New Map Reveals Hidden Fish Provinces of Middle America

Freshwater fishes are among the most vulnerable vertebrates on Earth, yet the maps that conservationists and evolutionary biologists use to understand them have long been inconsistent. Now, a new study of Middle America, the transition zone stretching from Mexico to the border between Panama and Colombia, has produced the most complete regionalisation yet of the region’s freshwater fish fauna, using every native species and two competing analytical methods to settle where the true boundaries of fish provinces lie. The results, published in Frontiers of Biogeography, confirm some classic divisions, overturn others and reveal a province that no previous scheme had listed.

The research team, led by Omar Mejía of the Instituto Politécnico Nacional in Mexico City, assembled more than 52,000 quality-filtered collection records for 685 native freshwater fish species from the Global Biodiversity Information Facility. The dataset was deliberately restricted to species that spend the critical phases of their life cycles in inland waters, with only records backed by vouchers in biological collections retained. Human observations were pruned, records located in the sea were deleted, geographic outliers were removed against published checklists, and every species name was updated to the latest nomenclature. The curation mattered: sloppy distribution data is the single largest source of error in biogeographic mapping.

With the cleaned database in hand, the researchers applied two of the most widely used techniques for identifying areas of endemism, regions of congruent, non-stochastic distributions of two or more taxa. The first, Parsimony Analysis of Endemicity, or PAE, builds area cladograms from a presence-absence matrix, treating each species’ distribution as a character and recognising areas of endemism as nodes supported by at least two synapomorphic taxa, species whose congruent distributions act like shared derived traits. The second, Endemicity Analysis, or EA, takes an optimality approach, explicitly evaluating the congruence of species distributions across grid cells and allowing the recognition of nested, overlapping and disjunct areas. The team ran both methods at 0.5-degree and 1-degree grid resolutions to test how scale affects the outcome.

The comparison produced a striking verdict. At 1-degree resolution, PAE regionalised 39 percent of Middle America and recovered 31 areas of endemism supported by 130 species from 19 families, with livebearers of the family Poeciliidae, cichlids and pupfishes of the family Cyprinodontidae the most represented. EA, by contrast, recovered 24 areas at a 30 percent consensus threshold and 45 at 50 percent, but when the authors inspected which EA consensus areas truly fulfilled the strict criterion of at least two species with an endemicity index of 1.0, meaning the species is present in every cell of the grid, only three to six regions survived. Overlap between the two methods’ polygons ranged from roughly 44 percent at coarse resolution to about 30 percent at fine resolution, leaving less than half the results congruent.

That shortfall led the authors to a conclusion that will resonate across biogeography: for this dataset, PAE outperformed EA. The finding is technically significant because EA has been criticised for inflating the number of areas in transition zones, where species distributions overlap extensively and consensus areas can be built from species that are not strictly sympatric. PAE’s hierarchical structure, which precludes overlapping areas, proved an advantage here rather than a limitation. The authors caution, however, that this verdict cannot be generalised to other biological groups or study regions, and that comparing both methods remains mandatory, since in some circumstances they are complementary.

The second half of the study tackled a different question: how should Middle America be divided into ichthyological provinces, geographic regions of relatively homogeneous fauna? Instead of arbitrary grid cells, the team used natural hydrological units, the FAO’s 16 basins and 307 sub-basins, plus Pfafstetter-coded hydrobasins, as study units. PAE on FAO basins regionalised an extraordinary 99 percent of the total surface of Middle America, recovering six areas of endemism supported by 59 species from 20 families. The authors then added two provinces well supported by the Pfafstetter level 4 analysis, for a total of eight ichthyological provinces and 38 sub-provinces, three of which nest within the Grijalva-Usumacinta sub-province.

The eight provinces read like a tour of the region’s evolutionary hotspots. The Lower Colorado province, supported by the endangered Colorado pikeminnow, bonytail and razorback sucker, and the Lower Santa Cruz-San Pedro province in the American Southwest, harbour depauperate but highly distinctive desert faunas. The Baja California province is defined by two endemic Fundulus killifishes. The Central Mexican Highlands province, supported by six endemic species including the recently described Cyprinodon inmemoriam and the Tequila splitfin relatives of endorheic basins wedged between the Sierra Madre ranges, is the province no previous scheme had listed. The Mexican Pacific Coast province, with 186 species, and the Mexican North Atlantic province, with 174, flank the highlands. The Isthmic-Peninsular province, richest in cichlids and poeciliids, harbours 205 species, while the Central American province, from the Motagua Basin to Panama, holds 236 species supported by 27 endemics.

Two results are likely to spark debate. First, the study recovered both ocean slopes of southern Mexico, Pacific and Atlantic, as a single Isthmic-Peninsular province rather than two independent ones as previously suggested, supported by 13 species including the firemouth cichlid Thorichthys meeki and the livebearer Phallichthys fairweatheri. Second, from southern Honduras to Panama, the team recovered a single Central American province, whereas earlier work had split this stretch into as many as nine provinces. The authors argue that the Sierra Madre Oriental acts as an effective barrier restricting the Mexican North Atlantic province to lowland Atlantic slopes, and that the congruence of their provinces with a recent phenetic regionalisation of North America, sharing indicator species such as Mayaheros beani and Pylodictis olivaris, supports a general-purpose regionalisation scheme.

Not everything went according to expectation. The team also ran a cluster analysis using Jaccard dissimilarity and UPGMA clustering, the phenetic approach many argue is best for large-scale regionalisation. Despite a very high co-phenetic correlation of 0.92, the ANOSIM significance tests failed to validate any of the six postulated provinces, because pairwise comparisons among areas were not significantly different. Only two sub-provinces, Choluteca and Lagos de Nicaragua, survived the finer-scale testing. The authors conclude that a natural region must include a historical relationship of the biota, and that provinces recognised by distinct sets of endemic taxa, as PAE delivers, better capture how life has been moulded by historic and contemporary forces.

For conservation planners, the map arrives at a critical moment. Middle America’s freshwater fishes face habitat loss, pollution, invasive species and climate change, and the region’s livebearing and pupfish lineages include some of the most imperilled vertebrates anywhere. By defining 38 sub-provinces, many supported by two to 13 strictly endemic species, the study gives managers a hierarchical framework for prioritising basins, from the Cuatro Ciénegas-like spring systems of Cuatro Ciénegas and the Laguna de Mayrán to the Nicaragua lake endemics and the Panama canal watershed. The authors stress that no universally accepted method exists for delimiting biogeographic regions, and that the selection of a proper approach must be evaluated against the nature of the study. But with 99 percent of Middle America now regionalised on the basis of its complete freshwater fish fauna, the reference system for understanding, and protecting, one of the planet’s great transition zones has just become considerably sharper.

Subject of Research: Biogeography of Middle American freshwater fishes: PAE and Endemicity Analysis reveal eight ichthyological provinces and 38 sub-provinces

Article Title: Analysis of endemicity and regionalisation of the freshwater ichthyofauna of Middle America

Article References: Bernal-Portillo, A., Pérez-Miranda, F., & Mejía, O. (2025). Analysis of endemicity and regionalisation of the freshwater ichthyofauna of Middle America. Frontiers of Biogeography, 18, Article e164902. https://doi.org/10.21425/fob.18.164902

Image Credits: AI Generated

DOI: 10.21425/fob.18.164902

Keywords: biogeography, freshwater fishes, areas of endemism, Parsimony Analysis of Endemicity, Endemicity Analysis, Middle America, ichthyological provinces, conservation, Analysis, endemicity, regionalisation, freshwater