Specimen collection is essential for modern science

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.

A new genus and species of shrew-like mouse (Rodentia: Muridae) from a new center of endemism in eastern Mindanao, Philippines

The Philippine archipelago hosts an exceptional diversity of murid rodents that have diversified following several independent colonization events. Here, we report the discovery of a new species of rodent from Mt. Kampalili on eastern Mindanao Island. Molecular and craniodental analyses reveal this species as a member of a Philippine "New Endemic" clade consisting of Tarsomys, Limnomys, and Rattus everetti (tribe Rattini). This new species of "shrew-mouse" is easily distinguished from its relatives in both craniodental and external characteristics including a long, narrow snout; small eyes and ears; short, dark, dense fur dorsally and ventrally; stout body with a tapering, visibly haired tail shorter than head and body length; stout forepaws; bulbous and nearly smooth braincase; narrow, tapering rostrum; short incisive foramina; slender mandible; and narrow, slightly opisthodont incisors. This new genus and species of murid rodent illustrates that murids of the tribe Rattini have exhibited greater species and morphological diversification within the Philippines than previously known and provides evidence that Mt. Kampalili represents a previously unrecognized center of mammalian endemism on Mindanao Island that is deserving of conservation action.

Molecular assessment of dietary niche partitioning in an endemic island radiation of tropical mammals

Island radiations represent unique evolutionary histories in unique ecological contexts. These radiations provide opportunities to investigate ecological diversification in groups that typically exhibit niche partitioning among their constituents, including partitioning of food resources. DNA metabarcoding produces finer levels of diet identification than traditional methods, allowing us to examine dietary niche partitioning in communities or clades in which species share superficially similar diets. Here, we use DNA metabarcoding to investigate dietary niche partitioning in an endemic radiation of mammals in the Philippines. Our data reveal niche partitioning as well as phylogenetically-uncorrelated adaptive evolution in this small mammal community. Because 70% of the focal species belong to the tribe Chrotomyini, an endemic Philippine radiation of murid rodents that feed extensively on earthworms, this study sheds light on dietary adaptation and its role in the co-occurrence of closely related species. Our results reveal fine-scale resource partitioning within this community; our data provide compelling evidence for niche partitioning of diet that was masked by previous diet categories and will help in further dissecting the model adaptive radiation of endemic small mammals on Luzon. This study reinforces the notion that DNA metabarcoding can be a valuable tool for investigating both ecological relationships and evolutionary ecology at the community and phylogenetic level, respectively.

Three new extinct species from the endemic Philippine cloud rat radiation (Rodentia, Muridae, Phloeomyini)

The 18 extant members of the Tribe Phloeomyini, the “cloud rats,” constitute an endemic Philippine radiation of arboreal herbivores that range in size from ca. 18 g to 2.7 kg, most occurring in cloud forest above 1,200 m elevation. Although calibrated phylogenies indicate that the Phloeomyini is estimated to have begun diversifying within the Philippines by ca. 10–11 million years ago, no extinct fossil species have been described, severely limiting our understanding of this distinctive radiation. Our studies of fossil and subfossil small mammal assemblages from the lowland Callao Caves complex in NE Luzon, Philippines, have produced specimens of Phloeomyini that date from ca. 67,000 BP to the Late Holocene (ca. 4,000 to 2,000 BP). We identify three extinct species that we name as new members assigned to the genera Batomys, Carpomys, and Crateromys, distinguished from congeners by body size, distinctive dental and other morphological features, and occupancy of a habitat (lowland forest over limestone) that differs from the high-elevation mossy forest over volcanic soils occupied by their congeners. Batomys cagayanensis n. sp. is known only from two specimens from ca. 67,000 BP; Carpomys dakal n. sp. and Crateromys ballik n. sp. were present from ca. 67,000 BP to the Late Holocene. These add to the species richness and morphological diversity of this endemic Philippine radiation of large folivores, and show specifically that the lowland fauna of small mammals on Luzon was more diverse in the recent past than it is currently, and that Luzon recently supported five species of giant rodents (ca. 1 kg or more). All three occurred contemporaneously with Homo luzonensis, and two, the new Carpomys and Crateromys, persisted until the Late Holocene when multiple exotic mammal species, both domestic and invasive, were introduced to Luzon, and new cultural practices (such as making pottery) became evident, suggesting that modern humans played a role in their extinction.

Philippine bats of the genus Kerivoula (Chiroptera: Vespertilionidae): Overview and assessment of variation in K. pellucida and K. whiteheadi

Bats of the genus Kerivoula (Mammalia, Chiroptera) are widespread in the Philippines with four reported species, but have been poorly known due to a paucity of specimens. We provide the first molecular phylogeny for Philippine Kerivoula, which supports the existence of four distinct clades that we treat as species (K. hardwickii, K. papillosa, K. pellucida, and K. whiteheadi); these four overlap broadly geographically. Each of these may be recognized on the basis of cytochrome b sequences and external and craniodental morphology. Detailed examination of K. pellucida shows little geographic differentiation within the Philippines, but they differ subtly from those on the Sunda Shelf. We consider K. whiteheadi to be composed of four recognizable clades, each restricted to a geographic region within the Philippines. We consider K. bicolor, from peninsular Thailand, and K. pusilla, from Borneo, to be distinct from K. whiteheadi. Our data indicate the presence of two species within the Philippines currently lumped as K. hardwickii; further study of these is needed. A calibrated phylogeny suggests that Kerivoula began arriving in the Philippines about 10 MYA, with each of the four current lineages arriving independently.

Interspecific diversity of testes mass and sperm morphology in the Philippine chrotomyine rodents: implications for differences in breeding systems across the species

The high diversity of native Philippine murid rodents includes an old endemic group, the chrotomyines, which are the sister group of the Australasian hydromyines. Herein we detail their interspecific diversity of relative testes mass (RTM) and sperm morphology. We find that in chrotomyines, as in the Australasian hydromyines, testes mass relative to body mass differs by an order of magnitude across the species and ranges from a large RTM in Soricomys and Chrotomys species to a small RTM in Apomys. Sperm morphology is associated with these findings, with individuals in species of Soricomys and Chrotomys producing relatively larger spermatozoa with a prominent apical hook and long tail, whereas, by contrast, the Apomys species have a sperm head that either has a very short or no apical hook and a shorter tail. These findings indicate coevolution of RTM with sperm morphological traits across the species, with the marked interspecific differences in RTM suggesting differences in the intensity of intermale sperm competition and hence breeding system. Thus, we hypothesise that species of Soricomys and Chrotomys that produce more streamlined spermatozoa with longer tails have a polyandrous or promiscuous mating system, whereas the Apomys species, which produce smaller and less streamlined spermatozoa, may exhibit monogamy.

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.

Two new species of shrew-rats (Rhynchomys: Muridae: Rodentia) from Luzon Island, Philippines

The murine genus Rhynchomys includes the large-bodied Philippine “shrew-rats,” highly specialized members of the vermivorous clade of Philippine murids. Four species are recognized, all of which are endemic to Luzon Island: R. soricoides from mountains within the Central Cordillera, R. isarogensis from Mt. Isarog on the Bicol Peninsula, R. banahao from Mt. Banahaw in south-central Luzon, and R. tapulao from Mt. Tapulao in the Zambales Mountains. Field surveys in 2006 and 2008 revealed two additional populations of Rhynchomys, one from Mt. Labo (1,544 m), a dormant stratovolcano at the base of the Bicol Peninsula, the other from Mt. Mingan (1,901 m), the highest peak in the central Sierra Madre of east-central Luzon. Assessment of external and craniodental features of available specimens from throughout Luzon support our description of the populations on Mt. Labo and Mt. Mingan as new species. All species of Rhynchomys are restricted to high-elevation, montane, and mossy forest habitats, separated by intervening lowlands. These discoveries highlight the importance of isolated highland areas in the historical diversification of Southeast Asian murines, and as current centers of endemism.

Tempo and mode of mandibular shape and size evolution reveal mixed support for incumbency effects in two clades of island-endemic rodents (Muridae: Murinae)

Existing radiations in a spatially limited system such as an oceanic island may limit the ecological opportunity experienced by later colonists, resulting in lower macroevolutionary rates for secondary radiations. Additionally, potential colonists may be competitively excluded by these incumbent (resident) species, unless they are biologically distinct (biotic filtering). The extant phenotypic diversity of secondary colonists may thus be impacted by lower rates of phenotypic evolution, exclusion from certain phenotypes, and transitions to new morphotypes to escape competition from incumbent lineages. We used geometric morphometric methods to test whether the rates and patterns of mandibular evolution of the Luzon "old endemic" rodent clades, Phloeomyini and Chrotomyini, are consistent with these predictions. Each clade occupied nearly completely separate shape space and partially separate size space. We detected limited support for decelerating and clade-specific evolutionary rates for both shape and size, with strong evidence for a shift in evolutionary mode within Chrotomyini. Our results suggest that decelerating phenotypic evolutionary rates are not a necessary result of incumbency interactions; rather, incumbency effects may be more likely to determine which clades can become established in the system. Nonincumbent clades that pass a biotic filter can potentially exhibit relatively unfettered evolution.

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.

Diversification rates of the "Old Endemic" murine rodents of Luzon Island, Philippines are inconsistent with incumbency effects and ecological opportunity

Diversity-dependent cladogenesis occurs when a colonizing lineage exhibits increasing interspecific competition as it ecologically diversifies. Repeated colonization of a region by closely related taxa may cause similar effects as species within each lineage compete with one another. This may be particularly relevant for secondary colonists, which could experience limited diversification due to competition with earlier, incumbent colonists over evolutionary time. We tested the hypothesis that an incumbent lineage may diminish the diversification of secondary colonists in two speciose clades of Philippine "Old Endemic" murine rodents-Phloeomyini and Chrotomyini-on the relatively old oceanic island of Luzon. Although phylogenetic analyses confirm the independent, noncontemporaneous colonization of Luzon by the ancestors of these two clades, we found no support for arrested diversification in either. Rather, it appears that diversification of both clades resulted from constant-rate processes that were either uniform or favored the secondary colonists (Chrotomyini), depending on the method used. Our results suggest that ecological incumbency has not played an important role in determining lineage diversification among Luzon murines, despite sympatric occurrence by constituent species within each lineage, and a substantial head start for the primary colonists.

Colonization and diversification of the white-browed shortwing (Aves: Muscicapidae: Brachypteryx montana) in the Philippines

Molecular phylogenetic approaches have greatly improved our knowledge of the pattern and process of biological diversification across the globe; however, many regions remain poorly documented, even for well-studied vertebrate taxa. The Philippine archipelago, one of the least-studied 'biodiversity hotspots', is an ideal natural laboratory for investigating the factors driving diversification in an insular and geologically dynamic setting. We investigated the history and geography of diversification of the Philippine populations of a widespread montane bird, the White-browed Shortwing (Brachypteryx montana). Leveraging dense archipelago-wide sampling, we generated a multi-locus genetic dataset (one nuclear and two mtDNA markers), which we analyzed using phylogenetic, population genetic, and coalescent-based methods. Our results demonstrate that Philippine shortwings (1) likely colonized the Philippines from the Sunda Shelf to Mindanao in the late Miocene or Pliocene, (2) diversified across inter-island barriers into three divergent lineages during the Pliocene and early Pleistocene, (3) have not diversified within the largest island, Luzon, contrary to patterns observed in other montane taxa, and (4) colonized Palawan from the oceanic Philippines rather than from Borneo, challenging the assumption of Palawan functioning exclusively as a biogeographic extension of the Sunda Shelf. Additionally, our finding that divergent (c. 4.0 mya) lineages are coexisting in secondary sympatry on Mindanao without apparent gene flow suggests that the speciation process is likely complete for these shortwing lineages. Overall, these investigations provide insight into how topography and island boundaries influence diversification within remote oceanic archipelagos and echo the results of many other studies in demonstrating that taxonomic diversity continues to be underestimated in the Philippines.

Oceanic island biogeography through the lens of the general dynamic model: assessment and prospect

The general dynamic model of oceanic island biogeography (GDM) has added a new dimension to theoretical island biogeography in recognizing that geological processes are key drivers of the evolutionary processes of diversification and extinction within remote islands. It provides a dynamic and essentially non-equilibrium framework generating novel predictions for emergent diversity properties of oceanic islands and archipelagos. Its publication in 2008 coincided with, and spurred on, renewed attention to the dynamics of remote islands. We review progress, both in testing the GDM's predictions and in developing and enhancing ecological-evolutionary understanding of oceanic island systems through the lens of the GDM. In particular, we focus on four main themes: (i) macroecological tests using a space-for-time rationale; (ii) extensions of theory to islands following different patterns of ontogeny; (iii) the implications of GDM dynamics for lineage diversification and trait evolution; and (iv) the potential for downscaling GDM dynamics to local-scale ecological patterns and processes within islands. We also consider the implications of the GDM for understanding patterns of non-native species diversity. We demonstrate the vitality of the field of island biogeography by identifying a range of potentially productive lines for future research.

The mammals of Mt. Amuyao: a richly endemic fauna in the Central Cordillera of northern Luzon Island, Philippines

Faunas of old oceanic islands often have extremely high levels of endemism and are considered highly susceptible to anthropogenic disruption. We surveyed the richly endemic small mammal fauna on Mt. Amuyao in the Central Cordillera of northern Luzon Island, Philippines. We tested hypotheses regarding elevational patterns of species richness and community composition, community response to habitat disturbance, and interactions of native and non-native mammals. Our study revealed greater species richness and faunal heterogeneity within the Central Cordillera than previously suspected. We documented 15 native species (14 rodents and 1 insectivore), and two species of non-native rodents. All of the native species are endemic to the Philippines, eight being restricted to the Cordillera. Twelve of the 14 native rodents belong to two ancient endemic clades, indicating that most of the regional diversity is the product of

Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats

Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule-coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries suggested by GMYC. In our simulations, GMYC performed relatively well (errors in estimated species diversity less than 25%) when the product of the haploid effective population size (N(e)) and speciation rate (SR; per lineage per million years) was less than or equal to 10(5), while interspecific variation in N(e) was twofold or less. However, at higher but also biologically relevant values of N(e) × SR and when N(e) varied tenfold among species, performance was very poor. GMYC analyses of mitochondrial DNA sequences from Philippine Hipposideros suggest actual diversity may be approximately twice the current estimate, and available echolocation call data are mostly consistent with GMYC delimitations. In conclusion, we consider the GMYC model useful under some conditions, but additional information on N(e), SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results.

The impact of conservation on the status of the world's vertebrates

Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.