Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies

Range contraction and expansion from glaciation has led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat los..., We identified G. bursarius samples analyzed by Alexander et al. (2024) that had high DNA content based on microsatellite amplification to increase the likelihood of reconstructing complete mitogenomes. These samples included 41 toes from museum specimens from the Illinois Natural History Survey collected between 1934 and 1985, and 12 tissue samples from G. bursarius illinoensis live-trapped in 2018-2019, following appropriate guidelines (UIUC IACUC #17190). We sampled seven G. bursarius subspecies from across the range, excluding only G. b. ozarkensis. We included three samples from other Geomys species (one G. breviceps dutcheri, and two Geomys jugossicularis) as outgroups. Geomys jugossicularis was previously considered within the G. bursarius clade but was determined to be an independent species.
Arbor Biosciences (arborbiosci.com; Ann Arbor, MI, USA) completed library preparation, mtDNA-bait enrichment and capture, and genome sequencing. Arbor Sciences created customized mtDNA-baits..., , Manuscript Title: Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies

Authors:
Nathan Alexander
Alida de Flamingh
Bradley J. Cosentino
Robert L. Schooley

The files contained herein include three alignments, a spreadsheet with sampling information (and is supplementary materials 1 in the published manuscript)

Alignments:

File Name: **Gopher_5_21_23_Subspecies_geo.nex**

Description: trimmed and alinged partial mitogenomes of 53 Geomys bursarius, 2 Geomys jugossicularis, and 1 Geomys breviceps dutcheri.
This file can be opened in MEGA v 11.03, PopArt v. 1.7

File Name: **COX1_alignment_subspecies.nex**

Description: individually aligned and compiled COX1 regions of 53 Geomys bursarius, 2 Geomys jugossicularis, and 1 Geomys breviceps dutcheri.
This file can be opened in PopArt v. 1.7

File Name: **Cytb_alignment_trimmed_subspecies.nexus**

Description: individually aligned, compiled, and tri...