Dataset Information

Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

ABSTRACT: The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81-1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41-0.78] with further internal separations at 0.32 Mya [0.22-0.43] and 0.16 Mya [0.17-0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics.

SUBMITTER: Lobon I

PROVIDER: S-EPMC4943195 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

Lobon Irene I Tucci Serena S de Manuel Marc M Ghirotto Silvia S Benazzo Andrea A Prado-Martinez Javier J Lorente-Galdos Belen B Nam Kiwoong K Dabad Marc M Hernandez-Rodriguez Jessica J Comas David D Navarro Arcadi A Schierup Mikkel H MH Andres Aida M AM Barbujani Guido G Hvilsom Christina C Marques-Bonet Tomas T

Genome biology and evolution 20160703 6

The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) ...[more]

PMID: 27345955

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Project description:Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000-80,000) and census sizes (5-50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.

Project description:The Philippines is a mega-diverse country that lies at the crossroads of past human migrations in the Asia-Pacific region and is believed to have never been connected to the Asian continent, even during the major sea-level subsidence of the Quaternary. As a result, the history of pig dispersal in the Philippines remains controversial, due to limited molecular studies and absence of archaeological evidence of pig domestication. This study provides the first comprehensive analysis of 184 complete mitochondrial DNA D-loop region from Philippine pigs to elucidate their early dispersal history by performing a phylogenetic comparison with wild boars and domestic pigs worldwide. The results showed a demographic signal of the ancestry of Philippine pigs that had a close genetic relationship with those from the mainland Southeast Asia and Northeast Asia, suggesting gene flow that may have resulted from human migration and trade. Here we have suggested two possible dispersal routes. One parallels the Neolithic expansion in Island Southeast Asia and Oceania via Northeast Asia, the other from the mainland Southeast Asia, into Palawan and Sulu Archipelago as early as prehistoric times via the Sundaic Region. Despite geographic barriers to migration, numerous genetic lineages have persisted across the Philippine islands, even justifying the recognition of a Philippine Lanyu subclade. The prehistoric population history suggests a demographic expansion that coincided with the interglacial periods of the Pleistocene and may have spread from the southern regions into the eastern and central regions of the Philippines. The intriguing signal of discrepancy discovered between the ancestral pattern and distribution range of the numerous endemic Philippine wild pigs opens a challenging new approach to illuminate complexity among these animals. Our study has contributed significantly towards completing the sparse molecular studies on Philippine pigs, an essential for creating win-win conservation measures.

Project description:BACKGROUND:Comparative broad-scale phylogeographic studies of aquatic organisms provide insights on biotic responses to the paleohydrological dynamics associated with climatic oscillations. These insights can be used to formulate a framework for understanding the evolutionary history of a species or closely related taxa as well as aid in predictive modeling of further responses to climate change. Anadromous fishes constitute interesting models for understanding the relative importance of environmental versus biological factors in shaping intraspecific genetic substructure on the interface between marine and freshwater realms. European shads, Alosa alosa and A. fallax are anadromous species that have persisted through historical large-scale environmental perturbations and now additionally face an array of anthropogenic challenges. A comprehensive phylogeographic investigation of these species is needed to provide insights on both the historical processes that have shaped their extant genetic structure and diversity, and the prospects for their future management and conservation. RESULTS:Despite introgressive hybridization, A. alosa and A. fallax are genetically divergent, congruent with previous studies. Three similarly divergent mtDNA clades were recognized within both A. fallax and A. alosa, most likely originating during common periods of isolation during the Pleistocene among the studied oceanographic regions. Periods of basin isolation apparently extended to the Black Sea as additional Alosa clades occur there. The present day geographic distribution of genetic diversity within European Alosa sp. suggests the existence of a strong but permeable barrier between the Atlantic and Mediterranean seas, as shown for a number of other aquatic species. Overall mtDNA diversity is considerably lower for A. alosa compared to A. fallax, suggesting that the former species is more sensitive to climatic as well as anthropogenic changes. For A. fallax, migration from the Mediterranean to the Atlantic was detected but not in the opposite direction, with colonization of the North Atlantic probably occurring after last glacial maximum. CONCLUSION:The similar haplotype network topologies between the two species support a common intraspecific history of isolation. Despite these similarities, A. alosa and A. fallax have clearly responded differently to the hydrological dynamics of the Pleistocene, as reflected in their distinct demographic histories. As the species additionally occupy different ecological niches it should not be surprising that they differ in resilience to natural or human-mediated climatic changes. For A. fallax, it is further clear that its demographic response to large-scale hydrological events is not synchronized between the Atlantic and Mediterranean basins. These regional and species-specific differences should be incorporated into future predictive modeling of biological response to climate change as well as current management concepts.

Dataset Information

Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

Publications

Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions.

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