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Bonfigli A, Cesare P, Volpe AR, Colafarina S, Forgione A, Aloisi M, Zarivi O, Poma AMG. Estimation of DNA Degradation in Archaeological Human Remains. Genes (Basel) 2023; 14:1238. [PMID: 37372418 DOI: 10.3390/genes14061238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained.
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Affiliation(s)
- Antonella Bonfigli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Patrizia Cesare
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Anna Rita Volpe
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Sabrina Colafarina
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Alfonso Forgione
- Department of Human Studies, University of L'Aquila, 67100 L'Aquila, Italy
| | - Massimo Aloisi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Osvaldo Zarivi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
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Towle I, Constantino PJ, Borths MR, Loch C. Tooth chipping patterns in Archaeolemur provide insight into diet and behavior. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:401-408. [PMID: 36790760 PMCID: PMC10107942 DOI: 10.1002/ajpa.24674] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/20/2022] [Accepted: 11/13/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Archaeolemur is a recently extinct genus of lemur that is often compared to some Cercopithecidae, especially baboons. This is due in part to their derived dentition, with large anterior teeth and reduced bilophodont molars. Research involving comparative morphology, analysis of coprolites, isotopes, and enamel structure, have suggested Archaeolemur had an omnivorous diet involving mechanically challenging items. Yet, microwear analysis of posterior teeth does not necessarily support this conclusion. MATERIALS AND METHODS In this macroscopic study, dental chipping was recorded on permanent teeth of Archaeolemur from different localities (53 individuals; 447 permanent teeth; including both A. edwardsi and A. majori specimens). This study aimed to compare chipping patterns across the dentition of Archaeolemur with chipping in other primates. RESULTS The results show enamel chipping was prevalent on the anterior teeth of Archaeolemur (38.9% of anterior teeth showed at least one fracture) yet rare in posterior teeth (9%). There was a decrease in chipping frequency across the dentition, moving distally from incisors (50%; 20/40), through caniniform teeth (30%; 15/50), premolars (9.5%; 16/169), and molars (8.5%; 16/188). DISCUSSION The results support previous research suggesting Archaeolemur had a varied omnivorous diet in which the anterior dentition was used for extensive food processing. This likely included mechanically challenging items such as tough/hard large fruits, small vertebrates, and crustaceans. Such a high rate of chipping in the anterior dentition is uncommon in other primates, with exception of hominins.
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Affiliation(s)
- Ian Towle
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Paul J Constantino
- Department of Biology, Saint Michael's College, Colchester, Vermont, USA
| | - Matthew R Borths
- Duke Lemur Center Museum of Natural History, Duke University, Durham, North Carolina, USA
| | - Carolina Loch
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
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Marciniak S, Mughal MR, Godfrey LR, Bankoff RJ, Randrianatoandro H, Crowley BE, Bergey CM, Muldoon KM, Randrianasy J, Raharivololona BM, Schuster SC, Malhi RS, Yoder AD, Louis EE, Kistler L, Perry GH. Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi. Proc Natl Acad Sci U S A 2021; 118:e2022117118. [PMID: 34162703 PMCID: PMC8255780 DOI: 10.1073/pnas.2022117118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal "subfossil" remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ∼160 kg) and other extraordinary Malagasy megafauna that survived into the past millennium. Yet, much about the evolutionary biology of these now-extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and subtropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here, we present a nuclear genome sequence (∼2× coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (∼85 kg). To support the testing of key phylogenetic and evolutionary hypotheses, we also generated high-coverage nuclear genomes for two extant lemurs, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemurs and 47 nonlemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and an extant folivore (a colobine monkey) and an herbivore (horse) in genes encoding proteins that function in plant toxin biodegradation and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.
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Affiliation(s)
- Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Mehreen R Mughal
- Bioinformatics and Genomics Intercollege Graduate Program, Pennsylvania State University, University Park, PA 16082
| | - Laurie R Godfrey
- Department of Anthropology, University of Massachusetts, Amherst, MA 01003
| | - Richard J Bankoff
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Heritiana Randrianatoandro
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Brooke E Crowley
- Department of Geology, University of Cincinnati, Cincinnati, OH 45220
- Department of Anthropology, University of Cincinnati, Cincinnati, OH 45220
| | - Christina M Bergey
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Department of Genetics, Rutgers University, New Brunswick, NJ 08854
| | | | - Jeannot Randrianasy
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Brigitte M Raharivololona
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 639798
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801
- Department of Ecology, Evolution and Behavior, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708
| | - Edward E Louis
- Department of Conservation Genetics, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107;
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560;
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802;
- Bioinformatics and Genomics Intercollege Graduate Program, Pennsylvania State University, University Park, PA 16082
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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Kapp JD, Green RE, Shapiro B. A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA. J Hered 2021; 112:241-249. [PMID: 33768239 PMCID: PMC8141684 DOI: 10.1093/jhered/esab012] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 11/12/2022] Open
Abstract
We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing platform that has been optimized for ancient and degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses directional splinted ligation of Illumina’s P5 and P7 adapters to convert natively single-stranded DNA and heat denatured double-stranded DNA into sequencing libraries in a single enzymatic reaction. To demonstrate its efficacy in converting degraded DNA molecules, we prepare 5 ancient DNA extracts into sequencing libraries using the SCR and 2 of the most commonly used approaches for preparing degraded DNA for sequencing: BEST, which targets and converts double-stranded DNA, and ssDNA2.0, which targets and converts single-stranded DNA. We then compare the efficiency with which each approach recovers unique molecules, or library complexity, given a standard amount of DNA input. We find that the SCR consistently outperforms the BEST protocol in recovering unique molecules and, despite its relative simplicity to perform and low cost per library, has similar performance to ssDNA2.0 across a wide range of DNA inputs. The SCR is a cost- and time-efficient approach that minimizes the loss of unique molecules and makes accessible a taxonomically, geographically, and a temporally broader sample of preserved remains for genomic analysis.
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Affiliation(s)
- Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
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Knigge RP, Vinyard CJ, McNulty KP. Mandibular symphyseal fusion in fossil primates: Insights from correlated patterns of jaw shape and masticatory function in living primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:322-336. [PMID: 32167167 DOI: 10.1002/ajpa.24048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/27/2020] [Accepted: 02/24/2020] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Variation in primate masticatory form and function has been extensively researched through both morphological and experimental studies. As a result, symphyseal fusion in different primate clades has been linked to either the recruitment of vertically directed balancing-side muscle force, the timing and recruitment of transversely directed forces, or both. This study investigates the relationship between jaw muscle activity patterns and morphology in extant primates to make inferences about masticatory function in extinct primates, with implications for understanding the evolution of symphyseal fusion. MATERIALS AND METHODS Three-dimensional mandibular landmark data were collected for 31 extant primates and nine fossil anthropoids and subfossil lemur species. Published electromyography (EMG) data were available for nine of the extant primate species. Partial least squares analysis and phylogenetic partial least squares analysis were used to identify relationships between EMG and jaw shape data and evaluate variation in jaw morphology. RESULTS Primates with partial and complete symphyseal fusion exhibit shape-function patterns associated with the wishboning motor pattern and loading regime, in contrast to shape-function patterns of primates with unfused jaws. All fossil primates examined (except Apidium) exhibit jaw morphologies suggestive of the wishboning motor pattern demonstrated in living anthropoids and indriids. DISCUSSION Partial fusion in Catopithecus, similar to indriids and some subfossil lemurs, may be sufficient to resist, or transfer, some amounts of transversely directed balancing-side muscle force at the symphysis, representing a transition to greater reliance on transverse jaw movement during mastication. Furthermore, possible functional convergences in physiological patterns during chewing (i.e., Archaeolemur) are identified.
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Affiliation(s)
- Ryan P Knigge
- Evolutionary Anthropology Lab, Department of Anthropology, University of Minnesota, Minneapolis, Minnesota.,Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri.,Department of Orthopaedic Surgery, University of Missouri, Columbia, Missouri
| | - Christopher J Vinyard
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio
| | - Kieran P McNulty
- Evolutionary Anthropology Lab, Department of Anthropology, University of Minnesota, Minneapolis, Minnesota
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6
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Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree. Syst Biol 2016; 65:772-91. [DOI: 10.1093/sysbio/syw035] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/30/2016] [Indexed: 01/14/2023] Open
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7
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Godfrey LR, Granatosky MC, Jungers WL. The Hands of Subfossil Lemurs. DEVELOPMENTS IN PRIMATOLOGY: PROGRESS AND PROSPECTS 2016. [DOI: 10.1007/978-1-4939-3646-5_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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8
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Druzhkova AS, Vorobieva NV, Trifonov VA, Graphodatsky AS. Ancient DNA: Results and prospects (The 30th anniversary). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415060046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Comparative and population mitogenomic analyses of Madagascar's extinct, giant ‘subfossil’ lemurs. J Hum Evol 2015; 79:45-54. [DOI: 10.1016/j.jhevol.2014.06.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 03/25/2014] [Accepted: 06/04/2014] [Indexed: 11/21/2022]
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10
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Boyer DM, Puente J, Gladman JT, Glynn C, Mukherjee S, Yapuncich GS, Daubechies I. A New Fully Automated Approach for Aligning and Comparing Shapes. Anat Rec (Hoboken) 2014; 298:249-76. [DOI: 10.1002/ar.23084] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 10/11/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Doug M. Boyer
- Department of Evolutionary Anthropology; Duke University; Durham North Carolina
| | - Jesus Puente
- Program in Applied and Computational Mathematics; Princeton University; Princeton New Jersey
| | - Justin T. Gladman
- NYCEP, New York Consortium in Evolutionary Primatology; New York New York
- PhD Program in Anthropology; Graduate Center, CUNY; New York New York
| | - Chris Glynn
- Department of Statistical Science; Duke University; Durham North Carolina
| | - Sayan Mukherjee
- Department of Statistical Science; Duke University; Durham North Carolina
- Department of Computer Science; Duke University; Durham North Carolina
- Department of Mathematics; Duke University; Durham North Carolina
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11
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Baab KL, Perry JMG, Rohlf FJ, Jungers WL. PHYLOGENETIC, ECOLOGICAL, AND ALLOMETRIC CORRELATES OF CRANIAL SHAPE IN MALAGASY LEMURIFORMS. Evolution 2014; 68:1450-68. [DOI: 10.1111/evo.12361] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 01/06/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Karen L. Baab
- Department of Anthropology; Stony Brook University; Social and Behavioral Sciences Building; 5th Floor Stony Brook New York 11794
- Interdepartmental Program in Anthropological Sciences; Stony Brook University; Stony Brook New York 11794
| | - Jonathan M. G. Perry
- Center for Functional Anatomy and Evolution; The Johns Hopkins University School of Medicine; Baltimore Maryland 21205
| | - F. James Rohlf
- Department of Ecology and Evolution; Stony Brook University; Stony Brook New York 11794
| | - William L. Jungers
- Interdepartmental Program in Anthropological Sciences; Stony Brook University; Stony Brook New York 11794
- Department of Anatomical Sciences; Stony Brook University; Stony Brook New York 11794
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12
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Masters J, Silvestro D, Génin F, DelPero M. Seeing the Wood through the Trees: The Current State of Higher Systematics in the Strepsirhini. Folia Primatol (Basel) 2013; 84:201-19. [DOI: 10.1159/000353179] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 05/21/2013] [Indexed: 11/19/2022]
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13
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Boyer DM, Seiffert ER, Gladman JT, Bloch JI. Evolution and allometry of calcaneal elongation in living and extinct primates. PLoS One 2013; 8:e67792. [PMID: 23844094 PMCID: PMC3701013 DOI: 10.1371/journal.pone.0067792] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 05/22/2013] [Indexed: 11/30/2022] Open
Abstract
Specialized acrobatic leaping has been recognized as a key adaptive trait tied to the origin and subsequent radiation of euprimates based on its observed frequency in extant primates and inferred frequency in extinct early euprimates. Hypothesized skeletal correlates include elongated tarsal elements, which would be expected to aid leaping by allowing for increased rates and durations of propulsive acceleration at takeoff. Alternatively, authors of a recent study argued that pronounced distal calcaneal elongation of euprimates (compared to other mammalian taxa) was related primarily to specialized pedal grasping. Testing for correlations between calcaneal elongation and leaping versus grasping is complicated by body size differences and associated allometric affects. We re-assess allometric constraints on, and the functional significance of, calcaneal elongation using phylogenetic comparative methods, and present an evolutionary hypothesis for the evolution of calcaneal elongation in primates using a Bayesian approach to ancestral state reconstruction (ASR). Results show that among all primates, logged ratios of distal calcaneal length to total calcaneal length are inversely correlated with logged body mass proxies derived from the area of the calcaneal facet for the cuboid. Results from phylogenetic ANOVA on residuals from this allometric line suggest that deviations are explained by degree of leaping specialization in prosimians, but not anthropoids. Results from ASR suggest that non-allometric increases in calcaneal elongation began in the primate stem lineage and continued independently in haplorhines and strepsirrhines. Anthropoid and lorisid lineages show stasis and decreasing elongation, respectively. Initial increases in calcaneal elongation in primate evolution may be related to either development of hallucal-grasping or a combination of grasping and more specialized leaping behaviors. As has been previously suggested, subsequent increases in calcaneal elongation are likely adaptations for more effective acrobatic leaping, highlighting the importance of this behavior in early euprimate evolution.
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Affiliation(s)
- Doug M Boyer
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America.
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14
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Kawashima T, Thorington RW, Sato F. Systematic and comparative morphologies of the extrinsic cardiac nervous system in lemurs (Primates: Strepsirrhini: Infraorder Lemuriformes, Gray, 1821) with evolutionary morphological implications. ZOOL ANZ 2013. [DOI: 10.1016/j.jcz.2012.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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15
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Molar size and diet in the Strepsirrhini: Implications for size-adjustment in studies of primate dental adaptation. J Hum Evol 2012; 63:796-804. [DOI: 10.1016/j.jhevol.2012.09.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 07/01/2012] [Accepted: 09/17/2012] [Indexed: 11/21/2022]
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The lemur revolution starts now: the genomic coming of age for a non-model organism. Mol Phylogenet Evol 2012; 66:442-52. [PMID: 22982436 DOI: 10.1016/j.ympev.2012.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/24/2012] [Accepted: 08/27/2012] [Indexed: 12/25/2022]
Abstract
Morris Goodman was a revolutionary. Together with a mere handful of like-minded scientists, Morris established himself as a leader in the molecular phylogenetic revolution of the 1960s. The effects of this revolution are most evident in this journal, which he founded in 1992. Happily for lemur biologists, one of Morris Goodman's primary interests was in reconstructing the phylogeny of the primates, including the tooth-combed Lorisifomes of Africa and Asia, and the Lemuriformes of Madagascar (collectively referred to as the suborder Strepsirrhini). This paper traces the development of molecular phylogenetic and evolutionary genetic trends and methods over the 50-year expanse of Morris Goodman's career, particularly as they apply to our understanding of lemuriform phylogeny, biogeography, and biology. Notably, this perspective reveals that the lemuriform genome is sufficiently rich in phylogenetic signal such that the very earliest molecular phylogenetic studies - many of which were conducted by Goodman himself - have been validated by contemporary studies that have exploited advanced computational methods applied to phylogenomic scale data; studies that were beyond imagining in the earliest days of phylogeny reconstruction. Nonetheless, the frontier still beckons. New technologies for gathering and analyzing genomic data will allow investigators to build upon what can now be considered a nearly-known phylogeny of the Lemuriformes in order to ask innovative questions about the evolutionary mechanisms that generate and maintain the extraordinary breadth and depth of biological diversity within this remarkable clade of primates.
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McLain AT, Meyer TJ, Faulk C, Herke SW, Oldenburg JM, Bourgeois MG, Abshire CF, Roos C, Batzer MA. An alu-based phylogeny of lemurs (infraorder: Lemuriformes). PLoS One 2012; 7:e44035. [PMID: 22937148 PMCID: PMC3429421 DOI: 10.1371/journal.pone.0044035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 07/31/2012] [Indexed: 11/30/2022] Open
Abstract
LEMURS (INFRAORDER: Lemuriformes) are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ∼55-60 million years ago (mya). Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primate-specific Short INterspersed Elements (SINEs), to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus) was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction) verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the exclusion of Eulemur and Varecia, with Varecia the sister lineage to the other three genera.
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Affiliation(s)
- Adam T McLain
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
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18
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Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 2012; 44:21. [PMID: 22697611 PMCID: PMC3390907 DOI: 10.1186/1297-9686-44-21] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 06/14/2012] [Indexed: 11/24/2022] Open
Abstract
In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
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Affiliation(s)
- Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Via F.lli Cervi 93, Segrate, Milan 20090, Italy
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Hughes S, Fernández H, Cucchi T, Duffraisse M, Casabianca F, Istria D, Pompanon F, Vigne JD, Hänni C, Taberlet P. A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices. PLoS One 2012; 7:e30272. [PMID: 22299033 PMCID: PMC3267719 DOI: 10.1371/journal.pone.0030272] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 12/14/2011] [Indexed: 12/02/2022] Open
Abstract
The goat (Capra hircus) is one of the earliest domesticated species ca. 10,500 years ago in the Middle-East where its wild ancestor, the bezoar (Capra aegagrus), still occurs. During the Neolithic dispersal, the domestic goat was then introduced in Europe, including the main Mediterranean islands. Islands are interesting models as they maintain traces of ancient colonization, historical exchanges or of peculiar systems of husbandry. Here, we compare the mitochondrial genetic diversity of both medieval and extant goats in the Island of Corsica that presents an original and ancient model of breeding with free-ranging animals. We amplified a fragment of the Control Region for 21 medieval and 28 current goats. Most of them belonged to the A haplogroup, the most worldwide spread and frequent today, but the C haplogroup is also detected at low frequency in the current population. Present Corsican goats appeared more similar to medieval goats than to other European goat populations. Moreover, 16 out of the 26 haplotypes observed were endemic to Corsica and the inferred demographic history suggests that the population has remained constant since the Middle Ages. Implications of these results on management and conservation of endangered Corsican goats currently decimated by a disease are addressed.
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Affiliation(s)
- Sandrine Hughes
- Paléogénomique et Evolution Moléculaire, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, INRA, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
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van Woerden J, van Schaik C, Isler K. Effects of Seasonality on Brain Size Evolution: Evidence from Strepsirrhine Primates. Am Nat 2010; 176:758-67. [DOI: 10.1086/657045] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Catlett KK, Schwartz GT, Godfrey LR, Jungers WL. "Life history space": a multivariate analysis of life history variation in extant and extinct Malagasy lemurs. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 142:391-404. [PMID: 20091842 DOI: 10.1002/ajpa.21236] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Studies of primate life history variation are constrained by the fact that all large-bodied extant primates are haplorhines. However, large-bodied strepsirrhines recently existed. If we can extract life history information from their skeletons, these species can contribute to our understanding of primate life history variation. This is particularly important in light of new critiques of the classic "fast-slow continuum" as a descriptor of variation in life history profiles across mammals in general. We use established dental histological methods to estimate gestation length and age at weaning for five extinct lemur species. On the basis of these estimates, we reconstruct minimum interbirth intervals and maximum reproductive rates. We utilize principal components analysis to create a multivariate "life history space" that captures the relationships among reproductive parameters and brain and body size in extinct and extant lemurs. Our data show that, whereas large-bodied extinct lemurs can be described as "slow" in some fashion, they also varied greatly in their life history profiles. Those with relatively large brains also weaned their offspring late and had long interbirth intervals. These were not the largest of extinct lemurs. Thus, we distinguish size-related life history variation from variation that linked more strongly to ecological factors. Because all lemur species larger than 10 kg, regardless of life history profile, succumbed to extinction after humans arrived in Madagascar, we argue that large body size increased the probability of extinction independently of reproductive rate. We also provide some evidence that, among lemurs, brain size predicts reproductive rate better than body size.
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Affiliation(s)
- Kierstin K Catlett
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA.
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Crowley BE, Carter ML, Karpanty SM, Zihlman AL, Koch PL, Dominy NJ. Stable carbon and nitrogen isotope enrichment in primate tissues. Oecologia 2010; 164:611-26. [PMID: 20628886 PMCID: PMC2955919 DOI: 10.1007/s00442-010-1701-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Accepted: 06/14/2010] [Indexed: 11/28/2022]
Abstract
Isotopic studies of wild primates have used a wide range of tissues to infer diet and model the foraging ecologies of extinct species. The use of mismatched tissues for such comparisons can be problematic because differences in amino acid compositions can lead to small isotopic differences between tissues. Additionally, physiological and dietary differences among primate species could lead to variable offsets between apatite carbonate and collagen. To improve our understanding of the isotopic chemistry of primates, we explored the apparent enrichment (ε*) between bone collagen and muscle, collagen and fur or hair keratin, muscle and keratin, and collagen and bone carbonate across the primate order. We found that the mean ε* values of proteinaceous tissues were small (≤1‰), and uncorrelated with body size or phylogenetic relatedness. Additionally, ε* values did not vary by habitat, sex, age, or manner of death. The mean ε* value between bone carbonate and collagen (5.6 ± 1.2‰) was consistent with values reported for omnivorous mammals consuming monoisotopic diets. These primate-specific apparent enrichment values will be a valuable tool for cross-species comparisons. Additionally, they will facilitate dietary comparisons between living and fossil primates.
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Affiliation(s)
- Brooke E Crowley
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.
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Kamilar JM, Muldoon KM. The climatic niche diversity of malagasy primates: a phylogenetic perspective. PLoS One 2010; 5:e11073. [PMID: 20552016 PMCID: PMC2884016 DOI: 10.1371/journal.pone.0011073] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 05/19/2010] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Numerous researchers have posited that there should be a strong negative relationship between the evolutionary distance among species and their ecological similarity. Alternative evidence suggests that members of adaptive radiations should display no relationship between divergence time and ecological similarity because rapid evolution results in near-simultaneous speciation early in the clade's history. In this paper, we performed the first investigation of ecological diversity in a phylogenetic context using a mammalian adaptive radiation, the Malagasy primates. METHODOLOGY/PRINCIPAL FINDINGS We collected data for 43 extant species including: 1) 1064 species by locality samples, 2) GIS climate data for each sampling locality, and 3) the phylogenetic relationships of the species. We calculated the niche space of each species by summarizing the climatic variation at localities of known occurrence. Climate data from all species occurrences at all sites were entered into a principal components analysis. We calculated the mean value of the first two PCA axes, representing rainfall and temperature diversity, for each species. We calculated the K statistic using the Physig program for Matlab to examine how well the climatic niche space of species was correlated with phylogeny. CONCLUSIONS/SIGNIFICANCE We found that there was little relationship between the phylogenetic distance of Malagasy primates and their rainfall and temperature niche space, i.e., closely related species tend to occupy different climatic niches. Furthermore, several species from different genera converged on a similar climatic niche. These results have important implications for the evolution of ecological diversity, and the long-term survival of these endangered species.
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Affiliation(s)
- Jason M Kamilar
- Department of Anthropology, Yale University, New Haven, Connecticut, USA.
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Subchondral Bone Apparent Density and Locomotor Behavior in Extant Primates and Subfossil Lemurs Hadropithecus and Pachylemur. INT J PRIMATOL 2010. [DOI: 10.1007/s10764-010-9401-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Fabre PH, Rodrigues A, Douzery EJP. Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol Phylogenet Evol 2009; 53:808-25. [PMID: 19682589 DOI: 10.1016/j.ympev.2009.08.004] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 07/08/2009] [Accepted: 08/03/2009] [Indexed: 11/18/2022]
Abstract
Here, we present a new primate phylogeny inferred from molecular supermatrix analyses of size 42 kb containing 70% of missing data, and representing 75% of primate species diversity. The supermatrix was analysed using a gene-partitioned maximum likelihood approach to obtain an exhaustive molecular phylogenetic framework. All clades recovered from recent molecular works were upheld in our analyses demonstrating that the presence of missing data did not bias our supermatrix inference. The resulting phylogenetic tree was subsequently dated with a molecular dating method to provide a timescale for speciation events. Results obtained from our relaxed molecular clock analyses concurred with previous works based on the same fossil constraints. The resulting dated tree allowed to infer of macroevolutionary processes among the primates. Shifts in diversification rate and speciation rates were determined using the SymmeTREE method and a birthdeath process. No significant asymmetry was detected for the primate clade, but significant shifts in diversification rate were identified for seven clades: Anthropoidea, Lemuriformes, Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian Macaca. Comparisons with previous primate supertree results reveal that (i) there was a diversification event at the root of the Lemuriformes, (ii) a higher diversification rate is detected for Cercopithecidae and Anthropoidea and (iii) a shift in diversification is always recovered for Macaca genus. Macroevolutionary inferences and primate divergence dates show that major primate diversification events occurred after the Paleogene, suggesting the extinction of ancient primate lineages.
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Affiliation(s)
- P-H Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, Place E. Bataillon, CC 064, 34095 Montpellier Cedex 5, France.
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