Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger pigeons' large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These results demonstrate the effect that selection can have on a vertebrate genome and contradict results that suggested that population instability contributed to this species's surprisingly rapid extinction

Mammal collections of the Western Hemisphere: A survey and directory of collections

As a periodic assessment of the mammal collection resource, the Systematic Collections Committee (SCC) of the American Society of Mammalogists undertakes decadal surveys of the collections held in the Western Hemisphere. The SCC surveyed 429 collections and compiled a directory of 395 active collections containing 5,275,155 catalogued specimens. Over the past decade, 43 collections have been lost or transferred and 38 new or unsurveyed collections were added. Growth in number of total specimens, expansion of genomic resource collections, and substantial gains in digitization and web accessibility were documented, as well as slight shifts in proportional representation of taxonomic groups owing to increasingly balanced geographic representation of collections relative to previous surveys. While we find the overall health of Western Hemisphere collections to be adequate in some areas, gaps in spatial and temporal coverage and clear threats to long-term growth and vitality of these resources have also been identified. Major expansion of the collective mammal collection resource along with a recommitment to appropriate levels of funding will be required to meet the challenges ahead for mammalogists and other users, and to ensure samples are broad and varied enough that unanticipated future needs can be powerfully addressed. © 2018 The Author(s)

Data from: Sympatric parasites have similar host-associated, but asynchronous, patterns of diversification

Parasitism is a common symbiotic interaction across diverse natural systems. Using a comparative evolutionary approach, we investigated the contributions of both host phylogeny and abiotic factors towards diversification of phylogenetically independent endoparasites that inhabit essentially the same physical space. We tested for host-parasite and parasite-parasite phylogenetic concordance in western North American chipmunks (Rodentia: Sciuridae) and two distantly related species of pinworms (Nematoda: Oxyurida). Deep structure in molecular phylogenies revealed signals of host-associated divergence in both parasite species, while shallower phylogeographic structure varied between the two parasites. This suggests that although these parasites experienced similar landscapes and cyclic climate processes, temporally distinctive diversification events were associated with differences in the initiation of their association with host lineages. When climate cycles initiate diversification, partially congruent, but asynchronous host-associated parasite phylogenies may emerge

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

Pinworm & host BUCKy trees and pinworm COI BEAST tree

H_cucullatum_COI_quadrivittatus_cytb_BUCKy.tre: BUCKy tree with concordance values for H. cucullatum COI MrBayes trees and quadrivittatus group cytb MrBayes trees H_cucullatum_R_eutamii_COI_BUCKy.tre: BUCKy tree with concordance values for H. cucullatum and R. eutamii COI MrBayes trees H_cucullatum_and_R_eutamii_COI_beast_rate_estimates_only.tre: BEAST tree of COI sequences for H. cucullatum and R. eutamii, used only to estimate relative rates H_cucullatum_COI_T_minimus_cytb_BUCKy.tre: BUCKy tree with concordance values for H. cucullatum COI MrBayes trees and T. minimus cytb MrBayes trees R_eutamii_COI_T_minimus_cytb_BUCKy.tre: BUCKy tree with concordance values for R. eutamii COI MrBayes trees and T. minimus cytb MrBayes trees R_eutamii_COI_quadrivittatus_cytb_BUCKy.tre: BUCKy tree with concordance values for R. eutamii COI MrBayes trees and quadrivittatus group cytb MrBayes tree

Rauschtineria eutamii DNA sequence alignments and phylogenies

R_eutamii_4loci_concatenated_MrBayes.tre: MrBayes tree of Rauschtineria eutamii concatenated loci COI, 12S, 18S, 28S R_eutamii_4loci_starbeast.tre: Starbeast species tree of Rauschtineria eutamii loci COI, 12S, 18S, 28S R_eutamii_COI_minimus_hosts_MrBayes.tre: MrBayes gene tree of COI for Rauschtineria eutamii individuals that corespond to Tamias minimus hosts (used in tanglegram) R_eutamii_COI_quadrivittatus_hosts_MrBayes.tre: MrBayes gene tree of COI for Rauschtineria eutamii individuals that corespond to quadrivittatus group hosts (used in tanglegram) Rauschtineria_eutamii_12S_MrBayes.tre: MrBayes gene tree of Rauschtineria eutamii 12S Rauschtineria_eutamii_12S_alignment.nex: DNA sequence alignment of Rauschtineria eutamii 12S Rauschtineria_eutamii_18S_MrBayes.tre: MrBayes gene tree of Rauschtineria eutamii 18S Rauschtineria_eutamii_18S_alignment.nex: DNA sequence alignment of Rauschtineria eutamii 18S Rauschtineria_eutamii_28S_MrBayes.tre: MrBayes gene tree of Rauschtineria eutamii 28S Rauschtineria_eutamii_28S_alignment.nex: DNA sequence alignment of Rauschtineria eutamii 28S Rauschtineria_eutamii_COI_MrBayes.tre: MrBayes gene tree of Rauschtineria eutamii COI Rauschtineria_eutamii_COI_RAxML.tre: RAxML gene tree of Rauschtineria eutamii COI Rauschtineria_eutamii_COI_alignment.nex: DNA sequence alignment of Rauschtineria eutamii CO

Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger pigeons' large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These results demonstrate the effect that selection can have on a vertebrate genome and contradict results that suggested that population instability contributed to this species's surprisingly rapid extinction