J.A. Esselstyn's research while affiliated with Louisiana State University and other places

Phylogenetic studies now routinely require manipulating and summarizing thousands of data files. For most of these tasks, currently available software requires considerable computing resources and substantial knowledge of command‐line applications. We develop an ultrafast and memory‐efficient software, SEGUL, that performs common phylogenomic dataset manipulations and calculates statistics summarizing essential data features. Our software is available as standalone command‐line interface (CLI) and graphical user interface (GUI) applications, and as a library for Rust, R and Python, with possible support of other languages. The CLI and library versions run native on Windows, Linux and macOS, including Apple ARM Macs. The GUI version extends support to include mobile iOS, iPadOS and Android operating systems. SEGUL leverages the high performance of the Rust programming language to offer fast execution times and low memory footprints regardless of dataset size and platform choice. The inclusion of a GUI minimizes bioinformatics barriers to phylogenomics while SEGUL's efficiency reduces economic barriers by allowing analysis on inexpensive hardware. Our support for mobile operating systems further enables teaching phylogenomics where access to computing power is limited.

We describe 3 new species of shrews (Eulipotyphla, Soricidae, Crocidura) from West Sumatra, Indonesia. Two of these taxa were found above 1,800 m on Mt. Singgalang. The third taxon was found above 1,660 m on Mt. Talamau, 65 km northwest of Mt. Singgalang. We also resurrect Crocidura aequicauda based on 2 specimens from Mts. Tujuh and Kerinci, which lie near the border between West Sumatra and Jambi provinces. Several methodological approaches support our findings: linear cranial morphometrics, landmark-based 2D geometric morphometrics, and molecular phylogenetics using both mtDNA and 6 nuclear exons. A multilocus species-tree analysis places the 3 new species and C. aequicauda in a clade with the Javan endemics C. monticola and C. umbra. Although the 2 taxa from Mt. Singgalang are recovered as sister species, 1 is nearly twice the size of the other, and they are divergent in several other morphological characters, such as tail length, cranium size, and pelage color and texture. Recently diverged yet morphologically disparate sister taxa living syntopically in an isolated habitat “island,” like the montane forests of Mt. Singgalang, is unusual in mammals but documented in other Crocidura on neighboring Java and Borneo; these 2 new taxa represent the first known case of this phenomenon on Sumatra. Our results bring the number of Sumatran Crocidura to 10, 9 of which are endemic to the island. All 3 of the new species appear to be endemic to a single mountain and were not detected in similar surveys of nearby mountains. If this local endemism pattern is common, it would indicate that Sumatra’s mammal diversity may be severely underestimated, largely due to the paucity of small-mammal surveys and museum specimens.

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Sperm competition can drive the rapid evolution of male reproductive traits, but it remains unclear how variation in sperm competition intensity shapes phenotypic and molecular diversity across clades. Old World mice and rats (subfamily Murinae) comprise one of the most rapid mammalian radiations and exhibit incredible diversity in sperm morphology and production. We sequenced exomes from 36 murine species and combined these data with published sequences to model the evolution of reproductive traits and genes across 78 murine species. We identified several independent shifts towards smaller relative testes mass, a trait reflective of reduced sperm competition. Several features of sperm morphology were associated with relative testes mass, suggesting that mating system evolution likely selects for convergent suites of traits related to sperm competitive ability. Molecular evolutionary rates of spermatogenesis proteins also correlated with relative testes mass, but in an unexpected direction. We predicted that sperm competition would result in rapid divergence among species with large relative testes mass, but instead found that many spermatogenesis genes evolve more rapidly in species with smaller relative testes mass due to relaxed purifying selection. While some reproductive genes showed evidence for pervasive positive selection, relaxed selection played a greater role underlying rapid evolution in small testes species. Our work demonstrates that sexual selection can impose strong purifying selection shaping the evolution of male reproduction.

It is a great pleasure to introduce this special feature honoring Dr. Alfred Lunt Gardner. Al’s many contributions to mammalogy span seven decades, two continents, and practically the entire tree of mammals. It is impossible to imagine what mammalogy in the Americas would look like without him. His academic contributions are as significant as his imposing stature. Al was born in Salem, Massachusetts in 1937 and spent his early childhood there. His first interests in natural history were sparked by his 3rd-grade teacher, an amateur ornithologist who kept a cabinet of specimens in her classroom (Gardner 2005). In 1947, the Gardner family relocated to a farm in North Andover, Massachusetts, where, according to Al, he “practically lived in the woods fishing, hunting, and trapping” (pg. 277, Gardner 2005). In his adolescent years, Al would spend considerable time in the outdoors, honing his trapping and skinning skills. By his freshman year of high school, he was selling furs and evading game wardens (Gardner 2005). In 1953, his family moved to Tucson, Arizona, where Al found a trove of new habitats and wildlife to explore. By 1955, Al graduated high school, signed up for the Army Reserves, and enrolled at the University of Arizona, where his mammalogical interests would be further stimulated by E. Lendell Cockrum and his graduate students.

Although Borneo has received more attention from biologists than most other islands in the Malay Archipelago, many questions regarding the systematic relationships of Bornean mammals remain. Using next-generation sequencing technology, we obtained mitochondrial DNA sequences from the holotype of Suncus ater , the only known specimen of this shrew. Several shrews collected recently in Sarawak are closely aligned, both morphologically and mitochondrially, with the holotype of S. ater . Phylogenetic analyses of mitochondrial sequences indicate that the S. ater holotype and new Sarawak specimens do not belong to the genus Suncus , but instead are most closely related to Palawanosorex muscorum . Until now Palawanosorex has been known only from the neighboring Philippine island of Palawan. Additional sequences from nuclear ultra-conserved elements from the new Sarawak specimens strongly support a sister relationship to P. muscorum . We therefore transfer ater to Palawanosorex . The new specimens demonstrate that P. ater is more widespread in northern Borneo than previously recorded. Continued sampling of Bornean mammal diversity and reexamination of type material are critical in understanding the evolutionary history of the biologically rich Malay Archipelago.

Faunivorous mammals with simple guts are thought to rely primarily on endogenously produced enzymes to digest food, in part because they lack fermentation chambers for facilitating mutualistic interactions with microbes. However, variation in microbial community composition along the length of the gastrointestinal tract has yet to be assessed in faunivorous species with simple guts. We tested for differences in bacterial taxon abundances and community compositions between the small intestines and colons of 26 individuals representing four species of shrew in the genus Crocidura. We sampled these hosts from a single locality on Sulawesi Island, Indonesia, to control for potential geographic and temporal variation. Bacterial community composition differed significantly between the two gut regions and members of the family Mycoplasmataceae contributed substantially to these differences. Three operational taxonomic units (OTUs) of an unclassified genus in this family were more abundant in the small intestine, whereas 1 OTU of genus Ureaplasma was more abundant in the colon. Species of Ureaplasma encode an enzyme that degrades urea, a metabolic byproduct of protein catabolism. Additionally, a Hafnia–Obesumbacterium OTU, a genus known to produce chitinase in bat gastrointestinal tracts, was also more abundant in the colon compared to the small intestine. The presence of putative chitinase- and urease-producing bacteria in shrew guts suggests mutualisms with microorganisms play a role in facilitating the protein-rich, faunivorous diets of simple gut mammals.

Although deer mice (Peromyscus spp.) are among the most studied small mammals, their species diversity and phylogenetic relationships remain unclear. The lack of taxonomic clarity is mainly due to a conservative morphology and because some taxa are rare, have restricted distributions, or are poorly sampled. One taxon, P. mexicanus, includes southern Mexican subspecies that have not had their systematic placement tested with genetic data. We analyzed the phylogenetic relationships and genetic structure of P. mexicanus populations using sequences of the mitochondrial gene cytochrome b. We inferred that P. mexicanus is paraphyletic, with P. m. teapensis, P. m. tehuantepecus, andP. m. totontepecus more closely related to P. gymnotis than to P. m. mexicanus. This highly divergent clade ranges from northeastern Oaxaca to northern Chiapas, including southern Veracruz, and southern Tabasco. In light of this group’s mitochondrial distinctiveness, cohesive geographic range, and previously reported molecular, biochemical, and morphological differences, we recommend it be treated as P. totontepecus. Our findings demonstrate the need for an improved understanding of the diversity and evolutionary history of these common and abundant members of North American small mammal communities.

Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus Pneumocystis are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that Pneumocystis cospeciate with their mammalian hosts suggests that thousands of Pneumocystis species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of Pneumocystis diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of Pneumocystis species sampled from 55 mammal species representing eight orders. Our results suggest that Pneumocystis species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate ≈4600 to 6250 Pneumocystis species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (~3.7%) mammal species have been screened for Pneumocystis, and many detected Pneumocystis lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of Pneumocystis to their mammal hosts and highlight an abundance of undescribed diversity.

Communities that occupy similar environments but vary in the richness of closely related species can illuminate how functional variation and species richness interact to fill ecological space in the absence of abiotic filtering, though this has yet to be explored on an oceanic island where the processes of community assembly may differ from continental settings. In discrete montane communities on the island of Sulawesi, local murine rodent (rats and mice) richness ranges from 7 to 23 species. We measured 17 morphological, ecological, and isotopic traits, both individually and grouped into 5 multivariate traits in 40 species, to test for the expansion or packing of functional space among nine murine communities. We employed a novel probabilistic approach for integrating intraspecific and community-level trait variance into functional richness. Trait-specific and phylogenetic diversity patterns indicate dynamic community assembly due to variable niche expansion and packing on multiple niche axes. Locomotion and covarying traits such as tail length emerged as a fundamental axis of ecological variation, expanding functional space and enabling the niche packing of other traits such as diet and body size. Though trait divergence often explains functional diversity in island communities, we found that phylogenetic diversity facilitates functional space expansion in some conserved traits such as cranial shape, while more labile traits are overdispersed both within and between island clades, suggesting a role of niche complementarity. Our results evoke interspecific interactions, differences in trait lability, and the independent evolutionary trajectories of each of Sulawesi’s 6 murine clades as central to generating the exceptional functional diversity and species richness in this exceptional, insular radiation. Bahasa Indonesia Abstract translation to be provided in subsequent version.