Population genetics and demographic history of red seaweed, Palmaria palmata, from the Canada-northwest Atlantic

doi:10.3724/SP.J.1003.2013.09029

Abstract

Abstract:

The paleoclimate change (e.g. the glacial fluctuation in the late Pleistocene) played an important role in shaping species’ population genetic structure, geographic distribution patterns, and gradient of diversity and composition. In this study, we sampled eight populations (138 individuals) of Palmaria palmata, a commercially and ecologically important red macroalga found on both sides of the North Atlantic coast, aiming to assess the genetic structure and demographic history through the integration of mitochondrial cox2-3 spacer and RAPD variation. Eleven mtDNA cox2-3 haplotypes were detected, one of which (C3) was common and located centrally in a haplotype network. It is shared by all populations and is regarded as ancestral. Two northern populations from the Gulf of St. Lawrence had highest levels of genetic diversity, and were significantly divergent from all other populations. AMOVA showed that highest genetic variation for cox2-3 occurred within populations, while less existed among groups. This was consistent with the results of a STRUCTURE clustering analysis of RAPD data. Our genetic diversity and haplotype network analyses indicated that multiple glacial refugia might have existed for the species along the Canada-north- west Atlantic coast. Furthermore, Bayesian skyline plot analysis based on cox2-3 spacer sequences indicated that population size underwent a slight increase over temporal and spatial scales. This occurred in approximately 0.18-0.13 million years ago. Pairwise genetic distance (K2P) between populations from the Gulf of St. Lawrence and the Bay of Fundy was 0.2%, indicating that they diverged from their common ancestor since about 0.36 million years ago. The evidence from our study suggests that climatic oscillations during the late Pleistocene had a drastic influence on the demography and genetic diversity of P. palmatain the Canada-northwest Atlantic.

Key words: Palmaria palmata, the Last Glacial Maximum, cox2-3, genetic structure, genetic diversity

Jingjing Li,Jie Zhang,Zimin Hu,Delin Duan. Population genetics and demographic history of red seaweed, Palmaria palmata, from the Canada-northwest Atlantic[J]. Biodiv Sci, 2013, 21(3): 306-314.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2013.09029

https://www.biodiversity-science.net/EN/Y2013/V21/I3/306

Figures/Tables 6

Fig. 1 Morphological characters of Palmaria palmata. (a) Living intertidal habitat of P. palmata from County Clare, Ireland in 2008. It is frequently found living on thallus of red marcroalga Chondrus crispus and brown macroalga Fucus serratus; (b) Purple morphological features of P. palmata from Bonne Bay, Canada.

Table 1 Sampling details of eight Palmaria palmata populations, including abbreviation codes, geographic location, sample size (N), number of haplotypes (Nh), types of haplotype (H), haplotype diversity (h), and nucleotide diversity (π)

简称 Code	种群 Population	经纬度 Locality	N	N_h	H	h (SD)	π (SD)
Gulf of St. Lawrence
LA	L’Anse Amour, Canada	52.32°N, 56.60°W	25	3	C1, C2, C3	0.640 (0.052)	0.0024 (0.0020)
BB	Bonne Bay, Canada	49.51°N, 57.92°W	31	3	C1, C3, C4	0.540 (0.043)	0.0018 (0.0017)
GP	Gaspe, Canada	48.88°N, 64.50°W	11	1	C3	0.000 (0.000)	0.0000 (0.0000)
RS	Rimouski, Canada	48.47°N, 68.51°W	24	2	C3, C5	0.083 (0.075)	0.0002 (0.0005)
Bay of Fundy
MB	Maces Bay, Canada	45.11°N, 66.75°W	8	2	C3, C6	0.250 (0.180)	0.0008 (0.0011)
VB	Victoria Beach, Canada	44.69°N, 65.75°W	9	3	C3, C7, C8	0.417 (0.191)	0.0014 (0.0016)
LT	Letete, Canada	45.06°N, 66.89°W	12	2	C3, C9	0.303 (0.148)	0.0009 (0.0012)
WH	White Head, Canada	44.63°N, 66.72°W	18	3	C3, C10, C11	0.451 (0.117)	0.0015 (0.0015)

Fig. 2 Distribution of mitochondrial cox2-3 haplotypes of Palmaria palmata populations and median-joining haplotype network. Population codes correspond to those in Table 1.

Table 2 Molecular variance (AMOVA) of Palmaria palmata populations. The eight populations were clustered into two groups: the Gulf of St. Lawrence and the Bay of Fundy.

变异来源 Source of variations	自由度 d.f.	变异组成 Variance components	变异百分比 % of variation	固定指数 Fixation indices
群组间 Among groups	1	0.0409	10.12	F_CT = 0.10118^NS
种群间 Among populations within groups	6	0.1246	34.09	Fsc = 0.37928^***
种群内 Within populations	130	0.2075	55.79	F_ST = 0.44509^***

Fig. 3 Population structuring analysis based on RAPD data with STRUCTURE. Each vertical bar indicates the multi-locus genotype of one individual, and colors represent the K virtual clusters. Population codes are the same as Table 1.

Fig. 4 Demographic history of Palmaria palmata. (a) Mismatch distributions of Palmaria palmata populations. The abscissa indicates the number of pairwise differences between compared sequences. The ordinate is the frequency for each value. Bars represent the observed distribution of pairwise differences, while the solid line shows the expected distribution; (b) Bayesian skyline plots show effective population size as a function of time. The upper and lower limits of grey trend represent the 95% confidence intervals of higher probability density (HPD) analysis.

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