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Relative positions and lengths of binary encoded indels and excluded regions (for the rpl16 intron) of unalignable sequence.
Source publication
The genus Mammillaria is likely the most species-rich and morphologically variable genus in the Cactaceae. There is doubt as to whether the genus is monophyletic, and past infrageneric treatments differ regarding generic circumscription. Phylogenetic questions about Mammillaria were addressed using chloroplast DNA sequence data from the rpl16 intro...
Context in source publication
Context 1
... alignment was carried out manually, following the principles of Kelchner and Clark (1997) for the alignment of noncoding DNA. Insertion/deletion events (indels) considered to be phylogenetically informative were coded in binary (presence/ absence) following the treatment of Graham et al. (2000) and added to the end of the data matrix (summarized in Table 1). There were two regions of doubtful homology in the rpl16 intron, which totaled 56 nucleotides. ...Citations
... Dependence on genetic indicators based on DNA is the criterion factor in identifying and diagnosing species because they are not provoked by external factors and are present in all stages of growth and all cells, so it was of interest to scientists, thus many evolutionary studies using genetic-based markers have been published in recent decades [13,14] to clear gene flow, evolutionary relationships, and phylogenetic taxonomy [12]. ...
... Estudios filogenéticos basados en el análisis de secuencias de cpDNA (intrón rpl16 e IGS psbA-trnH) sugieren que Mammillaria ser. Leucocephalae no es un grupo monofilético (Butterworth y Wallace, 2004). Posteriormente, Cervantes et al. (2021), utilizando también secuencias de cpDNA (intrón rpl16 e IGS psbA-trnH), recuperaron a los miembros de Mammillaria ser. ...
Antecedentes y Objetivos: Mammillaria es uno de los géneros más representativos de Cactaceae. En la región del Bajío, México, se distribuyen aproximadamente 70 especies y nueve subespecies, de las cuales siete especies y una subespecie corresponden a M. ser. Leucocephalae. En exploraciones recientes se encontraron individuos cuya morfología no concuerda con las especies descritas en los tratamientos taxonómicos actualizados. El objetivo de este trabajo es caracterizar y describir una nueva especie, con base en evidencia morfológica y medioambiental. Métodos: Se realizó trabajo de campo en junio de 2022. Se analizaron mediante el Análisis Canónico Discriminante (ACD) siete caracteres morfológicos. Además, se calcularon los residuos de Pearson para dos variables medioambientales y la significancia se estimó con una prueba de bondad de ajuste chi-cuadrada. El área de ocupación y la extensión de ocurrencia se calcularon para asignar la categoría de conservación según los criterios y categorías de la Lista Roja de la IUCN. Resultados clave: Se describe e ilustra a Mammillaria ariasii, similar a Mammillaria hahniana, de la cual difiere por el número de espinas radiales, la longitud de la espina central inferior y el color de los tépalos internos del perianto. La presencia de cristales extracelulares confirma su inclusión en M. ser. Leucocephalae. Mammillaria ariasii se caracteriza por habitar en suelos kastanozems háplico y relieves volcánicos en un área de ocupación aproximada de 28 km2 y de extensión de ocurrencia de 345 km2. Se proporciona una clave de identificación en donde se compara con otros miembros de Mammillaria ser. Leucocephalae. Conclusiones: Mammillaria ariasii es una nueva especie endémica del Bajío. De acuerdo con nuestros resultados debe ser considerada como especie en peligro (EN). Si bien es localmente abundante, debe tenerse en cuenta la erosión y la ganadería como factores potenciales de riesgo.
... The combination of these characters differentiates Stylothelae from the other series (Fitz-Maurice & Fitz-Maurice 2006, Hunt et al. 2006. Additionally, all species of M. series Stylothelae share the absence of the rpl16 intron, which is proposed as a synapomorphy of the group (Butterworth & Wallace 2004, Butterworth et al. 2007). This could be an indicator of chloroplast structure variation. ...
Background:
The chloroplast genomes of Cactaceae exhibit boundary modifications in the inverted repeat regions (IRs), gene inversions, and deletions. Among nine Mammillaria species, three distinct chloroplast structures have been identified, although not all of these correspond to the morphology-based classification of the genus.
Question:
Is there a distinct chloroplast genome structure in the species of Mammillaria series Stylothelae?
Studied species:
Mammillaria bocasana and M. erythrosperma.
Study site and dates:
Mexico from 2019 to 2023.
Methods:
Chloroplast DNA was sequenced, and chloroplast genomes were de novo assembled using the Fast-Plast program. Complete plastome sequences were annotated and verified. The sequences were aligned in MAUVE program to detect possible structural changes. A maximum likelihood phylogeny was executed to evaluate the relationships of the studied species.
Results:
The plastomes ranged from 107,368 bp in Mammillaria bocasana to 108,069 bp in M. erythrosperma. Both presented a quadripartite structure and contained 108 genes. The IRs were ~ 1,600 bp long and included the genes rpl2, rpl23 (pseudo), and trnI-CAU. MAUVE identified a ~ 21 kb inversion in the large single copy containing a block of genes related to photosynthesis. The phylogenetic analysis placed both species in a single clade separated from the other species within Mammillaria subg. Mammillaria.
Conclusions:
The studied species of Mammillaria series Stylothelae exhibited a different and synapomorphic chloroplast genome structure. Other Mammillaria chloroplast genome structures have evolved independently in different lineages.
... Stylothelae are morphologically characterized by a straight central spines with a hooked tip, bristles in the tubercle axils, widely spaced testa pits, the presence of alkaloids in flowers and fruits, and spring-to-summer flowering (Lüthy 1995, Hunt et al. 2006. Phylogenetic analyses based on cpDNA sequences (Butterworth & Wallace 2004, Bárcenas et al. 2011 have proved the polyphyly of the Hunt's broad concept of the series. Interestingly, species belonging to the narrow circumscription of the series (sensu Hunt et al. 2006) build up a monophyletic group (Butterworth & Wallace 2004). ...
... Phylogenetic analyses based on cpDNA sequences (Butterworth & Wallace 2004, Bárcenas et al. 2011 have proved the polyphyly of the Hunt's broad concept of the series. Interestingly, species belonging to the narrow circumscription of the series (sensu Hunt et al. 2006) build up a monophyletic group (Butterworth & Wallace 2004). The narrow circumscription of M. ser. ...
A new species of Mammillaria ser. Stylothelae is described and illustrated. Mammillaria monochrysacantha is distinguished from other species of the series by having a globose stem with fibrous roots, one single golden yellow hooked central spine, 28–32 tortuous hair-like radial spines, flowers with lanceolate pale yellow tepals, and non-arilloid seeds. We provided a comparison with other morphologically close and sympatric species of Mammillaria. The new species is endemic from the Sierra Gorda, Guanajuato, Mexico. We included data about its habitat and the status of conservation. Additionally, we integrated an identification key for M. ser. Stylothelae from Guanajuato, San Luis Potosí, and Querétaro, Mexico.
... Mammillaria is the most diverse genus in the family, with a variable number of species depending on the author; for example, Reppenhagen (1992) considered 320 species and, recently, Korotkova et al. (2021) recognized 143 species. A few studies have shown that Mammillaria s.l. is a polyphyletic group (Butterworth et al., 2002;Butterworth and Wallace, 2004). Nonetheless, Breslin et al. (2021) circumscribed Mammillaria s.s. to reflect a monophyletic group. ...
Species complexes consist of very close phylogenetic relatives, where morphological similarities make it difficult to distinguish between them using traditional taxonomic methods. Here, we focused on the long-standing challenge of species delimitation in the Mammillaria haageana complex, a group that presents great morphological diversity that makes its taxonomy a puzzle. Our work integrates genomic, morphological, and ecological data to establish the taxonomic limits in the M. haageana complex, and we also studied the evolutionary relationships with the remainder of the M. ser. Supertextae species. Our genetic analyses, as well as morphological and ecological evidence, led us to propose that the M. haageana complex is made up of six distinct entities (M. acultzingensis, M. conspicua, M. haageana, M. lanigera, M. meissneri, and M. san-angelensis), mainly as a result of ecological speciation. A recent taxonomic proposal considered these taxa as a single species; therefore, we propose their recognition at the species level. Our results also show a high level of incomplete lineage sorting rather than reticulation, which is especially likely in recently diverged species such as those comprising M. ser. Supertextae. The species hypotheses proposed here may be useful in future extinction risk assessments and conservation strategies.
... These six genera and Mammillaria compose the Mammilloid Clade [34]. Butterworth and Wallace [35] analyzed the phylogenetic relationships of 123 species of Mammilloid Clade (113 of them grouped in Mammillaria) based on two plastid loci (rpl16 intron and the intergenic spacer psbA-trnH). Their phylogenetic tree showed abundant polytomies and low support bootstrap values. ...
... The findings of this study have explained the phylogenetic relationships of the 103 taxa, particularly the 70 taxa sampled from the genus Mammillaria sensu Hunt [18] were polyphyletic, as was identified previously (e.g., [35,36]). However, based on our results, the monophyly of this genus can be identified within a subset of the 70 taxa sampled as Mammillaria. ...
Simple Summary
Cacti account for nearly 1440 species, most of them native to the American continent. These succulent plants are the most ubiquitous elements of the arid ecosystems. Mexico harbors the highest number of cacti species in the world (45%). Unfortunately, many of them are threatened by human activities. Although having this biodiversity relevance, presently the evolutionary processes of cacti have been poorly studied. Because the biological and conservation unit is the species, evolutionary studies provide relevant information. In this study, we analyzed how and when past events shaped the evolutionary relationships of 103 species. Our results showed that from 4.5 million years ago the arid regions of Mexico were the locations for abundant cacti speciation. From these lands, cacti have colonized most of the Mexican territories, the southern regions of the United States, as well as the Caribbean. The evolution of these plants was probably promoted by past temperatures that were comparable to the present ones. We identified different speciation and dispersal events in these fascinating plants. This study identified the Mexican Plateau as the place where the early stages of the evolutionary history of cacti occurred.
Abstract
Mexico harbors ~45% of world’s cacti species richness. Their biogeography and phylogenomics were integrated to elucidate the evolutionary history of the genera Coryphantha, Escobaria, Mammillaria, Mammilloydia, Neolloydia, Ortegocactus, and Pelecyphora (Mammilloid Clade). We analyzed 52 orthologous loci from 142 complete genomes of chloroplast (103 taxa) to generate a cladogram and a chronogram; in the latter, the ancestral distribution was reconstructed with the Dispersal-Extinction-Cladogenesis model. The ancestor of these genera arose ~7 Mya on the Mexican Plateau, from which nine evolutionary lineages evolved. This region was the site of 52% of all the biogeographical processes. The lineages 2, 3 and 6 were responsible for the colonization of the arid southern territories. In the last 4 Mya, the Baja California Peninsula has been a region of prolific evolution, particularly for lineages 8 and 9. Dispersal was the most frequent process and vicariance had relevance in the isolation of cacti distributed in the south of Mexico. The 70 taxa sampled as Mammillaria were distributed in six distinct lineages; one of these presumably corresponded to this genus, which likely had its center of origin in the southern part of the Mexican Plateau. We recommend detailed studies to further determine the taxonomic circumscription of the seven genera.
... Stylothelae (Hunt 2006) (= M. ser. Stylothelae group Crinita, Hunt 1981) represents a monophyletic group supported by chloroplast DNA sequences (Butterworth & Wallace 2004). Particularly, species of M. ser. ...
We describe a new endemic densely spined Mammillaria from San Luis Potosí, Mexico. The new species, named M. morentiniana, is distinctive by the presence of a globose to shortly cylindric stem with several glabrous, reddish central spines, radial spines that protrude from the plant like white needle-bristles, and small flowers with pale yellow, lanceolate tepals. We compare it with similar and sympatric species of M. ser. Stylothelae. We include data about habitat and the preliminary status of conservation of the new taxon.
Citation: González-Zamora P., Aquino D., Mohl J. & Sánchez D. 2022: A new endemic species of Mammillaria (Cactaceae) fromSan Luis Potosí, Mexico. – Willdenowia 52: 359–372.
Version of record first published online on 12 December 2022 ahead of inclusion in December 2022 issue.
... (Cactaceae) (Pilbeam, 1999;Barthlott et al., 2015), donde se han documentado al menos 143 especies y 61 subespecies (Korotkova et al., 2021). Estas se encuentran ampliamente distribuidas en el territorio nacional, mientras que solo algunas están presentes en Centroamérica, el norte de Sudamérica y las Antillas Mayores (Anderson, 2001;Butterworth y Wallace, 2004). En México, particularmente para el estado de Oaxaca, Hernández y Gómez-Hinostrosa ( R. Hunt), lo que convierte a Oaxaca en la tercera entidad federativa con el mayor número de especies endémicas del género, después de Baja California Sur con 10 y Tamaulipas con ocho. ...
Antecedentes y Objetivos:
En Oaxaca, México, se reportan 26 especies del género Mammillaria; siete de ellas endémicas. Mammillaria deherdtiana subsp. dodsonii está catalogada como amenazada. Los objetivos del trabajo fueron describir las características demográficas, reproductivas y aspectos etnobotánicos de su uso, así como los aspectos florísticos y bioclimáticos de las localidades estudiadas.
Métodos:
En enero de 2015 se encontraron dos localidades de Mammillaria deherdtiana subsp. dodsonii en la Sierra Norte. Entre enero y marzo se ubicaron cinco transectos de 5 m² en una de ellas, en los cuales se registró el número de individuos, se establecieron categorías de tamaño y se obtuvo la estructura poblacional. Para la marcha floral se eligieron diez flores y cada dos horas se registró el diámetro de la apertura del perianto. Se registraron las especies de plantas vasculares que crecían cerca de ella y se obtuvieron datos de las variables climáticas. Se entrevistó a los pobladores para documentar el conocimiento y uso que le dan a esta cactácea.
Resultados clave:
La estructura poblacional es multimodal. Los individuos juveniles conforman 65% y los adultos reproductivos 33% en la localidad estudiada. La antesis dura siete horas; se observó dicogamia y hercogamia, lo cual indica un sistema de cruza xenógamo. La subespecie es reconocida con nombres en español y zapoteco y es usada de manera ocasional como alimento, medicina y ornamento. Se registraron 15 especies pertenecientes al bosque de Pinus y Abies. Las preferencias ambientales de la subespecie son temperaturas de 9.6-12.7 °C y precipitación de 1009-1405 mm.
Conclusiones:
El sistema de cruza xenógamo resulta preocupante por la observación de un solo visitante floral. La presencia de cerdas y espinas radiales sugiere adaptaciones morfofisiológicas de esta subespecie al frío. Se sugiere profundizar en la presencia y efectividad de los polinizadores y en la dinámica de reclutamiento de la subespecie.
... Most of these taxa occur on or are entirely endemic to the Baja California peninsula and adjacent islands in the Gulf of California and Pacific Ocean (Rebman and Roberts, 2012). In this study, the Mammilloid clade (Butterworth and Wallace, 2004) is well-supported and composed of Cochemiea (K. Brandegee) Walton s.l., the Coryphantha clade, Cumarinia (F.M. Knuth) Buxb., and Mammillaria Haw. ...
... The Mammilloid clade is sister to a clade in Cacteae containing the well-supported, morphologically diverse and monotypic or often species-poor genera Acharagma (N.P. Taylor (Butterworth et al., 2002;Butterworth and Wallace, 2004;Bárcenas et al., 2011;Hernández-Hernández et al., 2011;Vázquez-Sánchez et al., 2013;Bárcenas et al., 2021;Breslin et al., 2021). This sister clade to the Mammilloid clade is biogeographically restricted almost without exception to the Mexican Plateau, through the Sierra Madre Oriental, into the Chihuahuan and Coahuilan regions of Mexico and the United States (Anderson, 2001;Vázquez-Sánchez et al., 2013). ...
... D. Aquino & Dan.Sanchez, were unavailable for sampling. Representative samples of Mammillaria s.s. were selected from each of the major subclades recovered in the phylogeny of Butterworth and Wallace (2004). Fifteen members of the Coryphantha clade were sampled, including Mammillaria sphacelata, which has been recovered as sister to that clade (Breslin et al. 2021). ...
Premise:
The Cactaceae of northwestern Mexico and the southwestern United States constitute a major component of the angiosperm biodiversity of the region. The Mammilloid clade, (Cactaceae, tribe Cacteae), composed of the genera Cochemiea, Coryphantha, Cumarinia, Mammillaria, and Pelecyphora is especially species rich. We sought to understand the timing, geographical and climate influences correlated with expansion of the Mammilloid clade, through the Sonoran Desert into Baja California.
Methods:
We reconstructed the historical biogeography of the Mammilloid clade, using Bayesian and maximum likelihood methods, based on a strongly supported molecular phylogeny. We also estimated divergence times, the timing of emergence of key characters, and diversification rates and rate shifts of the Mammilloid clade.
Key results:
We found that the most recent common ancestor of Cochemiea arrived in the Cape region of Baja California from the Sonoran Desert region approximately 5 million years ago, coinciding with the timing of peninsular rifting from the mainland, suggesting dispersal and vicariance as causes of species richness and endemism. The diversification rate for Cochemiea is estimated to be approximately 12 times that of the mean background diversification rate for angiosperms. Divergence time estimation shows that many of the extant taxa in Cochemiea and Baja California Mammillaria emerged from common ancestors 1 million to 200,000 years ago, having a mid-Pleistocene origin.
Conclusions:
Cochemiea and Mammillaria of the Baja California region are examples of recent, rapid diversification. Geological and climatic forces at multiple spatial and temporal scales are correlated with the western distributions of the Mammilloid clade. This article is protected by copyright. All rights reserved.
... Accordingly, in this study, we tested in silico these two probe sets (Angiosperm v.1 and Angiosperms353) in ten Caryophyllids species: nine species of cacti (Cactaceae) and the species Amaranthus hypochondriacus (Amaranthaceae), used in the phylogenetic analysis as an external group. We focused on cacti species because phylogenetic studies carried out with these taxa repeatedly result in unresolved phylogenetic trees [20][21][22]. This lack of phylogenetic resolution may be due to the fact that most of these studies used poor molecular sampling (1-12 loci), or may be due to other factors, such as the recent postulation of the origin of Cactaceae (30 to 35 Ma) based on the molecular-clock model [23,24]. ...
In angiosperms, huge advances in massive DNA sequencing technologies have impacted phylogenetic studies. Probe sets have been developed with the purpose of recovering hundreds of orthologous loci of targeted DNA sequences (TDS) across different plant lineages. We tested in silico the effectiveness of two universal probe sets in the whole available genomes of Caryophyllids, emphasizing phylogenetic issues in cacti species. A total of 870 TDS (517 TDS from Angiosperm v.1 and 353 from Angiosperms353) were individually tested in nine cacti species and Amaranthus hypochondriacus (external group) with ≥17 Gbp of available DNA data. The effectiveness was measured by the total number of orthologous loci recovered and their length, the percentage of loci discarded by paralogy, and the proportion of informative sites (PIS) in the alignments. The results showed that, on average, Angiosperms353 was better than Angiosperm v.1 for cacti species, since the former obtained an average of 275.6 loci that represent 123,687 bp, 2.48% of paralogous loci, and 4.32% of PIS in alignments, whereas the latter recovered 148.4 loci (37,683 bp), 10.38% of paralogous loci, and 3.49% of PIS. We recommend the use of predesigned universal probe sets for Caryophyllids, since these recover a high number of orthologous loci that resolve phylogenetic relationships.
