Article

Molecular and morphological systematics of the Bunomys division (Rodentia: Muridae), an endemic radiation on Sulawesi

Authors:
  • Research Center for Biosystematic and Evolution
To read the full-text of this research, you can request a copy directly from the authors.

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 placed B. fratrorum among other genera and inferred Paruromys as sister to the type species of Taeromys (T. celebensis). We resolve these issues by resurrecting Frateromys, a genus under which B. fratrorum was once placed, and returning Paruromys dominator to Taeromys. Within three species, F. fratrorum, T. callitrichus, and T. taerae, we recovered Pleistocene age divergences between populations sampled across the northern peninsula of Sulawesi; divergence between western and eastern populations of F. fratrorum may reflect the existence of two species.

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the authors.

... Furthermore, there have been no comprehensive studies of this species. Although a previous study about this species has been done by Handika et al. (2020), the study cannot fully explain the variation because it lacks a representative number of samples and distribution. Through this study, we aim to determine if there are any patterns to the morphological variations of the Paruromys dominator using more representative samples. ...
... This result agrees with those of Csanady and Mosansky (2018) and Musser (2014), who found that rodents have no sexual dimorphism in skull size or morphology. On the other hand, our findings reject < 2.2e-16 *** <2e-16 *** 1.77e-07 *** <2e-16 *** 3.44e-14 *** <2e-16 *** 3.24e-06 *** 8.39e-10 *** < 2.2e-16 *** 1.3e-08 *** 0.000289 *** 0.0123 * 5.7e-11 *** 0.532 <2e-16 *** 2.2e-16 *** This result is in line with the findings of a previous study on P. dominator (Handika et al. 2020). AGNES clustering showed that elevation also failed to correlate with the skull morphology in P. dominator. ...
Article
Full-text available
Correlations between natural geographic boundaries and variations in organisms' morphology have been well-documented in Sulawesi Island, which has a unique geological history and hundreds of endemic species. One of the widely distributed species of small mammals is Sulawesi giant rat (Paruromys dominator). Considering the geographic condition of Sulawesi, this species is a suitable model for studying geographic influences on morphological change. Moreover, there are no comprehensive studies on this species. Previous studies cannot fully explain the variability due to the lack of representative samples. Here, we measure 19 skull characteristics for 131 adult complete-skull specimens from six distribution areas in Sulawesi. We investigate the variation in skull characteristics using agglomeration nesting (AGNES) for cluster analysis and the standardized major axis (SMA) for allometry analysis. Our results show that P. dominator can be categorized into two groups, but distribution areas, elevation, or sex do not influence those. P. dominator in group 1 had a larger skull size than group 2. The two groups can be distinguished from four characteristics: breadth of mesopterygoid fossa (BMF), breadth of first upper molar (BM1), length of the auditory bulla (LB), and breadth of incisive foramina (BIF). The BMF and BM1 are related to mastication, and the LB and BIF are related to communication. We propose that the skull variation of this species is not correlated with geographical barriers but more clearly correlated with their feeding habits, mating behavior, and ability to escape predation. These findings were useful for future studies on the taxonomic status of P. dominator.
... Samples with "sp." were not identified to species for this study. Generic taxonomy for murines followsHandika et al. (2021). Taxonomy for Crocidura followsEsselstyn et al. (2021). ...
... The tribe Rattini is a minor component within this region and is mainly of relatively recent Asian origin. Recent discoveries, such as the description of four species of the Moluccan endemic murine genus Halmaheramys (Fabre et al., 2013(Fabre et al., , 2018Aplin et al., 2023), have highlighted that part of the Moluccan murine fauna is related to faunal elements of Asian rather than Sahulian origin, in particular the Sulawesian lineages Bunomys, Lenomys, Frateromys, Eropeplus and Taeromys, as well as the Philippine Bullimus and Sundaland Sundamys (Handika et al., 2021). In previous molecular studies, several Moluccan Rattus taxa were not placed in a phylogenetic framework, and therefore their affinities with Asian or Australo-Papuan faunas could not be assessed or clearly understood. ...
... Many of the inter-arm bays shrank in the last 4 million years leading to the coalescence of paleo-islands of Sulawesi, especially during the Pleistocene [88][89][90][91] . Many vertebrates show geographicbased population structure that re ects this history, such as Draco lizards [92] , Bunomys rodents [93] , Limnonectes frogs [94] , and studies on macaque monkeys and Celebes toads have led to the establishment of areas of endemism (AOEs [95][96][97][98] ), which are not re ected in Sulawesi rice paddy snakes. ...
Preprint
Full-text available
Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus ), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus , indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.
... However, Sulawesi biogeography is more interesting than even Wallace and other early investigators appreciated, because substantial regional in situ diversification also characterizes the Sulawesi biota. Many studies have identified examples of regional in situ diversification among terrestrial taxa including cicadas (Duffels 1990;de Boer and Duffels 1996), Chitaura grasshoppers (Walton et al. 1997;Butlin et al. 1998;Bridle et al. 2001), cockroaches (Maekawa et al. 2001), Limnonectes fanged frogs (Evans et al. 2003a, Setiadi et al. 2011, Celebes toads (Evans et al. 2003c(Evans et al. , 2008, Lamprolepis emerald skinks (Linkem et al. 2013), phalangers (Ruedas and Morales 2005), shrews (Esselstyn et al. 2009Eldridge et al. 2018), rodents (Esselstyn et al. 2012;Achmadi et al. 2013;Rowe et al. 2016aRowe et al. , 2019Giarla et al. 2018;Handika et al. 2021;Rowe et al. 2016b), tarsiers (Merker et al. 2009;Shekelle et al. 2010;Driller et al. 2015), anoas (Schreiber et al. 1999;Frantz et al. 2018), and forest pigs and babirusas (Frantz et al. 2018). In addition, there are impressive examples of in situ diversification in freshwater aquatic environments (von Rintelen et al. 2012), including in streams and the ancient deep-water rift lakes of central Sulawesi, as revealed by studies of aquatic snails (von Rintelen and Glaubrecht 2005;von Rintelen et al. 2007a, b, c;Glaubrecht and von Rintelen 2008), crabs (Schubart and Ng 2008), shrimps (von Rintelen et al. 2007a(von Rintelen et al. , 2010b, and fishes (Takehana et al. 2005;Mokodongan and Yamahira 2015;Mandagi et al. 2021;Utama et al. 2022). ...
Article
Full-text available
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of regional diversification, this has rarely been tested in the context of an explicit geological framework. Here we provide a tectonically-informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciation have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species - nine on Sulawesi proper and six on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present.
... The complexity of Sulawesi's geological history (Nugraha and Hall, 2018), its extensive ecogeographic variation (Whitten et al., 1987), and its tropical location are all factors that helped foster high levels of biodiversity. Researchers have also documented consistent geographical patterns of genetic partitioning among several ecologically and phylogenetically disparate animal taxa (e.g., toads, primates, and mice; Evans et al., 2003Evans et al., , 2008Merker et al., 2009;Giarla et al., 2018;Handika et al. 2021). The consistent locations of inter-and intraspecific genetic breaks on Sulawesi have led biologists to delineate several areas of endemism (Evans et al., 2003), which are largely defined by the boundaries between the central part of the island and the peninsulas. ...
Article
After nearly a decade of field inventories in which we preserved voucher specimens of the small terrestrial mammals of Sulawesi, we combined qualitative and quantitative analyses of morphological traits with molecular phylogenetics to better understand the diversity of shrews (Soricidae: Crocidura) on the island. We examined the morphology of 1368 specimens and obtained extensive molecular data from many of them, including mitochondrial DNA sequences from 851 specimens, up to five nuclear exons from 657 specimens, and thousands of ultraconserved elements from 90 specimens. By iteratively testing species limits using distinct character datasets and appropriate taxon sampling, we found clear, mostly consistent evidence for the existence of 21 species of shrews on Sulawesi, only seven of which were previously recognized. We divide these 21 species into five morphogroups, provide emended diagnoses of the seven previously named species, and describe 14 new species. The Long-Tailed Group contains Crocidura caudipilosa, C. elongata, C. microelongata, new species, and C. quasielongata, new species; the Rhoditis Group contains C. rhoditis, C. pseudorhoditis, new species, C. australis, new species, and C. pallida, new species; the Small-Bodied Group contains C. lea, C. levicula, C. baletei, new species, C. mediocris, new species, C. parva, new species, and C. tenebrosa, new species; the Thick-Tailed Group contains C. brevicauda, new species and C. caudicrassa, new species; and the Ordinary Group contains C. musseri, C. nigripes, C. normalis, new species, C. ordinaria, new species, and C. solita, new species. Documenting these endemic species reveals a local radiation (20 of the 21 species are members of an endemic clade) in which elevational gradients played a prominent role in either promoting speciation, or at a minimum, fostering the cooccurrence of phenotypically similar species. As now understood, the species-level diversity of Crocidura on Sulawesi is nearly three times the known diversity of any other insular shrew fauna. This study highlights the fact that if we wish to understand the true extent of biodiversity on Earth, large-scale, vouchered organismal inventories followed up with thorough examinations of genetic, morphological, and geographic traits are sorely needed in montane tropical regions, even for purportedly well-studied groups such as mammals.
Article
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.
Article
Based on molecular and morphological evidence, we describe a new species of murine rodent from Mt. Kampalili in easternmost Mindanao Island, Philippines. It is the third known species of Tarsomys, a genus endemic to Mindanao. The new species differs from congeners (T. apoensis and T. echinatus) in having smaller body size, shorter tail, smaller hind feet, soft and dense pelage of darker color, smaller skull with a broader zygomatic plate, shorter incisive foramina, and longer auditory bullae. The new species belongs to the “Tarsomys clade” of tribe Rattini that has diversified principally on Mindanao where, in addition to the 3 species of Tarsomys, it is represented by 2 species of Limnomys and 1 species of Baletemys. The Tarsomys clade also includes the Rattus everetti complex which is widespread throughout the oceanic portion of the Philippines and likely consists of at least 4 species. Molecular phylogenetic analysis strongly supports a sister relationship between this new species and T. apoensis, which diverged approximately 1.0 to 1.75 Ma. The phylogenetic position, morphological distinctness, and relatively ancient persistence of this species support within-island diversification as the most substantial contributor to existing species richness of small mammals in the Philippines.
Article
Full-text available
Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.
Article
Full-text available
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.
Article
Full-text available
BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The BEAGLE library defines a simple, but flexible, application programming interface (API), and includes a collection of efficient implementations for calculation under a variety of evolutionary models on different hardware devices. The library has been integrated into recent versions of popular phylogenetics software packages including BEAST and MrBayes and has been widely used across a diverse range of evolutionary studies. Here, we present BEAGLE 3 with new parallel implementations, increased performance for challenging data sets, improved scalability, and better usability. We have added new OpenCL and central processing unit-threaded implementations to the library, allowing the effective utilization of a wider range of modern hardware. Further, we have extended the API and library to support concurrent computation of independent partial likelihood arrays, for increased performance of nucleotide-model analyses with greater flexibility of data partitioning. For better scalability and usability, we have improved how phylogenetic software packages use BEAGLE in multi-GPU (graphics processing unit) and cluster environments, and introduced an automated method to select the fastest device given the data set, evolutionary model, and hardware. For application developers who wish to integrate the library, we also have developed an online tutorial. To evaluate the effect of the improvements, we ran a variety of benchmarks on state-of-the-art hardware. For a partitioned exemplar analysis, we observe run-time performance improvements as high as 5.9-fold over our previous GPU implementation. BEAGLE 3 is free, open-source software licensed under the Lesser GPL and available at https://beagle-dev.github.io.
Article
Full-text available
The murid rodent genus Rattus Fischer 1803 contains several species that are responsible for massive loss of crops and food, extinction of other species and the spread of zoonotic diseases to humans, as well as a laboratory species used to answer important questions in physiology, immunology, pharmacology, toxicology, nutrition, behaviour and learning. Despite the well-known significant impacts of Rattus, a definitive evolutionary based systematic framework for the genus is not yet available. The past 75 years have seen more dramatic changes in membership of Rattus than in almost any other genus of mammals. In fact, the Rattus genus has been a receptacle for any generalised Old World murine that lacked morphological specialisation and at one point, has included more than 560 species and/or subspecies, spread across Eurasia, Africa and the Australo-Papuan region. The dissolution of Rattus is ongoing as many of its constituent species and many genera of Rattini remain unsampled in any molecular study. To address this sampling limitation, we sequenced the mitochondrial cytochrome b (cytb) gene and examined phylogenetic relationships using both Bayesian and Maximum Likelihood algorithms for an expanded set of taxa within Rattus and among closely related genera. Here we place previously unsampled taxa in a phylogenetic context for the first time, including R. burrus, R. hoogerwerfi, R. lugens, and R. mindorensis within the Asian Rattus group, R. facetus within the Australo-Papuan Rattus radiation, and the undescribed ‘Bisa Rat’ described by Flannery as sister to the recently described genus Halmaheramys. We also present an exploratory foray into the wider topic of Rattus phylogenetics and propose that a reorganisation of the Rattus genus should require that it be a monophyletic group, include at least the type species R. norvegicus and R. rattus (plus their close allies); and exclude the Bandicota/Nesokia clade and other such specialised genera.
Article
Full-text available
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
Article
Full-text available
We describe a new species of murine rodent from a skull collected on Bisa Island and 3 specimens from Obi Island, North Maluku Province, Indonesia. Molecular and morphological data indicate a close relationship with Halmaheramys bokimekot (Fabre et al. 2013). The new species is characterized by its combination of large size; short tail with large scales; spiny, coarse, dark dorsal pelage with long black guard hairs; and a dark gray ventral pelage that contrasts slightly with the dorsum. The Bisa specimen displays unusual zygomatic arch morphology, which may be a disease-related deformity, or potentially a sexually dimorphic trait. The new species shares several external and cranio-mandibular features with its sister species from Halmahera that differ from those of Rattus species, including a spiny pelt, deep palatine sulci, a high rostrum and relatively flat dorsal profile, short incisive foramina, short palatal bridge, and molars with simple occlusal patterns. Although certain morphological characteristics of the new taxon suggest an affinity with the taxonomically diverse and geographically widespread Rattus, in other respects it clearly fits into the Wallacean clade containing Bunomys, Paruromys, and Taeromys, as indicated by molecular phylogenetic analyses. Along with the recent discovery of Halmaheramys, recognition of this new species from Bisa and Obi Islands underscores the north Moluccan region’s high endemism, conservation importance, and the urgent need for a better inventory of its biodiversity.
Article
Full-text available
We name two new tarsier species from the northern peninsula of Sulawesi. In doing so, we examine the biogeography of Sulawesi and remove the implausibly disjunct distribution of Tarsius tarsier. This brings tarsier taxonomy into better accordance with the known geological history of Sulawesi and with the known regions of biological endemism on Sulawesi and the surrounding island chains that harbor portions of the Sulawesi biota. The union of these two data sets, geological and biological, became a predictive model of biogeography, and was dubbed the Hybrid Biogeographic Hypothesis for Sulawesi. By naming these species, which were already believed to be taxonomically distinct, tarsier taxonomy better concords with that hypothesis and recent genetic studies. Our findings bring greater clarity to the conservation crisis facing the region.
Article
Full-text available
The interface of the Asian and Australian faunal zones is defined by a network of deep ocean trenches that separate intervening islands of the Philippines and Wallacea (Sulawesi, the Lesser Sundas, and the Moluccas). Studies of this region by Wallace marked the genesis of the field of biogeography, yet few workers have used molecular methods to investigate the biogeography of taxa whose distribution spans this interface. Some taxa, such as the fanged frogs of the ranid genus Limnonectes, have distributions on either side of the zoogeographical lines of Wallace and Huxley, offering an opportunity to ask how frequently these purported barriers were crossed and by what paths. To examine diversification of Limnonectes in Southeast Asia, the Philippines, and Wallacea, we estimated a phylogeny from mitochondrial DNA sequences obtained from a robust geographic sample. Our analyses suggest that these frogs dispersed from Borneo to the Philippines at least twice, from Borneo to Sulawesi once or twice, from Sulawesi to the Philippines once, and from the Philippines to Sulawesi once. Dispersal to the Moluccas occurred from Sulawesi and to the Lesser Sundas from Java/Bali. Species distributions are generally concordant with Pleistocene aggregate island complexes of the Philippines and with areas of endemism on Sulawesi. We conclude that the recognition of zoogeographic lines, though insightful, may oversimplify the biogeography of widespread taxa in this region.
Article
Full-text available
Island systems are important models for evolutionary biology because they provide convenient, discrete biogeographic units of study. Continental islands with a history of intermittent dry land connections confound the discrete definitions of islands and have led zoologists to predict (1) little differentiation of terrestrial organisms among continental shelf islands and (2) extinction, rather than speciation, to be the main cause of differences in community composition among islands. However, few continental island systems have been subjected to well-sampled phylogeographic studies, leaving these biogeographic assumptions of connectivity largely untested. We analyzed nine unlinked loci from shrews of the genus Crocidura from seven mountains and two lowland localities on the Sundaic continental shelf islands of Sumatra and Java. Coalescent species delimitation strongly supported all currently recognized Crocidura species from Sumatra (six species) and Java (five species), as well as one undescribed species endemic to each island. We find that nearly all species of Crocidura in the region are endemic to a single island and several of these have their closest relative(s) on the same island. Intra-island genetic divergence among allopatric, conspecific populations is often substantial, perhaps indicating species-level diversity remains underestimated. One recent (Pleistocene) speciation event generated two morphologically distinct, syntopic species on Java, further highlighting the prevalence of within-island diversification. Our results suggest that both between- and within-island speciation processes generated local endemism in Sundaland, supplementing the traditional view that the region's fauna is relictual and primarily governed by extinction. This article is protected by copyright. All rights reserved.
Article
Full-text available
Resumen Los lineamientos para el uso de especies de mamíferos de vida silvestre en la investigación con base en Sikes et al. (2011) se actualizaron. Dichos lineamientos cubren técnicas y regulaciones profesionales actuales que involucran el uso de mamíferos en la investigación y enseñanza; también incorporan recursos nuevos, resúmenes de procedimientos y requisitos para reportes. Se incluyen detalles acerca de captura, marcaje, manutención en cautiverio y eutanasia de mamíferos de vida silvestre. Se recomienda que los comités institucionales de uso y cuidado animal (cifras en inglés: IACUCs), las agencias reguladoras y los investigadores se adhieran a dichos lineamientos como fuente base de protocolos que involucren mamíferos de vida silvestre, ya sea investigaciones de campo o en cautiverio. Dichos lineamientos fueron preparados y aprobados por la ASM, en consulta con profesionales veterinarios experimentados en investigaciones de vida silvestre y IACUCS, de quienes cuya experiencia colectiva provee un entendimiento amplio y exhaustivo de la biología de mamíferos no-domesticados. La presente versión de los lineamientos y modificaciones posteriores están disponibles en línea en la página web de la ASM, bajo Cuidado Animal y Comité de Uso: (http://mammalogy.org/uploads/committee_files/CurrentGuidelines.pdf). Recursos adicionales relacionados con el uso de animales de vida silvestre para la investigación se encuentran disponibles en (http://www.mammalsociety.org/committees/animal-care-and-use#tab3).
Article
Full-text available
We document a new genus and species of shrew rat from the north peninsula of Sulawesi Island, Indonesia. The new taxon is known only from the type locality at 1,600 m elevation on Mt. Dako, in the district of Tolitoli. It is distinguished from all other Indonesian murines by its large, flat, pink nose with forward-facing nares. Relative to other Sulawesi murines, the species has extremely large ears (∼ 21% of head and body length), very long urogenital hairs, prominent and medially bowing hamular processes on the pterygoid bones, extremely long and procumbent lower incisors, and unusually long articular surfaces on the mandibular condyles. Morphologically, the new taxon is most similar to a group of endemic Sulawesi rats known commonly as "shrew rats." These are long faced, carnivorous murines, and include the genera Echiothrix, Melasmothrix, Paucidentomys, Sommeromys, and Tateomys. Our Bayesian and likelihood analyses of DNA sequences concatenated from 5 unlinked loci infer the new shrew rat as sister to a clade consisting of Melasmothrix, Paucidentomys, and Echiothrix, suggesting that Sulawesi shrew rats represent a clade. The Sulawesi water rat, Waiomys mamasae, was sister to the shrew rats in our analyses. Discovery of this new genus and species brings known shrew rat diversity on Sulawesi to 6 genera and 8 species. The extent of morphological diversity among these animals is remarkable considering the small number of species currently known.
Article
Full-text available
We collected specimens of Sommer's Sulawesi shrew-rat, Sommeromys macrorhinos, at three sites (1600, 2200, and 2600 m) and the Sulawesi small-bodied shrew-rat, Crunomys celebensis, at one site (1600 m) on Gunung Gandangdewata in the western block of the central core of Sulawesi during November 2011 and May 2012. Prior to 2011, S. macrorhinos was known only from the holotype, which was taken on 2 August 1973 at 2400 m near the summit of Gunung Tokala (upper montane forest). Previously, C. celebensis was known only from tropical lowland evergreen rain forest in the Danau Lindu valley and nearby upper drainage of the Sungai Miu in the northern portion of the west-central mountain block in Sulawesi's central core. The new specimens of S. macrorhinos and C. celebensis extend their known range of habitats to include the transition between lowland and montane forest. Because the original description of S. macrorhinos was based on a single specimen, we describe some external morphological features and provide measurements of new specimens as a supplement to the original description.
Article
Full-text available
Guidelines for use of wild mammal species are updated from the American Society of Mammalogists (ASM) 2007 publication. These revised guidelines cover current professional techniques and regulations involving mammals used in research and teaching. They incorporate additional resources, summaries of procedures, and reporting requirements not contained in earlier publications. Included are details on marking, housing, trapping, and collecting mammals. It is recommended that institutional animal care and use committees (IACUCs), regulatory agencies, and investigators use these guidelines as a resource for protocols involving wild mammals. These guidelines were prepared and approved by the ASM, working with experienced professional veterinarians and IACUCs, whose collective expertise provides a broad and comprehensive understanding of the biology of nondomesticated mammals in their natural environments. The most current version of these guidelines and any subsequent modifications are available at the ASM Animal Care and Use Committee page of the ASM Web site (http://mammalsociety.org/committees/index.asp).
Article
Full-text available
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree.
Article
Full-text available
AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub (www.github.com/AliView). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview Contact: anders.larsson@ebc.uu.se Supplementary information: Supplementary data are available at Bioinformatics online.
Article
Full-text available
The complex geological history of the Indonesian island Sulawesi has shaped the origin and subsequent diversification of its taxa. For the endemic freshwater snail Tylomelania a vicariant origin from the Australian margin has been hypothesized. Divergence time estimates from a mtDNA phylogeny based on a comprehensive island-wide sampling of Tylomelania fit regional tectonic constraints and support the 'out-of-Australia' vicariance hypothesis. The Banggai-Sula region of the Sula Spur, the Australian promontory colliding with West Sulawesi during the Miocene, is identified as a possible source area for the colonization of Sulawesi by the ancestor of Tylomelania. The molecular phylogeny also shows a rapid diversification of Tylomelania into eight major lineages with very little overlap in their distribution on the island. Haplotype networks provide further evidence for a strong spatial structure of genetic diversity in Tylomelania. Distribution boundaries of the major lineages do at best partially coincide with previously identified contact zones for other endemic species groups on Sulawesi. This pattern has likely been influenced by the poor dispersal capabilities and altitudinal distribution limits of this strict freshwater inhabitant. We suggest that late Miocene and Pliocene orogeny in large parts of Sulawesi has been the vicariant event driving primary diversification in Tylomelania.
Article
Full-text available
We describe Halmaheramys bokimekot Fabre, Pagès, Musser, Fitriana, Semiadi & Helgen gen. et sp. nov., a new genus and species of murine rodent from the North Moluccas, and study its phylogenetic placement using both molecular and morphological data. We generated a densely sampled mitochondrial and nuclear DNA data set that included most genera of Indo‐Pacific Murinae, and used probabilistic methodologies to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the topology and then used a Lagrange analysis to infer ancestral geographic areas. Finally, we combined the ancestral area reconstructions with temporal information to compare patterns of murine colonization among Indo‐Pacific archipelagos. We provide a new and comprehensive molecular phylogenetic reconstruction for Indo‐Pacific Murinae, with a focus on the Rattus division. Using previous results and those presented in this study, we define a new Indo‐Pacific group within the Rattus division, composed of Bullimus, Bunomys, Paruromys, Halmaheramys, Sundamys, and Taeromys. Our phylogenetic reconstructions revealed a relatively recent diversification from the Middle Miocene to Plio‐Pleistocene associated with several major dispersal events. We identified two independent Indo‐Pacific dispersal events from both western and eastern Indo‐Pacific archipelagos to the isolated island of Halmahera, which led to the speciations of H. bokimekot gen. et sp. nov. and Rattus morotaiensis Kellogg, 1945. We propose that a Middle Miocene collision between the Halmahera and Sangihe arcs may have been responsible for the arrival of the ancestor of Halmaheramys to eastern Wallacea. Halmaheramys bokimekot gen. et sp. nov. is described in detail, and its systematics and biogeography are documented and illustrated. © 2013 The Linnean Society of London
Article
Full-text available
The island of Sulawesi, in Indonesia, lies at the crossroads of the Indo-Australian Archipelago and has remained isolated from the Asian (Sunda) and Australian (Sahul) continental shelves for at least the last 10 million years. Of the 50 native species of rodents on Sulawesi, all are endemic and represent the evolution of a variety of ecological and morphological forms within the Muridae and Sciuridae. Carnivorous rodents have evolved, perhaps independently, in Muridae from the Philippines, Sulawesi, and Sahul, but semi-aquatic murids are only known from Sahul. Here we describe a new genus and species of insectivorous water rat from Sulawesi. Phylogenetic analyses demonstrate that it is related to the shrew rats of Sulawesi and represents an origin of aquatic carnivory that is independent from the evolution of water rats on Sahul. Many areas of Sulawesi have not been surveyed systematically and current lists of mammal species are likely to dramatically underestimate actual diversity.
Article
Full-text available
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
Article
Full-text available
The murine genera Celaenomys and Chrotomys comprise a group of semifossorial, vermivorous rodents endemic to the Philippines. Analysis of variation within this group supports the recognition of 4 named species occurring on the large islands of Luzon and Mindoro, as well as our description of a 5th species from Sibuyan, a small island in the central Philippines that has remained isolated from the other islands by deep water channels. Examination of cytochrome-b gene sequence data from 4 of the 5 taxa indicates that Celaenomys silaceus may be basal and sister to the other taxa but morphological and chromosomal data do not support the recognition of Celaenomys as a separate genus. Analysis of the sequence data indicates a relatively early separation of the Sibuyan species and a later split between 2 species of Chrotomys on Luzon. Diversification of Chrotomys appears to have involved speciation associated with both habitat vicariance on Luzon and overwater dispersal to neighboring islands. Most of the members of this clade are restricted to mid- or high-elevation forests, have limited geographic ranges within the archipelago, and some may be imperiled due to loss of natural habitat.
Article
Full-text available
Rhynchomys belongs to a unique assemblage of Philippine rodents that exhibit a combination of primitive features as well as unique morphological specializations. These nocturnal "shrew-rats," with highly specialized vermivorous and insectivorous food habits, are endemic to Luzon Island. Analyses of external, cranial, and dental features support the recognition of 4 species, 2 of which are described in this paper. All are restricted to high-elevation habitats, about 1, 100 in and above, in montane and mossy forest on northern, western, and southeastern Luzon. Habitat vicariance and subsequent divergence in isolation is the probable mode of diversification in Rhynchomys as well as in other murid clades whose members are restricted to high-elevation habitats. The discovery of locally endemic species of Rhynchomys both confirms the existence of multiple centers of endemism on Luzon and underscores the need to establish and maintain additional protected areas on the island.
Article
Full-text available
Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods such as the RAxML rapid bootstrap (RBS) and the Shimodaira–Hasegawa-like approximate likelihood ratio test have been introduced to speed up the bootstrap. Here, we suggest an ultrafast bootstrap approximation approach (UFBoot) to compute the support of phylogenetic groups in maximum likelihood (ML) based trees. To achieve this, we combine the resampling estimated log-likelihood method with a simple but effective collection scheme of candidate trees. We also propose a stopping rule that assesses the convergence of branch support values to automatically determine when to stop collecting candidate trees. UFBoot achieves a median speed up of 3.1 (range: 0.66–33.3) to 10.2 (range: 1.32–41.4) compared with RAxML RBS for real DNA and amino acid alignments, respectively. Moreover, our extensive simulations show that UFBoot is robust against moderate model violations and the support values obtained appear to be relatively unbiased compared with the conservative standard bootstrap. This provides a more direct interpretation of the bootstrap support. We offer an efficient and easy-to-use software (available at http://www.cibiv.at/software/iqtree) to perform the UFBoot analysis with ML tree inference.
Article
Aim To 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. Location Indo‐Australian Archipelago including the Sunda shelf of continental Asia, Sahul shelf of continental Australia, the Philippines and Wallacea of Indonesia. Taxon Order Rodentia, Family Muridae. Methods We 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. Results We 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 genus Rattus and their closest relatives, irrespective of colonization history. Main Conclusions Our 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.
Article
A laborious and difficult task in current tree of life reconstruction is to resolve evolutionary relationships of closely related congeneric species that originated from recent radiations. This is particularly difficult for forest species with long generation times and large effective population sizes such as conifers. The Qinghai-Tibetan Plateau (QTP) and adjacent areas are considered a species diversity center of Picea, harboring 11 species (including 5 varieties) of this genus, but evolutionary relationships of these species are far from being resolved due to recent radiations, morphological convergence, and frequent interspecific gene flow. In this study, we use these spruce species to test whether phylotranscriptomic analysis, combined with population genetic analysis, can disentangle their evolutionary relationships, and to explore whether reticulate evolution has occurred among them. Phylogenomic analyses indicate that all spruce species in the QTP and neighboring areas, except P. asperata and P. crassifolia, cluster together, and in particular, nearly all taxa (including varieties) reflect reciprocally monophyletic lineages, although the two species P. likiangensis and P. brachytyla are not monophyletic. We found that, compared to herbaceous plants, many more genes (a minimum of 600 OGs for Picea) are required to resolve interspecific relationships of conifers. Contrary to previous studies, our data do not support a hybrid origin of P. purpurea, but suggests a hybrid origin for P. brachytyla var. brachytyla and P. likiangensis var. rubescens. We emphasize that the species or species complex used for population genetic and phylogeographical studies should be monophyletic.
Article
Large rats are an important source of food in this area and their bones turn up in fossil material, especially sites linked with man. The species concerned are identified and contemporary specimens illustrated. Features by which species can be indentified (described here) include molars in particular. Some of the species are now far more uncommon than they were in the past.-K.Clayton
Article
Aim The Indonesian island of Sulawesi is home to thousands of endemic terrestrial animal species. Phylogeographical studies of some of these taxa revealed concordant distribution patterns (areas of endemism; AoEs), suggestive of a shared evolutionary or ecological mechanism driving divergence among various terrestrial taxa. Generally, AoEs have been attributed to Pleistocene marine incursions, geological fault zones and Sulawesi's history as an archipelago. We test, for the first time, the hypothesis that population divergences are associated with unsuitable climate spaces at the boundaries between these areas. Location Sulawesi, Indonesia. Taxon Maxomys musschenbroekii, a common murid rodent endemic to Sulawesi. Methods We sequenced a mitochondrial gene, four nuclear protein‐coding genes and hundreds of ultraconserved elements from individuals sampled across the island, which we used to build intraspecific phylogenies and identify population structure. To test climate‐related hypotheses, we used multiple regression to assess the extent to which genetic distances, over‐land geographical distances, environmental distances (derived from ecological niche model resistance surfaces) and areas of endemism are correlated. Results In all three genetic datasets, we inferred phylogeographical structure that is geographically concordant with previously defined AoEs. Ecological niche models showed a similar geography of suitability across the island since the Last Glacial Maximum, with varying levels of unsuitable climate space between AoEs. Genetic distances were more strongly correlated with environmental distances than geographical distances and interspecific divergences arose just in the past 1.5 Myr. Main Conclusions Population divergences within M. musschenbroekii are consistent with AoE definitions from other taxa. Stable areas of unsuitable habitat near AoE boundaries probably supplemented marine incursions in generating population structure within M. musschenbroekii and other co‐distributed species.
Article
Sulawesi has a remarkable biodiversity, an unusually rich endemic fauna, and is the largest island in Wallacea, just west of the Wallace Line. Alfred Russel Wallace himself suggested it could perhaps be the most remarkable island on the globe because of its peculiar fauna. It was home to extinct fossil fauna such as dwarf proboscideans, records significant Pleistocene faunal turnover, and evidence of early human occupation suggests an important role in hominid migration through the Sunda-Sahul region. Information on Neogene palaeogeography is essential for understanding biogeographic patterns, biodiversity and faunal changes. New palaeogeographic maps reflecting recent work on Sulawesi's complex geology and changes in tectonic interpretations are presented for intervals from the Early Miocene to Pleistocene, at 20, 15, 10, 8, 6, 5, 4, 3, 2, and 1. Ma. Additional maps illustrate the effects of glacially-driven sea level change in the last 1. Myr. They are based on a field-based investigation of sedimentary rocks in Sulawesi, accompanied by palaeontological, petrological and heavy mineral studies and U-Pb dating of detrital zircons, to date and determine depositional environments. The new results have been supplemented by re-evaluation of previous studies, including reports from oil company wells and seismic lines. Igneous rocks provided ages, indications of surface environment of eruptions, and location of magmatic activity. For most of the Neogene from the Early Miocene Sulawesi was a shallow marine area with a number of small islands, surrounded by relatively deep marine areas. Deep inter-arm bays began to form in the Late Miocene and the islands became larger. The most significant palaeogeographic change began in the Pliocene with an increase in the area and elevation of land accompanied by major subsidence of the inter-arm bays. The separate islands gradually coalesced in the Pleistocene to form the distinctive K-shaped island known today.
Article
Phylogeographic research on endemic primates and amphibians inhabiting the Indonesian island of Sulawesi revealed the existence of seven areas of endemism (AoEs). Here, we use phylogenetic and population genetic analyses of one mitochondrial gene and 15 nuclear loci to assess geographic patterns of genetic partitioning in a shrew (Crocidura elongata) that is endemic to Sulawesi, but occurs across the island. We uncover substantial genetic diversity in this species both between and within AoEs, but we also identify close relationships between populations residing in different AoEs. One of the earliest divergences within C. elongata distinguishes a high-elevation clade from low-elevation clades. In addition, on one mountain, we observe three distinct genetic groups from low, middle, and high elevations, suggesting divergence along a single elevational gradient. In general, our results show that C. elongata, like several other Sulawesi endemic taxa, harbors extensive genetic diversity. This diversity is structured in part by known AoE boundaries, but also by elevational gradients and geographic isolation within AoEs.
Article
Aim To investigate patterns of genetic and morphological differentiation in a ‘New Endemic’ Philippine rodent ( Bullimus ) and examine the dynamics on intra‐island speciation on oceanic islands. Location The Philippine archipelago, focusing on Luzon Island. Methods We examined patterns of genetic differentiation by sequencing one mitochondrial and three nuclear loci for an archipelago‐wide sampling of Bullimus , which we analysed using phylogenetic, population genetic, and coalescent‐based methods. We also measured 16 craniodental features for Bullimus luzonicus to examine morphological differentiation on Luzon. Results Time‐calibrated species tree analysis indicated that Bullimus colonized the southern Philippines during the late Pliocene or Pleistocene and diversified on Luzon during the last c . 540 kyr. We found substantial phylogeographical structure in B. luzonicus , most completely developed in the southern part of the island, where colonization initially occurred. Coalescent species delimitation analysis indicated strong support for genetic isolation among eight B. luzonicus populations, however, morphometric analyses suggested that only two or three of these populations were morphologically distinctive. Main conclusions Phylogeographical structure in B. luzonicus largely corresponded to Luzon's numerous isolated mountain ranges, which likely played a major role in driving diversification in central/northern Luzon over the last c . 230 kyr. The majority of B. luzonicus populations appear to be in the process of speciation, with only the furthest south population from Camarines Sur warranting elevation to species status. We found little evidence for diversification in B. bagobus on Mindanao, suggesting that Luzon may be an exceptional setting for murid rodent diversification.
Article
Mosaic-tailed rodents of the genus Melomys belong to the Australasian old endemic murine radiation and exhibit a rat-like morphology with arboreal or scansorial specializations. Here we report a new population of Melomys burtoni from the island of Halmahera (in the North Moluccas, Indonesia). Our molecular phylogenetic results highlight close relationships and recent evolutionary divergences among M. burtoni from Halmahera and the Australo-Papuan taxa M. burtoni and M. lutillus and other Moluccan taxa, including M. paveli. Multivariate as well as geometric morphometric analyses of cranial, and dental features support the recognition of M. burtoni from Halmahera as a slightly distinctive insular population, preventing us from elevating it as a new taxa. This population is recorded from lowland secondary forest and forest edge habitats in south-central Halmahera. As with other Moluccan endemic murines, colonization by an Australo-Papuan ancestor and subsequent isolation is the probable mode of diversification for M. burtoni in Halmahera. The discovery of Melomys in Halmahera fills a previously puzzling gap in knowledge of the murine fauna of the Moluccas and the biogeography of the Wallacean region.
Article
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Book
This new edition to the classic book by ggplot2 creator Hadley Wickham highlights compatibility with knitr and RStudio. ggplot2 is a data visualization package for R that helps users create data graphics, including those that are multi-layered, with ease. With ggplot2, it's easy to: • produce handsome, publication-quality plots with automatic legends created from the plot specification • superimpose multiple layers (points, lines, maps, tiles, box plots) from different data sources with automatically adjusted common scales • add customizable smoothers that use powerful modeling capabilities of R, such as loess, linear models, generalized additive models, and robust regression • save any ggplot2 plot (or part thereof) for later modification or reuse • create custom themes that capture in-house or journal style requirements and that can easily be applied to multiple plots • approach a graph from a visual perspective, thinking about how each component of the data is represented on the final plot This book will be useful to everyone who has struggled with displaying data in an informative and attractive way. Some basic knowledge of R is necessary (e.g., importing data into R). ggplot2 is a mini-language specifically tailored for producing graphics, and you'll learn everything you need in the book. After reading this book you'll be able to produce graphics customized precisely for your problems, and you'll find it easy to get graphics out of your head and on to the screen or page. New to this edition:< • Brings the book up-to-date with ggplot2 1.0, including major updates to the theme system • New scales, stats and geoms added throughout • Additional practice exercises • A revised introduction that focuses on ggplot() instead of qplot() • Updated chapters on data and modeling using tidyr, dplyr and broom
Article
In Bayesian phylogenetic analyses of genetic data, prior probability distributions need to be specified for the model parameters, including the tree. When Bayesian methods are used for molecular dating, available tree priors include those designed for species-level data, such as the pure-birth and birth-death priors, and coalescent-based priors designed for population-level data. However, molecular dating methods are frequently applied to data sets that include multiple individuals across multiple species. Such data sets violate the assumptions of both the speciation and coalescent-based tree priors, making it unclear which should be chosen and whether this choice can affect the estimation of node times. To investigate this problem, we used a simulation approach to produce data sets with different proportions of within- and between-species sampling under the multispecies coalescent model. These data sets were then analysed under pure-birth, birth-death, constant-size coalescent, and skyline coalescent tree priors. We also explored the ability of Bayesian model testing to select the best-performing priors. We confirmed the applicability of our results to empirical data sets from cetaceans, phocids, and coregonid whitefish. Estimates of node times were generally robust to the choice of tree prior, but some combinations of tree priors and sampling schemes led to large differences in the age estimates. In particular, the pure-birth tree prior frequently led to inaccurate estimates for data sets containing a mixture of inter- and intraspecific sampling, whereas the birth-death and skyline coalescent priors produced stable results across all scenarios. Model testing provided an adequate means of rejecting inappropriate tree priors. Our results suggest that tree priors do not strongly affect Bayesian molecular dating results in most cases, even when severely misspecified. However, the choice of tree prior can be significant for the accuracy of dating results in the case of data sets with mixed inter- and intraspecies sampling.
Article
We document a new genus and species of rodent (Muridae) from the west-central region of Sulawesi Island, Indonesia. The new taxon is known only from the type locality at around 1,600 m elevation on Mt. Gandangdewata of the Quarles Range, in the district of Mamasa. With phylogenetic analyses of DNA sequences from 5 unlinked loci, we infer that the new taxon is sister to the Sulawesi water rat, Waiomys mamasae , and nested within a clade of rodents from Sulawesi that otherwise feed exclusively on invertebrates. The new species is distinguishable from other rodents of Sulawesi by the combination of its small, slender body; soft, gray–brown fur; small, rounded ears; long, sparsely haired tail; long, fine mystacial vibrissae; gracile cranium; short rostrum; pronounced lacrimal bone; prominent, sickle-shaped coronoid process; and pale orange enamel on labial surface of incisors. Unlike its closest relatives, the new species feeds on both plant and animal matter, and may represent a rare evolutionary reversal of traits associated with a carnivorous diet in murids. Kami mendokumentasikan genus dan spesies hewan pengerat (Muridae) baru dari bagian tengah-barat Pulau Sulawesi, Indonesia. Takson baru ini hanya diketahui dari lokasi spesimen tipe pada ketinggian sekitar 1600 meter di Gunung Gandangdewata yang termasuk dalam rangkaian Pegunungan Quarlesi, Kabupaten Mamasa. Analisa filogenetik pada sekuen DNA dari 5 loci yang tidak terhubung menunjukkan bahwa takson baru ini merupakan kerabat dekat tikus air Sulawesi , Waiomys mamasae, dan berada pada kelompok hewan pengerat lainnya dari Sulawesi yang hanya memakan invertebrata. Spesies baru ini dibedakan dari hewan pengerat lainnya dari Sulawesi berdasarkan kombinasi beberapa karakter yaitu: tubuh ramping; rambut lembut abu-abu coklat; telinga kecil dan membulat; ekor panjang dan berambut jarang; kumis panjang dan tipis; tengkorak ramping; tulang hidung pendek; tulang lakrimal jelas; coronoid process tampak jelas dan berbentuk bulan sabit; dan enamel berwarna oranye muda pada penampang labial dari gigi seri. Tidak seperti kerabat terdekatnya, species baru ini memakan unsur tumbuhan maupun hewan, dan kemungkinan besar menunjukkan proses evolusi langka yang berbalik dari ciri yang diasosiasi dengan salah satu pemakan daging pada jenis Muridae.
Article
Island biogeography is the study of the distribution and dynamics of species in island environments. Due to their isolation from more widespread continental species, islands are ideal places for unique species to evolve, but they are also places of concentrated extinction. Not surprisingly, they are widely studied by ecologists, conservationists and evolutionary biologists alike. There is no other recent textbook devoted solely to island biogeography, and a synthesis of the many recent advances is now overdue. This second edition builds on the success and reputation of the first, documenting the recent advances in this exciting field and explaining how islands have been used as natural laboratories in developing and testing ecological and evolutionary theories. In addition, the book describes the main processes of island formation, development and eventual demise, and explains the relevance of island environmental history to island biogeography. The authors demonstrate the huge significance of islands as hotspots of biodiversity, and as places from which disproportionate numbers of species have been extinguished by human action in historical time. Many island species are today threatened with extinction, and this work examines both the chief threats to their persistence and some of the mitigation measures that can be put in play with conservation strategies tailored to islands.
Article
Two new species of of Bunomys are described, B. karokophilus and B. torajae, both from the west-central mountain region of central Sulawesi. The descriptions are presented within the context of a systematic review of Bunomys in which are provided characteristics of the genus and species (external form, secondary sexual traits, spermatozoa, stomach morphology, skull, dentition, chromosomes); diagnoses, geographic and elevational distributions; sympatric, syntopic, and parapatric distributional relationships; morphological, distributional, and in some cases ecological comparisons among the species; natural histories for certain species derived from field observations; parasites; allocation of generic and specific synonyms; and documentation of subfossils for two of the species.Eight species are recognized; all are nocturnal, terrestrial, and endemic to the island of Sulawesi. Bunomys chrysocomus has been collected from most regions of the island and inhabits both lowland tropical evergreen and montane rain forests (elevational range = 250–2200 m). Bunomys coelestis is endemic to montane forests on Gunung Lompobatang, the high volcano at the southern end of the southwestern peninsula (1829–2500 m). Bunomys prolatus has been reported only from mountain forest on Gunung Tambusisi at the western end of the eastern peninsula (1829 m). Bunomys torajae, n. sp., is described from a small sample collected in montane forest on Gunung Gandangdewata at the southern end of the west-central mountain block (2500–2600 m). Bunomys fratrorum is currently documented only from the northeastern area of the northern peninsula where it occupies habitats in lowland tropical evergreen and montane rain forests (coastal plain to 1982 m). Bunomys andrewsi has been collected primarily in lowland tropical evergreen rain forests in the core of Sulawesi and on the eastern, southeastern, and southwestern peninsula (coastal plain to 1600 m). Bunomys penitus is strictly montane and recorded only from the west-central mountain block and Pegunungan Mekongga on the southeastern peninsula (1285–2287 m). Bunomys karokophilus, n. sp., is currently known only from lowland tropical evergreen rain forest in the northern portion of the west-central mountain block (823–1150 m).Analyses of morphometric traits (cranial and dental measurements) results in a phenetic relationship among the species in which B. chrysocomus, B. coelestis, B. prolatus, and B. torajae, n. sp., form one group characterized by small physical size and small molars, and B. fratrorum, B. andrewsi, B. penitus, and B. karokophilus another group in which larger physical size and heavier molars are the phenetic definers. Whether or not the integrity of this phenetic pattern will withstand testing by analyses of DNA sequences, it remains a convenient arrangement in which to present and define the eight species.The morphological, elevational, and ecological relationships among the four species of Bunomys (B. chrysocomus, B. andrewsi, B. penitus, and B. karokophilus, n. sp.) collected along my transect area in the northern portion of the west-central mountain block (presently known as Lore Lindu National Park) and comparison between them and the elevational distributions of the other murids encountered along the transect are described.Finally, a brief introduction to the species of murid rodents that have been recorded from mainland Sulawesi and nearby islands is provided, which defines the murine faunal context for the species of Bunomys.The treatment of Bunomys offered here focuses on definitions of the species as outlined by phenetic traits, elevational and geographic distributions, and the natural history characteristics that are available for some of the species, and does not cover an analysis of the phylogenetic relationships between Bunomys and other Indoaustralian murines.
Article
Aim Phylogenetic endemism ( PE ) identifies geographic concentrations of evolutionarily isolated and spatially restricted biota. Locations with high PE hold elements of biodiversity with little representation elsewhere and whose loss would impact disproportionately on phylogenetic diversity. We aim to determine the global distribution of PE for the world's mammals and to test hypotheses regarding the role of past and present environment and isolation in creating current patterns of evolutionary and spatial isolation. Location Global land. Methods IUCN range polygons were combined with a mammal supertree to estimate PE and related measures at three resolutions. We tested the relationship between PE and predictors representing current and L ast G lacial M aximum ( LGM ) environment and isolation in a model selection framework, for all terrestrial mammals and separately for bats. Results We identified 12 centres of mammal PE , with implications for conservation decisions. Endemism of mammal evolutionary diversity peaks predominantly in tropical and S outhern H emisphere island and montane regions. PE was most strongly associated with energy availability, isolation, elevation and low variability of current climate. Post LGM climate stability was a surprisingly weak predictor of PE compared with LGM climate itself. When controlling for current species ranges, PE is more strongly explained by past climate and past isolation. Main conclusions While present conditions better explain species endemism, past climate and isolation are central to explaining PE . Isolation at the LGM was a significantly stronger predictor of PE than current isolation, confirming the key role of persistent barriers, even narrow ones such as W allace's L ine. This global evaluation of PE offers an innovative and effective way to capture and test the evolutionary underpinning of whole‐clade biogeography. With improving spatial and phylogenetic information, integrative measures such as PE offer a substantial contribution toward comprehending and conserving evolutionary diversity.
Article
The Sundaland core of SE Asia is a heterogeneous assemblage of Tethyan sutures and Gondwana fragments. Its complex basement structure was one major influence on Cenozoic tectonics; the rifting history of the north Australian margin was another. Fragments that rifted from Australia in the Jurassic collided with Sundaland in the Cretaceous and terminated subduction. From 90 to 45 Ma Sundaland was largely surrounded by inactive margins with localized strikeslip deformation, extension and subduction. At 45 Ma Australia began to move north, and subduction resumed beneath Sundaland. At 23 Ma the Sula Spur promontory collided with the Sundaland margin. From 15 Ma there was subduction hinge rollback into the Banda oceanic embayment, major extension, and later collision of the Banda volcanic arc with the southern margin of the embayment. However, this plate tectonic framework cannot be reduced to a microplate scale to explain Cenozoic deformation. Sundaland has a weak thin lithosphere, highly responsive to plate boundary forces and a hot weak deep crust has flowed in response to tectonic and topographic forces, and sedimentary loading. Gravity-driven movements of the upper crust, unusually rapid vertical motions, exceptionally high rates of erosion, and massive movements of sediment have characterized this region.
Article
Aim Widespread species found in disturbed habitats are often expected to be human commensals. In island systems, this association predicts that dispersal will be mediated by humans. We investigated the biogeographical relationships among populations of a widespread tree skink that inhabits coastal forest and human‐cultivated plantations in Southeast Asia. We sought to determine whether populations of the emerald tree skink, Lamprolepis smaragdina , dispersed via mechanisms that were not human‐mediated (‘natural’ dispersal) or whether dispersal was mediated by humans. The latter scenario predicts low levels of genetic differentiation across a species' range, coupled with a genetic signature of recent range expansion. Location Southeast Asia, the Philippines, Wallacea and the south‐western Pacific. Methods We analysed sequences of mitochondrial DNA from 204 samples collected throughout the range of this species. We use phylogenetic and population genetic methods to distinguish between predicted geographical patterns of genetic variation that might indicate natural or human‐mediated dispersal. Results In contrast to predictions derived from similar studies of taxonomy and natural history, we found L. smaragdina to be characterized by highly structured and seemingly geographically stable mitochondrial gene lineages. Main conclusions Our results demonstrate a novel pattern of widespread species distribution, never before observed in vertebrates of the Indo‐Australian Archipelago. Although this widespread and highly dispersive species is capable of long‐distance dispersal, and has a clear history of over‐water dispersal, it exhibits sharp genetic differentiation across its range. Our results suggest that random waif dispersal has been a pervasive ongoing phenomenon throughout the evolutionary history of this species.