The Effect of Defoliation on Seed Production of Six Costa Rican Tree Species

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/119092/1/ecy19735461363.pd

Coyote colonization of northern Virginia and admixture with Great Lakes wolves

Ecological invasions of generalist species often are facilitated by anthropogenic disturbance. Coyotes (Canis latrans) have benefitted from anthropogenic changes to North American ecosystems and have experienced a dramatic range expansion since the early 19th century. The region east of the Mississippi River has been colonized via 2 routes that have converged in the mid-Atlantic region during the past few decades. Coyotes using the northern route of expansion show molecular evidence of admixture with the Great Lakes wolf (GLW). We used noninvasive molecular techniques to detect the geographic origins of the recent coyote colonization of northern Virginia as a representative of the mid-Atlantic region and to detect signatures of admixture with GLWs. Of 455 individual canid scats screened, we sequenced a variable 282-base pair fragment of the mitochondrial control region from 126 coyote scats, assigned individual identities to samples using 6 microsatellite loci, and conducted phylogeographic analyses by comparing our sequences to previously published haplotypes. In 39 individuals identified in our scat surveys we detected 7 mitochondrial DNA haplotypes, all of which have been previously reported in diverse surrounding geographic localities. Phylogeographic analyses indicate multiple sources of colonization of northern Virginia. One common haplotype detected in northern Virginia is of wolf origin, indicating the presence of admixed coyotes and GLWs from the north

157kUCEs

BEAST xml file for 362 UCE loci dataset

Mitogene_Tree_DCSPrior

Mitogenome BEAST xml file from this publication

Data from: Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

Background: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi’s three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. Results: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace’s line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. Conclusions: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species

Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys, Nannosciurinae)

The plain long-nosed squirrels, genus Dremomys, are high elevation species in East and Southeast Asia. Here we present a complete molecular phylogeny for the genus based on nuclear and mitochondrial DNA sequences. Concatenated mitochondrial and nuclear gene trees were constructed to determine the tree topology, and date the tree. All speciation events within the plain-long nosed squirrels (genus Dremomys) were ancient (dated to the Pliocene or Miocene), and averaged older than many speciation events in the related Sunda squirrels, genus Sundasciurus. Within the plain long-nosed squirrels, the most recent interspecific split occurred 2.9 million years ago, older than some splits within Sunda squirrels, which dated to the Pleistocene. Our results demonstrate that the plain long-nosed squirrels are not monophyletic. The single species with a distinct distribution, the Bornean mountain ground squirrel (Dremomys everetti), which is endemic to the high mountains of Borneo, is nested within the Sunda squirrels with high support. This species diverged from its sister taxa in the Sunda squirrels 6.62 million years ago, and other plain long-nosed squirrels over 11 million years ago. Our analyses of morphological traits in these related genera support the re-classification of the Bornean mountain ground squirrel, Dremomys everetti, to the genus Sundasciurus, which changes its name to Sundasciurus everetti. Past inclusion in the plain long-nosed squirrels (Dremomys) reflects convergent evolution between these high elevation species.Funding was provided by the Spanish Government (CGL2010-21524)

Longitudinal fecal hormone monitoring of adrenocortical function in zoo housed fishing cats (Prionailurus viverrinus) during institutional transfers and breeding introductions.

The ex situ population of fishing cats (Prionailurus viverrinus) has become increasingly important for the conservation of this species. Unfortunately, captivity-induced stress is a concern and potential factor for lack of breeding success in this small felid, resulting in an unsustainable population. The objectives of this study were to: 1) validate an enzyme immunoassay for monitoring of fecal glucocorticoid metabolite (FGM) concentrations in the fishing cat; 2) identify potential exogenous stressors in the captive environment; 3) pinpoint management techniques that may lower FGM concentrations; and 4) determine if FGM concentrations are related to breeding success. Through a successful adrenocorticotrophic hormone challenge and additional laboratory methods, a cortisol enzyme immunoassay was validated as an effective tool for detecting FGM in this species. Between 2010 and 2013, longitudinal FGM monitoring was conducted in 26 fishing cats in the North American Species Survival Plan®. Exogenous stressors that elevated FGM concentrations included: chemical immobilizations; permanent transfers between facilities; construction; facility events; and fights/aggression among breeding pairs. Management factors that lowered FGM concentrations included: increased animal-keeper interaction through formal training; and providing indoor, off-exhibit, holding areas. In addition, social housing of individuals (either established breeding pairs or same sex pairs) decreased FGM concentrations. Individuals with breeding success (defined as observed copulations during the study period) also had lower FGM concentrations than unsuccessful individuals. Findings indicate that management factors play a role in lowering glucocorticoid (stress) levels in fishing cats, which may ultimately affect breeding success in the ex situ population

FcC_supermatrix

FasConCat supermatrix fasta file

28ConpleteGeneTrees

Subset of 28 UCE loci from complete data matrix