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Supplementary Text 1. Calibrations Used in Divergence Time Estimation in BEAST2

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Supplementary Text 1. Calibrations used in divergence time estimation in BEAST2. 1. Boreoeutheria (The crown group of all taxa, using Cavia porcellus as outgroup) Type: A secondary Calibration. Calibration: Uniform Distribution, 83-107 million years (Ma) Discussion. The common ancestor of Euarchontoglires and Laurasiatheria. Fossil record of the crown Placentalia is not very informative and could only calibrate the K/Pg boundary (61.7 Ma ± 0.1 Ma). We calibrated it based on the divergence time estimated in (Meredith, et al. 2011). The time estimated in (Meredith, et al. 2011) was 92.0 (82.9–107.6) Ma. 2. Laurasiatheria Type: A secondary Calibration. Calibration: Normal distribution. Mean: 85.75, sigma 4.4 Ma, so the 95%CI is 78.5-93 Ma. Discussion: Fossil record of the crown Laurasiatheria is not very informative and could only calibrate the K/Pg boundary (61.6 Ma). We calibrated it based on (Meredith, et al. 2011), which was at 84.6 (78.5–93.0) Ma. 3. Eulipotyphla (The crown group of Erinaceidae + Soricidae + Talpidae + Solenodontidae) Type: A secondary Calibration. Calibration: A normal distribution was used for this calibration with a mean of 78.3 Ma and a sigma of 4.6 Ma, and the 95%CI is 70.7-85.9 Ma. Discussion. Based on the results of (Meredith, et al. 2011), the 95% confidence intervals of Eulipotyphla are 70.7 to 85.8 Ma. 4. Most common recent ancestor (MCRA) of Soricidae + Erinaceidae + Talpidae Type: A secondary Calibration. Calibration: A normal distribution was used for this calibration with a mean of 75.76 Ma and sigma of 5.5 Ma, and the 95%CI is 66.7-84.8 Ma. Discussion. Based on the results of (Meredith, et al. 2011), the 95% confidence intervals are 66.7 to 84.8 Ma for this clade. 5. Stem Talpini Type: A fossil-based Calibration. Fossil Taxon and Specimen. Geotrypus minor (SMNS 47462; A1) from Ehrenstein 12, a fissure filling in a quarry in Ehrenstein, a sub-municipality of the city Blaustein near Ulm (Ziegler 2012). Minimum Age. 33.9 Ma (İslamoğlu, et al. 2010). All samples correlate with the Early Oligocene standard levels of Soumailles (MP 21) and Villebramar (MP 22) (Ziegler 2012). Calibration: An exponential distribution was used for this calibration with offset of 33.9 Ma and mean of 11.3 Ma (median=41.73 Ma, 95%CI=34.48 to 67.75 Ma). Discussion. Geotrypus minor is the oldest record of the genus and the smallest species of Geotrypus (Ziegler 2012). The genus was initially included in Scaptonychini, but later referred to Talpini (Ziegler 1990; van den Hoek Ostende 2001) because of their robust humeri. However, the overall shape of the humerus of G. minor is more similar to a shrew mole than to a true mole. It is more appropriate to place it on the stem rather than the crown of living Talpini. There is no reliable upper boundary for calibration, so we follow (Heath 2012), in which suggested “in the absence of prior knowledge of the true node to fossil age differences, it is advisable to assign a vague prior distribution to calibrated node ages”, i.e. to use exponential distribution with a mean value of: fossil age * 0.333. #note: this calibration is the same as calibration “10 Stem Talpini” in the Supplementary Text S4 in (He, et al. 2017). 6. MCRA of Soricidae Type: A secondary Calibration. Calibration: A normal distribution. We set the mean to 36 Ma, with standard deviation to 0.135 Ma, so that the median of prior is 35.7 Ma and 95% CI is 28.6-44.5 Ma. Discussion: We applied a second calibration following (Springer, et al. 2018), which focused on the divergence times of eulipotyphlans and estimated that the divergence between Crocidurinae and Soricinae occurred 36 million years ago (Ma) [95% confidence interval (CI) = 28.6-44.0 Ma]. This time is much older than a fossil calibration used in previous studies (Dubey, et al. 2007; He, et al. 2010), which was based on the assumption that Crocidosoricinae was the ancestor of Crocidurinae, Myosoricinae, and Soricinae. Crocidosoricinae is now recognized as a tribe of Myosoricinae (Crocidosoricini), thereby invalidating that assumption (Furio, et al. 2007). Fossils of both crocidurines and soricines are known from the Oligocene (< 34 Ma), and the oldest soricid fossil, Soricolestes soricavus is from Middle Eocene strata, Khaychin Formation (Lopatin 2002). Thus, the estimated divergence time in (Springer, et al. 2018) is congruent with fossil records. 7. MCRA of Anourosoricini and Nectogalini Type: A fossil-based Calibration. Fossil Taxon and Specimen. Darocasorex vandermeuleni (Naturalis, Leiden: 558887: left M1;558857: right m2; 558855: left m3) from Calatayud-Daroca Basin, east Central Spain. Level at transition local biozone G to H (MN 7/8 to 9), ∼11.5 Ma (van Dam 2010). Minimum Age. 12 Ma (van Dam 2010). Calibration. An exponential distribution for the prior of this calibration with offset of 12 Ma and a mean of 4 Ma (median=14.8 Ma, 95%CI=12.2-24.0 Ma). Discussion. Anourosoricini is a fossil rich group. In the Late Miocene at about 12-10 Ma, Darocasorex and Crusafontina (Anourosoricini) already existed (van Dam 2010). The oldest fossil of Nectogalini represented by Asoriculus (Nectogalini) from Europe at about MN10 (=8.7-9.7 Ma)(Fejfar and Sabol 2005; Rzebik-Kowalska and Lungu 2009). Thus, it is convincing that Anourosoricini diverged from Nectogalini and Notiosoricini more than 12 million years ago. We set the lower boundary to 12 million years ago. There is no reliable upper boundary for calibration, so we used exponential distribution with a mean value of: fossil age * 0.333. References Dubey S, Salamin N, Ohdachi SD, Barrière P, Vogel P. 2007. Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations. Molecular Phylogenetics and Evolution 44:126-137. Fejfar O, Sabol M. 2005. The Fossil Record of the Eurasian Neogene Insectivores (Erinaceomorpha, Soricomorpha, Mammalia), Part I.]: Czech Republic and Slovak Republic. Scripta Geologica. Special Issue 5:51-60. Furio M, Santos-Cubedo A, Minwer-Barakat R, Agusti J. 2007. Evolutionary history of the African soricid Myosorex (Insectivora : Mammalia) out of Africa. Journal of Vertebrate Paleontology 27:1018-1032. He K, Li YJ, Brandley MC, Lin LK, Wang YX, Zhang YP, Jiang XL. 2010. A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution. Molecular Phylogenetics and Evolution 56:734-746. He K, Shinohara A, Helgen KM, Springer MS, Jiang X-L, Campbell KL. 2017. Talpid Mole Phylogeny Unites Shrew Moles and Illuminates Overlooked Cryptic Species Diversity. Molecular Biology and Evolution 34:78-87. Heath TA. 2012. A hierarchical Bayesian model for calibrating estimates of species divergence times. Systematic Biology 61:793-809. İslamoğlu Y, Harzhauser M, Gross M, Jiménez-Moreno G, Coric S, Kroh A, Rögl F, van der Made J. 2010. From Tethys to Eastern Paratethys: Oligocene depositional environments, paleoecology and paleobiogeography of the Thrace Basin (NW Turkey). International Journal of Earth Sciences 99:183-200. Lopatin AV. 2002. The earliest shrew (Soricidae, Mammalia) from the Middle Eocene of Mongolia. Paleontologicheskii Zhurnal 6:78-87. Meredith RW, Janecka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simao TL, Stadler T, et al. 2011. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334:521-524. Rzebik-Kowalska B, Lungu A. 2009. Insectivore mammals from the Late Miocene of the Republic of Moldova. Acta Zoologica Cracoviensia-Series A: Vertebrata 52:11-60. Springer MS, Murphy WJ, Roca AL. 2018. Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Molecular Phylogenetics and Evolution 121:158-165. van Dam JA. 2010. The systematic position of Anourosoricini (Soricidae, Mammalia): paleontological and molecular evidence. Journal of Vertebrate Paleontology 30:1221-1228. van den Hoek Ostende LW. 2001. Insectivore faunas from the Lower Miocene of Anatolia-Part 8: Stratigraphy, palaeoecology, palaeobiogeography. Scripta Geologica 122:101-122. Ziegler R. 2012. Moles (Talpidae, Mammalia) from Early Oligocene karstic fissure fillings in South Germany. Geobios 45:501-513. Ziegler R. 1990. Talpidae (Insectivora, Mammalia) aus dem Oberoligozan und Untermiozan Suddeutschlands. Stuttgarter Beitraege zur Naturkunde Serie B (Geologie und Palaeontologie) 167:1-81. .
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  • Text Mining in R Salvador Mandujano 25

    Text Mining in R Salvador Mandujano 25

    www.mastozoologiamexicana.org La Portada La musaraña de Los Tuxtlas, Cryptotis nelsoni, es una de las especies de mamíferos más amenazadas en México. Esta imagen no solo simboliza uno de las características peculiares de las musarañas, el hocico pronunciado, sino lo muy poco que aun conocemos acerca de este grupo de pequeños mamíferos (Fotografía de Lázaro Guevara) Nuestro logo “Ozomatli” El nombre de “Ozomatli” proviene del náhuatl se refiere al símbolo astrológico del mono en el calendario azteca, así como al dios de la danza y del fuego. Se relaciona con la alegría, la danza, el canto, las habilidades. Al signo decimoprimero en la cosmogonía mexica. “Ozomatli” es una representación pictórica de los mono arañas (Ateles geoffroyi). La especie de primate de más amplia distribución en México. “ Es habitante de los bosques, sobre todo de los que están por donde sale el sol en Anáhuac. Tiene el dorso pequeño, es barrigudo y su cola, que a veces se enrosca, es larga. Sus manos y sus pies parecen de hombre; también sus uñas. Los Ozomatin gritan y silban y hacen visajes a la gente. Arrojan piedras y palos. Su cara es casi como la de una persona, pero tienen mucho pelo.” THERYA Volumen 10, número 1 enero 2019 EDITORIAL Las musarañas son importantes Lázaro Guevara 1 ARTICLES Differentiation pattern in the use of space by males and females of two species of small mammals (Peromyscus difficilis and P. melanotis) in a temperate forest Contenido Ivan Mijail De-la-Cruz, Alondra Castro-Campillo, Alejandro Zavala-Hurtado, Arturo Salame-Méndez and José Ramírez-Pulido 3 Spatial distribution of bat richness in Mexico at different taxonomic levels: biogeographical and conservation implications Kinberly Montserrat Barrios-Gómez, Ricardo López-Wilchis, Jhoana Díaz-Larrea and Luis Manuel Guevara-Chumacero 11 Analysis and trends of photo-trapping in Mexico: text mining in R Salvador Mandujano 25 Epizoic Arthropods of the Mexican Shrew, Sorex oreopolus (Mammalia: Soricidae) Griselda Montiel-Parra, Ana Lilia Carlos-Delgado, Ricardo Paredes-León and Tila M.