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Abdul-Latiff MAB, Md-Zain BM. Taxonomy, Evolutionary and Dispersal Events of Pig-Tailed Macaque, Macaca nemestrina (Linnaeus, 1766) in Southeast Asia with Description of a New Subspecies, Macaca nemestrina perakensis in Malaysia. Zool Stud 2021; 60:e50. [PMID: 35003344 PMCID: PMC8685347 DOI: 10.6620/zs.2021.60-50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 06/06/2021] [Indexed: 01/24/2023]
Abstract
The pig-tailed macaque, Macaca nemestrina, which is distributed in Peninsular Malaysia, Thailand, Borneo, and Sumatra, has been the subject of unstable and changing taxonomic entity in the M. nemestrina group. This species is involved with a human-macaque conflict in Malaysia and at the same time played an important role in the ethnozoological culture of Malaysian. Even so, comprehensive phylogenetic, population genetics and biogeographical analysis of M. nemestrina in Malaysia are non-existent after decades of intensive research on the genus itself. Thus, we conducted the first comprehensive genetic study of M. nemestrina in Malaysia, based on three mitochondrial loci-Cytochrome b (567 bp), D-loop (398 bp), and COI (577 bp)-from 27 individuals representing Malaysia, plus an additional 26 sequences of Southeast Asian macaques from Genbank. Comparative biogeographical analysis in this study supports the positions of M. nemestrina in M. nemestrina groups as opposed to the silenus or Sulawesi groups. Results from this study also indicate that Bornean populations are the first extant lineages to separate from the other examined lineages of M. nemestrina, M. leonina, M. pagensis, and M. siberu in Southeast Asia. Molecular clock analysis suggested that M. nemestrina arrived in the Malay Peninsula about 0.32 million years ago (MYA). Our results indicate that the population of pig-tailed macaque from Perak (west Peninsular Malaysia) differs genetically based on all phylogenetic and population genetic analyses. Morphologically, Perak's pig-tailed macaque shows brighter coloration than M. n. nemestrina. Thus, we proposed a new subspecies for Perak's pig-tailed macaque as Macaca nemestrina perakensis distributed in the state of Perak, Peninsular Malaysia. This research helps resolve the taxonomic position and population genetics of pig-tailed macaque in Malaysia, which contribute directly to conservation and management of the species in Malaysia.
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Affiliation(s)
- Muhammad Abu Bakar Abdul-Latiff
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. E-mail: (Md-Zain); or (Abdul-Latiff
- Oasis Integrated Group (OIG), Institute for Integrated Engineering (I2E), Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Johor, Malaysia
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84600, Muar, Johor, Malaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. E-mail: (Md-Zain); or (Abdul-Latiff
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Osada N, Matsudaira K, Hamada Y, Malaivijitnond S. Testing Sex-Biased Admixture Origin of Macaque Species Using Autosomal and X-Chromosomal Genomic Sequences. Genome Biol Evol 2021; 13:evaa209. [PMID: 33045051 PMCID: PMC8631084 DOI: 10.1093/gbe/evaa209] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 11/22/2022] Open
Abstract
The role of sex-specific demography in hybridization and admixture of genetically diverged species and populations is essential to understand the origins of the genomic diversity of sexually reproducing organisms. In order to infer how sex-linked loci have been differentiated undergoing frequent hybridization and admixture, we examined 17 whole-genome sequences of seven species representing the genus Macaca, which shows frequent inter-specific hybridization and predominantly female philopatry. We found that hybridization and admixture were prevalent within these species. For three cases of suggested hybrid origin of species/subspecies, Macaca arctoides, Macaca fascicularis ssp. aurea, and Chinese Macaca mulatta, we examined the level of admixture of X chromosomes, which is less affected by male-biased migration than that of autosomes. In one case, we found that Macaca cyclopis and Macaca fuscata was genetically closer to Chinese M. mulatta than to the Indian M. mulatta, and the admixture level of Chinese M. mulatta and M. fuscata/cyclopis was more pronounced on the X chromosome than on autosomes. Since the mitochondrial genomes of Chinese M. mulatta, M. cyclopis, and M. fuscata were found to cluster together, and the mitochondrial genome of Indian M. mulatta is more distantly related, the observed pattern of genetic differentiation on X-chromosomal loci is consistent with the nuclear swamping hypothesis, in which strong, continuous male-biased introgression from the ancestral Chinese M. mulatta population to a population related to M. fuscata and M. cyclopis generated incongruencies between the genealogies of the mitochondrial and nuclear genomes.
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Affiliation(s)
- Naoki Osada
- Faculty of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kazunari Matsudaira
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- Unit of Human Biology and Genetics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Department of Evolution and Phylogeny, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Suchinda Malaivijitnond
- Department of Biology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi Province, Thailand
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Mitogenomics of macaques (Macaca) across Wallace's Line in the context of modern human dispersals. J Hum Evol 2020; 146:102852. [DOI: 10.1016/j.jhevol.2020.102852] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/28/2020] [Accepted: 06/28/2020] [Indexed: 11/17/2022]
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Bodrov SY, Vasiljeva VK, Okhlopkov IM, Mamayev NV, Zakharov ES, Oleinikov AY, Genelt-Yanovskiy EA, Abramson NI. Evolutionary history of mountain voles of the subgenus Aschizomys (Cricetidae, Rodentia), inferred from mitochondrial and nuclear markers. Integr Zool 2019; 15:187-201. [PMID: 31631516 DOI: 10.1111/1749-4877.12415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we present an assessment of the evolutionary history and phylogenetic relationships of Asian mountain voles of the subgenus Aschizomys, genus Alticola, based on extensive sampling and phylogenetic analyses of data from mitochondrial and nuclear markers. Two species of this subgenus are widespread in the mountain areas of north-eastern Asia. However, both their distribution and taxonomic borders remained questionable for more than 100 years. Our study showed discordance in the phylogenetic patterns between nuclear and mtDNA markers. We found that mtDNA in A. lemminus is paraphyletic relative to A. macrotis, but nuclear markers demonstrated reciprocal monophyly. According to species distribution modeling, ranges of A. macrotis and A. lemminus experienced a secondary contact during the Last Glacial Maximum (approximately 22 kyr BP), and thus a hybridization event seems plausible during that period. Species tree analyses recovered a sister group relationship between the two species of the Aschizomys subgenus, with an estimated divergence date of around 0.8 Ma. Our results provided good support for currently recognized subspecies within both A. macrotis and A. lemminus based on mitochondrial and nuclear datasets. A new, yet undescribed form, supposedly of a subspecific status within A. lemminus, was found in the Bureinskiy Range in the Khabarovsk area. This finding expands the current species distribution range further to the southeast.
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Affiliation(s)
- Semen Yu Bodrov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Vera K Vasiljeva
- Institute for Biological Problems of Cryolithozone, Yakutsk, Sakha Republic (Yakutia), Russia
| | - Innokentiy M Okhlopkov
- Institute for Biological Problems of Cryolithozone, Yakutsk, Sakha Republic (Yakutia), Russia
| | - Nikolai V Mamayev
- Institute for Biological Problems of Cryolithozone, Yakutsk, Sakha Republic (Yakutia), Russia
| | - Evgeniy S Zakharov
- Institute for Biological Problems of Cryolithozone, Yakutsk, Sakha Republic (Yakutia), Russia
| | | | | | - Natalia I Abramson
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia.,Saint-Petersburg Scientific Center RAS, Saint Petersburg, Russia
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Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A, Melnick DJ. Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170351. [PMID: 29134059 PMCID: PMC5666242 DOI: 10.1098/rsos.170351] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/18/2017] [Indexed: 05/30/2023]
Abstract
Many genera of terrestrial vertebrates diversified exclusively on one or the other side of Wallace's Line, which lies between Borneo and Sulawesi islands in Southeast Asia, and demarcates one of the sharpest biogeographic transition zones in the world. Macaque monkeys are unusual among vertebrate genera in that they are distributed on both sides of Wallace's Line, raising the question of whether dispersal across this barrier was an evolutionary one-off or a more protracted exchange-and if the latter, what were the genomic consequences. To explore the nature of speciation over the edge of this biogeographic divide, we used genomic data to test for evidence of gene flow between macaque species across Wallace's Line after macaques colonized Sulawesi. We recovered evidence of post-colonization gene flow, most prominently on the X chromosome. These results are consistent with the proposal that gene flow is a pervasive component of speciation-even when barriers to gene flow seem almost insurmountable.
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Affiliation(s)
- Ben J. Evans
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S4K1
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th floor Schermerhorn Extension, 119th Street and Amsterdam Avenue, New York, NY 10027, USA
| | - Anthony J. Tosi
- Anthropology Department, Kent State University, 238 Lowry Hall, Kent, OH 44242, USA
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Jonathan Dushoff
- Biology Department, Life Sciences Building Room 328, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S4K1
| | - André Corvelo
- New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Don J. Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th floor Schermerhorn Extension, 119th Street and Amsterdam Avenue, New York, NY 10027, USA
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Ghenu AH, Bolker BM, Melnick DJ, Evans BJ. Multicopy gene family evolution on primate Y chromosomes. BMC Genomics 2016; 17:157. [PMID: 26925773 PMCID: PMC4772468 DOI: 10.1186/s12864-015-2187-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022] Open
Abstract
Background The primate Y chromosome is distinguished by a lack of inter-chromosomal recombination along most of its length, extensive gene loss, and a prevalence of repetitive elements. A group of genes on the male-specific portion of the Y chromosome known as the “ampliconic genes” are present in multiple copies that are sometimes part of palindromes, and that undergo a form of intra-chromosomal recombination called gene conversion, wherein the nucleotides of one copy are homogenized by those of another. With the aim of further understanding gene family evolution of these genes, we collected nucleotide sequence and gene copy number information for several species of papionin monkey. We then tested for evidence of gene conversion, and developed a novel statistical framework to evaluate alternative models of gene family evolution using our data combined with other information from a human, a chimpanzee, and a rhesus macaque. Results Our results (i) recovered evidence for several novel examples of gene conversion in papionin monkeys and indicate that (ii) ampliconic gene families evolve faster than autosomal gene families and than single-copy genes on the Y chromosome and that (iii) Y-linked singleton and autosomal gene families evolved faster in humans and chimps than they do in the other Old World Monkey lineages we studied. Conclusions Rapid evolution of ampliconic genes cannot be attributed solely to residence on the Y chromosome, nor to variation between primate lineages in the rate of gene family evolution. Instead other factors, such as natural selection and gene conversion, appear to play a role in driving temporal and genomic evolutionary heterogeneity in primate gene families. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2187-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana-Hermina Ghenu
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
| | - Benjamin M Bolker
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,Department of Mathematics & Statistics, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Don J Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th Floor Schermerhorn Extension, New York, 10027, USA
| | - Ben J Evans
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
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Das R, Hergenrother SD, Soto-Calderón ID, Dew JL, Anthony NM, Jensen-Seaman MI. Complete mitochondrial genome sequence of the Eastern gorilla (Gorilla beringei) and implications for african ape biogeography. J Hered 2014; 105:752-61. [PMID: 25189777 DOI: 10.1093/jhered/esu056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Western and Eastern species of gorillas (Gorilla gorilla and Gorilla beringei) began diverging in the mid-Pleistocene, but in a complex pattern with ongoing gene flow following their initial split. We sequenced the complete mitochondrial genomes of 1 Eastern and 1 Western gorilla to provide the most accurate date for their mitochondrial divergence, and to analyze patterns of nucleotide substitutions. The most recent common ancestor of these genomes existed about 1.9 million years ago, slightly more recent than that of chimpanzee and bonobo. We in turn use this date as a calibration to reanalyze sequences from the Eastern lowland and mountain gorilla subspecies to estimate their mitochondrial divergence at approximately 380000 years ago. These dates help frame a hypothesis whereby populations became isolated nearly 2 million years ago with restricted maternal gene flow, followed by ongoing male migration until the recent past. This process of divergence with prolonged hybridization occurred against the backdrop of the African Pleistocene, characterized by intense fluctuations in temperature and aridity, while at the same time experiencing tectonic uplifting and consequent shifts in the drainage of major river systems. Interestingly, this same pattern of introgression following divergence and discrepancies between mitochondrial and nuclear loci is seen in fossil hominins from Eurasia, suggesting that such processes may be common in hominids and that living gorillas may provide a useful model for understanding isolation and migration in our extinct relatives.
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Affiliation(s)
- Ranajit Das
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - Scott D Hergenrother
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - Iván D Soto-Calderón
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - J Larry Dew
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - Nicola M Anthony
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón)
| | - Michael I Jensen-Seaman
- From the Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (Das, Hergenrother, and Jensen-Seaman); Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148 (Soto-Calderón, Dew, and Anthony); and Biology Institute, University of Antioquia, AA.1226, Medellín, Colombia (Soto-Calderón).
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Evans BJ, Zeng K, Esselstyn JA, Charlesworth B, Melnick DJ. Reduced representation genome sequencing suggests low diversity on the sex chromosomes of tonkean macaque monkeys. Mol Biol Evol 2014; 31:2425-40. [PMID: 24987106 DOI: 10.1093/molbev/msu197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In species with separate sexes, social systems can differ in the relative variances of male versus female reproductive success. Papionin monkeys (macaques, mangabeys, mandrills, drills, baboons, and geladas) exhibit hallmarks of a high variance in male reproductive success, including a female-biased adult sex ratio and prominent sexual dimorphism. To explore the potential genomic consequences of such sex differences, we used a reduced representation genome sequencing approach to quantifying polymorphism at sites on autosomes and sex chromosomes of the tonkean macaque (Macaca tonkeana), a species endemic to the Indonesian island of Sulawesi. The ratio of nucleotide diversity of the X chromosome to that of the autosomes was less than the value (0.75) expected with a 1:1 sex ratio and no sex differences in the variance in reproductive success. However, the significance of this difference was dependent on which outgroup was used to standardize diversity levels. Using a new model that includes the effects of varying population size, sex differences in mutation rate between the autosomes and X chromosome, and GC-biased gene conversion (gBGC) or selection on GC content, we found that the maximum-likelihood estimate of the ratio of effective population size of the X chromosome to that of the autosomes was 0.68, which did not differ significantly from 0.75. We also found evidence for 1) a higher level of purifying selection on genic than nongenic regions, 2) gBGC or natural selection favoring increased GC content, 3) a dynamic demography characterized by population growth and contraction, 4) a higher mutation rate in males than females, and 5) a very low polymorphism level on the Y chromosome. These findings shed light on the population genomic consequences of sex differences in the variance in reproductive success, which appear to be modest in the tonkean macaque; they also suggest the occurrence of hitchhiking on the Y chromosome.
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Affiliation(s)
- Ben J Evans
- Biology Department, McMaster University, Hamilton, ON, Canada
| | - Kai Zeng
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, United Kingdom
| | - Jacob A Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Don J Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University
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Zikovitz AE, Agrawal AF. The condition dependency of fitness in males and females: the fitness consequences of juvenile diet assessed in environments differing in key adult resources. Evolution 2013; 67:2849-60. [PMID: 24094338 DOI: 10.1111/evo.12170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/03/2013] [Indexed: 11/29/2022]
Abstract
Variation in environmental or genetic quality leads to phenotypic variation in condition, but how much variation in fitness is created by this variation in condition? Using Drosophila melanogaster, we manipulated condition via alternative larval diets and then tested several key factors predicted to influence how much variation in fitness results from differences in condition. Specifically, we were interested in whether male and female fitness are affected equally by condition and whether the strength of selection on condition depends on the abundance of key resources limiting the reproductive output of each sex. We measured selection on condition in alternative assay contexts that varied in the abundance of adult food (a key resource for females) or in the abundance of females (a key resource for males). Overall, selection tended to be stronger on males than females. However, selection on males was weakened when the abundance of their key resource (females) was elevated. Increasing the abundance of the key resource for females (live yeast) elevated their reproductive output as expected but did not change the strength of selection in this sex. Instead, this manipulation increased selection on males, suggesting that this environmental factor indirectly affects selection on males via their interaction with females.
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Affiliation(s)
- Andrea E Zikovitz
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada
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Abstract
The effective population size (N(e)) quantifies the effectiveness of genetic drift in finite populations. When generations overlap, theoretical expectations for N(e) typically assume that the sampling of offspring genotypes from a given individual is independent among successive breeding events, even though this is not true in many species, including humans. To explore the effects on N(e) of nonindependent mate pairing across breeding events, we simulated the genetic drift of mitochondrial DNA, autosomal DNA, and sex chromosome DNA under three mating systems. Nonindependent mate pairing across breeding seasons has no effect when all adults mate pair for life, a small or moderate effect when females reuse stored sperm, and a large effect when there is intense male-male competition for reproduction in a harem social system. If adult females reproduce at a constant rate irrespective of the type of mate pairing, the general effect of nonindependent mate pairing is to decrease N(e) for paternally inherited components of the genome. These findings have significant implications for the relative N(e) values of different genomic regions, and hence for the expected levels of DNA sequence diversity in these regions.
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Martínez-Solano Í, Peralta-García A, Jockusch EL, Wake DB, Vázquez-Domínguez E, Parra-Olea G. Molecular systematics of Batrachoseps (Caudata, Plethodontidae) in southern California and Baja California: Mitochondrial-nuclear DNA discordance and the evolutionary history of B. major. Mol Phylogenet Evol 2012; 63:131-49. [DOI: 10.1016/j.ympev.2011.12.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 12/20/2011] [Accepted: 12/28/2011] [Indexed: 11/16/2022]
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Stelbrink B, Albrecht C, Hall R, von Rintelen T. THE BIOGEOGRAPHY OF SULAWESI REVISITED: IS THERE EVIDENCE FOR A VICARIANT ORIGIN OF TAXA ON WALLACE'S “ANOMALOUS ISLAND”? Evolution 2012; 66:2252-71. [DOI: 10.1111/j.1558-5646.2012.01588.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Osada N. Phylogenetic inconsistency caused by ancient sex-biased gene migration. PLoS One 2011; 6:e25549. [PMID: 21980490 PMCID: PMC3183042 DOI: 10.1371/journal.pone.0025549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 09/07/2011] [Indexed: 12/25/2022] Open
Abstract
Inferences of ancient sex-biased migration patterns using sex-linked genetic markers are usually difficult because of a stochastic process of allele fixation. Nevertheless, incongruent phylogenetic trees between different sex-linked markers and between sex-linked and autosomal markers are frequently interpreted as a signature of sex-biased migration without further statistical evaluation. I investigated the types of incongruent phylogenetic trees from which past sex-biased migration events can be statistically supported under the coalescent model. In the case of mammals, detecting a sex-biased migration pattern is not guaranteed by comparing the phylogenetic pattern of mitochondrial and Y-chromosomal loci. Likewise, evidence of introgression at a mitochondrial locus, but not at autosomal loci, does not support the hypothesis of an ancient female-biased migration pattern with statistical significance. In contrast, evidence of introgression at ≥ 5 unlinked autosomal loci, but not at a Y-chromosomal locus, would reject the null hypothesis of a sexually equal migration rate with statistical significance. A similar argument can be made to infer a male-biased migration pattern. Furthermore, the investigation of many recombining sex-biased markers such as X-chromosomal loci in mammals has the potential to efficiently detect ancient sex-biased demographic patterns.
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Affiliation(s)
- Naoki Osada
- Department of Population Genetics, National Institute of Genetics, Mishima, Japan.
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Piskol R, Stephan W. The role of the effective population size in compensatory evolution. Genome Biol Evol 2011; 3:528-38. [PMID: 21680889 PMCID: PMC3140890 DOI: 10.1093/gbe/evr057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The impact of the effective population size (Ne) on the efficacy of selection has been the focus of many theoretical and empirical studies over the recent years. Yet, the effect of Ne on evolution under epistatic fitness interactions is not well understood. In this study, we compare selective constraints at independently evolving (unpaired) and coevolving (paired) sites in orthologous transfer RNAs (tRNA molecules for vertebrate and drosophilid species pairs of different Ne. We show that patterns of nucleotide variation for the two classes of sites are explained well by Kimura's one- and two-locus models of sequence evolution under mutational pressure. We find that constraints in orthologous tRNAs increase with increasing Ne of the investigated species pair. Thereby, the effect of Ne on the efficacy of selection is stronger at unpaired sites than at paired sites. Furthermore, we identify a “core” set of tRNAs with high structural similarity to tRNAs from all major kingdoms of life and a “peripheral” set with lower similarity. We observe that tRNAs in the former set are subject to higher constraints and less prone to the effect of Ne, whereas constraints in tRNAs of the latter set show a large influence of Ne. Finally, we are able to demonstrate that constraints are relaxed in X-linked drosophilid tRNAs compared with autosomal tRNAs and suggest that Ne is responsible for this difference. The observed effects of Ne are consistent with the hypothesis that evolution of most tRNAs is governed by slightly to moderately deleterious mutations (i.e., |Nes| ≤ 5).
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Affiliation(s)
- Robert Piskol
- Section of Evolutionary Biology, Ludwig-Maximilian University, Munich, Germany.
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