Inferring the historical demography of southern African cheetahs (Acinonyx jubatus) using Bayesian analyses of molecular genetic data.

Gastrointestinal disease is omnipresent in captive cheetahs ( Acinonyx jubatus ), in contrast to its free-ranging populations. The current study aimed to evaluate the effect of diet type (meat-only whole prey) on gastrointestinal health in captive cheetahs by measuring faecal and serum concentrations of S100/calgranulins. This paper reports faecal S100A12 and calprotectin concentrations in 12 captive cheetahs fed supplemented beef versus whole rabbit for one month in a cross-over design. Also, serum S100A12 and calprotectin concentrations were determined in four cheetahs fed whole rabbit and six cheetahs fed supplemented beef, and these were compared to the faecal concentrations of the respective marker proteins. Both the immunoassay for canine calprotectin and canine S100A12 were precise and reproducible for use with serum samples and faecal extracts. Whereas the assay for S100A12 was linear and accurate, an inconsistent linearity of the canine calprotectin assay was observed and could be indicative of an insufficient cross-reactivity of the specific antibody used for this assay. Serum concentrations of S100A12 and calprotectin were not altered by diet type, and were not correlated with the respective concentrations in faeces. Numerically (P=0.241) greater calprotectin concentrations and greater (P=0.041) faecal S100A12 concentrations were detected in cheetahs fed supplemented beef compared with whole rabbit. These findings demonstrate that whole prey feeding may decrease intestinal inflammation in the captive cheetah. Consequently, the relation between diet type and intestinal inflammatory conditions in the captive cheetah warrants further investigation.

ObjectiveThis study aimed to investigate the diversity and sex-specific differences in the intestinal microbiota of cheetah (Acinonyx jubatus). MethodsFecal samples were collected from 9 healthy adult cheetahs (4 male and 5 female), and intestinal microbiota were assessed through high-throughput sequencing of the V3-V4 region of 16S rRNA gene. ResultsIn total, 599349 effective tags were obtained, with an average length of 405 bp. At 97% sequence similarity, 268 operational classification units (OTUs) were obtained and classified into the bacterial domain, including 10 phyla, 21 classes, 35 orders, 72 families, and 144 genera. Based on relative abundance, the 5 most abundant bacterial phyla were Firmicutes (accounting for approximately 42.29% of the total OTUs), Actinobacteria (31.54%), Fusobacteria (16.66%), Proteobacteria (5.30%), and Bacteroidetes (4.19%). The low abundance of phylum Bacteroidetes was the primary feature of the intestinal microbial community of the cheetah. The 5 most abundant families were Coriobacteriaceae (31.28%), Peptostreptococcaceae (17.66%), Fusobacteriaceae (15.46%), Lachnospiraceae (12.40%), and Clostridiaceae_1 (6.93%). The 5 most abundant genera were Collinsella (30.16%), Fusobacterium (15.46%), Peptoclostridium (11.46%), Blautia (8.28%), and Clostridium_sensu_stricto_1 (6.39%). Approximately 2.32% of the total OTUs were unclassified strains at the genus level. Alpha diversity analysis indicated that the Shannon indices of the intestinal microbiota ranged 2.93-4.41; Simpson indices, 0.72-0.91. The observed species and Shannon indices of the intestinal microbiota of male cheetahs were slightly greater than those of female cheetah. Beta diversity analysis revealed that the difference between sexes was greater than that within groups. However, cluster analysis revealed that intestinal microbes of cheetahs of the same sex were not clustered. ConclusionThe present results show the intestinal microbial diversity of cheetah, and indicate that intestinal microbiota of cheetah do not differ significantly on the basis of sex, thus providing a scientific basis for studies on the conservation of cheetahs and their digestive physiology and for rescuing and feeding cheetahs.

Afshar F, Sheidai M, Talebi SM, Keshavarzi M. 2015. Bayesian and Multivariate Analyses of combined molecular andmorphological data in Linum austriacum (Linaceae) populations: Evidence for infraspecific taxonomic groups. Biodiversitas 16: 179-187. Plant specimens of Linum austriacum (Linaceae) were collected from 16 geographical populations of nine provinces in Iran andused for morphological and molecular (ISSR) analyses. Different multivariate and Bayesian methods were used to studyinterpopulations differences. Analysis of variance test and Principal coordinate analysis plots indicated morphological difference of thepopulations. Mantel test revealed positive significant correlation between morphological and geographical distance of these populations.Pearson, coefficient of correlation showed significant correlations between basal leaf length, width and length/width ratio with latitudeand altitude of the studied populations. Bayesian analysis of combined molecular and morphological features revealed divergence of thestudied populations and consensus tree showed separation of 6 populations in different clusters. Canonical Variate Analysis plot of thesepopulations showed that Sang Sefid and Salmas populations differed greatly from the other populations. New ecotypes are suggested forthese populations.

Among the 30 known genera within subfamily Peiratinae, only the genus Sirthenea has a cosmopolitan distribution. The results of our studies are the first comprehensive analysis concerning one of the representatives of mentioned subfamily based on joint phylogenetic analyses of molecular and morphological data as well as molecular dating. A total of 32 species were included into the dataset with all known species of the genus Sirthenea. Material of over 400 dry specimens was examined for the morphological part of this study. The cosmopolitan distribution of Sirthenea and the inaccessibility of specimens preserved in alcohol required the extraction of DNA from the dried skeletal muscles of specimens deposited in 24 entomological collections. The oldest specimens used for the successful extraction and sequencing were collected more than 120 years ago in India. We performed Bayesian Inference analyses of molecular and morphological data separately, as well as combined analysis. The molecular and morphological data obtained during our research verify the correlation of the divergence dates of all known Sirthenea species. Results of the relaxed molecular clock analysis of the molecular data show that, the genus Sirthenea started diverging in the Late Cretaceous into two clades, which subsequently began to branch off in the Paleocene. Our results of phylogenetic analyses suggest that the fossula spongiosa and its development could be one of the most important morphological characters in the evolution of the genus, most likely associated with the ecological niche inhabited by Sirthenea representatives. Confirmation of the results obtained in our studies is the reconciliation of the evolutionary history of Sirthenea with the biogeographical processes that have shaped current global distribution of the genus.

The introduction of a sub-species or re-introduction of a species into an area where this species was extinct for decades is a challenging undertaking. It is therefore crucial to plan (re-) introductions carefully and to consider all current knowledge of the species (Breitenmoser et al., 2001) . This approach is particularly important when the species is threatened at a global level such as the cheetah (Acinonyx jubatus) (Durant et al., 2022) . The Asiatic cheetah (Acinonyx jubatus venaticus) has been extinct in India for 70 years and its government has introduced on September 17, 2022, eight cheetahs from Namibia and on February 18, 2023, 12 cheetahs from South Africa (Acinonyx jubatus jubatus) into their country. The cheetahs from Africa were brought to Kuno National Park (KNP), an unfenced area of $750 km 2 surrounded by villages with livestock farmers. The aim of this project is "to establish a free-ranging population of cheetahs in and around the Kuno NP" and for "this population to be managed as a metapopulation with other two to three established populations of cheetah in India with occasional 'immigrants' brought in from Africa, as and when needed" (Jhala et al., 2021) . Based on the prey density in the KNP, the carrying capacity for cheetahs was calculated to be 21 individuals, that is, $3 individuals/100 km 2 (Jhala et al., 2021) . Such high cheetah densities have not been recorded for other free-ranging African cheetah population roaming in unfenced areas, which typically occur at less than 1 individual/100 km 2 (Broekhuis et al., 2021; Weise et al., 2017) . On October 19, 2022, a critique on the cheetah reintroduction to India pointed out that even in prey-rich landscapes such as the Maasai Mara in Kenya, East Africa, the cheetah density is $1 individual/100 km 2 (Gopalaswamy et al., 2022) . On February 16, 2023, a response was published by Tordiffe et al. (2023) . A few weeks later, on March 27, 2023, one of the eight cheetahs from Namibia died, probably due to kidney failure, on March 29, 2023, four cubs were born by a female from Namibia and on April 2, 2023, a male from Namibia was walking 20 km out of the KNP into the adjacent villages.

The power of resolution of microsatellite markers and assignment tests to determine the geographic origin of cheetah ( Acinonyx jubatus) in Southern Africa

For more than two decades, the cheetah (Acinonyx jubatus) has been considered a paradigm of disease vulnerability associated with low genetic diversity, particularly at the immune genes of the major histocompatibility complex (MHC). Cheetahs have been used as a classic example in numerous conservation genetics textbooks as well as in many related scientific publications. However, earlier studies used methods with low resolution to quantify MHC diversity and/or small sample sizes. Furthermore, high disease susceptibility was reported only for captive cheetahs, whereas free-ranging cheetahs show no signs of infectious diseases and a good general health status. We examined whether the diversity at MHC class I and class II-DRB loci in 149 Namibian cheetahs was higher than previously reported using single-strand conformation polymorphism analysis, cloning, and sequencing. MHC genes were examined at the genomic and transcriptomic levels. We detected ten MHC class I and four class II-DRB alleles, of which nine MHC class I and all class II-DRB alleles were expressed. Phylogenetic analyses and individual genotypes suggested that the alleles belong to four MHC class I and three class II-DRB putative loci. Evidence of positive selection was detected in both MHC loci. Our study indicated that the low number of MHC class I alleles previously observed in cheetahs was due to a smaller sample size examined. On the other hand, the low number of MHC class II-DRB alleles previously observed in cheetahs was further confirmed. Compared with other mammalian species including felids, cheetahs showed low levels of MHC diversity, but this does not seem to influence the immunocompetence of free-ranging cheetahs in Namibia and contradicts the previous conclusion that the cheetah is a paradigm species of disease vulnerability.

Changing land use patterns in southern Africa have potential to dramatically alter the prospects for carnivore conservation. Understanding these influences is essential for conservation planning. We interviewed 250 ranchers in Namibia to assess human tolerance towards and the distribution of large carnivores. Cheetahs (Acinonyx jubatus), leopards (Panthera pardus) and brown hyaenas (Hyaena brunnea) were widely distributed on Namibian farmlands, spotted hyaenas (Crocuta crocuta) had a narrower distribution, and wild dogs (Lycaon pictus) and lions (Panthera leo) are largely limited to areas near source populations. Farmers were most tolerant of leopards and least tolerant of lions, wild dogs and spotted hyaenas. Several factors relating to land use correlated consistently with carnivore-presence and landowner tolerance. Carnivores were more commonly present and/or tolerated where; wildlife diversity and biomass were higher; income from wildlife was higher; income from livestock was lower; livestock biomass was lower; in conservancies; game fencing was absent; and financial losses from livestock depredation were lower. Efforts to create conditions whereby the costs associated with carnivores are lowest, and which confer financial value to them are likely to be the most effective means of promoting carnivore conservation. Such conditions are achieved where land owners pool land to create conservancies where livestock are replaced with wildlife (or where livestock husbandry is improved) and where wildlife generates a significant proportion of ranch income. Additional measures, such as promoting improved livestock husbandry and educational outreach efforts may also help achieve coexistence with carnivores. Our findings provide insights into conditions more conducive to the persistence of and tolerance towards large carnivores might be increased on private (and even communal) lands in Namibia, elsewhere in southern and East Africa and other parts of the world where carnivore conservation is being attempted on private lands.

The cheetah (Acinonyx jubatus) is listed as a vulnerable species by the International union for the conservation of nature (IUCN), including two critically endangered subspecies, the Saharan cheetah, and the Iranian cheetah, so it is imperative that we understand variation in cheetah morphology to make good decisions regarding the conservation of this species. Here, we aim to determine whether northeastern African cheetahs have smaller body sizes than southern African cheetahs. This study also adds to our knowledge of cheetah morphology from two cheetah populations that do not yet have comprehensive published data: Kenya, and northeastern Africa, including captive individuals. We calculated means and standard deviations on cranial and body measurements of live or in few cases, freshly dead, cheetahs from the aforementioned populations, plus previously published data on Namibian and Botswanan cheetahs and compared them to one another using multivariate analysis of variance. Results show that northeastern African cheetahs have smaller body sizes than southern and eastern African populations. We also found that captive cheetahs retain the morphological characteristics of their ancestral population- captive cheetahs from southern Africa have similar body sizes to wild southern African cheetahs and larger body sizes than captives from northeastern Africa. Other analyses regarding cheetah growth agree with previous studies on Namibian and Botswanan cheetah populations rates. As such, this study can serve as a baseline for the care of captive cheetah populations to maintain healthy weights and body proportions.

Molecular systematics of the marine gastropod families Trochidae and Calliostomatidae (Mollusca: Superfamily Trochoidea)

Genetic diversity in British populations ofSaxifraga rivularisL. (Saxifragaceae) was assessed using isozymes, RAPDs, inter-SSRs and RFLPs of two non-coding chloroplast DNA regions. Low levels of variation were detected: only five molecular phenotypes were recovered, polymorphic for a single RAPD band andPgdenzyme phenotype. The problem of drawing conservation recommendations from studies that show low levels of marker variation is discussed, and the importance of recognizing the limits of molecular genetic data in conservation biology is emphasized.

Conservation genetics of an arctic species,Saxifraga rivularisL., in Britain

Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN

Cladistic analyses employing the criterion of unweighted parsimony were performed on a matrix of morphological characters and on a combined data matrix of morphological and molecular characters (from the internal transcribed spacer region of the nuclear ribosomal DNA including the 5.8S ribosomal RNA gene and the flanking ITS-1 and ITS-2 regions) in order to infer relationships among the species of Sarcoscypha. The outgroup taxa for both analyses were Microstoma floccosum, Nanoscypha tetraspora, Nanoscypha sp., and Pithya cupressina. Fifteen morphological characters were identified and analyzed using NONA. These characters were combined with 104 informative molecular characters for a total of 119 phylogenetically informative characters in the combined analysis. An initial analysis of morphological data produced 166 most parsimonious trees. The consensus tree resolved the two Nanoscypha species plus S. striatispora as a monophyletic group, but showed no resolution among the remaining species of Sarcoscypha. A second analysis of the morphological data with only the core species of Sarcoscypha and with Pithya as the outgroup still showed little resolution. The analysis of molecular data alone produced a consensus tree with a toplogy much like that from a previously published analysis including fewer taxa and supported the transfer of S. striatispora to Nanoscypha. The analysis of combined morphological and molecular data produced two equally parsimonious trees. The only differences in the results from the combined and molecular analyses were: (i) the three accessions of S. austriaca formed a monophyletic group in the consensus tree from the combined analysis but not the molecular analysis, and (ii) Pithya cupressina was sister to Sarcoscypha in the combined analysis whereas Pithya, Nanoscypha, and Sarcoscypha formed an unresolved trichotomy in the consensus tree from the molecular analysis. Both the molecular and the combined analyses resolved two major clades within the core Sarcoscypha. All analyses placed S. striatispora outside the major clade formed from the remaining species of Sarcoscypha but nested within the Nanoscypha clade. A new combination is made for Sarcoscypha striatispora.

The cheetah (Acinonyx jubatus) has been considered a paradigm for disease vulnerability due to loss of genetic diversity. This species monomorphism has been suspected to be the basis for their general poor health and dwindling populations in captivity. North American and South African captive populations have high prevalences of hepatic veno-occlusive disease, glomerulosclerosis, gastritis, and systemic amyloidosis, diseases that are rare in other species. Unusually severe inflammatory reactions to common infectious agents have also been documented in captive cheetahs. The current study compared disease prevalences in free-ranging Namibian cheetahs with those in two captive populations of similar ages. The occurrence of diseases in the free-ranging population was determined from 49 necropsies and 27 gastric biopsies obtained between 1986 and 2003 and compared with prevalences in 147 North American and 80 South African captive cheetahs. Except for two cheetahs, the free-ranging population was in robust health with only mild lesions present, in contrast with significantly higher prevalences in the captive populations. Despite widespread heavy Helicobacter colonization in wild cheetahs, only 3% of the free-ranging population had moderate to severe gastritis, in contrast with 64% of captive cheetahs. No severe inflammatory reactions to viral infections were detected in the free-ranging animals. Because free-ranging Namibian cheetahs are as genetically impoverished as captive cheetahs, these findings caution against attributing loss of fitness solely to genetic factors and attest to the fundamental importance of extrinsic factors in wildlife health.