Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs.

Matsui, Atsushi; Rakotondraparany, Felix; Munechika, Isao; Hasegawa, Masami; Horai, Satoshi

doi:10.1016/j.gene.2008.08.024

Cited by 121Evolution and Paleontology StudiesPrimate Behavior and EcologyGenomics and Phylogenetic Studies

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs.

Open access

Matsui, Atsushi, Rakotondraparany, Felix, Munechika, Isao, Hasegawa, Masami, Horai, Satoshi·2009·Gene

DOI 10.1016/j.gene.2008.08.024

Open this paper in CoChat — free account

Abstract

Prosimians (tarsiers and strepsirrhini) represent the basal lineages in primates and have a close bearing on the origin of primates. Although major lineages among anthropoidea (humans, apes and monkeys) are well represented by complete mitochondrial DNA (mtDNA) sequence data, only one complete mtDNA sequence from a representative of each of the infraorders in prosimians has been described until quite recently, and therefore we newly determined complete mtDNA sequences from 5 lemurs, 4 lorises, one tarsier and one platyrrhini. These sequences were provided to phylogenetic analyses in combination with the sequences from the 15 primates species reported to the database. The position of tarsiers among primates could not be resolved by the maximum likelihood (ML) and neighbor-joining (NJ) analyses with several data sets. As to the position of tarsiers, any of the three alternative topologies (monophyly of haplorhini, monophyly of prosimians, and tarsiers being basal in primates) was not rejected at the significance level of 5%, neither at the nucleotide nor at the amino acid level. In addition, the significant variations of C and T compositions were observed across primates species. Furthermore, we used AGY data sets for phylogenetic analyses in order to remove the effect of different C/T composition bias across species. The analyses of AGY data sets provided a medium support for the monophyly of haplorhini, which might have been screened by the variation in base composition of mtDNA across species. To estimates the speciation dates within primates, we analyzed the amino acid sequences of mt-proteins with a Bayesian method of Thorne and Kishino. Divergence dates were estimated as follows for the crown groups: about 35.4 million years ago (mya) for lorisiformes, 55.3 mya for lemuriformes, 64.5 mya for strepsirrhini, 70.1 mya for haplorhini and 76.0 mya for primates. Furthermore, we reexamined the biogeographic scenarios which have been proposed for the origin of strepsirrhini (lemuriformes and lorisiformes) and for the dispersal of the lemuriformes and lorisiformes.

Integrity signals

Registry

Crossref · 10.1016/j.gene.2008.08.024

Cites

143 of 143 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Chiromyiformes diverged from a common ancestor with Lemuriformes shortly after colonisation of Madagascar.
“Chiromyiformes diverged from a common ancestor with Lemuriformes shortly after colonisation of Madagascar [14], [19]”
From A molecular phylogeny of living primates (2011) · cites this paper as [14]

Molecular Cloning: A Laboratory Manual
Sambrook, J., Fritsch, E., & Maniatis, T. (1989) · UCLA - Biblioteca de Ciencias de la Salud · Cited by 133,589 · see citing works
Molecular cloning: A laboratory manual
Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684 · see citing works
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
Felsenstein, J. (1985) · Evolution · doi:10.1111/j.1558-5646.1985.tb00420.x · Cited by 44,735 · cited 2× · see citing works
“The support for an internal edge was evaluated with the bootstrap probability (BP) (Felsenstein, 1985).”
Method
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
Thompson, J. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.24.4876 · Cited by 39,119 · cited 1× · see citing works
“Alignments for the 13 protein-coding sequences were performed using default settings in ClustalX (Thompson et al., 1997) and were adjusted manually with reference to codon boundaries of the aligned amino acid sequences.”
Method
Confidence Limits on Phylogenies: An Approach Using the Bootstrap
Felsenstein, J. (1985) · Evolution · doi:10.2307/2408678 · Cited by 19,371 · see citing works
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
Kumar, S. (2004) · Briefings in Bioinformatics · doi:10.1093/bib/5.2.150 · Cited by 11,642 · see citing works
Sequence and organization of the human mitochondrial genome
Anderson, S., Bankier, A. T., Barrell, B. G., de Bruijn, M. H. L., Coulson, A. R., Drouin, J., Eperon, I. C., Nierlich, D. P., Roe, B. A., Sanger, F., et al. (1981) · Nature · doi:10.1038/290457a0 · Cited by 9,640 · see citing works
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687 · see citing works
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 6,916 · cited 1× · see citing works
“For this purpose, we chose the Jones–Taylor– Thornton model (Jones et al., 1992) as a substitution model for amino acid sequences implemented in the program and used a monotreme and marsupials as outgroups.”
Method
MEGA2: molecular evolutionary genetics analysis software
Kumar, S., Tamura, K., Jakobsen, I. B., & Nei, M. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.12.1244 · Cited by 6,046 · see citing works
PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,344 · cited 1× · see citing works
“14d package (Yang, 1997).”
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
Shimodaira, H., & Hasegawa, M. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026201 · Cited by 4,237 · cited 1× · see citing works
“We performed tests of alternative trees in an ML framework with CONSEL program (Shimodaira and Hasegawa, 2001) using the nonparametric KH test (Kishino and Hasegawa, 1989), with correction for multiple comparisons of topologies defined a posteriori (SH test) (Shimodaira and Hasegawa, 1999).”
Method
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
Kishino, H., & Hasegawa, M. (1989) · Journal of Molecular Evolution · doi:10.1007/bf02100115 · Cited by 3,378 · cited 1× · see citing works
“We performed tests of alternative trees in an ML framework with CONSEL program (Shimodaira and Hasegawa, 2001) using the nonparametric KH test (Kishino and Hasegawa, 1989), with correction for multiple comparisons of topologies defined a posteriori (SH test) (Shimodaira and Hasegawa, 1999).”
Method
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
Felsenstein, J. (1978) · Systematic Biology · doi:10.1093/sysbio/27.4.401 · Cited by 3,221 · see citing works
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods.
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960 · cited 1× · see citing works
“, 1990)+Γ model (for the BASEML program in the PAML package) with 4–8 rate classes in the discrete approximation of the gamma model (Yang, 1994; Yang, 1996).”
Method
Molecular Systematics
Moore, D. S., Hillis, D. M., Moritz, C. C., & Mable, B. K. (1996) · Copeia · doi:10.2307/1447682 · Cited by 2,372 · see citing works
The general stochastic model of nucleotide substitution
Rodríguez, F., Oliver, J. L. T., Marín, A., & Medina, J. R. (1990) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(05)80104-3 · Cited by 2,325 · cited 1× · see citing works
“1985), and the general timereversible (GTR) (Rodriguez et al., 1990)+Γ model (for the BASEML program in the PAML package) with 4–8 rate classes in the discrete approximation of the gamma model (Yang, 1994; Yang, 1996).”
Method
Cases in which parsimony or compatibility methods will be positively misleading.
Felsenstein, J. (1978) · Systematic Zoology · doi:10.2307/2412923 · Cited by 2,230 · see citing works
Classification of mammals: above the species level
(1998) · Choice Reviews Online · doi:10.5860/choice.35-5657 · Cited by 2,103 · cited 1× · see citing works
“, 1998) and the whale/hippopotamus divergence (C3) (Thewissen, 1994; Mckenna and Bell, 1997; Bajpai and Gingerich, 1998; Waddell et al., 1999) as a calibration for their”
Background
CONSEL: for assessing the confidence of phylogenetic tree selection
Shimodaira, H., & Hasegawa, M. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.12.1246 · Cited by 2,051 · see citing works
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960 · cited 2× · see citing works
“(1997) and Goodman et al. (1998) suggested Otolemur and Nycticebus grouped together to the exclusion of Perodicticus using ɛ-globin and the β-globin sequences.”
BackgroundMethod
Compilation of tRNA sequences and sequences of tRNA genes
Sprinzl, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki012 · Cited by 1,916 · see citing works
Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes
Perna, N. T., & Kocher, T. D. (1995) · Journal of Molecular Evolution · doi:10.1007/bf01215182 · Cited by 1,642 · see citing works
Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes
Perna, N. T., & Kocher, T. D. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00186547 · Cited by 1,365 · cited 1× · see citing works
“The base composition bias of mtDNA from several mammal species has been reported (Perna and Kocher, 1995; Springer and Douzery, 1996; Schmitz et al., 2002; Philips and Penny, 2003; Gibson et al., 2005).”
Background
Molecular phylogenetics and the origins of placental mammals
Murphy, W. J., Eizirik, E., Johnson, W. E., Zhang, Y., Ryder, O. A., & O’Brien, S. J. (2001) · Nature · doi:10.1038/35054550 · Cited by 1,361 · cited 2× · see citing works
“, 2005) or with strepsirrhini (Eizirik et al., 2001; Murphy et al., 2001; Jow et al., 2002; Schmitz et al., 2002; Hudelot et al., 2003), although the position of tarsier depends on the molecular and morphological data sets.”
BackgroundResult
Estimating the rate of evolution of the rate of molecular evolution
Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317 · cited 2× · see citing works
“This method allows different rates on different branches (Thorne et al., 1998).”
Method
Primate adaptation and evolution
(1989) · Choice Reviews Online · doi:10.5860/choice.26-3889 · Cited by 1,246 · see citing works
Among-site rate variation and its impact on phylogenetic analyses
Yang, Z. (1996) · Trends in Ecology & Evolution · doi:10.1016/0169-5347(96)10041-0 · Cited by 1,202 · cited 1× · see citing works
“, 1990)+Γ model (for the BASEML program in the PAML package) with 4–8 rate classes in the discrete approximation of the gamma model (Yang, 1994; Yang, 1996).”
Method
Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence
Alfaro, M. E. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg028 · Cited by 1,136 · see citing works
A new hominid from the Upper Miocene of Chad, Central Africa
Brunet, M., Guy, F., Pilbeam, D. R., Mackaye, H. T., Likius, A., Djimdoumalbaye, A., Beauvilain, A., Blondel, C., Bocherens, H., Boisserie, J., et al. (2002) · Nature · doi:10.1038/nature00879 · Cited by 1,077 · see citing works
Likelihood-Based Tests of Topologies in Phylogenetics
Goldman, N., Anderson, J. P., & Rodrigo, A. G. (2000) · Systematic Biology · doi:10.1080/106351500750049752 · Cited by 1,076 · see citing works
Divergence time and evolutionary rate estimation with multilocus data.
Thorne, J. L., & Kishino, H. (2002) · Systematic Biology · doi:10.1080/10635150290102456 · Cited by 962 · cited 2× · see citing works
“The new version of the package (Thorne and Kishino, 2002) derives the posterior distribution of rates and times using a Markov chain Monte Carlo (MCMC) procedure that applies a probabilistic model to the estimation of change in nucleotide substitution rate over time.”
Method
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
Kishino, H., Miyata, T., & Hasegawa, M. (1990) · Journal of Molecular Evolution · doi:10.1007/bf02109483 · Cited by 887 · cited 1× · see citing works
“For the ML analyses, BPs were estimated by the RELL (resampling of estimated loglikelihoods) method (Kishino et al., 1990; Hasegawa and Kishino, 1994) with 10,000 bootstrap resamplings.”
Method
Placental mammal diversification and the Cretaceous–Tertiary boundary
Springer, M. S., Murphy, W. J., Eduardo Eizirik, C., & O’Brien, S. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334222100 · Cited by 837 · cited 1× · see citing works
“This result supports the estimateddates of theprevious studies concerning the inter-ordinal diversification of placental mammals (Hasegawa et al., 2003; Springer et al., 2003).”
Result
Compilation of tRNA sequences and sequences of tRNA genes
Sprinzl, M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.148 · Cited by 750 · see citing works
Toward a phylogenetic classification of Primates based on DNA evidence complemented by fossil evidence.
Goodman, M., Porter, C. A., Czelusniak, J., Page, S. L., Schneider, H., Shoshani, J., Gunnell, G., & Groves, C. P. (1998) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1998.0495 · Cited by 743 · see citing works
Synonymous and nonsynonymous rate variation in nuclear genes of mammals
Yang, Z., & Nielsen, R. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006320 · Cited by 679 · cited 1× · see citing works
“We also used the codon-substitution (CS)+Γ model (Goldman and Yang, 1994; Yang and Nielsen, 1998) implemented in PAML for the protein-encoding genes analyses.”
Method
Timing of Hot Spot—Related Volcanism and the Breakup of Madagascar and India
Storey, M., Mahoney, J. J., Saunders, A. D., Duncan, R. A., Kelley, S. P., & Coffin, M. F. (1995) · Science · doi:10.1126/science.267.5199.852 · Cited by 664 · cited 1× · see citing works
“Finally, Madagascar and India separated about 88 mya, in the middle Late Cretaceous (Storey, 1995) and the Seychelles separated from India (65mya) as India continued drifting northwards.”
Background
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
Suzuki, Y., Glazko, G. V., & Nei, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.212646199 · Cited by 647 · see citing works
Evolution of Tertiary Mammals of North America
(1998) · Cambridge University Press eBooks · doi:10.1017/cbo9780511529924 · Cited by 618 · see citing works
Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs.
Horai, S., Hayasaka, K., Kondo, R., Tsugane, K., & Takahata, N. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.2.532 · Cited by 588 · see citing works
Continental breakup and the ordinal diversification of birds and mammals
Hedges, S. B., Parker, P. H., Sibley, C. G., & Kumar, S. (1996) · Nature · doi:10.1038/381226a0 · Cited by 529 · cited 1× · see citing works
“extinction of the dinosaurs (Hedges et al., 1996).”
Primate Adaptation and Evolution
Dunbar, R., & Fleagle, J. G. (1999) · Journal of the Royal Anthropological Institute · doi:10.2307/2661176 · Cited by 519 · see citing works
Stratigraphic evidence for an early collision between northwest India and Asia
Beck, R. A. D., Burbank, D. W., Sercombe, W. J., Riley, G. W., Barndt, J. K., Berry, J. R., Afzal, J., Khan, A. M., Jurgen, H., Metje, J., et al. (1995) · Nature · doi:10.1038/373055a0 · Cited by 516 · see citing works
Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA
Adachi, J., & Hasegawa, M. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02498640 · Cited by 514 · see citing works
Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability
Douady, C. J. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg042 · Cited by 507 · see citing works
Late Paleocene-early Eocene climatic and biotic events in the marine and terrestrial records
Aubry, M., Lucas, S. G., & Berggren, W. A. (1998) · Columbia University Press eBooks · Cited by 486 · see citing works
The Separation of Madagascar and Africa
Rabinowitz, P. D., Coffin, M. F., & Falvey, D. A. (1983) · Science · doi:10.1126/science.220.4592.67 · Cited by 486 · cited 1× · see citing works
“Subsequently, the eastern continent continued to split, Antarctica–Australia separated about 130 mya and the separation of Madagascar fromAfricawas completed by about 120mya (Rabinowitz et al., 1983).”
Background
Late Miocene hominids from the Middle Awash, Ethiopia
Haile‐Selassie, Y. (2001) · Nature · doi:10.1038/35084063 · Cited by 479 · cited 1× · see citing works
“0 mya) (Aiello and Collard, 2001; Haile-Selassie, 2001; Brunet et al., 2002).”
Compilation of small ribosomal subunit RNA structures
Neefs, J., de Peer, Y. V., Rijk, P. D., Chapelle, S., & Wächter, R. D. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.13.3025 · Cited by 478 · cited 1× · see citing works
“12S and 16S rRNA sequences were performed using DIALIGN (Morgenstern, 2004) and were adjusted to the secondary structure models of mammalian 12S rRNA (Zwieb et al., 1981; Hixson and Brown, 1986; Neefs et al., 1993; Springer and Douzery, 1996) and 16S rRNA (Glotz et al.”
Method
Failure of the ILD to Determine Data Combinability for Slow Loris Phylogeny
Yoder, A. D., Irwin, J. A., & Payseur, B. A. (2001) · Systematic Biology · doi:10.1080/10635150116801 · Cited by 467 · cited 1× · see citing works
“, 2000, 2001a,b, 2002, 2003), lorisiformes (Yoder et al., 2001; Masters et al., 2005), and their biogeography (Yoder et al.”
Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution
Cooper, A., Lalueza‐Fox, C., Anderson, S., Rambaut, A., Austin, J. J., & Ward, R. H. (2001) · Nature · doi:10.1038/35055536 · Cited by 438 · cited 1× · see citing works
“A similar scenario (adapted from molecular data) has been suggested for the Indian frog (Biju and Bossuyt 2003, Hedges 2003) and the ratites, large flightless birds (Cooper et al. 2001).”
Method
Models of amino acid substitution and applications to mitochondrial protein evolution
Yang, Z., Nielsen, R., & Hasegawa, M. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025888 · Cited by 414 · cited 1× · see citing works
“(1979) amino acid distance with geometric formulae was used in calculating the acceptance rate of amino acid substitution (Yang et al., 1998).”
Method
Mammalian mitogenomic relationships and the root of the eutherian tree
Árnason, Ú., Adegoke, J. A., Bodin, K., Born, E. W., Esa, Y. B., Gullberg, A., Nilsson, M. A., Short, R. V., Xu, X., & Janke, A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.102164299 · Cited by 382 · cited 1× · see citing works
“Some data even suggested tarsiers to be a basal group of primates (Arnason et al., 2002).”
Background
The Primate fossil record
(2002) · Choice Reviews Online · doi:10.5860/choice.40-2181 · Cited by 371 · see citing works
Comparison of Likelihood and Bayesian Methods for Estimating Divergence Times Using Multiple Gene Loci and Calibration Points, with Application to a Radiation of Cute-Looking Mouse Lemur Species
Yang, Z., & Yoder, A. D. (2003) · Systematic Biology · doi:10.1080/10635150390235557 · Cited by 357 · see citing works
Compositional Bias May Affect Both DNA-Based and Protein-Based Phylogenetic Reconstructions
Foster, P. G., & Hickey, D. A. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006471 · Cited by 337 · cited 1× · see citing works
“If there are large variations in base composition across species, then conventional models may be unable to compensate for these variations (Foster and Hickey, 1999) and may prevent the recovery of the true evolutionary history.”
Background
A theory of human and primate evolution
(1989) · Choice Reviews Online · doi:10.5860/choice.27-1537 · Cited by 335 · see citing works
Using the fossil record to estimate the age of the last common ancestor of extant primates
Tavaré, S., Marshall, C. R., Will, O., Soligo, C., & Martin, R. D. (2002) · Nature · doi:10.1038/416726a · Cited by 330 · see citing works
Primate origins: plugging the gaps
Martin, R. D. (1993) · Nature · doi:10.1038/363223a0 · Cited by 325 · cited 1× · see citing works
“The common ancestor of primates should be earlier than the oldest known fossils (Martin, 1993), but adequate quantification is needed to interpret possible discrepancies between molecular and palaeontological estimates.”
Background
The biogeographic and tectonic history of India
Briggs, J. C. (2003) · Journal of Biogeography · doi:10.1046/j.1365-2699.2003.00809.x · Cited by 321 · see citing works
Two types of amino acid substitutions in protein evolution
Miyata, T., Miyazawa, S., & Yasunaga, T. (1979) · Journal of Molecular Evolution · doi:10.1007/bf01732340 · Cited by 321 · see citing works
Failure of the ILD to Determine Data Combinability for Slow Loris Phylogeny
Yoder, A. D., Irwin, J. A., & Payseur, B. A. (2001) · Systematic Biology · doi:10.1080/106351501300318003 · Cited by 317 · see citing works
The root of the mammalian tree inferred from whole mitochondrial genomes.
Phillips, M., & Penny, D. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00057-5 · Cited by 293 · see citing works
Madagascar: Heads It’s a Continent, Tails It’s an Island
de Wit, M. J. (2003) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev.earth.31.100901.141337 · Cited by 292 · see citing works
Fossil evidence for an ancient divergence of lorises and galagos
Seiffert, E. R., Simons, E. L., & Attia, Y. S. (2003) · Nature · doi:10.1038/nature01489 · Cited by 290 · see citing works
Single origin of Malagasy Carnivora from an African ancestor
Yoder, A. D., Burns, M. M., Zehr, S. M., Delefosse, T., Veron, G., Goodman, S. M., & Flynn, J. J. (2003) · Nature · doi:10.1038/nature01303 · Cited by 287 · cited 1× · see citing works
“Their recent study with Bayesian method suggested a 50–78 mya for the diversification of Malagasy primates (Yoder et al., 2003).”
New frog family from India reveals an ancient biogeographical link with the Seychelles
Biju, S. D., & Bossuyt, F. (2003) · Nature · doi:10.1038/nature02019 · Cited by 279 · cited 1× · see citing works
“A similar scenario (adapted from molecular data) has been suggested for the Indian frog (Biju and Bossuyt 2003, Hedges 2003) and the ratites, large flightless birds (Cooper et al. 2001). From the study of the divergence dates of salt-intolerant frogs, Van Bocxlaer et al. (2006) suggested that the timing of separation…”
Background
Nucleotide Bias Causes a Genomewide Bias in the Amino Acid Composition of Proteins
Singer, G. A. C., & Hickey, D. A. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026257 · Cited by 273 · cited 1× · see citing works
“If nonsynonymous positions are affected by compositional bias, then the encoded proteins will change their amino acid composition (Singer and Hickey, 2000).”
Background
Ancient single origin for Malagasy primates.
Yoder, A. D., Cartmill, M., Ruvolo, M., Smith, K., & Vilgalys, R. J. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.10.5122 · Cited by 268 · cited 2× · see citing works
“One is that strepsirrhini originated in Africa and succeeded the colonization to Madagascar and Asia by respective single immigration events, as mentioned by some studies (Yoder et al., 1996; Roos et al., 2004).”
Function, phylogeny, and fossils: Miocene hominoid evolution and adaptations
(1998) · Choice Reviews Online · doi:10.5860/choice.35-6224 · Cited by 266 · see citing works
Primate jumping genes elucidate strepsirrhine phylogeny.
Roos, C., Schmitz, J., & Zischler, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403852101 · Cited by 262 · cited 1× · see citing works
“One is that strepsirrhini originated in Africa and succeeded the colonization to Madagascar and Asia by respective single immigration events, as mentioned by some studies (Yoder et al., 1996; Roos et al., 2004).”
Background
Model misspecification and probabilistic tests of topology: evidence from empirical data sets.
Buckley, T. R. (2002) · Systematic Biology · doi:10.1080/10635150290069922 · Cited by 253 · see citing works
Primate evolution – in and out of Africa
Stewart, C., & Disotell, T. R. (1998) · Current Biology · doi:10.1016/s0960-9822(07)00367-3 · Cited by 247 · cited 2× · see citing works
“, 1997; Ward, 1997) suggest that the divergence between the Sivapithecus-orangutan and the African apes-human lineages occurred prior to 13 mya (Ward, 1997; Stewart and Disotell, 1998), which is the current consensus among paleoanthropologists.”
Background
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ
Morgenstern, B. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh373 · Cited by 234 · see citing works
Reconstruction of the Central Indian Ocean
Patriat, P., & Ségoufin, J. (1988) · Tectonophysics · doi:10.1016/0040-1951(88)90267-3 · Cited by 225 · cited 2× · see citing works
“Porter et al. (1997) and Goodman et al.”
Background
Molecular Dating and Biogeography of the Early Placental Mammal Radiation
Eizirik, E. (2001) · Journal of Heredity · doi:10.1093/jhered/92.2.212 · Cited by 220 · cited 2× · see citing works
“, 2005) or with strepsirrhini (Eizirik et al., 2001; Murphy et al., 2001; Jow et al., 2002; Schmitz et al., 2002; Hudelot et al., 2003), although the position of tarsier depends on the molecular and morphological data sets.”
BackgroundResult
Remarkable species diversity in Malagasy mouse lemurs (primates, Microcebus )
Yoder, A. D., Rasoloarison, R. M., Goodman, S. M., Irwin, J. A., Atsalis, S., Ravosa, M. J., & Ganzhorn, J. U. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.200121897 · Cited by 217 · cited 1× · see citing works
“Madagascar lemuriformes and AfroAsian lorisiformes have been enigmatic groups concerning the phylogenetic relationships among lemuriforms (Jung et al., 1992; Crovella et al., 1993; Yoder, 1994; Del Pero et al., 1995; Yoder et al., 2000; Yang and Yoder, 2003; Pastorini et al., 2000, 2001a,b, 2002, 2003), lorisiformes (…”
Background
Accuracies of the Simple Methods for Estimating the Bootstrap Probability of a Maximum-Likelihood Tree
Hasegawa, M., & Kishino, H. (1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040097 · Cited by 213 · cited 2× · see citing works
“For the ML analyses, BPs were estimated by the RELL (resampling of estimated loglikelihoods) method (Kishino et al., 1990; Hasegawa and Kishino, 1994) with 10,000 bootstrap resamplings.”
MethodResult
A comparison of the small ribosomal RNA genes from the mitochondrial DNA of the great apes and humans: sequence, structure, evolution, and phylogenetic implications.
(1986) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040379 · Cited by 210 · cited 1× · see citing works
“12S and 16S rRNA sequences were performed using DIALIGN (Morgenstern, 2004) and were adjusted to the secondary structure models of mammalian 12S rRNA (Zwieb et al., 1981; Hixson and Brown, 1986; Neefs et al., 1993; Springer and Douzery, 1996) and 16S rRNA (Glotz et al.”
Method
Handbook of Human Symbolic Evolution.
Dunbar, R., Lock, A., & Peters, C. R. (1998) · Journal of the Royal Anthropological Institute · doi:10.2307/3034175 · Cited by 198 · see citing works
Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes
Glotz, C., Zwieb, C. W., Brimacombe, R. L. C., Edwards, K., & Kössel, H. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.14.3287 · Cited by 197 · cited 1× · see citing works
“, 1993; Springer and Douzery, 1996) and 16S rRNA (Glotz et al., 1981; Burk et al., 2002), respectively.”
Handbook of human symbolic evolution
HAUSER, M. D. (1997) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(97)83203-x · Cited by 190 · see citing works
A Comprehensive Analysis of Mammalian Mitochondrial Genome Base Composition and Improved Phylogenetic Methods
Gibson, A., Gowri-Shankar, V., Higgs, P. G., & Rattray, M. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msi012 · Cited by 187 · cited 5× · see citing works
“, 2002; Gibson et al., 2005). Schmitz et al. (2002) suggested that tarsier and loris clustered apart from other primates andwere close to non-primatemammals by their base composition.”
BackgroundResultInfluential
Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species
Zwieb, C. W., Glotz, C., & Brimacombe, R. L. C. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.15.3621 · Cited by 186 · see citing works
A euprimate skull from the early Eocene of China
Ni, X., Wang, Y., Hu, Y., & Li, C. (2003) · Nature · doi:10.1038/nature02126 · Cited by 163 · cited 1× · see citing works
“Although some recent molecular phylogenies assume that primates originated far earlier than the K/T boundary, earliest fossil record suggests that primates began to diversify just after the K/T boundary around 55 mya (Ni et al., 2004).”
Background
A molecular approach to comparative phylogeography of extant Malagasy lemurs
Pastorini, J., Thalmann, U., & Martin, R. D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1031673100 · Cited by 163 · see citing works
New Sivapithecus humeri from Pakistan and the relationship of Sivapithecus and Pongo
Pilbeam, D. R., Rose, M. D., Barry, J. C., & Shah, S. M. I. (1990) · Nature · doi:10.1038/348237a0 · Cited by 161 · cited 1× · see citing works
“The orangutan lineage first appeared in the fossil record as Sivapithecus of about 12–13 mya (Kelley, 2002) but the fossil datings of Sivapithecus were once questioned (Pilbeam et al., 1990).”
Background
RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences
Hudelot, C., Gowri-Shankar, V., Jow, H., Rattray, M., & Higgs, P. G. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00061-7 · Cited by 156 · see citing works
A new Eocene archaeocete (Mammalia, Cetacea) from India and the time of origin of whales
Bajpai, S., & Gingerich, P. D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.26.15464 · Cited by 154 · cited 1× · see citing works
“, 1998) and the whale/hippopotamus divergence (C3) (Thewissen, 1994; Mckenna and Bell, 1997; Bajpai and Gingerich, 1998; Waddell et al., 1999) as a calibration for their”
Background
Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution
Jow, H., Hudelot, C., Rattray, M., & Higgs, P. G. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004221 · Cited by 154 · cited 2× · see citing works
“, 2005) or with strepsirrhini (Eizirik et al., 2001; Murphy et al., 2001; Jow et al., 2002; Schmitz et al., 2002; Hudelot et al., 2003), although the position of tarsier depends on the molecular and morphological data sets.”
BackgroundResult
Late Cretaceous Vicariance in Gondwanan Amphibians
Bocxlaer, I. V., Roelants, K., Biju, S. D., Nagaraju, J., & Bossuyt, F. (2006) · PLoS ONE · doi:10.1371/journal.pone.0000074 · Cited by 154 · see citing works
Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution.
Hasegawa, M., Thorne, J. L., & Kishino, H. (2003) · Genes & Genetic Systems · doi:10.1266/ggs.78.267 · Cited by 145 · cited 1× · see citing works
“This result supports the estimateddates of theprevious studies concerning the inter-ordinal diversification of placental mammals (Hasegawa et al., 2003; Springer et al., 2003).”
ResultSelf-citation
SINE Insertions in Cladistic Analyses and the Phylogenetic Affiliations of Tarsius bancanus to Other Primates
Schmitz, J., Ohme, M., & Zischler, H. (2001) · Genetics · doi:10.1093/genetics/157.2.777 · Cited by 145 · see citing works
Phylogeny and Evolution of Selected Primates as Determined by Sequences of the ε-Globin Locus and 5′ Flanking Regions
Porter, C. A., Page, S. L., Czelusniak, J., Schneider, H., Schneider, M. P. C., Sampaio, I., & Goodman, M. (1997) · International Journal of Primatology · doi:10.1023/a:1026328804319 · Cited by 142 · see citing works
Relative position of the cheirogaleidae in strepsirhine phylogeny: A comparison of morphological and molecular methods and results
Yoder, A. D. (1994) · American Journal of Physical Anthropology · doi:10.1002/ajpa.1330940104 · Cited by 136 · cited 1× · see citing works
“Madagascar lemuriformes and AfroAsian lorisiformes have been enigmatic groups concerning the phylogenetic relationships among lemuriforms (Jung et al., 1992; Crovella et al., 1993; Yoder, 1994; Del Pero et al., 1995; Yoder et al., 2000; Yang and Yoder, 2003; Pastorini et al., 2000, 2001a,b, 2002, 2003), lorisiformes (…”
Background
Events in Hominoid Evolution
Begun, D. R., Ward, C. V., & Rose, M. D. (1997) · Springer eBooks · doi:10.1007/978-1-4899-0075-3_18 · Cited by 135 · cited 1× · see citing works
“Recent statistical analyses of cranial and postcranial characters (Begun et al., 1997; Ward, 1997) suggest that the divergence between the Sivapithecus-orangutan and the African apes-human lineages occurred prior to 13 mya (Ward, 1997; Stewart and Disotell, 1998), which is the current consensus among paleoanthropologi…”
Background
A Fossil Lemur from the Oligocene of Pakistan
Marivaux, L., Welcomme, J., Antoine, P., Métais, G., Baloch, I. M., Benammi, M., Chaimanee, Y., Ducrocq, S., & Jaeger, J. (2001) · Science · doi:10.1126/science.1065257 · Cited by 135 · cited 1× · see citing works
“Bugtilemur fossil clearly suggested the important role of the Indian subcontinent in the early dispersal of lemuriformes and the evolution of strepsirrhine at IndoMadagascar block (Marivaux et al. 2001).”
Background
Late Cretaceous relatives of rabbits, rodents, and other extant eutherian mammals
Archibald, J. D., Averianov, A. O., & Ekdale, E. G. (2001) · Nature · doi:10.1038/35102048 · Cited by 131 · cited 1× · see citing works
“The maximum of 90 mya is based primarily on paleontological estimate for the antiquity of Zalambdalestidae which is regarded as the sister group of the Rodentia/ Lagomorpha clade and the minimum of 61 mya is based on the occurrence of cingulatan fossils of the ancestors of rodent and rabbit (the Eurymylidae and the Mi…”
Background
Compilation of tRNA sequences and sequences of tRNA genes
Sprinzl, M. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.1.68 · Cited by 131 · see citing works
Assessing the Cretaceous Superordinal Divergence Times within Birds and Placental Mammals by Using Whole Mitochondrial Protein Sequences and an Extended Statistical Framework
Waddell, P. J., Cao, Y., Hasegawa, M., & Mindell, D. P. (1999) · Systematic Biology · doi:10.1080/106351599260481 · Cited by 116 · cited 1× · see citing works
“, 1998) and the whale/hippopotamus divergence (C3) (Thewissen, 1994; Mckenna and Bell, 1997; Bajpai and Gingerich, 1998; Waddell et al., 1999) as a calibration for their”
Background
Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data
Cao, Y., Fujiwara, M., Nikaido, M., Okada, N., & Hasegawa, M. (2000) · Gene · doi:10.1016/s0378-1119(00)00427-3 · Cited by 112 · see citing works
Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates
Karanth, K. P., Delefosse, T., Rakotosamimanana, B., Parsons, T. J., & Yoder, A. D. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408354102 · Cited by 111 · see citing works
Evolution of the primate cytochrome c oxidase subunit II gene
Adkins, R., & Honeycutt, R. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00176084 · Cited by 107 · see citing works
Origins, Diversity and Relationships of Lemurs
Martin, R. D. (2000) · International Journal of Primatology · doi:10.1023/a:1005563113546 · Cited by 103 · cited 1× · see citing works
“Until 160 mya, Madagascar was a part of the southern supercontinent Gondwana and this supercontinent began to break up between Madagascar and Africa as a part of the initial breakup of Gondwanaland in the middle Jurassic (Martin, 2000).”
Background
Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP.
Poux, C., & Douzery, E. J. P. (2004) · American Journal of Physical Anthropology · doi:10.1002/ajpa.10322 · Cited by 103 · cited 4× · see citing works
“Recent studies of nuclear DNA seem to have established a consensus with respect to the phylogenetic position of tarsiers (Schmitz et al., 2001; Poux and Douzery, 2004).”
BackgroundMethodResultInfluential
An Assessment of Accuracy, Error, and Conflict with Support Values from Genome-Scale Phylogenetic Data
Taylor, D. J. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh156 · Cited by 94 · see citing works
The Complete Mitochondrial Sequence of Tarsius bancanus: Evidence for an Extensive Nucleotide Compositional Plasticity of Primate Mitochondrial DNA
Schmitz, J., Ohme, M., & Zischler, H. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004110 · Cited by 90 · cited 4× · see citing works
“The base composition bias of mtDNA from several mammal species has been reported (Perna and Kocher, 1995; Springer and Douzery, 1996; Schmitz et al., 2002; Philips and Penny, 2003; Gibson et al., 2005).”
BackgroundResultInfluential
The hominoid radiation in Asia
Kelley, J. (2002) · Medical Entomology and Zoology · Cited by 90 · see citing works
Evidence on primate phylogeny from ?-globin gene sequences and flanking regions
Porter, C. A., Sampaio, I., Schneider, H., Schneider, M. P. C., Czelusniak, J., & Goodman, M. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00166594 · Cited by 81 · see citing works
Accelerated Evolution of Cytochrome b in Simian Primates: Adaptive Evolution in Concert with Other Mitochondrial Proteins?
Andrews, T. D., Jermiin, L. S., & Easteal, S. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006382 · Cited by 78 · cited 1× · see citing works
“For mtDNA sequences, results from cytochrome b sequence analysis excluded tarsiers from primates (Andrews et al., 1998) and a COII sequence analysis indicated only a marginal affiliation of tarsiers with anthropoids (Adkins and Honeycutt, 1994).”
Chromosomal Evolution of Malagasy Lemurs
Rumpler, Y., Warter, S., Petter, J. J., Albignac, R., & Dutrillaux, B. (1988) · Folia Primatologica · doi:10.1159/000156336 · Cited by 78 · cited 1× · see citing works
“, 2002; Poux and Douzery, 2004) and karyotype comparisons (Rumpler et al., 1988).”
Background
Function, Phylogeny, and Fossils
Begun, D. R., Ward, C. V., & Rose, M. D. (1997) · Springer eBooks · doi:10.1007/978-1-4899-0075-3 · Cited by 73 · see citing works
Molecular Phylogeny of the Lemur Family Cheirogaleidae (Primates) Based on Mitochondrial DNA Sequences
Pastorini, J., Martin, R. D., Ehresmann, P., Zimmermann, E., & Forstner, M. R. J. (2001) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.2000.0904 · Cited by 72 · see citing works
Reconstructing the evolutionary history of the Lorisidae using morphological, molecular, and geological data
Masters, J. C., Anthony, N. M., de Wit, M. J., & Mitchell, A. (2005) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20149 · Cited by 71 · cited 2× · see citing works
“, 2000, 2001a,b, 2002, 2003), lorisiformes (Yoder et al., 2001; Masters et al., 2005), and their biogeography (Yoder et al.”
Result
Combing the primate record
Martin, R. D. (2003) · Nature · doi:10.1038/422388a · Cited by 70 · see citing works
Phylogeny of the Lemuridae: Effects of Character and Taxon Sampling on Resolution of Species Relationships within Eulemur
Yoder, A. D. (1999) · Cladistics · doi:10.1006/clad.1999.0105 · Cited by 62 · see citing works
The Taxonomy and Phylogenetic Relationships of Sivapithecus Revisited
Ward, S. (1997) · Springer eBooks · doi:10.1007/978-1-4899-0075-3_13 · Cited by 61 · cited 3× · see citing works
“, 1997; Ward, 1997) suggest that the divergence between the Sivapithecus-orangutan and the African apes-human lineages occurred prior to 13 mya (Ward, 1997; Stewart and Disotell, 1998), which is the current consensus among paleoanthropologists.”
Background
The Secondary Structure of Mammalian Mitochondrial 16S rRNA Molecules: Refinements Based on a Comparative Phylogenetic Approach
Burk, A., Douzery, E., & Springer, M. S. (2002) · Journal of Mammalian Evolution · doi:10.1023/a:1022649516930 · Cited by 59 · cited 2× · see citing works
“, 1993; Springer and Douzery, 1996) and 16S rRNA (Glotz et al., 1981; Burk et al., 2002), respectively.”
Background
Phylogeny of the Lemuridae: Effects of Character and Taxon Sampling on Resolution of Species Relationships within Eulemur
Yoder, A. D., & Irwin, J. A. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00271.x · Cited by 54 · cited 1× · see citing works
“, 1989) and DNA sequences (Del Pero et al., 1995; Yoder and Irwin, 1999; Wyner et al., 2000; Del Pero et al., 2001; Pastorini et al., 2002; Poux and Douzrey, 2004).”
Interrelationships of Mesozoic mammals
Kielan‐Jaworowska, Z. (1992) · Historical Biology · doi:10.1080/10292389209380427 · Cited by 52 · see citing works
The uniqueness of Daubentonia
OXNARD, C. E. (1981) · American Journal of Physical Anthropology · doi:10.1002/ajpa.1330540102 · Cited by 45 · cited 1× · see citing works
“Because of its morphological specializations, Daubentonia has sometimes been considered at the basal position of the strepsirrhini clade, thereby suggesting a diphyletic Lemuriformes (Groves, 1989; Adkins and Honeycutt, 1994) and even at the basal position of primates (Oxnard, 1981).”
Background
Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data.
Waddell, P. J., Kishino, H., & Ota, R. (2002) · PubMed · Cited by 44 · see citing works
Relationships among Brown Lemurs (Eulemur fulvus) Based on Mitochondrial DNA Sequences
Pastorini, J., Forstner, M. R. J., & Martin, R. D. (2000) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.2000.0796 · Cited by 43 · see citing works
Age differences and developmental trends in alarm peep responses by squirrel monkeys ( Saimiri sciureus )
McCowan, B., Franceschini, N. V., & Vicino, G. A. (2000) · American Journal of Primatology · doi:10.1002/1098-2345(200101)53:1 · Cited by 42 · see citing works
Phylogenetic relationships among the Malagasy lemuriforms (Primates: Strepsirrhini) as indicated by mitochondrial sequence data from the 12S rRNA gene
Delpero, M., Masters, J. C., Cervella, P., Crovella, S., Ardito, G., & Rumpler, Y. (2001) · Zoological Journal of the Linnean Society · doi:10.1111/j.1096-3642.2001.tb00624.x · Cited by 41 · see citing works
Phylogenetic aspects of Cetacean origins: A morphological perspective
Thewissen, J. (1994) · Journal of mammalian evolution · doi:10.1007/bf01473527 · Cited by 39 · cited 1× · see citing works
“, 1998) and the whale/hippopotamus divergence (C3) (Thewissen, 1994; Mckenna and Bell, 1997; Bajpai and Gingerich, 1998; Waddell et al., 1999) as a calibration for their”
Background
Szalatavus attricuspis, an Early Platyrrhine Primate
Rosenberger, A. L., Hartwig, W. C., & Wolff, R. G. (1991) · Folia Primatologica · doi:10.1159/000156552 · Cited by 37 · cited 1× · see citing works
“The split of platyrrhini/catarrhini and cercopithecoidea/hominoidea are often used as calibration points in dating among primates, and were at 35mya (Rosenberger et al., 1991) and at 25mya (Fleagle,1999) respectively.”
Background
The evolution of perissodactyla
Mein, P. (1992) · Geobios · doi:10.1016/s0016-6995(92)80057-k · Cited by 33 · see citing works
Highly repeated DNA analysis and systematics of the Lemuridae, a family of Malagasy prosimians
Crovella, S., Montagnon, D., & Rumpler, Y. (1993) · Primates · doi:10.1007/bf02381281 · Cited by 32 · cited 1× · see citing works
“Madagascar lemuriformes and AfroAsian lorisiformes have been enigmatic groups concerning the phylogenetic relationships among lemuriforms (Jung et al., 1992; Crovella et al., 1993; Yoder, 1994; Del Pero et al., 1995; Yoder et al., 2000; Yang and Yoder, 2003; Pastorini et al., 2000, 2001a,b, 2002, 2003), lorisiformes (…”
Background
Phylogenetic relationships among Malagasy lemurs as revealed by mitochondrial DNA sequence analysis
Pero, M. D., Crovella, S., Cervella, P., Ardito, G., & Rumpler, Y. (1995) · Primates · doi:10.1007/bf02382865 · Cited by 31 · see citing works
New strepsirrhine primate from the late Eocene of Peninsular Thailand (Krabi Basin)
Marivaux, L., Chaimanee, Y., Tafforeau, P., & Jaeger, J. (2006) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20376 · Cited by 29 · cited 1× · see citing works
“However, another interpretation suggested that Bugtilemur might be a very specialized adapiforms (Marivaux et al. 2006) and is needed more discussion.”
Background
Phylogenetic Relationships among Lemuriform Species Determined from Restriction Genomic DIMA Banding Patterns
Jung, K. Y., Crovella, S., & Rumpler, Y. (1992) · Folia Primatologica · doi:10.1159/000156634 · Cited by 28 · cited 2× · see citing works
“We followed Kielan-Jaworowska (1992) using monotremes as an outgroup for the mt-protein data and assigned 160±10mya (±: 1SE) for the Eutheria/ Marsupialia divergence (C1).”
BackgroundMethod
The coelacanth of frogs
Hedges, S. B. (2003) · Nature · doi:10.1038/425669a · Cited by 28 · see citing works
Our newest oldest ancestor?
Aiello, L. C., & Collard, M. (2001) · Nature · doi:10.1038/35069164 · Cited by 27 · see citing works
Phylogeny and Character Behavior in the Family Lemuridae
Wyner, Y. M., DeSalle, R., & Absher, R. (2000) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1999.0723 · Cited by 26 · cited 1× · see citing works
“, 1989) and DNA sequences (Del Pero et al., 1995; Yoder and Irwin, 1999; Wyner et al., 2000; Del Pero et al., 2001; Pastorini et al., 2002; Poux and Douzrey, 2004).”
Phylogenetic relationships among Lemuridae (Primates): evidence from mtDNA
Pastorini, J., Forstner, M. R. J., & Martin, R. D. (2002) · Journal of Human Evolution · doi:10.1006/jhev.2002.0587 · Cited by 25 · cited 3× · see citing works
“, 1989) and DNA sequences (Del Pero et al., 1995; Yoder and Irwin, 1999; Wyner et al., 2000; Del Pero et al., 2001; Pastorini et al., 2002; Poux and Douzrey, 2004).”
BackgroundResult
Determination of a complete lemur mitochondrial genome from feces
Matsui, A., Rakotondraparany, F., Hasegawa, M., & Horai, S. (2007) · Mammal Study · doi:10.3106/1348-6160(2007)32[7:doaclm]2.0.co;2 · Cited by 24 · cited 4× · see citing works
“Matsui et al. / Gene 441 (2009) 53–66”
BackgroundInfluentialSelf-citation
Phylogenetic relationships among Lemuridae (Primates): evidence from mtDNA
Pastorini, J. (2002) · Journal of Human Evolution · doi:10.1016/s0047-2484(02)90587-7 · Cited by 21 · see citing works
The Sinking Indian Raft: A Response to Thewissen and McKenna
Rage, J.-C., & Jaeger, J. (1995) · Systematic Biology · doi:10.1093/sysbio/44.2.260 · Cited by 20 · see citing works
Chromosomal evolution in prosimians
Rumpler, Y., Warter, S., Ishak, B., & Dutrillaux, B. (1989) · Human Evolution · doi:10.1007/bf02435444 · Cited by 17 · cited 1× · see citing works
“(Rumpler et al., 1989) and DNA sequences (Del Pero et al.”
Background
Chromosomes of lemuriformes. VI. Comparative karyology ofLemur fulvus: A g-banded karyotype ofLemur fulvus mayottensis (Schlegel 1866)
Hamilton, A. E., Tattersall, I., Sussman, R. W., & Buettner‐Janusch, J. (1980) · International Journal of Primatology · doi:10.1007/bf02692259 · Cited by 15 · cited 1× · see citing works
“fulvus subspecies (Hamilton et al., 1980).”
Perissodactyla and Proboscidea
Janis, C. M., Colbert, M. W., Coombs, M. C., Lambert, W. D., MacFadden, B. J., Mader, B. J., Prothero, D. R., Schoch, R. M., Shoshani, J., & Wall, W. P. (2010) · Cambridge University Press eBooks · doi:10.1017/cbo9780511529924.037 · Cited by 10 · see citing works

Flagged first, then by citations

Sorted by citations

A molecular phylogeny of living primates
Perelman, P., Johnson, W. E., Roos, C., Seuánez, H. N., Horvath, J. E., Moreira, M. A. M., Kessing, B., Pontius, J., Roelke, M., Rumpler, Y., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001342 · Cited by 1,414 · see citing works
Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes
Pozzi, L., Hodgson, J. A., Burrell, A. S., Sterner, K. N., Raaum, R. L., & Disotell, T. R. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.02.023 · Cited by 313 · see citing works
“As a consequence, most of the molecular studies to date employed a small set of calibration points, representing only a few nodes within the primate tree (e.g., Fabre et al., 2009; Matsui et al., 2009).”
Influential
Estimating the phylogeny and divergence times of primates using a supermatrix approach
Chatterjee, H. J., Ho, S. Y. W., Barnes, I., & Groves, C. P. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-259 · Cited by 305 · see citing works
“The oldest unambiguous primate fossil is dated at 55 million years [34,35], whereas molecular estimates often place the common primate ancestor in excess of 80 million years ago (MYA) [4,18].”
BackgroundInfluential
A Mitogenomic Phylogeny of Living Primates
Finstermeier, K., Zinner, D. P., Brameier, M., Meyer, M., Kreuz, E., Hofreiter, M., & Roos, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069504 · Cited by 266 · see citing works
Degeneration of Olfactory Receptor Gene Repertories in Primates: No Direct Link to Full Trichromatic Vision
Matsui, A., Go, Y., & Niimura, Y. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq003 · Cited by 221 · see citing works
“Recent molecular studies revealed the monophyly of haplorhines (Schmitz et al. 2001; Matsui et al. 2009), supporting the latter classification.”
ResultSelf-citation
African apes as reservoirs of Plasmodium falciparum and the origin and diversification of the Laverania subgenus
Duval, L., Fourment, M., Nerrienet, E., Rousset, D., Sadeuh‐Mba, S. A., Goodman, S. M., Andriaholinirina, N., Randrianarivelojosia, M., Paul, R. E. L., Robert, V., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005435107 · Cited by 149 · see citing works
“parasites acquired by host transfer from an evolutionary lineage that had diverged from the primate lineage before the divergence between lemurs (prosimians) and primates, which occurred before the Cretaceous/Tertiary boundary, ∼75–80 Mya (31, 32).”
BackgroundInfluential
The evolution of endothermy in Cenozoic mammals: a plesiomorphic‐apomorphic continuum
Lovegrove, B. G. (2011) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/j.1469-185x.2011.00188.x · Cited by 149 · see citing works
“Using a calibrated molecular clock phylogeny, the initial radiation of the lemuriforms and lorisiforms is estimated to have occurred 55.5 and 65.6 mya, respectively, based on protein sequences, and 35.4 and 33.1 mya, respectively, based on rRNA sequences (Matsui et al., 2009).”
BackgroundMethodInfluential
Acceleration of Olfactory Receptor Gene Loss in Primate Evolution: Possible Link to Anatomical Change in Sensory Systems and Dietary Transition
Niimura, Y., Matsui, A., & Touhara, K. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy042 · Cited by 134 · see citing works
Self-citation
The Genera and Species of Tarsiidae
Groves, C. P., & Shekelle, M. (2010) · International Journal of Primatology · doi:10.1007/s10764-010-9443-1 · Cited by 131 · see citing works
“Shekelle 2003; Shekelle et al. 2008a, 2010) have shown very deep divisions between what have now emerged as 3 species-groups, indicating that they separated from one another in the Middle or Late Miocene; more recently, Matsui et al .( 2009) provided molecular clock estimates for the split of Philippine and Western Ta…”
BackgroundInfluential
A multilocus phylogeny reveals deep lineages within African galagids (Primates: Galagidae)
Pozzi, L., Disotell, T. R., & Masters, J. C. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-72 · Cited by 93 · see citing works
“While most molecular studies have found lorises to be paraphyletic, the resolution of this node has been neither consistent nor robust [25,27,28,31,68,75,76,79].”
BackgroundInfluential
Pervasive incomplete lineage sorting illuminates speciation and selection in primates
Rivas-González, I., Rousselle, M. M. C., Li, F., Zhou, L., Dutheil, J. Y., Munch, K., Shao, Y., Wu, D., Schierup, M. H., & Zhang, G. (2023) · Science · doi:10.1126/science.abn4409 · Cited by 95 · see citing works
Are Tropical Small Mammals Physiologically Vulnerable to Arrhenius Effects and Climate Change?
Lovegrove, B. G., Canale, C. I., Levesque, D. L., Fluch, G., Řeháková‐Petrů, M., & Ruf, T. (2013) · Physiological and Biochemical Zoology · doi:10.1086/673313 · Cited by 92 · see citing works
Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons
Chan, Y.-C., Roos, C., Inoue‐Murayama, M., Inoue, E., Shih, C.-C., Pei, K. J., & Vigilant, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014419 · Cited by 91 · see citing works
Molecular Phylogenetics and Chronometrics of Tarsiidae Based on 12S mtDNA Haplotypes: Evidence for Miocene Origins of Crown Tarsiers and Numerous Species within the Sulawesian Clade
Shekelle, M., Meier, R., Wahyu, I., Wirdateti, & Ting, N. (2010) · International Journal of Primatology · doi:10.1007/s10764-010-9457-8 · Cited by 90 · see citing works
“More recently, Matsui et al. (2009) reported an even older molecular clock estimate for diversification of Philippine and Western Tarsiers, dating as far back as the Oligocene or possibly even the Eocene: 30.8±3.9 (23.4–38.6) Ma based on protein coding mtDNA, and 20.2±3.3 (14.5–27.4) Ma based on ribosomal RNA (rRNA) c…”
BackgroundResultInfluential
Remarkable ancient divergences amongst neglected lorisiform primates
Pozzi, L., Nekaris, K. A. I., Perkin, A. W., Bearder, S. K., Pimley, E. R., Schulze, H., Streicher, U., Nadler, T., Kitchener, A. C., Zischler, H., et al. (2015) · Zoological Journal of the Linnean Society · doi:10.1111/zoj.12286 · Cited by 87 · see citing works
“…with the galagids more closely related to either the Asian (Goodman et al., 1998; Yoder et al., 2001; Roos et al., 2004; Masters et al., 2007; Chatterjee et al., 2009; Matsui et al., 2009; Pozzi et al., 2014a, b) or the African lorisids (Dene et al., 1976; Finstermeier et al., 2013; this study).”
Background
Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene
Faure, É., Delaye, L., Tribolo, S., Levasseur, A., Seligmann, H., & Barthélémy, R.-M. (2011) · Biology Direct · doi:10.1186/1745-6150-6-56 · Cited by 86 · see citing works
“Divergence times (millions of years) shown are from the following references (superscripts match the corresponding nodes indicated by capital letters): [27](1), [28](2), [29](3), [30](4), [31](5), [32](6), [33](7) and [34](8).”
Background
Astragalar morphology of Afradapis, a large adapiform primate from the earliest late Eocene of Egypt
Boyer, D., Seiffert, E. R., & Simons, E. L. (2010) · American Journal of Physical Anthropology · doi:10.1002/ajpa.21328 · Cited by 83 · see citing works
Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
Meer, M. V., Kondrashov, A. S., Artzy‐Randrup, Y. A., & Kondrashov, F. A. (2010) · Nature · doi:10.1038/nature08691 · Cited by 83 · see citing works
The Evolution of Gibbons and Siamang
Reichard, U. H., Barelli, C., Hirai, H., & Nowak, M. G. (2016) · Developments in primatology · doi:10.1007/978-1-4939-5614-2_1 · Cited by 69 · see citing works
The Topographic Organization of Retinal Ganglion Cell Density and Spatial Resolving Power in an Unusual Arboreal and Slow-Moving Strepsirhine Primate, the Potto (Perodicticus potto)
Coimbra, J. P., Kaswera‐Kyamakya, C., Gilissen, E., Manger, P. R., & Collin, S. P. (2016) · Brain Behavior and Evolution · doi:10.1159/000443015 · Cited by 51 · see citing works
“…Cell Topography in the Potto (P. potto) Brain Behav Evol 2016;87:4–18 DOI: 10.1159/000443015 5 Introduction Strepsirhines (lemurs, galagos and lorisids) represent an early branch of the evolutionary radiation of primates, comprising ∼ 29% of their diversity [Mittermeier, 2013; Matsui et al., 2009].”
BackgroundInfluential
The rise and fall of a genus: Complete mtDNA genomes shed light on the phylogenetic position of yellow-tailed woolly monkeys, Lagothrix flavicauda, and on the evolutionary history of the family Atelidae (Primates: Platyrrhini)
Fiore, A. D., Chaves, P. B., Cornejo, F. M., Schmitt, C. A., Shanee, S., Cortés‐Ortiz, L., Fagundes, V., Roos, C., & Pacheco, V. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.03.028 · Cited by 51 · see citing works
Genomic data reject the hypothesis of a prosimian primate clade
Jameson, N. M., Hou, Z.-C., Sterner, K. N., Weckle, A. L., Goodman, M., Steiper, M. E., & Wildman, D. E. (2011) · Journal of Human Evolution · doi:10.1016/j.jhevol.2011.04.004 · Cited by 51 · see citing works
Phylogeny, Paleontology, and Primates: Do Incomplete Fossils Bias the Tree of Life?
Pattinson, D., Thompson, R. S., Piotrowski, A. K., & Asher, R. J. (2014) · Systematic Biology · doi:10.1093/sysbio/syu077 · Cited by 49 · see citing works
Avoidance of antisense, antiterminator tRNA anticodons in vertebrate mitochondria
Seligmann, H. (2010) · Biosystems · doi:10.1016/j.biosystems.2010.04.004 · Cited by 47 · see citing works
Evolution and biogeography of primates: a new model based on molecular phylogenetics, vicariance and plate tectonics
Heads, M. (2009) · Zoologica Scripta · doi:10.1111/j.1463-6409.2009.00411.x · Cited by 46 · see citing works
Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates
Melin, A. D., Matsushita, Y., Moritz, G. L., Dominy, N. J., & Kawamura, S. (2013) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2013.0189 · Cited by 44 · see citing works
“The genus Tarsius—represented today by a handful of species within insular Southeast Asia—belongs to a relict lineage with an origin approximately 56 Ma [2].”
Background
Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates
Janiak, M. C., Silva, F. E., Beck, R. M. D., de Vries, D., Kuderna, L. F. K., Torosin, N. S., Melin, A. D., Marquès‐Bonet, T., Goodhead, I., Messias, M. R., et al. (2022) · Molecular Ecology · doi:10.1111/mec.16554 · Cited by 40 · see citing works
Evolution, Ecology and Conservation of Lorises and Pottos
(2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526 · Cited by 37 · see citing works
Complete sequence and gene organization of the mitochondrial genome for Hubbard's sportive lemur (Lepilemur hubbardorum)
Lei, R., Shore, G. D., Brenneman, R. A., Engberg, S. E., Sitzmann, B. D., Bailey, C. A., Kimmel, L. M., Randriamampionona, R., Ranaivoarisoa, J. F., & Louis, E. E. (2010) · Gene · doi:10.1016/j.gene.2010.06.001 · Cited by 35 · see citing works
“Gene distributions for L. hubbardorumwere similar to the eight other lemur mitochondrial genomes (Arnason et al., 2002, 2008; Matsui et al., 2007, 2009) with all of the genes encoded on the H-strand, except for ND6 subunit gene and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr,…”
BackgroundMethodInfluential
Lumbar Vertebral Body Bone Microstructural Scaling in Small to Medium‐Sized Strepsirhines
Fajardo, R. J., DeSilva, J. M., Manoharan, R. K., Schmitz, J. E., MacLatchy, L., & Bouxsein, M. (2013) · The Anatomical Record · doi:10.1002/ar.22632 · Cited by 33 · see citing works
“The phylogenetic information and branch lengths for the analysis were culled from several sources, including Yoder (2004), Chatterjee (2009), Seiffert et al. (2003), Seiffert (2007), Masters et al. (2007), Smith and Cheverud (2002), Matsui et al. (2009), and Purvis (1995).”
Method
A Single Origin of Heterothermy in Mammals
Lovegrove, B. G. (2012) · Springer eBooks · doi:10.1007/978-3-642-28678-0_1 · Cited by 32 · see citing works
“Anthropoidea within Haplorrhini (Matsui et al. 2009). However, Rosa et al. (1996)”
BackgroundInfluential
Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data
Chan, Y.-C., Roos, C., Inoue‐Murayama, M., Inoue, E., Shih, C.-C., Pei, K. J., & Vigilant, L. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-82 · Cited by 33 · see citing works
“5 million years [15,92-94] and an assumed generation time of 15 years.”
Background
The evolution of mammalian body temperature: the Cenozoic supraendothermic pulses
Lovegrove, B. G. (2012) · Journal of Comparative Physiology B · doi:10.1007/s00360-011-0642-7 · Cited by 30 · see citing works
Organization of cholinergic, catecholaminergic, serotonergic and orexinergic nuclei in three strepsirrhine primates: Galago demidoff , Perodicticus potto and Lemur catta
Calvey, T., Patzke, N., Kaswera‐Kyamakya, C., Gilissen, E., Bertelsen, M. F., Pettigrew, J. D., & Manger, P. R. (2015) · Journal of Chemical Neuroanatomy · doi:10.1016/j.jchemneu.2015.10.002 · Cited by 28 · see citing works
“Strepsirrhines and, among the haplorhines, the Tarsiidae whose unique extant representative are the tarsiers, appear to have retained several plesiomorphic features of stem primates (Matsui et al., 2009; Rosa et al., 1996) .”
Background
Structural characterization of neutral and acidic oligosaccharides in the milks of strepsirrhine primates: greater galago, aye-aye, Coquerel’s sifaka and mongoose lemur
Taufik, E., Fukuda, K., Senda, A., Saito, T., Williams, C. V., Tilden, C., Eisert, R., Oftedal, O. T., & Urashima, T. (2012) · Glycoconjugate Journal · doi:10.1007/s10719-012-9370-9 · Cited by 27 · see citing works
“Nonetheless, type I oligosaccharide concentrations are clearly elevated in hominids, and become dominant in human milk, suggesting that evolutionary factors favoring type I oligosaccharides came into play early in hominid evolution and particularly after the divergence of humans from chimpanzees 6–7 mya [15, 38] The e…”
Background
Evolutionary Origins of Primate Vocal Communication: Diversity, Flexibility, and Complexity of Vocalizations in Basal Primates
Zimmermann, E. (2017) · Springer handbook of auditory research · doi:10.1007/978-3-319-59478-1_5 · Cited by 23 · see citing works
Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii
Schultz, D. T., Eizenga, J. M., Corbett-Detig, R. B., Francis, W. R., Christianson, L. M., & Haddock, S. H. D. (2020) · PeerJ · doi:10.7717/peerj.8356 · Cited by 23 · see citing works
Molecular Phylogenetic Relationships and Unveiling Novel Genetic Diversity among Slow and Pygmy Lorises, including Resurrection of Xanthonycticebus intermedius
Blair, M., Cao, G. T. H., López-Nandam, E. H., Veronese-Paniagua, D. A., Birchette, M. G., Kenyon, M., Md-Zain, B. M., Munds, R. A., Nekaris, K. A., Nijman, V., et al. (2023) · Genes · doi:10.3390/genes14030643 · Cited by 21 · see citing works
“tardigradus Red slender loris NC012763 Outgroup [54] NC012763”
Evolution of testis‐specific kinases TSSK 1B and TSSK 2 in primates
Shang, P., Hoogerbrugge, J. W., Baarends, W. M., & Grootegoed, J. A. (2012) · Andrology · doi:10.1111/j.2047-2927.2012.00021.x · Cited by 22 · see citing works
“From the above, we suggest that the TSSK branch of CaMK enzymes originated in the ancestor of all amniotes (birds, reptiles and mammals) after diversification of amphibians and amniotes, more than 300 MYA (million years ago).”
BackgroundInfluential
Phylogenetic Position of Tarsius bancanus Based on Partial Cytochrome b DNA Sequences
Md‐Zain, B. M., Lee, S. J., Lakim, M., Ampeng, A., & Mahani, M. C. (2010) · Journal of Biological Sciences · doi:10.3923/jbs.2010.348.354 · Cited by 22 · see citing works
The lemur revolution starts now: The genomic coming of age for a non-model organism
Yoder, A. D. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.08.024 · Cited by 18 · see citing works
“Similarly, it has been suggested that an island chain spanning the distance from Africa to Madagascar via the Davie Ridge may have offered opportunities for at least partially-terrestrial dispersal routes (Mccall, 1997).”
Mitogenomics of the family Cheirogaleidae and relationships to taxonomy and biogeography in Madagascar
Louis, E. E., & Lei, R. (2016) · Cambridge University Press eBooks · doi:10.1017/cbo9781139871822.004 · Cited by 16 · see citing works
Contrasting Evolutionary Dynamics of the Developmental Regulator PAX9, among Bats, with Evidence for a Novel Post-Transcriptional Regulatory Mechanism
Phillips, C. D., Butler, B., Fondon, J. W., Mantilla-Meluk, H., & Baker, R. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057649 · Cited by 16 · see citing works
Home Range, Activity Budgets and Habitat Use in the Bengal Slow Loris (Nycticebus bengalensis) in Bangladesh
Al-Razi, H., Hasan, S., Ahmed, T., & Muzaffar, S. B. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.019 · Cited by 14 · see citing works
Conserved sequences identify the closest living relatives of primates
Zhang, M., Li, M., Ayoola, A. O., Murphy, R. W., Wu, D., & Shao, Y. (2019) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2019.057 · Cited by 14 · see citing works
“We estimated divergence time using MCMCtree (dos Reis & Yang, 2011; Yang, 2007), with five fossil calibration points used to determine approximate likelihood calculations (Fan et al., 2013; Franzen et al., 2009; Matsui et al., 2009; Poux & Douzery, 2004; Vignaud et al., 2002).”
BackgroundMethodInfluential
Milk composition of captive vervet monkey (Chlorocebus pygerythrus) and rhesus macaque (Macaca mulatta) with observations on gorilla (Gorilla gorilla gorilla) and white handed gibbon (Hylobates lar)
Osthoff, G., Hugo, A., de Wit, M., Nguyen, T. P. M., & Seier, J. V. (2009) · Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology · doi:10.1016/j.cbpb.2008.12.015 · Cited by 14 · see citing works
The Use (and Misuse) of Phylogenetic Trees in Comparative Behavioral Analyses
Pozzi, L., Bergey, C. M., & Burrell, A. S. (2013) · International Journal of Primatology · doi:10.1007/s10764-013-9701-0 · Cited by 13 · see citing works
“…primate phylogenetic relationships, from the genus (Chiou et al. 2011; Meyer et al. 2011; Zinner et al. 2013), family (Chan et al. 2010; Raaum et al. 2005; Sterner et al. 2006), or even higher taxonomic levels (Arnason et al. 2008; Finstermeier et al. 2013; Hodgson et al. 2009; Matsui et al. 2009).”
Background
Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs
Canuti, M., Williams, C. V., Sagan, S. M., Munnink, B. B. O., Gadi, S. V., Verhoeven, J. T. P., Kellam, P., Cotten, M. L., Lang, A. S., Junge, R. E., et al. (2018) · Archives of Virology · doi:10.1007/s00705-018-4099-9 · Cited by 13 · see citing works
Phylogenomic Reconstruction of Sportive Lemurs (genusLepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography
Lei, R., Frasier, C. L., Hawkins, M. T. R., Engberg, S. E., Bailey, C. A., Johnson, S. E., McLain, A. T., Groves, C. P., Perry, G. H., Nash, S. D., et al. (2016) · Journal of Heredity · doi:10.1093/jhered/esw072 · Cited by 12 · see citing works
Locomotion and Posture in Ancestral Hominoids Prior to the Split of Hylobatids
Nowak, M. G., & Reichard, U. H. (2016) · Developments in primatology · doi:10.1007/978-1-4939-5614-2_3 · Cited by 11 · see citing works
Comparative Morphological Configuration of the Cardiac Nervous System in Lorises and Galagos (Infraorder Lorisiformes, Strepsirrhini, Primates) with Evolutionary Perspective
Kawashima, T., & Thorington, R. W. (2011) · The Anatomical Record · doi:10.1002/ar.21334 · Cited by 11 · see citing works
“…studies, divergence dates were estimated as follows for the crown groups: about 35.4 million years ago (mya) for Lorisiformes (Galagidae/Lorisidae), 55.3 mya for Aye-aye (Daubentonidae/ Lemuriformes), and 64.5 mya for Strepsirrhini (Lorisiformes/Daubentonidae-Lemuriformes; Matsui et al., 2009).”
BackgroundInfluential
Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements
Arab, M. A., Bernt, M., zu Siederdissen, C. H., Tout, K. R., & Stadler, P. F. (2017) · Algorithms for Molecular Biology · doi:10.1186/s13015-017-0113-0 · Cited by 10 · see citing works
“Species Accessions ̄̀ Literature Type Reference Maulisia mauli Normichthys operosus NC 011007 NC 011009 127 TDRL [10] Phaeognathus hubrichti Hydromantes brunus NC 006344 NC 006345 66 no duplication TDRL [38] [39] Galaxias maculatus Galaxiella nigrostriata NC 004594 NC 008448 62 duplication deletion [10] Jordanella flo…”
Background
The Toothcomb ofKaranisia clarki
López‐Torres, S., Selig, K., Burrows, A. M., & Silcox, M. T. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.008 · Cited by 9 · see citing works
Control Region Length Dynamics Potentially Drives Amino Acid Evolution in Tarsier Mitochondrial Genomes
Merker, S., Thomas, S. A., Völker, E., Perwitasari‐Farajallah, D., Feldmeyer, B., Streit, B., & Pfenninger, M. (2014) · Journal of Molecular Evolution · doi:10.1007/s00239-014-9631-2 · Cited by 9 · see citing works
New Insights on the Evolution of the Sweet Taste Receptor of Primates Adapted to Harsh Environments
Tamrin, N. A. M., Zainudin, R., Esa, Y. B., Alias, H., Isa, M. N. M., Croft, L., & Abdullah, M. T. (2020) · Animals · doi:10.3390/ani10122359 · Cited by 8 · see citing works
“Divergence (Node) [33] [34] [35] [20] [36] [37] [19] [22] [38]”
Importance of synonymous substitutions under dense taxon sampling and appropriate modeling in reconstructing the mitogenomic tree of Eutheria
Wu, J., Hasegawa, M., Zhong, Y., & Yonezawa, T. (2014) · Genes & Genetic Systems · doi:10.1266/ggs.89.237 · Cited by 8 · see citing works
“S7) gave a sister group relationship of Dermoptera to Simiiformes as in previous mitogenome analyses, and a sister group relationship of Tarsiidae to the clade formed by Dermoptera and Simiiformes.”
BackgroundMethodInfluential
What We Know (and Don’t Know) About the Fossil Records of Lorisids
López‐Torres, S., & Silcox, M. T. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.005 · Cited by 7 · see citing works
Molecular Evidence on Primate Origins and Evolution
Raaum, R. L. (2014) · Springer eBooks · doi:10.1007/978-3-642-39979-4_85 · Cited by 7 · see citing works
The Evolution of Social Organisation in Lorisiformes
Poindexter, S. A., & Nekaris, K. A. I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.012 · Cited by 7 · see citing works
Searching for the Haplorrhine Heterotherm: Field and Laboratory Data of Free-Ranging Tarsiers
Welman, S., Tuen, A. A., & Lovegrove, B. G. (2017) · Frontiers in Physiology · doi:10.3389/fphys.2017.00745 · Cited by 6 · see citing works
“With regards to their phylogeny, their position has been hotly debated and shuffled around the primate tree (Schwartz, 1984; Schmitz et al., 2001; Meireles et al., 2003; Simons, 2003; Yoder, 2003; Matsui et al., 2009; Perelman et al., 2011).”
Background
Trapping, Collaring and Monitoring the Lorisinae of Asia (Loris,Nycticebus) and Perodicticinae (Arctocebus,Perodicticus) of Africa
Nekaris, K. A. I., Munds, R. A., & Pimley, E. R. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.028 · Cited by 6 · see citing works
Molecular Advances in Lorisid Taxonomy and Phylogeny
Pozzi, L., Roos, C., & Blair, M. E. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.007 · Cited by 6 · see citing works
Molecular Phylogeny and Evolution in Primates
Matsui, A., & Hasegawa, M. (2011) · Primatology monographs · doi:10.1007/978-4-431-54011-3_16 · Cited by 6 · see citing works
Self-citation
Ranging Patterns of the Pygmy Slow Loris (Nycticebus pygmaeus) in a Mixed Deciduous Forest in Eastern Cambodia
Starr, C., & Nekaris, K. A. I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.023 · Cited by 5 · see citing works
Systematic and comparative morphologies of the extrinsic cardiac nervous system in lemurs (Primates: Strepsirrhini: Infraorder Lemuriformes, Gray, 1821) with evolutionary morphological implications
Kawashima, T., Thorington, R. W., & Sato, F. (2012) · Zoologischer Anzeiger · doi:10.1016/j.jcz.2012.04.001 · Cited by 5 · see citing works
“In the other strepsirrhines, the lemurs are divided into four families (Lemuriformes) and the Aye-aye alone constitutes its own family (Daubentoniidae), according to the most well-known standard classification (Groves, 2005); this has been confirmed by recent molecular evolutionary studies (Horvath et al., 2008; Matsu…”
BackgroundResultInfluential
Correction: Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons
Chan, Y.-C., Roos, C., Inoue‐Murayama, M., Inoue, E., Shih, C.-C., Pei, K. J., & Vigilant, L. (2013) · PLoS ONE · doi:10.1371/annotation/9ca325c6-7a42-4cfd-9085-125571708b5c · Cited by 5 · see citing works
Evolutionary transformation of the cervicobrachial plexus in the colugo (Cynocephalidae: Dermoptera) with a comparison to treeshrews (Tupaiidae: Scandentia) and strepsirrhines (Strepsirrhini: Primates).
Kawashima, T., Murakami, K., Takayanagi, M., & Sato, F. (2012) · PubMed · Cited by 4 · see citing works
Distribution and Conservation Status of Slow Lorises in Indo-China
Ni, Q., He, X., Wang, Y., & Meng, X. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.032 · Cited by 4 · see citing works
The whole mitochondrial genome of the Cynomolgus macaque(Macaca fascicularis)
Li, R., Wang, H., Yang, L.-Q., Zhang, B., Li, Y., Hu, J., & Kong, Q. (2013) · Mitochondrial DNA · doi:10.3109/19401736.2013.825777 · Cited by 4 · see citing works
“…Anthropoidea, Primates, and it has the closest genetic affinity with Macaca mulutta, followed by Macaca thibetana with NJ and ML analyses (Figure 1), this was in line with the taxonomy system based on different markers (Chatterjee et al., 2009; Matsui et al., 2009; Perelman et al., 2011).”
Result
The complete mitochondrial genome sequence of the black-capped capuchin (Cebus apella)
Bi, X., Huang, L., Jing, M., Zhang, L., Feng, P.-Y., & Wang, A. (2012) · Genetics and Molecular Biology · doi:10.1590/s1415-47572012005000034 · Cited by 4 · see citing works
“This size is intermediate to that of other primate mitogenomes (Matsui et al., 2009; Matsudaira and Ishida, 2010; Roos et al., 2011), with the longest being 17,149 bp (Eulemur macaco) (Matsui et al., 2009) and the shortest being 15,467 bp (Pygathrix nemaeus) (Roos et al., 2011).”
Background
Molecular Evidence of Primate Origins and Evolution
Raaum, R. L. (2013) · Springer eBooks · doi:10.1007/978-3-642-27800-6_85-1 · Cited by 4 · see citing works
“Four estimates from studies with questionable calibration, based mostly or solely on mtDNA sequence data, or with limited calibration within the primates can probably be dismissed out of hand (Bininda-Emonds et al. 2007; Fabre et al. 2009; Matsui et al. 2009; Perelman et al. 2011).”
BackgroundInfluential
The Soft-Tissue Anatomy of the Highly Derived Hand ofPerodicticusRelative to the More GeneralisedNycticebus
Boettcher, M. L., Leonard, K. C., Herrel, A., & Hartstone‐Rose, A. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.009 · Cited by 4 · see citing works
What Role Did Gum-Feeding Play in the Evolution of the Lorises?
Burrows, A. M., Nash, L. T., Hartstone‐Rose, A., Selig, K., Silcox, M. T., & López‐Torres, S. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.014 · Cited by 3 · see citing works
Characterization of the complete mitochondrial genome of the Macaroni penguin Eudyptes chrysolophus from the Barton Peninsula, King George Island, Antarctica
Kim, J.-U., & Kim, J.-H. (2021) · Mitochondrial DNA Part B · doi:10.1080/23802359.2021.1888329 · Cited by 3 · see citing works
“Complete mitochondrial genomes provide baseline information to understand genomic evolution and facilitate phylogenetic inference (Matsui et al. 2009) and taxonomic clarifications (Sebastian et al. 2018).”
Background
Exploring objective feature sets in constructing the evolution relationship of animal genome sequences
Li, X., Li, H., Yang, Z., Wu, Y., & Zhang, M. (2023) · BMC Genomics · doi:10.1186/s12864-023-09747-x · Cited by 3 · see citing works
“3A), the evolution relationship is consistent with the known conclusions about the evolution relationships of primates [43–46].”
Result
Positional Behaviour and Substrate Preference of Slow Lorises, with a Case Study ofNycticebus bengalensisin Northeast India
Das, N., & Nekaris, K. A. I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.021 · Cited by 4 · see citing works
Evolutionary Anatomy and Phyletic Implication of the Extrinsic Cardiac Nervous System in the Philippine Tarsier (Tarsius syrichta, Primates) in Comparisons With Strepsirrhines and New World Monkeys
Kawashima, T., Thorington, R. W., Murakami, K., & Sato, F. (2013) · The Anatomical Record · doi:10.1002/ar.22680 · Cited by 3 · see citing works
“Recent molecular phylogenetic studies have placed Tarsiers as the sister group of Strepsirrhini (with lemurs and lorises) (Arnason et al., 2008; Chatterjee et al., 2009) and of anthropoids (Matsui et al., 2009; Jameson et al., 2011; Meredith et al., 2011) (Table 1).”
Background
Husbandry and Reproductive Management Recommendations for Captive Lorises and Pottos (Nycticebus,LorisandPerodicticus)
Fitch‐Snyder, H. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.026 · Cited by 4 · see citing works
Fijaciones de los músculos caudo-mediales del antebrazo de primates: una revisión y adaptación a la terminología anatómica veterinaria
García, J. F. V., & Castañeda-Herrera, F. E. (2016) · Boletín Científico Centro de Museos Museo de Historia Natural · doi:10.17151/bccm.2016.20.1.10 · Cited by 3 · see citing works
Phylogenetic Position of North Sulawesi Tarsius sp. Based on Partial Cytochrome b Gene Sequences
Kamagi, D. D. W., Corebima, A. D., & Rengkuan, M. (2014) · Open Journal of Genetics · doi:10.4236/ojgen.2014.44030 · Cited by 2 · see citing works
Wildlife Trade Research Methods
Bergin, D., & Nijman, V. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.033 · Cited by 2 · see citing works
Using Accelerometers to Measure Nocturnal Primate Behaviour
Reinhardt, K. D., Campera, M., & Nekaris, K. A. I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.031 · Cited by 2 · see citing works
Thermoregulation in Lorises
Streicher, U., & Reinhardt, K. D. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.018 · Cited by 2 · see citing works
Evaluation of Field Techniques Used to Assess Populations of Pottos and Lorises
Kumara, H. N. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.029 · Cited by 2 · see citing works
Sexual Differences in Feeding and Foraging of Released Philippine Slow Loris (Nycticebus menagensis)
Anirudh, N. B., Brown, E. R., Sánchez, K. L., & Irpiandi, I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.022 · Cited by 2 · see citing works
Slow Lorises (Nycticebusspp.) as Photo Props on Instagram
Kitson, H., & Nekaris, K. A. I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.035 · Cited by 2 · see citing works
Seeing in the Dark
Veilleux, C. C. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.017 · Cited by 2 · see citing works
Whence and Whither: Acoustic Variability and Biogeography of Tarsiers in North Sulawesi
Kulander, O. (2000) · doi:10.15760/etd.6253 · Cited by 2 · see citing works
Outliers
Muchlinski, M. N., Hemingway, H. W., Grant, R. A., & Burrows, A. M. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.006 · Cited by 1 · see citing works
MakingScentsof Olfactory Sensitivity in Lorises and Pottos
Lundeen, I. K. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.010 · Cited by 1 · see citing works
Integrating Science and Puppetry to Inspire Teenagers in Rural Asia to Value Slow Lorises
Cardinal, C., Beasley, L., Kenyon, M., Imron, M. A., & Nekaris, K. A. I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.036 · Cited by 1 · see citing works
Mother–Infant Behaviours in Greater Slow Loris (Nycticebus coucang) Dyads Consisting of Mothers Pregnant at Confiscation and Their Sanctuary-Born Infants
Fuller, G. A., Eggen, W. F., Wirdateti, W., & Nekaris, K. A. I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.025 · Cited by 1 · see citing works
Nutrition of Lorisiformes
Cabana, F. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.016 · Cited by 2 · see citing works
Online Imagery and Loris Conservation
Feddema, K., & Nekaris, K. A. I. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.034 · Cited by 1 · see citing works
Developing a Rescue and Rehabilitation Centre as a Reaction to the Extensive Illegal Wildlife Trade in Slow Lorises
Příbrský, F. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.037 · Cited by 1 · see citing works
Evolutionary transformation of the cervicobrachial plexus in the colugo (Cynocephalidae: Dermoptera) with a comparison to treeshrews (Tupaiidae: Scandentia) and strepsirrhines (Strepsirrhini: Primates) What is the most important factor related to the specialised morphology of the cervicobrachial plexus in the colugo: its gliding locomotion, phylogenetic constraint, or semi-elongated neck?
Kawashima, T., Murakami, K., Takayanagi, M., & Sato, F. (2012) · Folia Morphologica
Studies on the transcriptional regulation of human sex hormone-binding globulin in testicular germ cells : mechanistic and evolutionary insights
Meyers, W. M. (2016) · cIRcle (University of British Columbia) · doi:10.14288/1.0308668
“(Ma) [185], [201], [202] or before 81-82 Ma [185], [203], [204].”
Testis-specific Protein Kinases TSSK1 and TSSK2 in Mouse Spermiogenesis
Shang, P. (2014) · RePub (Erasmus University Rotterdam)
Partial mtDNA sequencing data of vulnerable Cephalopachus bancanus from the Malaysian Borneo
Zahidin, M. A., Jalil, N. A., Naharuddin, N. M., Mohd‐Ridwan, A. R., Gani, M., & Abdullah, M. T. (2019) · Data in Brief · doi:10.1016/j.dib.2019.104133
“bancanus Western tarsier AB011077 [6] 4 Carlito syrichta Philippine's tarsier AB371090 [7] 5 C.”
Background
Sluggards and Drunkards?
Masters, J. C. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108676526.004

Genomic data reject the hypothesis of a prosimian primate clade
Jameson, N. M., Hou, Z.-C., Sterner, K. N., Weckle, A. L., Goodman, M., Steiper, M. E., & Wildman, D. E. (2011) · Journal of Human Evolution · doi:10.1016/j.jhevol.2011.04.004 · Cited by 51 · see citing works
Molecular evidence on Primate phylogeny from DNA sequences
Goodman, M., Baileym, W. J., Hayasaka, K., Stanhope, M. J., Slightom, J. L., & Czelusniak, J. (1994) · American Journal of Physical Anthropology · doi:10.1002/ajpa.1330940103 · Cited by 68 · see citing works
Estimating the phylogeny and divergence times of primates using a supermatrix approach
Chatterjee, H. J., Ho, S. Y. W., Barnes, I., & Groves, C. P. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-259 · Cited by 305 · see citing works
Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes
Pozzi, L., Hodgson, J. A., Burrell, A. S., Sterner, K. N., Raaum, R. L., & Disotell, T. R. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.02.023 · Cited by 313 · see citing works
A Mitogenomic Phylogeny of Living Primates
Finstermeier, K., Zinner, D. P., Brameier, M., Meyer, M., Kreuz, E., Hofreiter, M., & Roos, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069504 · Cited by 266 · see citing works

Authors: Matsui, A., Rakotondraparany, F., Munechika, I., Hasegawa, M., & Horai, S.
Affiliations: The Graduate University for Advanced Studies, SOKENDAI (JP)
University of Antananarivo (MG)
Research Institutue of Evolutionary Biology (JP)
Corresponding author: Matsui, Atsushi
ORCID: Hasegawa, Masami
Venue: Gene
Publisher: Elsevier BV
Published: 2009-07
Volume: 441
Issue: 1-2
Pages: 53-66
ISSN: 0378-1119 (ISSN-L)
DOI: 10.1016/j.gene.2008.08.024
OpenAlex: W2033726375
Cited by: 121
References: 139
Citations by year: 2024: 5 · 2023: 3 · 2022: 1 · 2021: 2 · 2020: 42 · 2019: 2 · 2018: 3 · 2017: 3 · 2016: 7 · 2015: 2 · 2014: 10 · 2013: 12 · 2012: 9
FWCI: 4.79
Type: journal article
Language: en
Open access: green
ir.soken.ac.jp
Licence: cc-by-nc-nd
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Gene (publishedVersion)
PubMed (publishedVersion)
SOKENDAI (Graduate University for Advanced Studies) (submittedVersion, cc-by-nc-nd)
Institutional Repositories DataBase (IRDB) (submittedVersion, cc-by-nc-nd)
Funders: Research Organization of Information and Systems
University of Tokyo
Japan Society for the Promotion of Science
Topics: Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Social Sciences › Psychology › Social Psychology › Primate Behavior and Ecology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: prosimians, primate phylogeny, mitochondrial DNA, tarsiers, lemurs, lorises, Strepsirrhini, Haplorhini, divergence time estimation, base composition bias, biogeography, Platyrrhini
MeSH terms: Animals, Base Composition, Base Sequence, Bayes Theorem, DNA, Mitochondrial, Biological Evolution, Humans, Molecular Sequence Data, Phylogeny, Primates, Genetic Speciation

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs.

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Cites

Cited by

Related

Record

About these checks