A new genus of rodent from Wallacea (Rodentia: Muridae: Murinae: Rattini), and its implication for biogeography and Indo-Pacific Rattini systematics

New insights into the mitogenomic phylogeny and evolutionary history of Murinae (Rodentia, Muridae) with the description of a new tribe

Murinae is the largest known subfamily of Muridae and includes 15 tribes and 3 genera (incertae sedis). Although the phylogeny of Murinae has been studied, its phylogenetic relationships have not been completely elucidated. We used phylogenetic framework and molecular dating methodologies with the vast majority of available mitochondrial genomes to disentangle the phylogenetic relationships and evolutionary history of Murinae. Sixteen tribes were identified within the Murinae subfamily. Among these, fifteen tribes were found to be consistent with those currently recognized. Hapalomyini (Clade A) was located at the base of the Murinae clade with strong nodal support contrary to previous studies, which showed that Phloeomyini diverged first. The Clade B consisted of Micromyini, Rattini, and the genus Vernaya. Vernaya cannot be accommodated in any existing tribe. The origin of Murinae dates back to 17.22 Ma. The split between Micromyini and Vernayini was dated to 11.69 Ma during the Miocene, indicating that they were both early branches of Murinae. Combined with the differences between Vernaya and its sister tribes (Micromyini and Rattini) in morphology, skull and teeth, we validated a new tribe, Vernayinitribe nov. We believe that it is necessary to combine morphological and molecular perspectives (especially from a genome-wide perspective) to determine the phylogenetic position of tribes with an uncertain taxonomic position in Murinae.

Comparative morphology of the rhinarium and upper lip in sigmodontine rodents: Refined nomenclature, intertribal variation in a phylogenetic framework, and functional inferences

Rodents have received substantial attention in the study of olfaction. However, the rhinarium, the naked part of the nose, which plays an important role in chemical, tactile, and thermal perception, has been relatively overlooked. This study presents a comprehensive analysis of the rhinarium morphology and spatially associated structures (i.e., upper lip, and philtrum) in sigmodontines, a diverse group within the Cricetidae rodents. The research covers 483 specimens representing 145 species, accounting for 74% of genera in the clade, including all 13 recognized tribes, three incertae sedis genera, and the murid representatives Mus musculus and Rattus norvegicus. The inconsistent use of terminology in describing rhinarium traits across the literature poses a challenge for comparative analyzes. To address this issue, a standardized terminology was proposed to characterize the rhinarium. A paired complex protuberance typically with epidermal ridges (i.e., rhinoglyphics), termed here the tubercle of Hill, was identified as a distinctive feature in muroid rhinaria. Comparative assessments among tribes revealed unique sets of features defining each major clade, encompassing variations in hairiness, dorsum nasi complexity, size and positioning of the tubercle of Hill, and other key attributes. Two primary rhinarium configurations were discerned: one shared by Oryzomyalia and Sigmodontini and another specific to Ichthyomyini. The former groups display a ventrally positioned rhinarium prominently featuring the tubercle of Hill and sculptured areola circularis. In contrast, Ichthyomyini exhibit a frontally directed rhinarium characterized by an enlarged dorsum nasi fused to the tubercle of Hill, resulting in a distinctive "cherry" appearance. Convergent rhinarium structures observed in fossorial species, characterized by well-developed plica alaris and hair fringes, are presumed to mitigate potential damage during digging. Conversely, semiaquatic carnivorous sigmodontines showcase an integrated apical structure in their rhinarium, facilitating enhanced somatosensory capabilities crucial for predation activities during diving expeditions.

New Guinea uplift opens ecological opportunity across a continent

Sahul unites the world's largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains untested across Sahul as a whole. To address this, we reconstruct the assembly of a recent and diverse radiation of rodents (Murinae: Hydromyini) spanning New Guinea, Australia, and oceanic islands. Using phylogenomic data from 270 specimens, including many recently extinct and highly elusive species, we find that the orogeny and expansion of New Guinea opened ecological opportunity and triggered diversification across a continent. After a single over-water colonization from Asia ca. 8.5 Ma, ancestral Hydromyini were restricted to the tropical rainforest of proto-New Guinea for 3.5 million years. Following a shift in diversification coincident with the orogeny of New Guinea ca. 5 Ma and subsequent colonization of Australia, transitions between geographic regions (n = 24) and biomes (n = 34) become frequent. Recurrent over-water colonization between mainland and islands demonstrate how islands can play a substantial role in the assembly of continental fauna. Our results are consistent with a model of increased ecological opportunity across Sahul following major geological uplift in New Guinea ca. 5 Ma, with sustained diversification facilitated by over-water colonization from the Pleistocene to present. We show how geological processes, biome transitions, and over-water colonization collectively drove the diversification of an expansive continental radiation.

Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents

Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining “ancestral-type” characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.

Molecular Evolution of Ecological Specialisation: Genomic Insights from the Diversification of Murine Rodents

Adaptive radiations are characterized by the diversification and ecological differentiation of species, and replicated cases of this process provide natural experiments for understanding the repeatability and pace of molecular evolution. During adaptive radiation, genes related to ecological specialization may be subject to recurrent positive directional selection. However, it is not clear to what extent patterns of lineage-specific ecological specialization (including phenotypic convergence) are correlated with shared signatures of molecular evolution. To test this, we sequenced whole exomes from a phylogenetically dispersed sample of 38 murine rodent species, a group characterized by multiple, nested adaptive radiations comprising extensive ecological and phenotypic diversity. We found that genes associated with immunity, reproduction, diet, digestion, and taste have been subject to pervasive positive selection during the diversification of murine rodents. We also found a significant correlation between genome-wide positive selection and dietary specialization, with a higher proportion of positively selected codon sites in derived dietary forms (i.e., carnivores and herbivores) than in ancestral forms (i.e., omnivores). Despite striking convergent evolution of skull morphology and dentition in two distantly related worm-eating specialists, we did not detect more genes with shared signatures of positive or relaxed selection than in a nonconvergent species comparison. Although a small number of the genes we detected can be incidentally linked to craniofacial morphology or diet, protein-coding regions are unlikely to be the primary genetic basis of this complex convergent phenotype. Our results suggest a link between positive selection and derived ecological phenotypes, and highlight specific genes and general functional categories that may have played an integral role in the extensive and rapid diversification of murine rodents.

Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland

Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.

Distribution pattern and phylogeography of tree rats Chiromyscus (Rodentia, Muridae) in eastern Indochina

The study combines available data on species distribution in eastern Indochina to investigate the phylogeographical genetic and morphological diversity of tree rats (Chiromyscus, Rodentia, Muridae) and to specify their natural ranges. We examined the diversity and distribution of tree rats over its range, based on recent molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, RAG1 and GHR) genes. The study presents the most complete and up-to-date data on the distribution and phylogeography of the genus in eastern Indochina. As revealed by mitochondrial genes, C. langbianis splits into at least four coherent geographically-distributed clades, whereas C. thomasi and C. chiropus form two distinctive mitochondrial clades each. Chiromyscus langbianis and C. chiropus show significant inconsistency in nuclear genes, whereas C. thomasi shows the same segregation pattern as can be traced by mitochondrial markers. The Northern and Southern phylogroups of C. thomasi appear to be distributed sympatrically with northern phylogroups of C. langbianis in most parts of eastern Indochina. The mitochondrial clades discovered are geographically subdivided and divergent enough to suspect independent subspecies within C. langbianis and C. thomasi. However, due to the insufficiency of obvious morphological traits, a formal description is not carried out here. The processes of recent fauna formation, species distribution patterns, dispersion routes and possible natural history in Indochina are discussed.

Markers for genetic change

Background and aims

Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question.

Methods

We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined.

Results

The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders.

Conclusions

Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.

A forgotten rodent from the Garden of Eden: what really happened to the long-tailed nesokia rat in the Mesopotamian marshes?

The greater part of expected mammalian extinctions will be of smaller-bodied mammals, including rats which are more generally known only as pests and carriers of pathogens. We address the long-tailed nesokia rat, which is among the least studied Palaearctic mammals. The species is known from merely five specimens, collected between March 1974 and January 1977 within a radius of 30 km around Qurna inside the seasonally flooded Mesopotamian marshes in southern Iraq. In the 1990s, this extensive aquatic habitat has been deliberately reduced to <15% of its original area and the IUCN expressed fear that such a disaster “almost certainly” caused the extinction of the long-tailed nesokia. Although the interventions after 2003 reversed the shrinking trend and marshes started to expand, the continuous presence of the long-tailed nesokia could not be unambiguously confirmed. We provide meagre evidence suggesting that the rat might be still present in the marshes. Next, our habitat modelling shows that the area of the long-tailed nesokia might be more extensive than expected with a highly suitable habitat covering 15,650 km2 of Mesopotamian marshland in Iraq (between Basra and Salah Ad Din provinces) and the Hawizeh Marshes in the adjacent Iranian Khuzestan.

Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support ($&gt;$ 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.

A simple skeletal measurement effectively predicts climbing behaviour in a diverse clade of small mammals

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.

Genome-Wide Microarray Analysis Suggests Transcriptomic Response May Not Play a Major Role in High- to Low-Altitude Acclimation in Harvest Mouse (Micromys minutus)

Simple Summary

Micromys minutus is a small rodent species that has a wide range of vertical distribution in Taiwan. By comparing the gene expression profile of the skeletal muscle tissues taken from individuals native to the high-altitude environment and those transferred to the low-altitude captive site, the Tnfrsf12a gene was demonstrated to have a differential expression pattern. Although this finding may be correlated with the altitude acclimation, the observation of only one gene transcript with significant alteration leads us to suggest that genetic response may not play a major role in altitude acclimation in M. minutus. Future comparative functional genomics studies involving other organ systems (in addition to skeletal muscles) and alarger sample size are warranted for better insight into the altitude acclimation of this small rodent species.

Abstract

The harvest mouse (Micromys minutus) is a small rodent species with a wide range of vertical distribution in Taiwan, extending from the sea level to 3100 m altitude. This species has recently suffered from habitat loss in high-altitude areas due to orchard cultivation, which may have resulted in mouse migration from high to low altitude. To investigate whether there is any physiological mechanism involved in altitude acclimation, rat cDNA microarray was used to compare transcriptomic patterns of the skeletal muscle tissues taken from individuals native to the high-altitude environment and those transferred to the low-altitude captive site. Of the 23,188 genes being analyzed, 47 (33 up-regulated and 14 down-regulated) were found to have differential expression (fold change > 4 or < −4, ANOVA p < 0.05). However, after multiple testing correction with a false discovery rate (FDR), only the result for Tnfrsf12a was found to be statistically significant (fold change = 13, FDR p < 0.05). The result was confirmed by quantitative polymerase chain reaction (q-PCR). The expression of Tnfrsf12a possibly relates to the skeletal muscle biology and thus can be correlated with altitude acclimation. However, finding only one gene transcript with significant alteration suggests that transcriptomic response may not play a major role in high- to low-altitude acclimation in harvest mouse.

What is in a genus name? Conceptual and empirical issues preclude the proposed recognition of Callibella (Callitrichinae) as a genus

In a recent article, Silva et al. (Zool Scr 47:133-143, 2018) proposed the relocation of the dwarf marmoset, Mico humilis, to the so far unrecognized genus Callibella. We contend that a taxonomic scheme that recognizes Callibella as if it were a valid genus is inadequately supported, and to some extent contradicted, by the ecological and morphological information provided by the authors. We discuss why the criterion of sympatry, invoked by Silva et al. to justify the recognition of Callibella at the genus level, is uninformative for taxonomic decisions above the species level. We also show that the morphological characteristics used by Silva et al. to separate Mico humilis from the other Mico are individually variable and present in every analyzed species of the genus. Moreover, we demonstrate that the Evolutionarily Distinct and Globally Endangered (EDGE) metric, employed by those authors to attempt to justify their taxonomic proposition, makes no sense in a taxonomic context. Conceptually, the use of autapomorphies and plesiomorphies to justify using Callibella goes against one of the main objectives of a meaningful classification, that is, to allow for all kinds of inferences based on previous observations (i.e., to be inductively projectible). Based on these arguments, we demonstrate that regarding Callibella as a subgenus of Mico is the most suitable way of making the Linnean taxonomy of marmosets congruent with the phylogenetic information available for the group.

Morphological Innovations and Vast Extensions of Mountain Habitats Triggered Rapid Diversification Within the Species-Rich Irano-Turanian Genus Acantholimon (Plumbaginaceae)

The Irano-Turanian floristic region spans a topographically complex and climatically continental territory, which has served as a source of xerophytic taxa for neighboring regions and is represented by a high percent of endemics. Yet, a comprehensive picture of the abiotic and biotic factors that have driven diversification within this biota remains to be established due to the scarcity of phylogenetic studies. Acantholimon is an important component of the subalpine steppe flora of the Irano-Turanian region, containing c. 200 cushion-forming sub-shrubby pungent-leaved species. Our recent molecular phylogenetic study has led to enlarging the circumscription of this genus to include eight mono- or oligospecific genera lacking the characteristic life-form and leaves. Using the same molecular phylogeny, here we investigate the tempo and mode of diversification as well as the biogeographic patterns in this genus, to test the hypothesis that a combination of key morphological innovations and abiotic factors is behind Acantholimon high species diversity. Molecular dating analysis indicates that Acantholimon s.l. started to diversify between the Late Miocene and the Pliocene and the biogeographic analysis points to an Eastern Iran-Afghanistan origin. Macroevolutionary models support the hypothesis that the high diversity of the genus is explained by accelerated diversification rates in two clades associated with the appearance of morphological key innovations such as a cushion life-form and pungent leaves; this would have favored the colonization of water-stressed, substrate-poor mountainous habitats along the newly uplifted IT mountains during the Mio-Pliocene. Given the apparent similarity of mountain habitats for most species of Acantholimon, we hypothesize that its current high species diversity responds to a scenario of non-adaptive radiation fueled by allopatric speciation rather than evolutionary radiation driven by ecological opportunity. Similar scenarios might underlie the high diversity of other speciose genera in the topographically complex Irano-Turanian landscape, though this remains to be tested with fine-grained distribution and climatic data.

Convergent evolution of an extreme dietary specialisation, the olfactory system of worm-eating rodents

Turbinal bones are key components of the mammalian rostrum that contribute to three critical functions: (1) homeothermy, (2) water conservation and (3) olfaction. With over 700 extant species, murine rodents (Murinae) are the most species-rich mammalian subfamily, with most of that diversity residing in the Indo-Australian Archipelago. Their evolutionary history includes several cases of putative, but untested ecomorphological convergence, especially with traits related to diet. Among the most spectacular rodent ecomorphs are the vermivores which independently evolved in several island systems. We used 3D CT-scans (N = 87) of murine turbinal bones to quantify olfactory capacities as well as heat or water conservation adaptations. We obtained similar results from an existing 2D complexity method and two new 3D methodologies that quantify bone complexity. Using comparative phylogenetic methods, we identified a significant convergent signal in the rostral morphology within the highly specialised vermivores. Vermivorous species have significantly larger and more complex olfactory turbinals than do carnivores and omnivores. Increased olfactory capacities may be a major adaptive feature facilitating rats' capacity to prey on elusive earthworms. The narrow snout that characterises vermivores exhibits significantly reduced respiratory turbinals, which may reduce their heat and water conservation capacities.

Fossils know it best: Using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Muridae)

Murid rodents (Rodentia: Muridae) represent the most diverse and abundant mammalian family. In this study, we provide a refined set of fossil calibrations which is used to reconstruct a dated phylogeny of the family using a multilocus dataset (six nuclear and nine mitochondrial gene fragments) encompassing 161 species representing 82 murid genera from four extant subfamilies (Deomyinae, Gerbillinae, Lophiomyinae and Murinae). In comparison with previous studies on murid or muroid rodents, our work stands out for the implementation of nine robust fossil constraints within the Muridae thanks to a thorough review of the fossil record. Before being assigned to specific nodes of the phylogeny, all potential fossil constraints were carefully assessed; they were also subjected to several cross-validation analyses. The resulting phylogeny is consistent with previous phylogenetic studies on murids, and recovers the monophyly of all sampled murid subfamilies and tribes. Based on nine controlled fossil calibrations, our inferred temporal timeframe indicates that the murid family likely originated in the course of the Early Miocene, 22.0-17.0 million years ago (Ma), and that most major lineages (i.e. tribes) started diversifying ca. 10 Ma. Historical biogeography analyses support the tropical origin for the family, with an initial internal split (vicariance event) between Afrotropical and Oriental (Indomalaya and Philippines) lineages. During the course of their diversification, the biogeographic pattern of murids is marked by several dispersal events toward the Australasian and the Palearctic regions. The Afrotropical region was also secondarily colonized at least three times from the Indomalaya, indicating that the latter region has acted as a major centre of diversification for the family.

A short review and worldwide list of wild albino rodents with the first report of albinism in Coendou rufescens (Rodentia: Erethizontidae)

Aberrant pelage color patterns such as albinism have been reported in some mammal groups including rodents, but in spite of the group’s richness, the phenomenon is relatively poorly documented in the literature. Albino specimens are reported in <2% of the species of rodents, four records of neotropical species were found (Delomys dorsalis, Heteromys anomalus, Octodon degus, Phyllotis andium). Of New World porcupines (Erethizontidae), albinism was documented only in the North American species Erethizon dorsatum. Here we report the first albino record from the Neotropics for this group, a stump-tailed porcupine (Coendou rufescens) in northern Ecuador.

Quaternary vertebrate faunas from Sumba, Indonesia: implications for Wallacean biogeography and evolution

Historical patterns of diversity, biogeography and faunal turnover remain poorly understood for Wallacea, the biologically and geologically complex island region between the Asian and Australian continental shelves. A distinctive Quaternary vertebrate fauna containing the small-bodied hominin Homo floresiensis, pygmy Stegodon proboscideans, varanids and giant murids has been described from Flores, but Quaternary faunas are poorly known from most other Lesser Sunda Islands. We report the discovery of extensive new fossil vertebrate collections from Pleistocene and Holocene deposits on Sumba, a large Wallacean island situated less than 50 km south of Flores. A fossil assemblage recovered from a Pleistocene deposit at Lewapaku in the interior highlands of Sumba, which may be close to 1 million years old, contains a series of skeletal elements of a very small Stegodon referable to S. sumbaensis, a tooth attributable to Varanus komodoensis, and fragmentary remains of unidentified giant murids. Holocene cave deposits at Mahaniwa dated to approximately 2000–3500 BP yielded extensive material of two new genera of endemic large-bodied murids, as well as fossils of an extinct frugivorous varanid. This new baseline for reconstructing Wallacean faunal histories reveals that Sumba's Quaternary vertebrate fauna, although phylogenetically distinctive, was comparable in diversity and composition to the Quaternary fauna of Flores, suggesting that similar assemblages may have characterized Quaternary terrestrial ecosystems on many or all of the larger Lesser Sunda Islands.

Sperm morphology of the Rattini – are the interspecific differences due to variation in intensity of intermale sperm competition?

It is widely accepted that in mammals a causal relationship exists between postcopulatory sexual selection and relative testes mass of the species concerned, but how much it determines sperm size and shape is debatable. Here we detailed for the largest murine rodent tribe, the Rattini, the interspecific differences in relative testes mass and sperm form. We found that residual testes mass correlates with sperm head apical hook length as well as its angle, together with tail length, and that within several lineages a few species have evolved highly divergent sperm morphology with a reduced or absent apical hook and shorter tail. Although most species have a relative testes mass of 1–4%, these derived sperm traits invariably co-occur in species with much smaller relative testes mass. We therefore suggest that high levels of intermale sperm competition maintain a sperm head with a long apical hook and long tail, whereas low levels of intermale sperm competition generally result in divergent sperm heads with a short or non-existent apical hook and shorter tail. We thus conclude that sexual selection is a major selective force in driving sperm head form and tail length in this large tribe of murine rodents.

Genetic diversity and evolution of Pneumocystis fungi infecting wild Southeast Asian murid rodents

Pneumocystis organisms are airborne-transmitted fungal parasites that infect the lungs of numerous mammalian species with strong host specificity. In this study, we investigated the genetic diversity and host specificity of Pneumocystis organisms infecting Southeast Asian murid rodents through PCR amplification of two mitochondrial genes and tested the co-phylogeny hypothesis among these fungi and their rodent hosts. Pneumocystis DNA was detected in 215 of 445 wild rodents belonging to 18 Southeast Asian murid species. Three of the Pneumocystis lineages retrieved in our phylogenetic trees correspond to known Pneumocystis species, but some of the remaining lineages may correspond to new undescribed species. Most of these Pneumocystis species infect several rodent species or genera and some sequence types are shared among several host species and genera. These results indicated a weaker host specificity of Pneumocystis species infecting rodents than previously thought. Our co-phylogenetic analyses revealed a complex evolutionary history among Pneumocystis and their rodent hosts. Even if a significant global signal of co-speciation has been detected, co-speciation alone is not sufficient to explain the observed co-phylogenetic pattern and several host switches are inferred. These findings conflict with the traditional view of a prolonged process of co-evolution and co-speciation of Pneumocystis and their hosts.

Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates

We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.

Masticatory muscle architecture in a water-rat from Australasia (Murinae, Hydromys) and its implication for the evolution of carnivory in rodents

Murines are well known for their generalist diet, but several of them display specializations towards a carnivorous diet such as the amphibious Indo-Pacific water-rats. Despite the fact that carnivory evolved repeatedly in this group, few studies have investigated associated changes in jaw muscle anatomy and biomechanics. Here, we describe the jaw muscles and cranial anatomy of a carnivorous water-rat, Hydromys chrysogaster. The architecture of the jaw musculature of six specimens captured both on Obi and Papua were studied and described using dissections. We identified the origin and insertions of the jaw muscles, and quantified muscle mass, fiber length, physiological cross-sectional area, and muscle vectors for each muscle. Using a biomechanical model, we estimated maximum incisor and molar bite force at different gape angles. Finally, we conducted a 2D geometric morphometric analyses to compare jaw shape, mechanical potential, and diversity in lever-arm ratios for a set of 238 specimens, representative of Australo-Papuan carnivorous and omnivorous murids. Our study reveals major changes in the muscle proportions among Hydromys and its omnivorous close relative, Melomys. Hydromys was found to have large superficial masseter and temporalis muscles as well as a reduced deep masseter and zygomatico-mandibularis, highlighting major functional divergence among omnivorous and carnivorous murines. Changes in these muscles are also accompanied by changes in jaw shape and the lines of action of the muscles. A more vertically oriented masseter, reduced masseteric muscles, as well as an elongated jaw with proodont lower incisors are key features indicative of a reduced propalinality in carnivorous Hydromys. Differences in the fiber length of the masseteric muscles were also detected between Hydromys and Melomys, which highlight potential adaptations to a wide gape in Hydromys, allowing it to prey on larger animals. Using a biomechanical model, we inferred a greater bite force in Hydromys than in Melomys, implying a functional shift between omnivory and carnivory. However, Melomys has an unexpected greater bite force at large gape compared with Hydromys. Compared with omnivorous Melomys, Hydromys have a very distinctive low mandible with a well-developed coronoid process, and a reduced angular process that projects posteriorly to the ascending rami. This jaw shape, along with our mechanical potential and jaw lever ratio estimates, suggests that Hydromys has a faster jaw closing at the incisor, with a higher bite force at the level of the molars. The narrowing of the Hydromys jaw explains this higher lever advantage at the molars, which constitutes a good compromise between a wide gape, a reduced anterior masseteric mass, and long fiber lengths. Lever arms of the superficial and deep masseter are less favourable to force output of the mandible in Hydromys but more favourable to speed. Compared with the small input lever arm defined between the condyle and the angular process, the relatively longer mandible of Hydromys increases the speed at the expense of the output force. This unique combination of morphological features of the masticatory apparatus possibly has permitted Hydromys to become a highly successful amphibious predator in the Indo-Pacific region.

Least speciose among the most speciose: Natural history correlates of monospecific and bispecific genera of Rodentia and Soricomorpha

Monospecific and bispecific genera are of special concern as they represent unique phylogenetic/evolutionary trajectories within larger clades. In addition, as phylogenetically older taxa are supposed to be exposed to higher rarity and extinction risk, monospecific and bispecific genera may be intrinsically more prone to extinction risks than multispecies genera, although extinction risks also depend on the ecological and biological strategy of the species. Here, the distribution across biogeographical zones and the levels of threat to 2 speciose orders of mammals (monospecific and bispecific genera of Rodentia and Soricomorpha) are investigated in order to highlight major patterns at the worldwide scale. In Rodentia, 39.7% of the genera (n = 490) were monospecific and 17.9% were bispecific. In Soricomorpha, 44.4% of the total genera (n = 45) were monospecific and 15% were bispecific. There was a positive correlation between the number of monospecific genera and the total number of genera per family. Peaks of monospecific and bispecific genera richness were observed in Neotropical, Oriental and Afrotropical regions in rodents and in the Palearctic region in soricomorphs. Range size was significantly uneven across biogeographic region in rodents (with larger ranges in Nearctic and Oriental regions and smaller ranges in the Australian region), but there was no difference across biogeographic regions in terms of range size in soricomorphs. Most of the monospecific and bispecific genera occurred in forest habitat in both taxa. The frequency distribution of the monospecific and bispecific genera across IUCN categories did not differ significantly from the expected pattern using the total rodent genera and the multispecies genera.

Rodent management issues in South Pacific islands: a review with case studies from Papua New Guinea and Vanuatu

Rodents are a key pest to agricultural and rural island communities of the South Pacific, but there is limited information of their impact on the crops and livelihoods of small-scale farmers. The rodent pest community is known, but the type and scales of damage to different crops on different islands are unknown. Knowledge about rodent pest management in other geographical regions may not be directly transferable to the Pacific region. Many studies on islands have largely focussed on the eradication of rodents from uninhabited islands for conservation benefits. These broadscale eradication efforts are unlikely to translate to inhabited islands because of complex social and agricultural issues. The livelihoods, culture and customs of poor small-scale farmers in the South Pacific have a large bearing on the current management of rodents. The aim of the present review was to describe the rodent problems, impacts and management of rodents on South Pacific islands, and identify gaps for further research. We compared and contrasted two case studies. The situation in Papua New Guinea is emergent as several introduced rodent species are actively invading new areas with wide-ranging implications for human livelihoods and conservation. In Vanuatu, we show how rodent damage on cocoa plantations can be reduced by good orchard hygiene through pruning and weeding, which also has benefits for the management of black pod disease. We conclude that (1) damage levels are unknown and unreported, (2) the impacts on human health are unknown, (3) the relationships between the pest species and their food sources, breeding and movements are not known, and (4) the situation in Papua New Guinea may represent an emergent crisis that warrants further investigation. In addition, there is a need for greater understanding of the invasive history of pest rodents, so as to integrate biological information with management strategies. Ecologically based rodent management can be achieved on Pacific Islands, but only after significant well funded large-scale projects are established and rodent ecologists are trained. We can learn from experiences from other locations such as Southeast Asia to guide the way.

Repeated evolution of carnivory among Indo-Australian rodents

Convergent evolution, often observed in island archipelagos, provides compelling evidence for the importance of natural selection as a generator of species and ecological diversity. The Indo-Australian Archipelago (IAA) is the world's largest island system and encompasses distinct biogeographic units, including the Asian (Sunda) and Australian (Sahul) continental shelves, which together bracket the oceanic archipelagos of the Philippines and Wallacea. Each of these biogeographic units houses numerous endemic rodents in the family Muridae. Carnivorous murids, that is those that feed on animals, have evolved independently in Sunda, Sulawesi (part of Wallacea), the Philippines, and Sahul, but the number of origins of carnivory among IAA murids is unknown. We conducted a comprehensive phylogenetic analysis of carnivorous murids of the IAA, combined with estimates of ancestral states for broad diet categories (herbivore, omnivore, and carnivore) and geographic ranges. These analyses demonstrate that carnivory evolved independently four times after overwater colonization, including in situ origins on the Philippines, Sulawesi, and Sahul. In each biogeographic unit the origin of carnivory was followed by evolution of more specialized carnivorous ecomorphs such as vermivores, insectivores, and amphibious rats.

Phylogeny and biogeography of species of Syphacia Seurat, 1916 (Nemata : Oxyurida : Oxyuridae) from the Australian Bioregion

Pinworm nematodes of the genus Syphacia (Nemata : Oxyurida : Oxyuridae) have a global distribution, and infect the caecum of rodents. Within the Australian Bioregion, 17 species of Syphacia infect a range of rodent hosts. Pinworms are traditionally thought to have coevolutionary relationships with their hosts, but the evolution and dispersal of Australian rodents and their helminths remains unclear. This combination of factors allowed us to investigate the likely relationships of Australian Syphacia species based on phylogenetic analysis, overlaid with the ecology and relationships of host species. We conducted a phylogenetic analysis using morphological characters of the species of Syphacia from the Australian Bioregion in order to examine the relationships between species, and to investigate how host evolution and phylogeny could inform (or be informed) by parasite phylogeny. Application of the taxon pulse theory of parasite speciation by matching host species to parasites shed some light on the timing of speciation of rodent hosts. We found that species of Syphacia had reasonably close host–parasite relationships, with additional evidence for ecological fitting or host switching occurring. Evidence provided here suggests strongly that most elements of the Stockholm Paradigm are at play in structuring the relationships we observe in this pinworm–mammal system.

Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents

Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of Pakistan, have served as one of the best-known fossil calibration points in molecular phylogenic studies. Although these fossils have been widely used as the 12 Ma date for the Mus/Rattus split or a more basal split, conclusive paleontological evidence for the nodal assignments has been absent. This study analyzes newly recognized characters that demonstrate lineage separation in the fossil record of Siwalik murines and examines the most reasonable nodal placement of the diverging lineages in a molecular phylogenetic tree by ancestral state reconstruction. Our specimen-based approach strongly indicates that Siwalik murines of the Karnimata clade are fossil members of the Arvicanthini-Otomyini-Millardini clade, which excludes Rattus and its relatives. Combining the new interpretation with the widely accepted hypothesis that the Progonomys clade includes Mus, the lineage separation event in the Siwalik fossil record represents the Mus/Arvicanthis split. Our test analysis on Bayesian age estimates shows that this new calibration point provides more accurate estimates of murine divergence than previous applications. Thus, we define this fossil calibration point and refine two other fossil-based points for molecular dating.

Syphacia (Syphacia) maxomyos sp. n. (Nematoda: Oxyuridae) from Maxomys spp. (Rodentia: Muridae) from Sulawesi and Sumatra, Indonesia

The present report describes Syphacia (Syphacia) maxomyos sp. n. (Nematoda: Oxyuridae) from two species of spiny rats, Maxomys musschenbroekii from Sulawesi and M. whiteheadi from Sumatra. It is characterized by a cephalic plate extending laterally with dorsoventral constriction and stumpy eggs with an operculum rim reaching pole. It is readily distinguishable by the former feature from all of hitherto known representatives of this genus in Indonesia, but it resembles parasites in Murini and Hydromyni rodents in continental Asia and Sahul. This is the first Syphacia species distributed in both the Sunda Shelf and Sulawesi with the exception of Syphacia muris, a cosmopolitan pinworm found in rodents of the of genus Rattus. It is surmised that S. maxomyos is specific to Maxomys and that it was introduced to Sulawesi by dispersal of some Maxomys from the Sunda Shelf.

Progress on research on rodents and rodent-borne zoonoses in South-east Asia

This review aims to synthesise knowledge regarding the taxonomy of South-east Asian murine rodents and the challenges associated with the identification of habitat preferences and associated rodent-borne diseases. Recent studies concerning the Rattini tribe have identified unclear species boundaries that would benefit from further investigation. The development of barcoding may allow more accurate identification of rodents, specifically for complex species. However, knowledge on the distribution and habitat specialisations of many common murine rodents is still scarce, particularly regarding the specific habitat preferences of most synanthropic rodent species (Rattus tanezumi or Rattus exulans). Several studies have analysed the prevalence of major rodent-borne diseases in South-east Asia and it appears that the greatest risk of rodent zoonoses are in the lowland rain-fed and irrigated landscapes, generally in and around rice fields.