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The majority of the parasite assessments of New World primates have been conducted through the identification of the eggs found in faeces, though many species of parasites have very similar eggs, leaving uncertainty in the diagnosis. Here, we present the results of a parasite survey of the three species of primates distributed in Mexico, combining non-invasive sampling with molecular techniques via DNA extraction of the eggs found in the faeces. Mitochondrial and ribosomal DNA were employed for species identification and Bayesian phylogenetic analysis. Nine parasite taxa were found in the three primate species: the nematodes Trypanoxyuris minutus, T. multilabiatus, T. pigrae, T. atelis, T. atelophora, Strongyloides sp., unidentified Ancylostomatid, unidentified Ascarid, and the trematode Controrchis biliophilus. We were able to extract and amplify DNA from the eggs of the five species of Trypanoxyuris reported for Mexican primates, two morphologically different trematode eggs, and Strongyloides sp. Phylogenetic analysis confirmed that the two types of trematode eggs belong to Controrchis biliophilus, a member of the family Dicrocoeliidae. For Strongyloides sp., phylogenetic analysis and genetic divergence showed an association between our samples and S. fuelleborni; however, no species could be established due to the lack of more DNA sequences from Strongyloides sp. occurring in Neotropical primates. The use of molecular and phylogenetic methods could help to overcome the limitations imposed by traditional non-invasive sampling because eggs are primarily obtained from the faeces; however, its utility relies on the extant genetic library and the contributions that expand such library. The information presented here could serve as a basis for future research on primate parasitology, allowing a more accurate parasite diagnosis and a more precise evaluation of their zoonotic potential.

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The current unprecedented rates of environmental perturbation, particularly in rain forest ecosystems, are jeopardizing the persistence of a variety of tropical species.The development of adequate conservation programs requires incorporating the evolutionary history and population genetic information of species, especially in those threatened by habitat loss and fragmentation. Mexican mantled howler monkeys (Alouatta palliata mexicana) represent the northernmost distribution of primates in America, a Critically Endangered species mainly inhabiting forest remnants. We assessed historical and contemporary patterns of genetic variation in A. p. mexicana populations from five regions across its geographic distribution in Mexico. We employed non-invasive sampling techniques and evaluated microsatellite loci and mitochondrial cytochrome b sequences from 127 individuals from 15 wild and two semi-captive populations. Our data demonstrate negative genetic effects on A. p. mexicana as a result of isolation, fragmentation, and small effective population size.Results revealed two mitochondrial lineages and three genetically differentiated nuclear clusters, along with reduced nuclear genetic diversity, limited gene flow, and significant inbreeding, associated with concurrent processes of historical dispersion and contemporary landscape changes. Accordingly, we argue that A. palliata mexicana in Mexico is an independently evolving unit that meets the criteria for being assigned as an Evolutionarily Significant Unit, crucial for the preservation of the howler monkeys' phylogenetic and functional diversity. The three genetic clusters identified are essential for the maintenance of the adaptive diversity and long-term survival of this howler subspecies. Our genetic approach and conservation recommendations may be useful for other endangered primates inhabiting fragmented populations.

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