Molecular phylogenetic inference of the howler monkey radiation (Primates: Alouatta)

Doyle, Esmeralda D.; Prates, Ivan; Sampaio, Iracilda; Koiffmann, Célia Priszkulnik; Silva, Wilson A.; Carnaval, Ana Carolina; Harris, Eugene E.

doi:10.1007/s10329-020-00854-x

Cited by 9 publications

(4 citation statements)

References 57 publications

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“…While in animals, inside the genus Sturnira Gray (Chiroptera) the S. parvidens lineage from tropical areas of Mexico to northern Costa Rica is closely related to their South American sisters (Hernández-Canchola and León-Paniagua 2017 ). Similarly, in the genus Alouatta Lacépède (Primates) a Mesoamerican clade is strongly supported, comprising A. paliatta and A. pigra (Doyle et al 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic and morphological analyses of Pilosocereus leucocephalus group s.s. (Cactaceae) reveal new taxonomical implications

et al. 2022

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Pilosocereus is one of the Cactaceae family’s most relevant genera in terms of the number of species and its wide geographical range in the Americas. Within Pilosocereus, five informal taxonomic groups have been recognized, one of which is P. leucocephalus group s.s., whose phylogenetic relationships remain unresolved. Therefore, our objectives are to recognize the circumscriptions of the species in P. leucocephalus group s.s. and to corroborate the monophyly and phylogenetic relationships of this group through a set of morphological and molecular characters. This study is based on representative sampling along the broad distribution of this group in Mexico and Central America using multivariate and phylogenetic analyses. The morphological characters identified to contribute to species recognition and group formation are branch diameter, areole length, the areole length-width ratio, the distance between areoles, the length of the longest radial spine, and branch and spines colors. The chloroplast markers rpl16, trnL-trnF, and petL-psbE and the nuclear marker AT1G18270 support the monophyly of the P. leucocephalus group s.s., and two probable synapomorphies are suggested, including one transversion in rpl16 and another in petL-psbE. Together, our results demonstrate that sampled species of P. leucocephalus group s.s. encompass six species distributed in Mexico and Central America: P. alensis and P. purpusii in the western region, P. chrysacanthus and P. collinsii in the central region, and P. gaumeri and P. leucocephalus in the eastern region. A taxonomic key to recognized species is provided.

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Section: Discussionmentioning

confidence: 99%

Phylogenetic and morphological analyses of Pilosocereus leucocephalus group s.s. (Cactaceae) reveal new taxonomical implications

et al. 2022

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“…This species is not found in Belize, but the related Alouatta pigra is common in our research area. The taxonomy of Alouatta is complex and has recently undergone revisions ( Doyle et al, 2021 ). It is not clear if any Alouatta pigra 16S references are contained in the Genbank nucleotide collection (the name does not exist in Genbank).…”

Section: Methodsmentioning

confidence: 99%

Out of thin air: surveying tropical bat roosts through air sampling of eDNA

Garrett

Watkins

Francis

et al. 2023

PeerJ

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Understanding roosting behaviour is essential to bat conservation and biomonitoring, often providing the most accurate methods of assessing bat population size and health. However, roosts can be challenging to survey, e.g., physically impossible to access or presenting risks for researchers. Disturbance during monitoring can also disrupt natural bat behaviour and present material risks to the population such as disrupting hibernation cycles. One solution to this is the use of non-invasive monitoring approaches. Environmental (e)DNA has proven especially effective at detecting rare and elusive species particularly in hard-to-reach locations. It has recently been demonstrated that eDNA from vertebrates is carried in air. When collected in semi-confined spaces, this airborne eDNA can provide remarkably accurate profiles of biodiversity, even in complex tropical communities. In this study, we deploy novel airborne eDNA collection for the first time in a natural setting and use this approach to survey difficult to access potential roosts in the neotropics. Using airborne eDNA, we confirmed the presence of bats in nine out of 12 roosts. The identified species matched previous records of roost use obtained from photographic and live capture methods, thus demonstrating the utility of this approach. We also detected the presence of the white-winged vampire bat (Diaemus youngi) which had never been confirmed in the area but was long suspected based on range maps. In addition to the bats, we detected several non-bat vertebrates, including the big-eared climbing rat (Ototylomys phyllotis), which has previously been observed in and around bat roosts in our study area. We also detected eDNA from other local species known to be in the vicinity. Using airborne eDNA to detect new roosts and monitor known populations, particularly when species turnover is rapid, could maximize efficiency for surveyors while minimizing disturbance to the animals. This study presents the first applied use of airborne eDNA collection for ecological analysis moving beyond proof of concept to demonstrate a clear utility for this technology in the wild.

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“…Even if the objective is not to verify the efficiency of the method, different studies have used the phenol-chloroform method to generate functional sequences. [73] analyzed hypervariable sequences for phylogeography study of Lutjanus analis and L. jocu, [74] produced multiplex PCR for the identification of the shark Isogomphodon oxyrhynchus, [75] evaluated the diversity of Neotropical anurans using DNA barcodes, [76] made the molecular phylogenetic inference of Primates Alouatta, and [77] identified the commercialization of the critically endangered species Pristis perotteti. However, despite these examples and the good acceptance by the scientific literature, the best concentration of extracted DNA does not always come from the phenol-chloroform method [69].…”

Section: Plos Onementioning

confidence: 99%

Quality analysis of genomic DNA and authentication of fisheries products based on distinct methods of DNA extraction

et al. 2023

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Molecular genetic techniques are an effective monitoring tool, but high-quality DNA samples are usually required. In this study, we compared three different protocols of DNA extraction: NaCl (saline); phenol-chloroform and commercial kit (Promega)—from three biological tissues of five individuals of Lutjanus purpureus under two methods of storage. The evaluated items included DNA concentration and purity, processing time and cost, as well as the obtaining of functional sequences. The highest average values of DNA concentration were obtained using the saline procedure and the commercial kit. Pure DNA was only obtained using the saline protocol, evaluated by the ratio of 260/280. The saline and phenol-chloroform protocols were the least expensive methods. The commercial kit costs are counterbalanced by the short time required. The procedure based on phenol-chloroform presented the worst results regarding DNA yield and the time required to perform all steps. The saline and commercial kit protocols showed similar results concerning the amount and quality of extracted DNA. Therefore, the final choice should be based on the available financial resources and the available time for carrying out each procedure of DNA extraction.

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Molecular phylogenetic inference of the howler monkey radiation (Primates: Alouatta)

Cited by 9 publications

References 57 publications

Phylogenetic and morphological analyses of Pilosocereus leucocephalus group s.s. (Cactaceae) reveal new taxonomical implications

Phylogenetic and morphological analyses of Pilosocereus leucocephalus group s.s. (Cactaceae) reveal new taxonomical implications

Out of thin air: surveying tropical bat roosts through air sampling of eDNA

Quality analysis of genomic DNA and authentication of fisheries products based on distinct methods of DNA extraction

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