Supporting Information Tables S1 & S2
Table S1 Polyploid complexes analyzed phylogenetically, not included in Mayrose et al.
(2011)
Aegilops/Triticum (Poaceae)
Given that the polyploid species of Triticum involve several species of Aegilops
as parents, the genus Triticum is clearly not monophyletic, Aegilops is also not
monophyletic (Petersen et al., 2006; Bordbar et al., 2011). We consider them together –
both exemplify considerable diversification at the polyploid level. Estimates of the
number of species in Aegilops varies from 22 to perhaps as many as 29 species
comprising both diploids and polyploids, using the higher species estimate, 11 are diploid
(2n = 14), 13 are tetraploid (2n = 28), and five are hexaploid (2n = 42). Triticum
comprises 11 species and includes three diploids (2n = 14), 6 tetraplods (2n = 28) and
two hexaploids (2n = 42) including T. aestivum (common wheat).
Consolea (Cactaceae)
Consolea (Cactaceae) is an entirely polyploid genus of 9 species (Areces-Mallea
2001), species range from hexaploid (2n = 66) to dodecaploid (2n = 132) (Negrón-Ortiz
2007, Baker et al., 2009, Majure et al., 2012a) relative to the base number of n = 11 for
all Cactaceae (Pinkava, 2002). Consolea forms a well-supported clade with the parents
being some member of Opuntia s.s. and another member of tribe Opuntieae outside of the
Tacinga-Brasiliopuntia-Opuntia clade (Majure et al., 2012b). However, using a genuslevel approach, as in Mayrose et al. (2011), hexaploid members (2n = 66) of the
Consolea clade would be diploid and those octoploid (2n = 88) and higher ploidal levels
(e.g., dodecaploids, 2n = 132) would be derived polyploids. Clearly the entire clade is
polyploid (Majure et al., 2012b).
Draba (Brassicaceae)
Draba L. (Brassicaceae) comprises approximately 400 species. Of the 43% of the
genus for which chromosome counts are available 78% are polyploid (Windham 2000,
2003, Jordon-Thaden & Koch, 2008). Draba ranges in ploidy from diploid (2n = 16) to
octadecaploid (18n = 144) with numerous stable levels in between (mostly 4n, 6n, 8n,
10n). Draba has a highly accelerated rate of speciation and polyploidization (JordonThaden & Koch, 2008). Polyploidy has also played a major role in each of the three
major clades (Jordon-Thaden et al., 2010). There is also strong evidence of cryptic
speciation within arctic polyploids as well as recurring polyploid formation, resulting in
high species diversity among polyploids (Grundt et al., 2006). High rates of speciation
and polyploidization in Draba since the Pleistocene indicates that polyploidy continues to
play an integral role in the diversification of the genus.
Elymus (Poaceae)
Elymus includes ~ 150 perennial species distributed in a wide range of ecological
habitats over the temperate and subtropic regions. In Triticeae, the basic number is x = 7
(Wang et al., 1995). The chromosome numbers in Elymus range from 2n = 4x = 28 to 2n
= 8x = 56 (~ half of the counts available have 2n = 42). The lowest number in Elymus is
actually already tetraploid (2n = 28), these would be considered diploid following
Mayrose et al. (2011). Several phylogenetic analyses of the genus have been published
(Liu et al., 2006, Zhang et al., 2009).
Festuca (Poaceae)
Festuca (Fescue) is one of the largest genera of Poaceae. It
comprises about 600 species and has a worldwide distribution. About 70% of species are
polyploid (with ploidal levels up to 12x); several phylogenetic analyses have been
conducted (Catalán et al., 2004, Šmarda et al., 2008).
Fragaria (Rosaceae)
Fragaria (Rosaceae) comprises 20 named species, 11 of which are diploid (2n =
14)—the remaining species are polyploid. Five are 4x, one is 6x, two are 8x, and one is
10x.
Gossypium (Malvaceae)
Gossypium (cotton, Malvaceae) consists of about 50 species – 45 diploid and 5
polyploid (tetraploid) and includes two polyploid species that were domesticated (G.
barbadense, G. hirsutum). Grover et al. (2012) recently demonstrated the monophyly of
the tetraploid species of Gossypium. Madlung (2013) recently noted Gossypium as a
good example of a polyploid radiation in his review.
Hedera (Araliaceae)
The genus Hedera (Araliaceae) is a polyploidy complex with approximately 16
taxa (Rutherford et al., 1993, Ackerfield & Wen, 2002, 2003). Clades of diploids (2n=
24) and polyploids (2n = 48, 72, 96, one species has 2n = 192) are geographically
structured suggesting recurrent genome duplication in this group. Approximately 60% of
Hedera species are polyploids (Vargas et al., 1999, Green et al., 2011).
Hordeum (Poaceae)
Hordeum (Poaceae) comprises 31 species with a nearly worldwide distribution.
About 50% of the species are polyploids (4x, 6x) or have both diploid and polyploid
forms (Blattner, 2004, Brassac et al., 2012).
Nicotiana (Solacnaceae)
Nicotiana (Solanaceae) comprises 75 naturally occurring species (40 diploids and
35 allopolyploids), the genus exhibits a mix of young as well as old polyploid members.
There are recently formed allotetraploids (less than 200,000 years, most of which are
associated with human habitation (e.g. N. tabacum). In sect. Repandae there are 4
polyploid species estimated to be 5 mya. Sect. Suaveolentes consists of 26 species, all
polyploid, and appears to still be diversifing. The clade has basal members with n = 24
and then descend to as low as n = 15 in two groups via reduction. The polyploids in this
clade are at least 10 my old (Clarkson et al., 2004, Chase et al., 2003, M. Chase pers.
Comm.).
Opuntia (Cactaceae)
Opuntia (Cactaceae) is a strictly New World genus distributed from southern
South America to Canada and consisting of around 200 species. Divergence time
estimation reveals a very young age for the genus as well at 5.6 ± 1.9 mya (Arakaki et al.,
2011). The base number in the family Cactaceae, and thus the genus Opuntia, does not
deviate from n = 11 (Pinkava 2002). The majority of species of Opuntia are polyploid
ranging from triploids (2n = 33) to nine-ploids (2n = 99). Of the 150 species with
reported chromosome numbers, 59 % were polyploid, 12 % were represented by both
diploid and polyploid counts, and only 29 % were recorded as diploid (Majure et al.,
2012a). Hybridization is common in Opuntia, and recent phylogenetic analyses recorded
numerous allopolyploid, interclade hybrids in the genus (Majure et al., 2012b). However,
polyploids are also very commonly derived from within clades as well. Nine of the ten
major clades of Opuntia consist of both diploid and polyploid taxa (Majure et al., 2012b).
Findings from Majure et al. (2012b) also emphasize the problems with including taxa
derived from reticulate evolution in the bifurcating framework of phylogenetic analyses.
Paeonia (Paeoniaceae)
Paeonia comprises 35 species distributed widely in five disjunct areas in the
northern hemisphere. Three sections are recognized within Paeonia (reviewed in Sang et
al., 1997). Section Oneapia, (2 species – both diploid), Section Moutan with six species,
all diploid), Section Paeonia consists of 27; one-third of the species in section Paeonia
are tetraploids. A phylogeny has been provided by Sang et al. (1997).
Rubus (Rosaceae)
Rubus (Rosaceae) includes ∼750 species, it is evolutionary complex and one of
the most systematically challenging genera of plants. Rubus is
taxonomically/evolutionary complex because of frequent hybridization, morphological
diversity, vegetative propagation, asexual seed production, and a high frequency of
polyploidy. Approximately 60% of all Rubus species are polyploid. A phylogenetic
framework was provided by Alice & Campbell (1999).
Tacinga (Cactaceae)
Tacinga (Cactaceae) is a genus of 8 species restricted to the Caatinga of Brazil
and northern Venezuela (Majure et al., 2013). Of those 8 species, 3 have been recorded
as polyploid (tetra- and hexaploid levels, 2n = 44, 66), and 2 species have been recorded
as diploid (2n = 22, Majure et al., 2012a). Tacinga forms a well-supported clade sister to
the Brasiliopuntia brasiliensis-Opuntia schickendantzii clade (Majure et al., 2012b),
although species relationships are not completely resolved phylogenetically.
Viola (Violaceae)
Viola (Violaceae) contains 500–600 species and comprises numerous hybrid and
polyploid complexes. From a putative base number of x = 6 or x = 7, extant chromosome
numbers range from 2n = 4 in V. modesta to at least 20-ploid 2n = ca. 160 in Viola
arborescens. Many members of Viola are considered high polyploids (with more than six
sets of nuclear chromosomes). The work of Marcussen et al. (2012) supported the
monophyly of the high polyploids, which resulted from allodecaploidization 9–14 Ma,
involving diploid and two paleotetraploid ancestors. Two of the high-polyploid lineages
remained decaploid, recurrent polyploidization with tetraploids within the last 5 Ma has
resulted in two 14-ploid lineages and one 18-ploid lineage (reviewed in Marcussen et al.,
2012). Polyploid speciation has been the major contributor to the diversification of this
genus (Marcussen et al., 2012).
Table S2 Other polyploid complexes in need of investigation
Genus
Family
References
Antennaria
Asteraceae
Bayer & Stebbins, 1987, Bayer et al.,
1996
Arctostaphylos
Ericaceae
Artemisia
Asteraceae
Bromus
Poaceae
Boykin et al., 2005
Torrell et al., 2001, Valles et al., 2001
Ainouche & Bayer, 1997, Fortune et
al., 2008
Campanula rotundifolia
Campanulaceae
Kovanda, 1977
Orobanchaceae
Heckard & Chuang, 1977, Chaung &
complex
Castilleja
Heckard, 1993, Tank & Olmstead,
2008
Clarkia
Onagraceae
Lewis, 1953, Lewis & Lewis, 1955,
Stebbins, 1971, Grant, 1981
Claytonia
Montiaceae
Lewis, 1970, Stebbins, 1971, Doyle,
1983
Crataegus
Rosaceae
Talent & Dickinson, 2005, Lo et al.,
2009, Lo et al., 2010
Crepis
Asteraceae
Babcock & Stebbins, 1938, Stebbins,
1950, 1971
Danthonia
Poaceae
Stebbins, 1971
Drosera
Droseraceae
Rivadavia et al., 2003
Galium anisophyllum
Rubiaceae
Stebbins, 1971
Glycine
Fabaceae
Doyle, 2012 (review)
Hieracium
Asteraceae
Fehrer et al., 2007, Fehrer et al., 2009
Iris
Iridaceae
Mitra, 1956, Stebbins, 1971
Micranthes
Saxifragaceae
Webb & Gornall, 1989, Soltis et al.,
complex
1996
Poa
Poaceae
Rubus
Rosaceae
Soreng, 2007, Soreng et al., 2010
Alice & Campbell, 1999, Alice et al.,
2001, Morden et al., 2003
Rumex paucifolius
Polygonaceae
Smith, 1968
Salicaceae
Azuma et al., 2000, Brunsfeld et al.,
complex
Salix
1991, Mabberley, 1997, Soltis & Soltis,
1990, Stebbins, 1971
Saxifraga
Saxifragaceae
Webb & Gornall, 1989, Soltis et al.,
1996
Tradescantia
Commelinaceae
Martínez & Ginzo, 1985
Vaccinium
Ericaceae
Lyrene et al., 2003
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