Scale(s) matter: Deconstructing an area of endemism for Middle American freshwater fishes

Elías, Diego J.; McMahan, Caleb D.; Matamoros, Wilfredo A.; Gómez‐González, Adan E.; Piller, Kyle R.; Chakrabarty, Prosanta

doi:10.1111/jbi.13941

Cited by 22 publications

(31 citation statements)

References 101 publications

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“…Particularly, with the mtCox1 marker, we identified differences in haplotype occurrence and their frequencies between the rainforest and delta zones (the upper and lower parts of the basin, respectively). These results are consistent with previous comparative phylogeographic analyses of the basin, which considered endemic species data and phylogeographic analyses for a selected group of organisms (mainly cichlids and poecilids), and report differences between the upper and lower parts of the Usumacinta River basin [29]. These results provide additional evidence that could indicate the existence of geographic structure for some of the freshwater fauna in the basin (e.g., Centropomus undecimalis) and support the hypothesis that the Usumacinta does not correspond to a single biogeographic unit [29].…”

Section: Mtdna Genetic Structuresupporting

confidence: 92%

“…The Usumacinta River basin is one of the largest basins in the Gulf of Mexico, whose biological diversity is outstanding for the Mesoamerican region [29,59], with more than 170 species, including 50 fish families, making it one of the most diverse river basins in Mexico [20]. Its hydrological connectivity allows the common snook to complete its life cycle.…”

Section: Discussionmentioning

confidence: 99%

“…In this sense, Ornelas-García et al [10] reported that despite the connectivity within the basin, the genetic diversity could be heterogeneously distributed, at least in Astyanax aeneus species, where the upper and lower basin present different levels of haplotype diversity, while the middle part of the basin presents the highest diversity, tentatively associated with a transition zone. Similarly, Elías et al [29] suggested that the upper and lower Usumacinta River basin does not correspond to a single biogeographic unit, based on endemic species diversity as well as the phylogeographic patterns obtained with some representative fish groups in the basin (i.e., cichlids and poeciliids).…”

Section: Introductionmentioning

confidence: 99%

“…Previous genetic studies of the common snook in the Usumacinta River basin recovered a single genetic pool, including samples from the San Pedro River, at the basin's floodplain, to the coastal area at Tabasco, Mexico [25]. However, other studies using freshwater species diversity and molecular data have suggested that the upper and lower part of the Usumacinta basin are different biogeographic units [10,[26][27][28][29]. In this sense, Ornelas-García et al [10] reported that despite the connectivity within the basin, the genetic diversity could be heterogeneously distributed, at least in Astyanax aeneus species, where the upper and lower basin present different levels of haplotype diversity, while the middle part of the basin presents the highest diversity, tentatively associated with a transition zone.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

et al. 2021

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The common snook is one of the most abundant and economically important species in the Usumacinta basin in the Gulf of Mexico, which has led to overfishing, threatening their populations. The main goal of the present study was to assess the genetic diversity and structure of the common snook along the Usumacinta River in order to understand the population dynamics and conservation status of the species. We characterized two mitochondrial markers (mtCox1 and mtCytb) and 11 microsatellites in the Usumacinta basin, which was divided into three zones: rainforest, floodplain and river delta. The mitochondrial data showed very low diversity, showing some haplotypic diversity differences between the rainforest and delta zones. In contrast, we consistently recovered two genetic clusters in the Usumacinta River basin with the nuclear data in both the DAPC and STRUCTURE analyses. These results were consistent with the AMOVA analyses, which showed significant differences among the genetic clusters previously recovered by DAPC and STRUCTURE. In terms of diversity distribution, the floodplain zone corresponded to the most diverse zone according to the mitochondrial and nuclear data, suggesting that this is a transition zone in the basin. Our results support the relevance of the molecular characterization and monitoring of the fishery resources at the Usumacinta River to better understand their connectivity, which could help in their conservation and management.

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Section: Mtdna Genetic Structuresupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

et al. 2021

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“…Another incongruence concerns the phylogenetic position of the upper Río Grijalva endemic cichlid Chiapaheros grammodes , a monotypic genus from Guatemala and Mexico ( Elías et al 2020 ). Data sets for UCEs and exons differ in taxon sampling but overall relationships within the herichthyines are largely the same except for those of Chiapaheros .…”

Section: Discussionmentioning

confidence: 99%

Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree

Alda

Ludt

Elías

et al. 2021

Genome Biology and Evolution

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Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different datasets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel dataset of ultraconserved elements (UCEs) and a recently published exon dataset of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of colonization and diversification in Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent datasets disagreed in areas with low phylogenetic signal that were overwhelmed by incomplete lineage sorting (ILS) and non-phylogenetic signals. For UCEs, high levels of ILS were found to be the major cause of gene tree discordance, whereas, for exons, non-phylogenetic signal is most likely caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.

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Does invasion by armored catfish shift trophic ecology of native fishes? Evidence from stable isotope analysis

Quintana

Keppeler

Winemiller

2023

Ecology

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Popular as aquarium fish, armored catfishes from South America (Pterygoplichthys spp.) have been introduced and become invasive in tropical and subtropical regions worldwide. These ecosystem engineers can deplete basal resources (e.g., periphyton and detritus), with potential negative effects for native fauna. We studied the trophic ecology of fishes in the Usumacinta River Basin, Guatemala, where Pterygoplichthys is now widespread and locally abundant. We analyzed stable isotopes (δ13C, δ15N) in fish tissues and basal resources to assess the potential impact of Pterygoplichthys on the trophic ecology of six co‐occurring native fishes that feed at a similar trophic level (Astyanax aeneus, Dorosoma petenense, Thorichthys pasionis, Oscura heterospila, Poecilia mexicana, and Gambusia sexradiata). The study was conducted during the dry season in the La Pasion (LPR; high invasion) and San Pedro (SPR; low invasion) rivers. We compared isotopic spaces occupied by native fish and Pterygoplichthys, estimated isotopic overlap, and evaluated the trophic displacement of native species. We also evaluated the relationships of environmental factors, including the relative biomass of the invasive catfish, with δ13C and δ15N signatures. Except for P. mexicana, native species had lower isotopic overlap with the catfish in LPR. Native fish isotopic spaces were compressed and shifted toward higher trophic positions in LPR relative to SPR. Benthic food resources were important for Pterygoplichthys in both rivers, and water‐column resources had greater relative importance (RI) for native species in LPR. Native fish δ13C was significantly associated with Pterygoplichthys biomass, conductivity, and water flow velocity; and water depth and sedimentation had a significant association with native fish δ15N. Findings provide evidence that invasive Pterygoplichthys, along with environmental factors, impact the trophic ecology of native fish in the Usumacinta Basin. Additional field research conducted over longer time periods and mesocosm experiments that account for fish assemblage and environmental variation could elucidate Pterygoplichthys impacts via food resource depletion or habitat alteration.

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Scale(s) matter: Deconstructing an area of endemism for Middle American freshwater fishes

Cited by 22 publications

References 101 publications

Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree

Does invasion by armored catfish shift trophic ecology of native fishes? Evidence from stable isotope analysis

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