Phylogeographical studies of the most species-rich region of the planet-the Amazon basin-have repeatedly uncovered genetically distinctive, allopatric lineages within currently named species, but understanding whether such lineages are reproductively isolated species is challenging. Here we harness the power of genome-wide data sets together with detailed phylogeographical sampling to both characterize the number of unique lineages and infer levels of reproductive isolation for three parapatric manakin species that make up the genus Pipra. The mitochondrial and nuclear genomes both support six distinctive lineages. The youngest lineages are now highly admixed with each other across major portions of their geographical ranges with one lineage now extinct in a genomically unadmixed state. In contrast, the oldest sets of lineages-dated to 1.4 million years-exhibit narrow hybrid zones. By fitting demographic models to parapatric lineage pairs we found that levels of gene flow and genomic homogenization decline with increasing evolutionary age. Only lineages descending from the basal node at 1.4 million years ago in the genus experience negligible gene flow, possess genomes resistant to homogenization and are separated by narrow hybrid zones. We conclude that a million years or more were required for Pipra manakins to become reproductively isolated. We suggest the six lineages be reclassified as two or three reproductively isolated species. Our unique approach to quantifying reproductive isolation in parapatric lineages could be applied broadly to other phylogeographical studies and would help determine species classification of the plethora of newly identified lineages in the Amazon basin and other regions.
机构:
Bharathidasan Univ, Sch Life Sci, Dept Bioinformat, Ind Syst Biol Lab, Tiruchirappalli, Tamil Nadu, IndiaBharathidasan Univ, Sch Life Sci, Dept Bioinformat, Ind Syst Biol Lab, Tiruchirappalli, Tamil Nadu, India
Saranya, Sivashanmuga Vadivel
Prathiviraj, R.
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Bharathidasan Univ, Sch Life Sci, Dept Bioinformat, Ind Syst Biol Lab, Tiruchirappalli, Tamil Nadu, IndiaBharathidasan Univ, Sch Life Sci, Dept Bioinformat, Ind Syst Biol Lab, Tiruchirappalli, Tamil Nadu, India
Prathiviraj, R.
Chellapandi, Paulchamy
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Bharathidasan Univ, Sch Life Sci, Dept Bioinformat, Ind Syst Biol Lab, Tiruchirappalli, Tamil Nadu, IndiaBharathidasan Univ, Sch Life Sci, Dept Bioinformat, Ind Syst Biol Lab, Tiruchirappalli, Tamil Nadu, India
机构:
Sun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Fudan Univ, Sch Life Sci, Key Lab Biodivers Sci & Ecol Engn, Minist Educ, Shanghai 200438, Peoples R ChinaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Wang, Xinfeng
He, Ziwen
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Sun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R ChinaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
He, Ziwen
Guo, Zixiao
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Sun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R ChinaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Guo, Zixiao
Yang, Ming
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Univ Washington, Dept Lab Med & Pathol, Seattle, WA 98195 USASun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Yang, Ming
Xu, Shaohua
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Sun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R ChinaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Xu, Shaohua
Chen, Qipian
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Sun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R ChinaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Chen, Qipian
Shao, Shao
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Sun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R ChinaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Shao, Shao
Li, Sen
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Sun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R ChinaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Li, Sen
Zhong, Cairong
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机构:
Hainan Acad Forestry, Hainan Acad Mangrove, Haikou 571100, Peoples R ChinaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Zhong, Cairong
Duke, Norman C.
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James Cook Univ, Townsville, QLD 4811, AustraliaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
Duke, Norman C.
Shi, Suhua
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Sun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R ChinaSun Yat sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangdong Key Lab Plant Resources,Southern Marine, Guangzhou 510275, Peoples R China
机构:
State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan UniversityState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Xinfeng Wang
Ziwen He
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机构:
State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen UniversityState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Ziwen He
Zixiao Guo
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机构:
State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen UniversityState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Zixiao Guo
Ming Yang
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机构:
Department of Laboratory Medicine& Pathology,University of WashingtonState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Ming Yang
Shaohua Xu
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State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen UniversityState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Shaohua Xu
Qipian Chen
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State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen UniversityState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Qipian Chen
Shao Shao
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State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen UniversityState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Shao Shao
Sen Li
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State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen UniversityState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Sen Li
Cairong Zhong
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机构:
Hainan Academy of Forestry (Hainan Academy of Mangrove)State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Cairong Zhong
Norman C.Duke
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Centre for Tropical Water and Aquatic Ecosystem Research,James Cook UniversityState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University
Norman C.Duke
Suhua Shi
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State Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen UniversityState Key Laboratory of Biocontrol,Guangdong Key Laboratory of Plant Resources, School of Life Sciences,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai), Sun Yat-sen University