Figure 4 - uploaded by Alireza Asem
Content may be subject to copyright.
Maximum parsimony haplotype network of ITS1 sequences. The size of each square/circle is proportional to the frequency of specimens. Each joining line between haplotypes is equal with single nucleotide substitutions. Black dots between haplotypes. Full-size DOI: 10.7717/peerj.7190/fig-4

Maximum parsimony haplotype network of ITS1 sequences. The size of each square/circle is proportional to the frequency of specimens. Each joining line between haplotypes is equal with single nucleotide substitutions. Black dots between haplotypes. Full-size DOI: 10.7717/peerj.7190/fig-4

Source publication
Article
Full-text available
Urmia Lake, the largest natural habitat of the brine shrimp Artemia urmiana, has progressively desiccated over the last two decades, resulting in a loss of 80% of its surface area and producing thousands of hectares of arid salty land. This ecological crisis has seriously affected the lake's native biodiversity. Artemia urmiana has lost more than 9...

Contexts in source publication

Context 1
... for 58 specimens revealed 56 haplotypes (H1-H56), which showed high variation in comparison with the other markers. The central haplotype (H1) covered only two specimens (3.5%) including a single specimen from each year. With the exception of H39 that was shared by two specimens from 2004, other haplotypes were unique to a single specimen (Fig. ...
Context 2
... 16S structure. Tajima's D and Fu and Li's D* were non-significant in the rainy period which could indicate 16S marker was at demographic equilibrium without selection in the rainy period. In contrast, a negative and significant neutrality value and expanded haplotype network indicated that 16S is involved in recent expansion in the drought period (Fig. 6). The negative and significant value of Fu Fs test suggested the excess of new mutations in the gene pool of 16S in both normal and drought ...

Citations

... Samples L. Sainz-Escudero et al. Additionally, to our data, all the available Artemia cox1 sequences available in GenBank (Valsala et al. 2005;Hou et al. 2006;Tizol-Correa et al. 2009;Muñoz et al. 2008Muñoz et al. , 2010Muñoz et al. , 2013Maniatsi et al. 2009Maniatsi et al. , 2011Maccari et al. 2013b;Eimanifar and Wink 2013;Eimanifar et al. 2014Eimanifar et al. , 2015Eimanifar et al. , 2016Asem et al. 2016Asem et al. , 2019Asem et al. , 2020Naganawa and Mura 2017;Horváth et al. 2018) and one of Branchinecta ferox used as outgroup (LT821334 [Rodríguez-Flores et al. 2017]) were retrieved in order to build a dataset represented by 1505 sequences, that allowed us to depict the structuring of the genus through the Neighbour Joining analysis and to perform phylogeographic analyses. Some dissimilar sequences that featured stop codons when traduced to amynoacids were removed from the analyses due to the existence of pseudogenes according to Rode et al. (2021). ...
Article
Full-text available
Brine shrimps ( Artemia ) have undergone geographic range and demographic expansions as a result of their interaction with humans since the beginning of salt harvesting. This interaction has favoured the expansion of some species but compromising the survival of others. Mediterranean native populations of Artemia salina from coastal salterns and lagoons are facing the presence and expansion of the introduced and invasive American species Artemia monica (= A . franciscana ). However, this species could not be the only threat. Parthenogenetic populations of the Asian species A . urmiana and A . sinica are widespread along the Mediterranean and other areas of the world. In this work, with the use of large cox1 and mitogenomic datasets, phylogenetic and phylogeographic inferences, and a time calibrated tree, we confirmed the Asian origin and recent arrival of the current Western Mediterranean parthenogenetic populations of Artemia . In addition, the replacement of Iberian populations of A . salina by Asiatic parthenogenetic populations lead us to recognize parthenogens as invasive. Current salterns development and commercial importance of Artemia make human-mediated introduction probable. These results demonstrate again the impact that changing human interests have on population expansion or decline of species adapted to anthropogenic habitats. Artemia salina decline makes urgent the implementation of conservation measures such as its use in fish farming and salt production or its inoculation in inland salterns.
... Our results revealed a negative and significant Tajima's D value (−2.304) only for the exotic population in AWWR (Table 6), which demonstrated an excess of rare haplotypes followed by population expansion or purifying selection (Nei and Kumar, 2000;Swanson et al., 2001;Akey et al., 2004;Cruciani et al., 2008;Levitan and Stapper, 2009;Asem et al., 2019). Given the greater numbers of polymorphic sites (12 sites), mutations (12 mutations), and haplotypes (12 haplotypes) in comparison with other localities, Tajima's D result might be ascribed to the demographic expansion of the Artemia population in AWWR. ...
... The negative values of Fu's Fs test and Fu and Li's D* test suggest the existence of rare recent mutations (Fu, 1997;Ramos-Onsins and Rozas, 2002;Zhao et al., 2008;Asem et al., 2019) and an excess of rare historical mutations in populations (Fu and Li, 1993;Fu, 1996;Zhao et al., 2008;Asem et al., 2019), respectively. The results of both neutrality tests were negative and significant for the AWWR population. ...
... The negative values of Fu's Fs test and Fu and Li's D* test suggest the existence of rare recent mutations (Fu, 1997;Ramos-Onsins and Rozas, 2002;Zhao et al., 2008;Asem et al., 2019) and an excess of rare historical mutations in populations (Fu and Li, 1993;Fu, 1996;Zhao et al., 2008;Asem et al., 2019), respectively. The results of both neutrality tests were negative and significant for the AWWR population. ...
Article
Full-text available
Artemia franciscana, native to America, has recently colonized as non-indigenous population in Asia, Europe, North Africa, and Australia. We evaluated the effects of the colonization of A. franciscana on genetic differentiation in new environments in the United Arab Emirates (UAE). We used the COI marker to determine the genetic structure and origins of exotic populations in the UAE. Results confirmed the colonization of A. franciscana in two localities. Invasive populations of A. franciscana had significantly lower genetic variation than native populations in the Great Salt Lake and San Francisco Bay. Results showed that the studied populations could not have colonized directly from natural American habitats, and they possibly were from secondary introduction events of other non-indigenous populations. Genetic analysis yielded different demographic patterns for the studied invasive populations. The population in Al Wathba Wetland Reserve (AWWR) demonstrated demographic expansion, whereas in Godolphin Lakes (GL), it reached a demographic equilibrium. Neutrality tests showed an excess of recent and historical mutations in the COI gene pool of invasive AWWR Artemia in the new environment. The results suggest that different ecological conditions in new environments can exert selective pressures during the introduction of an exotic population, which can affect genetic variation.
... (Perez et al., 1994;Valverde et al., 1994), a mitogenome of A. sinica (MK069595.1) (Asem et al., 2019), another of A. urmiana, and two mitogenomes from specimens of two populations of Tibet (identified as A. tibetiana, NC021382.1, JQ975177.1, ...
... Analyses of available nuclear DNA and mtDNA data A total of 428 nDNA sequences of the ITS region of Artemia Asem, Eimanifar & Sun, 2016, Asem et al., 2019Baxevanis, Kappas & Abatzopoulos, 2006;Eimanifar et al., 2014;Kappas et al., 2009;Maniatsi et al., 2009;Valsala, Sugathan & Bharathan, 2015;Vikas et al., 2012) and one of Streptocephalus proboscideus (Frauenfeld, 1873) (AY519840) used as outgroup, were downloaded from GenBank and aligned using MAFFT algorithm (Katoh & Toh, 2008). The resulting matrix was cleaned through Gblocks DNA information criterion (Castresana, 2000) excluding several contiguous non-conserved positions and allowing gap positions within the final blocks. ...
... published Artemia mitogenomes (Perez et al., 1994;Valverde et al., 1994;Zhang et al., 2013;Asem et al., 2019). ...
Article
Full-text available
High morphological plasticity in populations of brine shrimp subjected to different environmental conditions, mainly salinity, hindered for centuries the identification of the taxonomic entities encompassed within Artemia . In addition, the mismatch between molecular and morphological evolution rates complicates the characterization of evolutionary lineages, generating taxonomic problems. Here, we propose a phylogenetic hypothesis for Artemia based on two new complete mitogenomes, and determine levels of congruence in the definition of evolutionary units using nuclear and mtDNA data. We used a fossil of Artemia to calibrate the molecular clock and discuss divergence times within the genus. The hypothesis proposed herein suggests a more recent time frame for lineage splitting than previously considered. Phylogeographic analyses were performed using GenBank available mitochondrial and nuclear markers. Evidence of gen e flow, identified through discordances between nuclear and mtDNA markers, was used to reconsider the specific status of some taxa. As a result, we consider Artemia to be represented by five evolutionary units: Southern Cone, Mediterranean—South African, New World, Western Asian, and Eastern Asian Lineages. After an exhaustive bibliographical revision, unavailable names for nomenclatural purposes were discarded. The remaining available names have been assigned to their respective evolutionary lineage. The proper names for the evolutionary units in which brine shrimps are structured remain as follows: Artemia persimilis Piccinelli & Prosdocimi, 1968 for the Southern Cone Lineage, Artemia salina (Linnaeus, 1758) for the Mediterranean-SouthAfrican Lineage, Artemia urmiana Günther, 1899 for the Western Asian Lineage, and Artemia sinica Cai, 1989 for the Eastern Asian Lineage. The name Artemia monica Verrill, 1869 has nomenclatural priority over A. franciscana Kellogg, 1906 for naming the New World Lineage. New synonymies are proposed for A. salina ( = C. dybowskii Grochowski, 1896 n. syn. , and A. tunisiana Bowen & Sterling, 1978 n. syn. ), A. monica (= A. franciscana Kellogg, 1906 n. syn ., and A. salina var. pacifica Sars, 1904 n. syn. ); A. urmiana (= B. milhausenii Fischer de Waldheim, 1834 n. syn. , A. koeppeniana Fischer, 1851 n. syn. , A. proxima King, 1855 n. syn. , A. s. var. biloba Entz, 1886 n. syn. , A. s. var. furcata Entz, 1886 n. syn. , A. asiatica Walter, 1887 n. syn. , A. parthenogenetica Bowen & Sterling, 1978 n. syn. , A. ebinurica Qian & Wang, 1992 n. syn. , A. murae Naganawa, 2017 n. syn. , and A. frameshifta Naganawa & Mura, 2017 n. syn. ). Internal deep nuclear structuring within the A. monica and A. salina clades, might suggest the existence of additional evolutionary units within these taxa.
... Our results revealed a negative and significant Tajima's D value (−2.304) only for the exotic population in AWWR (Table 6), which demonstrated an excess of rare haplotypes followed by population expansion or purifying selection (Nei and Kumar, 2000;Swanson et al., 2001;Akey et al., 2004;Cruciani et al., 2008;Levitan and Stapper, 2009;Asem et al., 2019). Given the greater numbers of polymorphic sites (12 sites), mutations (12 mutations), and haplotypes (12 haplotypes) in comparison with other localities, Tajima's D result might be ascribed to the demographic expansion of the Artemia population in AWWR. ...
... The negative values of Fu's Fs test and Fu and Li's D* test suggest the existence of rare recent mutations (Fu, 1997;Ramos-Onsins and Rozas, 2002;Zhao et al., 2008;Asem et al., 2019) and an excess of rare historical mutations in populations (Fu and Li, 1993;Fu, 1996;Zhao et al., 2008;Asem et al., 2019), respectively. The results of both neutrality tests were negative and significant for the AWWR population. ...
... The negative values of Fu's Fs test and Fu and Li's D* test suggest the existence of rare recent mutations (Fu, 1997;Ramos-Onsins and Rozas, 2002;Zhao et al., 2008;Asem et al., 2019) and an excess of rare historical mutations in populations (Fu and Li, 1993;Fu, 1996;Zhao et al., 2008;Asem et al., 2019), respectively. The results of both neutrality tests were negative and significant for the AWWR population. ...
Article
Full-text available
Artemia franciscana, native to America, has recently colonized as non-indigenous population in Asia, Europe, North Africa, and Australia. We evaluated the effects of the colonization of A. franciscana on genetic differentiation in new environments in the United Arab Emirates (UAE). We used the COI marker to determine the genetic structure and origins of exotic populations in the UAE. Results confirmed the colonization of A. franciscana in two localities. Invasive populations of A. franciscana had significantly lower genetic variation than native populations in the Great Salt Lake and San Francisco Bay. Results showed that the studied populations could not have colonized directly from natural American habitats, and they possibly were from secondary introduction events of other non-indigenous populations. Genetic analysis yielded different demographic patterns for the studied invasive populations. The population in Al Wathba Wetland Reserve (AWWR) demonstrated demographic expansion, whereas in Godolphin Lakes (GL), it reached a demographic equilibrium. Neutrality tests showed an excess of recent and historical mutations in the COI gene pool of invasive AWWR Artemia in the new environment. The results suggest that different ecological conditions in new environments can exert selective pressures during the introduction of an exotic population, which can affect genetic variation.
... 21 found that GSL represented a unimodal mismatch distribution and have recorded this population was under demographic expansion. This difference can be attributed using sequences in different period from GSL. Asem et al. 56 have proved ecological variation could alter genetic structure of Artemia from Urmia Lake. It seems a comprehensive study needs to be performed on population genetic of both native American Artemia in GSL and SFB to estimate ability of genetic variation in two major sources in long-term. ...
Preprint
Artemia franciscana, native to America, has recently colonized non-indigenous populations in Eurasia, Mediterranean regions and Australia. In present we sought to evaluate the potential effects of colonization of A. franciscana on genetic differentiation in the new environments in UAE. We used the COI marker to determine population genetic structure and identify the origins of exotic populations in UAE. Our findings have confirmed the colonization of both localities by A. franciscana. Genetic variation of invasive A. franciscana were exclusively lower than native population in Great Salt Lake and San Francisco Bay. Results have showed the studied population could not possibly have colonized directly from natural American localities, perhaps resulting from secondary introduction events from other non-indigenous populations. Genetic analysis have yielded different demographic patterns for invasive studied populations. Al Wathba Wetland Reserve (AWWR) population have represented demographic expansion. In contrast, Godolphin Lakes (GL) population was at demographic equilibrium. Neutrality tests have documented the excess of both recent and historical mutations in the COI gene pool of invasive AWWR Artemia throughout establishment in the new environment.
... The aim of the present study was to further perform an analysis based on population genetic approaches to determine the intra-and inter-specific genetic variations of native and invasive Artemia populations from Iran and neighboring regions (14 sites) using Inter-Simple Sequence Repeats (ISSRs) genomic fingerprinting. Genomic fingerprinting by ISSR has been demonstrated to be a useful molecular tool to recognize DNA polymorphisms among Artemia taxa [27][28][29][30]. We hypothesize that the establishment of an exotic species in the new geographical habitats should be accompanied by intra-species genetic divergence to better adapt to the new environmental conditions. ...
... These results have also been documented by Eimanifar and Wink [28]. The high level of haplotype variation might be attributed to the evolutionary life history of A. urmiana [30] and/or its large population size [28]. Urmia Lake has undergone considerable changes in environmental conditions, such as salinity and temperature [41,42], which could have influenced genetic variation and population size during evolution. ...
... Overall, our ISSR results have documented that invasive A. franciscana populations had distinctly higher genetic variation than Western Asian native parthenogenetic populations. On the other hand, native A. franciscana from Great Salt Lake (GSL) have represented higher variation than examined invasive populations in this study, as the percentage of polymorphic loci differed from 67-81% vs. 30.95-46.83% (see [29]). ...
Article
Full-text available
Due to the rapid developments in the aquaculture industry, Artemia franciscana, originally an American species, has been introduced to Eurasia, Africa and Australia. In the present study, we used a partial sequence of the mitochondrial DNA Cytochrome Oxidase subunit I (mt-DNA COI) gene and genomic fingerprinting by Inter-Simple Sequence Repeats (ISSRs) to determine the genetic variability and population structure of Artemia populations (indigenous and introduced) from 14 different geographical locations in Western Asia. Based on the haplotype spanning network, Artemia urmiana has exhibited higher genetic variation than native parthenogenetic populations. Although A. urmiana represented a completely private haplotype distribution, no apparent genetic structure was recognized among the native parthenogenetic and invasive A. franciscana populations. Our ISSR findings have documented that despite that invasive populations have lower variation than the source population in Great Salt Lake (Utah, USA), they have significantly revealed higher genetic variability compared to the native populations in Western Asia. According to the ISSR results, the native populations were not fully differentiated by the PCoA analysis, but the exotic A. franciscana populations were geographically divided into four genetic groups. We believe that during the colonization, invasive populations have experienced substantial genetic divergences, under new ecological conditions in the non-indigenous regions.
... Recently, Asem et al. (2019) used four molecular markers (Na+/K+ ATPase, COI, 16s rRNA and ITS1) to investigate the effects of environmental changes on Artemia genetic variability in the Urmia Lake. ...
Article
Full-text available
Up to date, the true phylogenetic relationships among the Artemia species are under debate. In this study, some morphometric and molecular (Inter-simple sequence repeats, ISSR) variations were analyzed to evaluate the biodiversity among some Egyptian Artemia species comparatively with other brine shrimps (A. parthenogenetica, A. salina and A. franciscana). The highest and lowest Wilks' lambda values were calculated for the Length of furca and the abdominal length. The cluster analysis based on the Artemia morphological variations was an agreement with the re-constructed dendrogram based on ISSR markers. The ISSR variations were comparatively analyzed with the Artemia species Cytochrome oxidase subunit I gene (COI) sequence variations. Based on the COI consensus sequences, the distance value between A. salina and A. parthenogenetica was higher than the distance value between A. salina and A. franciscana. The ISSR could be an effective method in Artemia molecular characterization and evolutionary studies. The results could be helpful in the conservation of the evaluated Artemia species. The combination of more informative molecular markers with the selected morphometric characters should be carried out to understand the true evolutionary variations in the Artemia resources.