high rates of endemism at the species and generic levels. The influence of island size, altitude, isolation and other factors on the development of the land snail faunas is discussed. The effect of land use changes on the land snail fauna over the last 150 years is evaluated. Current threats include recent changes in agricultural practice leading to the destruction of snail habitats in both forest and plantation areas. The potential threat posed by introduced species is also discussed. The Gulf of Guinea snail faunas appear to be in relatively good health in comparison to many other island snail faunas. However, the uniqueness of the faunas makes it imperative that further ecological and taxonomic research is undertaken both to understand the processes by which they developed and to evaluate the current status of many species in terms of distribution and threats.