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Effects of selective timber harvest on amphibian species diversity in Budongo Forest Reserve, Uganda
... In addition, the application of arboricide chemicals was done in the 1950 s and 1960 s to selectively eliminate non-commercial tree species (Plumptre, 1996). At present, Budongo Central Forest Reserve is a mosaic of large areas (compartments) of several-hundred-hectares which were logged and treated with arboricide at different times, as well as unlogged compartments (Lukwago et al., 2020). Biodiversity and emerging communities in these naturally regenerating areas have been studied for a wide range of taxa including trees (Plumptre, 1996;Bahati, 1998;Sheil, 2001;Mwavu et al., 2008;Kirika et al., 2010), climbers (Babweteera et al., 2000), primates (Plumptre and Reynolds, 1994), birds (Owiunji and Plumptre, 1998;Dale et al., 2000;Owiunji, 2000Owiunji, , 2001Uwimbabazi et al., 2013), amphibians (Lukwago et al., 2020), a wide range of canopy arthropods (Wagner, 2001), including canopy beetles (Wagner, 2000) and canopy ants (Schultz and Wagner, 2002). ...
... At present, Budongo Central Forest Reserve is a mosaic of large areas (compartments) of several-hundred-hectares which were logged and treated with arboricide at different times, as well as unlogged compartments (Lukwago et al., 2020). Biodiversity and emerging communities in these naturally regenerating areas have been studied for a wide range of taxa including trees (Plumptre, 1996;Bahati, 1998;Sheil, 2001;Mwavu et al., 2008;Kirika et al., 2010), climbers (Babweteera et al., 2000), primates (Plumptre and Reynolds, 1994), birds (Owiunji and Plumptre, 1998;Dale et al., 2000;Owiunji, 2000Owiunji, , 2001Uwimbabazi et al., 2013), amphibians (Lukwago et al., 2020), a wide range of canopy arthropods (Wagner, 2001), including canopy beetles (Wagner, 2000) and canopy ants (Schultz and Wagner, 2002). However, published data on fruit-feeding butterflies is currently lacking. ...
... The 51-year-old compartment W22 has thick undergrowth, and upper-storey canopy trees are scarce. Compartment N15 (primary forest) is a strict nature reserve and has probably not experienced any form of illegal logging (Plumptre and Reynolds, 1994;Lukwago et al., 2020). ...
Understanding of how biodiversity can recover after anthropogenic disturbances, such as selective logging, is important for planning conservation strategies for tropical forests and for more sustainable timber harvest re-gimes. However, the knowledge of insect community compositions in regenerating logged forests is still limited, especially in the Afrotropics. Here, we evaluated the recovery patterns of fruit-feeding butterfly communities in four different-aged secondary forest compartments and one primary forest compartment in the Budongo Central Forest Reserve, Uganda. In each compartment, butterflies were sampled monthly for five consecutive months in 2017 using traps baited with fermented bananas. A total of 3,778 individuals, representing 82 species (78 identified at the species level and four morphogroups) were recorded. The fruit-feeding butterfly community composition differed among forest compartments and study months. Fruit-feeding butterfly communities of the oldest 72-year-old secondary forest compartment were similar to the primary forest compartment. In the younger secondary forest compartments the seasonal variation was large; especially the communities of the “core” rainy season months were distinct from the communities in primary and oldest secondary forest. The majority of in-dividuals captured from both primary and secondary forests represented forest-dependent species. Primary forests are irreplaceable for preserving the diversity of tropical forests in the long-term. Nevertheless, our study demonstrates that selective logging can allow fruit-feeding butterfly community composition to recover if enough time (>70 years) is allowed for recovery.
... The study was conducted in northwestern Uganda where large-scale deforestation for fertilizer-based sugarcane cultivation has been documented for several decades. The long-term mean annual temperature for the study area is about 25 • C while the annual precipitation is about 1700 mm (Lukwago et al., 2020). Rainfall in the region follows a bimodal distribution pattern divided into two main wet seasons (March to May and August to November), and an extended (December to February) and a short dry season (June to July; Lukwago et al., 2020). ...
... The long-term mean annual temperature for the study area is about 25 • C while the annual precipitation is about 1700 mm (Lukwago et al., 2020). Rainfall in the region follows a bimodal distribution pattern divided into two main wet seasons (March to May and August to November), and an extended (December to February) and a short dry season (June to July; Lukwago et al., 2020). ...
Tropical deforestation for fertilizer-based agriculture has greatly increased in the last decades resulting in significant greenhouse gas (GHG; carbon dioxide (CO 2), methane (CH 4), and nitrous oxide (N 2 O)) emissions. Unfortunately , empirical studies on soil GHG fluxes from African deforestation hotspots are still limited, creating uncertainties in global GHG budgets. Therefore, we assessed how soil GHG fluxes along with their auxiliary controls (water filled pore space (WFPS), temperature, and mineral nitrogen (N)) differed between the forest and sugarcane plantations. This assessment was based on monthly (forest) and intensive (sugarcane) GHG and auxiliary measurements between May 2019 and June 2020. Measurements were conducted in four reference forest plots and 12 sugarcane plots randomly assigned to three fertilization treatment groups (low, standard, and high), representing the fertilization gradient used by sugarcane farmers in Uganda. Despite the use of different fertilization rates as treatments for the sugarcane experiment, neither auxiliary controls nor soil GHG fluxes significantly differed among the treatments. Soil CO 2 effluxes were higher under sugarcane (17.6 ± 0.0 Mg C ha-1 yr-1) compared to forest (14.5 ± 0.1 Mg C ha-1 yr-1 ; p < 0.001) because of the higher autotrophic respiration from the sugarcane's fine root biomass and the microbial decomposition of the sugarcane's larger soil organic carbon (SOC) stocks. Conversely, soil CH 4 uptake under sugarcane (− 1.1 ± 0.0 kg C ha-1 yr-1) was three times lower than under forest (− 3.1 ± 0.0 kg C ha-1 yr-1 ; p < 0.001), owing to the likely alteration of methanotroph abundance upon conversion. Likewise, soil N 2 O emissions were smaller under sugarcane (1.3 ± 0.0 kg N ha-1 yr-1) compared to forest (1.8 ± 0.0 kg N ha-1 yr-1 ; p < 0.001) because excess N from fertilizer addition in the sugarcane was either lost through leaching or taken up by the sugarcane crop. Only seasonal variability in WFPS, among the auxiliary controls, affected CH 4 uptake at both sites (p < 0.001) and soil CO 2 effluxes under sugarcane (p = 0.018). Noteworthy, soil N 2 O fluxes from both sites were unaltered by the seasonality-mediated changes in auxiliary controls. We conclude that even with the increased SOC sequestration and the lower N 2 O emissions under sugarcane compared to forest, the forest-sugarcane conversion resulted in a yearly net C loss of 2.8 Mg CO 2-eq ha-1 from soils to atmosphere, largely arising from the higher soil CO 2 effluxes and to a smaller extent from a reduced CH 4 uptake under sugarcane.
... The forest reserve spans over 825 km 2 and is extensively diverse with respect to forest communities, with Cynometra alexandri, Chrysophyllum albidum, Maesopsis eminii, and Diospyros abyssinica as the dominant tree species (Eggeling, 1947). The long-term mean annual temperature and precipitation over the study area is 25 • C and 1700 mm, respectively (Lukwago et al., 2020). Rainfall is distributed into two rainy seasons (i.e., March to May and August to November) punctuated by a strong dry season (December to February) and a weak dry season (June to July; Lukwago et al., 2020). ...
... The long-term mean annual temperature and precipitation over the study area is 25 • C and 1700 mm, respectively (Lukwago et al., 2020). Rainfall is distributed into two rainy seasons (i.e., March to May and August to November) punctuated by a strong dry season (December to February) and a weak dry season (June to July; Lukwago et al., 2020). It is worth noting that the amount of rainfall received during the field campaign (2385 mm; Fig. 2d) was higher than the long-term mean annual precipitation for this region. ...
Soil macronutrient availability is one of the abiotic controls that alters the exchange of greenhouse gases (GHGs) between the soil and the atmosphere in tropical forests. However, evidence on the macronutrient regulation of soil GHG fluxes from central African tropical forests is still lacking, limiting our understanding of how these biomes could respond to potential future increases in nitrogen (N) and phosphorus (P) deposition. The aim of this study was to disentangle the regulation effect of soil nutrients on soil GHG fluxes from a Ugandan tropical forest reserve in the context of increasing N and P deposition. Therefore, a large-scale nutrient manipulation experiment (NME), based on 40 m×40 m plots with different nutrient addition treatments (N, P, N + P, and control), was established in the Budongo Central Forest Reserve. Soil carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes were measured monthly, using permanently installed static chambers, for 14 months. Total soil CO2 fluxes were
partitioned into autotrophic and heterotrophic components through a root
trenching treatment. In addition, soil temperature, soil water content, and
nitrates were measured in parallel to GHG fluxes. N addition (N and N + P) resulted in significantly higher N2O fluxes in the transitory phase (0–28 d after fertilization; p<0.01) because N fertilization likely increased soil N beyond the microbial immobilization and plant nutritional demands, leaving the excess to be nitrified or denitrified. Prolonged N fertilization, however, did not elicit a significant response in background (measured more than 28 d after fertilization) N2O fluxes. P fertilization marginally and significantly increased transitory (p=0.05) and background (p=0.01)
CH4 consumption, probably because it enhanced methanotrophic activity. The addition of N and P (N + P) resulted in larger CO2 fluxes in the transitory phase (p=0.01), suggesting a possible co-limitation of both N and P on soil respiration. Heterotrophic (microbial) CO2 effluxes were significantly higher than the autotrophic (root) CO2 effluxes (p<0.01) across all treatment plots, with microbes contributing about two-thirds of the total soil CO2 effluxes. However, neither heterotrophic nor autotrophic
respiration significantly differed between treatments. The results from this study suggest that the feedback of tropical forests to the global soil GHG budget could be disproportionately altered by increases in N and P
availability over these biomes.
... Conventional selective logging, in particular, reduces forest structural heterogeneity, causing increased temperatures and reduced humidity (Meijide et al., 2018;Mollinari et al., 2019), leading to increased desiccation risk and reduced microhabitat heterogeneity (Gardner et al., 2007). Although anuran communities may exhibit limited disturbance following CL (Fredericksen and Fredericksen, 2004;Vallan et al., 2004), studies in Malaysia (Gillespie et al., 2012;Faruk et al., 2013;Konopik et al., 2015), Uganda (Lukwago et al., 2020), and Guyana (Ernst et al., 2006) identified major shifts in community composition, including reduced richness and diversity of forest specialists following CL. Community recovery following conventional selective logging is highly variable, but amphibian community composition in South America and Ivory Coast sites had not returned to unlogged community states even 30 years after logging (Ernst et al., 2006). ...
... Whilst the results of our multi-species occupancy models yielded highly variable results, our diversity profiles conformed to previous studies of amphibian responses to different logging types. Species richness and evenness in CL sites remained low even 18 -21 years after logging, similar to Ugandan (Lukwago et al., 2020), Guyana (Ernst et al., 2006) and Malaysian (Konopik et al., 2015) amphibian communities. In conjunction with our habitat and species occupancy results, this suggests a considerably longer recovery period following CL for anuran richness and evenness compared to RIL. ...
Unsustainable timber management, primarily via Conventional selective Logging (CL), has resulted in severe habitat degradation and biodiversity loss. Sustainable techniques, principally Reduced Impact Logging (RIL), are therefore essential for conserving highly threatened, physiologically sensitive taxa such as amphibians. In this study we compare the effects of CL and RIL on stream amphibians across a regeneration gradient in two forest reserves in Sabah, Malaysian Borneo. We analysed data from a community of stream amphibians across 29 transects subject to either CL (18-21 years since logging) or RIL (4-21). Multi-species occupancy modelling determined community and species responses to logging types, regeneration times and logging associated environmental factors. Diversity profiles, which capture representative diversity indices whilst accounting for community evenness, were calculated using occupancy model results. Our results indicated that several species and community occupancy generally responded negatively to logging associated covariates (lower aboveground carbon density and higher siltation). Stream breeding species occupancy was generally lower in CL compared to RIL sites, with higher generalist breeding species occupancy in CL sites. Diversity profiles identified higher anuran diversity and evenness in RIL compared to CL sites of the same age (18-21 years). Furthermore, anuran diversity and evenness exhibited a distinct recovery from 4 to 21 years following RIL. Our results provide strong evidence that RIL reduces the negative impacts on stream habitats, amphibian occupancy and diversity compared to CL, and suggest a far quicker recovery after RIL. We believe RIL presents a promising alternative for sustainable tropical timber management and stream amphibian conservation.
... Recently, Lukwago et al. (2020) found that historical forest management practices, such as selective logging and arboricide treatment, led to a reduction in species diversity and a general alteration of diversity metrics for amphibian communities in Budongo Forest Reserve, a relatively undisturbed protected area in western Uganda. Here, we examined amphibian communities in the Mabira Forest Reserve of central Uganda with the goal of documenting the responses of species to forest degradation. ...
... 2020) distributed into two rainy seasons (i.e. March to May and August to November), a strong dry season (December to February), and a weak dry season (June to July) (Lukwago et al., 2020). It is worth noting that the amount of rainfall received during the field campaign (2385 mm, Fig. 2d) was higher than the long-term mean annual precipitation for this region. ...
Tropical forests contribute significantly to the emission and uptake of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). However, studies on the soil environmental controls of greenhouse gases (GHGs) from African tropical forest ecosystems are still rare. The aim of this study was to disentangle the regulation effect of soil nutrients on soil GHG fluxes in a tropical forest in northwestern Uganda. Therefore, a large-scale nutrient manipulation experiment (NME) based on 40 m × 40 m plots with different nutrient addition treatments (nitrogen (N), phosphorus (P), N + P, and control) was established. Soil CO2, CH4, and N2O fluxes were measured monthly using permanently installed static chambers for 14 months. Total soil CO2 fluxes were partitioned into autotrophic and heterotrophic components through a root trenching treatment. In addition, soil temperature, soil water content, and mineral N were measured in parallel to GHG fluxes. N addition (N, N + P) resulted in significantly higher N2O fluxes in the transitory phase (0–28 days after fertilization, p
Tropical deforestation for fertilizer-based agriculture has greatly increased in the last decades resulting in significant anthropogenic greenhouse gas (GHG) emissions. Unfortunately, empirical studies on soil GHG fluxes (carbon dioxide (C2), methane (CH4), and nitrous oxide (N2O)) from African tropical deforestation hotspots are still limited, creating uncertainties in global GHG budgets. Therefore, we quantified soil GHG fluxes and their potential auxiliary controls (water-filled pore space (WFPS), temperature and mineral nitrogen) from four forest plots and 12 replicate plots of a completely randomized design (CRD) experiment premised in a neighboring 20-year-old sugarcane plantation in northwestern Uganda. Despite the use of different fertilization rates (low, standard, and high) as treatments for the sugarcane CRD experiment, neither auxiliary controls nor soil GHG fluxes significantly differed among the CRD treatments. Soil CO2 effluxes were higher in the sugarcane (17.6 ± 0.0 Mg C ha-1 yr-1) than in the forest (14.5 ± 0.1 Mg C ha-1 yr-1; p < 0.001) because of the increased autotrophic respiration from the sugarcane’s fine root biomass and the likely exposure of its larger SOC stocks to microbial decomposition through ploughing operations. Conversely, soil CH4 uptake was three times lower in the sugarcane (-1.1 ± 0.0 kg C ha-1 yr-1) than in the forest (-3.1 ± 0.0 kg C ha-1 yr-1; p < 0.001), which we suspect was due alteration of the methanotroph abundance upon the conversion. Likewise, soil N2O emissions were smaller in the sugarcane (1.3 ± 0.0 kg N ha-1 yr-1) than the forest (1.8 ± 0.0 kg N ha-1 yr-1; p < 0.001) which is likely because excess N from fertilizer addition in the sugarcane was either lost through leaching or taken up by the sugarcane crop. Only seasonal variability in WFPS, among the auxiliary controls, affected CH4 uptake at both sites and soil CO2 effluxes in the sugarcane (p = 0.018). Noteworthy, soil N2O fluxes from both sites were unaltered by the seasonality-mediated changes in auxiliary controls. Overall, our results suggest that forest conversion for sugarcane cultivation alters soil GHG fluxes by increasing soil CO2 emissions and reducing both soil CH4 sink strength and soil N2O emissions.
Tropical biodiversity is under threat from a wide variety of anthropogenic stressors.
Understanding the effect of major stressors—most notably land use change, over‐
harvesting, emergence of novel pathogens, and climate change—is a major goal of
tropical biology. However, to do so requires baseline data with which to compare
present‐day patterns. Unfortunately, the tropics suffer from a lack of basic histori‐
cal data; the few studies which have published such data have proven invaluable.
In 1989, Fauth et al. described their studies of reptile and amphibian diversity and
population demographics across tropical elevational gradients in Costa Rica. Since
then, Fauth et al.'s basic ecological data have been widely used to document shifting
patterns of species composition and abundance. Here, 30 years later, we argue that
(a) collecting foundational ecological data remains incredibly important, especially
in the tropics, and especially in those taxa which are generally understudied (e.g.,
reptiles and amphibians), (b) despite being one of the original goals of the 1989 study,
the mechanisms driving biogeographical patterns of diversity remain unclear (both in
the tropics and globally), and (c) that revisiting sites of historic biodiversity surveys—
particularly those along gradients of environmental change—is incredibly important
to our understanding of how tropical diversity is currently, and will continue to be, af‐
fected by activities in the Anthropocene. In its simplest terms, there has never been a
time where the collection of basic data in the tropics has ever been more important.
Biodiversity loss is a major challenge. Over the past century, the average rate of vertebrate extinction has been about 100-fold higher than the estimated background rate and population declines continue to increase globally. Birth and death rates determine the pace of population increase or decline, thus driving the expansion or extinction of a species. Design of species conservation policies hence depends on demographic data (e.g., for extinction risk assessments or estimation of harvesting quotas). However, an overview of the accessible data, even for better known taxa, is lacking. Here, we present the Demographic Species Knowledge Index, which classifies the available information for 32,144 (97%) of extant described mammals, birds, reptiles, and amphibians. We show that only 1.3% of the tetrapod species have comprehensive information on birth and death rates. We found no demographic measures, not even crude ones such as maximum life span or typical litter/clutch size, for 65% of threatened tetrapods. More field studies are needed; however, some progress can be made by digitalizing existing knowledge, by imputing data from related species with similar life histories, and by using information from captive populations. We show that data from zoos and aquariums in the Species360 network can significantly improve knowledge for an almost eightfold gain. Assessing the landscape of limited demographic knowledge is essential to prioritize ways to fill data gaps. Such information is urgently needed to implement management strategies to conserve at-risk taxa and to discover new unifying concepts and evolutionary relationships across thousands of tetrapod species.
Uganda is one of the most species rich countries in Africa because of the presence of several major biomes. However, it is also a country that has lost much of its natural habitat to agriculture. Uganda is a country that has been better surveyed for its biodiversity than many African countries, but despite this, there has not been a comprehensive analysis of the critical sites that contribute to biodiversity conservation at a global, as well as at a national level. We here present such an assessment using mammals, birds, reptiles, amphibians, and plants as surrogate taxa. We identified 36 terrestrial sites that are of sufficient global importance to qualify as Key Biodiversity Areas (KBAs), using the Global Standard for the Identification of KBAs, which complement an additional nine freshwater sites. National red listing of species and ecosystems was used to identify sites of national importance for conservation. We employ a conservation planning approach using Marxan to identify the minimum set of sites needed to conserve all the globally and nationally threatened species and nationally threatened habitats in Uganda. The findings show that most of the remaining natural habitat in Uganda is important for the conservation of globally and nationally threatened species and threatened habitat. Large areas of irreplaceable habitat occur outside protected areas, although more extensive surveys of these areas would likely reduce the area that is irreplaceable. Priority areas for conservation of both globally and nationally threatened species are identified for the first time in Uganda. Our analysis shows that most natural habitat remaining in the country is critical for the conservation of the rich biodiversity of this country.
The demise of amphibians?
Rapid spread of disease is a hazard in our interconnected world. The chytrid fungus Batrachochytrium dendrobatidis was identified in amphibian populations about 20 years ago and has caused death and species extinction at a global scale. Scheele et al. found that the fungus has caused declines in amphibian populations everywhere except at its origin in Asia (see the Perspective by Greenberg and Palen). A majority of species and populations are still experiencing decline, but there is evidence of limited recovery in some species. The analysis also suggests some conditions that predict resilience.
Science , this issue p. 1459 ; see also p. 1386
Uganda is one of the most species rich countries in Africa because of the presence of several major biomes. However, it is also a country that has lost much of its natural habitat to agriculture. Uganda is a country that has been better surveyed for its biodiversity than many African countries, but despite this, there has not been a comprehensive analysis of the critical sites that contribute to biodiversity conservation at a global, as well as at a national level. We here present such an assessment using mammals, birds, reptiles, amphibians, and plants as surrogate taxa. We identified 36 terrestrial sites that are of sufficient global importance to qualify as Key Biodiversity Areas (KBAs), using the Global Standard for the Identification of KBAs, which complement an additional nine freshwater sites. National red listing of species and ecosystems was used to identify sites of national importance for conservation. We employ a conservation planning approach using Marxan to identify the minimum set of sites needed to conserve all the globally and nationally threatened species and nationally threatened habitats in Uganda. The findings show that most of the remaining natural habitat in Uganda is important for the conservation of globally and nationally threatened species and threatened habitat. Large areas of irreplaceable habitat occur outside protected areas, although more extensive surveys of these areas would likely reduce the area that is irreplaceable. Priority areas for conservation of both globally and nationally threatened species are identified for the first time in Uganda. Our analysis shows that most natural habitat remaining in the country is critical for the conservation of the rich biodiversity of this country.
Aim
Lack of biological information is a silent but strong impediment for planning how to rescue amphibians from extinction. Currently, 24% of all amphibian species are assigned to the Data Deficient (DD) category of IUCN. Here, we aim to identify priority areas for amphibian research that could help gather information on these species and overcome such knowledge gap.
Location
Global.
Taxon
Amphibians.
Methods
We mapped the distribution of 1578 DD amphibian species and then defined priority research areas as those areas with high and complementary concentration of amphibian DD species that could be considered important areas for studying (and therefore conserving) such species. To evaluate the performance of the proposed priority research areas, we calculated the percentage of species overlapping these areas, considering all amphibian DD species; recently described species and geographically restricted DD species. We also determined the proportion of priority research areas falling inside each continent and country of the world. Finally, we estimated the level protection of these species and of human pressure on natural ecosystems found within our priority research areas.
Results
We showed that gathering biological information of species from just 0.4% of the world area could clarify the conservation status of more than 80% of DD amphibians. Most identified priority research areas overlap with regions under high human pressure and only a small percentage of DD amphibian species might cope with those altered conditions.
Main conclusions
Knowledge shortfalls represent a major issue for amphibian conservation globally, however, the picture could radically change if research efforts and investments are geographically strategically distributed. This study brings the first application of a complementary‐based tool, which has been originally designed and implemented in conservation planning, aimed at generating information that help researchers to fill knowledge gaps as efficiently as possible.
The scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. As extinction is non-random across the tree of life, it is important to prioritise threatened species which represent large amounts of evolutionary history. The EDGE metric prioritises species based on their Evolutionary Distinctiveness (ED), which measures the relative contribution of a species to the total evolutionary history of their taxonomic group, and Global Endangerment (GE), or extinction risk. EDGE prioritisations rely on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic trees of large taxonomic groups are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to estimate missing ED scores for species absent from a phylogenetic tree whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogenetic tree, the new method provided the closest estimates of their “true” ED score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous methods. The previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogenetic tree. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst limiting uncertainty and anticipating future phylogenetic advances.
Human activities continue to erode the tree of life, requiring us to prioritize research and conservation. Amphibians represent key victims and bellwethers of global change, and the need for action to conserve them is drastically outpacing knowledge. We provide a phylogeny incorporating nearly all extant amphibians (7,238 species). Current amphibian diversity is composed of both older, depauperate lineages and extensive, more recent tropical radiations found in select clades. Frog and salamander diversification increased strongly after the Cretaceous-Palaeogene boundary, preceded by a potential mass-extinction event in salamanders. Diversification rates of subterranean caecilians varied little over time. Biogeographically, the Afro- and Neotropics harbour a particularly high proportion of Gondwanan relicts, comprising species with high evolutionary distinctiveness (ED). These high-ED species represent a large portion of the branches in the present tree: around 28% of all phylogenetic diversity comes from species in the top 10% of ED. The association between ED and imperilment is weak, but many species with high ED are now imperilled or lack formal threat status, suggesting opportunities for integrating evolutionary position and phylogenetic heritage in addressing the current extinction crisis. By providing a phylogenetic estimate for extant amphibians and identifying their threats and ED, we offer a preliminary basis for a quantitatively informed global approach to conserving the amphibian tree of life.
The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages
occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals. Haplotype networks were reconstructed and species boundaries were investigated using three species-delimitation approaches: Bayesian generalized mixed Yule-coalescent model (bGMYC), the Poisson Tree Process model (PTP) and a cluster algorithm (SpeciesIdentifier). Estimates of similarity in bioclimatic niche were calculated from species-distribution models (MAXENT) and multivariate statistics (Principal Component Analysis, Discriminant Function Analysis). Ancestral-area reconstructions were performed on the phylogeny using probabilistic approaches implemented in BioGeoBEARS. We detected high levels of genetic differentiation yielding ten distinct lineages or operational taxonomic units, and Central Africa was found to be a diversity hotspot for these frogs. Most speciation events took place throughout the Miocene, including ‘‘out-of-Africa” overseas dispersal events to Madagascar in the East and to São Tomé in the West. Bioclimatic niche was remarkably well
conserved, with most species tolerating similar temperature and rainfall conditions common to the Central African region. The P. mascareniensis complex provides insights into how bioclimatic niche shaped the current biogeographic patterns with niche conservatism being exhibited by the Central African radiation and niche divergence shaping populations in West Africa and Madagascar. Central Africa, including the Albertine Rift region, has been an important center of diversification for this species complex.
A molecular phylogeny of the Afrotropical anuran genus Amietia based on 323 16S sequences indicates that there are 19 species, including four not yet described. No genetic material was available for the nominal A. inyangae. We consider them to represent full species, and define them based on 16S genetic distances, as well as differences in morphology, tadpoles and advertisement call where known. An analysis based on two mitochondrial and two nuclear genes (12S, 16S, 28S and tyrosinase exon 1), from 122 samples, confirmed the phylogenetic relationships suggested by the 16S tree. We recognise and (re-) describe the following species: Amietia angolensis (Bocage, 1866), A. chapini (Noble, 1924), A. delalandii (Duméril & Bibron, 1841), A. desaegeri (Laurent, 1972), A. fuscigula (Duméril & Bibron, 1841), A. hymenopus (Boulenger, 1920), A. inyangae (Poynton, 1966), A. johnstoni (Günther, 1893), A. moyerorum sp. nov., A. nutti (Boulenger, 1896), A. poyntoni Channing & Baptista, 2013, A. ruwenzorica (Laurent, 1972), A. tenuoplicata (Pickersgill, 2007), A. vandijki (Visser & Channing, 1997), A. vertebralis (Hewitt, 1927), and A. wittei (Angel, 1924). Three further candidate species of Larson et al. (2016) await formal naming. We provisionally regard A. amieti (Laurent, 1976) as a junior synonym of A. chapini (Noble, 1924). Amietia lubrica (Pickersgill, 2007) is shown to be a junior synonym of A. nutti, while A. quecketti (Boulenger, 1895) is shown to be a junior synonym of A. delalandii (Duméril & Bibron, 1841), and A. viridireticulata (Pickersgill, 2007) is placed as a junior synonym of A. tenuoplicata (Pickersgill, 2007). On the basis of similarity of 16S sequences, we assign A. sp. 1, A. sp. 3 and A. sp. 6 of Larson et al (2016) to the nomina A. chapini (Noble, 1924), A. desaegeri (Laurent, 1972), and A. nutti (Boulenger, 1896) respectively.
The toad species
Sclerophrys capensis
Tschudi, 1838 was erected for a single specimen from South Africa which has never been properly studied and allocated to a known species. A morphometrical and morphological analysis of this specimen and its comparison with 75 toad specimens referred to five South African toad species allowed to allocate this specimen to the species currently known as
Amietophrynus rangeri
. In consequence, the nomen
Sclerophrys
must replace
Amietophrynus
as the valid nomen of the genus, and
capensis
as the valid nomen of the species. This work stresses the usefulness of natural history collections for solving taxonomic and nomenclatural problems.
The Anthropocene is characterized by a widespread biodiversity crisis that is rivaling prehistoric mass extinctions. Amphibians are the most threatened class of vertebrates. In addition to traditional threats such as land-use conversion and pollution, climate change and introduced diseases are expected to further reduce amphibian biodiversity. The fungal disease chytridiomycosis has caused the rapid extirpation of tens to possibly hundreds of amphibian species. Recent advances have revealed a deep evolutionary history and considerable variation in the virulence of strains of the fungal pathogen, patterns that need to be reconciled with the rapid spread of disease and demise of host populations. A conservation priority is surveillance of a newly discovered species of chytrid fungus that is killing European salamanders. The accelerated discovery of new amphibian species challenges existing conservation resources, but it is an opportunity to fill geographical gaps and to enhance programs aimed at preserving amphibian biodiversity.
Quantitative and qualitative samples of amphibian and lizard faunas were taken from forest litter in Costa Rica and compared with similar samples collected in Borneo, the Philippines, and Panama. Animal abundance is about ten times greater in Costa Rican lowland wet forest than in Borneo. Radically different routes and rates of energy flow are postulated to account for the difference. In a series of upland (1010-1425 m) samples in the Philippines, the number of litter lizards and frogs increases with elevation. A single upland (1200 m) Costa Rican sample contains about three times as many animals per 100 m2 as two lowland sites. This increase with altitude correlates well with hypotheses that overall tropical forest productivity is greatest at intermediate elevations. Herpetofaunal densities are greater in wet areas compared to dry sites and flat terrain compared to slopes. These observations are linked to the greater variation and lesser total litter fall in dry sites and/or slopes. The number of species of amphibians and lizards regularly inhabiting the litter is similar in all wet lowland forests studied. Increasing elevation and decreasing rainfall correlate with faunas having fewer species. The former is seen as the result of the differential ability of lowland species to invade uplands, and the latter as a decrease in the kind and duration of frog-spawning sites. Reduced equitability with increasing elevation is principally due to the much greater proportional increase of the commonest species. In the evolution of American and Bornean-Philippine wet lowland faunas, frogs with direct development (Eleutherodactylus) have radiated in the former in the same fashion that skinks have in the latter.
The effectiveness of pitfall versus funnel traps was examined using drift fence data from five studies that employed different array designs, fencing materials, and numbers of traps in diverse Florida habitats. In general, salamanders, anurans, lizards, and snakes were captured more frequently than expected in funnel traps than in pitfall traps. In most studies, hylid frogs (Hyla, Acris, and Pseudacris) were captured significantly more often in funnel traps, but other anuran groups were captured either more often in funnel traps or equally as often in both types of traps. Most lizards and medium-sized and large snake species were captured more often in funnel traps, but semifossorial lizard (Le, Eumeces egregius) and snake (e.g, Tantilla relicta) species were usually captured in pitfall traps. Too few turtle and small snake species were trapped to draw conclusions. Other studies that found funnel traps to be less effective than pitfall traps for some herpetofauna used funnel traps that were smaller or that might have been poorly constructed or installed. Reptiles had similar mortality rates in both types of traps, but in drier habitats, anurans were more prone to dying in funnel than in pitfall traps, despite the presence of shade covers and sponges. Overall herpetofaunal mortality rates were higher in funnel traps than pitfall traps, but this difference was significant only for the study with the longest interval between checking traps in terrestrial habitats. Traps should be checked at least every three days to minimize mortality. In the Coastal Plain of the southeastern United States, most species can be effectively sampled by using only funnel traps, but pitfall traps should be added in xeric upland habitats to increase the chance of capturing semifossorial or fossorial reptiles.
We examine the systematics of multiple populations of the Albertine Rift endemic amphibian Hyperolius castaneus, which currently incorporates four subspecies. Standard morphometric data were analyzed with principal components analyses and analyses of covariance. Phylogenetic analyses of two mitochondrial (16S, cyt b) and one nuclear (RAG1) genes were analyzed from 41 samples representing three subspecies. Results indicated some significant morphometric differences between the nominate subspecies H. c. castaneus and the Itombwe Plateau subspecies H. c. constellatus, and phylogenetic analyses of molecular data recovered these taxa as reciprocally monophyletic groups. We recognize these two allopatric populations as recently diverged, but distinct species, H. castaneus and H. constellatus. The subspecies H. c. submarginatus from the Kabobo Plateau is transferred to the synonymy of H. constellatus, but the status of the unsampled subspecies H. c. rhodogaster, described from mid-elevations of the western Itombwe Plateau, remains problematic. The phylogeographic pattern of our study resembles some, but not all, Albertine Rift vertebrates that have been examined with molecular data. Hyperolius constellatus is restricted to the Itombwe and Kabobo plateaus, which are of special conservation concern because of high levels of amphibian diversity and endemism, and multiple threats from deforestation, mining activities and road construction.
We live amid a global wave of anthropogenically driven biodiversity loss: species and population extirpations and, critically,
declines in local species abundance. Particularly, human impacts on animal biodiversity are an under-recognized form of global
environmental change. Among terrestrial vertebrates, 322 species have become extinct since 1500, and populations of the remaining
species show 25% average decline in abundance. Invertebrate patterns are equally dire: 67% of monitored populations show 45%
mean abundance decline. Such animal declines will cascade onto ecosystem functioning and human well-being. Much remains unknown
about this “Anthropocene defaunation”; these knowledge gaps hinder our capacity to predict and limit defaunation impacts.
Clearly, however, defaunation is both a pervasive component of the planet’s sixth mass extinction and also a major driver
of global ecological change.
Zoonotic pathogens cause an estimated 70% of emerging and re-emerging infectious diseases in humans. In sub-Saharan Africa, bushmeat hunting and butchering is considered the primary risk factor for human-wildlife contact and zoonotic disease transmission, particularly for the transmission of simian retroviruses. However, hunting is only one of many activities in sub-Saharan Africa that bring people and wildlife into contact. Here, we examine human-animal interaction in western Uganda, identifying patterns of injuries from animals and contact with nonhuman primates. Additionally, we identify individual-level risk factors associated with contact. Nearly 20% (246/1,240) of participants reported either being injured by an animal or having contact with a primate over their lifetimes. The majority (51.7%) of injuries were dog bites that healed with no long-term medical consequences. The majority (76.8%) of 125 total primate contacts involved touching a carcass; however, butchering (20%), hunting (10%), and touching a live primate (10%) were also reported. Red colobus (Piliocolobus rufomitratus tephrosceles) accounted for most primate contact events. Multivariate logistic regression indicated that men who live adjacent to forest fragments are at elevated risk of animal contact and specifically primate contact. Our results provide a useful comparison to West and Central Africa where "bushmeat hunting" is the predominant paradigm for human-wildlife contact and zoonotic disease transmission.
AimTo apply mathematical models to the task of predicting extinction risk for species currently listed as ‘Data Deficient’ (DD) by the International Union for the Conservation of Nature (IUCN). We demonstrate this approach by applying it globally to amphibians, the vertebrate group recognized as being most extinction threatened and having the largest proportion of DD species. We combine model predictions with current extinction risk knowledge to highlight regions of greatest disparity between known and predicted risk, where potential species extinctions may be overlooked.LocationGlobal.Methods
Using global amphibian distribution data obtained from the IUCN and species trait data, we apply machine learning randomForest models to predict extinction risk of DD species from life history traits, environmental variables and habitat loss. These models are trained using data for species that have been assigned to an extinction risk category (other than DD) by the IUCN. We then combine predictions for DD species with IUCN assessment data in a GIS framework to highlight anomalies between current knowledge of amphibian extinction risk and our model predictions.ResultsWe show that DD amphibian species are likely to be more threatened with extinction than their fully assessed counterparts. Regions in South America, central Africa and North Asia are particularly at risk due to lack of species knowledge and higher extinction risk than currently recognized.Main conclusionsApplication of predictive models ranking regions and species most in need of primary research allows prioritization of limited resources in an informed context, minimizing risk of unnoticed species' extinction.
Conservation policy typically excludes people from national parks and manages encroachment by law enforcement. However, local people continue to extract resources from protected areas by boundary encroachment and poaching. This paper quantifies the patterns of illegal resource extraction from Kibale National Park in Uganda, the demand for Park resources by communities bordering the Park, and examines whether designated resource access agreements reduce illegal extraction. Sections of the Park boundary were examined and human entry trails, wood extraction, livestock grazing, and animal poaching signs were quantified. Levels of illegal extraction were compared with the demand for and admitted illegal access to resources inside the Park, collected in a survey of households located near the Park. Extraction was also compared between villages with and without negotiated resources access agreements. The most wanted and extracted resource from the Park was wood for fuel and construction. Implementation of resource access agreements with local community associations was found to be an effective means of reducing illegal extraction, but only if the association members profited from the agreement.
Censuses were made of breeding birds on islands in Pymatuning Lake, a reservoir at the Pennsylvania-Ohio border. For these islands the variation of the number of resident avian species with island size is that which one would expect if the birds were distributed randomly, with the probability of a breeding pair residing on an island proportional to the area of the island and independent of the presence of other pairs. This type of random placement of individuals can yield species-area relations which differ from those commonly used for analysis of biogeographic data. -from Authors
Extinctions are normal biological phenomena. Both mass extinctions in geological time and local extinctions in ecological time are well documented, but rates of extinction have increased in recent years—especially in vertebrates, including amphibians—as illustrated by recent reports of their population declines and range reductions. We suggest that long-term population data are necessary for rigorously evaluating the significance of the amphibian declines. Due to the physiological constraints, relatively low mobility, and site fidelity of amphibians, we suggest that many amphibian populations may be unable to recolonize areas after local extinction.
Las extinciones son un fenómeno biológico normal. Extinciones en masa en una escala temporal geológica y extinciones locales en una escala temporal ecológica, están bien documentadas, pero en años recientes las tasas de exinción han incrementado, especialmente en vertebrados, incluyendo a los anfibios tal como ha sido ejemplificado en reportes recientes sobre la declinación de su población y la reducción de su área de distribución. Nosotros sugerimos que datos poblacionales a largo plozo son necesarios para evaluar rigurosamente la significancia de la declinación en anfibios. Nosotros sugerimos que muchas de las poblaciones de anfibios son incapaces de recolonizar áreas después de extinciones locales debido a las restricciones fisiológicas, la relativamente baja movilidad y la filopatría de los anfibios.
In the face of accelerating declines in amphibian populations, it is crucial to be able to effectively identify conservation priorities, both in terms of species and localities. Rapid assessment of amphibian community structure is therefore essential. Visual encounter survey (VES) and standardized visual transect sampling (SVTS) are becoming increasingly important in the measurement and monitoring of tropical anuran communities. In the present paper we compare the performance of SVTS along seven tropical forest transects where frog communities are currently being monitored: Lalut Birai (Borneo, Indonesia), Kakamega Forest National Reserve (Kenya, Africa), Taï National Park (Ivory Coast, Africa; two transects) and Ambolokopatrika-Betaolana Rainforest (Madagascar, three transects). We compared species lists generated from the transects with those from the entire study areas. Species richness was estimated using different incidence- and abundance-based richness estimators: ACE, ICE, Chao1, Chao2, First-order jackknife, Michaelis Menton Estimators (MMMeans and MMRuns). Only a few transect characteristics had a significant effect on species richness estimate accuracy. Species saturation was significantly enhanced by the number of transect walks (ncounts). The relative standard deviation of the First-order jackknife estimator significantly decreased with an increasing daily species richness and a combined effect of daily species richness and the overall abundance of frogs. Comparison of transect and forest species lists show that terrestrial species are best represented by VES/SVTS. We recommend that a transect census should be performed on at least 20 independent walks. Different species richness estimators should be applied simultaneously since their behavior/effectiveness under a wide array of transect parameters is still unknown. Accepted 25 June 2004.
A review is given on the literature of relationships between common forest harvesting practices and the distribution and abundance of amphibians. Emphasis is on the problems commonly encountered in the experimental design and measurement of forest amphibian populations, including a notable lack of pretreatment data. Several aspects of amphibian-forestry relationships in need of further research are outlined. Management recommendations relevant to conserving upland and riparian zone amphibian habitat during forest harvesting are offered.
Abundance and distribution of frogs inhabiting the litter layer of an area of primary lowland rain forest in Central Amazonia were studied over a period of 15 months by sampling 498 plots each 5m × 5m. The litter frog fauna of the area consists of 23 species, but only 12 of these were encountered in the plots, and 84% of the frogs encountered belonged to only six species. Total abundance and diversity within the plot data are strongly seasonal and peak in the late wet season. Both are positively correlated with litter volume and moisture. Most of this variation is due to seasonality of reproduction, as indicated by patterns of occurrence of juveniles of the most abundant species.
These results indicate that the plot sampling method docs not sample the entire fauna adequately. Since this technique has been used to study other tropical forest litter herpetofaunas, however, comparison with other studies may be useful. Species diversity of litter frogs appears to be approximately the same in lowland primary forest sites studied, averaging around 20 ‘regular’ species. Abundances, however, vary widely. Central American communities contain 14–15 frogs (100m) ⁻² , African 9–10, South American 4–6, and South-east Asian 1–2. These differences may be due to differential nutrient availability in forests of different ages and/or on different soils.
INTRODUCTION In theory there is no disagreement about the neces-sity to standardize ecological field methods and data acquisition in order to guarantee comparability be-tween different studies, as well as to enhance the power of predictions resulting therefrom. The need for standardization of techniques across and within studies has continuously been emphasized by several authors (e.g., Heyer et al. 1994, Adis et al. 1998). Those who are involved in community ecological field research know well that this is a crucial factor when it comes to generalizing results in order to make them accessible to those who urgently need scientific guide-lines to back up their practical efforts. This becomes especially important when looking at phenomena such as the well known world-wide amphibian de-cline, which seems to have affected even populations in pristine habitats and continues to affect or even wipe out whole populations with terrifying rapidity (Houlahan et al. 2000, Kiesecker et al. 2001, Pounds 2001). In these cases synergistic efforts are urgently needed, calling for unified methods and data output (Alford & Richards 1999, Parris 1999, DAPTF 2002). However, in reality there still is a lack of studies that can be compared without reservations, especially studies that were conducted in different parts of the world, although precisely this kind of comparison is ECOTROPICA 10: 1–14, 2004 © Society for Tropical Ecology Abstract: The need for standardization of field methods within and across studies has been recognized by the majority of ecologists throughout the world. However, comparable studies based on a standardized protocol are still scarce. We provide a guideline for effectively sampling and monitoring tropical forest amphibians and give recommendations for standardization. Based on a four-year study on amphibians in Taï National Park, Côte d'Ivoire, we evaluate commonly used techniques, and offer a catalogue of efficient techniques, along with suggestions for improvement of particular methods, with regard to study objectives and specific amphibian guilds. For simple short-term surveys we recommend visual and acoustic encounter surveys, accompanied by opportunistic trapping. The transect design introduced here proved to be most adequate for representative sampling and appeared to be appropriate for most studies that involve multivariate data. It is especially useful for long-term studies. Transects furthermore provide an effective method of investigating at least leaf litter frogs, not only at their breeding sites but also throughout the whole range of habitats used by them, thus generating a much more complete picture of an amphibian community than is possible with other methods. Accepted 4 February 2004.
A study of the effects of gap size and age on climber abundance and diversity was carried out in Budongo Forest Reserve in Uganda. Data were collected from compartments N5, W21, B1 and B3. Stump records were used to locate and estimate the ages of 78 gaps. Sample plots 5 × 5 m were set up in the gaps to assess climber abundance and diversity.
Climbers were more abundant and diverse in gaps that were more than 400 m2, 15 months old and had more than 25% canopy opening. Momordica foetida was the most abundant climber species occurring on stems, branches and crowns of seedlings and saplings. Therefore, in order to keep natural regeneration free from climber tangles and produce good quality timber, climber control should be a major activity in tropical high forest management.
Résumé
On a réalisé une étude des effets de la taille et de l'ancienneté des trouées sur l'abondance des plantes grimpantes dans la Réserve forestière de Budongo, en Ouganda. On a récolté des données dans les compartiments N5, W21, B1 et B3. On a utilisé le relevé des souches pour situer et estimer l'âge de 78 percées. On a créé des plots échantillons de 5/5 m dans les percées pour évaluer l'abondance et la diversité des plantes grimpantes.
Ces plantes sont plus abondantes et plus diverses dans les percées qui ont plus de 400 m2, plus de 15 mois et ont plus de 25% d'ouverture de la canopée. Momordica foetidaétait l'espèce grimpante la plus abondante sur les jeunes pousses, les branches et les couronnes des jeunes plants et des jeunes arbres. C'est pourquoi, afin de préserver la régénération naturelle de l'enchevêtrement des plantes grimpantes et de produire du bois de bonne qualité, il faudrait consacrer au contrôle des plantes grimpantes une part majeure des activités de gestion des hautes forêts tropicales.
The dramatic increase in anthropogenic activity severely threatens the biodiversity and life-support services that underpin human well-being. The broadened focus of protecting ecosystem services (ESs) better aligns the interests of people and biodiversity conservation. In this study, we used species richness as a surrogate for biodiversity and mapped the key ESs in East Africa with the goal to assess the spatial congruence between biodiversity and ESs, and evaluate the representation of current protected areas (PAs) network for biodiversity and ESs. The results showed that PAs well represented for species richness and regulating services but underrepresented for provisioning services. The PAs network occupies 10.96% of East Africa's land surface, and captures 20.62-26.37% of conservation priorities for vertebrate and plant species. It encompasses more than 16.23% of priority areas for three regulating services, but only 6.17% and 5.22% for crop and livestock production, respectively. Strong correlations and high overlaps exist between species richness and regulating services, particularly for carbon storage, water yield and plants. Thus, we believe that actions taken to conserve biodiversity also will protect certain ESs, which in turn will create new incentives and funding sources for the conservation of biodiversity. Overall, our results have wide-ranging policy implications and can be used to optimize conservation strategies for both biodiversity and multiple ESs in East Africa.
The tropics contain the overwhelming majority of Earth's biodiversity: their terrestrial, freshwater and marine ecosystems hold more than three-quarters of all species, including almost all shallow-water corals and over 90% of terrestrial birds. However, tropical ecosystems are also subject to pervasive and interacting stressors, such as deforestation, overfishing and climate change, and they are set within a socio-economic context that includes growing pressure from an increasingly globalized world, larger and more affluent tropical populations, and weak governance and response capacities. Concerted local, national and international actions are urgently required to prevent a collapse of tropical biodiversity.
Coordinated efforts by ecologists and natural resource managers are necessary to balance the conservation of biological diversity with the potential for sustained economic development. Because some amphibians have suffered world-wide declines during the last 20 years, it is important to consider biologically based management strategies that will preserve local and regional populations. This paper provides a brief overview of potential threats to local and regional populations, the state of knowledge on population and landscape processes, and the critical elements needed for an effective management plan for amphibians. Local population dynamics and ecological connectivity of amphibian metapopulations must be considered in effective management plans. There are 3 critical factors to consider in a management plan (1) the number or density of individuals dispersing from individual wetlands, (2) the diversity of wetlands with regard to hydroperiod, and (3) the probability of dispersal among adjacent wetlands or the rescue and recolonization of local populations. Wetland losses reduce the total number of sites where pond-breeding amphibians can reproduce and recruit juveniles into the breeding population. Loss of small, temporary wetlands (
We investigated the distribution of species of the genus Ptychadena at nine sites at the upper Nile and its catchment in Rwanda. For species delimitation, we chose an integrative approach, combining morphological and bioacoustic data and DNA barcoding (mitochondrial 16S rRNA gene). We identified three species using independent evidence from the three different data sets: Ptychadena anchietae, Ptychadena porosissima, and a species of the Ptychadena mascareniensis group. The latter is undistinguishable genetically, bioacoustically, and morphologically from populations from Uganda, Kenya, and Egypt. We resurrect the name Ptychadena nilotica for these populations. The species differs strongly genetically from topotypic P. mascareniensis, and from clades referred to as P. cf. mascareniensis from Western and Central Africa. Morphologically, the three Rwandan species can be differentiated by their quantitative morphometrics (discriminant analysis, success rate: 98.3%) and by a number of qualitative characters of external morphology which are useful for identification in the field. The specific features of the advertisement call differ unequivocally among the three species and allow detection and identification in the field. We also provide quantitative descriptions of temporal and frequency structure of the release calls of two of the species and the distress calls of all three species. Finally, we compare the 16S sequences obtained from Rwandan specimens with those deposited in GenBank to estimate geographical distribution of taxa in Africa.
Information content may be used as a measure of the diversity of a many-species biological collection. The diversity of small collections, all of whose members can be identified and counted, is defined by Brillouin's measure of information. With larger collections it becomes necessary to estimate diversity; what is estimated is Shannon's measure of information which is a function of the population proportions of the several species. Different methods of estimation are appropriate for different types of collections. If the collection can be randomly sampled and the total number of species is known, Basharin's formula may be used. With a random sample from a population containing an unknown number of species, Good's method is sometimes applicable. With a patchy population of sessile organisms, such as a plant community, random samples are unobtainable since the contents of a randomly placed quadrat are not a random sample of the parent population. To estimate the diversity of such a community a method is proposed whereby the sample size is progressively increased by addition of new quadrats; as this is done the diversity of the pooled sample increases and then levels off. The mean increment in total diversity that results from enlarging the sample still more then provides an estimate of the diversity per individual in the whole population.
Information content may be used as a measure of the diversity of a many-species biological collection. The diversity of small collections, all of whose members can be identified and counted, is defined by Brillouin's measure of information. With larger collections it becomes necessary to estimate diversity; what is estimated is Shannon's measure of information which is a function of the population proportions of the several species. Different methods of estimation are appropriate for different types of collections. If the collection can be randomly sampled and the total number of species is known, Basharin's formula may be used. With a random sample from a population containing an unknown number of species, Good's method is sometimes applicable. With a patchy population of sessile organisms, such as a plant community, random samples are unobtainable since the contents of a randomly placed quadrat are not a random sample of the parent population. To estimate the diversity of such a community a method is proposed whereby the sample size is progressively increased by addition of new quadrats; as this is done the diversity of the pooled sample increases and then levels off. The mean increment in total diversity that results from enlarging the sample still more then provides an estimate of the diversity per individual in the whole population.
Anthropogenic habitat alteration has long been neglected as a factor in the analysis of predictability patterns in biological communities. We tested this factor by investigating anuran leaf litter assemblages in primary and secondary forests of Tai National Park, Ivory Coast, during two years. We measured predictability of assemblage composition by analyzing correlations between the off-diagonal elements of distance matrices based on (1) species distribution, (2) environmental characteristics, and (3) geographic distance. Pairwise correlations between matrices were significant in all cases when considering data pooled across time and habitats. A different pattern emerged when data were split according to season and disturbance level (i.e., primary vs. secondary habitats). Assemblage composition in primary habitats was correlated with geographic proximity of sites exclusively, indicating otherwise stochastic recruitment from a regional species pool at the local community level. In contrast, assemblage composition in secondary habitats was predictable based on environmental parameters, not geographical proximity. This can be inferred to be the result of a strong local site filter effect (i.e., physiologically more-restrictive conditions within secondary forest habitats, especially due to an altered microclimate). Results were consistent throughout seasons. The observed transition in predictability patterns indicates that anthropogenic disturbance not only affects system descriptors, such as species richness, abundance, and diversity, but may also alter the system's dynamics.
1. The Budongo Forest Reserve has been logged selectively for over 60 years. Most compartments in the Reserve have records of the volume of timber removed, the date of harvesting, and of treatments carried out to encourage regeneration of valuable timber species. 2. Line transect surveys of the five diurnal primates resident in this forest were carried out in eight of these compartments; two of which had never been logged and six of which had been harvested at approximately 10-year intervals since 1940. 3. Densities were calculated using the computer package DISTANCE. It was found that the 'Hazard Rate Model' fitted the observer-primate distance data better than other models. Densities over the whole forest were as follows: Cercopithecus mitis sthuhlmannii 43.9 km(-2); C. ascanius schmidti 33.3 km(-2); Colobus guereza occidentalis 39.3 km(-2); Papio anubis 11.7 km(-2); Pan troglodytes schweinfurthii 1.3 km(-2). 4. Only C. guereza showed any significant correlation between logging date and animal density, and none of the primates showed any correlation with the volume of timber removed. For three of the primates (C. guereza, C. mitis and C. ascanius) there were significantly higher numbers in the logged compartments when compared with those that were not logged. 5. Cercopithecus mitis and C. ascanius showed significant correlations between the percentage of different forest types and the densities of the primates in each compartment. In particular there was a positive correlation with the 'mixed' forest type that foresters have been encouraging through their management practices. It is concluded that these two primates and C. guereza have benefited from logging in Budongo and that logging has had little effect on the other two primates.
The Niger Delta (Southern Nigeria) is the main oil-producing region in sub-Saharan Africa. Its biodiversity is very important for the concomitant presence of rainforests and mangroves, and many endemic flora and fauna. Six sites in southern Nigeria, four currently affected by oil industry development but formerly inside the rainforest belt and two in pristine protected areas, were surveyed for amphibians during 1996-2002, in both dry and rainy seasons. Amphibian species diversity was reliably assessed at all study sites, as shown by species accumulation curves. The total number of species found in the two pristine sites was much higher than that found in the four developed sites. Nevertheless, a total of over 6300 amphibian specimens belonging to 28 species were captured at these four sites. Species included three Bufonidae (genera Bufo and Nectophryne), two Pipidae (Silurana and Hymenochirus), nine Ranidae (Hylarana, Ptychadena, Aubria, Conraua, Hoplobatrachus, and Phrynobatrachus), one Arthroleptidae (Arthroleptis), one Rhacophoridae (Chiromantis), one Microhylidae (Phrynomantis), and eleven Hyperoliidae (Hyperolius, Afrixalus, Leptopelis, Phlyctimantis, and Opisthothylax). The four developed study sites were similar in terms of species composition; the most common species were Silurana tropicalis (accounting for about 74% of the total number of specimens captured), Bufo maculatus, Ptychadena spp., Hylarana albolabris, Hoplobatrachus occipitalis, Hyperolius cf. concolor and Afrixalus dorsalis. Greater numbers of species and individuals were captured in the rainy season than in the dry season. In terms of chemo-physical properties of the water at their breeding sites, both adult and larval anurans of several species (e. g., Silurana, Bufo and Ptychadena) were highly adaptable, being able to thrive in anoxic and slightly acidic water with dissolved oxygen from 0.50-1.50 mg l-1 and pH from 5.9-7.2.
ABSTRACTI compared species richness and habitat correlates of leaf-litter herpetofaunal abundance in undisturbed and selectively logged forests, and an abandoned pine plantation in Kibale National Park, Uganda. I sampled 50 randomly located 25 m2 litter plots in each area during the wet and dry seasons in 1997. Ten anuran, five lizard, and three snake species were captured in plots over the study. Assemblage composition was most similar at logged and unlogged sites. The logged forest herpetofauna had higher species richness and abundance than the unlogged forest, but diversity was greater in the unlogged forest due to greater evenness. In contrast, the pine plantation site had the highest richness, abundance, and evenness of the three study sites, but species composition was distinct from the other areas. Herpetofaunal densities were significantly lower in all three areas during the dry season than in the wet season. During the dry season, soil moisture, litter mass, topography, shrub cover, and number of fallen logs were significant positive predictors of herpetofaunal presence in litter plots, but only soil moisture was significant in the wet season. The interaction of moisture and topography appears to be important in determining seasonal patterns of litter herpetofaunal distribution. Comparison of litter herpetofaunal studies across the tropics have shown that mid-elevation faunas generally support fewer species than lowland faunas. Compared with other tropical mid-elevation litter faunas, Kibale supports an intermediate number of species, but at lower densities than observed at any other mid-elevation site reported in the literature.
Species richness is a fundamental measurement of community and regional diversity, and it underlies many ecological models and conservation strategies. In spite of its importance, ecologists have not always appreciated the effects of abundance and sampling effort on richness measures and comparisons. We survey a series of common pitfalls in quantifying and comparing taxon richness. These pitfalls can be largely avoided by using accumulation and rarefaction curves, which may be based on either individuals or samples. These taxon sampling curves contain the basic information for valid richness comparisons, including category–subcategory ratios (species-to-genus and species-to-individual ratios). Rarefaction methods – both sample-based and individual-based – allow for meaningful standardization and comparison of datasets. Standardizing data sets by area or sampling effort may produce very different results compared to standardizing by number of individuals collected, and it is not always clear which measure of diversity is more appropriate. Asymptotic richness estimators provide lower-bound estimates for taxon-rich groups such as tropical arthropods, in which observed richness rarely reaches an asymptote, despite intensive sampling. Recent examples of diversity studies of tropical trees, stream invertebrates, and herbaceous plants emphasize the importance of carefully quantifying species richness using taxon sampling curves.