1
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Kenyon-Flatt B, von Cramon-Taubadel N. Intrageneric taxonomic distinction based on morphological variation in the macaque (Macaca) skeleton. Anat Rec (Hoboken) 2024; 307:118-140. [PMID: 37439127 DOI: 10.1002/ar.25283] [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: 11/07/2022] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Taxonomic classification is important for understanding the natural world, yet current methods for species assessment often focus on craniodental morphology rather than the entire skeleton. Moreover, it is currently unknown how much variation could, or should, exist intragenerically. Here, we tested whether taxonomy can be accurately predicted based on patterns of morphological variation in macaques (H1 ) and whether postcranial bones reflect subgeneric macaque taxonomy similarly, or better, than the cranium (H2 ). Data included 3D scans of cranial and postcranial bones for eight macaque species (Macaca arctoides, Macaca fascicularis, Macaca fuscata, Macaca mulatta, Macaca nemestrina, Macaca nigra, Macaca radiata, and Macaca sylvanus). Fixed anatomical and semilandmarks were applied to scans of eight skeletal elements (crania = 45; mandible = 31; scapula = 66; humerus = 38; radius = 33; os coxa = 28; femur = 40; tibia = 40). For each skeletal element, regression analyses were performed to minimize the effects of sexual dimorphism. Between-groups principal components analysis was used to visualize the major patterns of among-species morphological variation, while the strength of correct taxon classification was measured with discriminant function analysis. Results suggested accepting the alternate hypothesis that different macaque species can be distinguished morphologically. Both cranial and many postcranial elements appeared to possess a taxonomic signal, and the limb bones-especially the upper limb-are reported to be more useful for taxonomic assessment than previously realized. Theoretically, certain behaviors and/or ecogeographical factors, as well as phylogeny, influenced skeletal morphology in macaques, likely contributing to taxonomic distinctions among different species.
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Affiliation(s)
- Brittany Kenyon-Flatt
- School of Nursing, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, New York, USA
| | - Noreen von Cramon-Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, New York, USA
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2
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Yan X, Terai Y, Widayati KA, Itoigawa A, Purba LHPS, Fahri F, Suryobroto B, Imai H. Functional divergence of the pigmentation gene melanocortin-1 receptor (MC1R) in six endemic Macaca species on Sulawesi Island. Sci Rep 2022; 12:7593. [PMID: 35534524 PMCID: PMC9085793 DOI: 10.1038/s41598-022-11681-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 04/28/2022] [Indexed: 11/20/2022] Open
Abstract
Coat color is often highly variable within and between animal taxa. Among hundreds of pigmentation-related genes, melanocortin-1 receptor (MC1R) plays key roles in regulating the synthesis of the dark eumelanin and the red-yellow pheomelanin. The six species of macaques that inhabit Sulawesi Island diverged rapidly from their common ancestor, M. nemestrina. Unlike most macaques, Sulawesi macaques commonly have a dark coat color, with divergence in shade and color pattern. To clarify the genetic and evolutionary basis for coat color in Sulawesi macaques, we investigated the MC1R sequences and functional properties, including basal cAMP production and α-MSH-induced activity in vitro. We found fixed non-synonymous substitutions in MC1R in each species. Furthermore, we found that six species-specific variants corresponded with variation in agonist-induced and basal activity of MC1R. Inconsistent with the dark coat color, four substitutions independently caused decreases in the basal activity of MC1R in M. hecki, M. nigra, M. tonkeana, and M. ochreata. Selective analysis suggested MC1R of M. nigra and M. nigrescens underwent purifying selection. Overall, our results suggest that fixed differences in MC1R resulted in different functional characteristics and might contribute to divergence in color among the six Sulawesi macaque species.
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Affiliation(s)
- Xiaochan Yan
- Molecular Biology Section, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan
| | - Yohey Terai
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan
| | | | - Akihiro Itoigawa
- Molecular Biology Section, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan
| | | | - Fahri Fahri
- Department of Biology, Tadulako University, Palu, Indonesia
| | | | - Hiroo Imai
- Molecular Biology Section, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan.
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3
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Montani ME, Tomasco IH, Barberis IM, Romano MC, Barquez RM, Díaz MM. A new species of Molossus (Chiroptera: Molossidae) from Argentina. J Mammal 2021. [DOI: 10.1093/jmammal/gyab078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Abstract
Fourteen species of bats in the genus Molossus currently are recognized in the Neotropical region; only three are known from Argentina. Here, we describe a new species based on specimens collected in the province of Santa Fe, Argentina, in the Pampa ecoregion. The new species can be distinguished from its congeners by its general strong orange coloration, forearm length > 41 mm, dorsal hairs bicolor and long (~5 mm), infraorbital foramen laterally oriented, and long and forward-projected (pincer-like) upper incisors. The external and cranial morphology of the new species are described and comparisons made with other species of similar size and with those present in its distributional area. Wilcoxon tests and multivariate analyses (nonmetric multidimensional scaling ordination and PERMANOVA) were carried out to determine the morphometric differences between the new species and other seven species of Molossus. The species tree, estimated by *BEAST from the concatenation of mitochondrial and nuclear genes, suggests that Molossus sp. nov. is basal within the clade formed by {{M. aztecus, M. rufus}, {{M. currentium, M. pretiosus}, M. sinaloae}} with a posterior probability of 0.82.
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Affiliation(s)
- M Eugenia Montani
- Instituto de Investigaciones de Biodiversidad Argentina (PIDBA), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina
- PCMA (Programa de Conservación de los Murciélagos de Argentina), Miguel Lillo 205, 4000 Tucumán, Argentina
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, San Lorenzo 1949, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, C.C. 14, S2125ZAA Zavalla, Santa Fe, Argentina
| | - Ivanna H Tomasco
- Instituto de Investigaciones de Biodiversidad Argentina (PIDBA), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400 Montevideo, Uruguay
| | - Ignacio M Barberis
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (C1425FQB), Ciudad Autónoma de Buenos Aires, Argenitna
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental Villarino, C.C. 14, S2125ZAA Zavalla, Santa Fe, Argentina
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), UNR - CONICET, Campo Experimental Villarino, C.C. 14, S2125ZAA Zavalla, Santa Fe, Argentina
| | - Marcelo C Romano
- Centro de Investigaciones en Biodiversidad y Ambiente (ECOSUR), Pje. Sunchales 329, 2000 Rosario, Santa Fe, Argentina
| | - Rubén M Barquez
- Instituto de Investigaciones de Biodiversidad Argentina (PIDBA), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina
- PCMA (Programa de Conservación de los Murciélagos de Argentina), Miguel Lillo 205, 4000 Tucumán, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (C1425FQB), Ciudad Autónoma de Buenos Aires, Argenitna
| | - M Mónica Díaz
- Instituto de Investigaciones de Biodiversidad Argentina (PIDBA), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000 Tucumán, Argentina
- PCMA (Programa de Conservación de los Murciélagos de Argentina), Miguel Lillo 205, 4000 Tucumán, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (C1425FQB), Ciudad Autónoma de Buenos Aires, Argenitna
- Fundación Miguel Lillo, Miguel Lillo 251, 4000 Tucumán, Argentina
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4
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Horoiwa M, Mandagi IF, Sutra N, Montenegro J, Tantu FY, Masengi KWA, Nagano AJ, Kusumi J, Yasuda N, Yamahira K. Mitochondrial introgression by ancient admixture between two distant lacustrine fishes in Sulawesi Island. PLoS One 2021; 16:e0245316. [PMID: 34111145 PMCID: PMC8192020 DOI: 10.1371/journal.pone.0245316] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Sulawesi, an island located in a biogeographical transition zone between Indomalaya and Australasia, is famous for its high levels of endemism. Ricefishes (family Adrianichthyidae) are an example of taxa that have uniquely diversified on this island. It was demonstrated that habitat fragmentation due to the Pliocene juxtaposition among tectonic subdivisions of this island was the primary factor that promoted their divergence; however, it is also equally probable that habitat fusions and resultant admixtures between phylogenetically distant species may have frequently occurred. Previous studies revealed that some individuals of Oryzias sarasinorum endemic to a tectonic lake in central Sulawesi have mitochondrial haplotypes that are similar to the haplotypes of O. eversi, which is a phylogenetically related but geologically distant (ca. 190 km apart) adrianichthyid endemic to a small fountain. In this study, we tested if this reflects ancient admixture of O. eversi and O. sarasinorum. Population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that O. eversi and O. sarasinorum are substantially reproductively isolated from each other. Comparison of demographic models revealed that the models assuming ancient admixture from O. eversi to O. sarasinorum was more supported than the models assuming no admixture; this supported the idea that the O. eversi-like mitochondrial haplotype in O. sarasinorum was introgressed from O. eversi. This study is the first to demonstrate ancient admixture of lacustrine or pond organisms in Sulawesi beyond 100 km. The complex geological history of this island enabled such island-wide admixture of lacustrine organisms, which usually experience limited migration.
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Affiliation(s)
- Mizuki Horoiwa
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ixchel F. Mandagi
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Nobu Sutra
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
- Graduate School of Hasanuddin University, Makassar, Indonesia
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Fadly Y. Tantu
- Faculty of Animal Husbandry and Fisheries, Tadulako University, Palu, Indonesia
| | | | | | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Nina Yasuda
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
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5
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Ali JR, Heaney LR. Wallace's line,
Wallacea
, and associated divides and areas: history of a tortuous tangle of ideas and labels. Biol Rev Camb Philos Soc 2021; 96:922-942. [DOI: 10.1111/brv.12683] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 12/27/2022]
Affiliation(s)
- Jason R. Ali
- Department of Earth Sciences University of Hong Kong Pokfulam Road Hong Kong China
| | - Lawrence R. Heaney
- Field Museum of Natural History 1400 S Lake Shore Drive Chicago IL 60605‐2496 U.S.A
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6
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Supriatna J, Shekelle M, Fuad HA, Winarni NL, Dwiyahreni AA, Farid M, Mariati S, Margules C, Prakoso B, Zakaria Z. Deforestation on the Indonesian island of Sulawesi and the loss of primate habitat. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01205] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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7
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Handika H, Achmadi AS, Esselstyn JA, Rowe KC. Molecular and morphological systematics of the Bunomys division (Rodentia: Muridae), an endemic radiation on Sulawesi. ZOOL SCR 2020. [DOI: 10.1111/zsc.12460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Heru Handika
- Department of Biological Sciences Museum of Natural Science Louisiana State University Baton Rouge LA USA
- Sciences Department Museums Victoria Melbourne VIC Australia
- School of Biosciences University of Melbourne Parkville, Melbourne VIC Australia
| | - Anang S. Achmadi
- Museum Zoologicum Bogoriense Indonesian Institute of Sciences Cibinong Indonesia
| | - Jacob A. Esselstyn
- Department of Biological Sciences Museum of Natural Science Louisiana State University Baton Rouge LA USA
| | - Kevin C. Rowe
- Sciences Department Museums Victoria Melbourne VIC Australia
- School of Biosciences University of Melbourne Parkville, Melbourne VIC Australia
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8
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Using occupancy-based camera-trap surveys to assess the Critically Endangered primate Macaca nigra across its range in North Sulawesi, Indonesia. ORYX 2020. [DOI: 10.1017/s0030605319000851] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractPrimates are one of the most threatened groups of mammals. Understanding their patterns of population occurrence and abundance, especially in response to threats, is critical for informing conservation action. The crested black macaque Macaca nigra is the only Critically Endangered species of Sulawesi's seven endemic macaques. Little is known about its distribution or its response to deforestation and hunting. We conducted a camera-trap survey across the entire species range using an occupancy-based analytical approach to (1) establish the first range-wide baseline of occurrence, (2) investigate how environmental and anthropogenic factors influence occurrence, (3) identify priority conservation subpopulations, and (4) test the efficacy of the sampling and analytical protocol for temporal monitoring of M. nigra using occupancy as the state variable. From 9,753 camera-trap days, M. nigra was detected on 473 days at 77 of the 111 camera locations. Species occupancy was 0.66 and highest inside protected areas and closed canopy forest. We identified eight distinct subpopulations, based on distribution and forest fragment size. To inform future monitoring, we used a power analysis to determine if our effort would allow us to detect inter-annual occupancy declines of 10%, and found that 90 camera locations surveyed for 3 months (8,100 camera days) across three consecutive seasons is the effort required to detect such change with 80% certainty. Our study underscores the importance of well-managed protected areas and intact forests for the long-term survival of the crested black macaque, and tests the effectiveness of camera traps to monitor primates at the landscape scale.
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9
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Mitogenomics of macaques (Macaca) across Wallace's Line in the context of modern human dispersals. J Hum Evol 2020; 146:102852. [DOI: 10.1016/j.jhevol.2020.102852] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/28/2020] [Accepted: 06/28/2020] [Indexed: 11/17/2022]
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10
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Roos C, Kothe M, Alba DM, Delson E, Zinner D. The radiation of macaques out of Africa: Evidence from mitogenome divergence times and the fossil record. J Hum Evol 2019; 133:114-132. [DOI: 10.1016/j.jhevol.2019.05.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 04/14/2019] [Accepted: 05/31/2019] [Indexed: 01/30/2023]
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11
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Hosoishi S, Ogata K. Cryptic Diversity in the Widespread Asian Ant Crematogaster rothneyi (Hymenoptera: Formicidae) Inferred from Morphological and Genetic Evidence. Zool Stud 2019; 58:e11. [PMID: 31966312 PMCID: PMC6778772 DOI: 10.6620/zs.2019.58-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/07/2019] [Indexed: 11/18/2022]
Abstract
The myrmicine species Crematogaster rothneyi is one of the most widely distributed ants in Asia, but it has rarely been collected in the field. Its distribution range covers South and Southeast Asia, extending approximately 5,000 km from India in the west to Sulawesi in the east. Despite this wide distribution range, C. rothneyi has been treated as a single taxonomic species, and no combined morphological or molecular analysis has been conducted to assess whether any intraspecific variation exists. The sequence divergences of C. rothneyi populations, mainly obtained from Southeast Asia, were investigated by analyzing 387 bp and 175 bp sequences of the 12S ribosomal RNA and cytochrome c oxidase subunit (COI) genes, respectively. Phylogenetic analysis indicated that the C. rothneyi populations were separated into three groups: group I from Thailand and Cambodia, group II from Bangladesh and Myanmar, and group III from Krakatau and Sulawesi. Groups II and III were recovered as a single clade, sister to group I. The interspecific divergences were 7.3% to 8.5% for 12S and 14.5% to 23.3% for COI between most C. rothneyi specimens and Cambodian specimens, while divergence for 12S was 3.5% between Thai and Cambodian specimens. The Thai specimens are not morphologically differentiated, and are considered conspecific to C. rothneyi. We describe the Cambodian series as a new species, Crematogaster yaharai sp. nov., based on unique antennal morphology and mesosomal sculpture patterns with molecular evidence. Crematogaster rothneyi civa Forel, 1902 is synonymized under C. rothneyi. Crematogaster rothneyi is widespread and has sister species, suggesting recent diversification within the Indochinese Peninsula.
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Affiliation(s)
- Shingo Hosoishi
- Institute of Tropical Agriculture, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395 Japan.
| | - Kazuo Ogata
- Institute of Tropical Agriculture, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka 819-0395 Japan.
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12
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Affiliation(s)
- Bayu Broto
- Department of Wildlife, Fisheries, and Conservation Biology; University of Maine; 5755 Nutting Hall Orono ME 04469 USA
| | - Alessio Mortelliti
- Department of Wildlife, Fisheries, and Conservation Biology; University of Maine; 5755 Nutting Hall Orono ME 04469 USA
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13
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Abduriyim S, Zibibulla G, Eli S, Ismayil Z, Halik M. Phylogeny and genetic structure of the goitered gazelle (Artiodactyla, Bovidae) in north-western China indicated by the hypervariable mitochondrial control region. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1470583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Shamshidin Abduriyim
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Guzalnur Zibibulla
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Subinur Eli
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Zorigul Ismayil
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Mahmut Halik
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
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14
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Frantz LAF, Rudzinski A, Nugraha AMS, Evin A, Burton J, Hulme-Beaman A, Linderholm A, Barnett R, Vega R, Irving-Pease EK, Haile J, Allen R, Leus K, Shephard J, Hillyer M, Gillemot S, van den Hurk J, Ogle S, Atofanei C, Thomas MG, Johansson F, Mustari AH, Williams J, Mohamad K, Damayanti CS, Wiryadi ID, Obbles D, Mona S, Day H, Yasin M, Meker S, McGuire JA, Evans BJ, von Rintelen T, Ho SYW, Searle JB, Kitchener AC, Macdonald AA, Shaw DJ, Hall R, Galbusera P, Larson G. Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events. Proc Biol Sci 2018; 285:rspb.2017.2566. [PMID: 29643207 PMCID: PMC5904307 DOI: 10.1098/rspb.2017.2566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/16/2018] [Indexed: 11/13/2022] Open
Abstract
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2–3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
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Affiliation(s)
- Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK .,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Anna Rudzinski
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Allowen Evin
- Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, Cedex 05, France.,Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - James Burton
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK.,IUCN SSC Asian Wild Cattle Specialist Group and Chester Zoo, Cedar House, Caughall Road, Upton by Chester, Chester CH2 1LH, UK
| | - Ardern Hulme-Beaman
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | - Ross Barnett
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Rodrigo Vega
- Ecology Research Group, Section of Life Sciences, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury CT1 1QU, Kent, UK
| | - Evan K Irving-Pease
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Richard Allen
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Kristin Leus
- Copenhagen Zoo, IUCN SSC Conservation Breeding Specialist Group-Europe, Roskildevej 38, Postboks 7, 2000 Frederiksberg, Denmark.,European Association of Zoos and Aquaria, PO Box 20164, 1000 HD Amsterdam, The Netherlands
| | - Jill Shephard
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium.,Environment and Conservation Sciences, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - Mia Hillyer
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium.,Molecular Systematics Unit/Terrestrial Zoology, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Sarah Gillemot
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Jeroen van den Hurk
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Sharron Ogle
- Edinburgh Medical School: BMTO, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Cristina Atofanei
- Ecology Research Group, Section of Life Sciences, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury CT1 1QU, Kent, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Abdul Haris Mustari
- Department of Forest Resources Conservation and Ecotourism, Faculty of Forestry, Bogor Agricultural University, PO Box 168, Bogor 16001, Indonesia
| | - John Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy, Southern Australia 5371, Australia
| | - Kusdiantoro Mohamad
- Faculty of Veterinary Medicine, Bogor Agricultural University, Jalan Agatis, IPB Campus, Darmaga, Bogor 16680, Indonesia
| | - Chandramaya Siska Damayanti
- Faculty of Veterinary Medicine, Bogor Agricultural University, Jalan Agatis, IPB Campus, Darmaga, Bogor 16680, Indonesia
| | | | - Dagmar Obbles
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - Stephano Mona
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005 Paris, France.,EPHE, PSL Research University, Paris, France
| | | | | | - Stefan Meker
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Thomas von Rintelen
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853, USA
| | - Andrew C Kitchener
- Department of Natural Sciences, Chambers Street, National Museums Scotland, Edinburgh EH1 1JF, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Alastair A Macdonald
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK
| | - Darren J Shaw
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK
| | - Robert Hall
- SE Asia Research Group, Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Peter Galbusera
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
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Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A, Melnick DJ. Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170351. [PMID: 29134059 PMCID: PMC5666242 DOI: 10.1098/rsos.170351] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/18/2017] [Indexed: 05/30/2023]
Abstract
Many genera of terrestrial vertebrates diversified exclusively on one or the other side of Wallace's Line, which lies between Borneo and Sulawesi islands in Southeast Asia, and demarcates one of the sharpest biogeographic transition zones in the world. Macaque monkeys are unusual among vertebrate genera in that they are distributed on both sides of Wallace's Line, raising the question of whether dispersal across this barrier was an evolutionary one-off or a more protracted exchange-and if the latter, what were the genomic consequences. To explore the nature of speciation over the edge of this biogeographic divide, we used genomic data to test for evidence of gene flow between macaque species across Wallace's Line after macaques colonized Sulawesi. We recovered evidence of post-colonization gene flow, most prominently on the X chromosome. These results are consistent with the proposal that gene flow is a pervasive component of speciation-even when barriers to gene flow seem almost insurmountable.
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Affiliation(s)
- Ben J. Evans
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S4K1
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th floor Schermerhorn Extension, 119th Street and Amsterdam Avenue, New York, NY 10027, USA
| | - Anthony J. Tosi
- Anthropology Department, Kent State University, 238 Lowry Hall, Kent, OH 44242, USA
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Jonathan Dushoff
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S4K1
| | - André Corvelo
- New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Don J. Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th floor Schermerhorn Extension, 119th Street and Amsterdam Avenue, New York, NY 10027, USA
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16
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Engelhardt A, Muniz L, Perwitasari-Farajallah D, Widdig A. Highly Polymorphic Microsatellite Markers for the Assessment of Male Reproductive Skew and Genetic Variation in Critically Endangered Crested Macaques ( Macaca nigra). INT J PRIMATOL 2017; 38:672-691. [PMID: 28845069 PMCID: PMC5550527 DOI: 10.1007/s10764-017-9973-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/11/2017] [Indexed: 11/24/2022]
Abstract
Genetic analyses based on noninvasively collected samples have become an important tool for evolutionary biology and conservation. Crested macaques (Macaca nigra), endemic to Sulawesi, Indonesia, are important for our understanding of primate evolution as Sulawesi macaques represent an exceptional example of primate adaptive radiation. Crested macaques are also Critically Endangered. However, to date we know very little about their genetics. The aim of our study was to find and validate microsatellite markers useful for evolutionary, conservation, and other genetic studies on wild crested macaques. Using fecal samples of 176 wild macaques living in the Tangkoko Reserve, Sulawesi, we identified 12 polymorphic microsatellite loci through cross-species polymerase chain reaction amplification with later modification of some of these primers. We tested their suitability by investigating and exploring patterns of paternity, observed heterozygosity, and evidence for inbreeding. We assigned paternity to 63 of 65 infants with high confidence. Among cases with solved paternity, we found no evidence of extragroup paternity and natal breeding. We found a relatively steep male reproductive skew B index of 0.330 ± 0.267; mean ± SD) and mean alpha paternity of 65% per year with large variation across groups and years (29–100%). Finally, we detected an excess in observed heterozygosity and no evidence of inbreeding across our three study groups, with an observed heterozygosity of 0.766 ± 0.059 and expected heterozygosity of 0.708 ± 0.059, and an inbreeding coefficient of −0.082 ± 0.035. Our results indicate that the selected markers are useful for genetic studies on wild crested macaques, and possibly also on other Sulawesi and closely related macaques. They further suggest that the Tangkoko population of crested macaques is still genetically variable despite its small size, isolation, and the species’ reproductive patterns. This gives us hope that other endangered primate species living in small, isolated populations may also retain a healthy gene pool, at least in the short term.
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Affiliation(s)
- Antje Engelhardt
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF, Liverpool, UK.,Junior Research Group of Primate Sexual Selection, German Primate Center, 37077 Göttingen, Germany.,Courant Research Center Evolution of Social Behavior, Georg August University, 37077 Göttingen, Germany
| | - Laura Muniz
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Dyah Perwitasari-Farajallah
- Primate Research Centre, Bogor Agricultural University, Bogor, Indonesia.,Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany.,German Center for Integrative Biodiversity Research, 04103 Leipzig, Germany
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17
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Hawkins MTR, Leonard JA, Helgen KM, McDonough MM, Rockwood LL, Maldonado JE. Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens. BMC Evol Biol 2016; 16:80. [PMID: 27075887 PMCID: PMC4831120 DOI: 10.1186/s12862-016-0650-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 04/03/2016] [Indexed: 01/06/2023] Open
Abstract
Background The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi’s three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. Results Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace’s line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. Conclusions The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0650-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melissa T R Hawkins
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA. .,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA. .,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, 22030, USA.
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana(EBD-CSIC), 41092, Sevilla, Spain
| | - Kristofer M Helgen
- Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Molly M McDonough
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Larry L Rockwood
- Department of Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Jesus E Maldonado
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, P.O. Box 37012, Washington, DC, 20013-7012, USA
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18
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Mokodongan DF, Yamahira K. Origin and intra-island diversification of Sulawesi endemic Adrianichthyidae. Mol Phylogenet Evol 2015; 93:150-60. [DOI: 10.1016/j.ympev.2015.07.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 07/26/2015] [Accepted: 07/27/2015] [Indexed: 11/17/2022]
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19
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Driller C, Merker S, Perwitasari-Farajallah D, Sinaga W, Anggraeni N, Zischler H. Stop and Go - Waves of Tarsier Dispersal Mirror the Genesis of Sulawesi Island. PLoS One 2015; 10:e0141212. [PMID: 26559527 PMCID: PMC4641617 DOI: 10.1371/journal.pone.0141212] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/05/2015] [Indexed: 11/18/2022] Open
Abstract
The Indonesian island of Sulawesi harbors a highly endemic and diverse fauna sparking fascination since long before Wallace’s contemplation of biogeographical patterns in the region. Allopatric diversification driven by geological or climatic processes has been identified as the main mechanism shaping present faunal distribution on the island. There is both consensus and conflict among range patterns of terrestrial species pointing to the different effects of vicariant events on once co-distributed taxa. Tarsiers, small nocturnal primates with possible evidence of an Eocene fossil record on the Asian mainland, are at present exclusively found in insular Southeast Asia. Sulawesi is hotspot of tarsier diversity, whereby island colonization and subsequent radiation of this old endemic primate lineage remained largely enigmatic. To resolve the phylogeographic history of Sulawesi tarsiers we analyzed an island-wide sample for a set of five approved autosomal phylogenetic markers (ABCA1, ADORA3, AXIN1, RAG1, and TTR) and the paternally inherited SRY gene. We constructed ML and Bayesian phylogenetic trees and estimated divergence times between tarsier populations. We found that their arrival at the Proto-Sulawesi archipelago coincided with initial Miocene tectonic uplift and hypothesize that tarsiers dispersed over the region in distinct waves. Intra-island diversification was spurred by land emergence and a rapid succession of glacial cycles during the Plio-Pleistocene. Some tarsier range boundaries concur with spatial limits in other taxa backing the notion of centers of faunal endemism on Sulawesi. This congruence, however, has partially been superimposed by taxon-specific dispersal patterns.
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Affiliation(s)
- Christine Driller
- Institute of Anthropology, Johannes-Gutenberg University Mainz, Mainz, Germany
- * E-mail:
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Dyah Perwitasari-Farajallah
- Primate Research Center, Bogor Agricultural University, Bogor, Indonesia
- Department of Biology, Bogor Agricultural University, Bogor, Indonesia
| | - Walberto Sinaga
- Primate Research Center, Bogor Agricultural University, Bogor, Indonesia
| | - Novita Anggraeni
- School of Graduate Studies, Bogor Agricultural University, Bogor, Indonesia
| | - Hans Zischler
- Institute of Anthropology, Johannes-Gutenberg University Mainz, Mainz, Germany
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20
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Low Genetic Diversity and Strong Geographical Structure of the Critically Endangered White-Headed Langur (Trachypithecus leucocephalus) Inferred from Mitochondrial DNA Control Region Sequences. PLoS One 2015; 10:e0129782. [PMID: 26057239 PMCID: PMC4461268 DOI: 10.1371/journal.pone.0129782] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 05/13/2015] [Indexed: 11/29/2022] Open
Abstract
Many Asian colobine monkey species are suffering from habitat destruction and population size decline. There is a great need to understand their genetic diversity, population structure and demographic history for effective species conservation. The white-headed langur (Trachypithecus leucocephalus) is a Critically Endangered colobine species endemic to the limestone karst forests in southwestern China. We analyzed the mitochondrial DNA (mtDNA) control region sequences of 390 fecal samples from 40 social groups across the main distribution areas, which represented one-third of the total extant population. Only nine haplotypes and 10 polymorphic sites were identified, indicating remarkably low genetic diversity in the species. Using a subset of 77 samples from different individuals, we evaluated genetic variation, population structure, and population demographic history. We found very low values of haplotype diversity (h = 0.570 ± 0.056) and nucleotide diversity (π = 0.00323 ± 0.00044) in the hypervariable region I (HVRI) of the mtDNA control region. Distribution of haplotypes displayed marked geographical pattern, with one population (Chongzuo, CZ) showing a complete lack of genetic diversity (having only one haplotype), whereas the other population (Fusui, FS) having all nine haplotypes. We detected strong population genetic structure among habit patches (ΦST = 0.375, P < 0.001). In addition, the Mantel test showed a significant correlation between the pairwise genetic distances and geographical distances among social groups in FS (correlation coefficient = 0.267, P = 0.003), indicting isolation-by-distance pattern of genetic divergence in the mtDNA sequences. Analyses of demographic history suggested an overall stable historical population size and modest population expansion in the last 2,000 years. Our results indicate different genetic diversity and possibly distinct population history for different local populations, and suggest that CZ and FS should be considered as one evolutionarily significant unit (ESU) and two management units (MUs) pending further investigation using nuclear markers.
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21
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Merker S, Thomas S, Völker E, Perwitasari-Farajallah D, Feldmeyer B, Streit B, Pfenninger M. Control region length dynamics potentially drives amino acid evolution in tarsier mitochondrial genomes. J Mol Evol 2014; 79:40-51. [PMID: 25008552 DOI: 10.1007/s00239-014-9631-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 11/25/2022]
Abstract
Patterns and processes of molecular evolution critically influence inferences in phylogeny and phylogeography. Within primates, a shift in evolutionary rates has been identified as the rationale for contrasting findings from mitochondrial and nuclear DNA studies as to the position of Tarsius. While the latter now seems settled, we sequenced complete mitochondrial genomes of three Sulawesi tarsiers (Tarsius dentatus, T. lariang, and T. wallacei) and analyzed substitution rates among tarsiers and other primates to infer driving processes of molecular evolution. We found substantial length polymorphism of the D-loop within tarsier individuals, but little variation of predominant lengths among them, regardless of species. Length variation was due to repetitive elements in the CSB domain-minisatellite motifs of 35 bp length and microsatellite motifs of 6 bp length. Amino acid evolutionary rates were second highest among major primate taxa relative to nucleotide substitution rates. We observed many radical possibly function-altering amino acid changes that were rarely driven by positive selection and thus potentially slightly deleterious or neutral. We hypothesize that the observed pattern of an increased amino acid evolutionary rate in tarsier mitochondrial genomes may be caused by hitchhiking of slightly deleterious mutations with favored D-loop length variants selected for maximizing replication success within the cell or the mitochondrion.
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Affiliation(s)
- Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191, Stuttgart, Germany,
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22
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Evans BJ, Zeng K, Esselstyn JA, Charlesworth B, Melnick DJ. Reduced representation genome sequencing suggests low diversity on the sex chromosomes of tonkean macaque monkeys. Mol Biol Evol 2014; 31:2425-40. [PMID: 24987106 DOI: 10.1093/molbev/msu197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In species with separate sexes, social systems can differ in the relative variances of male versus female reproductive success. Papionin monkeys (macaques, mangabeys, mandrills, drills, baboons, and geladas) exhibit hallmarks of a high variance in male reproductive success, including a female-biased adult sex ratio and prominent sexual dimorphism. To explore the potential genomic consequences of such sex differences, we used a reduced representation genome sequencing approach to quantifying polymorphism at sites on autosomes and sex chromosomes of the tonkean macaque (Macaca tonkeana), a species endemic to the Indonesian island of Sulawesi. The ratio of nucleotide diversity of the X chromosome to that of the autosomes was less than the value (0.75) expected with a 1:1 sex ratio and no sex differences in the variance in reproductive success. However, the significance of this difference was dependent on which outgroup was used to standardize diversity levels. Using a new model that includes the effects of varying population size, sex differences in mutation rate between the autosomes and X chromosome, and GC-biased gene conversion (gBGC) or selection on GC content, we found that the maximum-likelihood estimate of the ratio of effective population size of the X chromosome to that of the autosomes was 0.68, which did not differ significantly from 0.75. We also found evidence for 1) a higher level of purifying selection on genic than nongenic regions, 2) gBGC or natural selection favoring increased GC content, 3) a dynamic demography characterized by population growth and contraction, 4) a higher mutation rate in males than females, and 5) a very low polymorphism level on the Y chromosome. These findings shed light on the population genomic consequences of sex differences in the variance in reproductive success, which appear to be modest in the tonkean macaque; they also suggest the occurrence of hitchhiking on the Y chromosome.
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Affiliation(s)
- Ben J Evans
- Biology Department, McMaster University, Hamilton, ON, Canada
| | - Kai Zeng
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom
| | - Jacob A Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Don J Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University
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23
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von Rintelen T, Stelbrink B, Marwoto RM, Glaubrecht M. A snail perspective on the biogeography of Sulawesi, Indonesia: origin and intra-island dispersal of the viviparous freshwater gastropod Tylomelania. PLoS One 2014; 9:e98917. [PMID: 24971564 PMCID: PMC4090239 DOI: 10.1371/journal.pone.0098917] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/09/2014] [Indexed: 11/25/2022] Open
Abstract
The complex geological history of the Indonesian island Sulawesi has shaped the origin and subsequent diversification of its taxa. For the endemic freshwater snail Tylomelania a vicariant origin from the Australian margin has been hypothesized. Divergence time estimates from a mtDNA phylogeny based on a comprehensive island-wide sampling of Tylomelania fit regional tectonic constraints and support the ‘out-of-Australia’ vicariance hypothesis. The Banggai-Sula region of the Sula Spur, the Australian promontory colliding with West Sulawesi during the Miocene, is identified as a possible source area for the colonization of Sulawesi by the ancestor of Tylomelania. The molecular phylogeny also shows a rapid diversification of Tylomelania into eight major lineages with very little overlap in their distribution on the island. Haplotype networks provide further evidence for a strong spatial structure of genetic diversity in Tylomelania. Distribution boundaries of the major lineages do at best partially coincide with previously identified contact zones for other endemic species groups on Sulawesi. This pattern has likely been influenced by the poor dispersal capabilities and altitudinal distribution limits of this strict freshwater inhabitant. We suggest that late Miocene and Pliocene orogeny in large parts of Sulawesi has been the vicariant event driving primary diversification in Tylomelania.
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Affiliation(s)
- Thomas von Rintelen
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- * E-mail:
| | - Björn Stelbrink
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Ristiyanti M. Marwoto
- Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, LIPI, Cibinong, Bogor, Indonesia
| | - Matthias Glaubrecht
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
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24
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Lane-deGraaf KE, Kennedy RC, Arifin SMN, Madey GR, Fuentes A, Hollocher H. A test of agent-based models as a tool for predicting patterns of pathogen transmission in complex landscapes. BMC Ecol 2013; 13:35. [PMID: 24063811 PMCID: PMC3850893 DOI: 10.1186/1472-6785-13-35] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 09/09/2013] [Indexed: 11/17/2022] Open
Abstract
Background Landscape complexity can mitigate or facilitate host dispersal, influencing patterns of pathogen transmission. Spatial transmission of pathogens through landscapes, therefore, presents an important but not fully elucidated aspect of transmission dynamics. Using an agent-based model (LiNK) that incorporates GIS data, we examined the effects of landscape information on the spatial patterns of host movement and pathogen transmission in a system of long-tailed macaques and their gut parasites. We first examined the role of the landscape to identify any individual or additive effects on host movement. We then compared modeled dispersal distance to patterns of actual macaque gene flow to both confirm our model’s predictions and to understand the role of individual land uses on dispersal. Finally, we compared the rate and the spread of two gastrointestinal parasites, Entamoeba histolytica and E. dispar, to understand how landscape complexity influences spatial patterns of pathogen transmission. Results LiNK captured emergent properties of the landscape, finding that interaction effects between landscape layers could mitigate the rate of infection in a non-additive way. We also found that the inclusion of landscape information facilitated an accurate prediction of macaque dispersal patterns across a complex landscape, as confirmed by Mantel tests comparing genetic and simulated dispersed distances. Finally, we demonstrated that landscape heterogeneity proved a significant barrier for a highly virulent pathogen, limiting the dispersal ability of hosts and thus its own transmission into distant populations. Conclusions Landscape complexity plays a significant role in determining the path of host dispersal and patterns of pathogen transmission. Incorporating landscape heterogeneity and host behavior into disease management decisions can be important in targeting response efforts, identifying cryptic transmission opportunities, and reducing or understanding potential for unintended ecological and evolutionary consequences. The inclusion of these data into models of pathogen transmission patterns improves our understanding of these dynamics, ultimately proving beneficial for sound public health policy.
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Affiliation(s)
- Kelly E Lane-deGraaf
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
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25
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Fabre PH, Pagès M, Musser GG, Fitriana YS, Fjeldså J, Jennings A, Jønsson KA, Kennedy J, Michaux J, Semiadi G, Supriatna N, Helgen KM. A new genus of rodent from Wallacea (Rodentia: Muridae: Murinae: Rattini), and its implication for biogeography and Indo-Pacific Rattini systematics. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12061] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Pierre-Henri Fabre
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum; University of Copenhagen; Universitetsparken 15 DK-2100 Copenhagen Denmark
| | - Marie Pagès
- Laboratoire de génétique des microorganismes; Université de Liège; 4000 Liège Belgique
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet; CS 30016 34988 Montferrier-sur-Lez Cedex France
| | - Guy G. Musser
- Division of Vertebrate Zoology (Mammalogy); American Museum of Natural History; New York NY 10024 USA
| | - Yuli S. Fitriana
- Museum Zoologicum Bogoriense; Research Center For Biology; Indonesian Institute of Sciences (LIPI); Jl.Raya Jakarta-Bogor Km.46 Cibinong 16911 Indonesia
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum; University of Copenhagen; Universitetsparken 15 DK-2100 Copenhagen Denmark
| | - Andy Jennings
- Muséum National d'Histoire Naturelle; Département Systématique et Evolution CP 51; 57 Rue Cuvier 75231 Paris France
| | - Knud A. Jønsson
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum; University of Copenhagen; Universitetsparken 15 DK-2100 Copenhagen Denmark
| | - Jonathan Kennedy
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum; University of Copenhagen; Universitetsparken 15 DK-2100 Copenhagen Denmark
| | - Johan Michaux
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet; CS 30016 34988 Montferrier-sur-Lez Cedex France
| | - Gono Semiadi
- Museum Zoologicum Bogoriense; Research Center For Biology; Indonesian Institute of Sciences (LIPI); Jl.Raya Jakarta-Bogor Km.46 Cibinong 16911 Indonesia
| | - Nanang Supriatna
- Museum Zoologicum Bogoriense; Research Center For Biology; Indonesian Institute of Sciences (LIPI); Jl.Raya Jakarta-Bogor Km.46 Cibinong 16911 Indonesia
| | - Kristofer M. Helgen
- National Museum of Natural History; Smithsonian. Institution; P.O. Box 37012 MRC 108 Washington DC 20013-7012 USA
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Malaivijitnond S, Arsaithamkul V, Tanaka H, Pomchote P, Jaroenporn S, Suryobroto B, Hamada Y. Boundary zone between northern and southern pig-tailed macaques and their morphological differences. Primates 2012; 53:377-89. [PMID: 22820844 DOI: 10.1007/s10329-012-0316-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 06/28/2012] [Indexed: 11/24/2022]
Abstract
Based on previous conflicting reports that the two forms of pig-tailed macaque (northern and southern) exist as separate species, subspecies, or forms, and that their boundary zone lies in Thailand, a survey of the distribution range and morphology of pig-tailed macaques in Thailand was conducted during 2003-2010. We first conducted a questionnaire survey. Questionnaires were sent to 7,410 subdistricts throughout Thailand. We then traveled to 72 of the 123 subdistricts reporting the presence of pig-tailed macaques. However, due to a lack of reports of the presence of free-ranging pig-tailed macaques living south of the Isthmus of Kra, a survey of pet pig-tailed macaques was also conducted during 16-24 September 2011. Furthermore, 35 wild northern pig-tailed macaques inhabiting northern Thailand (13°13'N, 101°03'E) were temporarily caught and their morphological characters were measured and then compared to those of the southern form captured from Sumatra, Indonesia. Although largely allopatric, the ranges of the northern and southern pig-tailed macaques in Thailand were found to have a partially sympatric boundary at the Surat Thani-Krabi depression (8-9°30'N). Morphologically, these two forms were very distinctive, with different morphological characters such as the crown patch, the white color of the triangle above the eyes, the red streak at the external rim of the eyes, pelage color, ischial callosity, tail length and carriage, facial height, and limb length in both sexes, and patterns of sex skin swelling and reddening in females. These differences in morphological characters between the northern and southern forms should help settle the problems of their taxonomy.
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Affiliation(s)
- Suchinda Malaivijitnond
- Primate Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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Abstract
If island biogeography has a sweet spot, it's where islands generate their own species diversity rather than merely taking on mainland immigrants. In birds and other highly dispersive taxa, however, this 'zone of radiation', may be vanishingly small. Darwin's finches and Hawaiian Honeycreepers are among only a handful of examples of island radiation in birds (Price 2008), suggesting that winged powers of dispersal make sufficient isolation from mainland colonists unlikely, while also hindering speciation within and among isolated islands. Nevertheless, two studies in this issue of Molecular Ecology join a string of other recent analyses suggesting that island radiation in birds remains under-appreciated (see also Moyle et al. 2009; Kisel & Barraclough 2010; Rosindell & Phillimore 2011). Melo et al. (2011) use a phylogenetic analysis of white-eyes on islands in the Gulf of Guinea to identify two previously overlooked island radiations, and reveal replicated adaptive divergence on islands where species occur in pairs. Sly et al. (2011), meanwhile, consider possible explanations for speciation and geographic differentiation within a large island, and find the same type of oceanic barriers that are critical to bird speciation across archipelagos may also contribute to divergence that appears to have occurred within a single island.
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Affiliation(s)
- Richard E Glor
- Department of Biology, University of Rochester, RC Box 270211, Rochester, NY 14627, USA.
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Stelbrink B, Albrecht C, Hall R, von Rintelen T. THE BIOGEOGRAPHY OF SULAWESI REVISITED: IS THERE EVIDENCE FOR A VICARIANT ORIGIN OF TAXA ON WALLACE'S “ANOMALOUS ISLAND”? Evolution 2012; 66:2252-71. [DOI: 10.1111/j.1558-5646.2012.01588.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Setiadi MI, McGuire JA, Brown RM, Zubairi M, Iskandar DT, Andayani N, Supriatna J, Evans BJ. Adaptive radiation and ecological opportunity in Sulawesi and Philippine fanged frog (Limnonectes) communities. Am Nat 2011; 178:221-40. [PMID: 21750386 DOI: 10.1086/660830] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Because island communities are derived from mainland communities, they are often less diverse by comparison. However, reduced complexity of island communities can also present ecological opportunities. For example, amphibian diversity on Sulawesi Island is lower than it is in the Philippines, but Sulawesi supports a surprising diversity of Sulawesi fanged frogs (Limnonectes). Here we examine molecular, morphological, and geographical variation of fanged frogs from these two regions. Using genealogical concordance, morphology, and a Bayesian approach to species delimitation, we identified 13 species on Sulawesi, only four of which have been previously described. After evolutionary history is accounted for, a model with multiple body size optima in sympatric species is favored over a "random-walk" model of body size evolution. Additionally, morphological variation is higher among sympatric than nonsympatric species on Sulawesi but not in the Philippines. These findings suggest that adaptive radiation of fanged frogs on Sulawesi was driven by natural selection to infiltrate ecological niches occupied by other frog lineages in the Philippines. This supports a role of ecological opportunity in community assembly: diversification in mature communities, such as the Philippines, is limited by a dearth of unoccupied ecological niches. On Sulawesi, evolutionary novelties originated in a predictable and replicated fashion in response to opportunities presented by a depauperate ancestral community.
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Affiliation(s)
- Mohammad I Setiadi
- Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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30
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Burton JA, Nietsch A. Geographical Variation in Duet Songs of Sulawesi Tarsiers: Evidence for New Cryptic Species in South and Southeast Sulawesi. INT J PRIMATOL 2010. [DOI: 10.1007/s10764-010-9449-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Evans BJ, Pin L, Melnick DJ, Wright SI. Sex-linked inheritance in macaque monkeys: implications for effective population size and dispersal to Sulawesi. Genetics 2010; 185:923-37. [PMID: 20407130 PMCID: PMC2907209 DOI: 10.1534/genetics.110.116228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 04/19/2010] [Indexed: 11/18/2022] Open
Abstract
Sex-specific differences in dispersal, survival, reproductive success, and natural selection differentially affect the effective population size (N(e)) of genomic regions with different modes of inheritance such as sex chromosomes and mitochondrial DNA. In papionin monkeys (macaques, baboons, geladas, mandrills, drills, and mangabeys), for example, these factors are expected to reduce N(e) of paternally inherited portions of the genome compared to maternally inherited portions. To explore this further, we quantified relative N(e) of autosomal DNA, X and Y chromosomes, and mitochondrial DNA using molecular polymorphism and divergence information from pigtail macaque monkeys (Macaca nemestrina). Consistent with demographic expectations, we found that N(e) of the Y is lower than expected from a Wright-Fisher idealized population with an equal proportion of males and females, whereas N(e) of mitochondrial DNA is higher. However, N(e) of 11 loci on the X chromosome was lower than expected, a finding that could be explained by pervasive hitchhiking effects on this chromosome. We evaluated the fit of these data to various models involving natural selection or sex-biased demography. Significant support was recovered for natural selection acting on the Y chromosome. A demographic model with a skewed sex ratio was more likely than one with sex-biased migration and explained the data about as well as an ideal model without sex-biased demography. We then incorporated these results into an evaluation of macaque divergence and migration on Borneo and Sulawesi islands. One X-linked locus was not monophyletic on Sulawesi, but multilocus data analyzed in a coalescent framework failed to reject a model without migration between these islands after both were colonized.
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Affiliation(s)
- Ben J Evans
- Department of Biology, McMaster University, Life Sciences Building, Hamilton, Ontario L8S 4K1, Canada.
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Setiadi MI, Hamidy A, Abidin Z, Susanto D, Brown RM, Peterson AT, Li X, Evans BJ. Genetic structure of herpetofauna on Halmahera Island, Indonesia: implications for Aketajawe-Lolobata National Park. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2010; 24:553-562. [PMID: 20015261 DOI: 10.1111/j.1523-1739.2009.01384.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Genetic variation within species--a priority for biodiversity conservation--is influenced by natural selection, demography, and stochastic events such as genetic drift. We evaluated the role of these factors in 14 codistributed species of reptiles and amphibians on the Indonesian island of Halmahera by testing whether their molecular variation was correlated with geographic distance, ecology, riverine barriers, or Halmahera's paleoisland precursors. We found support for isolation by distance effects in four species. Two of these four were also significantly affected either by rivers or by ecology. A fifth species was significantly affected by ecology and a sixth was significantly affected by Halmahera's paleoislands. These findings--the most comprehensive survey of multispecies genetic variation on Halmahera to date--bode well for the efficacy of the recently established Aketajawe-Lolobata National Park in conserving a substantial component of vertebrate genetic variation on this island. Future success of conservation efforts will depend crucially, of course, on funding for and enforcement of conservation management of this park.
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Affiliation(s)
- Mohammad Iqbal Setiadi
- Center for Environmental Genomics, Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
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Juliandi B, Suryobroto B, Perwitasari-Farajallah D. The ischial callosities of Sulawesi macaques. Am J Primatol 2009; 71:1021-31. [PMID: 19746442 DOI: 10.1002/ajp.20745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Berry Juliandi
- Division of Animal Biosystematic and Ecology, Department of Biology, Bogor Agricultural University, Bogor, Indonesia.
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35
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Chatterjee HJ, Ho SYW, Barnes I, Groves C. Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evol Biol 2009; 9:259. [PMID: 19860891 PMCID: PMC2774700 DOI: 10.1186/1471-2148-9-259] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 10/27/2009] [Indexed: 12/05/2022] Open
Abstract
Background The primates are among the most broadly studied mammalian orders, with the published literature containing extensive analyses of their behavior, physiology, genetics and ecology. The importance of this group in medical and biological research is well appreciated, and explains the numerous molecular phylogenies that have been proposed for most primate families and genera. Composite estimates for the entire order have been infrequently attempted, with the last phylogenetic reconstruction spanning the full range of primate evolutionary relationships having been conducted over a decade ago. Results To estimate the structure and tempo of primate evolutionary history, we employed Bayesian phylogenetic methods to analyze data supermatrices comprising 7 mitochondrial genes (6,138 nucleotides) from 219 species across 67 genera and 3 nuclear genes (2,157 nucleotides) from 26 genera. Many taxa were only partially represented, with an average of 3.95 and 5.43 mitochondrial genes per species and per genus, respectively, and 2.23 nuclear genes per genus. Our analyses of mitochondrial DNA place Tarsiiformes as the sister group of Strepsirrhini. Within Haplorrhini, we find support for the primary divergence of Pitheciidae in Platyrrhini, and our results suggest a sister grouping of African and non-African colobines within Colobinae and of Cercopithecini and Papionini within Cercopthecinae. Date estimates for nodes within each family and genus are presented, with estimates for key splits including: Strepsirrhini-Haplorrhini 64 million years ago (MYA), Lemuriformes-Lorisiformes 52 MYA, Platyrrhini-Catarrhini 43 MYA and Cercopithecoidea-Hominoidea 29 MYA. Conclusion We present an up-to-date, comprehensive estimate of the structure and tempo of primate evolutionary history. Although considerable gaps remain in our knowledge of the primate phylogeny, increased data sampling, particularly from nuclear loci, will be able to provide further resolution.
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Affiliation(s)
- Helen J Chatterjee
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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36
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Petit RJ, Excoffier L. Gene flow and species delimitation. Trends Ecol Evol 2009; 24:386-93. [PMID: 19409650 DOI: 10.1016/j.tree.2009.02.011] [Citation(s) in RCA: 473] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/19/2009] [Accepted: 02/23/2009] [Indexed: 10/20/2022]
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Elucidating geological and biological processes underlying the diversification of Sulawesi tarsiers. Proc Natl Acad Sci U S A 2009; 106:8459-64. [PMID: 19451646 DOI: 10.1073/pnas.0900319106] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Because of their exceptionally long independent evolution, a range diminution of their Eocene relatives, and a remarkable subsequent diversification in Southeast Asia, tarsiers are of particular importance to evolutionary primatologists. Little is known, however, on the processes shaping the radiation of these small enigmatic primates-especially on the Indonesian island of Sulawesi, their center of endemism. Geological reconstructions and progress in applying DNA sequence information to divergence dating now provide us with the tools and background to comprehend tarsier dispersal. Here, we describe effects of plate-tectonic movements, Pleistocene sea level changes, and hybridization on the divergence of central Sulawesi tarsiers. We analyzed 12 microsatellites, the cytochrome b gene, the hypervariable region I of the mitochondrial control region, and the sex-determining region on the Y-chromosome from 144 specimens captured along a transect crossing a species boundary and a contact zone between 2 microplates. Based on these differentially inherited genetic markers, geographic information, and recordings of vocalizations, we demonstrate that the species boundary coincides with a tectonic suture. We estimate the most recent common ancestor of the 2 taxa to have lived 1.4 Mya, we describe asymmetrical introgressive hybridization, and we give evidence of unbiased dispersal in one species and male-biased dispersal in another species. This study exemplifies that the distribution of tarsier acoustic forms on Sulawesi is consistent with the allocation of genetic variability and that plate-tectonic and glacial events have left traceable marks in the biogeography of this island's unique fauna.
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Evans BJ, McGuire JA, Brown RM, Andayani N, Supriatna J. A coalescent framework for comparing alternative models of population structure with genetic data: evolution of Celebes toads. Biol Lett 2008; 4:430-3. [PMID: 18511406 DOI: 10.1098/rsbl.2008.0166] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Isolation of populations eventually leads to divergence by genetic drift, but if connectivity varies over time, its impact on diversification may be difficult to discern. Even when the habitat patches of multiple species overlap, differences in their demographic parameters, molecular evolution and stochastic events contribute to differences in the magnitude and distribution of their genetic variation. The Indonesian island of Sulawesi, for example, harbours a suite of endemic species whose intraspecific differentiation or interspecific divergence may have been catalysed by habitat fragmentation. To further test this hypothesis, we have performed phylogenetic and coalescent-based analyses on molecular variation in mitochondrial and nuclear DNA of the Celebes toad (Bufo celebensis). Results support a role for habitat fragmentation that led to a population structure in these toads that closely matches distributions of Sulawesi macaque monkeys. Habitat fragmentation, therefore, may also have affected other groups on this island.
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Affiliation(s)
- Ben J Evans
- Department of Biology, McMaster University, Hamilton, ON, Canada.
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MODOLO LARA, MARTIN ROBERTD, VAN SCHAIK CARELP, VAN NOORDWIJK MARIAA, KRÜTZEN MICHAEL. When dispersal fails: unexpected genetic separation in Gibraltar macaques (Macaca sylvanus). Mol Ecol 2008; 17:4027-38. [DOI: 10.1111/j.1365-294x.2008.03890.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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Bilgin R, Karataş A, Çoraman E, Morales JC. The mitochondrial and nuclear genetic structure of Myotis capaccinii (Chiroptera: Vespertilionidae) in the Eurasian transition, and its taxonomic implications. ZOOL SCR 2008. [DOI: 10.1111/j.1463-6409.2008.00326.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Crandall KA, Robison HW, Buhay JE. Avoidance of extinction through nonexistence: the use of museum specimens and molecular genetics to determine the taxonomic status of an endangered freshwater crayfish. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9546-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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Osterholz M, Walter L, Roos C. Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups. BMC Evol Biol 2008; 8:58. [PMID: 18298809 PMCID: PMC2268674 DOI: 10.1186/1471-2148-8-58] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 02/25/2008] [Indexed: 11/16/2022] Open
Abstract
Background The evolutionary history of the Asian colobines is less understood. Although monophyly of the odd-nosed monkeys was recently confirmed, the relationships among the langur genera Presbytis, Semnopithecus and Trachypithecus and their position among Asian colobines remained unclear. Moreover, in Trachypithecus various species groups are recognized, but their affiliations are still disputed. To address these issues, mitochondrial and Y chromosomal sequence data were phylogenetically related and combined with presence/absence analyses of retroposon integrations. Results The analysed 5 kb fragment of the mitochondrial genome allows no resolution of the phylogenetic relationships among langur genera, but five retroposon integrations were detected which link Trachypithecus and Semnopithecus. According to Y chromosomal data and a 573 bp fragment of the mitochondrial cytochrome b gene, a common origin of the species groups T. [cristatus], T. [obscurus] and T. [francoisi] and their reciprocal monophyly is supported, which is also underpinned by an orthologous retroposon insertion. T. [vetulus] clusters within Semnopithecus, which is confirmed by two retroposon integrations. Moreover, this species group is paraphyletic, with T. vetulus forming a clade with the Sri Lankan, and T. johnii with the South Indian form of S. entellus. Incongruence between gene trees was detected for T. [pileatus], in that Y chromosomal data link it with T. [cristatus], T. [obscurus] and T. [francoisi], whereas mitochondrial data affiliates it with the Semnopithecus clade. Conclusion Neither relationships among the three langur genera nor their position within Asian colobines can be settled with 5 kb mitochondrial sequence data, but retroposon integrations confirm at least a common origin of Semnopithecus and Trachypithecus. According to Y chromosomal and 573 bp mitochondrial sequence data, T. [cristatus], T. [obscurus] and T. [francoisi] represent true members of the genus Trachypithecus, whereas T. [vetulus] clusters within Semnopithecus. Due to paraphyly of T. [vetulus] and polyphyly of Semnopithecus, a split of the genus into three species groups (S. entellus - North India, S. entellus - South India + T. johnii, S. entellus - Sri Lanka + T. vetulus) seems to be appropriate. T. [pileatus] posses an intermediate position between both genera, indicating that the species group might be the result of ancestral hybridization.
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Affiliation(s)
- Martin Osterholz
- Department of Primate Genetics, German Primate Center, Kellnerweg 4, 37077 Goettingen, Germany.
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Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys. Mol Phylogenet Evol 2007; 46:466-74. [PMID: 18180172 DOI: 10.1016/j.ympev.2007.11.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2007] [Revised: 10/24/2007] [Accepted: 11/15/2007] [Indexed: 11/22/2022]
Abstract
Evidence of incongruence between mitochondrial and nuclear gene trees is now becoming documented with increasing frequency. Among the Old World monkeys, this discordance has been well demonstrated in the Cercopithecinae, but has not yet been investigated in the Colobinae. The mitochondrial relationships between the colobine genera have recently been clarified and cluster Presbytis and Trachypithecus as sister taxa to the exclusion of Semnopithecus. This is incongruent with previous morphological hypotheses that suggest the latter two are sister taxa, and perhaps even congeneric. In addition to analyzing a previously published 10,896 bp mitochondrial dataset, we sequenced and analyzed a 4297 bp fragment of the X-chromosome in order to test the competing mitochondrial and morphological phylogenetic hypotheses. The results from the mitochondrial dataset again support a Presbytis+Trachypithecus group while the X-chromosomal dataset supported a Semnopithecus+Trachypithecus group. A Shimodaira-Hasegawa test performed on both datasets indicates that the mitochondrial and X-chromosomal trees are significantly better at explaining their respective datasets than alternative topologies (p<0.05). We suggest that differential lineage sorting or ancient hybridization may be the cause of this strong discordance between the mitochondrial and X-chromosomal markers in these taxa.
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Ziegler T, Abegg C, Meijaard E, Perwitasari-Farajallah D, Walter L, Hodges JK, Roos C. Molecular phylogeny and evolutionary history of Southeast Asian macaques forming the M. silenus group. Mol Phylogenet Evol 2006; 42:807-16. [PMID: 17208017 DOI: 10.1016/j.ympev.2006.11.015] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 11/09/2006] [Accepted: 11/16/2006] [Indexed: 10/23/2022]
Abstract
The 12 presently recognized taxa forming the Macaca silenus group represent the most diverse lineage within the genus Macaca. The present study was set up to clarify the phylogenetic relationships of the extant members of the M. silenus group and to explain their geographical distribution patterns seen today. A combined approach involving the analysis of one paternal (TSPY) and two maternal (cyt b and 12S-16S rRNA) molecular markers enabled us to resolve the phylogenetic relationships within this lineage. Our Y chromosomal marker is not informative enough to allow detailed conclusion. Based on our mitochondrial data, however, M. pagensis, endemic to the three southern Mentawai islands (Sipora, North- and South Pagai), split off early (2.4-2.6 mya) and represents a sister clade to the macaques from the northern Mentawai island of Siberut and from those of the Southeast Asian mainland, which diverged in a radiation-like splitting event about 1.5-1.7 mya. By combining our new results with available data on behavioural as well as climate and sea level changes in Southeast Asia during the Plio- and Pleistocene, we have developed two scenarios for the evolutionary history of this primate group, which may help explain the current geographical distribution of its members.
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Affiliation(s)
- Thomas Ziegler
- Department of Reproductive Biology, German Primate Centre, Kellnerweg 4, 37077 Göttingen, Germany
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45
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Kawamoto Y, Shotake T, Nozawa K, Kawamoto S, Tomari KI, Kawai S, Shirai K, Morimitsu Y, Takagi N, Akaza H, Fujii H, Hagihara K, Aizawa K, Akachi S, Oi T, Hayaishi S. Postglacial population expansion of Japanese macaques (Macaca fuscata) inferred from mitochondrial DNA phylogeography. Primates 2006; 48:27-40. [PMID: 17119867 DOI: 10.1007/s10329-006-0013-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Accepted: 07/31/2006] [Indexed: 10/23/2022]
Abstract
We investigated the diversity and phylogeography of mitochondrial DNA (mtDNA) in Japanese macaques (Macaca fuscata), an endemic species in Japan that has the northernmost distribution of any non-human primate species. DNA samples from 135 localities representing the entire range of this species were compared. A total of 53 unique haplotypes were observed for the 412-bp partial mtDNA control region sequence, with length variation distinguishing the two subspecies. Clustering analyses suggested two putative major haplogroups, of which one was geographically distributed in eastern Japan and the other in western Japan. The populations in the east showed lower mtDNA diversity than those in the west. Phylogeographical relationships of haplotypes depicted with minimum spanning network suggested differences in population structure. Population expansion was significant for the eastern but not the western population, suggesting establishment of the ancestral population was relatively long ago in the west and recent in the east. Based on fossil evidence and past climate and vegetation changes, we inferred that the postulated population expansion may have taken place after the last glacial period (after 15,000 years ago). Mitochondrial DNA showed contrasting results in both variability and phylogenetic status of local populations to those of previous studies using protein variations, particularly for populations in the periphery of the range, with special inference on habitat change during the glacial period in response to cold adaptation.
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Affiliation(s)
- Yoshi Kawamoto
- Primate Research Institute, Kyoto University, Kanrin, Inuyama, Aichi, 484-8506, Japan.
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Arnold ML, Meyer A. Natural hybridization in primates: one evolutionary mechanism. ZOOLOGY 2006; 109:261-76. [PMID: 16945512 DOI: 10.1016/j.zool.2006.03.006] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Revised: 03/06/2006] [Accepted: 03/15/2006] [Indexed: 11/15/2022]
Abstract
The role and importance of natural hybridization in the evolutionary histories of animal taxa is still debated. This results largely from a history of zoological investigations that assumed, rather than documented, a limited evolutionary role for this process. However, it is now becoming apparent that, just as for plants, the creative effects of reticulate evolution are widespread in animal taxa as well. This conclusion is supported by the documentation of numerous instances of the formation of new taxa and the genetic enrichment through introgressive hybridization. In the present review, we use primates as a paradigm for how natural hybridization can affect the evolution of species complexes and remains a footprint on genomes. Findings for a number of groups, including basal (e.g. lemurs) and derived (e.g. Old World apes) lineages, demonstrate that introgression and hybrid speciation have caused a reticulate pattern that is still detectable in the, often mosaic, genomes of primates. For example, results from genetic analyses of our own species demonstrate the process of past introgressive hybridization with the progenitors of our sister taxa (i.e. chimpanzees and gorillas) and most likely also our extinct, close relatives in the hominid lineage.
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Affiliation(s)
- Michael L Arnold
- Department of Genetics, Life Sciences Building, University of Georgia, Athens, GA 30602, USA.
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Schillaci MA, Froehlich JW, Supriatna J, Jones-Engel L. The effects of hybridization on growth allometry and craniofacial form in Sulawesi macaques. J Hum Evol 2005; 49:335-69. [PMID: 15996717 DOI: 10.1016/j.jhevol.2005.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2004] [Revised: 04/08/2005] [Accepted: 04/25/2005] [Indexed: 11/19/2022]
Abstract
The present research investigates the effects of hybridization between Macaca maurus and M. tonkeana on adult male form and patterns of growth allometry. Comparisons of adult hybrid mean phenotypic values with the adult averages of the parental species indicate a condition of heterosis for cranial vault length and crown-rump length. Negative heterosis is indicated for body mass. Regression parameters describing growth allometry are generated for four craniofacial measurement variables and one body measurement using both least squares and reduced major axis regression. Comparisons of hybrid and parental regression slopes and intercepts using analysis of covariance and t-tests suggest that there is a hybrid pattern of growth allometry characterized by an increase in regression slope values coupled with lower intercept values compared to those of the parental species and the parental averages for most regression parameters. Multivariate analyses of the adult and ontogenetic morphometric data indicate significant differences across species taxa in form and shape during development and adulthood. Our finding of significant differences between hybrids and their parental taxa in growth allometry and craniofacial form and shape during development challenges the assumption often made regarding the reproductive and taxonomic significance of observed ontogenetic divergence between Neandertals and modern humans. We propose that anthropological primatology, with its goal of developing nonhuman primate models for investigating human evolution, can provide a biologically relevant means by which to empirically estimate the taxonomic significance of morphological and ontogenetic divergence observed in the hominid fossil record.
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Affiliation(s)
- Michael A Schillaci
- Department of Social Sciences, University of Toronto at Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada.
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Gaines CA, Hare MP, Beck SE, Rosenbaum HC. Nuclear markers confirm taxonomic status and relationships among highly endangered and closely related right whale species. Proc Biol Sci 2005; 272:533-42. [PMID: 15846869 PMCID: PMC1578701 DOI: 10.1098/rspb.2004.2895] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2004] [Accepted: 08/11/2004] [Indexed: 11/12/2022] Open
Abstract
Right whales (genus: Eubalaena) are among the most endangered mammals, yet their taxonomy and phylogeny have been questioned. A phylogenetic hypothesis based on mitochondrial DNA (mtDNA) variation recently prompted a taxonomic revision, increasing the number of right whale species to three. We critically evaluated this hypothesis using sequence data from 13 nuclear DNA (nuDNA) loci as well as the mtDNA control region. Fixed diagnostic characters among the nuclear markers strongly support the hypothesis of three genetically distinct species, despite lack of any diagnostic morphological characters. A phylogenetics analysis of all data produced a strict consensus cladogram with strong support at nodes that define each right whale species as well as relationships among species. Results showed very little conflict among the individual partitions as well as congruence between the mtDNA and nuDNA datasets. These data clearly demonstrate the strength of using numerous independent genetic markers during a phylogenetics analysis of closely related species. In evaluating phylogenetic support contributed by individual loci, 11 of the 14 loci provided support for at least one of the nodes of interest to this study. Only a single marker (mtDNA control region) provided support at all four nodes. A study using any single nuclear marker would have failed to support the proposed phylogeny, and a strong phylogenetic hypothesis was only revealed by the simultaneous analysis of many nuclear loci. In addition, nu DNA and mtDNA data provided complementary levels of support at nodes of different evolutionary depth indicating that the combined use of mtDNA and nuDNA data is both practical and desirable.
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Affiliation(s)
- C A Gaines
- Department of Biology, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA.
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Piganeau G, Gardner M, Eyre-Walker A. A broad survey of recombination in animal mitochondria. Mol Biol Evol 2004; 21:2319-25. [PMID: 15342796 DOI: 10.1093/molbev/msh244] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recombination in mitochondrial DNA (mtDNA) remains a controversial topic. Here we present a survey of 279 animal mtDNA data sets, of which 12 were from asexual species. Using four separate tests, we show that there is widespread evidence of recombination; for one test as many as 14.2% of the data sets reject a model of clonal inheritance and in several data sets, including primates, the recombinants can be identified visually. We show that none of the tests give significant results for obligate clonal species (apomictic pathogens) and that the sexual species show significantly greater evidence of recombination than asexual species. For some data sets, such as Macaca nemestrina, additional data sets suggest that the recombinants are not artifacts. For others, it cannot be determined whether the recombinants are real or produced by laboratory error. Either way, the results have important implications for how mtDNA is sequenced and used.
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Affiliation(s)
- Gwenaël Piganeau
- Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, UK.
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