An 1896 specimen helps clarify the phylogenetic placement of the Mexican endemic Hooper’s deer mouse

Abstract

Hooper’s deer mouse, Peromyscus hooperi, is the sole member of the Peromyscus hooperi species group. This species is endemic to México where it is restricted to the grassland transition zone in the states of Coahuila, Zacatecas, and San Luis Potosí. Previous studies using mitochondrial and nuclear genes (Cytb, Adh1-I2, Fgb-I7 and Rbp3) did not resolve the phylogenetic relationships of this relatively poorly known species. It was hypothesized that P. hooperi is sister to P. crinitus, and these two taxa are related to P. melanotis, P. polionotus, P. maniculatus, P. keeni, P. leucopus, P. gossypinus, P. eremicus, P. californicus, and Osgoodomys banderanus. Based on morphological characters, karyotypes, and allozymes, P. hooperi does not align with either subgenera Haplomylomys or Peromyscus. However, its unique characteristics (e. g., phallus, karyotype) have been recognized, and therefore it has been retained as its own species group. To better resolve the phylogenetic placement of P. hooperi, we performed target-enrichment and high-throughput sequencing and obtained several thousand nuclear ultraconserved elements and a complete mitogenome from a specimen collected in 1896 by Nelson and Goldman in Coahuila, México. We compared these data with 21 other species of neotomines using genome-wide data. Contrary to previous studies, we found high nodal support for the placement of P. hooperi as sister to a clade that includes Podomys floridanus, Neotomodon alstoni, Habromys simulatus, H. ixtlani, Peromyscus mexicanus, P. megalops, P. melanophrys, P. perfulvus, P. aztecus, P. attwateri, P. pectoralis, and P. boylii. We dated a Pliocene divergence of P. hooperi from its sister group at approximately 3.98 mya, and after the split of P. crinitus at ca. 4.31 mya from other peromyscines. We demonstrated that genome-wide data improve the phylogenetic signal, independently of taxon sampling, for a phylogenetically problematic species such as P. hooperi. We recommend that future genomic studies expand taxon sampling, including members of the subgenus Haplomylomys, to confirm the phylogenetic relationships of P. hooperi and the genetic status of its populations.

Novel genomic resources contribute to the systematics of threatened arboreal deer mice of the genus Habromys Hooper & Musser, 1964 (Cricetidae, Neotominae) within a neotomine–peromyscine phylogeny

“…Therefore, our data support the hypothesis that Peromyscus is paraphyletic ( Bradley et al 2007 ; Miller and Engstrom 2008 ; Platt et al 2015 ; Sullivan et al 2017 ; Castañeda-Rico et al 2022b ). In addition, we corroborated previous results by Castañeda-Rico et al (2022b , 2023 ) where members of the genus Habromys are sisters to P. aztecus , a member of the Peromyscus aztecus species group, and this clade is sister to a clade comprising members of the Peromyscus truei species group ( P. attwateri and P. pectoralis ). The difference between those previous studies and ours is that they only included H. simulatus in the UCE-based phylogeny and H. ixtlani in the mitogenome-based phylogeny (one sample for each dataset).…”

“…In contrast, in this study, we have expanded our sampling and have included two species ( H. simulatus and H. lophurus ) in the UCE-based phylogeny and three species ( H. simulatus , H. ixtlani , and H. lophurus ) in the mitogenome phylogeny. Another difference among these studies is that Castañeda-Rico et al (2022b , 2023 ) did not test for the monophyly of the genus; however, these additional three species enabled us to confirm the monophyly of Habromys . The sister relationship between the genus Habromys and P. aztecus coincides with Osgood (1909) , who recognized a close affinity between H. lophurus + H. lepturus + H. simulatus and forms of the Peromyscus aztecus species group.…”

“…To determine the phylogenetic position of H. lophurus , a Bayesian Inference ( BI ) analysis was performed using MrBayes v3.2.6 ( Ronquist et al 2012 ) under the best model and partition scheme (by gene and codon position – 6 partitions) selected by PartitionFinder v2.1.1 ( Lanfear et al 2016 ) for the mitogenome dataset and without partitions for the UCE dataset. We included previously published Neotominae and Sigmodontinae mitogenomes and UCEs downloaded from GenBank; KY707304 and KY707303 ( Sullivan et al 2017 ), MT078816 – MT078819 PRJNA606805 ( Castañeda-Rico et al 2020 ), OL685394 PRJNA818347 ( Castañeda-Rico et al 2022a ), ON528108 – ON528119 PRJNA838631 ( Castañeda-Rico et al 2022b ), and OP432689 PRJNA880321 ( Castañeda-Rico et al 2023 ). The final datasets included 21 and 20 species for mitogenomes and UCE, respectively (Table 1 ).…”