Genetic relationships among American species of the genus Prosopis (Mimosoideae, Leguminosae) inferred from ITS sequences: evidence for long-distance dispersal
TL;DR: This work aimed to determine whether American Prosopis sections arose in North or South America, and to explain the current distribution of their species on the basis of their genetic relationships.
Abstract: Aim The genus Prosopis includes 44 species and has a pseudoamphitropical, disjunct distribution. We aimed to determine whether American Prosopis sections arose in North or South America, and to explain the current distribution of their species on the basis of their genetic relationships.
Location South-western USA, Mexico, Caribbean Antilles, Peru–Ecuador, central and northern Argentina, south-western Argentina (Patagonia) and Cuyo, south-western Asia and northern Africa.
Methods Internal transcribed spacer fragments from 21 species of Prosopis were sequenced and the data were used to analyse the phylogenetic relationships using Microlobius and Mimosa as outgroups. Genetic distances were calculated to estimate the degree of divergence. Dispersal–vicariance (DIVA) analysis was conducted to help understand the biogeographical history of the genus.
Main conclusions The sections Strombocarpa and Algarobia are not monophyletic. Prosopis argentina (section Monilicarpa) and the species of Algarobia are included in single clade. The phylogeny, DIVA analysis, and the pattern of genetic distances indicate that the ancestral area for the American species was wide, from south-western USA to Central and northern Argentina. Successive vicariance events split this area, and long-distance dispersal episodes (perhaps mediated by birds) led to recolonizations from North to South America, and vice versa.
Citations
More filters
TL;DR: The objective of this study is to further outline the determinants of plant genetic structure by distinguishing the effects of mating system on gene flow and on genetic drift, and to confirm that mating system is the main influencing factor of FST.
Abstract: Understanding the mechanisms that control species genetic structure has always been a major objective in evolutionary studies. The association between genetic structure and species attributes has received special attention. As species attributes are highly taxonomically constrained, phylogenetically controlled methods are necessary to infer causal relationships. In plants, a previous study controlling for phylogenetic signal has demonstrated that Wright's FST, a measure of genetic differentiation among populations, is best predicted by the mating system (outcrossing, mixed-mating or selfing) and that plant traits such as perenniality and growth form have only an indirect influence on FST via their association with the mating system. The objective of this study is to further outline the determinants of plant genetic structure by distinguishing the effects of mating system on gene flow and on genetic drift. The association of biparental inbreeding and inbreeding depression with population genetic structure, mating system and plant traits are also investigated. Based on data from 263 plant species for which estimates of FST, inbreeding (FIS) and outcrossing rate (tm) are available, we confirm that mating system is the main influencing factor of FST. Moreover, using an alternative measure of FST unaffected by the impact of inbreeding on effective population size, we show that the influence of tm on FST is due to its impact on gene flow (reduced pollen flow under selfing) and on genetic drift (higher drift under selfing due to inbreeding). Plant traits, in particular perenniality, influence FST mostly via their effect on the mating system but also via their association with the magnitude of selection against inbred individuals: the mean inbreeding depression increases from short-lived herbaceous to long-lived herbaceous and then to woody species. The influence of perenniality on mating system does not seem to be related to differences in stature, as proposed earlier, but rather to differences in generation time. Plant traits correlated with generation time affect both inbreeding depression and mating system. These in turn modify genetic drift and gene flow and ultimately genetic structure.
164 citations
Cites background from "Genetic relationships among America..."
...The details of the topology at lower taxonomic levels were then grafted according to phylogenetic information obtained from various sources, generally from specific phylogenetic studies at the family level or below [27-45]....
[...]
TL;DR: The phylogenetic hypotheses were used to infer the biogeographic history, divergence times, and potential reticulate evolution of Opuntieae, including Opuntia s.s.s, which originated in southwestern South America and expanded to the Central Andean Valleys and the desert region of western North America during the Pliocene.
Abstract: Premise of the study: The opuntias (nopales, prickly pears) are not only culturally, ecologically, economically, and medicinally important, but are renowned for their taxonomic diffi culty due to interspecifi c hybridization, polyploidy, and morphological variability. Evolutionary relationships in these stem succulents have been insuffi ciently studied; thus, delimitation of Opuntia s.s. and major subclades, as well as the biogeographic history of this enigmatic group, remain unresolved. Methods: We sequenced the plastid intergenic spacers atpB-rbcL, ndhF-rpl32 , psbJ-petA , and trnL-trnF , the plastid genes matK and ycf1 , the nuclear gene ppc , and ITS to reconstruct the phylogeny of tribe Opuntieae, including Opuntia s.s. We used phylogenetic hypotheses to infer the biogeographic history, divergence times, and potential reticulate evolution of Opuntieae. Key results: Within Opuntieae, a clade of Tacinga , Opuntia lilae , Brasiliopuntia , and O. schickendantzii is sister to a well-supported Opuntia s.s., which includes Nopalea . Opuntia s.s. originated in southwestern South America (SA) and then expanded to the Central Andean Valleys and the desert region of western North America (NA). Two major clades evolved in NA, which subsequently diversifi ed into eight subclades. These expanded north to Canada and south to Central America and the Caribbean, eventually returning back to SA primarily via allopolyploid taxa. Dating approaches suggest that most of the major subclades in Opuntia s.s. originated during the Pliocene. Conclusions: Opuntia s.s. is a well-supported clade that includes Nopalea . The clade originated in southwestern SA, but the NA radiation was the most extensive, resulting in broad morphological diversity and frequent species formation through reticulate evolution and polyploidy.
161 citations
Cites background from "Genetic relationships among America..."
...…United States/northern Mexico ( Johnston, 1940 ; Axelrod, 1948 ; Raven, 1963 ; Solbrig, 1972 ; Lia et al., 2001 ; Simpson et al., 2005 ; Bessega et al., 2006 ; Moore et al., 2006 ; Hawkins et al., 2007 ), although there is still speculation as to why such disjunctions occur ( Solbrig,…...
[...]
...…suggest that these North – South American disjunctions must have formed via long-distance dispersal events ( Raven, 1963 ; Simpson et al., 2005 ; Bessega et al., 2006 ; Moore et al., 2006 ), since very few species of the overall fl oras are shared between the two areas (e.g., 2%; Raven, 1972…...
[...]
TL;DR: The authors reviewed advances in the study of two major intercontinental disjunct biogeographic patterns: (i) between Eurasian and western North American deserts with the Mediterranean climate (the Madrean-Tethyan disjunctions); and (ii) between the temperate regions of North and South America (the amphitropical disjunitions).
Abstract: The present paper reviews advances in the study of two major intercontinental disjunct biogeographic patterns: (i) between Eurasian and western North American deserts with the Mediterranean climate (the Madrean- Tethyan disjunctions); and (ii) between the temperate regions of North and South America (the amphitropical disjunctions). Both disjunct patterns have multiple times of origin. The amphitropical disjunctions have largely resulted from long-distance dispersal, primarily from the Miocene to the Holocene, with available data indicating that most lineages dispersed from North to South America. Results of recent studies on the Mediterranean disjuncts between the deserts of Eurasia and western North America support the multiple modes of origin and are mostly consistent with hypotheses of long-distance dispersal and the North Atlantic migration. Axelrod's Madrean-Tethyan hypothesis, which implies vicariance between the two regions in the early Tertiary, has been favored by a few studies. The Beringian migration corridor for semiarid taxa is also supported in some cases.
148 citations
TL;DR: An evaluation of the limitations of the dispersal–vicariance analysis implemented in the software diva is needed, especially in relation to several newer alternatives.
Abstract: Aim Analytical methods are commonly used to identify historical processes of vicariance and dispersal in the evolution of taxa. Currently, dispersal-vicariance analysis implemented in the software ...
104 citations
Cites background from "Genetic relationships among America..."
...Many of these studies have inferred vicariance events at the base of the tree, where the true history could have been either vicariance or speciation by dispersal (e.g. Drovetski, 2003; Sanmartı́n, 2003; Bessega et al., 2006; Biswas & Pawar, 2006; Guo & Wang, 2007; Musilová et al., 2008)....
[...]
TL;DR: A combined approach including molecular phylogeny, molecular dating, and character optimization analysis was applied to study Prosopis diversification and evolution, suggesting that prosopis is not a natural group.
Abstract: The genus Prosopis is an important member of arid and semiarid environments around the world. To study Prosopis diversification and evolution, a combined approach including molecular phylogeny, molecular dating, and character optimization analysis was applied. Phylogenetic relationships were inferred from five different molecular markers (matK-trnK, trnL-trnF, trnS-psbC, G3pdh, NIA). Taxon sampling involved a total of 30 Prosopis species that represented all Sections and Series and the complete geographical range of the genus. The results suggest that Prosopis is not a natural group. Molecular dating analysis indicates that the divergence between Section Strombocarpa and Section Algarobia plus Section Monilicarpa occurred in the Oligocene, contrasting with a much recent diversification (Late Miocene) within each of these groups. The diversification of the group formed by species of Series Chilenses, Pallidae, and Ruscifoliae is inferred to have started in the Pliocene, showing a high diversification rate. The moment of diversification within the major lineages of American species of Prosopis is coincident with the spreading of arid areas in the Americas, suggesting a climatic control for diversification of the group. Optimization of habitat parameters suggests an ancient occupation of arid environments by Prosopis species. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 621–640.
86 citations
Cites background or result from "Genetic relationships among America..."
...The only cladistic analysis performed (Bessega et al., 2006) suggested that most of the groups taxonomically recognized are not monophyletic....
[...]
...The results obtained in the present study are consistent with the only previous cladistic analysis involving Prosopis species (Bessega et al., 2006) in showing that the Section Algarobia is not monophyletic, and that P. argentina (Section Monilicarpa) is close to species of Section Algarobia....
[...]
...3) but not in that of Bessega et al. (2006)....
[...]
...In addition, none of these studies have evaluated the nature of the Prosopis generic limits as either outgroups were not included (Ramírez et al., 1999; Bessega et al., 2005), or these were distantly related to Prosopis species (Bessega et al., 2006)....
[...]
...…Biological Journal of the Linnean Society, 2008, 93, 621–640 © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 621–640 by species of Series Ruscifoliae, Chilenses, and Pallidae (mesquite clade) is not monophyletic in the analysis of Bessega et al. (2006)....
[...]
References
More filters
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
57,055 citations
"Genetic relationships among America..." refers methods in this paper
...4.0b10; Swofford, 1998) to create a matrix of distances among sequences (with Kimura 2-parameter model, then neighbor (the neighbour-joining method of Saitou & Nei, 1987) was used to infer the network of relationships from the distance matrix using the program phylip (ver....
[...]
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Abstract: The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
40,349 citations
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Abstract: CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.
38,522 citations
"Genetic relationships among America..." refers methods in this paper
...Sequences were edited with the computational program bioedit (Hall, 1999) and initial alignment was performed using clustalx (Thompson et al., 1997) with the default Journal of Biogeography 33, 1905–1915 1907 ª 2006 The Authors....
[...]
35,309 citations
01 Jan 1990
26,241 citations