The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing

Background The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains scarce. Complicating factors include limitations on sample collection and a lack of high-quality reference sequences. Here, we used nanopore adaptive sampling to resequence the L. rosalia mitogenome from feces, a sample which can be collected non-invasively. Results Adaptive sampling doubled the fraction of both host-derived and mitochondrial sequences compared to sequencing without enrichment. 258x coverage of the L. rosalia mitogenome was achieved in a single flow cell by targeting the unfinished genome of the distantly related emperor tamarin (Saguinus imperator) and the mitogenome of the closely related black lion tamarin (Leontopithecus chrysopygus). The L. rosalia mitogenome has a length of 16,597 bp, sharing 99.68% sequence identity with the L. chrysopygus mitogenome. A total of 38 SNPs between them were identified, with the majority being found in the non-coding D-loop region. DNA methylation and hydroxymethylation were directly detected using a neural network model applied to the raw signal from the MinION sequencer. In contrast to prior reports, DNA methylation was negligible in mitochondria in both CpG and non-CpG contexts. Surprisingly, a quarter of the 642 CpG sites exhibited DNA hydroxymethylation greater than 1% and 44 sites were above 5%, with concentration in the 3′ side of several coding regions. Conclusions Overall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.

The Mitochondrial Genome and Epigenome of the Golden Lion Tamarin from Fecal DNA using Nanopore Adaptive Sequencing

The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains scarce. Complicating factors include limitations on sample collection and a lack of high-quality reference sequences. Here, we used nanopore adaptive sampling to resequence the L. rosalia mitogenome from feces, a sample which can be collected non-invasively. Adaptive sampling doubled the fraction of both host-derived and mitochondrial sequences compared to sequencing without enrichment. 258x coverage of the L. rosalia mitogenome was achieved in a single flow cell by targeting the unfinished genome of the distantly related emperor tamarin (Saguinus imperator) and the mitogenome of the closely related black lion tamarin (Leontopithecus chrysopygus). The L. rosalia mitogenome has a length of 16,597 bp, sharing 99.68% sequence identity with the L. chrysopygus mitogenome. A total of 38 SNPs between them were identified, with the majority being found in the non-coding D-loop region. DNA methylation and hydroxymethylation were directly detected using a neural network model applied to the raw signal from the MinION sequencer. In contrast to prior reports, DNA methylation was negligible in mitochondria in both CpG and non-CpG contexts. Surprisingly, a quarter of the 642 CpG sites exhibited DNA hydroxymethylation greater than 1% and 44 sites were above 5%, with concentration in the 3’ side of several coding regions. Overall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.

Ecology of the Atlantic Forest

Extending along the southern coast of Brazil, into Argentina and Paraguay, the Atlantic Forest is a domain that once covered 150 Mha and includes many distinct forest subtypes and ecosystems. Its large latitudinal (29˚) and altitudinal (0–2,800 m above sea level) range, as well as complex topography in the region, has created microclimates within forest subtypes, which has led to biodiversity specifically adapted to narrow ecological ranges. The region is incredibly species-rich and is home to charismatic or economically important species such as the black and golden lion tamarin, the red-browned Amazon parrot, and the highly prized palm heart from Euterpe edulis. Through widespread human-driven change dating back to the arrival of European settlers in 1500, this realm has been extensively reduced, fragmented, and modified. Nowadays, this region is home to about 130 million people (60 percent of the Brazilian population) and is responsible for producing 70 percent of Brazil’s GDP, putting a strain on natural resources and providing challenges to conservation. Due to its high levels of endemic species coupled with a high threat of habitat loss and fragmentation, the Atlantic Forest has been identified as a “biodiversity hotspot.” Numerous studies have assessed the effects of habitat transformation on biodiversity and the consensus is that the majority of species are negatively affected. It is puzzling however that few species have actually gone extinct in the wild, even if some extinctions might have gone undetected. Extinctions do not immediately follow habitat change, there is often a time lag of many decades between habitat transformation and extinction. This may suggest that many species in the Atlantic Forest are “living deads,” as despite their presence the available habitat no longer supports their requirements. It also suggests that there is a window of opportunity to restoring the domain to avert extinctions before they are realized. Current research and policy actions are geared toward optimizing restoration and increasing the extent of native forest cover, bringing hope to the conservation of this unique domain.

Yellow fever in Brazil threatens successful recovery of endangered golden lion tamarins

The golden lion tamarin is an endangered primate endemic to Brazil’s Atlantic Forest. Centuries of deforestation reduced numbers to a few hundred individuals in isolated forest fragments 80 km from Rio de Janeiro city. Intensive conservation action including reintroduction of zoo-born tamarins into forest fragments 1984–2000, increased numbers to about 3,700 in 2014. Beginning in November 2016, southeastern Brazil experienced the most severe yellow fever epidemic/epizootic in the country in 80 years. In May 2018, we documented the first death of a golden lion tamarin due to yellow fever. We re-evaluated population sizes and compared them to results of a census completed in 2014. Tamarin numbers declined 32%, with ca. 2,516 individuals remaining in situ. Tamarin losses were significantly greater in forest fragments that were larger, had less forest edge and had better forest connectivity, factors that may favor the mosquito vectors of yellow fever. The future of golden lion tamarins depends on the extent of additional mortality, whether some tamarins survive the disease and acquire immunity, and the potential development of a vaccine to protect the species against yellow fever.

Spatial Response to Linear Infrastructures by the Endangered Golden Lion Tamarin

Linear infrastructures are a primary driver of economic development. However, they also can negatively affect wildlife by mortality and the barrier effect. In this paper, we address how paved and unpaved roads, high-tension power lines, and gas/oil pipelines affect home range size, core areas, and movement in an endangered primate, the golden lion tamarin (GLT). Location data were recorded using radio telemetry on 16 groups in two protected areas and in privately owned forest fragments. The GLT’s home range, not core area, increased in size for the groups that occupied locations far from linear infrastructures; home range was also significantly influenced by available forest size. None of the home ranges contained a road, but home ranges did contain power lines. GLTs used the surrounding landscape near all types of infrastructure. Movement analysis showed that most of the step lengths (distances between subsequent locations) were less than 100 m between two consecutive locations, but step length was longer for roads and longer for groups in fully forested habitats. Tamarins avoided paved roads when in close proximity to this type of infrastructure; this behavior increased in areas without adequate adjacent forest habitat. Our results show that linear infrastructures differ in their level of impact: roads can act as a barrier, whereas other types of infrastructure have minimal effect on movement and home range. We discuss these differences in impact in terms of structure, maintenance schedules, and edge effects of infrastructure.

Living and lost mammals of Rio de Janeiro's largest biological reserve: an updated species list of Tinguá

The Tinguá Biological Reserve (TBR) is the largest protected area of this category in Rio de Janeiro state. Here, for the first time, we present the historical composition of terrestrial mammals' assemblage of TBR region. An inventory was conducted using transect surveys, nonstandard transects, survey of museum specimens and informal reports. Considering all the data, eighty-five species were recorded, placing TBR as the second one in the number of mammals recorded in "Serra do Mar" ecoregion of Atlantic Forest and in the Rio de Janeiro state. Among the species with historical records are the jaguar (Panthera onca) and the golden-lion-tamarin (Leontopithecus rosalia) while the current presence of the maned wolf (Chrysocyon brachyurus) was recorded for the first time. Priority studies should focus on Chiroptera, Rodentia and Didelphimorphia orders, especially in the most remote areas of the reserve, and long-term surveys of endangered species. Besides hunting, fragmentation of its interior by roads, pipelines and transmission lines and exotic species, TBR is also threatened by the urban growth around it and the pressure to reduce its area and its protection category, demanding greater attention by the high levels of governance of protected areas in Brazil.