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Article: Genomic Insights into Cultivated Mexican Vanilla planifolia Reveal High Levels of Heterozygosity Stemming from Hybridization

Ellestad, Paige / Pérez-Farrera, Miguel Angel / Buerki, Sven

Plants. 2022 Aug. 11, v. 11, no. 16

2022

Abstract: Although vanilla is one of the most valuable spices, there is a lack of understanding of the genomic variability of the main vanilla producing species, Vanilla planifolia, within its cultivated origin, Mexico. High genomic heterozygosity levels within ... ...

Abstract	Although vanilla is one of the most valuable spices, there is a lack of understanding of the genomic variability of the main vanilla producing species, Vanilla planifolia, within its cultivated origin, Mexico. High genomic heterozygosity levels within the globally cultivated ‘Daphna’ genome have raised questions on the possibility of a hybrid origin and analogous genomic signatures of vanilla cultivated within its origin. This study investigated these questions by assessing whether the genomic structure of Mexican V. planifolia reflected domestication events. Whole genome re-sequencing was used to compare genome complexity between 15 cultivated accessions from different regions and gene pools. Results showed high levels of heterozygosity, ranging from 2.48% to 2.85%, in all but one accession, which exhibited a low level (0.403%). Chromosome-level comparative analyses revealed genomic variability among samples, but no signals of chromosome rearrangements. These findings support the hypotheses that cultivated vanilla resulted from hybridization and that multiple domestication events have shaped cultivated vanilla leading to the formation of landraces. High cultural diversity within this region further supports the occurrence of multiple domestication processes. These results may help to improve breeding and conservation efforts aiming to preserve the genetic diversity of this beloved spice threatened by climate change.
Keywords	Vanilla planifolia ; chromosomes ; climate change ; domestication ; genes ; genetic variation ; genomics ; heterozygosity ; hybridization ; hybrids ; landraces ; multicultural diversity ; sequence analysis ; spices ; Mexico
Language	English
Dates of publication	2022-0811
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants11162090
Database	NAL-Catalogue (AGRICOLA)

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Article: Genomic Insights into Cultivated Mexican

Ellestad, Paige / Pérez-Farrera, Miguel Angel / Buerki, Sven

Plants (Basel, Switzerland)

2022 Volume 11, Issue 16

Abstract: Although vanilla is one of the most valuable spices, there is a lack of understanding of the genomic variability of the main vanilla producing species, ...

Abstract	Although vanilla is one of the most valuable spices, there is a lack of understanding of the genomic variability of the main vanilla producing species,
Language	English
Publishing date	2022-08-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants11162090
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Article ; Online: A new species of Anthurium (Araceae) from Mexico and resurrection of Anthurium macdougallii

Jiménez, Pedro Díaz / Pérez‐Farrera, Miguel Ángel / Croat, Thomas B. / Aguilar‐Rodríguez, Pedro A.

Nordic Journal of Botany. 2023 Mar., v. 2023, no. 3 p.e03737-

2023

Abstract: Anthurium hentrichianum Díaz Jim., Pérez‐Farr. & Croat a new species belonging to A. section Andiphilum (Schott) Croat from the Sierra de Juarez, north of Oaxaca, Mexico is described and illustrated. This new species is characterized by its large size ( ... ...

Abstract	Anthurium hentrichianum Díaz Jim., Pérez‐Farr. & Croat a new species belonging to A. section Andiphilum (Schott) Croat from the Sierra de Juarez, north of Oaxaca, Mexico is described and illustrated. This new species is characterized by its large size (up to 80 cm long), broadly sulcate petioles with acute margins, long geniculum (2.0–3.5 cm long) and broadly ovate to oblong‐triangular blades (56–68 cm long) with basal, and primary lateral veins usually tinged red‐purple on the lower surface. Based on a detailed review of herbarium specimens, and a comparison with specimens collected at the type localities of A. andicola Liebm. and A. macdougallii Matuda, we conclude that A. macdougallii, a taxon currently considered to be a synonym of A. andicola is a distinct species, and A. oaxacamonticola Matuda is synonymized to A. macdougallii. Anthurium andicola and A. macdougallii are re‐described with a more complete description, using fertile, living and dry material collected at its type localities.
Keywords	Anthurium ; herbaria ; new species ; Mexico
Language	English
Dates of publication	2023-03
Publishing place	Blackwell Publishing Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2406507-9
ISSN	1756-1051 ; 0107-055X
ISSN (online)	1756-1051
ISSN	0107-055X
DOI	10.1111/njb.03737
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Article ; Online: Ceratophila, a new genus of erotylid beetles (Erotylidae: Pharaxonothinae) inhabiting male cones of the cycad Ceratozamia (Cycadales: Zamiaceae).

Tang, William / Skelley, Paul / PÉrez-Farrera, Miguel Angel

Zootaxa

2018 Volume 4508, Issue 2, Page(s) 151–178

Abstract: Ceratophila new genus (Erotylidae: Pharaxonothinae) inhabiting male cones of the Mesoamerican cycad genus Ceratozamia Brongniart (Zamiaceae) is described for seven new species and compared to other genera of the Pharaxonothinae. Ceratophila differs from ... ...

Abstract	Ceratophila new genus (Erotylidae: Pharaxonothinae) inhabiting male cones of the Mesoamerican cycad genus Ceratozamia Brongniart (Zamiaceae) is described for seven new species and compared to other genera of the Pharaxonothinae. Ceratophila differs from other genera of the Pharaxonothinae in many characters, most notable of which are: lateral pronotal carina thicker anteriorly in lateral view; head with supraocular and transverse occipital lines; elytra lacking a basal bead; and stridulatory files at base of head narrowly separated. Ceratophila has the male genitalia laterally compressed with a short median lobe and flagellum, similar to other Erotylidae. In comparison, the most superficially similar pharaxonothine genus Pharaxonotha Reitter has: lateral pronotal carina thin along entire length; head lacking supraocular lines, but with transverse occipital lines; elytra with distinct basal bead; stridulatory files at base of head widely separated; and unique male genitalia that are dorsoventrally flattened with a long median lobe and flagellum. Ceratophila contains two subgenera, which differ most notably in external characters and sexual dimorphism. Members of Ceratophila (Ceratophila), the nominal subgenus, have: more cylindrical bodies, pronotum evenly convex dorsally; the pronotum lacking basal longitudinal grooves on disc; metatibiae that are distinctly triangularly dilated toward apex; and no apparent external sexual dimorphism. In comparison, members of Ceratophila (Vovidesa) new subgenus have: dorsoventrally flattened bodies; the pronotum explanate (concave) along lateral margins; the pronotum with basal longitudinal grooves on disc; metatibiae weakly or not dilated toward apex; and with all tibiae in males showing strong sexual dimorphism. Four new species are described within the subgenus Ceratophila: C. (C.) chemnicki, C. (C.) gregoryi, C. (C.) picipennis, C. (C.) sanchezae; and three new species are described within the subgenus Vovidesa: C. (V.) chiapensis, C. (V.) mixeorum, C. (V.) vazquezi. Keys to genera, subgenera and species of known adults based on morphology are provided.
MeSH term(s)	Animal Distribution ; Animal Structures ; Animals ; Body Size ; Coleoptera ; Cycadopsida ; Male ; Organ Size ; Zamiaceae
Language	English
Publishing date	2018-10-31
Publishing country	New Zealand
Document type	Journal Article
ISSN	1175-5334
ISSN (online)	1175-5334
DOI	10.11646/zootaxa.4508.2.1
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Article ; Online: Morphological variation between the two species of the palm genus Gaussia (Arecaceae) from Mesoamerica

Santos‐Hernández, Nancy Gabriela / Pérez‐Farrera, Miguel Ángel / Eguiarte, Luis E. / Vovides, Andrew P. / Gutiérrez‐Ortega, José Said

Nordic Journal of Botany. 2022 Dec., v. 2022, no. 12 p.e03770-

2022

Abstract: Palms (Arecaceae) represent a challenge for studies of morphological variation for several various reasons. For instance, the height of many species makes them difficult to collect, and in some cases, the size of the leaves or the presence of spines make ...

Abstract	Palms (Arecaceae) represent a challenge for studies of morphological variation for several various reasons. For instance, the height of many species makes them difficult to collect, and in some cases, the size of the leaves or the presence of spines make them hard to process and preserve in herbaria. Arecaceae is one of the most diverse families of monocots (ca 2600 species), and many of its species remain poorly studied. The genus Gaussia has five recognized species. Their distributions are restricted to Central America and the Caribbean islands, and for most of them, their taxonomic descriptions are the only information available. Two species – Gaussia maya and G. gomez‐pompae – are exclusively distributed in Mesoamerica. They occur allopatrically and their populations are isolated from each other. The aim of this work was to evaluate the levels of intra‐ and inter‐population morphological variation in both species and determine the possible factors that influence such a variation. We examined the morphological variation of 13 vegetative structures of 155 adult individuals from nine populations of G. maya and G. gomez‐pompae. The differentiation among populations was significant for almost all the variables and was consistent with an isolation‐by‐distance pattern. A linear discriminant analysis, Mahalanobis distances and UPGMA cluster analysis based on Euclidean distances among populations showed that three morphological groups could be distinguished. One group contained only individuals of G. maya, the second only G. gomez‐pompae, while the third group represents a yet unknown taxon. Pairwise differentiation tests clarified the morphological distinction among the three groups. This work highlights the importance of quantifying morphological variation between populations of little‐studied palms.
Keywords	Arecaceae ; adults ; botany ; cluster analysis ; discriminant analysis ; Caribbean ; Central America
Language	English
Dates of publication	2022-12
Publishing place	Blackwell Publishing Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2406507-9
ISSN	1756-1051 ; 0107-055X
ISSN (online)	1756-1051
ISSN	0107-055X
DOI	10.1111/njb.03770
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The phylogenetic reconstruction of the Neotropical cycad genus Ceratozamia (Zamiaceae) reveals disparate patterns of niche evolution.

Gutiérrez-Ortega, José Said / Pérez-Farrera, Miguel Angel / Matsuo, Ayumi / Sato, Mitsuhiko P / Suyama, Yoshihisa / Calonje, Michael / Vovides, Andrew P / Kajita, Tadashi / Watano, Yasuyuki

Molecular phylogenetics and evolution

2023 Volume 190, Page(s) 107960

Abstract: The cycad genus Ceratozamia comprises 40 species from Mexico, Guatemala, Belize, and Honduras, where cycads occur throughout climatically varied montane habitats. Ceratozamia has the potential to reveal the history and processes of species ... ...

Abstract	The cycad genus Ceratozamia comprises 40 species from Mexico, Guatemala, Belize, and Honduras, where cycads occur throughout climatically varied montane habitats. Ceratozamia has the potential to reveal the history and processes of species diversification across diverse Neotropical habitats in this region. However, the species relationships within Ceratozamia and the ecological trends during its evolution remain unclear. Here, we aimed to clarify the phylogenetic relationships, the timing of clade and species divergences, and the niche evolution throughout the phylogenetic history of Ceratozamia. Genome-wide DNA sequences were obtained with MIG-seq, and multiple data-filtering steps were used to optimize the dataset used to construct an ultrametric species tree. Divergence times among branches and ancestral niches were estimated. The niche variation among species was evaluated, summarized into two principal components, and their ancestral states were reconstructed to test whether niche shifts among branches can be explained by random processes, under a Brownian Motion model. Ceratozamia comprises three main clades, and most species relationships within the clades were resolved. Ceratozamia has diversified since the Oligocene, with major branching events occurring during the Miocene. This timing is consistent with fossil evidence, the timing estimated for other Neotropical plant groups, and the major geological events that shaped the topographic and climatic variation in Mexico. Patterns of niche evolution in the genus do not accord with the Brownian Motion model. Rather, non-random evolution with shifts towards more seasonal environments at high latitudes, or shifts towards humid or dry environments at low latitudes explain the diversification of Ceratozamia. We present a comprehensive phylogenetic reconstruction for Ceratozamia and identify for the first time the environmental factors involved in clade and species diversification within the genus. This study alleviates the controversies regarding the species relationships in the genus and provides the first evidence that latitude-associated environmental factors may influence processes of niche evolution in cycads.
MeSH term(s)	Phylogeny ; Zamiaceae/genetics ; Phylogeography ; Ecosystem ; Time Factors
Language	English
Publishing date	2023-11-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2023.107960
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Article ; Online: Spatio-temporal evolution of climbing habit in the Dahlia-Hidalgoa group (Coreopsidae, Asteraceae).

Sánchez-Chávez, Erandi / Rodríguez, Aaron / Castro-Castro, Arturo / Pérez-Farrera, Miguel Angel / Sosa, Victoria

Molecular phylogenetics and evolution

2019 Volume 135, Page(s) 166–176

Abstract: In this paper we focus on Hidalgoa, a small genus distributed in cloud forest from Mexico to Colombia with the uncommon climbing habit of enlarging its petioles. This genus belongs to tribe Coreopsideae (Asteraceae), a group mostly from the Neotropics ... ...

Abstract	In this paper we focus on Hidalgoa, a small genus distributed in cloud forest from Mexico to Colombia with the uncommon climbing habit of enlarging its petioles. This genus belongs to tribe Coreopsideae (Asteraceae), a group mostly from the Neotropics with a few taxa in Oceania and Polynesia. The phylogenetic position of Hidalgoa has not yet been determined though it will most probably be closely related to Dahlia. The aim of this paper is to understand the ecological and evolutionary consequences of the shift to a climbing growth form using a spatio-temporal approach to phylogenetic analyses, and by testing evolutionary models for ecological niche. Our results identified that Hidalgoa formed a sub- clade in a grade with Dahlia, with divergence occurring in the Pliocene. The ancestral life form for this clade was cryptophytic (e.g. geophytes). Analyses using the climate variables most important to the elements of the Dahlia-Hidalgoa clade indicate that they share the same preferences. Moreover, visualization by traitgrams of the significant climate variables shows no departure among clades. These results suggest that no evolutionary or ecological consequences have yet manifested, and that Hidalgoa can be considered a climbing Dahlia.
MeSH term(s)	Base Pairing/genetics ; Climate ; Colombia ; Dahlia/classification ; Dahlia/physiology ; Ecosystem ; Mexico ; Models, Biological ; Phylogeny ; Polynesia ; Principal Component Analysis ; Species Specificity ; Time Factors
Language	English
Publishing date	2019-03-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2019.03.012
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Article: Ups and downs: Genetic differentiation among populations of the Podocarpus (Podocarpaceae) species in Mesoamerica

Ornelas, Juan Francisco / Ortiz-Rodriguez, Andrés Ernesto / Ruiz-Sanchez, Eduardo / Sosa, Victoria / Pérez-Farrera, Miguel Ángel

Molecular phylogenetics and evolution. 2019 Sept., v. 138

2019

Abstract: The biogeographical history of Mesoamerican cloud forests is complex, encompassing a diverse and heterogeneous mixture of species with temperate and tropical origins. The dynamic geological landscape and climate change from the Miocene to the Pleistocene ...

Abstract	The biogeographical history of Mesoamerican cloud forests is complex, encompassing a diverse and heterogeneous mixture of species with temperate and tropical origins. The dynamic geological landscape and climate change from the Miocene to the Pleistocene affected the distributions and composition of cloud forests in the region, and contributed to divergence events at different time scales. We assessed genetic variation of 29 populations of P. matudae, and closely related P. guatemalensis and P. oleifolius (Podocarpaceae) by sequencing 255 samples of the psbA-trnH and trnL-F intergenic spacer regions across the species ranges. We conducted phylogenetic, population and spatial genetic analyses as well as divergence time estimation and ecological niche modelling (ENM) to test the generality of demographic and genetic scenarios for cloud forest-adapted species. The results revealed genetic differentiation among species, with some individuals of P. oleifolius and P. guatemalensis placed in the P. matudae group and some P. oleifolius in the P. guatemalensis group. Predictions of ENMs under past climatic conditions and a strong signal of spatial expansion suggest that the highland P. matudae and P. oleifolius populations experienced expansions into lower elevation during the Last Glacial Maximum (LGM). Contrary to predictions by the two precipitation models and elevational ups and downs for cloud forest taxa during the LGM, genetic differentiation and predicted distribution of suitable habitat support the hypotheses that P. matudae and P. oleifolius remained in situ during the LGM primarily within the current fragmented distribution of the cloud forest and spread into the lowlands during the LGM, whereas the distribution of suitable habitat for P. guatemalensis had no major changes upwards from the Last Inter Glacial (LIG) to current conditions.
Keywords	Miocene epoch ; Pleistocene epoch ; Podocarpus matudae ; Podocarpus oleifolius ; altitude ; climate change ; climatic factors ; genetic analysis ; genetic variation ; geographical distribution ; intergenic DNA ; landscapes ; lowlands ; models ; niches ; phylogeny ; prediction ; tropical montane cloud forests ; Central America
Language	English
Dates of publication	2019-09
Size	p. 17-30.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2019.05.025
Database	NAL-Catalogue (AGRICOLA)

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Article: Phylogenetic analyses and morphological characteristics support the description of a second species of Tridimeris (Annonaceae)

Ortiz-Rodriguez, Andres Ernesto / Escobar-Castellanos, Marcos Alberto / Pérez-Farrera, Miguel Angel

PhytoKeys. 2016 Nov. 8, v. 74

2016

Abstract: Based on phylogenetic and morphological evidence, Tridimerischiapensis Escobar-Castellanos & Ortiz-Rodr., sp. n. (Annonaceae), a new species from the karst forest of southern Mexico, is described and illustrated. The new species differs from ... ...

Abstract	Based on phylogenetic and morphological evidence, Tridimerischiapensis Escobar-Castellanos & Ortiz-Rodr., sp. n. (Annonaceae), a new species from the karst forest of southern Mexico, is described and illustrated. The new species differs from Tridimerishahniana, the only described species in the genus, in that the latter has flowers with sepals densely tomentose outside, one (rarely two) carpel(s) per flower and fruits densely covered with golden-brown hairs, while Tridimerischiapensis has flowers with glabrous sepals outside, two to five carpels per flower and glabrous fruits. Furthermore, a shallow triangular white patch at the base of the inner petals is found in Tridimerischiapensis, a morphological character shared with the sister genus Sapranthus but absent in Tridimerishahniana. Geographically, both species occur allopatrically. With just one known locality and seven individuals of Tridimerischiapensis recorded in one sampling hectare, and based on application of the criteria established by the IUCN, we conclude tentatively that the species is critically endangered.
Keywords	Annonaceae ; calyx ; carpels ; corolla ; forests ; fruits ; karsts ; new species ; phylogeny ; plant taxonomy ; scientific illustration ; taxon descriptions ; trichomes ; Mexico
Language	English
Dates of publication	2016-1108
Size	p. 79-95.
Publishing place	Pensoft Publishers
Document type	Article
ZDB-ID	2579891-1
ISSN	1314-2003 ; 1314-2011
ISSN (online)	1314-2003
ISSN	1314-2011
DOI	10.3897/phytokeys.74.10371
Database	NAL-Catalogue (AGRICOLA)

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Article: Speciation along a latitudinal gradient: The origin of the Neotropical cycad sister pair

Gutiérrez-Ortega, José Said / Molina-Freaner, Francisco / Martínez, José F / Pérez-Farrera, Miguel Angel / Vovides, Andrew P / Hernández-López, Antonio / Tezuka, Ayumi / Nagano, Atsushi J / Watano, Yasuyuki / Takahashi, Yuma / Murakami, Masashi / Kajita, Tadashi

Ecology and evolution

2021 Volume 11, Issue 11, Page(s) 6962–6976

Abstract: Latitude is correlated with environmental components that determine the distribution of biodiversity. In combination with geographic factors, latitude-associated environmental variables are expected to influence speciation, but empirical evidence on how ... ...

Abstract	Latitude is correlated with environmental components that determine the distribution of biodiversity. In combination with geographic factors, latitude-associated environmental variables are expected to influence speciation, but empirical evidence on how those factors interplay is scarce. We evaluated the genetic and environmental variation among populations in the pair of sister species
Language	English
Publishing date	2021-05-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.7545
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