Presence (x) of the accepted species of Alstroemeria in the administrative political regions of Chile.
The genus Alstroemeria encompasses approximately 80 species endemic to South America, with 2 centers of diversity (Chile and Brazil). In Chile, Alstroemeria represents one of the most diverse genera of vascular monocotyledons, comprising more than 50 recognized or accepted taxa (36 species, 11 subspecies and 10 varieties) from which ca. 82% are endemic to the Mediterranean zone of central Chile, one of the world’s diversity hotspots. The taxonomy of the genus is very difficult due to the great variability of the vegetative and floral traits. Moreover, a number of taxa have been recently described and several nomenclatural changes have been proposed. In order to elucidate the taxonomy of some Chilean complexes of Alstroemeria, an integrative approach including morphology, colorimetry, cytogenetic, multivariate statistical analyses of morphological variation and DNA-molecular studies have been conducted. In this chapter, we review the literature concerning these approaches; a checklist of the species growing in Chile is provided including all published names, references to the original protologues, accepted names, synonyms and the biogeographic status (endemic or native) of the accepted taxa; maps illustrating the diversity of the genus in South America and its distribution in Chile were constructed.
- Chilean hotspot
- geographical distribution
- South America
The family Alstroemeriaceae Dumort. nom. Cons., belongs to the monocotyledon angiosperm clade (Subclass: Liliopsida, Order: Liliales) [1, 2]. It is distributed in Central and South America , and comprises about 200 species distributed in the genera Alstroemeria L., Bomarea Mirb., Leontochir Phil. and Schickendantzia Pax . Some authors recognized Taltalia Ehr. Bayer as an independent genus [5, 6] while others included Taltalia and Schickendantzia in Alstroemeria . Genera have been classified in two subfamilies: (a) Subfamily: Luzuriagoideae with Drymophila R. Br. and Luzuriaga Ruiz & Pav. and (b) Subfamily: Alstroemerioideae with Alstroemeria and Bomarea (incl. Leontochir) [3, 8] or treated Luzuriagoideae as a separate family Luzuriagaceae . Alstroemeria comprises about 80 species endemic to South America (southern South America and Eastern Brazil); Bomarea includes 120 species in Central and South America; Luzuriaga comprises 4 species (3 species in Chile, 1 in New Zealand) and Drymophila 1 species from Australia and Tasmania . Phylogenetic studies using morphology and DNA sequences (rps16, rbcL) recognized Alstroemeria as monophyletic and certainly different from Leontochir and Bomarea; moreover, three subclades of Alstroemeria have been recognized that correspond to northern Chile, central Chile and Brazil . Alstroemeria was established by Linnaeus in 1762 in honor to the Swedish botanist Claus von Alströmer . It has its boreal distribution in Venezuela (3°N) and its austral limit in the Patagonia of Chile and Argentina, with two main distribution centers in the continent: Brazil (and adjacent areas of Paraguay and Argentina) and Chile (and the adjacent countries Peru, Bolivia and Argentina) [11, 12, 13, 14, 15]. In Chile, Alstroemeria represents 1 of the most diverse genera of vascular monocotyledons, comprising more than 50 recognized or accepted taxa (36 species, 11 subspecies and 10 varieties) from which about ca. 82% are endemic to the Mediterranean zone of central Chile . Due to the beauty of their flowers, Chilean species of Alstroemeria, locally known as “astromelias or lirios del campo” are appreciated all over the world as ornamental plants [16, 17, 18]. Many hybrids and cultivars have been developed in several countries, such as, The Netherlands, England, United States and Japan . The taxonomy of the genus is very complex due to the great variability both in vegetative and floral characters . Moreover, several taxa have been recently described (e.g., A. werdermannii var. flavicans , A. philippi var. albicans , A. philippi subsp. adrianae , A. hookeri subsp. sansebastiana , A. marticorenae , A. traudliae ) or nomenclatural changes have been made, affecting the rank status of many taxa. Due to its geographical isolation, Chile contains a unique flora which includes an extraordinary number of endemic plants. Furthermore, the area between the Regions of Atacama and Biobío comprises about 60% of the vascular species of the Chilean flora, with nearly 50% endemic to Chile . In this area, identified as a hotspot of biodiversity , lives most of the Chilean species of Alstroemeria. This area harbors most of the Chilean population, and is characterized by a strong disturbance triggered mainly by agriculture, industry and forestry. In this chapter, we reviewed the taxonomic literature to make an updated checklist of the species growing in Chile and their synonyms. In addition, we construct distribution maps based on the literature as well as on the database of the Herbarium of the University of Concepción (CONC). Recent studies integrating different source of evidence, such as morphometry, cytogenetic, colorimetry and molecular data for better taxonomic species delimitation are discussed.
The database of the Herbarium of the University of Concepción (CONC) was used to construct preliminary lists of species and the geographic distribution of each taxon. This database contains the following fields: (1) Taxon name; (2) Collector’s name; (3) Collector’s number; (4) Latitude; (5) Longitude; (6) Elevation; (7) Administrative region; (8) Locality; (9) Collection date (month); (10) Collection date (Year); (11) Herbarium and (12) Herbarium number. A total of 714 specimens were included in the CONC-DB. In addition to historical specimens, plants were collected and photographed in the field and kept in CONC. A checklist is provided including all published combinations, references to original publication, accepted names and biogeographic status (endemic or native). Maps illustrating the diversity of the genus in South America and distribution in Chile were constructed based on data taken from the CONC-DB and literature [14, 15, 23], using the software DIVA-GIS 7.5.0.
3. Taxonomy and distribution of the genus Alstroemeria in Chile
3.1. General morphology
Alstroemeria comprises mostly perennial species. In 1998, Bayer  established the monotypic genus Taltalia to separate the annual A. graminea Phil., endemic to northern Chile, from Alstroemeria. Perennial species have cylindrical rhizomes, from which two kinds of roots born: thin roots and thick roots which contain starch (Figure 1A); A. ligtu (locally known as “liuto”) was used by indigenous people (Mapuches or Araucanos) to produce starch from the thick roots. According to Molina , the farmers made from the roots of this plant “a white, light, nutritious and so healthy flour that they usually gave it to the sick persons…” . Aerial stems are erect or decumbent. The leaves are often resupinated, that is, twisted from the petiole or the leaf blade so the lower surface becomes functionally the upper surface; sometimes the leaves form basal rosettes; leaf blades thin or thick, sometimes with papillae; the blade varies in shape from linear to elliptic or ovate; fertile stems usually have reduced leaves but sterile stems have well developed leaves (Figure 1B). The flowers are slightly zygomorphic (Figure 1C-D), with six free tepals in two verticils; the three outer tepals are similar in shape and color; the inner three tepals are differentiated in two upper inner tepals and one lower inner tepal. Upper inner tepals with colored lines (nectar guides) on a lighter background (Figure 1D). Stamens 3: the ovary is inferior, 3-carpellate, 3-loculate. The fruit is a six-ribbed loculicidal capsule (Figure 1C) with explosive dehiscence, with numerous globose seeds (Figure 2).
3.2. Colorimetric studies in Chilean Alstroemeria
In Alstroemeria, the flowers varies in color from white to yellow, pink, red, purple and violet according to the species [11, 14]; color is regulated by several pigments including anthocyanin-like 6-hydroxydelphinidine 3-rutinoside, 6-hydroxycyanidin 3-rutinoside, delphinidin 3-malonylglucoside among others, carotenoids and flavonoids . In some groups of plants, as occurs in Alstroemeria, it is possible that the taxonomic characters traditionally used do not have sufficient discriminant power to differentiate very close species or varieties within a species complex. In such cases, it may be useful to have characteristics that pose a new perspective on the problem. It has been shown that the color of the corolla, objectively measured, had high taxonomic value when the traditional characters were less informative to distinguish cryptic taxa . In Alstroemeria, the color of the flower has often been used in keys and descriptions [11, 14, 15, 22, 23], however, most of the time, the described color corresponds to a subjective perception of the same by the human eye. The color of the flowers is taxonomically significant in Alstroemeria [14, 29, 30]; the outer tepals and the lower inner tepals are similar in shape and color but the upper internal tepals are different, showing unique patterns of maculae (actually nectar guides) that are species specific; however, some species showed variability in the background color , because it depends on several ecological factors such as temperature and pH . In order to describe objectively the color (mainly the background color) of the different tepals (external, upper internal and lower internal), the CIElab system  has been used in some species complexes of Chilean Alstroemeria [29, 30] (Figure 3). The CIE (Commission Internationale de l’Eclairage) color system uses three coordinates to locate a given color in the color space. The spectrophotometer registers the reflected wavelengths as numerical values (spectral curve) from which the coordinates that place a given color in the color space are calculated. The color expressed in the CIELab scale uses the Cartesian coordinates L*, a* and b*. L* expresses the luminosity, a* denotes the green/red value and b* the blue/yellow value. The degree of luminosity of L* determines that a color appears lighter or darker and is expressed in a scale from 0 (black or total absorption) to 100 (white). The axis a* moves from negative values (green) to positive values (red) while axis b* moves from blue (negative values) to yellow (positive values). The color expressed in the CIELCh scale uses polar coordinates (L*, C*, h°), derived from the CIELab scale. C* denotes chroma (saturation, intensity) and h° denotes hue, expressed as angular measures. Chroma is the distance of the color from the axes a* and b* of L*, calculated as (a*2 + b*2)1/2 and represents the color saturation; the hue, h° is calculated as arctg (b*/a*). In A. magnifica complex, the colorimetric study of the flower helped to elucidate the taxonomic position of A. pulchra var. maxima. This taxon, originally described by Philippi in 1864 , was transferred by Bayer in 1987 to A. magnifica with the subspecific rank (A. magnifica subsp. maxima) .
The colorimetric differences between A. magnifica and A. pulchra as shown in the reflectance spectra were due mainly to the parameters a* and b* indicating that A. magnifica have tepals comparatively more intense violet than those of A. pulchra var. maxima. Our results suggest that the color of the flowers can be used as a new taxonomic character in Alstroemeria and that var. maxima probably belongs to A. pulchra as originally proposed and not to A. magnifica . Colorimetric studies were carried out also in A. presliana . This species comprises two subspecies: subsp. presliana and subsp. australis. Alstroemeria presliana subsp. presliana grows in Chile (Regions of Maule and Biobío) and Argentina (Neuqén) ; subsp. australis in endemic to Chile (Regions of Biobío and Araucanía) [11, 14].
Although the color of the flowers is one of the most important characters to distinguish the subspecies , there is a huge variability in color in the flowers of both subspecies. Differences in the spectral reflectance curves were detected between 440 and 540 nm and between 660 and 700 nm in the outer and lower inner tepals. Upper internal tepals differ mainly between 640 and 700 nm. The color measured in the CIELab space is related to the content of anthocyanins so that the flowers containing delphinidin-3-glucosides take on a more blue hue than those containing exclusively cyanidin-3-glucosides . The presence of delphinidin-3-glucosides detected in subsp. presliana but not in subsp. australis  could explain the bluer hue observed in subsp. presliana in comparison with subsp. australis and the difference observed in the parameter b*, which takes negative values in subsp. presliana and positive values in subsp. australis both in outer and lower inner tepals. On the other hand, in the upper inner tepals, b* was positive (yellow), reaching higher values in subsp. australis and therefore denoting a more intense yellow color in subsp. australis than in subsp. presliana .
3.3. Geographical distribution
In Chile, there are 38 species of Alstroemeria and 16 infraspecific taxa (8 subspecies and 8 varieties) and 1 nothospecies (A. x chrysantha) . Nevertheless, more than 116 species have been described, most of which are considered synonyms or are names of uncertain application because there is no original material (types) in herbaria (see Checklist below). The description of such high number of taxa can be explained by the extent of morphological variation, especially of the flowers, which harbors most of the characters useful to taxonomy, and because microevolutionary processes are still active so that species are not yet completely separated. Chile shares only few taxa with its neighboring countries (Argentina, Bolivia and Peru). In Peru, five species have been mentioned [14, 36, 37], one of which is also present in Chile: A. violacea. In Bolivia, three species are found, one of which growth in Chile: A. aurea (, under A. aurantiaca). In Argentina, there are 10 species , 5 shared with Chile: A. andina var. venustula, A. aurea, A. patagonica, A. presliana subsp. presliana, A. pseudospathulata. Thus, more than 88% of the genus is represented by taxa endemic to Chile (Figure 4). In Chile, Alstroemeria spreads from 20°S (Tarapacá Region) to 53°S (Magallanes Region) [14, 23]. Most taxa have a very restricted distribution in Chile (Table 1). The vast majority of the species are distributed in north (Tarapacá-Coquimbo) and central (Valparaíso-Biobío) Chile (Figure 5); only six species growth in southern Chile (Araucanía-Magallanes). The most boreal taxa are A. lutea and A. violacea that reach the Region of Tarapacá (20°S) in northern Chile. Alstroemeria lutea is restricted to the coast of the Tarapacá Region (Iquique) whereas A. violacea extends southern to 28°S in the Atacama Region; this species if known also from Peru (Arequipa) [14, 23, 37]. The regions with the largest number of taxa are Atacama (14 taxa), Coquimbo (26), Valparaíso (19) and Metropolitan (14) (Figure 6). The number of taxa decreases abruptly southern the Maule Region where 12 taxa are found; in Los Ríos and Los Lagos, only one species has been collected (A. aurea) and A. patagonica is found in Aysén and Magallanes being the most austral species of the genus Alstroemeria in the world. The latter species grow from 46°30′S to 52°45′S  and also in Argentina (Neuquén to Tierra del Fuego) [14, 34]. Alstroemeria aurea is the species with the widest distribution in Chile (this species spreads over 10 regions, from the O’Higgins Region, 34°12′S to Torres del Paine National Park, Magallanes Region, 51°21′S). Alstroemeria revoluta, the second widely distributed species, spreads from Valparaíso (La Campana National Park, 32°57′S) to Araucanía Region (Traiguén-Galvarino, 38°16′S) and A. versicolor ranges from the Metropolitan Region (Rio Clarillo National Reserve, 33°40′S) to Araucanía (Malleco, Renaico, 37°48′S). With these exceptions, most species show very narrow distribution, some of them being confined to a single region, such as A. lutea (Tarapacá Region), A. kingii, A. philippi var. albicans and A. polyphylla (Atacama Region), A. andina var. venustula, A. hookeri subsp. maculata, A. magnifica, A. schizanthoides var. alba and A. mollensis, A. traudliae (Coquimbo Region), A. marticorenae (Valparaíso Region), A. achirae (Maule Region), A. hookeri subsp. sansebastiana (Biobío Region), A. presliana subsp. australis (Araucanía Region, Nahuelbuta National Park). For the latitudinal distribution of each species, see reference (, Figure 5). Altitudinally, the genus Alstroemeria spreads from the sea level to nearly 4000 m.a.s.l. although most species are found below 2000 m.a.s.l. Alstroemeria andina, A. crispata, A. exerens, A. pallida, A. parvula, A. spathulata and A. umbellata can be found above 3000 m of elevation.
|2a||A. andina var. andina||x||x|
|2b||A. andina var. venustula||x|
|3a||A. angustifolia var. angustifolia||x||x|
|3b||A. angustifolia var. velutina||x||x|
|12a||A. hookeri subsp. hookeri||x||x||x|
|12b||A. hookeri subsp. maculata||x|
|12c||A. hookeri subsp. recumbens||x||x|
|12d||A. hookeri subsp. sansebastiana||x|
|15a||A. ligtu subsp. ligtu||x||x||x|
|15b||A. ligtu subsp. simsii||x||x||x||x|
|15c||A. ligtu subsp. splendens||x||x|
|18a||A. magnifica var. magnifica||x|
|18b||A. magnifica var. sierrae||x|
|18c||A. magnifica var. tofoensis||x|
|25a||A. philippi subsp. adrianae||x||x|
|25b||A. philippii var. albicans||x|
|25c||A. philippii var. philippii||x||x|
|27a||A. presliana subsp. australis||x|
|27b||A. presliana subsp. presliana||x||x||x|
|29a||A. pulchra subsp. lavandulacea||x||x|
|29b||A. pulchra subsp. pulchra||x||x||x||x||x|
|29c||A. pulchra var. maxima||x||x||x|
|31a||A. schizanthoides var. alba||x|
|31b||A. schizanthoides var. schizanthoides||x||x|
|37a||A. werdermannii subsp. flavicans||x||x|
|37b||A. werdermannii subsp. werdermannii||x||x|
|38||A. x chrysantha||x||x||x|
4. Cytogenetic studies in Chilean Alstroemeria
Cytogenetic studies in Alstroemeria have proved to be useful in delimiting species, since each studied taxon has a unique karyotype. These studies have contributed to the delimitation of the different taxa, as well as to the understanding of the chromosomal processes that determine the divergence among them . Recent studies at the infraspecific level, in taxonomic complexes of the genus, have also been shown to be useful in the recognition of these taxa, either due to differences in the chromosomal architecture or in the asymmetry indexes of the chromosomes [40, 41]. Strasburger  was the first researcher to perform chromosome studies in Alstroemeria and until 1989 the number of cytological published papers involved no more than 10 different species . In the last 25 years, a wide variety of cytogenetic studies have been carried out in the genus, including physical location of repetitive DNA sequences in A. aurea [16, 44, 45], meiosis and mitosis , karyology [47, 48, 49], variation and size of the genome , fluorescent in situ hybridization [39, 51, 52] and cytotaxonomy [40, 41, 52, 53, 54, 55, 56, 57, 58]. In 15 geographically isolated populations of five species of Alstroemeria (A. aurea, A. hookeri, A. ligtu, A. pelegrina and A. presliana) collected in Chile, karyotypes and variation of RAPD markers have been investigated. Tandemly repeated DNA sequences—5S and 18/25S rDNA genes and the sequence A001-1 were used to characterize karyotypes by fluorescence in situ hybridization (FISH). Ten somatic metaphases per population were used for measurement of chromosome length. Differences in RAPD marker bands were used for characterization of populations, creating a similarity index. FISH with all three DNA probes shows a high degree of polymorphism among and sometimes also within accessions of A. aurea, A. hookeri and A. ligtu. The number of chromosome pairs showing 5S rDNA signals is more different for the investigated species A. aurea, A. hookeri, A. ligtu, A. pelegrina and A. presliana with 5, 7, 5, 3 and 7, respectively, than the number of 18/25S rDNA signals in this succession with 7, 7, 6, 5 and 7 chromosome pairs, showing a high evolutionary dynamics within the genus. Furthermore, among the four populations of A. hookeri, accession 4181 was different in arm length of chromosome 3. RAPD markers (index of similarity) also showed a greater genetic distance of accession 4181 from the other three accessions of A. hookeri .
The study of the chromosomes in Alstroemeria has already helped to clarify a number of taxonomic issues within the genus. For example, study of karyotypes in the A. hookeri complex permitted change a subspecies to the species rank (A. cummingiana), the recognition of a new subspecies (A. hookeri subsp. sansebastiana) and description of a new species (A. marticorenae) [19, 22, 40, 41]. Similar situation occurred in the A. presliana complex, where after completing a comparative karyotypic study in 11 populations, it was suggested that A. presliana subsp. australis, endemic to the cordillera of Nahuelbuta, should be raised to species rank .
A number of cytological studies have been completed in the Alstroemeria ligtu complex. Buitendijik and Ramanna  and Buitendjik et al.  found variation in the DNA content and polymorphism of C bands in the chromosomes of subsp. ligtu, subsp. simsii and subsp. splendens. Zhou et al. , utilizing FISH, completed the characterization of the genomic DNA of eight highly repetitive sequences in subsp. ligtu and simsii, showing detailed karyotypes with localization of specific DNA sequences. DAPI staining and acetic orcein, completed a comparative karyotype study of five populations of subsp. ligtu from the Region of Biobío and one population of subsp. simsii from the Region of Valparaiso . The six populations studied revealed an asymmetric karyotype with 2n = 2x = 16 chromosomes. The populations of subsp. ligtu have a haploid formula of four metacentric chromosomes (chromosomes 1 and 2 with microsatellites), one submetacentric with a microsatellite and three telocentric with microsatellites. The population of subsp. simsii is characterized by having five metacentric chromosomes (chromosome 2 with a microsatellite and 6 with a secondary constriction) and three telocentric chromosomes with satellites. Baeza et al.  analyzed four populations of subsp. ligtu, defining localization on the chromosomes of the ribosomal genes 5S and 18-45S. Low polymorphic hybridization sites were detected in the populations, and only chromosome 1 presented a polymorphic site of 5S and 18/25S rDNA in the proximal and distal positions, respectively. Three subspecies are recognized within A. ligtu complex: subsp. ligtu, subsp. splendens and subsp. simsii. Fourteen populations were collected throughout its distributional range. Chromosome number, karyotype formulae, karyotypes, ideograms, intrachromosomal asymmetry index MCA, and interchromosomal asymmetry index CVCL were calculated [57, 58]. All studied populations showed 2n = 2x = 16 chromosomes. Subspecies ligtu and simsii are clearly differentiated from each other in MCA and together from subsp. splendens with CVCL. Intrachromosomal asymmetry index revealed two population groups within subsp. splendens. These populations also differ in karyotype formulae, habitat, soil type and distribution. We concluded that a fourth subspecies should be described from populations located in the lower part of the cordillera de los Andes in the Region of Maule. Populations of higher elevations correspond to those already described as subsp. splendens . A comparative karyotype study was carried out among four populations of A. diluta subsp. diluta and three populations of A. diluta subsp. chrysantha. The seven populations presented an asymmetric karyotype, with 2n = 2x = 16 chromosomes, and with same karyotype formulae: 3 m + 1sm + 1st + 3 t. The architecture of the karyotype between the subspecies is the same. The scatter plot among MCA versus CVCL shows different groupings between populations of the two subspecies, and the total chromosomes length (TCL) is highest in the populations of subsp. chrysantha. According to the results obtained, the populations growing in Valparaíso Region should be considered belong to subsp. diluta . We analyzed the karyotypes of 10 populations of A. magnifica complex along its natural distribution. All the populations showed an asymmetric karyotype, with 2n = 16 chromosomes but with 3 different karyotype formulae. Alstroemeria magnifica var. magnifica and A. magnifica var. sierrae presented the same karyotype formula, and A. magnifica var. magenta and A. magnifica var. tofoensis each had a different formula. The scatter plot among CVCL versus MCA shows different groupings between populations of the four varieties. Based on these results it is possible to consider raising Alstroemeria magnifica var. magenta to species rank and A. magnifica var. tofoensis to subspecies; A. magnifica var. magnifica and A. magnifica var. sierrae should each remain as varieties. Nevertheless, these taxonomic changes should be considered tentative, as additional sources of evidence become available.
5. Molecular studies in Alstroemeria
During recent years, an increasing accessibility to molecular data and the development of a vast range of bioinformatics analysis has favored the successful implementation of genetic tools in the identification and conservation of biological diversity . Dominant molecular markers based on random fragment alleles e.g. Inter Simple Sequence Repeat (ISSR), Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) have been used for characterizing genetic diversity in Alstroemeria [60, 61, 62], becoming the marker of choice for the identification of cultivar varieties with ornamental value [63, 64, 65] and conducting population genetic analyses [66, 67]. The use of DNA sequences has been more related to the construction of phylogenetic hypotheses and establishment of biogeographic patterns [8, 9]. Interestingly, near 30% of the Chilean species of Alstroemeria form species complexes, comprising from two to four infraspecific taxa each. This pattern is likely explained by adaptation to a wide range of environmental heterogeneity present in Chile , which is possibly driving processes of microevolutionary divergence . Given the complexity of interpreting the integrity within and among these species complexes, we started several initiatives for applied genetic studies with the purpose of disentangling the discernibility of intraspecific patterns of divergence, especially in groups highly regarded for their ornamental and conservation value.
5.1. Molecular markers in assessing genetic diversity for conservation in Alstroemeria
A priority goal in conservation is to evaluate levels of apportionment of genetic diversity in targeted species, given the association between population genetic diversity and their potential for local adaptation and evolutionary resilience. Genetic variability is the result of the dynamics of gene flow, for which a homogeneous distribution of allelic frequencies is expected under high levels of gene flow among populations . Interestingly, this situation is rarely found in nature, since the strong effect that geographic isolation and selection represents for local populations of plants. As a result, it is not surprising that peripheral populations tend to increase gene differentiation and population structure levels; hence, contributing to the local isolation that eventually could result in different isolated species (Figure 7) .
Such patterns of isolation and divergence are no exception in Alstroemeria, for which high levels of structuration are documented. For example, Alstroemeria hookeri represents a species complex that comprises four subspecies, two of them (subspecies recumbens and maculata) distributed in North-Central of Chile and two (subspecies hookeri and sansebastiana) in southern Chile. Based on ISSR (Inter Simple Sequence Repeat) markers, high levels of population structure were found among southern subspecies (Figure 8, Table 2); also concomitant with previous findings found with allozymes markers . Similarly, high levels of within population diversity was found in A. presliana complex using AFLP markers (Table 2), exhibiting significant levels of among population variability and moderate levels of genetic population structure (Table 2). This complex comprises of two varieties (var. presliana and var. australis), both separately distributed across Coastal and Andean mountain ranges in Chile (Figure 9). The results from both complexes showed the existence of two heterogeneous genetic groups with no evident spatial congruence suggesting genetic differentiation among varieties or subspecies. Interestingly, several populations are individually differentiated in their genetic profiles, despite of occurring closely enough with other neighbored populations to sustain substantial levels of gene flow (Figure 9).
|Within pop.||Among pop.|
|A. hookeri||hookeri||0.052||0.582||41.71||58.28||Allozymes/Ruiz et al. |
Among explanations of the observed patterns of genetic diversity found in Alstroemeria, strategies of reproduction and dispersal become plausible enough to be considered. Alstroemeria species have a restricted capacity of seed and pollen dispersal , which in combination with their vegetative reproduction by rhizomes [14, 67], could contribute to maintaining restricted levels of gene flow and sustaining high levels of genetic structure among populations . The sum of these factors implies that local populations could be subject to strong geographic and ecological isolation, which would explain the diversity of infraspecific taxa found in this and other species complexes . In general, moderate to high levels of among population genetic diversity were detected in the studied Alstroemeria species complexes. From a conservation perspective, this pattern suggests that protection initiatives should consider as many populations as possible, in order to preserve the largest proportion of total species genetic diversity.
5.2. Molecular phylogenetic studies in Alstroemeria
Phylogenetic studies provide a theoretical framework to understand the relationships among populations and species. It is desirable that taxa must represent monophyletic lineages, thus reflecting the genetic, evolutionary and biogeographical integrity of lineages and species. Under such premise, several phylogenetic studies in Alstroemeria have been conducted integrating a diverse array of molecular, morphological and cytological data [8, 9]. Chacón et al.  conducted the most recent and comprehensive phylogenetic studies in genus Alstroemeria, based on DNA sequences and cytological data. From taxonomic and evolutionary perspective, three are the most relevant results: (1) Samples belonging to the same species were retrieved as monophyletic; (2) a biogeographic break exists between Brazilian and Chilean species groups and (3) a relatively recent divergence has occurred with the most species of the genus, being diverged during the last 8 millions of years. Interestingly, some of these results have been confirmed from previous initiatives, especially those reflecting the monophyly of the Brazilian species group with alternative molecular markers (i.e., AFLP) .
Despite the promising of these results, species from the Chilean group were mostly underrepresented, making difficult to obtain relevant evidence of local patterns of diversification, particularly to those depicting evolutionary trends or taxonomic integrity in species complexes. Nonetheless, while some progress has been achieved scrutinizing chloroplast sequences (rpl32-trnl), discordant results challenge the hypothesis integrity previously stated in several of these groups. While Alstroemeria hookeri and A. presliana complexes are retrieved as monophyletic clades, other groups like A. magnifica and A. ligtu are retrieved as paraphyletic (Figure 10).
5.3. Molecular markers in eliciting taxonomic status in Alstroemeria species complex
The delimitation of species is a fundamental step for conducting natural and applied sciences, as they represent the main study unit for most areas of research (global evaluations of biodiversity, assessment and initiatives for biological conservation, etc.) . In this sense, molecular approaches in taxonomy have been used under the assumption that observed divergent patterns of genetic variation are the direct result of breaks in gene flow, leading to phenotypic and genotypic differences that sustain isolated and differentiated species and populations . The simultaneous use of multiple molecular markers and criteria of delimitation has improved the taxonomic work, particularly helping to contextualize the role of microevolutionary processes in the species generation. As previously stated, species of Alstroemeria share attributes that could heavily influence patterns of micro evolutionary isolation and divergence, such as restricted seed and pollen dispersal and vegetative reproduction by rhizomes. Therefore, the wide distribution of taxonomic complexes in areas with contrasting topography and climatic conditions implies the existence of restrictions for gene flow, where substantial effects of ecogeographic isolation and divergence are expected in local diversification patterns . Hence, micro evolutionary processes are currently underway and active , probably producing decoupled or unnoticeable patterns of divergence. Traditional taxonomic treatment in Alstroemeria has heavily relied on the interpretation of floral diversity and vegetative attributes, which has resulted in an important number of recognized taxa and species complexes described . Nonetheless, because active of micro-evolutionary divergence may not ensure congruence among the diverse phenotypic and genotypic characters, it is likely that an under or overrepresentation of taxa is currently occurring in Alstroemeria. Therefore, given that molecular data could reflect patterns of divergence more accordingly to the dynamic of local gene flow, an interesting approach is to evaluate taxonomic boundaries integrating both molecular and phenotypic data as potential taxonomic characters. Recent molecular and phenotypic integrated studies conducted in Alstroemeria complexes resulted beneficial when multiple sources of evidence are placed to solve questions about the integrity or the validity of previous taxonomic treatments. For example, when morphometric, cytogenetic and molecular data were employed in A. hookeri complex taxa [41, 67], all analyzed characters were partially consistent with the recognition of the new subspecies Alstroemeria hookeri subsp. sansebastiana , and supported the hypothesis of Muñoz & Moreira  of elevating Alstroemeria hookeri ssp. cummingiana to species level. Subsequent investigations were also conducted in other three complexes (A. ligtu, A. magnifica and A. presliana), eliciting similar evidence with significant taxonomic impact. In the A. magnifica complex, evidence from morphology, colorimetry and cytology support the change of the taxonomic status of A. magnifica var. magenta. Preliminary analyses based on chloroplast sequences (rpl32-trnL) also supported this observation, validating the separation of var. magenta from the other A. magnifica varieties (Figure 11). In the A. ligtu complex, a new entity was discovered based on cytogenetic data, and its taxonomic status was redefined [57, 58]. The molecular data, based on chloroplast DNA (rpl32-trnL region) support the separation of Coastal populations of A. ligtu subsp. ligtu from populations of the inland distribution range (Figure 12). Finally, in A. presliana, same chloroplast markers also confirm the lack of structure observed with AFLP data; nonetheless, both of them seem not concordant with previous studies conducted with phenotypic data [18, 30]. It is likely that different sources of divergence are shaping idiosyncratic processes of differentiation among species complexes of Alstroemeria, suggesting that a case by case evaluation might be required before reaching a consensus for a more genus-wide taxonomic perspective.
5.4. Perspectives and future work
Previous studies have demonstrated that a consensus about the integrity of the taxa of Alstroemeria is far from being reached, as different patterns of differentiation may difficult to be elicited separately. In this sense, molecular markers have provided a natural framework to contextualize their evolutionary process, reconciling discordance observed from different character sources. Nonetheless, despite of their utility, molecular markers are not exempt of limitations that should be addressed in subsequent studies. One of the main limitations to reach a robust taxonomic hypothesis is the recurrent difficulty to obtain consistent molecular markers adaptable enough for interspecific and intraspecific analyses. These difficulties arise from the extraordinary large and complex genomic architecture of Alstroemeria, which is likely comprised of a large proportion of repetitive DNA (18–34 pg.) . Our experience suggests that most nuclear markers tend to recurrently fail to retrieve single and readable copies through recurrent Sanger sequencing techniques, especially for the Internal Transcribed Spacer or ITS. Similarly, fragment analyses also exhibit levels of difficulties for consistent scoring, since the effect that repetitive DNA has in the proportion of cut sites with restriction enzymes . Since a more widespread consensus exist about the necessity of integrating different sources of molecular evidence and methodologies in species delimitation analyses , further work is required in the design of reliable and stable molecular markers for the study of natural species of Alstroemeria.
With the onset of new and more accessible technologies for genome sequencing (Next Generation Sequencing or NGS), new possibilities have opened for the generation of more representative analyses of genetic diversity [76, 77]. Unfortunately, such techniques have been not widely implemented in Alstroemeria, except important breakthroughs like the sequencing and the annotation of the chloroplast genome in A. aurea . The generation of single nuclear polymorphisms (SNP) in non-model organisms has been the approach of choice for high-throughput genome sequencing, adding improved genome representation and resolution for inter and intraspecific levels relationships . The implementation of SNPs might result in a significant improvement in the estimation of genetic diversity and species limits in Alstroemeria, as SNPs represent codominant markers capable of providing a higher statistical power and an easier species comparability considering the available genomic resources compared to AFLP . For taxonomic purposes, SNP could greatly improve the use of DNA barcodes to identify species through the use of specific DNA regions, especially when traditional approaches of taxonomy fail . Obviously, the use of NGS and SNP techniques in Alstroemeria requires adjustments to overcome the limitations imposed by genome size and complexity, for which recent alternatives have been shown from the study of other equally complex organisms . As such, the perspective of solving the taxonomic problems with molecular techniques in Alstroemeria remains promising, yet keeping in perspective its own limitations and challenges to reach the require tools to finally approach the inherent dynamics of macro and micro evolutionary patterns in this group.
6. Concluding remarks
Genetic divergence and population structure estimated with AFLPs and ISSR, have demonstrated the importance of molecular markers for conservation purposes in Alstroemeria. Integrative use of molecular data with other source of evidence (morphology, cytology and morphometry) give a best interpretation of lineage divergence with better argumentation for taxonomic delimitation in species complexes of Alstroemeria. Due to the high proportion of species complex in genus Alstroemeria in Chile, is necessary to carry out phylogenetic studies including the most infraspecifc taxa and more representative sampling, in addition with a major representation of the genome in the analyses. More efforts are needed in producing more stable molecular markers, in order to further implement integrative analyses. In this sense, it is likely that NGS will play a pivotal role helping to overcome present limitations of molecular work in Alstroemeria.
We gratefully acknowledge the Curators and Director of the Herbarium CONC for providing access to the studied specimens. This work was supported by the projects Fondecyt 1130349 “Morphological, molecular and cytogenetic overview of some species complexes of the genus Alstroemeria in Chile” and VRID-ENLACE 217.111.063-1.0 “Integrative taxonomy in the genus Alstroemeria L. (Alstroemeriaceae): The use of morphological, colorimetric, cytological and molecular approaches on several Chilean complexes”. We acknowledge Nicolás Villalobos for technical support.
Checklist of the Chilean species of Alstroemeria
Accepted names were written in bold, synonyms in italics. Names written in normal fonts corresponds to those whose acceptance or status has not yet been clarified. (E) = Endemic to Chile. (N) = Native.
Alstroemeria achirae Muñoz-Schick & Brink, Gayana, Bot. 57(1): 56. 2000 (E)
Alstroemeria albiflora C. Presl, Reliq. Haenk. 1(2): 121. 1827 = Alstroemeria pallida Graham
Alstroemeria amoena Salisb., Prodr. Stirp. Chap. Allerton 248. 1796 = Alstroemeria pelegrina L.
Alstroemeria andina Phil., Linnaea 29: 69. 1858.
subsp. venustula (Phil.) Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 74. 1987 = Alstroemeria andina Phil. var. venustula (Phil.) Muñoz-Schick, Not. Mens. Mus. Nac. Hist. Nat. 352: 22. 2003.
var. andina (E)
var. venustula (Phil.) Muñoz-Schick, Not. Mens. Mus. Nac. Hist. Nat. 352: 22. 2003. (N)
Alstroemeria angustifolia Herb., Amaryllidaceae 96. 1837.
subsp. velutina Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 165. 1987.
var. acuminata Herb., Amaryllidaceae 97. 1837 = Alstroemeria angustifolia var. angustifolia
var. angustifolia (E)
var. conferta Herb., Amaryllidaceae 97. 1837 = Alstroemeria angustifolia var. angustifolia
var. intermedia Herb., Amaryllidaceae 97. 1837 = Alstroemeria angustifolia var. angustifolia
var. solliana Herb., Amaryllidaceae 97. 1837 = Alstroemeria angustifolia var. angustifolia
var. velutina (Ehr. Bayer) Muñoz-Schick, Mitt. Bot. Staatssamml. München 24: 165. 1987. (E)
Alstroemeria aulica Ravenna, Onira 4(10): 41. 2000.
Alstroemeria aurantiaca D. Don, Brit. Fl. Gard., ser. 2, t. 205. 1835 = Alstroemeria aurea Graham
Alstroemeria araucana Phil., Anales Univ. Chile 43: 547. 1873 = Alstroemeria aurea Graham
Alstroemeria aurea Graham, Edinburgh Philos. J. 181. 1833. (N)
var. valparadisiaca Herb., Amaryllidaceae 98. 1837 = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeri aurea Meyen, Reise Erde 1: 311. 1834, hom. Illeg. = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria bicolor Hook., Exot. Fl. 2(9): t. 95. 1824 = Alstroemeria pulchra Sims subsp. pulchra
Alstroemeria bilabiata Ravenna, Phytologia 64(4): 282. 1988.
Alstroemeria cantillanica Ravenna, Phytologia 64(4): 285. 1988.
Alstroemeria chilensis Lem., Fl. Serres 1(5): 98. 1845 = Alstroemeria ligtu L. subsp. ligtu
Alstroemeria chillanensis Grau & Ehr. Bayer, Mitt. Bot. Staatssamml. München 18: 220. 1982 = Alstroemeria presliana Herb. subsp. presliana
Alstroemeria chiloensis Phil., Linnaea 29: 71. 1858 = Alstroemeria aurea Graham
Alstroemeria ciliata Poepp., Fragm. Syn. Pl. 6. 1833 = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria citrina Phil., Linnaea 22: 264. 1864 (E)
Alstroemeria concolor Steud., Berberid. Amer. Austr. 53. 1857
Alstroemeria x chrysantha (Ehr. Bayer) J.M. Watson & A.R. Flores, Fl. Silvtr. Chile 1: 90. 2015.(E)
Alstroemeria crispata Phil., Linnaea 29: 70. 1858 (E)
Alstroemeria crocea Phil., Linnaea 33: 262. 1864, non Ruiz & Pav. 1802 = Alstroemeria pseudospathulata Ehr. Bayer
Alstroemeria cummingiana Herb., Amaryllidaceae 96. 183 (E)
Alstroemeria decora Ravenna, Onira 4(10): 42. 2000.
Alstroemeria dentata Klotzsch ex Kunth, Enum. Pl. 5: 780. 1850, nom. Nud. = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria diazii Phil., Linnaea 33: 261. 1864 = Alstroemeria exerens Meyen
Alstroemeria diazii auct. Non Phil., Fl. Patagonica 2: 162. 1969 = Alstroemeria presliana Herb. subsp. presliana
Alstroemeria diluta Ehr. Bayer, Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 178. 1987
subsp. chrysantha Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 178. 1987 (E) = Alstroemeria x chrysantha (Ehr. Bayer) J.M. Watson & A.R. Flores
subsp. diluta (E)
Alstroemeria discolor Ravenna, Onira 4(10): 44. 2000.
Alstroemeria epulauquensis Ravenna, Phytologia 64(4): 283. 1988 = Alstroemeria presliana Herb. subsp. presliana
Alstroemeria exerens Meyen, Reise Erde 1: 34. 1834 (E)
Alstroemeria exserens Meyen, Reise Erde 1: 34. 1834 = Alstroemeria exerens Meyen
Alstroemeria flava Phil., Linnaea 33: 263. 1864 = Alstroemeria ligtu subsp. ligtu
Alstroemeria flos-martini Ker Gawl., Bot. Reg. 9: t. 731. 1823 = Alstroemeria pulchra Sims subsp. pulchra
Alstroemeria garaventae Ehr. Bayer, Gattung Alstroemeria in Chile 60. 1987 (E)
Alstroemeria gayana Phil., Linnaea 29: 71. 1857 = Alstroemeria magnifica Herb. var. magnifica
Alstroemeria graminea Phil., Anales Univ. Chile 93: 161. 1896 (E)
Alstroemeria haemantha Ruiz & Pav., Fl. Peruv. 3: 60. 1802 = Alstroemeria ligtu L.
var. haemantha = Alstroemeria ligtu L.subsp. ligtu
var. pilosa Herb., Amaryllidaceae 100. 1837 = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
var. simsiana Herb., Amaryllidaceae 99. 1837 = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria haemantha auct. Non Ruiz & Pav. = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria herbertiana M. Roem., Fam. Nat. Syn. Monogr. 250. 1847 = Alstroemeria revoluta Ruiz & Pav.
Alstroemeria hirtella Phil., Linnaea 29: 70. 1858, hom. Illeg. = Alstroemeria leporina Ehr. Bayer & Grau
Alstroemeria hookeri Lodd., Bot. Cab. 13: t. 1272. 1827
subsp. cummingiana (Herb.) Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 157. 1987 = Alstroemeria cummingiana Herb.
subsp. hookeri (E)
subsp. maculata Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 153. 1987 (E)
subsp. recumbens (Herb.) Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 149. 1987 (E)
subsp. sansebastiana C.M. Baeza & E. Ruiz, Gayana, Bot. 68(2): 313. 2011 (E)
Alstroemeria hookeriana Schult., Syst. Veg. 7(1): 733. 1829 = Alstroemeria hookeri Lodd. subsp. hookeri
Alstroemeria huemulina Ravenna, Phytologia 64(4): 285. 1988
Alstroemeria inconspicua Phil., Anales Univ. Chile 43: 546. 1783 = Alstroemeria revoluta Ruiz & Pav.
Alstroemeria jocunda Ravenna, Phytologia 64(4): 284. 1988
Alstroemeria kingii Phil., Anales Univ. Chile 43: 548. 1873 (E)
Alstroemeria lacrima-solis Ravenna, Phytologia 64(4): 283. 1988 = Alstroemeria pseudospathulata Ehr. Bayer
Alstroemeria leporina Ehr. Bayer & Grau, Mitt. Bot. Staatssamml. München 18: 222. 1982 (E)
Alstroemeria ligtu L., Pl. Alströmeria 10. 1762.
Fma. pulchra (Sims) Voss, Bot. Mag. 50: t. 2421. 1823 = Alstroemeria pulchra Sims subsp. pulchra
subsp. incarnata Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 131. 1987, nom. Illeg. = Alstroemeria ligtu L. subsp. splendens Muñoz-Schick
subsp. ligtu (E)
subsp. simsii (Spreng.) Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 122. 1987 (E)
subsp. splendens Muñoz-Schick, Notic. Mens. Mus. Nac. Hist. Nat. 352: 22. 2003 (E)
var. andina Phil., Linnaea 33: 261. 1864 = Alstroemeria pallida Graham
var. pulchra (Sims) Baker, Handb. Amaryllideae: 139. 1888 = Alstroemeria pulchra Sims subsp. pulchra
Alstroemeria ligtu auct. Non L., Trab. Inst. Bot. Farmacol. 33: 26. 1915 = Alstroemeria aurea Graham
Alstroemeria lothiana Utinet. J. Jardins Jahrgang 1841: 348. = Alstroemeria ligtu subsp. ligtu
Alstroemeria lutea Muñoz-Schick, Gayana, Bot. 57(1): 55. 2000 (E)
Alstroemeria macreana Herb., Amaryllidaceae 90. 1837 = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria magenta Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 191. 1987 = Alstroemeria magnifica Herb. var. magenta (Ehr. Bayer) Muñoz-Schick
Alstroemeria magnifica Herb., Bot. Reg. 29: 64. 1843
subsp. gayana (Phil.) Ehr. Bayer, Gatt. Alstroemeria Chile 252. 1987 = Alstroemeria magnifica Herb. var. magnifica
var. magnifica (E)
var. magenta (Ehr. Bayer) Muñoz-Schick, Notic. Mens. Mus. Nac. Hist. Nat. 352: 22. 2003 = Alstroemeria magenta Ehr. Bayer
var. sierrae (Muñoz) Muñoz-Schick, Notic. Mens. Mus. Nac. Hist. Nat. 352: 22. 2003 (E)
var. tofoensis Muñoz-Schick, Notic. Mens. Mus. Nac. Hist. Nat. 352: 22. 2003 (E)
Alstroemeria magenta Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 191. 1987 (E)
Alstroemeria magna Ravenna, Phytologia 64(4): 284. 1988
Alstroemeria marticorenae Negritto & C.M. Baeza, Syst. Bot. 40(1): 70. 2015 (E)
Alstroemeria meyeniana Schauer, Nova Acta Acad. Caes. Leop.-Carol. German. Nat. Cur. Suppl. 1: 440. 1843 = Alstroemeria versicolor Ruiz & Pav.
Alstroemeria mollensis Muñoz-Schick & Brinck, Gayana, Bot. 60(2): 102. 2003 (E)
Alstroemeria monantha Ravenna, Phytologia 64(4): 286. 1988
Alstroemeria mutabilis Kunze, Enum. Pl. 5: 777. 1850 = Alstroemeria aurea Graham
Alstroemeria nana Rendle, J. Bot. 42: 325. 1904 = Alstroemeria patagonica Phil.
Alstroemeria nidularis Ravenna, Phytologia 64(4): 282. 1988
Alstroemeria nivalis Phil., Linnaea 29: 69. 1858, hom. Illeg. = Alstroemeria pallida Graham
Alstroemeria nubigena Phil., Linnaea 29: 69. 1858 = Alstroemeria pallida Graham
Alstroemeria oxyphylla Ravenna, Phytologia 64(4): 286. 1988, nom. Superfl. = Alstroemeria pseudospathulata Ehr. Bayer
Alstroemeria pallens Phil., Linnaea 33: 265. 1864 = Alstroemeria exerens Meyen
Alstroemeria pallida Graham, Edinburgh New Philos. J. 344. 1829 (E)
Alstroemeria parvula Phil., Linnaea 33: 261. 1864 (E)
Alstroemeria patagonica Phil., Anales Univ. Chile 84: 160. 1894 (N)
fma. Biflora Ravenna, Sellowia 19: 34. 1967 = Alstroemeria patagonica Phil.
Alstroemeria paupercula Phil., Fl. Atacam. 51. = Alstroemeria violacea Phil.
Alstroemeria pelegrina L., Sp. Pl. (ed. 2) 1: 461. 1762 (E)
var. albescens Herb. Amaryllidaceae 91. 1837. = Alstroemeria pelegrina L.
Alstroemeria philippii Baker, Handb. Amaryllidae 140. 1888
subsp. adrianae J.M. Watson & A.R. Flores, Herbertia 63: 102. 2009 (E)
subsp. philippii (E)
var. albicans Muñoz-Schick, Alstroemerias Chile 41. 2003 (E)
var. philippii (E)
Alstroemeria poetica Ravenna, Phytologia 64(4): 285. 1988
Alstroemeria polpaicana Ravenna, Phytologia 64(4): 283. 1988
Alstroemeria polyphylla Phil., Anales Univ. Chile 93: 160. 1896 (E)
Alstroemeria presliana Herb., Enum. Pl. 5: 773. 1850
subsp. presliana (N)
subsp. australis Ehr. Bayer, Gatt. Alstroemeria Chile 122. 1987 (E)
Alstroemeria pseudospathulata Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 49. 1987 (N)
Alstroemeria pulchella auct. Non L.f. = Alstroemeria ligtu subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria pulchella L.f. var. pilosa Lindl., Edwards’s Bot. Reg. 17: t. 1410. 1831 = Alstroemeria ligtu subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria pulchra Sims, Bot. Mag. 50, t. 2421. 1823
subsp. lavandulacea Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 187. 1987 (E)
subsp. maxima (Phil.) Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 202 t.14, 18. 1987 (E)
subsp. pulchra (E)
var. maxima Phil., Linnaea 33: 266. 1864–65 (E)
Alstroemeria pygmaea auct. Non Herb., Svenska Exped. Magell. 3(5): 205. 1901 = Alstroemeria patagonica Phil.
Alstroemeria quillotensis Herb., Amaryllidaceae 97, t.2., f.2, 1837 = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria recumbens Herb., Amaryllidaceae 97, t.3. 1837 = Alstroemeria hookeri Lodd. subsp. recumbens (Herb.) Ehr. Bayer
Alstroemeria reflexa M. Roem., Fam. Nat. Syn. Monogr. 4: 252. 1847 = Alstroemeria revoluta Ruiz & Pav.
Alstroemeria revoluta Ruiz & Pav., Fl. Peruv. 3: 59. 1802 (E)
Alstroemeria rosea Hook., Exot. Fl. 3(27): t.181. 1825 = Alstroemeria hookeri Lodd. subsp. hookeri
Alstroemeria rosea Phil., Sert. Mendoc. Alt. 43. 1871 = Alstroemeria pallida Graham
Alstroemeria sabulosa Ravenna, Phytologia 64(4): 281. 1988
Alstroemeria schizanthoides Grau, Ehr. Bayer, Mitt. Bot. Staatssamml. München 18: 213. 1982
var. alba Muñoz-Schick, Notic. Mens. Mus. Nac. Hist. Nat. 352: 22. 2003 (E)
var. schizanthoides (E)
Alstroemeria sericantha Schauer, Nov. Actorum Acad. Caes. Nat. Cut. 19(Suppl. 1): 441. 1843 = Alstroemeria umbellata Meyen
Alstroemeria sierrae Muñoz, Fl. Silvestr. Chile: 64. 1966 = Alstroemeria magnifica Herb. var. sierrae (Muñoz) Muñoz-Schick
Alstroemeria simsii Spreng., Syst. Veg. [Sprengel] 2: 80. 1825 = Alstroemeria ligtu L. subsp. simsii (Spreng.) Ehr. Bayer
Alstroemeria sotoana Phil., Anales Univ. Chile 93: 159. 1896 = Alstroemeria versicolor Ruiz & Pav.
Alstroemeria spathulata C. Presl, Reliq. Haenk. 1(2): 122, t.22, f.2., 1827 (E)
Alstroemeria spathulata auct. Non C. Presl, Fl. Patag. 2: 162. 1969 = Alstroemeria pseudospathulata Ehr. Bayer
Alstroemeria spectabilis Ravenna, Phytologia 64(4): 284. 1988
Alstroemeria stenopetala Phil., Anales Univ. Chile 43: 547. 1873 = Alstroemeria aurea Graham
Alstroemeria timida Ravenna, Phytologia 64(4): 281. 1988
Alstroemeria tigrina Phil., Linnaea 29: 68. 1857 = Alstroemeria versicolor Ruiz & Pav.
Alstroemeria traudliae J.M. Watson & A.R. Flores, Fl. Sylvestr. Chil. 1: 118. 2015 (E)
Alstroemeria tricolor Hook., Exot. Fl. 1(5): t. 65. 1823 = Alstroemeria pulchra Sims subsp. pulchra
Alstroemeria umbellata Meyen, Reise Erde 1: 356. 1835 (E)
Alstroemeria venusta Ravenna, Phytologia 64(4): 282. 1988
Alstroemeria venustula Phil., Linnaea 33: 260. 1864 = Alstroemeria andina Phil. var. venustula (Phil.) Muñoz-Schick
Alstroemeria versicolor Ruiz & Pav., Fl. Peruv. 3: 59. 1802 (E)
Alstroemeria violacea Phil., Fl. Atacam. 51. 1860 (N)
Alstroemeria violacea Knight & Perry, nom. Nud. = Alstroemeria violacea Phil.
Alstroemeria werdermannii Ehr. Bayer, Gatt. Alstroemeria Chile 87. 1986
var. werdermannii (E)
var. flavicans Muñoz-Schick, Gayana, Bot. 57(1): 57, f.3. 2000 = A. werdermannii Ehr. Bayer subsp. flavicans (Muñoz-Schick) J.M. Watson & A.R. Flores (E)
subsp. flavicans (Muñoz-Schick) J.M. Watson & A.R. Flores, Fl. Silvestr. Chile 1: 122. 2015.
Alstroemeria xanthina Phil., Anales Univ. Chile 43: 546. 1873 = Alstroemeria versicolor Ruiz & Pav.
Alstroemeria yaelae Ravenna, Phytologia 64(4): 282. 1988
Alstroemeria zoellneri Ehr. Bayer, Mitt. Bot. Staatssamml. München 24: 245, t. 143–144. 1987(E)
Taltalia graminea (Phil.) Ehr. Bayer, Sendtnera 5: 7, f. 1–4. 1998 = Alstroemeria graminea Phil.