Phylogeographical Structure in Mitochondrial DNA of Legume Pod Borer (Maruca vitrata) Population in Tropical Asia and Sub-Saharan Africa.

This study was undertaken to assess the genetic diversity and host plant races of M. vitrata population in South and Southeast Asia and sub-Saharan Africa. The cytochrome c oxidase subunit 1 (cox1) gene was used to understand the phylogenetic relationship of geographically different M. vitrata population, but previous studies did not include population from Southeast Asia, the probable center of origin for Maruca, and from east Africa. Extensive sampling was done from different host plant species in target countries. Reference populations from Oceania and Latin America were used. An amplicon of 658 bp was produced by polymerase chain reaction, and 64 haplotypes were identified in 686 M. vitrata individuals. Phylogenetic analysis showed no difference among the M. vitrata population from different host plants. However, the results suggested that M. vitrata has formed two putative subspecies (which cannot be differentiated based on morphological characters) in Asia and sub-Saharan Africa, as indicated by the high pairwise FST values (0.44-0.85). The extremely high FST values (≥ 0.93) of Maruca population in Latin America and Oceania compared to Asian and African population seem to indicate a different species. On the continental or larger geographical region basis, the genetic differentiation is significantly correlated with the geographical distance. In addition, two putative species of Maruca, including M. vitrata occur in Australia, Indonesia and Papua New Guinea. The negative Tajima's D and Fu's FS values showed the recent demographic expansion of Maruca population. The haplotype network and Automatic Barcode Gap Discovery analyses confirmed the results of phylogenetic analysis. Thus, this study confirmed the presence of three putative Maruca species, including one in Latin America, one in Oceania (including Indonesia) and M. vitrata in Asia, Africa and Oceania. Hence, the genetic differences in Maruca population should be carefully considered while designing the pest management strategies in different regions

Result of AMOVA analysis of <i>Maruca vitrata</i> populations from 22 host plants in South- and Southeast Asia as well as sub-Saharan Africa, based on <i>coxI</i> sequence data.

<p>* significant at <i>P</i> < 0.05</p><p>** highly significant at <i>P</i> < 0.01</p><p>Result of AMOVA analysis of <i>Maruca vitrata</i> populations from 22 host plants in South- and Southeast Asia as well as sub-Saharan Africa, based on <i>coxI</i> sequence data.</p

Pairwise <i>FS</i>_<i>T</i> values (below diagonal) and distance matrix (above diagonal; in the unit of kilometer) comparing populations of <i>Maruca vitrata</i> (country based analysis).

<p>* <i>F</i>_<i>ST</i> values were significant at <i>P</i> < 0.05</p><p>** highly significant at <i>P</i> < 0.01</p><p>Pairwise <i>FS</i>_<i>T</i> values (below diagonal) and distance matrix (above diagonal; in the unit of kilometer) comparing populations of <i>Maruca vitrata</i> (country based analysis).</p

Phylogenetic relationship among <i>Maruca</i> sp. based upon a 615 bp mitochondrial coxI gene fragments using maximum parsimony (MP) algorithm.

<p>Countries abbreviated for the reference population in the phylogenetic tree are as follows: CAM—Cameroon; NGA—Nigeria; GAB—Gabon; KEN—Kenya; GHA—Ghana; AUS—Australia; PAK—Pakistan; CN—China; PHI—Philippines; CR—Costa Rica; BRZ—Brazil; MEX—Mexico; ARG—Argentina; PAN—Panama; INDO—Indonesia; PNG—Papua New Guinea. Groups are marked as below: Red—Group 1; Blue—Group 2; Purple—Group 3; Green—Group 4. Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124057#pone.0124057.t001" target="_blank">Table 1</a> for the <i>M</i>. <i>vitrata</i> population details used in this study.</p

List of number of samples studied, number of haplotypes, haplotype diversity (<i>h</i>), nucleotide diversity (π), Tajima’s <i>D</i> and Fu’s <i>F</i>_<i>S</i> tests for <i>Maruca vitrata</i> populations from four selected continents / regions.

<p>** values were significant at P < 0.01</p><p>*** values were significant at P < 0.001</p><p>List of number of samples studied, number of haplotypes, haplotype diversity (<i>h</i>), nucleotide diversity (π), Tajima’s <i>D</i> and Fu’s <i>F</i>_<i>S</i> tests for <i>Maruca vitrata</i> populations from four selected continents / regions.</p

List of number of samples studied, number of haplotypes, haplotype diversity (<i>h</i>), nucleotide diversity (π), Tajima’s <i>D</i> and Fu’s <i>F</i>_<i>S</i> tests for <i>Maruca vitrata</i> populations from ten countries in South and Southeast Asia, and sub-Saharan Africa.

<p>** values were significant at P < 0.01</p><p>*** values were significant at P < 0.001</p><p>List of number of samples studied, number of haplotypes, haplotype diversity (<i>h</i>), nucleotide diversity (π), Tajima’s <i>D</i> and Fu’s <i>F</i>_<i>S</i> tests for <i>Maruca vitrata</i> populations from ten countries in South and Southeast Asia, and sub-Saharan Africa.</p

Pairwise <i>FS</i>_<i>T</i> values (below diagonal) and distance matrix (above diagonal; in the unit of kilometer) comparing populations of <i>Maruca vitrata</i> (continent or larger geographical region based analysis).

<p>* <i>F</i>_<i>ST</i> values were significant at <i>P</i> < 0.05</p><p>** highly significant at <i>P</i> < 0.01</p><p>Pairwise <i>FS</i>_<i>T</i> values (below diagonal) and distance matrix (above diagonal; in the unit of kilometer) comparing populations of <i>Maruca vitrata</i> (continent or larger geographical region based analysis).</p

Genetic isolation-by-distance analysis by regression of genetic differentiation (<i>FST</i>) vs. geographic distance (km) (A) among <i>Maruca vitrata</i> population from different countries in Asia and Africa, and (B) among <i>Maruca</i> population from different continents or larger geographical regions.

<p>Genetic isolation-by-distance analysis by regression of genetic differentiation (<i>FST</i>) vs. geographic distance (km) (A) among <i>Maruca vitrata</i> population from different countries in Asia and Africa, and (B) among <i>Maruca</i> population from different continents or larger geographical regions.</p

Result of AMOVA analysis of <i>Maruca</i> populations from four selected continents / regions based on <i>coxI</i> sequence data.

<p>* significant at <i>P</i> < 0.05</p><p>** highly significant at <i>P</i> < 0.01</p><p>Result of AMOVA analysis of <i>Maruca</i> populations from four selected continents / regions based on <i>coxI</i> sequence data.</p

ABGD analysis- K2P divergence based Neighbor-joining tree based on <i>coxI</i> haplotypes.

<p>CN5 marked in red box is the population collected from Central Java, Indonesia, whereas two populations in green box (HQ571111 and LEPKP101) have originated from Kalimantan, Indonesia.</p