Predicting future climate change impacts on the potential distribution of the black howler monkey (Alouatta pigra): an endangered arboreal primate.

Climate change is one of the main factors affecting biodiversity worldwide at an alarming rate. In addition to increases in global extreme weather events, melting of polar ice caps, and subsequent sea level rise, climate change might shift the geographic distribution of species. In recent years, interest in understanding the effects of climate change on species distribution has increased, including species which depend greatly on forest cover for survival, such as strictly arboreal primates. Here, we generate a series of species distribution models (SDMs) to evaluate future projections under different climate change scenarios on the distribution of the black howler monkey (Alouatta pigra), an endemic endangered primate species. Using SDMs, we assessed current and future projections of their potential distribution for three Social Economic Paths (SSPs) for the years 2030, 2050, 2070, and 2090. Specifically, we found that precipitation seasonality (BIO15, 30.8%), isothermality (BIO3, 25.4%), and mean diurnal range (BIO2, 19.7.%) are the main factors affecting A. pigra distribution. The future climate change models suggested a decrease in the potential distribution of A. pigra by projected scenarios (from - 1.23 to - 12.66%). The highly suitable area was the most affected above all in the more pessimist scenario most likely related to habitat fragmentation. Our study provides new insights into the potential future distribution and suitable habitats of Alouatta pigra. Such information could be used by local communities, governments, and non-governmental organizations for conservation planning of this primate species.

The complete chloroplast genome sequence of Psittacanthus schiedeanus (Cham. & Schltdl.) G.Don. (Santalales: Loranthaceae), the first plastome of a mistletoe species in the Psittacantheae tribe.

Psittacanthus schiedeanus (Cham. & Schltdl.) G.Don., 1834, is a mistletoe species in the Loranthaceae, characteristic of the canopy in cloud forest edges and widely distributed in northern Mesoamerica. Here, we report the complete chloroplast genome sequence of P. schiedeanus, the first for a species in the Psittacantheae tribe. The circularized quadripartite structure of the P. schiedeanus chloroplast genome was 122,586 bp in length and included a large single-copy region of 72,507 bp and two inverted repeats of 21,283 bp separated by a small single-copy region of 7,513 bp. The genome contained 112 genes, of which 96 are unique, including 65 protein-coding genes, 27 transfer RNA, and four ribosomal RNA. The overall GC content in the plastome of P. schiedeanus is 36.9%. Based on 43 published complete chloroplast genome sequences for species in the families Loranthaceae and Santalaceae (Santalales), the maximum-likelihood phylogenetic tree with high-support bootstrap values indicated that P. schiedeanus in the Psittacantheae tribe is sister to the tribe Lorantheae. The chloroplast genome provided in this study represents a valuable resource for genetic, phylogenetic and conservation studies of Psittacanthus species, and an important advance for unraveling the evolutionary history of these hemiparasitic plants.

Transcriptional Basis for Haustorium Formation and Host Establishment in Hemiparasitic Psittacanthus schiedeanus Mistletoes.

The mistletoe Psittacanthus schiedeanus, a keystone species in interaction networks between plants, pollinators, and seed dispersers, infects a wide range of native and non-native tree species of commercial interest. Here, using RNA-seq methodology we assembled the whole circularized quadripartite structure of P. schiedeanus chloroplast genome and described changes in the gene expression of the nuclear genomes across time of experimentally inoculated seeds. Of the 140,467 assembled and annotated uniGenes, 2,000 were identified as differentially expressed (DEGs) and were classified in six distinct clusters according to their expression profiles. DEGs were also classified in enriched functional categories related to synthesis, signaling, homoeostasis, and response to auxin and jasmonic acid. Since many orthologs are involved in lateral or adventitious root formation in other plant species, we propose that in P. schiedeanus (and perhaps in other rootless mistletoe species), these genes participate in haustorium formation by complex regulatory networks here described. Lastly, and according to the structural similarities of P. schiedeanus enzymes with those that are involved in host cell wall degradation in fungi, we suggest that a similar enzymatic arsenal is secreted extracellularly and used by mistletoes species to easily parasitize and break through tissues of the host.

Phylogeography and population differentiation in Hepatozoon canis (Apicomplexa: Hepatozoidae) reveal expansion and gene flow in world populations.

BACKGROUND: Hepatozoon canis is a protozoan transmitted to dogs and other wild carnivores by the ingestion of ticks containing mature oocysts and is considered the principal cause of canine hepatozoonosis in the world. Here, we examined ribosomal RNA 18S gene sequence variation to determine the genetic differences and phylogeographic diversity of H. canis from various geographical areas around the world. METHODS: We used 550 publicly available sequences of H. canis from 46 countries to assess haplotype relationships, geographical structure, genetic diversity indices, and relationships among populations. We performed neutrality tests and pairwise comparisons of fixation index (FST) values between groups and pairwise comparisons of FST values between populations. To determine whether populations are structured, analyses of molecular variance (AMOVAs) and spatial analysis of molecular variance (SAMOVA) were performed. RESULTS: The dataset of H. canis yielded 76 haplotypes. Differentiation among populations indicated that there is no phylogeographical structure (GST = 0.302 ± 0.0475). Moreover, when samples were grouped by continents a significant FST was obtained, meaning that populations were genetically differentiated. The AMOVA showed that 57.4% of the genetic variation was explained by differences within populations when all locations were treated as a single group and revealed that there is no population structure when populations are grouped into two, three, and four groups (FCT, p > 0.05), suggesting that dispersal between populations is high. SAMOVA revealed significant FCT values for groups K = 5. The Tajima's D and Fu's Fs show that populations have undergone recent expansion, and the mismatch distribution analysis showed population expansion (multimodal distribution). CONCLUSIONS: The current molecular data confirmed that H. canis does not show phylogeographic or population structure. The haplotypes exhibit low genetic differentiation, suggesting a recent expansion due to gene flow among populations. These results provide pivotal information required for future detailed population genetic analysis or to establish control strategies of this parasite.

Detection of Antimicrobial Resistance Genes in Escherichia coli Isolated from Black Howler Monkeys (Alouatta pigra) and Domestic Animals in Fragmented Rain-Forest Areas in Tabasco, Mexico.

The appearance and spread of antimicrobial resistance (AMR) in bacteria in natural environments and wildlife are related to agricultural and livestock activities and are a global health and conservation problem. We assessed the presence of AMR genes in Escherichia coli isolated from black howler monkeys (Alouatta pigra), sheep (Ovis aries), cattle (Bos taurus), and horses (Equus caballus) from a highly fragmented forest in southern Mexico. Fresh fecal samples were collected using swabs, seeded on eosin-methylene blue agar, and E. coli colonies identified by PCR; multiplex-PCR was performed on E. coli DNA for the detection of 10 AMR genes from four families (sulfonamides, tetracycline, ß-lactamase, and chloramphenicol). We detected E. coli in 94% (48/51) of fecal samples, of which 33% (16/48) tested positive for at least one AMR gene. We detected AMR genes in at least one individual from each sampled animal species, with the most prevalent genes being tet(B) 18% (9/48), sul2 14% (7/48), sul1, and blaTEM 12% (6/48). Sheep samples contained AMR genes from the four families of antibiotics detected in this study and 50% (5/10) tested positive for the presence of at least one gene. A total of 12% (2/16) of fecal samples from black howler monkeys tested positive for AMR genes. The presence of AMR genes in A. pigra and domestic animals has not been reported in the Balancán area of Tabasco, Mexico. Transmission of AMR bacteria from domestic animals to monkeys is rare; however, this is a potential health risk for wildlife and species conservation.

West Nile Virus Prevalence in Wild Birds from Mexico.

West Nile virus (WNV) emerged in the Americas with its introduction in 1999 and now is considered endemic across the continent. In 2002, WNV was detected in Mexico, where its occurrence and mortality are considerably lower compared with the US. However, continuous national surveillance programs in Mexico are nonexistent. Birds are considered the primary hosts and primary geographic dispersers of this pathogen. A total of 200 cloacal and tracheal samples from wild migratory or resident birds were retrospectively analyzed using reverse transcription PCR to detect WNV from birds collected in Mexico from 2008 to 2009. The overall prevalence was 8% (16/200), and positive samples were from Oaxaca, Chiapas, and Tamaulipas in Ruby-throated Hummingbird ( Archilochus colubris), Double-crested Cormorant ( Phalacrocorax auritus), Ring-billed Gull ( Larus delawarensis), and Mourning Dove ( Zenaida macroura). Analysis of the partial sequence of the envelope gene from one of the samples from Oaxaca provided evidence that the virus belonged to the WN99 genotype. Taken together, these results demonstrated that WNV circulated in wild birds from northern and southern Mexico during the 2008-09 season, providing further information about the presence of WNV in Mexico.

Tracking Host Trees: The Phylogeography of Endemic Psittacanthus sonorae (Loranthaceae) Mistletoe in the Sonoran Desert.

The host dependence of mistletoes suggests that they track the distributions of their hosts. However, the factors that determine the geographic distribution of mistletoes are not well understood. In this study, the phylogeography of Psittacanthus sonorae was reconstructed by sequencing one nuclear (ITS) and two plastid (trnL-F and atpB-rbcL) regions of 148 plants from populations separated by the Sea of Cortez. Divergence time and gene flow were estimated to gain insight into the historical demography and geographic structuring of genetic variation. We also described and mapped the spatial distribution of suitable habitat occupied by P. sonorae and its most common host Bursera microphylla in the Sonoran Desert, along with their responses to Quaternary climate fluctuations using environmental data and ecological niche modeling (ENM). We detected environmental and genetic differentiation between the peninsular and continental P. sonorae populations. Population divergence occurred during the Pleistocene, around the time of the Last Glacial Maximum. No signals of population growth were detected, with net gene flow moving from the continent to the peninsula. ENM models indicate decoupled responses by the mistletoe and its main host to past climate changes. For the Last Interglacial to the present, most models produce only partial areas of overlap on both the peninsula and the continent. Our results support a scenario of Late-Pleistocene isolation and divergence with asymmetrical gene flow between peninsular and continental P. sonorae populations. Continental populations migrated to the peninsula and the spatial isolation probably produced genetic differentiation under different environmental conditions.

Molecular detection of Bifidobacterium spp. in faeces of black howler monkeys (Alouatta pigra).

BACKGROUND: Bifidobacterium genus are considered to be beneficial bacteria for their hosts; however, knowledge about the specific species that are part of the gut microbiome of howler monkeys is scarce. Polymerase chain reaction (PCR) is a useful technique for the identification of non-cultivable or difficult to grow bacterial species. With the goal of detecting species of the genus Bifidobacterium in black howler monkeys, we used PCR on DNA derived from faecal samples. METHODS: We collected and extracted DNA from 40 faecal samples. Using specific primers, we performed PCR and nested PCR to detect members of the Bifidobacterium genus and a subset of species: Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium longum and Bifidobacterium animalis subsp. animalis. RESULTS: 97.5% (39/40) of the samples were positive for Bifidobacterium spp. We found B longum in 100% of the analysed samples. CONCLUSIONS: This is the first report of B longum in black howler monkey faeces.

A mistletoe tale: postglacial invasion of Psittacanthus schiedeanus (Loranthaceae) to Mesoamerican cloud forests revealed by molecular data and species distribution modeling.

BACKGROUND: Ecological adaptation to host taxa is thought to result in mistletoe speciation via race formation. However, historical and ecological factors could also contribute to explain genetic structuring particularly when mistletoe host races are distributed allopatrically. Using sequence data from nuclear (ITS) and chloroplast (trnL-F) DNA, we investigate the genetic differentiation of 31 Psittacanthus schiedeanus (Loranthaceae) populations across the Mesoamerican species range. We conducted phylogenetic, population and spatial genetic analyses on 274 individuals of P. schiedeanus to gain insight of the evolutionary history of these populations. Species distribution modeling, isolation with migration and Bayesian inference methods were used to infer the evolutionary transition of mistletoe invasion, in which evolutionary scenarios were compared through posterior probabilities. RESULTS: Our analyses revealed shallow levels of population structure with three genetic groups present across the sample area. Nine haplotypes were identified after sequencing the trnL-F intergenic spacer. These haplotypes showed phylogeographic structure, with three groups with restricted gene flow corresponding to the distribution of individuals/populations separated by habitat (cloud forest localities from San Luis Potosí to northwestern Oaxaca and Chiapas, localities with xeric vegetation in central Oaxaca, and localities with tropical deciduous forests in Chiapas), with post-glacial population expansions and potentially corresponding to post-glacial invasion types. Similarly, 44 ITS ribotypes suggest phylogeographic structure, despite the fact that most frequent ribotypes are widespread indicating effective nuclear gene flow via pollen. Gene flow estimates, a significant genetic signal of demographic expansion, and range shifts under past climatic conditions predicted by species distribution modeling suggest post-glacial invasion of P. schiedeanus mistletoes to cloud forests. However, Approximate Bayesian Computation (ABC) analyses strongly supported a scenario of simultaneous divergence among the three groups isolated recently. CONCLUSIONS: Our results provide support for the predominant role of isolation and environmental factors in driving genetic differentiation of Mesoamerican parrot-flower mistletoes. The ABC results are consistent with a scenario of post-glacial mistletoe invasion, independent of host identity, and that habitat types recently isolated P. schiedeanus populations, accumulating slight phenotypic differences among genetic groups due to recent migration across habitats. Under this scenario, climatic fluctuations throughout the Pleistocene would have altered the distribution of suitable habitat for mistletoes throughout Mesoamerica leading to variation in population continuity and isolation. Our findings add to an understanding of the role of recent isolation and colonization in shaping cloud forest communities in the region.

First molecular evidence of Hepatozoon canis in domestic dogs and ticks in fragmented rainforest areas in Mexico.

The tick-borne pathogens of the genus Hepatozoon affect domestic animals and wildlife; their prevalence has risen around the world in the past years. In Mexico there is not enough data available about their surveillance. This study aimed to detect the prevalence of Hepatozoon by PCR in domestic animals and ticks from a fragmented rainforest area from southeast Mexico and analyze the phylogeographic structure of the parasites detected. The total prevalence of H. canis in mammals was 9.7% (20/206; 95% Confidence limits: 6.0-14.6%), being dogs the species with the highest prevalence, of 63.3% (19/30; 95% Confidence limits: 43.9-80.1%). The phylogenetic analysis revealed that sequences from this study were closer to the sequence of H. canis of domestic origin, rather than from wild origin, but in an independent cluster. Haplotypes from our study were geographically restricted to Mexico and the closest haplotype was from Brazil. Ticks that resulted positive by PCR were identified as Amblyomma cajennense (A. mixtus) and Rhipicephalus turanicus. Under fragmented and disturbed conditions of habitat in Balancan, the presence of H. canis may represent a potential risk for other species of domestic and wildlife animals. To the knowledge of the authors, this study represents the first molecular finding of H. canis in Mexico in both domestic animals and ticks. This research lays the groundwork for further studies in order to elucidate the relationships between domestic hosts, wildlife and ticks and describe the life cycle of this parasite in the area.