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Kai H, Takada N, Thomson V, Suzuki H. Region-Specific Genetic Diversity of Black Rats ( Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events. Zoolog Sci 2024; 41:290-301. [PMID: 38809868 DOI: 10.2108/zs230065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/27/2023] [Indexed: 05/31/2024]
Abstract
Among the six mitochondrial DNA lineages of the black rat (Rattus rattus Complex; RrC), lineages II and IV are widespread in Southeast and East Asia. This study explored their demographic history using 17 new sequences from the Miyako Islands in the Ryukyu archipelago, together with 178 publicly available cytochrome b sequences. We defined six and two haplotype groups showing rapid population expansion signals in Lineages II and IV, respectively. The six haplotype groups of Lineage II were represented by haplotypes from 1) Myanmar/Bangladesh/Northeast India, 2) Laos, 3) Thailand, 4) Indonesia/Philippines, 5) Vietnam/southern China, and 6) the Ryukyu archipelago. These expansion times were estimated using time-dependent evolutionary rates to be 115,300 years ago (ya), 128,500 ya, 9600 ya, 10,600 ya, 7200 ya, and 1400 ya, respectively, although all had large confidence intervals. The two groups of Lineage IV were recovered from the mainland and islands of Southeast Asia with predicted expansion times of 197,000 ya and 5800 ya, respectively. These results suggest that climatic fluctuations during the last 200,000 years of the Quaternary, affected the population dynamics in subtropical areas at different times. Furthermore, the results of the younger rapid expansion events of RrC suggest the possibility of agricultural advancement and dispersal of Neolithic farmers to different areas within the mainland and islands of Southeast Asia during the Holocene. A subset of rats from the Miyako Islands were found to have the same lineage IV haplotypes as those in Southeast Asia, suggesting a recent introduction of these new lineages.
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Affiliation(s)
- Hajime Kai
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nobuhiro Takada
- Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Vicki Thomson
- Centre for Conservation Ecology and Genomics, University of Canberra, Bruce, ACT 2617, Australia
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan,
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2
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Smith SM, Heaney LR, Angielczyk KD. Small skeletons show size-specific scaling: an exploration of allometry in the mammalian lumbar spine. Proc Biol Sci 2024; 291:20232868. [PMID: 38628132 PMCID: PMC11021941 DOI: 10.1098/rspb.2023.2868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
Studies of vertebrate bone biomechanics often focus on skeletal adaptations at upper extremes of body mass, disregarding the importance of skeletal adaptations at lower extremes. Yet mammals are ancestrally small and most modern species have masses under 5 kg, so the evolution of morphology and function at small size should be prioritized for understanding how mammals subsist. We examined allometric scaling of lumbar vertebrae in the small-bodied Philippine endemic rodents known as cloud rats, which vary in mass across two orders of magnitude (15.5 g-2700 g). External vertebral dimensions scale with isometry or positive allometry, likely relating to body size and nuances in quadrupedal posture. In contrast to most mammalian trabecular bone studies, bone volume fraction and trabecular thickness scale with positive allometry and isometry, respectively. It is physiologically impossible for these trends to continue to the upper extremes of mammalian body size, and we demonstrate a fundamental difference in trabecular bone allometry between large- and small-bodied mammals. These findings have important implications for the biomechanical capabilities of mammalian bone at small body size; for the selective pressures that govern skeletal evolution in small mammals; and for the way we define 'small' and 'large' in the context of vertebrate skeletons.
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Affiliation(s)
- S. M. Smith
- Field Museum of Natural History, 1400 S DuSable Lake Shore Drive, Chicago, IL 60605, USA
| | - L. R. Heaney
- Field Museum of Natural History, 1400 S DuSable Lake Shore Drive, Chicago, IL 60605, USA
| | - K. D. Angielczyk
- Field Museum of Natural History, 1400 S DuSable Lake Shore Drive, Chicago, IL 60605, USA
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3
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Hazzi NA, Hormiga G. Molecular phylogeny of the tropical wandering spiders (Araneae, Ctenidae) and the evolution of eye conformation in the RTA clade. Cladistics 2023; 39:18-42. [PMID: 36200603 DOI: 10.1111/cla.12518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 01/13/2023] Open
Abstract
Tropical wandering spiders (Ctenidae) are a diverse group of cursorial predators with its greatest species richness in the tropics. Traditionally, Ctenidae are diagnosed based on the presence of eight eyes arranged in three rows (a 2-4-2 pattern). We present a molecular phylogeny of Ctenidae, including for the first time representatives of all of its subfamilies. The molecular phylogeny was inferred using five nuclear (histone H3, 28S, 18S, Actin and ITS-2) and four mitochondrial (NADH, COI, 12S and 16S) markers. The final matrix includes 259 terminals, 103 of which belong to Ctenidae and represent 28 of the current 49 described genera. We estimated divergence times by including fossils as calibration points and biogeographic events, and used the phylogenetic hypothesis obtained to reconstruct the evolution of the eye conformation in the retrolateral tibial apophysis (RTA) clade. Ctenidae and its main lineages originated during the Paleocene-Eocene and have diversified in the tropics since then. However, in some analyses Ctenidae was recovered as polyphyletic as the genus Ancylometes Bertkau, 1880 was placed as sister to Oxyopidae. Except for Acantheinae, in which the type genus Acantheis Thorell, 1891 is placed inside Cteninae, the four recognized subfamilies of Ctenidae are monophyletic in most analyses. The ancestral reconstruction of the ocular conformation in the retrolateral tibial apophysis clade suggests that the ocular pattern of Ctenidae has evolved convergently seven times and that it has originated from ocular conformations of two rows of four eyes (4-4) and the ocular pattern of lycosids (4-2-2). We also synonymize the monotypic genus Parabatinga Polotov & Brescovit, 2009 with Centroctenus Mello-Leitão, 1929. We discuss some of the putative morphological synapomorphies of the main ctenid lineages within the phylogenetic framework offered by the molecular phylogenetic results of the study.
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Affiliation(s)
- Nicolas A Hazzi
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Fundación Ecotonos, Cra 72 No. 13ª-56, Cali, Colombia
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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4
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Nasir MH, Bhassu S, Mispan MS, Bakar SA, Jing KJ, Omar H. Molecular Identification and Genetic Variation of Rattus Species From Oil Palm Plantations of Malaysia Based on Mitochondrial Cytochrome Oxidase Subunit I (COI) Gene Sequences. Zoolog Sci 2022; 39:554-561. [PMID: 36495490 DOI: 10.2108/zs210093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
Rats (Rattus species) are the most notorious vertebrate pests in Malaysian oil palm plantations. Although many studies have been conducted on Asian rats, little attention has been paid to their species composition and phylogenetic relationships in oil palm plantations in Peninsular Malaysia. We determined the mitochondrial cytochrome oxidase subunit I (COI) gene sequence (708 bp) for 216 individual rats collected from five oil palm plantations in Peninsular Malaysia. Phylogenetic analysis in conjunction with comparison with sequences from the nucleotide sequence database revealed five distinct lineages in the Malaysian oil plantations: Rattus tiomanicus, Rattus argentiventer, Rattus exulans, Rattus tanezumi, and a taxon corresponding to the Malayan house rat, which was most frequently observed (∼50%). The last taxon has traditionally been classified as a synonym of Rattus rattus (Rattus rattus diardii) or Rattus tanezumi, but our phylogenetic analysis placed it as an independent lineage, which is not particularly closely related to R. rattus or R. tanezumi, and which we refer to as Rattus diardii. The construction of the network showed that there is considerable genetic variation within the lineages of R. diardii and R tiomanicus, suggesting that these two species are native to the Malay Peninsula.
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Affiliation(s)
- Mohamad Harris Nasir
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Animal Genetics and Genome Evolutionary Laboratory (AGAGEL), Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Subha Bhassu
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Centre for Biotechnology in Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Animal Genetics and Genome Evolutionary Laboratory (AGAGEL), Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Muhamad Shakirin Mispan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Centre for Biotechnology in Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sazaly Abu Bakar
- Tick Cell Biobank Asia Outpost, Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Khoo Jing Jing
- Tick Cell Biobank Asia Outpost, Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Hasmahzaiti Omar
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia, .,Centre for Biotechnology in Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia.,Museum of Zoology (Block J14), Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
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Reilly SB, Karin BR, Stubbs AL, Arida E, Arifin U, Kaiser H, Bi K, Hamidy A, Iskandar DT, McGuire JA. Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago. Evolution 2022; 76:2281-2301. [PMID: 35932243 DOI: 10.1111/evo.14592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 01/22/2023]
Abstract
The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semipermeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation, rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence capture to generate a dataset of 1154 nuclear genes (∼1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three pairs of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and nonstepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection.
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Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Evy Arida
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Umilaela Arifin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Zoology Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Hinrich Kaiser
- Department of Biology, Victor Valley College, 18422 Bear Valley Road, Victorville, California, 92395, USA.,Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Amir Hamidy
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Djoko T Iskandar
- Basic Sciences Commission, Indonesian Academy of Sciences, 11, Jl. Medan Merdeka, Selatan Jakarta, 10110, Indonesia.,School of Life Sciences and Technology, Institut Teknologi Bandung, 10 Jalan Ganesha, Bandung, 40132, Indonesia
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
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6
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Rowsey DM, Duya MRM, Ibañez JC, Jansa SA, Rickart EA, Heaney LR. A new genus and species of shrew-like mouse (Rodentia: Muridae) from a new center of endemism in eastern Mindanao, Philippines. J Mammal 2022; 103:1259-1277. [PMID: 36660555 PMCID: PMC9841421 DOI: 10.1093/jmammal/gyac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/13/2022] [Indexed: 01/17/2023] Open
Abstract
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.
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Affiliation(s)
| | - Mariano Roy M Duya
- Institute of Biology, University of the Philippines–Diliman, Quezon City, Philippines
| | - Jayson C Ibañez
- Philippine Eagle Foundation, Philippine Eagle Center, Malagos, Baguio District Davao City, Philippines
| | - Sharon A Jansa
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric A Rickart
- Natural History Museum of Utah, University of Utah, Salt Lake City, Utah, USA
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7
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Abstract
Phylogenetic models have long assumed that lineages diverge independently. Processes of diversification that are of interest in biogeography, epidemiology, and genome evolution violate this assumption by affecting multiple evolutionary lineages. To relax the assumption of independent divergences and infer patterns of divergences predicted by such processes, we introduce a way of conceptualizing, modeling, and inferring phylogenetic trees. We apply the approach to genomic data from geckos distributed across the Philippines and find support for patterns of shared divergences predicted by repeated fragmentation of the archipelago by interglacial rises in sea level. Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.
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8
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Breed WG, Leigh CM, Peirce EJ. The highly divergent spermatozoon of the Palawan spiny rat, Maxomys panglima has an extremely long tail. Reprod Fertil Dev 2022; 34:526-530. [PMID: 35201976 DOI: 10.1071/rd21255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/28/2021] [Indexed: 11/23/2022] Open
Abstract
CONTEXT Sperm morphology varies greatly across mammalian species and this variability is especially evident in murid rodents with both sperm head shape and tail length being sexually selected traits. The Palawan spiny rat, Maxomys panglima has a longer sperm tail than that currently recorded for any other mammalian species. AIMS The aim of the current study was to determine the sperm morphology of an individual Palawan spiny rat, M. panglima . METHODS Light and transmission electron microscopy were carried out. KEY RESULTS We found that the sperm tail of M. panglima has an average length of 380μm with the midpiece being approximately 185μm in length with comparatively small mitochondria but very large coarse fibres. Furthermore, the sperm head has a less acutely flexed apical hook than that of most other murid rodents including those of several other Maxomys species. CONCLUSIONS The Palawan spiny rat has a highly divergent sperm morphology with an extremely long tail. It may turn out to be an important species for testing various hypotheses of sperm form and function in mammals. IMPLICATIONS These findings suggest markedly different selective pressures may have resulted in this unique sperm morphology, the functional significance of which remains to be determined.
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Affiliation(s)
- W G Breed
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - C M Leigh
- Adelaide Microscopy, University of Adelaide, Adelaide, SA 5005, Australia
| | - E J Peirce
- School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia
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9
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Fortela EB, Gonzalez JCT. Re-examination of the current distribution of two endemic malkohas from Greater Luzon PAIC, the Philippines. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2021. [DOI: 10.1016/j.japb.2021.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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10
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Ochoa J, Mijares ASB, Piper PJ, Reyes MC, Heaney LR. Three new extinct species from the endemic Philippine cloud rat radiation (Rodentia, Muridae, Phloeomyini). J Mammal 2021. [DOI: 10.1093/jmammal/gyab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
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.
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Affiliation(s)
- Janine Ochoa
- Department of Anthropology, University of the Philippines, Diliman, Quezon CityPhilippines
| | - Armand S B Mijares
- Archaeological Studies Program, University of the Philippines, Diliman, Quezon City, Philippines
- National Museum of the Philippines, Manila, Philippines
| | - Philip J Piper
- Archaeological Studies Program, University of the Philippines, Diliman, Quezon City, Philippines
- National Museum of the Philippines, Manila, Philippines
| | | | - Lawrence R Heaney
- National Museum of the Philippines, Manila, Philippines
- Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL, USA
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11
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Woods R, Barnes I, Brace S, Turvey ST. Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents. Mol Biol Evol 2021; 38:84-95. [PMID: 33035304 PMCID: PMC7783164 DOI: 10.1093/molbev/msaa189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining “ancestral-type” characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.
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Affiliation(s)
- Roseina Woods
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom.,Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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12
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Yao L, Witt K, Li H, Rice J, Salinas NR, Martin RD, Huerta-Sánchez E, Malhi RS. Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:21-33. [PMID: 32643146 DOI: 10.1002/ajpa.24099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/10/2020] [Accepted: 05/15/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVES Long-tailed macaques (Macaca fascicularis) are widely distributed throughout the mainland and islands of Southeast Asia, making them a useful model for understanding the complex biogeographical history resulting from drastic changes in sea levels throughout the Pleistocene. Past studies based on mitochondrial genomes (mitogenomes) of long-tailed macaque museum specimens have traced their colonization patterns throughout the archipelago, but mitogenomes trace only the maternal history. Here, our objectives were to trace phylogeographic patterns of long-tailed macaques using low-coverage nuclear DNA (nDNA) data from museum specimens. METHODS We performed population genetic analyses and phylogenetic reconstruction on nuclear single nucleotide polymorphisms (SNPs) from shotgun sequencing of 75 long-tailed macaque museum specimens from localities throughout Southeast Asia. RESULTS We show that shotgun sequencing of museum specimens yields sufficient genome coverage (average ~1.7%) for reconstructing population relationships using SNP data. Contrary to expectations of divergent results between nuclear and mitochondrial genomes for a female philopatric species, phylogeographical patterns based on nuclear SNPs proved to be closely similar to those found using mitogenomes. In particular, population genetic analyses and phylogenetic reconstruction from the nDNA identify two major clades within M. fascicularis: Clade A includes all individuals from the mainland along with individuals from northern Sumatra, while Clade B consists of the remaining island-living individuals, including those from southern Sumatra. CONCLUSIONS Overall, we demonstrate that low-coverage sequencing of nDNA from museum specimens provides enough data for examining broad phylogeographic patterns, although greater genome coverage and sequencing depth would be needed to distinguish between very closely related populations, such as those throughout the Philippines.
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Affiliation(s)
- Lu Yao
- American Museum of Natural History, New York, New York, USA
| | - Kelsey Witt
- Brown University, Providence, Rhode Island, USA.,University of California Merced, Merced, California, USA
| | - Hongjie Li
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan Rice
- University of California Merced, Merced, California, USA
| | - Nelson R Salinas
- American Museum of Natural History, New York, New York, USA.,Instituto de Hidrología, Metereología y Estudios Ambientales IDEAM, Bogotá, Colombia
| | - Robert D Martin
- The Field Museum of Natural History, Chicago, Illinois, USA.,University of Zürich, Zürich, Switzerland
| | | | - Ripan S Malhi
- University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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13
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Ge D, Feijó A, Abramov AV, Wen Z, Liu Z, Cheng J, Xia L, Lu L, Yang Q. Molecular phylogeny and morphological diversity of the Niviventer fulvescens species complex with emphasis on species from China. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe Niviventer fulvescens species complex (NFSC), a group of abundant and taxonomically ambiguous rodent taxa, is distributed from Southeast Asia to south-eastern China. We combined molecular and morphological datasets to clarify the species composition and variation of the NFSC. Our phylogenetic analyses, using molecular data, recovered eight genetic lineages in the NFSC, including a novel, distinct lineage from Jilong, Tibet, China, which is described as a new species, N. fengi sp. nov. The species status of N. fengi is supported by a species delimitation analysis, and it is morphologically distinguished from other members of the NFSC by its greyish dorsal fur, soft hairs covering the whole body and a hairy tail. NFSC species bearing well-developed spines are found at lower elevations. A comprehensive taxonomic revision of the NFSC within China is provided, represented by five species: N. cremoriventer, N. fulvescens, N. huang, N. mekongis comb. nov. and N. fengi. A further study of this species complex, including samples from Southeast Asia, is needed.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia; Joint Russian–Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhengjia Liu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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14
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Rowsey DM, Keenan RM, Jansa SA. Dietary morphology of two island-endemic murid rodent clades is consistent with persistent, incumbent-imposed competitive interactions. Proc Biol Sci 2020; 287:20192746. [PMID: 32097592 DOI: 10.1098/rspb.2019.2746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A lineage colonizing a geographic region with no competitors may exhibit rapid diversification due to greater ecological opportunity. The resultant species diversity of this primary-colonizing (incumbent) clade may limit subsequent lineages' ability to persist unless these non-incumbent lineages are ecologically distinct. We compare the diversity in diet-related mandibular morphology of two sympatric murid rodent clades endemic to Luzon Island, Philippines-incumbent Phloeomyini and secondary-colonizing Chrotomyini-to the mandibular morphological diversity of Sahul Hydromyini, the sister clade of Chrotomyini and the incumbent murid lineage on the supercontinent of Sahul. This three-clade comparison allows us to test the hypothesis that incumbent lineages can force persistent ecological distinction of subsequent colonists at the time of colonization and throughout the subsequent history of the two sympatric clades. We find that Chrotomyini forms a subset of the diversity of their clade plus Sahul Hydromyini that minimizes overlap with Phloeomyini. We also infer that this differentiation extends to the stem ancestor of Chrotomyini and Sahul Hydromyini, consistent with a biotic filter imposed by Phloeomyini. Our work illustrates that incumbency has the potential to have a profound influence on the ecomorphological diversity of colonizing lineages at the island scale even when the traits in question are evolving at similar rates among independently colonizing clades.
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Affiliation(s)
- Dakota M Rowsey
- Department of Ecology, Evolution, and Behavior & Bell Museum of Natural History, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108, USA.,Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Ryan M Keenan
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, 2003 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Sharon A Jansa
- Department of Ecology, Evolution, and Behavior & Bell Museum of Natural History, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108, USA
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15
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Breed WG, Hassan H, Gonzalez M, McLennan HJ, Leigh CM, Heaney LR. Interspecific diversity of testes mass and sperm morphology in the Philippine chrotomyine rodents: implications for differences in breeding systems across the species. Reprod Fertil Dev 2019; 31:705-711. [PMID: 30475689 DOI: 10.1071/rd18278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/23/2018] [Indexed: 01/16/2023] Open
Abstract
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.
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Affiliation(s)
- William G Breed
- Robinson Research Institute, School of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Hazirah Hassan
- Robinson Research Institute, School of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Macarena Gonzalez
- Robinson Research Institute, School of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Hanna J McLennan
- Robinson Research Institute, School of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Chris M Leigh
- Robinson Research Institute, School of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Lawrence R Heaney
- Field Museum of Natural History, Division of Mammals, 1400 South Lake Shore Drive, Chicago, Illinois 60605, USA
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16
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Nations JA, Heaney LR, Demos TC, Achmadi AS, Rowe KC, Esselstyn JA. A simple skeletal measurement effectively predicts climbing behaviour in a diverse clade of small mammals. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractArboreal 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.
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Affiliation(s)
- Jonathan A Nations
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | | | | | - Anang S Achmadi
- Museum Zoologicum Bogoriense, Research Centre for Biology, Cibinong, Jawa Barat, Indonesia
| | - Kevin C Rowe
- Sciences Department, Museum Victoria, Melbourne, VIC, Australia
| | - Jacob A Esselstyn
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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17
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Rickart EA, Balete DS, Timm RM, Alviola PA, Esselstyn JA, Heaney LR. Two new species of shrew-rats (Rhynchomys: Muridae: Rodentia) from Luzon Island, Philippines. J Mammal 2019. [DOI: 10.1093/jmammal/gyz066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Abstract
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.
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Affiliation(s)
- Eric A Rickart
- Natural History Museum of Utah, University of Utah, Salt Lake City, UT, USA
| | | | - Robert M Timm
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Phillip A Alviola
- Institute of Biological Sciences, University of the Philippines, Los Baños, Laguna, Philippines
| | - Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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18
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Oaks JR, Siler CD, Brown RM. The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago. Evolution 2019; 73:1151-1167. [PMID: 31017301 PMCID: PMC6767427 DOI: 10.1111/evo.13754] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/10/2019] [Indexed: 01/05/2023]
Abstract
A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the "species-pump" model, in which repeated bouts of cospeciation are driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. To test this prediction, we collected comparative genomic data from 16 pairs of insular gecko populations. We analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation have not been an important mechanism of speciation for gekkonid lizards across the Philippine Archipelago.
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Affiliation(s)
- Jamie R. Oaks
- Department of Biological Sciences & Museum of Natural HistoryAuburn UniversityAuburnAlabama36849
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of BiologyUniversity of OklahomaNormanOklahoma73072
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas66045
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19
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Rowsey DM, Heaney LR, Jansa SA. Tempo and mode of mandibular shape and size evolution reveal mixed support for incumbency effects in two clades of island-endemic rodents (Muridae: Murinae). Evolution 2019; 73:1411-1427. [PMID: 30985908 DOI: 10.1111/evo.13737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/04/2019] [Indexed: 12/26/2022]
Abstract
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.
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Affiliation(s)
- Dakota M Rowsey
- Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota, 55108.,Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108
| | | | - Sharon A Jansa
- Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota, 55108.,Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, 55108
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20
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Dong J, Kergoat GJ, Vicente N, Rahmadi C, Xu S, Robillard T. Biogeographic patterns and diversification dynamics of the genus Cardiodactylus Saussure (Orthoptera, Grylloidea, Eneopterinae) in Southeast Asia. Mol Phylogenet Evol 2018; 129:1-14. [DOI: 10.1016/j.ympev.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/27/2018] [Accepted: 06/02/2018] [Indexed: 10/14/2022]
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21
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Phylogeography of the black rat Rattus rattus in India and the implications for its dispersal history in Eurasia. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1830-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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New Supple Skink, GenusLygosoma(Reptilia: Squamata: Scincidae), from Indochina and Redescription ofLygosoma quadrupes(). J HERPETOL 2018. [DOI: 10.1670/16-064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Aghová T, Kimura Y, Bryja J, Dobigny G, Granjon L, Kergoat GJ. Fossils know it best: Using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Muridae). Mol Phylogenet Evol 2018; 128:98-111. [PMID: 30030180 DOI: 10.1016/j.ympev.2018.07.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022]
Abstract
Murid rodents (Rodentia: Muridae) represent the most diverse and abundant mammalian family. In this study, we provide a refined set of fossil calibrations which is used to reconstruct a dated phylogeny of the family using a multilocus dataset (six nuclear and nine mitochondrial gene fragments) encompassing 161 species representing 82 murid genera from four extant subfamilies (Deomyinae, Gerbillinae, Lophiomyinae and Murinae). In comparison with previous studies on murid or muroid rodents, our work stands out for the implementation of nine robust fossil constraints within the Muridae thanks to a thorough review of the fossil record. Before being assigned to specific nodes of the phylogeny, all potential fossil constraints were carefully assessed; they were also subjected to several cross-validation analyses. The resulting phylogeny is consistent with previous phylogenetic studies on murids, and recovers the monophyly of all sampled murid subfamilies and tribes. Based on nine controlled fossil calibrations, our inferred temporal timeframe indicates that the murid family likely originated in the course of the Early Miocene, 22.0-17.0 million years ago (Ma), and that most major lineages (i.e. tribes) started diversifying ca. 10 Ma. Historical biogeography analyses support the tropical origin for the family, with an initial internal split (vicariance event) between Afrotropical and Oriental (Indomalaya and Philippines) lineages. During the course of their diversification, the biogeographic pattern of murids is marked by several dispersal events toward the Australasian and the Palearctic regions. The Afrotropical region was also secondarily colonized at least three times from the Indomalaya, indicating that the latter region has acted as a major centre of diversification for the family.
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Affiliation(s)
- Tatiana Aghová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Zoology, National Museum, Václavské náměstí 68, 115 79 Prague, Czech Republic.
| | - Yuri Kimura
- Department of Geology and Paleontology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba 305-0005, Ibaraki, Japan
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Gauthier Dobigny
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ. Montpellier, Montpellier, France; Ecole Polytechnique d'Abomey-Calavi, Abomey-Calavi University, 01BP2009 Cotonou, Benin
| | - Laurent Granjon
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Gael J Kergoat
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
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24
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Rowsey DM, Heaney LR, Jansa SA. Diversification rates of the "Old Endemic" murine rodents of Luzon Island, Philippines are inconsistent with incumbency effects and ecological opportunity. Evolution 2018; 72:1420-1435. [PMID: 29845633 DOI: 10.1111/evo.13511] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/18/2018] [Indexed: 12/31/2022]
Abstract
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.
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Affiliation(s)
- Dakota M Rowsey
- Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota 55108
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108
| | - Lawrence R Heaney
- Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, Illinois 60605
| | - Sharon A Jansa
- Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota 55108
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108
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25
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Adhikari P, Han SH, Kim YK, Kim TW, Thapa TB, Subedi N, Kunwar A, Banjade M, Oh HS. New record of the Oriental house rat, Rattus tanezumi, in Nepal inferred from mitochondrial Cytochrome B gene sequences. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:386-390. [PMID: 33474178 PMCID: PMC7800815 DOI: 10.1080/23802359.2018.1436991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study determines the presence of R. tanezumi from in Nepal using morphological and molecular analyses. Morphologically, it is indistinguishable with R. rattus owing to similar fur colour and morphometric data. However, molecular identification and phylogenetic analysis using sequences of the mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene revealed two different species R. rattus and R. tanezumi from collected specimens. The genetic distance between R. rattus and R. tanezumi was found 0.043. In phylogenetic tree, the clade of R. tanezumi is distinguished into two sub-clades, R. tanezumi found in Nepal, and East Asian countries, China, Laos, Thailand, Viet Nam, and South Korea have genetic distance 0.031, suggesting the different lineages of R. tanezumi. This study confirmed the R. tanezumi present in Nepal. Our findings suggest that morphological analysis and molecular study should be carried out simultaneously for accurate identification of small sized cryptic mammals like R. tanezumi and R. rattus.
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Affiliation(s)
- Pradeep Adhikari
- Faculty of Science Education, Jeju National University, Jeju, Republic of Korea.,National Institute of Ecology, Seocheon, Republic of Korea
| | - Sang-Hyun Han
- Educational Science Research Institute, Jeju National University, Jeju, Republic of Korea.,Species Restoration Technology Institute, Korea National Park Service, Yeongju, Republic of Korea
| | - Yoo-Kyung Kim
- Educational Science Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Tae-Wook Kim
- Species Restoration Technology Institute, Korea National Park Service, Yeongju, Republic of Korea
| | - Tej Bahadur Thapa
- Central Department of Zoology, Tribhuvan University, Kathmandu, Nepal
| | - Naresh Subedi
- National Trust for Nature Conservation, Lalitpur, Nepal
| | - Amar Kunwar
- Small Mammals Conservation and Research Foundation, Kathmandu, Nepal
| | - Maniram Banjade
- Faculty of Science Education, Jeju National University, Jeju, Republic of Korea
| | - Hong-Shik Oh
- Faculty of Science Education, Jeju National University, Jeju, Republic of Korea
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26
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Weinell JL, Brown RM. Discovery of an old, archipelago-wide, endemic radiation of Philippine snakes. Mol Phylogenet Evol 2018; 119:144-150. [DOI: 10.1016/j.ympev.2017.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 11/10/2017] [Accepted: 11/15/2017] [Indexed: 11/26/2022]
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27
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Kyriazis CC, Alam B, Wjodyla M, Hackett S, Hosner P, Mays HL, Heaney LR, Reddy S. Colonization and diversification of the white-browed shortwing (Aves: Muscicapidae: Brachypteryx montana) in the Philippines. Mol Phylogenet Evol 2018; 121:121-131. [PMID: 29305243 DOI: 10.1016/j.ympev.2017.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 12/01/2017] [Accepted: 12/24/2017] [Indexed: 10/18/2022]
Abstract
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.
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Affiliation(s)
- Christopher C Kyriazis
- Biology Department, Loyola University Chicago, 1050 W. Sheridan Road, Chicago, IL 60660, USA
| | - Bushra Alam
- Biology Department, Loyola University Chicago, 1050 W. Sheridan Road, Chicago, IL 60660, USA
| | - Mark Wjodyla
- Biology Department, Loyola University Chicago, 1050 W. Sheridan Road, Chicago, IL 60660, USA
| | - Shannon Hackett
- Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Peter Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Herman L Mays
- Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA; Cincinnati Museum Center, Cincinnati, OH 45203, USA
| | - Lawrence R Heaney
- Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, 1050 W. Sheridan Road, Chicago, IL 60660, USA.
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Pahl T, McLennan HJ, Wang Y, Achmadi AS, Rowe KC, Aplin K, Breed WG. Sperm morphology of the Rattini – are the interspecific differences due to variation in intensity of intermale sperm competition? Reprod Fertil Dev 2018; 30:1434-1442. [DOI: 10.1071/rd17431] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/05/2018] [Indexed: 01/16/2023] Open
Abstract
It is widely accepted that in mammals a causal relationship exists between postcopulatory sexual selection and relative testes mass of the species concerned, but how much it determines sperm size and shape is debatable. Here we detailed for the largest murine rodent tribe, the Rattini, the interspecific differences in relative testes mass and sperm form. We found that residual testes mass correlates with sperm head apical hook length as well as its angle, together with tail length, and that within several lineages a few species have evolved highly divergent sperm morphology with a reduced or absent apical hook and shorter tail. Although most species have a relative testes mass of 1–4%, these derived sperm traits invariably co-occur in species with much smaller relative testes mass. We therefore suggest that high levels of intermale sperm competition maintain a sperm head with a long apical hook and long tail, whereas low levels of intermale sperm competition generally result in divergent sperm heads with a short or non-existent apical hook and shorter tail. We thus conclude that sexual selection is a major selective force in driving sperm head form and tail length in this large tribe of murine rodents.
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29
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Fabre PH, Reeve AH, Fitriana YS, Aplin KP, Helgen KM. A new species of Halmaheramys (Rodentia: Muridae) from Bisa and Obi Islands (North Maluku Province, Indonesia). J Mammal 2017. [DOI: 10.1093/jmammal/gyx160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Pan T, Zhang Y, Wang H, Wu J, Kang X, Qian L, Chen J, Rao D, Jiang J, Zhang B. The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification. PeerJ 2017; 5:e3995. [PMID: 29177111 PMCID: PMC5701547 DOI: 10.7717/peerj.3995] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/16/2017] [Indexed: 11/20/2022] Open
Abstract
Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus.
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Affiliation(s)
- Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Yanan Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Jun Wu
- Ministry of Environmental Protection, Nanjing Institute of Environmental Sciences, Nanjing, Jiangsu, China
| | - Xing Kang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Lifu Qian
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Jinyun Chen
- Department of Life Science, Huainan Normal University, Huainan, Anhui, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China.,School of Biosciences, Cardiff University, Cardiff, United Kingdom
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31
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Yao L, Li H, Martin RD, Moreau CS, Malhi RS. Tracing the phylogeographic history of Southeast Asian long-tailed macaques through mitogenomes of museum specimens. Mol Phylogenet Evol 2017; 116:227-238. [PMID: 28863929 DOI: 10.1016/j.ympev.2017.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/23/2017] [Accepted: 08/13/2017] [Indexed: 12/01/2022]
Abstract
The biogeographical history of Southeast Asia is complicated due to the continuous emergences and disappearances of land bridges throughout the Pleistocene. Here, we use long-tailed macaques (Macaca fascicularis), which are widely distributed throughout the mainland and islands of Southeast Asia, asa model for better understanding the biogeographical patterns of diversification in this geographically complex region. A reliable intraspecific phylogeny including individuals from localities on oceanic islands, continental islands, and the mainland is needed to trace relatedness along with the pattern and timing of colonization in this region. We used high-throughput sequencing techniques to sequence mitochondrial genomes (mitogenomes) from 95 Southeast Asian M. fascicularis specimens housed at natural history museums around the world. To achieve a comprehensive picture, we more than tripled the mitogenome sample size for M. fascicularis from previous studies, and for the first time included documented samples from the Philippines and several small Indonesian islands. Confirming the result from a previous, recent intraspecific phylogeny for M. fascicularis, the newly reconstructed phylogeny of 135 specimens divides the samples into two major clades: Clade A includes haplotypes from the mainland and some from northern Sumatra, while Clade B includes all insular haplotypes along with lineages from southern Sumatra. This study resolves a previous disparity by revealing a disjunction in the origin of Sumatran macaques, with separate lineages originating within the two major clades, suggesting that at least two major migrations to Sumatra occurred. However, our dated phylogeny reveals that the two major clades split ∼1.88Ma, which is earlier than in previously published phylogenies. Our new data reveal that most Philippine macaque lineages diverged from the Borneo stock within the last ∼0.06-0.43Ma. Finally, our study provides insight into successful sequencing of DNA across museums and shotgun sequencing of DNA specimens asa method to sequence the mitogenome.
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Affiliation(s)
- Lu Yao
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA.
| | - Hongjie Li
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
| | - Robert D Martin
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA; Institute of Evolutionary Medicine, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Corrie S Moreau
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA; Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 607 S. Mathews Ave., 109 Davenport Hall, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W Gregory Dr., Urbana, IL 61820, USA
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32
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Camacho-Sanchez M, Leonard JA, Fitriana Y, Tilak MK, Fabre PH. The generic status of Rattus annandalei (Bonhote, 1903) (Rodentia, Murinae) and its evolutionary implications. J Mammal 2017. [DOI: 10.1093/jmammal/gyx081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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33
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34
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Reyes MC, Ingicco T, Piper PJ, Amano N, Pawlik AF. First fossil evidence of the extinct Philippine cloud ratCrateromys paulus(Muridae: Murinae: Phloeomyini) from Ilin Island, Mindoro, and insights into its Holocene abundance. P BIOL SOC WASH 2017. [DOI: 10.2988/17-00012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Marian C. Reyes
- (MCR) National Museum of the Philippines, Padre Burgos St., Manila 1000, Philippines,
- (MCR, AFP) Archaeological Studies Program, Albert Hall, University of the Philippines, Diliman, Quezon City 1101, Philippines
| | - Thomas Ingicco
- (TI) Département de Préhistoire/UMR 7194, Muséum national d'Histoire naturelle, Musée de l'Homme 17, Place du Trocadéro 75116 Paris, France
| | - Philip J. Piper
- (PJP) School of Archaeology and Anthropology, AD Hope Bldg#14, The Australian National University, Canberra, Australia ACT 2601
| | - Noel Amano
- (NA) Max Planck Institute for the Science of Human History, Jena, 07745, Germany
| | - Alfred F. Pawlik
- (MCR, AFP) Archaeological Studies Program, Albert Hall, University of the Philippines, Diliman, Quezon City 1101, Philippines
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35
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Martin SA, Alhajeri BH, Steppan SJ. Dietary adaptations in the teeth of murine rodents (Muridae): a test of biomechanical predictions. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12822] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Stephanie A. Martin
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
- Biology Department; Austin Community College; Austin TX USA
| | - Bader H. Alhajeri
- Department of Biological Sciences; Kuwait University; Safat 13110 Kuwait
| | - Scott J. Steppan
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
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36
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Evidence of a complex phylogeographic structure in the Indomalayan pencil-tailed tree mouse Chiropodomys gliroides (Rodentia: Muridae) in eastern Indochina. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Rowe KC, Achmadi AS, Esselstyn JA. A new genus and species of omnivorous rodent (Muridae: Murinae) from Sulawesi, nested within a clade of endemic carnivores. J Mammal 2016. [DOI: 10.1093/jmammal/gyw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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38
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Borregaard MK, Amorim IR, Borges PAV, Cabral JS, Fernández-Palacios JM, Field R, Heaney LR, Kreft H, Matthews TJ, Olesen JM, Price J, Rigal F, Steinbauer MJ, Triantis KA, Valente L, Weigelt P, Whittaker RJ. Oceanic island biogeography through the lens of the general dynamic model: assessment and prospect. Biol Rev Camb Philos Soc 2016; 92:830-853. [PMID: 26923215 DOI: 10.1111/brv.12256] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 01/28/2016] [Accepted: 02/02/2016] [Indexed: 01/06/2023]
Abstract
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.
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Affiliation(s)
- Michael K Borregaard
- School of Geography and the Environment, University of Oxford, South Parks Road, OX1 3QY, Oxford, U.K.,Center for Macroecology, Evolution and Climate, National Museum of Natural History, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Isabel R Amorim
- Departamento de Ciências Agrárias, cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Rua Capitão João d'Ávila, São Pedro, 9700-042, Angra do Heroísmo, Terceira, Azores, Portugal
| | - Paulo A V Borges
- Departamento de Ciências Agrárias, cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Rua Capitão João d'Ávila, São Pedro, 9700-042, Angra do Heroísmo, Terceira, Azores, Portugal
| | - Juliano S Cabral
- Biodiversity, Macroecology and Conservation Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany.,Synthesis Centre of the German Centre for Integrative Biodiversity Research (iDiv), Deutscher Platz 5e, 04103, Leipzig, Germany
| | - José M Fernández-Palacios
- Island Ecology and Biogeography Research Group, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Richard Field
- School of Geography, University of Nottingham, NG7 2RD, Nottingham, U.K
| | - Lawrence R Heaney
- Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL, 60605, U.S.A
| | - Holger Kreft
- Biodiversity, Macroecology and Conservation Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Thomas J Matthews
- School of Geography and the Environment, University of Oxford, South Parks Road, OX1 3QY, Oxford, U.K.,Departamento de Ciências Agrárias, cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Rua Capitão João d'Ávila, São Pedro, 9700-042, Angra do Heroísmo, Terceira, Azores, Portugal
| | - Jens M Olesen
- Department of Bioscience - Genetics, Ecology and Evolution, Aarhus University, Ny Munkegade 114.2, DK-8000, Aarhus C, Denmark
| | - Jonathan Price
- Department of Geography and Environmental Studies, University of Hawaii at Hilo, 200 West Kawili Street, Hilo, HI, 96720, U.S.A
| | - Francois Rigal
- Departamento de Ciências Agrárias, cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Rua Capitão João d'Ávila, São Pedro, 9700-042, Angra do Heroísmo, Terceira, Azores, Portugal.,Environment and Microbiology Team, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
| | - Manuel J Steinbauer
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
| | - Konstantinos A Triantis
- School of Geography and the Environment, University of Oxford, South Parks Road, OX1 3QY, Oxford, U.K.,Departamento de Ciências Agrárias, cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Rua Capitão João d'Ávila, São Pedro, 9700-042, Angra do Heroísmo, Terceira, Azores, Portugal.,Department of Ecology and Taxonomy, Faculty of Biology, National and Kapodistrian University, GR-15784, Athens, Greece
| | - Luis Valente
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Haus 26, D-14476, Potsdam, Germany
| | - Patrick Weigelt
- Biodiversity, Macroecology and Conservation Biogeography, University of Göttingen, Büsgenweg 1, 37077, Göttingen, Germany
| | - Robert J Whittaker
- School of Geography and the Environment, University of Oxford, South Parks Road, OX1 3QY, Oxford, U.K.,Center for Macroecology, Evolution and Climate, National Museum of Natural History, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
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39
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Rowe KC, Achmadi AS, Esselstyn JA. Repeated evolution of carnivory among Indo-Australian rodents. Evolution 2016; 70:653-65. [PMID: 26826614 DOI: 10.1111/evo.12871] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 12/30/2022]
Abstract
Convergent evolution, often observed in island archipelagos, provides compelling evidence for the importance of natural selection as a generator of species and ecological diversity. The Indo-Australian Archipelago (IAA) is the world's largest island system and encompasses distinct biogeographic units, including the Asian (Sunda) and Australian (Sahul) continental shelves, which together bracket the oceanic archipelagos of the Philippines and Wallacea. Each of these biogeographic units houses numerous endemic rodents in the family Muridae. Carnivorous murids, that is those that feed on animals, have evolved independently in Sunda, Sulawesi (part of Wallacea), the Philippines, and Sahul, but the number of origins of carnivory among IAA murids is unknown. We conducted a comprehensive phylogenetic analysis of carnivorous murids of the IAA, combined with estimates of ancestral states for broad diet categories (herbivore, omnivore, and carnivore) and geographic ranges. These analyses demonstrate that carnivory evolved independently four times after overwater colonization, including in situ origins on the Philippines, Sulawesi, and Sahul. In each biogeographic unit the origin of carnivory was followed by evolution of more specialized carnivorous ecomorphs such as vermivores, insectivores, and amphibious rats.
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Affiliation(s)
- Kevin C Rowe
- Sciences Department, Museum Victoria, Melbourne, Australia.
| | - Anang S Achmadi
- Research Center for Biology, Museum Zoologicum Bogoriense, Cibinong, Jawa Barat, Indonesia
| | - Jacob A Esselstyn
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
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40
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Patterson BD, Norris RW. Towards a uniform nomenclature for ground squirrels: the status of the Holarctic chipmunks. MAMMALIA 2016. [DOI: 10.1515/mammalia-2015-0004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe chipmunks are a Holarctic group of ground squirrels currently allocated to the genus
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41
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Pagès M, Fabre PH, Chaval Y, Mortelliti A, Nicolas V, Wells K, Michaux JR, Lazzari V. Molecular phylogeny of South-East Asian arboreal murine rodents. ZOOL SCR 2015. [DOI: 10.1111/zsc.12161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie Pagès
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège; 4000 Liège (Sart Tilman) Belgique
- INRA; UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet, CS 30016 34988 Montferrier-sur-Lez Cedex France
- Institut des Sciences de l’Évolution de Montpellier; Université de Montpellier; CNRS; IRD; EPHE; 34095 Montpellier France
| | - Pierre-Henri Fabre
- Harvard Museum of Comparative Zoology; 26 Oxford Street Cambridge MA 02138 USA
- Smithsonian Institution; PO Box 37012, MRC 108 Washington DC 20013-7012 USA
| | - Yannick Chaval
- INRA; UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet, CS 30016 34988 Montferrier-sur-Lez Cedex France
| | - Alessio Mortelliti
- Department of Wildlife, Fisheries, and Conservation Biology; University of Maine; 5755 Nutting Hall, Room 228 Orono ME 04469 USA
| | - Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité; ISYEB - UMR 7205, CNRS; MNHN; UPMC; EPHE; Muséum national d'Histoire naturelle; Sorbonne Universités 57 rue Cuvier, CP 51 75005 Paris France
| | - Konstans Wells
- Environmental Futures Research Institute; Griffith University; Brisbane Qld 4111 Australia
| | - Johan R. Michaux
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège; 4000 Liège (Sart Tilman) Belgique
- CIRAD; TA C- 22/E - Campus international de Baillarguet 34398 Montpellier Cedex 5 France
| | - Vincent Lazzari
- Institut de paléoprimatologie; Paléontologie Humaine: Evolution et paléoenvironnements - UMR CNRS 7262 INEE; 86022 6 rue Michel Brunet Poitier France
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42
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Hawkins MTR, Helgen KM, Maldonado JE, Rockwood LL, Tsuchiya MTN, Leonard JA. Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys, Nannosciurinae). Mol Phylogenet Evol 2015; 94:752-764. [PMID: 26524259 DOI: 10.1016/j.ympev.2015.10.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 10/19/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
Abstract
The plain long-nosed squirrels, genus Dremomys, are high elevation species in East and Southeast Asia. Here we present a complete molecular phylogeny for the genus based on nuclear and mitochondrial DNA sequences. Concatenated mitochondrial and nuclear gene trees were constructed to determine the tree topology, and date the tree. All speciation events within the plain-long nosed squirrels (genus Dremomys) were ancient (dated to the Pliocene or Miocene), and averaged older than many speciation events in the related Sunda squirrels, genus Sundasciurus. Within the plain long-nosed squirrels, the most recent interspecific split occurred 2.9 million years ago, older than some splits within Sunda squirrels, which dated to the Pleistocene. Our results demonstrate that the plain long-nosed squirrels are not monophyletic. The single species with a distinct distribution, the Bornean mountain ground squirrel (Dremomys everetti), which is endemic to the high mountains of Borneo, is nested within the Sunda squirrels with high support. This species diverged from its sister taxa in the Sunda squirrels 6.62 million years ago, and other plain long-nosed squirrels over 11 million years ago. Our analyses of morphological traits in these related genera support the re-classification of the Bornean mountain ground squirrel, Dremomys everetti, to the genus Sundasciurus, which changes its name to Sundasciurus everetti. Past inclusion in the plain long-nosed squirrels (Dremomys) reflects convergent evolution between these high elevation species.
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Affiliation(s)
- Melissa T R Hawkins
- Smithsonian Conservation Biology Institute, Center for Conservation and Evolutionary Genetics, National Zoological Park, Washington DC 20008, USA; Division of Mammals, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington DC 20013-7012, USA; Estación Biológica de Doñana (EBD-CSIC), Conservation and Evolutionary Genetics Group, Avda. Americo Vespucio s/n, Sevilla 41092, Spain; George Mason University, Department of Environmental Science and Policy, 4400 University Drive, Fairfax, VA 20030, USA.
| | - Kristofer M Helgen
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington DC 20013-7012, USA
| | - Jesus E Maldonado
- Smithsonian Conservation Biology Institute, Center for Conservation and Evolutionary Genetics, National Zoological Park, Washington DC 20008, USA; Division of Mammals, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington DC 20013-7012, USA
| | - Larry L Rockwood
- George Mason University, Department of Biology, 4400 University Drive, Fairfax, VA 20030, USA
| | - Mirian T N Tsuchiya
- Smithsonian Conservation Biology Institute, Center for Conservation and Evolutionary Genetics, National Zoological Park, Washington DC 20008, USA; Division of Mammals, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington DC 20013-7012, USA; George Mason University, Department of Environmental Science and Policy, 4400 University Drive, Fairfax, VA 20030, USA
| | - Jennifer A Leonard
- Estación Biológica de Doñana (EBD-CSIC), Conservation and Evolutionary Genetics Group, Avda. Americo Vespucio s/n, Sevilla 41092, Spain
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43
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Esselstyn JA, Achmadi AS, Handika H, Rowe KC. A hog-nosed shrew rat (Rodentia: Muridae) from Sulawesi Island, Indonesia. J Mammal 2015. [DOI: 10.1093/jmammal/gyv093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents. Sci Rep 2015; 5:14444. [PMID: 26411391 PMCID: PMC4585935 DOI: 10.1038/srep14444] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/14/2015] [Indexed: 12/03/2022] Open
Abstract
Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of Pakistan, have served as one of the best-known fossil calibration points in molecular phylogenic studies. Although these fossils have been widely used as the 12 Ma date for the Mus/Rattus split or a more basal split, conclusive paleontological evidence for the nodal assignments has been absent. This study analyzes newly recognized characters that demonstrate lineage separation in the fossil record of Siwalik murines and examines the most reasonable nodal placement of the diverging lineages in a molecular phylogenetic tree by ancestral state reconstruction. Our specimen-based approach strongly indicates that Siwalik murines of the Karnimata clade are fossil members of the Arvicanthini-Otomyini-Millardini clade, which excludes Rattus and its relatives. Combining the new interpretation with the widely accepted hypothesis that the Progonomys clade includes Mus, the lineage separation event in the Siwalik fossil record represents the Mus/Arvicanthis split. Our test analysis on Bayesian age estimates shows that this new calibration point provides more accurate estimates of murine divergence than previous applications. Thus, we define this fossil calibration point and refine two other fossil-based points for molecular dating.
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Magallón S, Gómez-Acevedo S, Sánchez-Reyes LL, Hernández-Hernández T. A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. THE NEW PHYTOLOGIST 2015; 207:437-453. [PMID: 25615647 DOI: 10.1111/nph.13264] [Citation(s) in RCA: 493] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/21/2014] [Indexed: 05/03/2023]
Abstract
The establishment of modern terrestrial life is indissociable from angiosperm evolution. While available molecular clock estimates of angiosperm age range from the Paleozoic to the Late Cretaceous, the fossil record is consistent with angiosperm diversification in the Early Cretaceous. The time-frame of angiosperm evolution is here estimated using a sample representing 87% of families and sequences of five plastid and nuclear markers, implementing penalized likelihood and Bayesian relaxed clocks. A literature-based review of the palaeontological record yielded calibrations for 137 phylogenetic nodes. The angiosperm crown age was bound within a confidence interval calculated with a method that considers the fossil record of the group. An Early Cretaceous crown angiosperm age was estimated with high confidence. Magnoliidae, Monocotyledoneae and Eudicotyledoneae diversified synchronously 135-130 million yr ago (Ma); Pentapetalae is 126-121 Ma; and Rosidae (123-115 Ma) preceded Asteridae (119-110 Ma). Family stem ages are continuously distributed between c. 140 and 20 Ma. This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous. While substantial amounts of angiosperm morphological and functional diversity have deep evolutionary roots, extant species richness was probably acquired later.
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Affiliation(s)
- Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sandra Gómez-Acevedo
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luna L Sánchez-Reyes
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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van Tuinen M, Torres CR. Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families. Front Genet 2015; 6:203. [PMID: 26106406 PMCID: PMC4459087 DOI: 10.3389/fgene.2015.00203] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 05/25/2015] [Indexed: 11/13/2022] Open
Abstract
Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age. While many studies have stressed this concern with regard to deep nodes in the Tree of Life, the inference that molecular divergence time estimation of shallow nodes is less sensitive to erroneous model choice has not been tested explicitly in a Bayesian framework. Because of available divergence time estimation methods that permit fossil priors across any phylogenetic node and the present increase in efficient, cheap collection of species-level genomic data, insight is needed into the performance of divergence time estimation of shallow (<10 MY) nodes. Here, we performed multiple sensitivity analyses in a multi-locus data set of aquatic birds with six fossil constraints. Comparison across divergence time analyses that varied taxon and locus sampling, number and position of fossil constraint and shape of prior distribution showed various insights. Deviation from node ages obtained from a reference analysis was generally highest for the shallowest nodes but determined more by temporal placement than number of fossil constraints. Calibration with only the shallowest nodes significantly underestimated the aquatic bird fossil record, indicating the presence of saturation. Although joint calibration with all six priors yielded ages most consistent with the fossil record, ages of shallow nodes were overestimated. This bias was found in both mtDNA and nDNA regions. Thus, divergence time estimation of shallow nodes may suffer from bias and low precision, even when appropriate fossil priors and best available substitution models are chosen. Much care must be taken to address the possible ramifications of substitution saturation across the entire Tree of Life.
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Affiliation(s)
- Marcel van Tuinen
- Department of Biology and Marine Biology, University of North Carolina at WilmingtonWilmington, NC, USA
- Centre of Evolutionary and Ecological Studies, Marine Evolution and Conservation Group, University of GroningenGroningen, Netherlands
| | - Christopher R. Torres
- Department of Biology and Marine Biology, University of North Carolina at WilmingtonWilmington, NC, USA
- National Evolutionary Synthesis CenterDurham, NC, USA
- Department of Integrative Biology, University of Texas at AustinAustin, TX, USA
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Hughes M, Rubite RR, Blanc P, Chung KF, Peng CI. The Miocene to Pleistocene colonization of the Philippine archipelago by Begonia sect. Baryandra (Begoniaceae). AMERICAN JOURNAL OF BOTANY 2015; 102:695-706. [PMID: 26022484 DOI: 10.3732/ajb.1400428] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY One third of the species-rich Philippine flora is endemic, and most of the islands in the archipelago have never been connected to a continental region. We currently lack any well-sampled angiosperm phylogenies that span the archipelago, prohibiting the formation of informed hypotheses as to the evolution of this rich and highly endemic flora. METHODS We produced time-calibrated phylogenetic trees from both nuclear (ITS) and chloroplast (ndhA intron, ndhF-rpl32 spacer, rpl32-trnL spacer, trnC-trnD spacer) regions of 41 species of Begonia sect. Baryandra, all except one endemic to the Philippines. Historical biogeography was reconstructed across the chloroplast phylogeny using a Bayesian binary method of character optimization. Comparison of phylogenies from the two genomes permitted insight into the prevalence of hybridization in the group. KEY RESULTS The Philippine archipelago was colonized by Begonia sect. Baryandra in the late Miocene, via long-distance dispersal from western Malesia and a point of entry likely to be in the northwestern region of the archipelago. Palawan, Luzon, and Panay all bear early-branching lineages from this initial colonization. There have been Plio-Pleistocene dispersals from these islands into Borneo and Mindanao. Hybridization was common between species as evidenced by haplotype sharing and phylogenetic incongruence. CONCLUSIONS The phylogenies show a high degree of geographic structure, which millions of years of exposure to typhoons have not blurred, showing long-term species and population stability. The recent dispersals to Mindanao are congruent with the geologically recent arrival of the island at its current latitude in the southern Philippines.
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Affiliation(s)
- Mark Hughes
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, UK, EH3 5LR
| | - Rosario Rivera Rubite
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Padre Faura, Manila, Philippines
| | | | - Kuo-Fang Chung
- National Taiwan University, School of Forestry and Resource Conservation, Daan, Taipei 106, Taiwan
| | - Ching-I Peng
- Biodiversity Research Center, Academia Sinica, Nangang, Taipei 115, Taiwan
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Makarikov AA, Tkach VV, Villa SM, Bush SE. Description of two new species of Hymenolepis Weinland, 1858 (Cestoda: Hymenolepididae) from rodents on Luzon Island, Philippines. Syst Parasitol 2015; 90:27-37. [PMID: 25557745 DOI: 10.1007/s11230-014-9528-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/23/2014] [Indexed: 11/26/2022]
Abstract
Our helminthological examination of murid rodents on Luzon Island, Philippines, revealed a remarkable diversity of Hymenolepis Weinland, 1858. Here we describe two new species based on specimens from murid rodents Rattus everetti (Günther) and Apomys datae (Meyer) collected from Luzon Island. Hymenolepis alterna n. sp. differs from all known species of Hymenolepis in having irregularly alternating genital pores. This feature has not been reported from any previously known member of Hymenolepis. Additionally, Hymenolepis alterna n. sp. also differs from other Hymenolepis spp. in the relative position of both poral and antiporal dorsal osmoregulatory canals which are shifted towards the middle of the proglottis in relation to the ventral canals on both sides of the proglottides, and in having curved or twisted external seminal vesicle, covered externally by a dense layer of intensely stained cells. Hymenolepis bilaterala n. sp. differs from all known species of Hymenolepis in the relative position of both poral and antiporal dorsal osmoregulatory canals, which are shifted bilaterally towards the margins of proglottides in relation to the ventral canals, and in possession of testes situated in a triangle and eggs with very thin outer coat. A total of seven species of Hymenolepis are known from the Philippine archipelago. This total includes the cosmopolitan species Hymenolepis diminuta (Rudolphi, 1819), which was likely introduced to the island with invasive rats. Strikingly, all seven known species occur on the island of Luzon alone. By comparison, only six Hymenolepis spp. are known from the whole Palaearctic and seven from the Nearctic despite a much better level of knowledge of rodent helminths in these zoogeographical regions, as well as vast territories, diverse landscapes and very rich rodent fauna. This suggests that Hymenolepis spp. may have undergone an unusually active radiation in the Philippines. Possible explanations of this phenomenon are discussed.
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Affiliation(s)
- Arseny A Makarikov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze Str. 11, 630091, Novosibirsk, Russian Federation
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Veron G, Patou ML, Tóth M, Goonatilake M, Jennings AP. How many species of Paradoxurus
civets are there? New insights from India and Sri Lanka. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12085] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Géraldine Veron
- UMR 7205 ISYEB; CNRS MNHN UPMC EPHE; Institut de Systématique, Evolution, Biodiversité; Muséum National d'Histoire Naturelle, CP 51; Paris Cedex 05 France
| | - Marie-Lilith Patou
- UMR 7205 ISYEB; CNRS MNHN UPMC EPHE; Institut de Systématique, Evolution, Biodiversité; Muséum National d'Histoire Naturelle, CP 51; Paris Cedex 05 France
| | - Mária Tóth
- Department of Zoology; Hungarian Natural History Museum; Budapest Hungary
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Balakirev AE, Abramov AV, Rozhnov VV. Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia, Muridae) inferred from molecular data, with description of a new species. Zookeys 2014; 451:109-36. [PMID: 25493050 PMCID: PMC4258623 DOI: 10.3897/zookeys.451.7210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 09/03/2014] [Indexed: 12/05/2022] Open
Abstract
Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscuschiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscuschiropus (the type species of Chiromyscus), Chiromyscuslangbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name Chiromyscusthomasi sp. n.
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Affiliation(s)
- Alexander E. Balakirev
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- A.N. Severtsov’s Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Alexei V. Abramov
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, Saint Petersburg 199034, Russia
| | - Viatcheslav V. Rozhnov
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- A.N. Severtsov’s Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
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