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Machine learning approaches identify male body size as the most accurate predictor of species richness. BMC Biol 2020; 18:105. [PMID: 32854698 PMCID: PMC7453550 DOI: 10.1186/s12915-020-00835-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness -the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera. RESULTS We test the predictive power of 22 variables from spiders' morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness. CONCLUSIONS We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly.
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Wehenkel C, Mariscal-Lucero SDR, González-Elizondo MS, Aguirre-Galindo VA, Fladung M, López-Sánchez CA. Tall Pinus luzmariae trees with genes from P. herrerae. PeerJ 2020; 8:e8648. [PMID: 32149029 PMCID: PMC7049253 DOI: 10.7717/peerj.8648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/27/2020] [Indexed: 11/20/2022] Open
Abstract
CONTEXT Pinus herrerae and P. luzmariae are endemic to western Mexico, where they cover an area of more than 1 million hectares. Pinus herrerae is also cultivated in field trials in South Africa and South America, because of its considerable economic importance as a source of timber and resin. Seed quality, afforestation success and desirable traits may all be influenced by the presence of hybrid trees in seed stands. AIMS We aimed to determine the degree of hybridization between P. herrerae and P. luzmariae in seed stands of each species located in the Sierra Madre Occidental, Durango, Mexico. METHODS AFLP molecular markers from samples of 171 trees across five populations were analyzed with STRUCTURE and NewHybrids software to determine the degree of introgressive hybridization. The accuracy of STRUCTURE and NewHybrids in detecting hybrids was quantified using the software Hybridlab 1.0. Morphological analysis of 131 samples from two populations of P. herrerae and two populations of P. luzmariae was also conducted by Random Forest classification. The data were compared by Principal Coordinate Analysis (PCoA) in GenAlex 6.501. RESULTS Hybridization between Pinus herrerae and P. luzmariae was observed in all seed stands under study and resulted in enhancement of desirable silvicultural traits in the latter species. In P. luzmariae, only about 16% molecularly detected hybrids correspond to those identified on a morphological basis. However, the morphology of P. herrerae is not consistent with the molecularly identified hybrids from one population and is only consistent with 3.3 of those from the other population. CONCLUSIONS This is the first report of hybrid vigour (heterosis) in Mexican pines. Information about hybridization and introgression is essential for developing effective future breeding programs, successful establishment of plantations and management of natural forest stands. Understanding how natural hybridization may influence the evolution and adaptation of pines to climate change is a cornerstone to sustainable forest management including adaptive silviculture.
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Affiliation(s)
- Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Samantha del Rocío Mariscal-Lucero
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
- Instituto Tecnológico del Valle del Guadiana, Tecnológico Nacional de México, Durango, Mexico
| | | | - Víctor A. Aguirre-Galindo
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
| | | | - Carlos A. López-Sánchez
- Department of Organisms and Systems Biology, University of Oviedo, Polytechnic School of Mieres, Asturias, Spain
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Pinedo-Alvarez C, Renteria-Villalobos M, Aguilar-Soto V, Vega-Mares JH, Melgoza-Castillo A. Distribution dynamics of Picea chihuahuana Martínez populations under different climate change scenarios in Mexico. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Antúnez P, Wehenkel C, López-Sánchez CA, Hernández-Díaz JC. The Role of Climatic Variables for Estimating Probability of Abundance of Tree Species. POLISH JOURNAL OF ECOLOGY 2017. [DOI: 10.3161/15052249pje2017.65.3.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Pablo Antúnez
- División de Estudios de Posgrado-Instituto de Estudios Ambientales, Universidad de la Sierra Juárez, Avenida Universidad S/N, Ixtlán de Juárez, 68725 Oaxaca, México
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Km 5.5 Carretera Mazatlán, 34160 Durango, México
| | - Carlos A. López-Sánchez
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Km 5.5 Carretera Mazatlán, 34160 Durango, México
| | - José C. Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Km 5.5 Carretera Mazatlán, 34160 Durango, México
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Dominguez-Guerrero IK, Del Rocío Mariscal-Lucero S, Hernández-Díaz JC, Heinze B, Prieto-Ruiz JÁ, Wehenkel C. Discrimination of Picea chihuahuana Martinez populations on the basis of climatic, edaphic, dendrometric, genetic and population traits. PeerJ 2017. [PMID: 28626616 PMCID: PMC5470581 DOI: 10.7717/peerj.3452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background Picea chihuahuana, which is endemic to Mexico, is currently listed as “Endangered” on the Red List. Chihuahua spruce is only found in the Sierra Madre Occidental (SMO), Mexico. About 42,600 individuals are distributed in forty populations. These populations are fragmented and can be classified into three geographically distinct clusters in the SMO. The total area covered by P. chihuahuana populations is less than 300 ha. A recent study suggested assisted migration as an alternative to the ex situ conservation of P. chihuahuana, taking into consideration the genetic structure and diversity of the populations and the predictions regarding the future climate of the habitat. However, detailed background information is required to enable development of plans for protecting and conserving species and for successful assisted migration. Thus, it is important to identify differences between populations in relation to environmental conditions. The genetic diversity of populations, which affect vigor, evolution and adaptability of the species, must also be considered. In this study, we examined 14 populations of P. chihuahuana, with the overall aim of discriminating the populations and form clusters of this species. Methods Each population was represented by one 50 × 50 m plot established in the center of its respective location. Climate, soil, dasometric, density variables and genetic and species diversities were assessed in these plots for further analyses. The putatively neutral and adaptive AFLP markers were used to calculate genetic diversity. Affinity Propagation (AP) clustering technique and k-means clustering algorithm were used to classify the populations in the optimal number of clusters. Later stepwise binomial logistic regression was applied to test for significant differences in variables of the southern and northern P. chihuahuana populations. Spearman’s correlation test was used to analyze the relationships among all variables studied. Results The binomial logistic regression analysis revealed that seven climate variables, the geographical longitude and sand proportion in the soil separated the southern from northern populations. The northern populations grow in more arid and continental conditions and on soils with lower sand proportion. The mean genetic diversity using all AFLP studied of P. chihuahuana was significantly correlated with the mean temperature in the warmest month, where warmer temperatures are associated to larger genetic diversity. Genetic diversity of P. chihuahuana calculated with putatively adaptive AFLP was not statistically significantly correlated with any environmental factor. Discussion Future reforestation programs should take into account that at least two different groups (the northern and southern cluster) of P. chihuahuana exist, as local adaptation takes place because of different environmental conditions.
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Affiliation(s)
| | | | - José Ciro Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Berthold Heinze
- Federal Research Centre for Forests, Natural Hazards and Landscape (BFW), Vienna, Austria
| | - José Ángel Prieto-Ruiz
- Facultad de Ciencias Forestales, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
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Lucas-Borja ME, Ahrazem O, Candel-Pérez D, Moya D, Fonseca T, Hernández Tecles E, De Las Heras J, Gómez-Gómez L. Evaluation of fire recurrence effect on genetic diversity in maritime pine (Pinus pinaster Ait.) stands using Inter-Simple Sequence Repeat profiles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 572:1322-1328. [PMID: 26822471 DOI: 10.1016/j.scitotenv.2016.01.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/17/2016] [Accepted: 01/17/2016] [Indexed: 06/05/2023]
Abstract
The management of maritime pine in fire-prone habitats is a challenging task and fine-scale population genetic analyses are necessary to check if different fire recurrences affect genetic variability. The objective of this study was to assess the effect of fire recurrence on maritime pine genetic diversity using inter-simple sequence repeat markers (ISSR). Three maritime pine (Pinus pinaster Ait.) populations from Northern Portugal were chosen to characterize the genetic variability among populations. In relation to fire recurrence, Seirós population was affected by fire both in 1990 and 2005 whereas Vila Seca-2 population was affected by fire just in 2005. The Vila Seca-1 population has been never affected by fire. Our results showed the highest Nei's genetic diversity (He=0.320), Shannon information index (I=0.474) and polymorphic loci (PPL=87.79%) among samples from twice burned populations (Seirós site). Thus, fire regime plays an important role affecting genetic diversity in the short-term, although not generating maritime pine genetic erosion.
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Affiliation(s)
- M E Lucas-Borja
- Department of Agricultural Technology and Science and Genetics, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain
| | - O Ahrazem
- Department of Agricultural Technology and Science and Genetics, Faculty of Pharmacy, Institute of Botany, University of Castilla-La Mancha, Campus Universitario s/n, Albacete, E-02071, Spain
| | - D Candel-Pérez
- Department of Agricultural Technology and Science and Genetics, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain.
| | - D Moya
- Department of Vegetal Production, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain
| | - T Fonseca
- Department of Forestry Sciences and Landscape Architecture, University of Trás-os-Montes e Alto Douro, 5001-801, Vila Real, Portugal
| | - E Hernández Tecles
- Department of Vegetal Production, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain
| | - J De Las Heras
- Department of Vegetal Production, ETSIAM, University of Castilla-La Mancha, Campus Universitario s/n, Albacete E-02071, Spain
| | - L Gómez-Gómez
- Department of Agricultural Technology and Science and Genetics, Faculty of Pharmacy, Institute of Botany, University of Castilla-La Mancha, Campus Universitario s/n, Albacete, E-02071, Spain
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Ávila-Flores IJ, Hernández-Díaz JC, González-Elizondo MS, Prieto-Ruíz JÁ, Wehenkel C. Degree of Hybridization in Seed Stands of Pinus engelmannii Carr. In the Sierra Madre Occidental, Durango, Mexico. PLoS One 2016; 11:e0152651. [PMID: 27064490 PMCID: PMC4827862 DOI: 10.1371/journal.pone.0152651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 03/17/2016] [Indexed: 11/24/2022] Open
Abstract
Hybridization is an important evolutionary force, because interspecific gene transfer can introduce more new genetic material than is directly generated by mutations. Pinus engelmannii Carr. is one of the nine most common pine species in the pine-oak forest ecoregion in the state of Durango, Mexico. This species is widely harvested for lumber and is also used in reforestation programmes. Interspecific hybrids between P.engelmannii and Pinus arizonica Engelm. have been detected by morphological analysis. The presence of hybrids in P. engelmannii seed stands may affect seed quality and reforestation success. Therefore, the goals of this research were to identify introgressive hybridization between P. engelmannii and other pine species in eight seed stands of this species in Durango, Mexico, and to examine how hybrid proportion is related to mean genetic dissimilarity between trees in these stands, using Amplified Fragment Length Polymorphism (AFLP) markers and morphological traits. Differences in the average current annual increment of putative hybrids and pure trees were also tested for statistical significance. Morphological and genetic analyses of 280 adult trees were carried out. Putative hybrids were found in all the seed stands studied. The hybrids did not differ from the pure trees in vigour or robustness. All stands with putative P. engelmannii hybrids detected by both AFLPs and morphological traits showed the highest average values of the Tanimoto distance, which indicates: i) more heterogeneous genetic material, ii) higher genetic variation and therefore iii) the higher evolutionary potential of these stands, and iv) that the morphological differentiation (hybrid/not hybrid) is strongly associated with the Tanimoto distance per stand. We conclude that natural pairwise hybrids are very common in the studied stands. Both morphological and molecular approaches are necessary to confirm the genetic identity of forest reproductive material.
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Affiliation(s)
- Israel Jaime Ávila-Flores
- Doctorado Institucional en Ciencias Agropecuarias y Forestales, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
| | - José Ciro Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
| | - Maria Socorro González-Elizondo
- CIIDIR Unidad Durango, Instituto Politécnico Nacional, Sigma 119 Fracc, 20 de Noviembre II, Durango, Durango, México, C.P., 34220
| | - José Ángel Prieto-Ruíz
- Facultad de Ciencias Forestales, Universidad Juárez del Estado de Durango, Blv. Durango y Ave, Papaloapan s/n. Col. Valle del Sur, Durango, Durango, México, C.P., 34120
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
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Wehenkel C, Brazão-Protázio JM, Carrillo-Parra A, Martínez-Guerrero JH, Crecente-Campo F. Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico). PLoS One 2015; 10:e0140442. [PMID: 26496189 PMCID: PMC4619678 DOI: 10.1371/journal.pone.0140442] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/25/2015] [Indexed: 11/17/2022] Open
Abstract
The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests.
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Affiliation(s)
- Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
| | | | - Artemio Carrillo-Parra
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - José Hugo Martínez-Guerrero
- Facultad de Medicina Veterinaria y Zootecnia, Cuerpo Académico de Fauna Silvestre, Universidad Juárez del Estado de Durango, Durango, México
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