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Ghimire P, Palacios C, Trimble J, Lamichhaney S. Museum genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens. G3 (BETHESDA, MD.) 2024; 14:jkae081. [PMID: 38626302 DOI: 10.1093/g3journal/jkae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/16/2024] [Accepted: 04/05/2024] [Indexed: 04/18/2024]
Abstract
The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia spp.) and examine their genetic composition and taxonomic status and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences; however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollynecks are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspecies Ciconia episcopus neglecta and Ciconia episcopus episcopus, suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds.
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Affiliation(s)
- Prashant Ghimire
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
| | - Catalina Palacios
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
| | - Jeremiah Trimble
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
- School of Biomedical Sciences, Kent State University, Kent, OH 44240, USA
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Baeza JA, Macdonald-Shedd A, Latorre-Cárdenas MC, Griffin E, Gutiérrez-Rodríguez C. The first genomic resource for the ‘near threatened’ Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae. J NAT HIST 2023. [DOI: 10.1080/00222933.2023.2186809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Castillo-Chora VDJ, Sánchez-González LA, Mastretta-Yanes A, Prieto-Torres DA, Navarro-Sigüenza AG. Insights into the importance of areas of climatic stability in the evolution and maintenance of avian diversity in the Mesoamerican dry forests. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
We analysed the phylogeographic structure of five resident bird lineages distributed in the seasonally dry tropical forests (SDTF) of Mesoamerica to test whether they show patterns of synchronous and geographically coincident genetic divergence during the Quaternary. We generated phylogenetic trees, estimated divergence times and analysed the genetic structure of populations (based on sequences of mitochondrial genes), as well as estimating historical distributions (range extension and areas of long-term climate stability) during the Late Pleistocene. We tested and selected the phylogeographic divergence scenarios that best explain the current divergence patterns of taxa using the Approximate Bayesian Computation (ABC) approach. For most species, phylogenetic trees and haplotype networks showed a clear genetic structure associated with geographical distribution. Overall, the divergence times ranged from 0.29–2.0 Mya, suggesting that diversification of populations occurred at different times during the Pleistocene. The palaeodistribution models predicted at least two areas of climatic stability within the current SDTF that probably allowed glacial-interglacial persistence of isolated bird populations along the Mexican Pacific, thus promoting their genetic divergence. The results provide information relevant to the identification of diversification hotspots for the Mesoamerican SDTF avifauna.
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Affiliation(s)
- Vicente De J Castillo-Chora
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México
| | - Luis A Sánchez-González
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
| | - Alicia Mastretta-Yanes
- CONACYT—CONABIO, Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Liga Periférico-Insurgentes Sur No. 4903, Parques del Pedregal, Tlalpan, Mexico City, México
| | - David A Prieto-Torres
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, A.P., Mexico City, México
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Prado-Ortiz LE, Valdespino C, Romano M, González-Romero A. Quantification of immunoreactive testosterone and estradiol-17ß metabolites to identify the sex of Neotropical otters (Lontra longicaudis annectens) in the field. Anim Reprod Sci 2020; 222:106607. [PMID: 33017800 DOI: 10.1016/j.anireprosci.2020.106607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 01/24/2023]
Abstract
Before there was use of ultrasonographic imaging, determination of the ratio of estrogens to androgens in the same individual was a technique used for differentiating the sex of monomorphic animals in captivity, with larger estrogen concentrations in the females. Due to species-specific differences in both concentration and changes throughout the year of these hormones, corroboration of the method is needed in each case. In this study, there was use of a chemo-immuno assay to quantify sex steroids in fecal samples collected from seven (five females and two males) Neotropical otters, Lontra longicaudis. The reproductive season for this species was determined to be between October and March, with increased estradiol in the females and relatively greater concentrations of testosterone in the males as compared with other seasons of the year. Results from utilization of a k-means analysis procedure indicated that the use of steroid ratios in fecal samples to differentiate otter sex is an effective technique when there are evaluations during the breeding season. The estrogen to androgen ratios during this period, however, are the inverse of what was expected, with there being larger testosterone concentrations in the female otters. The ratio of estrogens to androgens in feces of captive otters can be effectively used to determine the sex of otters in the field. We propose this method is reliable for sex determination in wild otter populations during the reproductive season.
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Affiliation(s)
- L E Prado-Ortiz
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología A. C., Carretera Antigua a Coatepec # 351, El haya, 91070 Xalapa, Veracruz, Mexico
| | - C Valdespino
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología A. C., Carretera Antigua a Coatepec # 351, El haya, 91070 Xalapa, Veracruz, Mexico.
| | - M Romano
- D. Fisiología, Biofísica y Neurociencias, CINVESTAV, Mexico
| | - A González-Romero
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología A. C., Carretera Antigua a Coatepec # 351, El haya, 91070 Xalapa, Veracruz, Mexico
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Vázquez-López M, Morrone JJ, Ramírez-Barrera SM, López-López A, Robles-Bello SM, Hernández-Baños BE. Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae). Zookeys 2020; 952:129-157. [PMID: 32774114 PMCID: PMC7394775 DOI: 10.3897/zookeys.952.51785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/02/2020] [Indexed: 11/26/2022] Open
Abstract
The integration of genetic, morphological, behavioral, and ecological information in the analysis of species boundaries has increased, allowing integrative systematics that better reflect the evolutionary history of biological groups. In this context, the goal of this study was to recognize independent evolutionary lineages within Euphonia affinis at the genetic, morphological, and ecological levels. Three subspecies have been described: E. affinis godmani, distributed in the Pacific slope from southern Sonora to Guerrero; E. affinis affinis, from Oaxaca, Chiapas and the Yucatan Peninsula to Costa Rica; and E. affinis olmecorum from Tamaulipas and San Luis Potosi east to northern Chiapas (not recognized by some authors). A multilocus analysis was performed using mitochondrial and nuclear genes. These analyses suggest two genetic lineages: E. godmani and E. affinis, which diverged between 1.34 and 4.3 My, a period in which the ice ages and global cooling fragmented the tropical forests throughout the Neotropics. To analyze morphometric variations, six morphometric measurements were taken, and the Wilcoxon Test was applied to look for sexual dimorphism and differences between the lineages. Behavioral information was included, by performing vocalization analysis which showed significant differences in the temporal characteristics of calls. Finally, Ecological Niche Models were estimated with MaxEnt, and then compared using the method of Broennimann. These analyses showed that the lineage distributed in western Mexico (E. godmani) has a more restricted niche than the eastern lineage (E. affinis) and thus we rejected the hypotheses of niche equivalence and similarity. Based on the combined evidence from genetic, morphological, behavioral, and ecological data, it is concluded that E. affinis (with E. olmecorum as its synonym) and E. godmani represent two independent evolutionary lineages.
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Affiliation(s)
- Melisa Vázquez-López
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Juan J. Morrone
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Sandra M. Ramírez-Barrera
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Anuar López-López
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Sahid M. Robles-Bello
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
| | - Blanca E. Hernández-Baños
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 70-399. 04510 Mexico City, MexicoUniversidad Nacional Autónoma de MéxicoMexicoMexico
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Bolívar-Leguizamón SD, Silveira LF, Derryberry EP, Brumfield RT, Bravo GA. Phylogeography of the Variable Antshrike (Thamnophilus caerulescens), a South American passerine distributed along multiple environmental gradients. Mol Phylogenet Evol 2020; 148:106810. [DOI: 10.1016/j.ympev.2020.106810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/23/2020] [Accepted: 03/25/2020] [Indexed: 12/21/2022]
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Latorre-Cardenas MC, Gutiérrez-Rodríguez C, Rico Y. Estimating genetic and demographic parameters relevant for the conservation of the Neotropical otter, Lontra longicaudis, in Mexico. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Moreno-Contreras I, Sánchez-González LA, Arizmendi MDC, Prieto-Torres DA, Navarro-Sigüenza AG. Climatic Niche Evolution in the Arremon brunneinucha Complex (Aves: Passerellidae) in a Mesoamerican Landscape. Evol Biol 2020. [DOI: 10.1007/s11692-020-09498-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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