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Map showing the distribution of Pinus section Parrya based on Critchfield and Little (1966). Species records are based on herbarium collections and data from field studies. The individual sample sites are indicated by triangles (Appendix 1). Colors represent North American subsections that belong to section Parrya.
Contexts in source publication
Context 1
... hybridization and gene flow have been reported in species of Pinus subsection Cembroides (e.g. Mirov 1967;Lanner 1974aLanner , 1974bLanner and Phillips 1992;Malusa 1992). Some populations of P. edulis (predominantly two needles per fascicle) and P. monophylla (predominantly singleneedled) occur in sympatry (Fig. 1) in the eastern Great Basin where trees of P. edulis with both single needles and two needles per fascicle have been observed (Lanner 1974a). In a study of natural hybridization in pinyon pines in northwestern Arizona, Lanner and Phillips (1992) analyzed variation in morphological characters over different years. Based on differences ...
Context 2
... Lanner (treated here as a synonym of P. quadrifolia). According to Lanner (1974b), this would explain extreme needle number variation in P. quadrifolia, a characteristic that is frequently observed in pine artificial hybrids when parents differ in this character ( Keng and Little 1961). The geographical distributions of the taxa overlap broadly (Fig. 1), with sympatric populations common in Baja California (e.g. in the Sierra Juárez), suggesting that putative hybrids of several types co-exist in a hybrid swarm (Lanner 1974b). Farjon and Styles (1997) reported that pollen dispersal occurs in April and May in P. monophylla and in March and April in P. quadrifolia, which would allow for ...
Context 3
... of México and the Oregon State University Herbarium (OSC). The individuals represent all taxa of Pinus subsection Cembroides recognized by Gernandt et al. (2005). For outgroups we included three individuals representing two of three species of subsection Balfourianae and three of P. nelsonii, the only member of subsection Nelsoniae (Fig. 1). These two subsections were recovered as the sister group of subsection Cembroides in previous phylogenetic analyses and together with subsection Cembroides are classified in section Parrya (Gernandt et al. 2005). We also included representative species from section Quinquefoliae: subsections Gerardianae Loudon (2), Krempfianae Little ...
Context 4
... Allowing for a single reticulation resulted in a reduction from 8084 to 7619 lineages and involved introgression from P. monophylla into P. edulis (Fig. 4B). Allowing for two reticulations resulted in a reduction to 7453 lineages (Fig. 4C). The first reticulation involved introgression from P. fallax into P. cembroides subsp. cembroides (Fig. 4C: H1) and the second involved introgression from P. edulis into P. lagunae (Fig. 4C: H2). Allowing for three reticulations resulted in a reduction to 7211 lineages (Fig. 4D). The first reticulation (Fig. 4D: H1) involved introgression from P. culminicola into P. quadrifolia, the second involved introgression from a possible extinct taxon ...
Context 5
... in a reduction to 7453 lineages (Fig. 4C). The first reticulation involved introgression from P. fallax into P. cembroides subsp. cembroides (Fig. 4C: H1) and the second involved introgression from P. edulis into P. lagunae (Fig. 4C: H2). Allowing for three reticulations resulted in a reduction to 7211 lineages (Fig. 4D). The first reticulation (Fig. 4D: H1) involved introgression from P. culminicola into P. quadrifolia, the second involved introgression from a possible extinct taxon into P. lagunae (Fig. 4D: H2), and the third involved introgression from a possible extinct taxon into P. cembroides subsp. cembroides (Fig. 4D: ...
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... Posteriormente, se depuró la BDO eliminando datos sin coordenadas, mal georreferenciados y duplicados (de una especie) en pixeles de 1 km 2 . Se consideraron como válidas las entidades taxonómicas definidas en publicaciones recientes (Buck et al., 2020(Buck et al., , 2023Farjon, 2018;Montes et al., 2019Montes et al., , 2022Pérez-de la Rosa & Gernandt, 2017;Willyard et al., 2017Willyard et al., , 2021 y se consultaron sitios especializados (http://www.worldfloraonline.org/, https://powo.science.kew.org/) ...
... Tales variaciones pueden deberse a: 1) metodología: solo se contabilizaron las especies dentro de los pixeles incluidos en CRP_1 y no para toda la península, por lo que especies como P. lagunae (Rob-Pass.) Passini no están incluidas en la cifra mencionada (9 especies); 2) taxonomía: el nivel taxonómico empleado fue especie, con base en las entidades reconocidas por Farjon (2018) y estudios recientes sobre delimitacion de especies (Buck et al., 2020(Buck et al., , 2023Montes et al., 2019Montes et al., , 2022Willyard et al., 2017Willyard et al., , 2021. El número de especies observado (9, 21, 17, 16) en algunas regiones como CRP_1, 2, 3 y 7 es cercano a las 7, 20, 14 y 15 mencionadas por Sáenz-Ceja Tabla 1 Valores de los criterios considerados para la asignación de un valor de importancia (V.I.) para centros de riqueza de especies de Pinus (CRP) en México. ...
Identifying centers of diversification is useful for species germplasm conservation planning. The study objective was to determine the localities that acted as centers of diversification of the Pinus genus in Mexico and to identify current areas with the highest pine species richness. An occurrence database (BDO) and fossil records (RF) were built for the species. From this, a mesh of ~10 × 10 km was created and Centers of Pine Richness (CRP), Centers of Genetic Richness (CRG) and Centers of High Diversity (CAD) were determined. The spatial coincidence of CRG, CAD and
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... These include angiosperm-specific probe sets that target hundreds of nuclear genes [17,22] and one recently developed to enrich more than 400 nuclear genes across flagellate land plants [18]. While there are bait kits developed specifically for specific conifer families (e.g., Pinaceae; [23]), we are not aware of a conifer-specific bait set that targets the entire clade. ...
Conifers are an ecologically and economically important seed plant group that can pro-vide significant insights into the evolution of land plants. Molecular phylogenetics has developedas an important approach in evolutionary studies, although there have been relatively few studiesof conifers that employ large-scale data sourced from multiple nuclear genes. Target enrichmentsequencing (target capture, exon capture, or Hyb-Seq) has developed as a key approach in modernphylogenomic studies. However, until now, there has been no bait set that specifically targets theentire conifer clade. REMcon is a target sequence capture probe set intended for family- and species-level phylogenetic studies of conifers that target c. 100 single-copy nuclear loci. We tested the REM-con probe set using 69 species, including 44 conifer genera across six families and four other gym-nosperm taxa, to evaluate the efficiency of target capture to efficiently generate comparable DNAsequence data across conifers. The recovery of target loci was high, with, on average, 94% of thetargeted regions recovered across samples with high read coverage. A phylogenetic analysis of thesedata produced a well-supported topology that is consistent with the current understanding of rela-tionships among conifers. The REMcon bait set will be useful in generating relatively large-scalenuclear data sets consistently for any conifer lineage.
... The most widespread piñon pine in the Mogollon Highlands, known variously as Pinus edulis var. fallax (Little Montes et al. 2019Montes et al. , 2022, is tolerant of higher temperatures and lower moisture than other closely related piñon species. Here, we call this species the Mogollon Highlands piñon, Pinus 3 fallax (after Buck et al. 2023), to call attention to its narrow distribution and unique characters. ...
... Recent efforts for sequencing low copy genes have relied on PCR techniques using primers designed from genes retrieved from transcriptomes or other next generation sequencing approaches (e.g., Zeng et al., 2014;Fu et al., 2016). The ability to amplify selected nuclear genes represent an advance in the field, as researchers are now able to incorporate nuclear genes in evolutionary studies with non-model organisms without being restricted by complex data processing or high sequencing costs (Zhang et al., 2012;Liu et al., 2015;Waselkov et al., 2018;Montes et al., 2019). ...
... Исследование однонуклеотидного полиморфизма (SNP) в низкокопийных районах геномов (DArTseq-технология) показало отсутствие различий между экземплярами P. quadrifolia и P. juarezensis, которые таким образом являются конспецифичными (Buck et al., 2020). Анализ низкокопийных ядерных генов у единичных образцов видов этой группы не выявил гибридов P. quadrifolia × P. californiarum (Montes et al., 2019), но увеличение выборок видов до нескольких десятков и анализ SNPs ядерной ДНК вдоль всего генома позволил обнаружить незначительное количество межвидовых гибридов P. quadrifolia × P. californiarum и P. quadrifolia × P. monophylla, как морфологически промежуточных, так и сходных с одним из родителей (Buck et al., 2020). Было высказано предположение, что морфологическая промежуточность признаков у гибридов наблюдается в случаях, когда у них генетический вклад обоих родителей примерно равен, а когда один из них преобладает в результате интрогрессий (т.е. ...
01.11.2023 г. После доработки 07.11.2023 г. Принята к публикации 07.11.2023 г. Межвидовая гибридизация широко распространена у растений и является важнейшим фактором их эволюции. Долгое время основным критерием гибридного происхождения растения считалась промежуточность заметных морфологических признаков. Однако, по мере внедрения в систематику ме-тодов химии и молекулярной биологии и изучения все больших выборок, все чаще выявляются рас-тения химически и генетически гибридные, но внешне неотличимые от предполагаемых родителей, или имеющие необычное сочетание признаков, не позволяющее по морфологии опознать гибрид-ность и родителей. Последующее более пристальное исследование таких выявленных "молекулярных гибридов", применение морфометрии, часто позволяют найти и морфологические, зачастую количественные или микроскопические, признаки, подтверждающие гибридную природу данных растений. Выявление и изучение криптических гибридов важно для систематики сложных таксономических групп с широкой фенотипической пластичностью, с большим количеством сходных ви-дов, с упрощенной морфологией. Оно помогает лучше понять условия, при которых может происходить гибридизация, и важно в практическом плане, в особенности для борьбы с инвазионными видами, для охраны редких и угрожаемых видов и др. Ключевые слова: криптогибриды, растения, межвидовая гибридизация, морфологическая промежуточность признаков, "молекулярные гибриды".
long time, the main criterion for the hybrid origin of a plant was considered to be the morphological intermediacy of noticeable external characters. However, as the methods of chemistry and molecular biology are introduced into systematics and larger samples are studied, the researches increasingly identify the plants which
are chemically and genetically hybrid, but are outwardly indistinguishable from the hypothetical parents or have an unusual combination of traits that does not allow us to recognize the hybridity and the parents by morphology. Subsequent closer study of such identified “molecular hybrids” with application of morphometry often
makes it possible to find morphological, often quantitative or microscopic characteristics which confirm the hybrid nature of these plants as well. Identification and study of cryptic hybrids is important for the systematics of complex taxonomic groups with wide phenotypic plasticity, with a large number of similar species, and
simplified morphology. It helps to better understand the conditions under which hybridization can occur, and is important in practical terms, especially for the control of invasive species, for the protection of rare and endangered species, etc.
... While hybridization between fallax-type and P. edulis has been proposed (Lanner & Phillips, 1992;LaHood, 1995), no genetic studies have found evidence of admixture between the two taxa (Duran et al., 2012;Montes et al., 2019) and Montes et al. (2022) found no genetic differentiation between them, implying that the two are one taxon. Fallax-type typically has one needle per fascicle with two resin canals (Little, 1968;Cole et al., 2008), whereas P. edulis has two needles and two resin canals. ...
... This method produces a higher number of informative single nucleotide polymorphisms (SNPs) across the genome that are then compared with a reference genome (Buck et al., 2020). We selected P. lambertiana as the reference genome (GCA_001447015.2) because of its relatively close evolutionary relationship with the pinyon subsection Cembroides (Montes et al., 2019;Jin et al., 2021) compared to that of P. taeda. A lowdensity DArTseq assay of 353 individuals (Table S1) subset from across the distribution (Fig. 2b) resulted in 24 109 SNPs, coded as '0' (homozygous to reference allele), '1' (homozygous to alternative allele), '2' (heterozygous), and '-' (fragment missing). ...
... This novel hybridization event was not detected in other genetic studies (i.e. Montes et al., 2019Montes et al., , 2022 likely due to their lower sample sizes and taxonomically focused sampling design targeting 'type' individuals. However, the hybrid origin of P. 9fallax may explain their study's nuclear phylogenetic findings wherein P. 9fallax samples never formed a monophyletic group, but instead grouped with either P. edulis or P. californiarum (Montes et al., 2022). ...
Multispecies interbreeding networks, or syngameons, have been increasingly reported in natural systems. However, the formation, structure, and maintenance of syngameons have received little attention. Through gene flow, syngameons can increase genetic diversity, facilitate the colonization of new environments, and contribute to hybrid speciation.
In this study, we evaluated the history, patterns, and consequences of hybridization in a pinyon pine syngameon using morphological and genomic data to assess genetic structure, demographic history, and geographic and climatic data to determine niche differentiation.
We demonstrated that Pinus edulis, a dominant species in the Southwestern US and a barometer of climate change, is a core participant in the syngameon, involved in the formation of two drought‐adapted hybrid lineages including the parapatric and taxonomically controversial fallax‐type. We found that species remain morphologically and genetically distinct at range cores, maintaining species boundaries while undergoing extensive gene flow in areas of sympatry at range peripheries.
Our study shows that sequential hybridization may have caused relatively rapid speciation and facilitated the colonization of different niches, resulting in the rapid formation of two new lineages. Participation in the syngameon may allow adaptive traits to be introgressed across species barriers and provide the changes needed to survive future climate scenarios.
... The circumscription of recognized species in Pinus subsect. Cembroides differs in recent works (Gernandt et al., 2005;Farjon and Filer, 2013;Gernandt and Pérez de la Rosa, 2014;Montes et al., 2019) and the taxonomic ranges used for pinyon pines has varied widely, due in part to placing emphasis on different molecular and structural characters (Malusa, 1992;Farjon and Styles, 1997;Gernandt et al., 2005;Farjon and Filer, 2013). Disagreements in the classification of some taxa include whether or not to elevate P. cembroides Zucc. ...
... orizabensis D.K. Bailey and P. cembroides subsp. lagunae (Robert-Passini) D.K. Bailey (here treated as P. lagunae (Robert-Passini) Passini), to the rank of species (Gernandt et al., 2005;Farjon and Filer, 2013;Montes et al., 2019). Similarly, phylogenetic analyses clearly support separating P. discolor D.K. Bailey & F.G. Hawksw. ...
... and P. johannis M.F. Robert from P. cembroides (Gernandt et al., 2003(Gernandt et al., , 2005Parks et al., 2012;Montes et al., 2019) although they have been treated as infraspecific taxa of P. cembroides (Farjon and Filer, 2013 (Malusa, 1992). Pinus californiarum has been treated as an independent lineage, as a synonym of P. monophylla, or as a variety, P. monophylla var. ...
Premise:
Accurate species delimitation is essential for evolutionary biology, conservation, and biodiversity management. We studied species delimitation in North American pinyon pines, Pinus subsection Cembroides, a natural group with high levels of incomplete lineage sorting.
Methods:
We used coalescent-based methods and multivariate analyses of low-copy number nuclear genes and nearly complete high-copy number plastomes generated with the Hyb-Seq method. The three coalescent-based species delimitation methods evaluated were the Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Process (PTP), and Trinomial Distribution of Triplets (Tr2). We also measured admixture in populations with possible introgression.
Results:
Our results show inconsistencies among GMYC, PTP, and Tr2. The single-locus based GMYC analysis of plastid DNA recovered a higher number of species (up to 24 entities, including singleton lineages and clusters) than PTP and the multi-locus coalescent approach. The PTP analysis identified 10 species whereas Tr2 recovered 13, which agreed closely with taxonomic treatments.
Conclusions:
We found that PTP and GMYC identified species with low levels of ILS and high morphological divergence (P. maximartinezii, P. pinceana, and P. rzedowskii). However, GMYC method oversplit species by identification of more divergent samples as singletons. Moreover, both PTP and GMYC were incapable of identifying some species that are readily identified morphologically. We suggest that the divergence times between lineages within North American pinyon pines are so disparate that GMYC results are unreliable. Results of the Tr2 method coincided well with previous delimitations based on morphology, DNA, geography, and secondary chemistry.
... This method has been used to characterize hundreds of genes for phylogenetic studies of the three most species-rich clades of exclusively North American pines, subsects. Australes, Ponderosae, and Cembroides (Gernandt et al. 2018; Montes et al. 2019;Willyard et al. 2021) and to study population genetics and local adaptation (Peláez et al. 2020). ...
Genetic and evolutionary questions are being addressed in pines using a host of high-throughput sequencing strategies, including whole-genome sequencing, transcriptome sequencing, and target enrichment of nuclear genes. Some of the questions being addressed include the genetic basis of pathogen and drought resistance, differential expression, genetic mapping, phylogeography, and phylogenetics. Pine genomes are enormous, ranging from 20 to 40 Gb. At present, draft genomes are available for only two pine species, P. taeda (loblolly pine) and P. lambertiana (sugar pine), but most other approximately 80 species of North American pines have been represented in evolutionary studies based on complete plastomes, low-copy nuclear genes, and transcriptomes. A number of online databases have been developed and made publicly available for comparative studies of pines and other conifers.Keywords
Pinus
Genome sequencesPlastid genomesTranscriptomesGenomic databases
... Pinus remota (Little) D.K. Bailey & Hawksw. también pertenece a la subsección Cembroides, que incluye a las especies de pinos conocidas como piñoneros (Gernandt et al., 2003(Gernandt et al., , 2005Montes et al., 2019). Los árboles tienen un tamaño medio de tipo arbóreo-arbustivo y forman poblaciones que crecen de manera dispersa y fragmentada en dos regiones de Norteamérica: una en los Estados Unidos de América al suroeste de Texas y la otra en México, en el noreste y sureste de Chihuahua, Coahuila y oeste de Nuevo León (Perry, 1991;Farjon y Styles, 1997;Farjon, 2013). ...
Antecedentes y Objetivos:
El decremento y fragmentación de las poblaciones resulta en la pérdida de variación e incremento de la diferenciación genética. Pinus remota es una especie arbórea-arbustiva de distribución restringida con poblaciones dispersas y fragmentadas. Los objetivos del presente estudio fueron: evaluar los niveles de variación genética, la endogamia y el tamaño efectivo de las poblaciones, probar la hipótesis de la existencia de cuellos de botella asociados a la disminución de la variación genética de las poblaciones y analizar la estructura genética y su asociación con la distribución geográfica de las poblaciones.
Métodos:
El estudio se realizó en siete poblaciones representativas de su distribución natural en México, con muestras de acículas de 112 árboles analizadas con cinco microsatélites de núcleo. Los datos se evaluaron con parámetros de la genética de poblaciones y métodos de aproximación Bayesiana.
Resultados clave:
La heterocigosidad promedio esperada (He=0.557) fue más alta que la observada (Ho=0.375). Las poblaciones no se encuentran en equilibro Hardy-Weinberg, con una endogamia significativa (FIS=0.259) y tamaños efectivos reducidos (Ne entre 375-425); están estructuradas en tres grupos genéticos (FST=0.158), con valores altos del índice Mc (0.186-0.283), sugiriendo eventos de declinamiento demográfico ancestral (entre 11,910 y 23,820 años atrás), asociados con los cambios climáticos del Pleistoceno.
Conclusiones:
El estudio demuestra que P. remota contiene una variación genética considerable, pero estructurada espacialmente y asociada a cuellos de botella ancestrales. Además, se confirma que P. catarinae es su sinónimo. La especie ha sido capaz de subsistir y adaptarse a condiciones ambientales locales. Con este conocimiento se plantean estrategias para la conservación de las poblaciones remanentes de la especie.
... The accuracy of any evolutionary or ecological inference is heavily dependent on a fully resolved phylogeny and reliable estimates of species divergence times. Unfortunately, due to the slow evolutionary rates of conifers (3), the phylogenetic relationships of most subsections and species of pines are far from being resolved (10,(20)(21)(22)(23)(26)(27)(28), which hinders us from studying their spatiotemporal evolution. ...
... The phylogenies inferred from the CDS and CDS (first + second) datasets, using either concatenation or coalescent methods, are highly resolved (ultrafast bootstrap [UFBoot] > 95% and local posterior probability [LPP] > 95% for most nodes) and topologically consistent, except that Pinus nelsonii and a few species within subsections show discordant placements ( Fig. 1 and SI Appendix, Figs. S1-S4), which could be attributed to incomplete lineage sorting, hybridization among closely related species, or other unknown factors (22,(27)(28)(29). ...
Significance
Understanding what determines the distribution of biodiversity remains one of the great challenges in evolutionary biology and ecology. The Northern Hemisphere conifers do not follow a latitudinal diversity gradient and show a unique distribution pattern, that is most species are distributed at middle latitudes. To reveal the mechanisms underlying this pattern, we investigate the spatiotemporal evolution of the largest conifer genus Pinus . We find that the midlatitude region has been an evolutionary museum for Pinus , and particularly, topography has played the most important role in pine diversification. Moreover, our results indicate that pine’s preference of warm and somewhat drier habitats could be helpful for their adaptation to the Anthropocene climate warming, which is important for biodiversity conservation and forest management.
