Bonar et al. 2024 Proximate drivers of migration propensity: a meta-analysis across species

This code accompanies the paper "Proximate drivers of migration propensity: a meta-analysis across species" by Bonar et al. The purpose of this code is to generate meta-analyitical models that measure the effect of internal and external factors on propensity to migrate across species.Data files include raw data and calculated Cohen's d effect sizes</p

Caw Ridge, Alberta (Month) Feature ID (RSV) Matrix

Count matrix of the given feature IDs from the fecal microbiome of mountain goats at Caw Ridge, Alberta classified for each month across June, July, and August. Included are the feature ID, confidence of classification from QIIME2, taxon assignment, and sequence

Population and Origin Feature ID (RSV) Matrix

Count matrix of the given feature IDs from the fecal microbiome of mountain goats ranging from Alaska, USA to Alberta, Canada (four populations - three wild, one captive). Included are the feature ID, confidence of classification from QIIME2, taxon assignment, and sequence

Newick Rooted Tree File

Newick Rooted Tree File of the mountain goat fecal microbiom

The biogeography of Dromiciops in southern South America: Middle Miocene transgressions, speciation and associations with Nothofagus

The current distribution of the flora and fauna of southern South America is the result of drastic geological events that occurred during the last 20 million years, including marine transgressions, glaciations and active vulcanism. All these have been associated with fragmentation, isolation and subsequent expansion of the biota, south of 35°S, such as the temperate rainforest. This forest is mostly dominated by Nothofagus trees and is the habitat of the relict marsupial monito del monte, genus Dromiciops, sole survivor of the order Microbiotheria. Preliminary analyses using mtDNA proposed the existence of three main Dromiciops lineages, distributed latitudinally, whose divergence was initially attributed to recent Pleistocene glaciations. Using fossil-calibrated dating on nuclear and mitochondrial genes, here we reevaluate this hypothesis and report an older (Miocene) biogeographic history for the genus. We performed phylogenetic reconstructions using sequences from two mitochondrial DNA and four nuclear DNA genes in 159 specimens from 31 sites across Chile and Argentina. Our phylogenetic analysis resolved three main clades with discrete geographic distributions. The oldest and most differentiated clade corresponds to that of the northern distribution (35.2°S to 39.3°S), which should be considered a distinct species (D. bozinovici, sensu D'Elía et al. 2016). According to our estimations, this species shared a common ancestor with D. gliroides (southern clades) about ~13 million years ago. Divergence time estimates for the southern clades (39.6°S to 42.0°S) ranged from 9.57 to 6.5 Mya. A strong genetic structure was also detected within and between clades. Demographic analyses suggest population size stability for the northern clade (D. bozinovici), and recent demographic expansions for the central and southern clades. All together, our results suggest that the diversification of Dromiciops were initiated by the Middle Miocene transgression (MMT), the massive marine flooding that covered several lowlands of the western face of Los Andes between 37 and 48°S. The MMT resulted from an increase in global sea levels at the Miocene climatic optimum, which shaped the biogeographic origin of several species, including Nothofagus forests, the habitat of Dromiciops.Fil: Quintero Galvis, Julian F.. Universidad Austral de Chile; ChileFil: Saenz Agudelo, Pablo. Universidad Austral de Chile; ChileFil: Celis Diez, Juan L.. Pontificia Universidad Católica de Valparaíso; ChileFil: Amico, Guillermo Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Vazquez, Miriam Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Shafer, Aaron B.A.. Trent University; CanadáFil: Nespolo, Roberto F.. Universidad Austral de Chile; Chile. Pontificia Universidad Católica de Chile; Chil

DNA methylation networks underlying mammalian traits

Using DNA methylation profiles ( n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species