Discordance Between Spatial Distributions of Y-Chromosomal and Mitochondrial Haplotypes in African Green Monkeys (Chlorocebus spp.): A Result of Introgressive Hybridization or Cryptic Diversity?

Introgressive hybridization may cause substantial discordances among phylogenies based on different genetic markers. Such discordances have been found in diverse mammal species including primates. A recent study of mitochondrial DNA (mtDNA) revealed several poly- and paraphyletic relationships in African green monkeys (Chlorocebus), suggesting contemporary and/or ancient introgressive hybridization among almost all parapatric species of the genus. However, mtDNA analyses alone do not allow us to draw conclusions concerning introgression events. In this study we analyzed two Y chromosomal (Y-chr) markers for 30 African green monkey samples and compared the resulting genetic relationships to those based on published mtDNA data. In line with the results for mtDNA, we found no Y-chr evidence of hypothesized hybridization among Chlorocebus sabaeus and C. tantalus in the northern part of the contact zone in West Africa, and we found two distinct and distantly related Y-chr haplotypes within the range of C. tantalus, suggesting possible cryptic genetic diversity rather than ancient introgressive hybridization in this species. In contrast, Y-chr data revealed monophyletic relationships within Chlorocebus pygerythrus from East Africa, suggesting that mtDNA paraphylies found in this species are most likely to be the result of ancient introgressive hybridization and subsequent cytonuclear extinction of an earlier taxon. Our results accentuate the importance of analyzing sex chromosomal data in addition to mtDNA to obtain more information on the potential outcomes of hybridization with respect to genetic and species diversity. Analysis of more diverse nuclear marker sets is needed to obtain a more complete picture of the African green monkey evolution.     

Geographic distribution of microsatellite alleles in geladas (Primates,Cercopithecidae): Evidence for three evolutionary units

The subspecific taxonomy and distribution of geladas (Theropithecus gelada Rüppell, 1835) remains uncertain. Recent molecular studies based on mitochondrial sequence data revealed a geographically structured, three-deme population, suggesting that there are three evolutionary units of geladas. However, mitochondrial distributions do not always recover population relationships, particularly in taxa with a complex history of isolation and gene flow. We therefore analysed the nuclear genetic population structure of the global gelada population based on 20 microsatellite loci in 43 samples from across its geographic range. F_ST values, a STRUCTURE analysis and a principal coordinate analysis (PCoA) confirmed the three-deme population structure corresponding to the mitochondrial population structure. Therefore, our analyses provide additional support for three evolutionary units in geladas, corresponding to (a) a northern (north of Lake Tana, primarily in the Simien Mountains, previously classified as Theropithecus gelada gelada Rüppell, 1835), (b) a central (between Addis Ababa and the highlands east of Lake Tana, previously classified as Theropithecus gelada obscurus Heuglin, 1863) and (c) a southern (south of the Rift Valley, previously tentatively classified as Theropithecus gelada arsi Shotake et al., 2016, Anthropological Science, 124, 157) population. These results pave the way for future conservation decisions and highlight that the gelada population boundaries need more fine-grained genetic sampling and phenotypic analyses, in particular for their taxonomic ranking.     

Group Composition of Guinea Baboons (<Emphasis Type="Italic">Papio papio</Emphasis>) at a Water Place Suggests a Fluid Social Organization

Baboon social systems are among the most studied in primates. Solid knowledge of the hamadryas and savannah baboon systems has accumulated, leading to a dichotomic view of baboon social systems. Hamadryas baboons live in multilayered troops based on 1-male units whereas savannah baboons live in multimale multifemale groups based on a network of related females. Less attention has been paid to their West African congenerics, the Guinea baboons, Papio papio. To fill this gap, in 2007 we initiated a long-term study of a baboon troop ranging in the Niokolo Koba National Park in southeastern Senegal. Earlier studies suggested a tendency for a multilayered social system in Guinea baboons, similar to the hamadryas baboon organization. Therefore, as a first approach to analyzing variability in party size and composition, we observed members of the troop crossing an open area from a fixed point for 3 mo during the dry and wet seasons. We counted individuals and recorded changes in composition of both arriving and departing parties. Party size and composition were highly variable on both a daily and a seasonal basis; 45.9% of the arriving parties changed in composition while crossing the open area, either splitting into smaller parties or fusing into larger ones, suggesting a fluid organization. Our data support the existence of neither a hamadryas baboon-like multilayered social organization nor a stable medium-sized multimale multifemale group as in savannah baboons. In light of our data we may need to revise the dichotomic view of baboon social systems and include space for greater variability of their social systems.     

Mutation Profiling in Cholangiocarcinoma: Prognostic and Therapeutic Implications

Background

Cholangiocarcinoma (CCA) is clinically heterogeneous; intra and extrahepatic CCA have diverse clinical presentations. Next generation sequencing (NGS) technology may identify the genetic differences between these entities and identify molecular subgroups for targeted therapeutics.

Methods

We describe successful NGS-based testing of 75 CCA patients along with the prognostic and therapeutic implications of findings. Mutation profiling was performed using either a) NGS panel of hotspot regions in 46 cancer-related genes using a 318-chip on Ion PGM Sequencer or b) Illumina HiSeq 2000 sequencing platform for 3,769 exons of 236 cancer-related genes plus 47 introns from 19 genes to an average depth of 1000X. Clinical data was abstracted and correlated with clinical outcome. Patients with targetable mutations were referred to appropriate clinical trials.

Results

There were significant differences between intrahepatic (n = 55) and extrahepatic CCA (n = 20) in regard to the nature and frequency of the genetic aberrations (GAs). IDH1 and DNA repair gene alterations occurred more frequently in intrahepatic CCA, while ERBB2 GAs occurred in the extrahepatic group. Commonly occurring GAs in intrahepatic CCA were TP53 (35%), KRAS (24%), ARID1A (20%), IDH1 (18%), MCL1 (16%) and PBRM1 (11%). Most frequent GAs in extrahepatic CCA (n = 20) were TP53 (45%), KRAS (40%), ERBB2 (25%), SMAD4 (25%), FBXW7 (15%) and CDKN2A (15%). In intrahepatic CCA, KRAS, TP53 or MAPK/mTOR GAs were significantly associated with a worse prognosis while FGFR GAs correlated with a relatively indolent disease course. IDH1 GAs did not have any prognostic significance. GAs in the chromatin modulating genes, BAP1 and PBRM1 were associated with bone metastases and worse survival in extrahepatic CCA. Radiologic responses and clinical benefit was noted with EGFR, FGFR, C-met, B-RAF and MEK inhibitors.

Conclusion

There are significant genetic differences between intra and extrahepatic CCA. NGS can potentially identify disease subsets with distinct prognostic and therapeutic implications.     

Life history traits and parental care in Lepilemur ruficaudatus

In this study we investigated the importance of biparental care for the evolution and/or maintenance of pair-living in red-tailed sportive lemurs (Lepilemur ruficaudatus), a nocturnal folivorous lemur. Between 2000 and 2005, we collected data on life history traits from a total of 14 radio-collared pairs of adults and their offspring in Kirindy forest, western Madagascar. Predation rate varied between years with a minimum of 0% and a maximum of 40% per year. Patterns of parental care were quantified during simultaneous focal observations of both pair-partners in 2003 and 2004. Mating activity was limited to the months of May and June, as indicated by conspicuous changes of vulval morphology and male mate guarding behavior. After a gestation length of about 5 months, which is much longer than expected for a lemur of this body mass, single infants were born in November. Lactation lasted for about 50 days. Apart from lactation, females provided infant care by warming, grooming and transporting infants orally. Infants were parked in dense vegetation while females foraged. Males were seen only rarely in proximity to infants and we found no evidence for direct infant care provided by social fathers. We conclude that the necessity of direct infant care cannot explain the evolution and/or maintenance of pair-living in Lepilemur ruficaudatus.     

Do leucocytes reflect condition in nestling burrowing parrots Cyanoliseus patagonus in the wild?

The different leucocyte types are an important part of the immune system. Thus, they have been used in ecological studies to assess immune function and physiological stress in wild birds. It is generally assumed that increased stress and decreased condition are associated with an increase in the ratio of heterophils to lymphocytes, the H/L ratio. We studied leucocyte profiles in relation to body condition in nestling Burrowing Parrots (Cyanoliseus patagonus) in North-eastern Patagonia, Argentina. As in other wild parrots, heterophils were the most numerous leucocyte type, suggesting strong investment into innate immunity. Leucocyte profiles did not change with the age, while nestlings in better body condition increased the number of heterophils. Because the number of lymphocytes was independent of body condition, as a result we observed a positive correlation between body condition and the H/L ratio. The total number of leucocytes relative to erythrocytes increased in nestlings in better body condition, indicating a larger overall investment into immune function in well-nourished nestlings. The observed heterophilic profiles of nestling Burrowing Parrots together with the positive relationship between H/L ratio and body condition may indicate a favoured investment in a robust innate immunity that reduces the risk of infection taking hold in these long-lived birds.     

Chloroplast DNA variation in the shrub Justicia areysiana (Acanthaceae) endemic to the monsoon affected coastal mountains of the southern Arabian Peninsula

The monsoon affected mountains of the southern Arabian Peninsula harbour in climatically favoured refugia vegetation elements of palaeo-African origin. To understand better the temporal and spatial differentiation of these refugia, chloroplast variation in Justicia areysiana Deflers (Acanthaceae), a shrub species endemic to the Yemeni and Omani mountains close to the Arabian Sea, was studied using PCR-RFLP and chloroplast microsatellite diversity. Eleven haplotypes were characterized and show a distinct geographical distribution pattern with a deep split between populations from south Yemeni fog oases and those from Hawf Mountains/Dhofar region in east Yemen and south Oman. Very limited haplotype diversity within populations (h_S = 0.15) and a high level of population differentiation (G_ST = 0.81) demonstrate the strong genetic isolation of populations from each other. Past oscillations between humid and arid periods connected with glacial and interglacial episodes in the Pleistocene and Holocene are considered responsible for the observed patterns of genetic variation.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 437–444.     

Social Organization of Lepilemur ruficaudatus

We characterize the spatial organization of red-tailed sportive lemurs (Lepilemur ruficaudatus) as a key aspect of their social organization and social system. Sportive lemurs are small (<1000 g), nocturnal and folivorous primates endemic to Madagascar. We studied a population of 57 individually-marked individuals in Kirindy Forest, western Madagascar, between 1995 and 2001. We radio-tracked 20 males and 26 females of the marked population to obtain detailed information on the size and location of their home ranges. Census data and morphometric measurements provided complementary data sets. Males and females occupied small (<1 ha) home-ranges. Long-term records from 9 individuals revealed home-range stability over several years. In 4 cases home ranges overlapped extensively with that of one member of the opposite sex; in 2 cases, a spatial association of 1 male and 2 females occurred. However, home ranges overlapped very little with neighboring individuals of both sexes. During the study period, spatially associated individuals used on average 5.6 sleeping trees within 117 days, but they spent on average only about every fourth night together. The data suggest that home ranges in red-tailed sportive lemurs are exclusively used by pairs or trios and that the modal social organization of red-tailed sportive lemurs is pair-living.