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Abstract It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass (RTM), presumably reflecting reduced sperm competition. Several sperm traits were associated with RTM, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller RTM due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction and that broad patterns of molecular evolution may help identify genes that contribute to male fertility. 

Abstract 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. 

Abstract 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. 

Abstract AimTo determine the historical dynamics of colonization and whether the relative timing of colonization predicts diversification rate in the species‐rich, murine rodent communities of Indo‐Australia. LocationIndo‐Australian Archipelago including the Sunda shelf of continental Asia, Sahul shelf of continental Australia, the Philippines and Wallacea of Indonesia. TaxonOrder Rodentia, Family Muridae. MethodsWe used a fossil‐calibrated molecular phylogeny and Bayesian biogeographical modelling to infer the frequency and temporal sequence of biogeographical transitions among Sunda, Sahul, the Philippines and Wallacea. We estimated diversification rates for each colonizing lineage using a method‐of‐moments estimator of net diversification and Bayesian mixture model estimates of diversification rate shifts. ResultsWe identified 17 biogeographical transitions, including nine originating from Sunda, seven originating from Sulawesi and broader Wallacea and one originating from Sahul. Wallacea was colonized eight times, the Phillipines five times, Sunda twice and Sahul twice. Net diversification rates ranged from 0.2 to 2.12 species/lineage/My with higher rates in secondary and later colonizers than primary colonizers. The highest rates were in the genusRattusand their closest relatives, irrespective of colonization history. Main ConclusionsOur inferences from murines demonstrate once again the substantial role of islands as sources of species diversity in terrestrial vertebrates of the IAA with most speciation events occurring on islands. Sulawesi and broader Wallacea have been a major source of colonists for both island and continental systems. Crossings of Wallace's Line were more common than subsequent transitions across Lydekker's Line to the east. While speciation following colonization of oceanic archipelagos and large islands is consistent with adaptive radiation theory and ideas regarding ecological opportunity, we did not observe a strong signal of incumbency effects. Rather, subsequent colonists of landmasses radiated unhindered by previous radiations. 

Abstract Sulawesi is the largest, most topographically complex island in the Wallacean biogeographic zone, and it has a rich fauna of endemic small mammals, dominated by rodents of the family Muridae. Among murids, the Bunomys division is the most species‐rich radiation on Sulawesi. In total, the division contains 11 genera and 32 species, five and 20 of which are endemic to Sulawesi. We combined a five‐locus phylogeny and linear cranial morphology to better understand the taxonomy and local scales of endemism within the Bunomys division on Sulawesi. Phylogenetic analyses of mitochondrial and nuclear DNA placedB. fratrorumamong other genera and inferredParuromysas sister to the type species ofTaeromys(T. celebensis). We resolve these issues by resurrectingFrateromys, a genus under whichB. fratrorumwas once placed, and returningParuromys dominatortoTaeromys. Within three species,F. fratrorum, T. callitrichus,andT. taerae, we recovered Pleistocene age divergences between populations sampled across the northern peninsula of Sulawesi; divergence between western and eastern populations ofF. fratrorummay reflect the existence of two species. 

Abstract Arboreal locomotion allows access to above-ground resources and might have fostered the diversification of mammals. Nevertheless, simple morphological measurements that consistently correlate with arboreality remain indefinable. As such, the climbing habits of many species of mammals, living and extinct, remain speculative. We collected quantitative data on the climbing tendencies of 20 species of murine rodents, an ecologically and morphologically diverse clade. We leveraged Bayesian phylogenetic mixed models (BPMMs), incorporating intraspecific variation and phylogenetic uncertainty, to determine which, if any, traits (17 skeletal indices) predict climbing frequency. We used ordinal BPMMs to test the ability of the indices to place 48 murine species that lack quantitative climbing data into three qualitative locomotor categories (terrestrial, general and arboreal). Only two indices (both measures of relative digit length) accurately predict locomotor styles, with manus digit length showing the best fit. Manus digit length has low phylogenetic signal, is largely explained by locomotor ecology and might effectively predict locomotion across a multitude of small mammals, including extinct species. Surprisingly, relative tail length, a common proxy for locomotion, was a poor predictor of climbing. In general, detailed, quantitative natural history data, such as those presented here, are needed to enhance our understanding of the evolutionary and ecological success of clades. 

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 as five 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 six murine clades as central to generating the exceptional functional diversity and species richness in this exceptional, insular radiation. 

Zoonotic diseases, including those carried by mammalian hosts, pose a significant threat to human health worldwide and substantial investment in wildlife disease surveillance is aimed at identifying the risk of spillover from wildlife to human populations where they interact. However, host species diversity is highest in the most intact habitats away from human habitation and most of the potential host species within these habitats are unsampled for infections. This is particularly true in biodiverse tropical ecosystems where the prevalence and identity of infections are the least known. We screened for presence of trypanosomes in 2,335 specimens from 66 species of rodents and shrews sampled from 11 mountain areas on the tropical island of Sulawesi, Indonesia. Our sampling spanned from the edge of human occupation into the most intact forests available on the island with sampling elevations ranging from 220 to 2,700 m. The two most common Trypanosoma species we detected were a native species from the Theileri clade (19.0 % of samples) and an introduced species from the Lewisi clade (5.1 % of murid rodent samples). Both species were detected at all elevations, extending from village edges to mountain peaks, but both reached their highest prevalence above 2,000 m elevation in the most intact forest away from human habitation. If these patterns with trypanosome infections are typical of other zoonotic diseases, wildlife disease surveillance would need to shift resources to study host-pathogen dynamics in more remote ecosystems. Sampling focused on the breadth of biodiversity, such as collected by and housed in natural history collections, is needed to further our understanding of zoonotic diseases and their prevalence. 

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 ofSuncus ater, the only known specimen of this shrew. Several shrews collected recently in Sarawak are closely aligned, both morphologically and mitochondrially, with the holotype ofS. ater. Phylogenetic analyses of mitochondrial sequences indicate that theS. aterholotype and new Sarawak specimens do not belong to the genusSuncus, but instead are most closely related toPalawanosorex muscorum. Until nowPalawanosorexhas 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 toP. muscorum. We therefore transferatertoPalawanosorex. The new specimens demonstrate thatP. ateris 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. 

Abstract 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.