A case study of apparent conflict between molecular phylogenies: the interrelationships of African elephants

Recent molecular phylogenies of the African elephants suggest that there is an evolutionary structure within Loxodonta africana. Some nuclear results ( Roca et al., 2001 ) support the separation of the forest African elephant subspecies L. a. cyclotis as a species distinct from the savannah elephant L. a. africana, on the basis of the recognition of both forming highly divergent (reciprocally monophyletic) clades. Conversely, a mitochondrial survey ( Eggert et al., 2002 ), while admitting a geographic partitioning of the genetic structure within African elephants, suggests retaining the status quo. They recognize three diagnosible entities (western, central and south‐eastern Africa) with non‐overlapping ranges within L. africana sensu lato. In order to address these conflicting views (historical fragmentation and speciation or isolation by distance, respectively), we have sequenced two datasets of 1961 bp (for 50 elephants) and about 3700 bp, respectively (for 20 elephants) of the mitochondrial DNA for both forms of elephants (cyclotis and africana). They span the cytochrome b gene, the control region and several RNAs. When compared with former mtDNA data, they provide the most comprehensive view of the African elephant phylogeny (78 mtDNA haplotypes, of which 44 are new) and provide the first insight into populations from the Democratic Republic of Congo. The genetic diversity of mtDNA was appraised and the stability of alternative phylogenetic trees was investigated. Our results are inconsistent with both those prior studies. They revealed two highly divergent molecular clades referred to as F and S, that do not conform to the morphological delineations of cyclotis and africana. A non‐negligible proportion of specimens of L. a. africana display haplotypes prevailing in forest elephant populations (clade F). The geographic distribution of clades and areas of their co‐occurrence support the hypothesis of incomplete isolation between forest and savannah African elephant populations, followed by recurrent interbreeding between the two forms. We state that the conclusions of prior studies resulted from insufficient character and/or geographic sampling. We conclude that there is no satisfying argument which can recognize two or more species of African elephants. We briefly comment on the meaning of such an attitude in a conservation viewpoint. © The Willi Hennig Society 2005.     

Savanna trees in Namibia—Factors controlling their distribution at the arid end of the spectrum

This study reviewed the distribution of ten common savanna trees in Namibia. Tree distributions were investigated in relation to bioclimatic, topographic and edaphic variables at a national scale. The factors of importance at these broad geographic scales appeared to be rainfall, substrate and, likely, the incidence of frost. Baikiaea plurijuga, Burkea africana, Guibourtia coleosperma and Pterocarpus angolensis seem to reach their bioclimatic limits in Namibia.At the local level, plant traits become important and contribute to explaining distribution patterns. High water and/or nitrogen use efficiency (Acacia erioloba, Colophospermum mopane), dual water obtaining strategies (Faidherbia albida), fire tolerance (e.g. Acacia species, Burkea africana and Pterocarpus angolensis) and drought tolerance (Boscia albitrunca) are some key attributes providing additional explanations for current distributions.Amongst the selected trees and at broad geographic scales, below-ground adaptations are governed by rainfall regime in combination with coarse-textured soils, whereby shallow-rooted trees prevail in the Kalahari sandveld. Deep-rooted species are found largely on non-sandy soils. Physiological performance of many trees appears to be directly linked to rainfall regime and trees may hence show varying performance throughout their distribution range. Insight into plant functional attributes of trees in Namibia is required to develop appropriate management strategies in the light of climate change. Modelling climate change impacts should consider the relative contribution of bioclimatic versus local environmental factors that explain the current distribution patterns of the selected trees.     

Not as Ubiquitous as We Thought: Taxonomic Crypsis,Hidden Diversity and Cryptic Speciation in the Cosmopolitan Fungus Thelonectria discophora (Nectriaceae,Hypocreales, Ascomycota)

The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions.     

Geonemy,ecology, reproductive biology and morphology of the tardigrade <Emphasis Type="Italic">Hypsibius zetlandicus</Emphasis> (Eutardigrada: Hypsibiidae) with erection of <Emphasis Type="Italic">Borealibius</Emphasis> gen. n.

The morphology, biology and geographic distribution of Hypsibius zetlandicus (Murray 1907) are considered. Scanning electron microscopy (SEM) and/or light microscopy (LM) analyses have been carried out on H. zetlandicus and the type species of Hypsibius: Hypsibius dujardini (Doyère 1840), with particular emphasis on the buccal–pharyngeal apparatuses. Some unusual characteristics of this apparatus in H. zetlandicus lead us to the erection of the new genus Borealibius, to which H. zetlandicus (Borealibius zetlandicus comb. n.) is transferred. In the light of new discoveries of this species from polar, sub-polar and alpine regions, and based on the available bibliographic references, we hypothesize a boreo–alpine distribution for this species. The presence of traits that are unusual and rare (in other tardigrade species) have been observed whilst analyzing the reproductive biology and ecology of B. zetlandicus (i.e., the presence of hermaphroditism, parental care and the colonization of very different substrates).     

管壳缝类硅藻中国新记录属种——非洲南氏藻

利用光学和电子显微镜对采自黄海水域的1个管壳缝类硅藻——非洲南氏藻进行了形态学研究,并对其地理分布进行了讨论.结果表明:(1)该种壳体带面呈矩形,壳面窄椭圆形,具有钝圆的末端.(2)壳缝居中,由两条等长的分支组成.(3)管壳缝由复杂、接合的肋突支撑,但无龙骨.(4)每条线纹仅有1个孔纹,壳套上最多有1列孔纹.(5)目前...     

Effects of diet,habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis)

The gut microbiome, or the community of microorganisms inhabiting the digestive tract, is often unique to its symbiont and, in many animal taxa, is highly influenced by host phylogeny and diet. In this study, we characterized the gut microbiome of the African savanna elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), sister taxa separated by 2.6–5.6 million years of independent evolution. We examined the effect of host phylogeny on microbiome composition. Additionally, we examined the influence of habitat types (forest versus savanna) and diet types (crop‐raiding versus noncrop‐raiding) on the microbiome within L. africana. We found 58 bacterial orders, representing 16 phyla, across all African elephant samples. The most common phyla were Firmicutes, Proteobacteria, and Bacteroidetes. The microbiome of L. africana was dominated by Firmicutes, similar to other hindgut fermenters, while the microbiome of L. cyclotis was dominated by Proteobacteria, similar to more frugivorous species. Alpha diversity did not differ across species, habitat type, or diet, but beta diversity indicated that microbial communities differed significantly among species, diet types, and habitat types. Based on predicted KEGG metabolic pathways, we also found significant differences between species, but not habitat or diet, in amino acid metabolism, energy metabolism, and metabolism of terpenoids and polyketides. Understanding the digestive capabilities of these elephant species could aid in their captive management and ultimately their conservation.     

Testing the regeneration niche hypothesis with Gesneriaceae (tribe Sinningiae) in Brazil: Implications for the conservation of rare species

The germination requirements of sexually reproducing plants are regulated by environmental factors such as temperature. Those factors acting at the germination phase are part of the regeneration niche, which is fundamental in the processes that contribute to habitat suitability and geographic distribution. We tested the hypothesis that rarity is associated with regeneration niche in three species of plants in the family Gesneriaceae (tribe Sinningieae), Sinningia rupicola (Mart.) Wiehler, Paliavana sericiflora Benth and Sinningia allagophylla (Mart.) Wiehler, which vary in their distribution and habitat specificity but share a small zone of sympatry in rocky fields south of Belo Horizonte in Minas Gerais, Brazil. The regeneration niche was tested using a seed germination experiment under controlled light conditions at seven fixed temperatures (10–40°C at 5°C intervals). Each of the three species germinated differently at the various temperatures. The species with the smallest geographic range, S. rupicola, also had the most restricted germination: germination peaked at 15°C when relatively few seeds germinated (45%), and even fewer germinated at other temperatures. The regeneration niche was wider in P. sericiflora and wider still in S. allagophylla, with germination greater than 90% between 15–25°C and greater than 80% between 15–30°C, respectively. Our germination results provide qualified support for the hypothesis of correlation of the regeneration niche with geographic distribution of related plant taxa, with important conservation implications for rare and endangered species.     

Morphological and phylogenetic study of algal partners associated with the lichen-forming fungus <Emphasis Type="Italic">Tephromela atra</Emphasis> from the Mediterranean region

Recent DNA sequence analyses have revealed the diversity of algal partners in lichen symbioses. Although morphologically similar, different genetic lineages of photobionts are detected in wide geographic ranges of the same lichen fungal species. We studied the photobiont of the genus Trebouxia, which are known as partners of diverse lichen-forming fungal species in the Mediterranean region. We studied the phylogeny of these algae with a multilocus dataset including three loci: ITS, rbcL, and actin type I gene. The two lineages found, informally named Trebouxia sp. 1 and Trebouxia sp. 2, are related to Trebouxia arboricola/decolorans. The cultivation under axenic conditions succeeded only for one of them so far. We used light microscopy, confocal laser scanning microscopy and transmission electron microscopy for phenotypic characterisation. The ultrastructural characters currently used to describe species in the genus do not support the segregation of Trebouxia sp.1 from Trebouxia arboricola. The preferential presence in Mediterranean climates of these strains suggests eco-physiological adaptation. Despite their asexuality in long living lichen symbioses, coccoid algal lichen partners have apparently diversified genetically and physiologically.     

Modelling the potential distribution of endangered Prunus africana (Hook.f.) Kalkm. in East Africa

Continued harvesting and climate change are affecting the distributions of many plant species and may lead to numerous extinctions over the next century. Endangered species are likely to be a special concern, but the extent to which they are sensitive to climate is currently unclear. Species distribution modelling, if carefully implemented, can be used to assess climate sensitivity and potential climate change impacts, of tree species. We used MaxEnt algorithm for species distribution modelling to assess the potential distribution and climate change risks for a threatened Prunus africana, in East Africa. Data from different herbaria on its distribution were linked to data on climate to test hypotheses on the factors determining its distribution. Predictive models were developed and projected onto a climate scenario for 2050 to assess climate change risks. Precipitation of driest quarter and annual precipitation appeared to be the main factors influencing its distribution. Climate change was predicted to result in reductions of the species' habitats (e.g. Erasmus et al., Glob. Change Biol. 2002; 8 : 679). Prunus africana distribution is thus highly vulnerable to a warming climate and highlights the fact that both in‐situ and ex‐situ conservation will be a solution to global warming.     

Can biotic interactions cause allopatry? Niche models,competition, and distributions of South American mouse opossums

Based on our own empirical data and a literature review, we explore the possibility that biotic interactions, specifically competition, might be responsible for creating, and/or maintaining, geographic isolation. Ecological niche modeling was first used to test whether the distributions of 2 species of Neotropical marsupials (Marmosa robinsoni and M. xerophila) fit the predicted geographic pattern of competitive exclusion: one species predominates in areas environmentally suitable for both species along real contact zones. Secondly, we examined the connectivity among populations of each species, interpreted in the light of the niche models. The results show predominance of M. xerophila along its contact zone with M. robinsoni in the Península de Paraguaná in northwestern Venezuela. There, M. robinsoni has an extremely restricted distribution despite climatic conditions suitable for both species across the peninsula and its isthmus. The latter two results suggest that M. xerophila may be responsible for the geographic isolation of the peninsular populations of M. robinsoni with respect to other populations of the latter species in northwestern Venezuela. These results may represent an example of allopatry caused, or at least maintained, by competition. Our results and a review of numerous studies in which biotic interactions restrict species distributions (including at the continental scale) support a previously overlooked phenomenon: biotic interactions can isolate populations of a species. We propose 2 general mechanisms, intrusion and contraction, to classify allopatric conditions caused by various classes of biotic interactions. We present a necessary modification of the concept of ecological vicariance to include biotic interactions as possible vicariant agents regardless of whether genetic differentiation occurs or not.     

Two foliar idioblasts of taxonomic significance in Cercidium and Parkinsonia (Leguminosae: Caesalpinioideae)

Leaf anatomy was surveyed for idioblasts in Cercidium (eight to nine species) and Parkinsonia (four to six species), two problematic genera of caesalpinioid legumes variously merged and separated for over a century. Leaflets from 16 accessions (11 dried and five liquid-preserved) of ten species were cleared (protoplasts removed chemically) and stained, supplemented by resin-embedded sections and scanning electron microscopy. Four Parkinsonia species had large, dimorphic, living subepidermal idioblasts (SI)—one form adaxially restricted, the other form abaxial. The fifth species, P. africana, had tiny scalelike leaflets without idioblasts. Idioblast contents are unknown but visibly different from those of adjacent cells. All five Cercidium species lacked SIs, but instead had veinlet idioblasts (VI). These large idioblasts varied in size and abundance, but in C. floridum and C. texanum they were especially large, spheroidal to ovate, thick-walled, and devoid of protoplasm at maturity. VIs occurred mostly as pairs or clusters, with individual cells joined by a large gap resembling a simple perforation plate. Almost all VI units abutted minor veins, but no perforation plate joined the proximal VI to a tracheary element. Cells similar to SIs occur in other Caesalpinieae genera, but VIs are unique to Cercidium. The mutually exclusive distribution of SIs and VIs supports the view that Cercidium and Parkinsonia are different.     

Predicting the potential invasive range of light brown apple moth (Epiphyas postvittana) using biologically informed and correlative species distribution models

The light brown apple moth (Epiphyas postvittana) is a highly polyphagous species that has invaded several geographic regions across the globe and has stimulated substantial concern over possible impacts for agriculture in the US. We aimed to predict the potential geographic range of E. postvittana to better understand the threat of this species in the US and globally. We used the mechanistic simulation modelling method CLIMEX and the correlative niche modelling method Maxent to predict the geographic distribution of E. postvittana in its native range and globally and tested model projections using known invasion data. Different predictor variable data sets and threshold dependent and independent measures of environmental suitability were considered in model evaluation. Models accurately predicted known invasive localities of E. postvittana across the globe. Overall predictions of environmental suitability were largely congruent across models, although there were some notable differences. Ephiphyas postvittana clearly has the potential to establish in many regions of the globe, although some previous analyses of the potential distribution of this species appear overly pessimistic. Additional studies of the biology of this species in invaded areas, including interactions with natural enemies and the capacity to adapt to novel climatic conditions, are ultimately needed to more fully understand its potential economic and environmental impacts.     

Host plant distributions and climate interact to affect the predicted geographic distribution of a Neotropical termite

Species distribution models (SDMs) have been widely used in the scientific literature. The majority of SDMs use climate data or other abiotic variables to forecast the potential distribution of a species in geographic space. Biotic interactions can affect the predicted spatial distribution of a species in many ways across multiple spatial scales, and incorporating these predictors in an SDM is a current topic in the scientific literature. Constrictotermes cyphergaster is a widely distributed termite in the Neotropics. This termite species nests in plants and more frequently nests in some arboreal species. Thus, this species is an excellent model to evaluate the influence of biotic interactions in SDMs. We evaluate the influences of climate and the geographic distribution of host plants on the potential distribution of C. cyphergaster. Three correlative models (MaxEnt) were built to predict the geographic distribution of the termite: (1) climate data, (2) biotic data (i.e., the geographic distribution of host plants), and (3) climate and biotic data. The models that were generated indicate that the potential geographic distribution of C. cyphergaster is concentrated in the Cerrado and Caatinga regions. In addition, path analysis and multiple regression revealed the importance of the direct effects of biological interactions in the geographic distribution of the termite, while climate affected the distribution of the termite mainly through indirect effects by influencing the geographic distributions of host plants. The current study endorses the importance of including biological interactions in SDMs. We recommend using biotic predictors in SDM studies of insect species, mainly because insects have important environmental services and biotic interaction data can improve the macroecological studies of this group.     

Cultural characteristics, morphology, and variation within Claviceps africana and C. sorghi from India

Sorghum ergot in India is caused by Claviceps africana and C. sorghi. The distributions of these two species in India is not known. Eighty-nine sorghum ergot isolates were cultured from young sphacelia obtained from male sterile sorghum plants artificially inoculated using inoculum collected in the field. Based on cultural characteristics, the isolates were separated into two groups which differed distinctly in the morphology of their sphacelia, conidia, and sclerotia. Marked differences also were observed in rates of secondary conidial production and disease spread between the groups. In combination with molecular evidence, our results confirm that the isolates placed in Group I represent C. africana and Group II isolates represent C. sorghi. C. africana was found to be widely distributed in all sorghum growing areas of India. The species first described as occuring in India, C. sorghi, appears to be restricted to a few locations in the states of Maharashtra, Andhra Pradesh, and Karnataka.     

The role of abiotic and biotic factors in determining coexistence of multiple pollinators in the yucca–yucca moth mutualism

The determinants of a species' geographic distribution are a combination of both abiotic and biotic factors. Environmental niche modeling of climatic factors has been instrumental in documenting the role of abiotic factors in a species' niche. Integrating this approach with data from species interactions provides a means to assess the relative roles of abiotic and biotic components. Here, we examine whether the high host specificity typically exhibited in the active pollination mutualism between yuccas and yucca moths is the result of differences in climatic niche requirements that limit yucca moth distributions or the result of competition among mutualistic moths that would co‐occur on the same yucca species. We compared the species distribution models of two Tegeticula pollinator moths that use the geographically widespread plant Yucca filamentosa. Tegeticula yuccasella occurs throughout eastern North America whereas T. cassandra is restricted to the southeastern portion of the range, primarily occurring in Florida. Species distribution models demonstrate that T. cassandra is restricted climatically to the southeastern United States and T. yuccasella is predicted to be able to live across all of eastern North America. Data on moth abundances in Florida demonstrate that both moth species are present on Y. filamentosa; however, T. cassandra is numerically dominant. Taken together, the results suggest that moth geographic distributions are heavily influenced by climate, but competition among pollinating congeners will act to restrict populations of moth species that co‐occur.     

Predicting the risk of non-target damage to a close relative of a target weed using sequential no-choice tests,paired-choice tests and olfactory discrimination experiments

We investigated host-plant utilisation by the candidate biocontrol agent Paradibolia coerulea (Coleoptera: Chrysomelidae) on the target plant Spathodea campanulata Beauv. (Bignoniaceae) and a closely related non-target plant, Kigelia africana (Lam.) Benth. (Bignoniaceae). Paired-choice and sequential no-choice experiments were performed and coupled with olfactory discrimination experiments to test the insects’ responses to volatiles from both plant species as well as to cues from conspecific beetles. Although K. africana was utilised by P. coerulea, S. campanulata was preferred for both adult feeding and oviposition. Interestingly, whereas females were attracted to olfactory cues emitted by S. campanulata, males demonstrated no such olfactory discrimination. Females were also attracted to cues deposited by males, and males were deterred by cues from other males, but neither sex responded to female olfactory cues. Very few eggs were recorded on K. africana and none of the larvae that hatched on K. africana survived the first instar. Both S. campanulata and K. africana are suitable for adult feeding, but persistent utilisation of K. africana in the field is unlikely because larval development is only possible on S. campanulata and because the adult females are strongly attracted to volatiles emitted by the target plant. Nevertheless, if P. coerulea is released as a biocontrol agent, spill-over adult feeding could potentially occur on K. africana growing sympatrically with S. campanulata. Because P. coerulea cannot complete its development on K. africana, non-target damage will only occur where the target plant is present, with an intensity dependent on densities of adult beetles locally.     

Structural diversity and regeneration of the endangered Prunus africana (Rosaceae) in Zimbabwe

Prunus africana is endemic to Africa and was included in Appendix II of the Convention on International Trade in Endangered Species (CITES) in 1995. In Zimbabwe, the species was reported to be rare and confined to the Eastern Highlands. The objective of this study was to assess size–class distribution and regeneration levels and to characterize structural diversity of P. africana. Given the clustered nature of the species, adaptive cluster sampling was used based on the assumption that there were more P. africana trees in the neighbourhood of reference trees. Each cluster was terminated when there were no more P. africana trees within a distance of 500 m. Data on diameter and height were collected in each cluster using standard forestry procedures. Regeneration was determined by counting seedlings and saplings within a radial distance of 14 m from the mother tree. Structural indices, that ie, diameter and height differentiation and mingling were determined for a structural group of four trees. Findings from this study indicated poor regeneration, fewer P. africana trees in small and large size classes, dominance of positive height and diameter differentiation and high mingling. These findings have implications on management and conservation of P. africana in Zimbabwe.     

Diversity and distribution patterns of aquatic macrophytes in selected ecosystems of south western Nigeria

The present study investigates the macrophytes diversity from selected aquatic ecosystems in South-Western Nigeria using quadrat method. The survey revealed two major aquatic ecosystem types (mangrove and freshwater swamp) and recorded a total of 83 species belonging to 77 genera and 41 families. Three species (Sacciolepis africana, Ipomoea asarifolia and Commelina diffusa) were found present in all the surveyed areas. However, species such as Acrostichum aureum, Avicennia germinans and Rhizophora racemosa were restricted in its distribution. Poaceae and Ludwigia were the dominant family and genus, respectively. In addition, our study recorded Hallea ledermannii classified as vulnerable by IUCN Red List. Diversity analysis revealed high species richness in all the studied locations especially in Lagos State. Similar diversity pattern was observed for Osun and Oyo States. Further, our results reflect that macrophytes assemblages in South-Western Nigeria could be influenced by human activities. Hence, we recommend further studies that would test hypothesis on how human activities affect the diversity and distribution of flora in the area. Additionally, conservation of the aquatic environments of the region appears necessary. The findings of this study provide insights on the patterns of macrophyte diversity in South-Western Nigeria, thus, forms a guideline for initiating effective conservation policies in the area.     

Extreme isolation by distance in a montane frog <Emphasis Type="Italic">Rana cascadae</Emphasis>

Given the recent interest in declining amphibian populations, it is surprising that there are so few data on genetic drift and gene flow in anuran species. We used seven microsatellite loci to investigate genetic structure and diversity at both large and small geographic scales, and to estimate gene flow in the Cascades frog, Rana cascadae. We sampled 18 sites in a hierarchical design (inter-population distances ranging from 1–670 km) to test for isolation by distance and to determine the geographic scale over which substantial gene flow occurs. Eleven of these sites were sampled as three fine-scale clusters of three, three, and five sites separated by pairwise distances of 1–23 km to estimate number of migrants exchanged per generation via F _ST and by a coalescent approach. We found R. cascadae exhibits a strong pattern of isolation by distance over the entire species range, and that there is a sharp drop in migrants exchanged between sites separated by greater than 10 km. These data, in conjunction with results of other recent studies, suggest that montane habitats promote unusually strong genetic isolation among frog populations. We discuss our results in light of future management and conservation of R. cascadae.