Changing places: how the results of new field work in the Rubeho Mountains influence conservation priorities in the Eastern Arc Mountains of Tanzania

The Rubeho Mountains are a poorly studied mountain block within the Eastern Arc Mountain range of Tanzania and Kenya. We present the results of field surveys for vertebrates undertaken during the period February 2000 to December 2002. One hundred and twelve man‐days of surveys recorded 35 mammal, 107 bird, ten reptile and nine amphibian species, including eleven species endemic and seven near‐endemic to the Eastern Arc, with one species new to science. Of these, nine species are regarded as threatened with extinction. The new survey data significantly elevate the biological importance of the Rubehos within the Eastern Arc range. Further analyses highlight how the overall biological ranking of the Eastern Arc mountain blocks is correlated with survey effort. The majority of the forest habitat on the Rubehos is contained in three national (Central Government) Forest Reserves (Mang'alisa, Mafwomero and Ukwiva). Our surveys recorded high levels of disturbance to the forest habitat in all three reserves and we draw attention to the need for additional conservation investment in this area.     

Biogeography and diversity among montane populations of mouse shrew (Soricidae: Myosorex) in Tanzania

We assess variation in morphological and molecular characters among three species of Myosorex (the mouse shrew) –Myosorex geata, Myosorex kihaulei, and Myosorex zinki– as a means to test previously proposed biogeographic hypotheses for Tanzanian ‘sky islands’ and systematic hypotheses for Tanzanian mouse shrews. We analyse 17 cranial and dental variables using multivariate statistics and perform phylogenetic and phylogeographic analyses on sequences of mitochondrial and nuclear DNA; samples are drawn from every known Tanzanian population of Myosorex. Morphometric and phylogenetic analyses reveal that M. zinki is distinct, but that currently isolated populations of M. geata and M. kihaulei are relatively similar to one another, and may not have been isolated over geological time scales. Analyses of molecular variance identify statistically significant, but limited, genetic variation within and between isolated populations of M. geata and M. kihaulei. Between two putative regional biogeographic boundaries, greater genetic variation is explained by grouping populations on either side of the Ruaha River than by grouping populations on either side of the Makambako Gap. Our results are in agreement with recent studies illustrating the close relationship between faunas of the Southern Highlands and southern Eastern Arc Mountains, diminishing the apparent importance of the Makambako Gap as a historical biogeographic barrier. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 669–680.     

Carbon storage,structure and composition of miombo woodlands in Tanzania’s Eastern Arc Mountains

We determine the aboveground biomass and carbon storage (ABGC) of trees and the herbaceous layer in miombo woodland in the Eastern Arc Mountains (EAM) of Tanzania. In four 1‐ha sample plots in Nyanganje and Kitonga Forests, we measured all trees ≥10 cm diameter alongside height and wood mass density. The plots contained an average of 20 tree species ha^?1 (range 11–29) and 344 stems ha^?1 (range 281–382) with Shannon diversity values of 1.05 and 1.25, respectively. We weighted nine previously published woody savannah allometric models based on whether: (i) the model was derived from the same geographical region; (ii) the model included tree height/wood mass density in addition to stem diameter; and (iii) sample size was used to fit the model. The weighted mean ABGC storage from the nine models range from 13.5 ± 2 to 29.8 ± 5 Mg ha^?1. Measured ABGC storage in the herbaceous layer, using the wet combustion method, adds 0.55 ± 0.02 Mg C ha^?1. Estimates suggest that EAM miombo woodlands store a range of 13–30 Mg ha^?1 of carbon. Although the estimates suggest that miombo woodlands store significant quantities of carbon, caution is required as this is the first estimate based on in situ data.     

Extremely divergent song types in the genus Aerotegmina Hemp (Orthoptera: Tettigoniidae: Hexacentrinae) and the description of a new species from the Eastern Arc Mountains of Tanzania (East Africa)

The genus Aerotegmina comprises a group of African canopy-dwelling, predatory bushcrickets (katydids) that is known for its inflated tegmina and the unusually loud and low-frequency calling song of its type species. Here, we describe the songs of another two species of the genus which are much larger than the type species and have an even lower peak frequency. In addition, small and large species differ in song structure. While the type species and closely related forms have a broad banded, multi-peak song with strong components in the audio and ultrasonic range, the species treated here have an extremely narrow banded, resonant song with a carrier frequency of 2 kHz. With Q-values above 100 these sounds belong to the purest songs ever recorded in Orthoptera. Besides describing songs, stridulatory organs and a new species we discuss the possible functions of the song type. A key to the species of Aerotegmina is provided.     

Seasonal elevational movements of Eastern Olive Sunbird Cyanomitra olivacea in the Uluguru Mountains,Tanzania

Little is known about the seasonal elevational movements for most tropical avifauna species. Seasonal elevational movements of the Eastern Olive Sunbird Cyanomitra olivacea were studied along an elevational gradient from 600 to 1 500?m above sea level in the Uluguru Mountains, Tanzania, between May 2005 and February 2006. The recapture of ringed individuals along an elevational gradient across seasons provided evidence for the seasonal elevational movement of the Eastern Olive Sunbird in the Uluguru Mountains and the first documented evidence for this species in the Eastern Arc Mountains as a whole. Due to forest fragmentation and lack of corridors connecting high- and low-altitude forests in the Uluguru Mountains, the results have implications for conservation of the forest along the entire elevational gradient as well as for other forest bird species that have been documented to make seasonal elevational movements in the Uluguru Mountains and the entire Eastern Arc Mountains.     

Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

Understanding the evolutionary history of the species in a particular region provides insights into how that fauna was formed. Of particular interest to biogeographers is examining the impact a geographical barrier had in generating temporal genetic diversity among codistributed species. We examined the impact a major New World barrier, the Isthmus of Tehuantepec (IT) in southern Mexico, had on a regional bird fauna. Specifically, genetic data from 10 montane-forest bird taxa were analysed using approximate Bayesian computation (ABC) to test the hypothesis of simultaneous intraspecific diversification at the IT. Because effective population size (N_e) has the greatest impact on coalescent times, thereby affecting tests of divergence among codistributed taxa, we chose priors for both current and ancestral N_e using empirical estimates of theta. The ABC method detected two discrete diversification events. Subsequent analysis with the number of diversification events constrained to two suggests that four taxa diverged in an older event, with the remaining six diverging more recently. Application of a range of mutation rates from 2.0 to 5.0% Myr⁻¹ places both events within the Pleistocene or Late Pliocene, suggesting that fluctuations in montane habitat induced by climate cycles and a late Pliocene seaway may have fractured this montane bird fauna. The results presented here suggest this avian fauna responded in a relatively concerted fashion over the last several million years.     

The shaping of genetic variation in edge‐of‐range populations under past and future climate change

With rates of climate change exceeding the rate at which many species are able to shift their range or adapt, it is important to understand how future changes are likely to affect biodiversity at all levels of organisation. Understanding past responses and extent of niche conservatism in climatic tolerance can help predict future consequences. We use an integrated approach to determine the genetic consequences of past and future climate changes on a bat species, Plecotus austriacus. Glacial refugia predicted by palaeo‐modelling match those identified from analyses of extant genetic diversity and model‐based inference of demographic history. Former refugial populations currently contain disproportionately high genetic diversity, but niche conservatism, shifts in suitable areas and barriers to migration mean that these hotspots of genetic diversity are under threat from future climate change. Evidence of population decline despite recent northward migration highlights the need to conserve leading‐edge populations for spearheading future range shifts.     

Genetic structure offers insights into the evolution of migration and the taxonomy of the Barred Long‐tailed Cuckoo Cercococcyx montanus species complex

Barred Long‐tailed Cuckoo (Cercococcyx montanus) currently comprises two morphologically distinct subspecies, one resident in the Albertine Rift (montanus) and one in east and southeast Africa (patulus) in which there are migrations that are poorly understood. Based on nuclear and mitochondrial DNA sequences, we find that two specimens collected in relatively low‐elevation forest in the Albertine Rift were correctly identified from plumage as the migratory subspecies whose closest known breeding area is > 800 km to the east. We discuss ways in which this unique migratory pattern could have evolved and argue that migration was gained and then lost in the C. montanus complex. Based on consistent morphological and genetic differences, we suggest that Barred Long‐tailed Cuckoo is best treated as two species, one of which (C. montanus) is a non‐migratory Albertine Rift endemic.     

Effects of a hydropower plant on Coleopteran diversity and abundance in the Udzungwa Mountains, Tanzania

The effects of river flow diversion on biodiversity were assessed using Coleoptera as an indicator group in three habitats of the Kihansi Gorge (Udzungwa Mountains, Tanzania), before and after commissioning of a hydropower plant. Data collected using sweep netting and pitfall traps showed that the effect of diversion of the river flow was site-specific, affecting particularly the spray habitat. Rarefaction analysis of both sweep netting and pitfall samples indicated that the expected richness of Coleoptera declined significantly in all habitats after commissioning of the power plant. Sweep netting and pitfall samples showed that the highest Shannon–Wiener diversity index value before the diversion of the river flow was in the spray zone, but the index value decreased after diversion. Changes in the other two habitats were less prominent. Analysis of variance using diversity index values from five pitfall samples in each habitat type before and after commissioning indicated that there were no statistically significant differences in the diversity index between the two sampling periods or among the three habitat types. Renkonen's similarity index between habitats showed that pitfall samples had higher similarity (87%) than did samples from sweep netting (69%). It is suggested that for mitigation purposes, artificial spray systems, which have been installed in other wetlands of the Kihansi Gorge, also be installed to cover the whole Lower Wetland in which this study was undertaken. In order to maintain overall biodiversity in the Kihansi Gorge, it is suggested that the ecosystem conservation approach be prioritised.     

Genetic Divergence During Long‐term Isolation in Highly Diverse Populations of Tropical Trees Across the Eastern Arc Mountains of Tanzania

The Eastern Arc Mountains are believed to support some of the oldest tropical forest in the world. The current distribution of this forest is highly fragmented due to a combination of long‐term effects of past changes in global climate and more recent deforestation. We sought to explore the hypothesized antiquity and long‐term isolation of the Eastern Arc montane forests based on an assessment of the geographical distribution and interspecies similarity of chloroplast DNA sequence variation in five forest trees. Data were used to investigate regional patterns of diversity and population structure based on intraspecific phylogenies, and results were interpreted against hypotheses on ecosystem age and connectivity. Regional diversity was high, with up to 22 chloroplast DNA haplotypes being recorded within a species across the sampled populations. Geographical concordance of genetic and geographic structure was weak to absent in all species and there was little similarity of genetic structure between species. Haplotype sharing between mountain blocks was extremely limited. The generally weak phylogeographical structure, in conjunction with high regional diversity and genetic uniqueness of individual mountain forests does not support the assumption of widespread genetic connectivity of the mountain forests, indicating instead a pattern of past isolation and ongoing diversification. Our findings substantially add to understanding patterns of diversity in this region and lend weight to calls to use more sophisticated biodiversity assessments when setting regional conservation and research funding priorities.     

Effects of fire on understorey birds in Kimboza Forest Reserve in the eastern foothills of the Uluguru Mountains,Tanzania

Fire is one of the main threats facing the long‐term survival of the forests in the Eastern Arc Mountains. Yet, our understanding of how it affects fauna, particularly birds, is still poor. A fire that originated on surrounding farmland burned approximately half of Kimboza Forest Reserve between 13 and 15 October 2010. To better understand how birds respond to fire, a short‐term study of understorey bird diversity and abundance in this forest reserve was conducted by comparing burned and unburned sites twenty months post‐fire. Capture rates were significantly higher at the unburned site compared to the burned site. Bird species diversity was also higher at the unburned site than at the burned site. Despite the brevity of the study, the results suggest that fire has negative effects on forest avifauna and forest fires need to be prevented at Kimboza Forest Reserve as they affect the distribution and diversity of understorey birds.     

Phylogeny,phylogeography and geographical variation in the Crocidura monax (Soricidae) species complex from the montane islands of Tanzania,with descriptions of three new species

We assess morphological and multilocus genetic variation among 11 isolated montane populations of white‐toothed shrews from Tanzania that have been referred to either Crocidura monax Thomas or C. montis Thomas. The montane sites we sampled represent ‘sky‐islands’ from two geologically distinct archipelagos (Northern Highlands and the Eastern Arc Mountains) and are a significant component of the Eastern Afromontane Biodiversity Hotspot. We used multivariate analyses of morphometric traits and phylogenetic and species‐delimitation analyses of multilocus DNA sequence data to assess species‐level diversity. Our species delimitation analyses included a novel, pairwise validation approach that avoids potential biases associated with specifying a guide tree. These analyses reveal several distinct lineages, which we treat as six allopatric species. Each species is restricted to one, two or four mountains. We use available names to recognize C. monax, C. tansaniana Hutterer and C. usambarae Dippenaar, while naming and describing three new species. Our results demonstrate the effectiveness of combining morphological and genetic data to uncover and describe hidden diversity in a cryptic mammalian system. © 2015 The Linnean Society of London     

multi‐dice: r package for comparative population genomic inference under hierarchical co‐demographic models of independent single‐population size changes

Population genetic data from multiple taxa can address comparative phylogeographic questions about community‐scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co‐demographic models that directly test multi‐taxa hypotheses within a single, unified analysis. This approach has been applied to classical phylogeographic data sets such as mitochondrial barcodes as well as reduced‐genome polymorphism data sets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD‐seq and GBS. A strategy for the latter had been accomplished by adapting the site frequency spectrum to a novel summarization of population genomic data across multiple taxa called the aggregate site frequency spectrum (aSFS), which potentially can be deployed under various inferential frameworks including approximate Bayesian computation, random forest and composite likelihood optimization. Here, we introduce the r package multi‐dice , a wrapper program that exploits existing simulation software for flexible execution of hierarchical model‐based inference using the aSFS, which is derived from reduced genome data, as well as mitochondrial data. We validate several novel software features such as applying alternative inferential frameworks, enforcing a minimal threshold of time surrounding co‐demographic pulses and specifying flexible hyperprior distributions. In sum, multi‐dice provides comparative analysis within the familiar R environment while allowing a high degree of user customization, and will thus serve as a tool for comparative phylogeography and population genomics.     

Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent‐wide lineage admixture

Genetic admixture is supposed to be an important trigger of species expansions because it can create the potential for selection of genotypes suitable for new climatic conditions. Up until now, however, no continent‐wide population genetic study has performed a detailed reconstruction of admixture events during natural species expansions. To fill this gap, we analysed the postglacial history of Alnus glutinosa, a keystone species of European swamp habitats, across its entire distribution range using two molecular markers, cpDNA and nuclear microsatellites. CpDNA revealed multiple southern refugia located in the Iberian, Apennine, Balkan and Anatolian Peninsulas, Corsica and North Africa. Analysis of microsatellites variation revealed three main directions of postglacial expansion: (i) from the northern part of the Iberian Peninsula to Western and Central Europe and subsequently to the British Isles, (ii) from the Apennine Peninsula to the Alps and (iii) from the eastern part of the Balkan Peninsula to the Carpathians followed by expansion towards the Northern European plains. This challenges the classical paradigm that most European populations originated from refugial areas in the Carpathians. It has been shown that colonizing lineages have met several times and formed secondary contact zones with unexpectedly high population genetic diversity in Central Europe and Scandinavia. On the contrary, limited genetic admixture in southern refugial areas of A. glutinosa renders rear‐edge populations in the Mediterranean region more vulnerable to extinction due to climate change.     

Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species

The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.     

The evolution of sexual and parthenogenetic Warramaba: a window onto Plio–Pleistocene diversification processes in an arid biome

Environmental changes over the Plio‐Pleistocene have been key drivers of speciation patterns and genetic diversification in high‐latitude and mesic environments, yet comparatively little is known about the evolutionary history of species in arid environments. We applied phylogenetic and phylogeographic analyses to understand the evolutionary history of Warramaba grasshoppers from the Australian arid zone, a group including sexual and parthenogenetic lineages. Sequence data (mitochondrial COI) showed that the four major sexual lineages within Warramaba most likely diverged in the Pliocene, around 2–7 million years ago. All sexual lineages exhibited considerable phylogenetic structure. Detailed analyses of the hybrid parthenogenetic species W. virgo and its sexual progenitors showed a pattern of high phylogenetic diversity and phylogeographic structure in northern lineages, and low diversity and evidence for recent expansion in southern lineages. Northern sexual lineages persisted in localized refugia over the Pleistocene, with sustained barriers promoting divergence over this period. Southern parts of the present range became periodically unsuitable during the Pleistocene, and it is into this region that parthenogenetic lineages have expanded. Our results strongly parallel those for sexual and parthenogenetic lineages of the gecko Heteronotia from the same region, indicating a highly general effect of Plio‐Pleistocene environmental change on diversification processes in arid Australia.     

Multilocus molecular DNA variation in Winifred's Warbler Scepomycter winifredae suggests cryptic speciation and the existence of a threatened species in the Rubeho–Ukaguru Mountains of Tanzania

Winifred's Warbler Scepomycter winifredae has a disjunct but very restricted distribution in the mountains of central Tanzania. It was once known only from the Uluguru Mountains. Subsequently, this rare warbler has been recorded from the Ukaguru Mountains, and more recently from the Rubeho Mountains, as well as from Mwanihana Forest on the eastern scarp of the Udzungwa Highlands (single record). These three localities are isolated from the Uluguru Mountains by more than 100 km of lowland savannah. Here we characterize the populations morphologically and estimate demographic parameters using a multilocus molecular approach. Birds from the Uluguru Mountains differed from those of the Rubeho–Ukaguru Mountains in mtDNA by 1.6% (uncorrected) sequence divergence, or at 16 sites: one at each of the first and second codon positions, and at 14 third codon position sites. Five autosomal introns were also sequenced for a total of 2922 bp of nuclear DNA. No single nucleotide polymorphisms were completely fixed between the Uluguru and Rubeho–Ukaguru populations. Results from our coalescent analyses suggest that there is currently unlikely to be any exchange of birds between the Uluguru and Rubeho–Ukaguru populations and that the shared nuclear alleles are a consequence of lineage sorting not yet having been completed due to the recent divergence (upper Pleistocene) between these two populations. In view of the lack of gene flow between the Uluguru and Rubeho–Ukaguru populations, and morphological diagnosability, we propose to recognize the latter populations as a separate species, which we name Rubeho Warbler Scepomycter rubehoensis .     

The Indian Ocean dipole – the unsung driver of climatic variability in East Africa

A growing body of evidence suggests that an independent ocean circulation system in the Indian Ocean, the Indian Ocean dipole (IOD), is partly responsible for driving climate variability of the surrounding landmasses. The IOD had traditionally been viewed as an artefact of the El Niño–Southern Oscillation (ENSO) system although increasingly the evidence is amassing that it is separate and distinct phenomenon. We review the causes of the IOD, how it develops within the Indian Ocean, the relationships with ENSO, and the consequences for East African climate dynamics and associated impacts on ecosystems, in particular along the Eastern Arc Mountains of Kenya and Tanzania. We evaluate current research initiatives focussed on characterizing and constraining the IOD and examine how effective these will be in determining climate change impacts on East African ecosystems and how such predictive capacity can be used in developing policy.