Cytb alignment by group (sets)

Nexus file of 762 samples of DNA sequence data for the cytochrome b gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies). Also includes a taxon set conforming to the 21 jumping mice lineages and 4 species

BRCA alignment

Ninety-two samples of sequence data from the BRCA gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies)

SDM_records

High-quality, natural history museum-based samples obtained from MANIS (Jan-2011) and down-sampled (aka thinned) to 10km radius to offset sampling bias. Taxa are lineage-based assignments for each species used in niche modeling

ApoB alignment

Ninety-two samples of sequence data from the ApoB gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies)

MYH6 alignment

Ninety-two samples of sequence data from the MYH6 gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies)

Collecting event cascade.

<p>Holistic sampling and extended specimens begin with a more comprehensive collecting event that captures multiple specimens, samples, and data about event context. These begin a cascade of subsamples, preparations, and diverse data records that may be located in different collections, institutions, data repositories, and publications. All these descendants and associated derivative data are linked to the original collecting event and, as a result, to each other.</p

GBA alignment

Ninety-two samples of sequence data from the GBA gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies)

The role of natural history biorepositories in pathogen biology and mitigation.

<p>Host–parasite collections provide an exemplar of how museums can stimulate better coordination and participation in pathobiology across multiple institutions. Their roles range from sample providers to sample users (research) to informatics resources and contributing to the mitigation of public health crises. In this model, specimens are provided to natural history repositories by existing public health networks, fieldwork, and rural communities. Frozen and traditional collections become central to pathobiology research aimed at identifying pathogens, discovering zoonotic host associations, and delineating the potential spatial extent of the pathogen. Detailed questions about the pathogen ecology and evolutionary history can then be addressed to provide a framework for more effective public health response in increasingly dynamic environments. Relational web-accessible databases at museums facilitate complex linkages between all associated materials and allow careful tracking of all studies and their derived data (e.g., GenBank).</p

The role of biological collections in integrated pest management.

<p>The process of diagnosing an agricultural pest and then finding, testing, mass-producing, and releasing a control agent takes place in different settings and institutions. For the process to succeed, each participant in the process must be using the same host plants, pest species, and control agent species. Morphological and genetic comparisons with reference collections and databases can reveal the inadvertent introduction of look-alike or cryptic species into the process.</p

Heteroxynema cucullatum DNA sequence alignments and phylogenies

H_cucullatum_3loci_concatenated_MrBayes.tre: MrBayes tree of Heteroxynema cucullatum concatenated loci COI, ITS+, 28S H_cucullatum_3loci_starbeast.tre: Starbeast species tree of Heteroxynema cucullatum loci COI, ITS+, 28S H_cucullatum_COI_quadrivittatus_hosts_MrBayes.tre: MrBayes gene tree of COI for Heteroxynema cucullatum individuals that corespond to quadrivittatus group hosts (used in tanglegram) H_cucullatum_COI_T_minimus_hosts_MrBayes.tre: MrBayes gene tree of COI for Heteroxynema cucullatum individuals that corespond to Tamias minimus hosts (used in tanglegram) Heteroxynema_cucullatum_28S_MrBayes.tre: MrBayes gene tree of Heteroxynema cucullatum 28S Heteroxynema_cucullatum_28S_alignment.nex: DNA sequence alignment of Heteroxynema cucullatum 28S Heteroxynema_cucullatum_COI_MrBayes.tre: MrBayes gene tree of Heteroxynema cucullatum COI Heteroxynema_cucullatum_COI_RAxML.tre: RAxML gene tree of Heteroxynema cucullatum COI Heteroxynema_cucullatum_COI_alignment.nex: DNA sequence alignment of Heteroxynema cucullatum COI Heteroxynema_cucullatum_ITS_MrBayes.tre: MrBayes gene tree of Heteroxynema cucullatum ITS+ Heteroxynema_cucullatum_ITS_alignment.nex: DNA sequence alignment of Heteroxynema cucullatum ITS