Not only climate. The importance of biotic interactions in shaping species distributions at macro scales

Abiotic factors are usually considered key drivers of species distribution at macro scales, while biotic interactions are mostly used at local scales. A few studies have explored the role of biotic interactions at macro scales, but all considered a limited number of species and obligate interactions. We examine the role of biotic interactions in large-scale SDMs by testing two main hypotheses: (1) biotic factors in SDMs can have an important role at continental scale; (2) the inclusion of biotic factors in largescale SDMs is important also for generalist species. We used a maximum entropy algorithm to model the distribution of 177 bat species in Africa calibrating two SDMs for each species: one considering only abiotic variables (noBIO-SDMs) and the other (BIO-SDMs) including also biotic variables (trophic resource richness). We focused the interpretation of our results on variable importance and response curves. For each species, we also compared the potential distribution measuring the percentage of change between the two models in each pixel of the study area. All models gave AUC >0.7, with values on average higher in BIO-SDMs compared to noBIO-SDMs. Trophic resources showed an importance overall higher level than all abiotic predictors in most of the species (~68%), including generalist species. Response curves were highly interpretable in all models, confirming the ecological reliability of our models. Model comparison between the two models showed a change in potential distribution for more than 80% of the species, particularly in tropical forests and shrublands. Our results highlight the importance of considering biotic interactions in SDMs at macro scales. We demonstrated that a generic biotic proxy can be important for modeling species distribution when species-specific data are not available, but we envision that a multi-scale analysis combined with a better knowledge of the species might provide a better understanding of the role of biotic interactions

New records of bat species using Gatkop Cave in the maternal season

Eight bat species were recorded at Gatkop Cave, in the northern part of South Africa in December 2011 (Cloeotis percivali, Hipposideros caffer, Myotis tricolor, Miniopterus natalensis, Nycteris thebaica, Rhinolophus blasii, Rhinolophus smithersi, and Rhinolophus simulator). With the exception of M. natalensis, R. simulator and Myo. tricolor, the other five species were recorded for the first time at Gatkop Cave during this time of the year, when thousands of M. natalensis use the cave as a maternity and nursery roost. Previously it was suggested the large numbers of M. natalensis using Gatkop Cave during the maternal period excluded other bat species. The reason for this recorded change in species roost composition at Gatkop Cave during the maternal period in relation to previous records made from the late 1960s and the mid 1980s is not clear, two possible reasons are the loss of other roosts, or these species were previously present but were not captured as a result of the particular methods used.http://www.degruyter.com/view/j/mamm2017-02-25am2017Centre for Wildlife Managemen

The excreted microbiota of bats : evidence of niche specialisation based on multiple body habitats

Animal-associated microbiotas form complex communities, which play crucial functions for their host, including susceptibility to infections. Despite increasing attention to bats as reservoirs of zoonotic pathogens, their microbiota is poorly documented, especially for samples potentially implicated in pathogen transmission such as urine and saliva. Here, using low-biomass individual samples, we examined the composition and structure of bacterial communities excreted by insectivorous bats, focusing on three body habitats (saliva, urine and faeces). We show that niche specialisation occurs as bacterial community composition was distinct across body habitats with the majority of phylotypes being body habitat specific. Our results suggest that urine harbours more diverse bacterial communities than saliva and faeces and reveal potentially zoonotic bacteria such as Leptospira, Rickettsia, Bartonella and Coxiella in all body habitats. Our study emphasised that, in addition to the traditional use of gut-associated samples such as faeces, both urine and saliva are also of interest because of their diverse microbiota and the potential transmission of pathogenic bacteria. Our results represent a critical baseline for future studies investigating the interactions between microbiota and infection dynamics in bats.This work was supported by the National Research Foundation (NRF) of South Africa [Grant UID 78566 (NRF RISP grant for the ABI3500), UID 91496 and UID 92524], and by the Grant or Cooperative Agreement Number, [1U2GGH001874-01], funded by the Centers for Disease Control and Prevention. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Preventionor the Department of Health and Human Services. MD’s postdoctoral fellowship is funded by a Capacity Building Grant from the National Research Foundation, South Africa [Grant UID 92524].http://femsec.oxfordjournals.org2018-01-31hb2017Centre for Wildlife ManagementMedical Virolog

Bat species (Mammalia: Chiroptera) occurring at Telperion Nature Reserve

Mist nets, harp traps and roost searches resulted in the eight bat species being recorded in Telperion Nature Reserve, which is in a transition between the Savanna and Grassland biomes. The majority of these were species in the family Vespertilionidae. Anabat release calls were recorded from three species. Sexual dimorphism in external body size, and in two of the Anabat release call parameters (Fc and Sc), were observed in Neoromicia capensis. This species was roosting in larger numbers in buildings than previously recorded for vegetation roosts. The low capture rate and lack of certain bat families was most likely the result of capture bias, even though the Grassland biome is known to have fewer species than the Savanna biome.E. Oppenheimer and Sonhttp://www.journals.co.za/content/journal/nfi_ditsongam2020Mammal Research InstituteMedical Virolog

Synchronized shift of oral, faecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction

Seasonal reproduction is a period of extreme physiological and behavioural changes, yet we know little about how it may affect host microbial communities (i.e. microbiota) and pathogen transmission. Here, we investigated shifts of the bacterial microbiota in saliva, urine and faeces during the seasonal reproduction of bats in South Africa, and test for an interaction in shedding patterns of both bacterial (Leptospira) and viral (adeno- and herpesviruses) agents. Based on a comparative approach in two cave-dwelling bat species and high-throughput sequencing of the 16S rRNA gene, we demonstrated a clear signature in microbiota changes over the reproduction season, consistent across the multiple body habitats investigated, and associated with the sex, age and reproductive condition of bats. We observed in parallel highly dynamic shedding patterns for both bacteria and viruses, but did not find a significant association between viral shedding and bacterial microbiota composition. Indeed, only Leptospira shedding was associated with alterations in both the diversity and composition of the urinary microbiota. These results illustrate how seasonal reproduction in bats substantially affects microbiota composition and infection dynamics, and have broad implications for the understanding of disease ecology in important reservoir hosts, such as bats.In part by the National Research Foundation (NRF) of South Africa: the NRF-DST South African Research Chair held by Prof Markotter, grant no. 98339, as well as grant numbers 92524, 85756 and 91496, and grant UID 78566 (NRF RISP grant for the ABI3500). This research was partially supported by the Cooperative Agreement Number [5 NU2GGH001874-02-00], funded by the Centers for Disease Control and Prevention, USA. M.D.’s postdoctoral fellowship was funded by a Capacity Building Grant from the National Research Foundation, South Africa (grant no. UID 92524).http://rsos.royalsocietypublishing.orgam2018Centre for Wildlife ManagementMammal Research InstituteMedical Virolog

Host conservation through their parasites: molecular surveillance of vector-borne microorganisms in bats using ectoparasitic bat flies

Most vertebrates host a wide variety of haematophagous parasites, which may play an important role in the transmission of vector-borne microorganisms to hosts. Surveillance is usually performed by collecting blood and/or tissue samples from vertebrate hosts. There are multiple methods to obtain samples, which can be stored for decades if properly kept. However, blood sampling is considered an invasive method and may possibly be harmful to the sampled individual. In this study, we investigated the use of ectoparasites as a tool to acquire molecular information about the presence and diversity of infectious microorganism in host populations. We tested the presence of three distinct vector-borne microorganisms in both bat blood and bat flies: Bartonella bacteria, malaria-like Polychromophilus sp. (Apicomplexa), and Trypanosoma sp. (Kinetoplastea). We detected the presence of these microorganisms both in bats and in their bat flies, with the exception of Trypanosoma sp. in South African bat flies. Additionally, we found Bartonella sp. in bat flies from one population in Spain, suggesting its presence in the host population even if not detected in bats. Bartonella and Polychromophilus infection showed the highest prevalence in both bat and bat fly populations. Single, co- and triple infections were also frequently present in both. We highlight the use of haematophagous ectoparasites to study the presence of infectious microorganism in host blood and its use as an alternative, less invasive sampling method

Diversity of Bartonella and Rickettsia spp. in bats and their blood-feeding ectoparasites from South Africa and Swaziland

In addition to several emerging viruses, bats have been reported to host multiple bacteria but their zoonotic threats remain poorly understood, especially in Africa where the diversity of bats is important. Here, we investigated the presence and diversity of Bartonella and Rickettsia spp. in bats and their ectoparasites (Diptera and Siphonaptera) collected across South Africa and Swaziland. We collected 384 blood samples and 14 ectoparasites across 29 different bat species and found positive samples in four insectivorous and two frugivorous bat species, as well as their Nycteribiidae flies. Phylogenetic analyses revealed diverse Bartonella genotypes and one main group of Rickettsia, distinct from those previously reported in bats and their ectoparasites, and for some closely related to human pathogens. Our results suggest a differential pattern of host specificity depending on bat species. Bartonella spp. identified in bat flies and blood were identical supporting that bat flies may serve as vectors. Our results represent the first report of bat-borne Bartonella and Rickettsia spp. in these countries and highlight the potential role of bats as reservoirs of human bacterial pathogens.S1 Table. Details of the blood samples analyzed for Bartonella and Rickettsia in South Africa and Swaziland. Not all individuals sampled were taken as museum vouchers, and some vouchers have not yet been lodged in a public repository; in such instances identification based on morphology was limited to external features only, and hence identification to species level was not always possible. Acronyms used in Sample ID and Field/Museum number: UP—Virological Research Group, University of Pretoria; ECJS—Ernest Seamark, AfricanBats; NC— Northern Cape, Davis Jacobs, University of Cape Town; TM- Ditsong National Museum of Natural History, Pretoria (formerly Transvaal Museum); CHIR KNP: Skukuza Biological Reference Collection.The National Research Foundation (NRF) of South Africa (Grant UID: 78566 (NRF RISP grant for the ABI3500) and Grant UID 91496 and 92524) and the Poliomyelitis Research Foundation (PRF) (Grant number 12/14). MD’s postdoctoral fellowship is funded by the National Research Foundation, South Africa (NRF – N00595). Remove selectedhttp://www.plosone.orgCentre for Wildlife ManagementMedical VirologyMicrobiology and Plant Patholog

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

The use of incidence data to estimate bat (Mammalia: Chiroptera) species richness and taxonomic diversity and distinctness within and between the biomes of South Africa, Lesotho and Swaziland

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Master of Science. Johannesburg, 2013.Species richness and estimates of species richness were calculated based on assemblages of bats, within the biomes of South Africa, Lesotho and Swaziland following the vegetation classification of Mucina and Rutherford (2006). Similarity indices were used to explore the various relationships between the assemblages between the various biomes. Taxonomic diversity and distinctness examined the various assemblages within each of the biomes to investigate which biomes contained assemblages that were taxonomically diverse and/or taxonomically distinct compared to all species known to occur within South Africa, Lesotho and Swaziland. The Desert biome had the lowest recorded species richness (5 species), and there was insufficient data to calculate estimates of species richness for this biome. While the Albany had 11 species recorded with species estimates (Est.) ranging between 11-12, then in increasing order - Nama-Karoo (12 species, Est. 13-25 species), Succulent-Karoo (13 species, Est. 15-30 species), Fynbos (17 species, Est. 18-25 species), Indian Ocean Coastal Belt (31 species, Est. 32-36 species), Forest (32 species, Est. 37-46 species), Grassland (39 species, Est. 42-54 species), Azonal (45 species, Est. 49-63 species) and Savanna (57 species, Est. 59-67 species). The mean recorded estimates (based on the averages of all models) and rounding up to a full species indicates that the Albany biome contains the lowest expected species richness of 12 species, then Fynbos and Nama-Karoo (21 species), Succulent-Karoo (22 species), Indian Ocean Coastal Belt (34 species), Forest (43 species), Grassland (49 species), Azonal (54 species) and Savanna (64 species). Sample completeness was calculated for each of the biomes which indicates in ascending order that the Albany biome is 93.2% complete followed by the Indian Ocean Coastal Belt biome (91.1%), Savanna biome (89.9%), Azonal biome (84.1%), Fynbos biome (81.5%), Grassland biome (80.7%), Forest biome (75.8%), Succulent-Karoo biome (61.3%), and Nama-Karoo biome (59.9%). This showed that the Albany biome was found to be the only biome that has been sufficiently sampled. The Jaccard and Sørensen pair wise indices resulted in the clustering of the biomes with similar species richness, due to the large range in species richness (5-57 species) between the biomes. The Lennon et al. (2001) index which is not affected by large species richness between the samples indicated that the Desert and Nama-Karoo assemblages were most dissimilar to one another, while the Indian Ocean Coastal Belt assemblage was the most similar to the remaining biome assemblages. The Albany biome assemblage and Azonal biome assemblage were shown to the most dissimilar to one another. The Grassland, Nama-Karoo and Savanna biomes contribute to higher taxonomic diversity, while the Albany, Azonal, Fynbos, Nama-Karoo and Succulent-Karoo biomes contain lower species richness generally but represent a higher taxonomic distinctness from the chiroptera assemblages in the Grassland and Savanna biomes. The Desert, Forest and Indian Ocean Coastal Belt biomes do not iv contain bat assemblages that are neither taxonomically distinct nor diverse when compared to the taxa of South Africa, Lesotho and Swaziland. The bat assemblage within the Nama-Karoo are both taxonomically diverse and distinct from chiroptera assemblages found within the other nine biomes, requiring a greater focus on conservation actions for the bat species assemblage located within this biome