Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses

Abstract

Systematically investigating the impacts of Pleistocene sea-level fluctuations on mangrove plants may provide a better understanding of their demographic history and useful information for their conservation. Therefore, we conducted population genomic analyses of 88 nuclear genes to explore the population dynamics of a mangrove tree Lumnitzera racemosa across the Indo-West Pacific region. Our results revealed pronounced genetic differentiation in this species between the populations from the Indian Ocean and the Pacific Ocean, which may be attributable to the long-term isolation between the western and eastern coasts of the Malay Peninsula during sea-level drops in the Pleistocene glacial periods. The mixing of haplotypes from the two highly divergent groups was identified in a Cambodian population at almost all 88 nuclear genes, suggesting genetic admixture of the two lineages at the boundary region. Similar genetic admixture was also found in other populations from Southeast Asia based on the Bayesian clustering analysis of six nuclear genes, which suggests extensive and recent secondary contact of the two divergent lineages in Southeast Asia. Computer simulations indicated substantial migration from the Indian Ocean towards the South China Sea, which likely results in the genetic admixture in Southeast Asia.

Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata

“…It is thus easily to imagine that seeds from both the SCS and the Indian Ocean could rapidly re-colonize the seashore of the Java Sea via drift on sea currents, resulting in secondary contact of the two previously isolated lineages in this area. Similar genetic admixture of SCS and Indian Ocean groups was observed in two mangrove species Rhizophora apiculata (Yahya et al, 2014) and Lumnitzera racemosa (Li et al, 2016), as well as the false clown anemonefish ( Amphiprion ocellaris , Timm and Kochzius, 2008) and reef communities (Hoeksema, 2007). …”

Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species

“…Within SE Asia, populations on the western side of Malay Peninsula were separable from those on the eastern side, suggesting that the Malay Peninsula acted as a land barrier to the dispersal of R. apiculata , which is consistent with previous studies on Rhizophora species (Inomata et al, 2009 ; Ng et al, 2015 ; Wee et al, 2015 ). This pattern of population differentiation is also evident in other sea water dispersed mangrove species, such as Ceriops species (Ge and Sun, 2001 ; Liao et al, 2007 ; Huang et al, 2008 , 2012 ), B. gymnorhiza (Minobe et al, 2009 ; Urashi et al, 2013 ), and Lumnitzera species (Su et al, 2006 , 2007 ; Li et al, 2016 ). Similarly, genetic structure of R. mangle, R. racemosa , and R. samoensis in the AEP region is influenced by the Central American Isthmus and the American continent land masses (Núñez-Farfán et al, 2002 ; Takayama et al, 2013 ).…”

Genetic structures across a biogeographical barrier reflect dispersal potential of four Southeast Asian mangrove plant species

“…Present-day mangrove populations along the Malacca Strait most likely resulted from a northto-south migration event no earlier than circa 10,000 years ago by individuals from the closest refugia in the Andaman Sea. Genetic admixture between divergent lineages from the Pacific and Indian Oceans has thus been observed along the Malacca Strait in S. alba (Yang et al, 2017) and L. racemosa (Li et al, 2016). The genetic admixture was likely facilitated by present-day ocean circulation that flows from the South China Sea into the Andaman Sea via the Malacca Strait for at least a quarter of the year (Rizal et al, 2012).…”