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Lizardo V, García Trejo EA, Morrone JJ. Niche conservatism and convergence in birds of three cenocrons in the Mexican Transition Zone. PeerJ 2024; 12:e16664. [PMID: 38188173 PMCID: PMC10768671 DOI: 10.7717/peerj.16664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024] Open
Abstract
Background The niche conservatism hypothesis postulates that physiological and phylogenetic factors constrain species distributions, creating richness hotspots with older lineages in ancestral climatic conditions. Conversely, niche convergence occurs when species successfully disperse to novel environments, diversifying and resulting in areas with high phylogenetic clustering and endemism, low diversity, and lower clade age. The Mexican Transition Zone exhibits both patterns as its biotic assembly resulted from successive dispersal events of different biotic elements called cenocrons. We test the hypothesis that biogeographic transitionallity in the area is a product of niche conservatism in the Nearctic and Typical Neotropical cenocrons and niche convergence in the Mountain Mesoamerican cenocron. Methods We split the avifauna into three species sets representing cenocrons (sets of taxa that share the same biogeographic history, constituting an identifiable subset within a biota by their common biotic origin and evolutionary history). Then, we correlated richness, endemism, phylogenetic diversity, number of nodes, and crowning age with environmental and topographic variables. These correlations were then compared with the predictions of niche conservatism versus niche convergence. We also detected areas of higher species density in environmental space and interpreted them as an environmental transition zone where birds' niches converge. Results Our findings support the expected predictions on how niches evolved. Nearctic and Typical Neotropical species behaved as predicted by niche conservatism, whereas Mountain Mesoamerican species and the total of species correlations indicated niche convergence. We also detected distinct ecological and evolutionary characteristics of the cenocrons on a macroecological scale and the environmental conditions where the three cenocrons overlap in the Mesoamerican region.
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Affiliation(s)
- Viridiana Lizardo
- Museum of Zoology ‘Alfonso L. Herrera’, Department of Evolutionary Biology, School of Sciences, Universidad Nacional Autónoma de México, Mexico City, CdMx, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, CdMx, México
| | - Erick Alejandro García Trejo
- Unit of Informatics for Biodiversity, Department of Evolutionary Biology, School of Sciences, Universidad Nacional Autónoma de México, Mexico City, CdMx, México
| | - Juan J. Morrone
- Museum of Zoology ‘Alfonso L. Herrera’, Department of Evolutionary Biology, School of Sciences, Universidad Nacional Autónoma de México, Mexico City, CdMx, México
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Nuñez LP, Gray LN, Weisrock DW, Burbrink FT. The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini). Mol Phylogenet Evol 2023:107844. [PMID: 37301486 DOI: 10.1016/j.ympev.2023.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.
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Affiliation(s)
- Leroy P Nuñez
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA.
| | - Levi N Gray
- Fort Collins Science Center, United States Geological Survey, Guam, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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Benites P, Zaldívar-Riverón A, Meza-Lázaro RN, Samacá-Sáenz E, Gutiérrez-Rodríguez J, Hernández-López A. Multiple introgression events during the diversification history of the edible mexican grasshopper genus sphenarium (orthoptera: pyrgomorphidae). Mol Phylogenet Evol 2023; 183:107774. [PMID: 36972795 DOI: 10.1016/j.ympev.2023.107774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Speciation with gene flow often leads to ambiguous phylogenetic reconstructions, reticulate patterns of relatedness and conflicting nuclear versus mitochondrial (mt) lineages. Here we employed a fragment of the COI mtDNA gene and nuclear genome-wide data (3RAD) to assess the diversification history of Sphenarium, an orthopteran genus of great economic importance in Mexico that is presumed to have experienced hybridisation events in some of its species. We carried out separate phylogenetic analyses to evaluate the existence of mito-nuclear discordance in the species relationships, and also assessed the genomic diversity and population genomic structure and investigated the existence of interspecific introgression and species limits of the taxa involved based on the nuclear dataset. The species delineation analyses discriminated all the currently recognised species, but also supported the existence of four undescribed species. The mt and nuclear topologies had four discordant species relationships that can be explained by mt introgression, where the mt haplotypes of S. purpurascens appear to have replaced those of S. purpurascens A and B, S. variabile and S. zapotecum. Moreover, our analyses supported the existence of nuclear introgression events between four species pairs that are distributed in the Sierra Madre del Sur province in southeast Mexico, with three of them occurring in the Tehuantepec Isthmus region. Our study highlights the relevance of genomic data to address the relative importance of allopatric isolation versus gene flow in speciation.
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Affiliation(s)
- Pilar Benites
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Rubi N Meza-Lázaro
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Ernesto Samacá-Sáenz
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México; Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Coyoacán, 04510 Ciudad de México, México
| | | | - Antonio Hernández-López
- Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Guanajuato, México
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DeRaad DA, McCormack JE, Chen N, Peterson AT, Moyle RG. Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays. Syst Biol 2022; 71:1453-1470. [PMID: 35552760 DOI: 10.1093/sysbio/syac034] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (A. californica) and Woodhouse's Scrub-Jay (A. woodhouseii), result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting to better understand the systematics of other groups with similarly complex evolutionary histories.
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Affiliation(s)
- Devon A DeRaad
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence KS, 66045, USA
| | - John E McCormack
- Moore Laboratory of Zoology,Occidental College, Los Angeles, CA, 90041, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - A Townsend Peterson
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence KS, 66045, USA
| | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence KS, 66045, USA
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Integrating Earth–life systems: a geogenomic approach. Trends Ecol Evol 2022; 37:371-384. [DOI: 10.1016/j.tree.2021.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/04/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
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García‐Sotelo UA, García‐Vázquez UO, Espinosa D. Historical biogeography of the genus Rhadinaea (Squamata: Dipsadinae). Ecol Evol 2021; 11:12413-12428. [PMID: 34594509 PMCID: PMC8462180 DOI: 10.1002/ece3.7988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/31/2021] [Accepted: 06/28/2021] [Indexed: 11/12/2022] Open
Abstract
Multiple geological and climatic events have created geographical or ecological barriers associated with speciation events, playing a role in biological diversification in North and Central America. Here, we evaluate the influence of the Neogene and Quaternary geological events, as well as the climatic changes in the diversification of the colubrid snake genus Rhadinaea using molecular dating and ancestral area reconstruction. A multilocus sequence dataset was generated for 37 individuals of Rhadinaea from most of the biogeographical provinces where the genus is distributed, representing 19 of the 21 currently recognized species, and two undescribed species. Our analyses show that the majority of the Rhadinaea species nest in two main clades, herein identified as "Eastern" and "Southern". These clades probably diverged from each other in the early Miocene, and their divergence was followed by 11 divergences during the middle to late Miocene, three divergences during the Pliocene, and six divergences in the Pleistocene. The ancestral distribution of Rhadinaea was reconstructed across the Sierra Madre del Sur. Our phylogenetic analyses do not support the monophyly of Rhadinaea. The Miocene and Pliocene geomorphology, perhaps in conjunction with climate change, appears to have triggered the diversification of the genus, while the climatic changes during the Miocene probably induced the diversification of Rhadinaea in the Sierra Madre del Sur. Our analysis suggests that the uplifting of the Trans-Mexican Volcanic Belt and Chiapan-Guatemalan highlands in this same period resulted in northward and southward colonization events. This was followed by more recent, independent colonization events in the Pliocene and Pleistocene involving the Balsas Basin, Chihuahuan Desert, Pacific Coast, Sierra Madre Occidental, Sierra Madre Oriental, Sierra Madre del Sur, Trans-Mexican Volcanic Belt, and Veracruz provinces, probably driven by the climatic fluctuations of the time.
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Affiliation(s)
- Uriel A. García‐Sotelo
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Facultad de Estudios Superiores ZaragozaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Uri O. García‐Vázquez
- Facultad de Estudios Superiores ZaragozaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - David Espinosa
- Facultad de Estudios Superiores ZaragozaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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Alvarez-Alvarez EA, Rodríguez-Godínez R, Sierra-Morales P, Medina-Valdivia SA, Vázquez-Salgado E, Brito-Millán M, Almazán-Núñez RC. Patterns of Bird Diversity and Endemism Along an Elevational Gradient in the Southern Mexican Highlands. Zool Stud 2020; 59:e69. [PMID: 34221145 PMCID: PMC8231403 DOI: 10.6620/zs.2020.59-69] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 11/11/2020] [Indexed: 11/18/2022]
Abstract
Knowledge of bird species diversity along elevational gradients is key for understanding the distributional limits of species and, ultimately, for promoting measures that conserve biodiversity. In the present study, we evaluated changes in bird species richness, diversity, and endemism along an elevational gradient in the Sierra Madre del Sur in southern Mexico -a globally recognized biodiversity hotspot. Monthly bird surveys were carried out at localities with elevations of 1600, 1800, 2000, and 2200 m over the course of one year (2014-2015) covering an area of 2000 km2 (10 circular plots with a radius of 25 m per elevation site). Diversity was calculated in terms of effective number of species or Hill numbers, while the composition of bird species along the elevational gradient was analyzed by non-metric multidimensional scaling, and endemic bird species turnover was assessed with faunal congruence curves. Overall, a total of 118 bird species belonging to 35 families were recorded along the elevational gradient. Although we found that bird richness and diversity increased with increasing elevation, we also observed significant turnover in bird composition and endemic species, which were likely linked to forest types and conditions, as well as proximity of sites to urban centers. Assessing biodiversity patterns across elevational gradients in a well-recognized biodiversity reservoir advances both understanding of ecological patterns and aids conservation efforts and management of biological resources.
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Affiliation(s)
- Edson A Alvarez-Alvarez
- Laboratorio Integral de Fauna Silvestre (área de Ornitología), Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Ciudad Universitaria Sur, 39090, Chilpancingo de los Bravo, Guerrero, México. E-mail: (Almazán-Núñez); (Alvarez-Alvarez); (Rodríguez-Godínez); (Sierra-Morales); (Vázquez-Salgado)
| | - Rosalba Rodríguez-Godínez
- Laboratorio Integral de Fauna Silvestre (área de Ornitología), Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Ciudad Universitaria Sur, 39090, Chilpancingo de los Bravo, Guerrero, México. E-mail: (Almazán-Núñez); (Alvarez-Alvarez); (Rodríguez-Godínez); (Sierra-Morales); (Vázquez-Salgado)
| | - Pablo Sierra-Morales
- Laboratorio Integral de Fauna Silvestre (área de Ornitología), Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Ciudad Universitaria Sur, 39090, Chilpancingo de los Bravo, Guerrero, México. E-mail: (Almazán-Núñez); (Alvarez-Alvarez); (Rodríguez-Godínez); (Sierra-Morales); (Vázquez-Salgado)
| | - Sandy A Medina-Valdivia
- Centro de Ciencias de Desarrollo Regional, Universidad Autónoma de Guerrero, Calle Pino s/n, Col. El roble, 39040, Acapulco, Guerrero, México. E-mail: (Medina-Valdivia)
| | - Estefanía Vázquez-Salgado
- Laboratorio Integral de Fauna Silvestre (área de Ornitología), Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Ciudad Universitaria Sur, 39090, Chilpancingo de los Bravo, Guerrero, México. E-mail: (Almazán-Núñez); (Alvarez-Alvarez); (Rodríguez-Godínez); (Sierra-Morales); (Vázquez-Salgado)
| | - Marlene Brito-Millán
- University of California Institute for Mexico and the United States (UC MEXUS), Cuerpo Académico Biodiversidad y Gestión Ambiental Sustentable, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Ciudad Universitaria Sur, 39090, Chilpancingo de los Bravo, Guerrero, México. E-mail: (Brito-Millán)
| | - R Carlos Almazán-Núñez
- Laboratorio Integral de Fauna Silvestre (área de Ornitología), Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n, Ciudad Universitaria Sur, 39090, Chilpancingo de los Bravo, Guerrero, México. E-mail: (Almazán-Núñez); (Alvarez-Alvarez); (Rodríguez-Godínez); (Sierra-Morales); (Vázquez-Salgado)
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Zamudio-Beltrán LE, Licona-Vera Y, Hernández-Baños BE, Klicka J, Ornelas JF. Phylogeography of the widespread white-eared hummingbird (Hylocharis leucotis): pre-glacial expansion and genetic differentiation of populations separated by the Isthmus of Tehuantepec. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
AbstractThe Pleistocene glacial cycles had a strong influence on the demography and genetic structure of many species, particularly on northern-latitude taxa. Here we studied the phylogeography of the white-eared hummingbird (Hylocharis leucotis), a widely distributed species of the highlands of Mexico and Central America. Analysis of mitochondrial DNA (mtDNA) sequences was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. Analyses of 108 samples from 11 geographic locations revealed population structure and genetic differentiation among populations separated by the Isthmus of Tehuantepec (IT) and the Motagua-Polochic-Jocotán (MPJ) fault barriers. ENM predicted a widespread distribution of suitable habitat for H. leucotis since the Last Inter Glacial (LIG), but this habitat noticeably contracted and fragmented at the IT. Models for historical dispersal corridors based on population genetics data and ENM revealed the existence of corridors among populations west of the IT; however, the connectivity of populations across the IT has changed little since the LIG. The shallow geographic structure on either side of the isthmus and a star-like haplotype network, combined with the long-term persistence of populations across time based on genetic data and potential dispersal routes, support a scenario of divergence with migration and subsequent isolation and differentiation in Chiapas and south of the MPJ fault. Our findings corroborate the profound effects of Pleistocene climatic fluctuations on the evolutionary history of montane taxa but challenge the generality of expanded suitable habitat (pine-oak forests) during glacial cycles.
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Affiliation(s)
- Luz E Zamudio-Beltrán
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yuyini Licona-Vera
- Departamento de Biología Evolutiva, Instituto de Ecología, Asociación Civil (INECOL), Xalapa, Veracruz, Mexico
| | - Blanca E Hernández-Baños
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - John Klicka
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología, Asociación Civil (INECOL), Xalapa, Veracruz, Mexico
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