Comparative life histories and microhabitat use in three sympatric sculpins (Cottidae:Cottus) in northeastern California

Synopsis Life histories of three sculpins endemic to the Pit River system, northeastern California, are detailed.Cottus pitensis is widely distributed throughout the drainage. This species is typically found in rapidly flowing, shallow water on coarse substrate. It grows to a large size, >100 mm, and lives to 5 years. Spawning occurs annually, in early spring. Fecundity is relatively low, <320 oocytes.Cottus asperrimus is restricted to a large population in Fall River and smaller concentrations in Hat Creek and Pit River. It is a relatively small fish, <80 mm, and lives to 5 years. It occurs in deep, slow-moving, often spring-fed streams, typically on fine substrates. Spawning lasts from autumn to early spring. Males establish nests on hard substrates and guard several clutches of eggs. Fecundity ranges from 140–580 oocytes.Cottus klamathensis macrops is relatively rare in the drainage. The largest concentration is in the Hat Creek system, smaller populations exist in Fall River and Pit River. This sculpin is found on coarse substrate, often where aquatic vegetation is abundant. It is typically found in slow, relatively shallow water. It grows to >100mm and lives to 5 years. Males guard eggs during the short spawning season beginning in late winter. Fecundity in this species reaches a maximum of 650 oocytes. Life history strategies vary within the genus, yet the life histories of these sculpins are more similar to each other than they are to many of their congeners. This within-group similarity may have resulted from exposure of all three species to similar environmental pressures. This is predicted by life-history theory.     

Identifying sources of dissolved organic carbon in agriculturally dominated rivers using radiocarbon age dating: Sacramento–San Joaquin River Basin, California

We used radiocarbon measurements of dissolved organic carbon (DOC) to resolve sources of riverine carbon within agriculturally dominated landscapes in California. During 2003 and 2004, average Δ¹⁴C for DOC was ?254‰ in agricultural drains in the Sacramento–San Joaquin Delta, ?218‰ in the San Joaquin River, ?175‰ in the California State Water Project and ?152‰ in the Sacramento River. The age of bulk DOC transiting the rivers of California’s Central Valley is the oldest reported for large rivers and suggests wide-spread loss of soil organic matter caused by agriculture and urbanization. Using DAX 8 adsorbent, we isolated and measured ¹⁴C concentrations in hydrophobic acid fractions (HPOA); river samples showed evidence of bomb-pulse carbon with average Δ¹⁴C of 91 and 76‰ for the San Joaquin and Sacramento Rivers, respectively, with older HPOA, ?204‰, observed in agricultural drains. An operationally defined non-HPOA fraction of DOC was observed in the San Joaquin River with seasonally computed Δ¹⁴C values of between ?275 and ?687‰; the source of this aged material was hypothesized to be physically protected organic-matter in high clay-content soils and agrochemicals (i.e., radiocarbon-dead material) applied to farmlands. Mixing models suggest that the Sacramento River contributes about 50% of the DOC load in the California State Water Project, and agricultural drains contribute approximately one-third of the load. In contrast to studies showing stabilization of soil carbon pools within one or two decades following land conversion, sustained loss of soil organic matter, occurring many decades after the initial agricultural-land conversion, was observed in California’s Central Valley.     

Persistence of historical population structure in an endangered species despite near‐complete biome conversion in California's San Joaquin Desert

Genomic responses to habitat conversion can be rapid, providing wildlife managers with time‐limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near‐complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt‐nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site‐associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid‐adapted taxa in one of the world's most compromised landscapes.     

Cryptic species and co‐diversification in sand scorpions from the Karakum and Kyzylkum deserts of Central Asia

Little is known about species diversification within the deserts of Central Asia. For example, the degree of lineage divergence and timing of population differentiation, as well as potential biogeographic barriers driving diversification, are nearly unknown. Here, we analysed a multi‐locus data set for a widespread sand scorpion (Mesobuthus gorelovi) to evaluate cryptic species diversity and phylogeographic patterns across the Karakum and Kyzylkum deserts. We also combined these data with previously published sequence data to test for a signal of co‐diversification. A consensus species delimitation approach indicated that the widespread M. gorelovi is likely composed of up to five distinct species that began to diversify at the Miocene–Pliocene boundary. We observed shared patterns of lineage divergence across the Amu Darya River region in three scorpion taxa and found support for a shared history of assemblage diversification across this biogeographic barrier. Thus, major river systems appear to facilitate diversification among desert scorpions.     

Characterization of microsatellite loci in Sacramento perch (Archoplites interruptus)

We characterized 23 polymorphic tetranucleotide microsatellite loci for Sacramento perch (Archoplites interruptus). This species is extirpated in its native range, the Sacramento–San Joaquin Delta (California, USA), and is therefore targeted for recovery. A concerted effort is currently underway to re‐establish self‐sustaining populations of Sacramento perch in its native range. These microsatellites will be used to analyse the population structure of the species and, in conjunction with life history and physiological data, develop a comprehensive recovery plan.     

Phylogeography of a stream-dwelling frog (Pseudacris cadaverina) in southern California

Recent phylogeographic studies of animal taxa in California have revealed common geographic patterns of evolutionary divergence and genetic diversity that are generally attributable to landscape influences. However, there remains a paucity of knowledge on the evolution of freshwater taxa in southern California. Here, we investigate phylogeographic patterns in a stream-dwelling frog (Pseudacris cadaverina). Two hundred and twenty-one individuals were collected from 46 populations across the species’ range in southern California. Using 1100 bp of sequence data from cytochrome b and tRNA-Glu, we conducted phylogenetic analyses, analysis of molecular variance, and nested clade phylogeographic analysis to gain insight into the factors contributing to the distribution of genetic diversity in P. cadaverina. We tested for evidence of two putative phylogeographic breaks and tested hypotheses that genetic diversity in this species is partitioned into (1) major watersheds, (2) mountain ranges, and (3) coastal and desert regions. Our results suggest that the eastern Transverse Ranges are the center of origin for extant P. cadaverina lineages and that the observed genetic structure in this species was established during the Pleistocene Epoch. There is strong support for three major haplotype groups and a Transverse Range break in P. cadaverina that is concordant with breaks found in numerous other taxa. The distribution of genetic diversity in P. cadaverina is due in large part to the separation of populations into different major watersheds and mountain ranges. Gene flow appears to be generally limited among disjunct populations throughout the region and some desert populations have been isolated by historical habitat fragmentation.     

Temperature preferences and oxygen consumption of three species of sculpin (Cottus) from the Pit River drainage,California

Synopsis I examined the temperature preferences and routine metabolic rates of Pit sculpin, Cottius pitensis, marbled sculpin, C. klamathensis macrops, and rough sculpin, C. asperrimus, of the Pit River drainage of California to determine if the distributional patterns of these species can be explained on the basis of physiological or behavioral responses to temperature. The routine metabolic rates of these species did not increase significantly between 10 and 15°C, indicating an area of thermal compensation. Metabolic rates then rapidly increased between 15 and 20°C (Q₁₀ values>4.0) followed by little increase between 20 and 25°C (Q₁₀ values >2.0), indicating another area of thermal compensation. The final temperature preferenda of Pit, marbled and rough sculpin were 11.2, 12.1 and 13.5°C, respectively. Marbled and rough sculpin appear to be more stenothermal than Pit sculpin. At acclimation temperatures of 10, 15 and 20°C the acute preferred temperatures of marbled and rough sculpin ranged from 11.1 to 14.7° C and 13.3 to 14.4°C, respectively. Values for Pit sculpin ranged from 9.9 to 16.4°C at acclimation temperatures of 10, 15 and 20°C. The distributions of marbled and rough sculpin are consistent with their behavioral and metabolic responses to temperature. The widespread distribution of Pit sculpin is consistent with its greater tolerance of high temperatures and eurythermal behavior, but the absence of Pit sculpin from habitats dominated by marbled and rough sculpin is not consistent with a temperature related explanation.     

Phylogeography and diversification of an Amazonian understorey hummingbird: paraphyly and evidence for widespread cryptic speciation in the Plio‐Pleistocene

Straight‐billed Hermit Phaethornis bourcieri inhabits the understorey of upland terra firme forest throughout most of the Amazon basin. Currently, two allopatric taxa regarded as subspecies are recognized: P. b. bourcieri and P. b. major. However, the validity, interspecific limits and evolutionary history of these taxa are not yet fully elucidated. We use molecular characters to propose a phylogenetic hypothesis for populations and taxa grouped under Phaethornis bourcieri. Our results showed that P. bourcieri is part of the ‘Ametrornis’ clade, along with Phaethornis philippii and Phaethornis koepckeae, and that the subspecies major is more closely related to the latter two species than to populations grouped under nominate bourcieri. Our phylogenetic hypotheses recovered three main reciprocally monophyletic clades under nominate bourcieri separated by the lower Negro River and the Branco River or the Branco–Negro interfluve (clades B and C) and the upper Amazon (Solimões) or lower Marañon/Ucayali Rivers (clades C and D). Based on multi‐locus phylogeographic and population genetics approaches, we show that P. b. major is best treated as a separate species, and that P. b. bourcieri probably includes more than one evolutionary species, whose limits remain uncertain. The diversification of the ‘Ametrornis’ clade (P. bourcieri, P. philippii and P. koepckeae) is centred in the Amazon and appears to be closely linked to the formation of the modern Amazon drainage during the Plio‐Pleistocene.     

Characterization of microsatellite loci for five members of the minnow family Cyprinidae found in the Sacramento–San Joaquin Delta and its tributaries

Two microsatellite‐enriched libraries [(CAGA)_n, (TAGA)_n] were constructed using pooled DNA from three cyprinid species native to the Sacramento–San Joaquin Delta of California: Sacramento splittail (Pogonichthys macrolepidotus); Sacramento pikeminnow (Ptychocheilus grandis); and tui chub (Siphateles bicolor). Primers were designed for 105 loci and tested for levels of polymorphism in five cyprinid species found in the Delta: Sacramento splittail, Sacramento pikeminnow, tui chub, hitch (Lavinia exilicauda), and Sacramento blackfish (Orthodon microlepidotus). Fifty‐one loci were polymorphic for at least one species and 31 loci were polymorphic for multiple species. The number of polymorphic loci per species ranged from 16 to 26.     

Lineage-specific late pleistocene expansion of an endemic subtropical gossamer-wing damselfly, Euphaea formosa, in Taiwan

Background  

Pleistocene glacial oscillations have significantly affected the historical population dynamics of temperate taxa. However, the general effects of recent climatic changes on the evolutionary history and genetic structure of extant subtropical species remain poorly understood. In the present study, phylogeographic and historical demographic analyses based on mitochondrial and nuclear DNA sequences were used. The aim was to investigate whether Pleistocene climatic cycles, paleo-drainages or mountain vicariance of Taiwan shaped the evolutionary diversification of a subtropical gossamer-wing damselfly, Euphaea formosa.     

Pleistocene climatic fluctuations drive isolation and secondary contact in the red diamond rattlesnake (Crotalus ruber) in Baja California

Aim

Many studies have investigated the phylogeographic history of species on the Baja California Peninsula, and they often show one or more genetic breaks that are spatially concordant among many taxa. These phylogeographic breaks are commonly attributed to vicariance as a result of geological or climatic changes, followed by secondary contact when barriers are no longer present. We use restriction‐site associated DNA sequence data and a phylogeographic model selection approach to explicitly test the secondary contact hypothesis in the red diamond rattlesnake, Crotalus ruber.

Location

Baja California and Southern California.

Methods

We used phylogenetic and population clustering approaches to identify population structure. We then used coalescent methods to simultaneously estimate population parameters and test the fit of phylogeographic models to the data. We used ecological niche models to infer suitable habitat for C. ruber at the Last Glacial Maximum (LGM).

Results

Crotalus ruber is composed of distinct northern and southern populations with a boundary near the town of Loreto in Baja California Sur. A model of isolation followed by secondary contact provides the best fit to the data, with both divergence and contact occurring in the Pleistocene. We also identify a genomic signature of northern range expansion in the northern population, consistent with LGM niche models showing that the northern‐most portion of the range of C. ruber was not suitable habitat during the LGM.

Main conclusions

We provide the first explicitly model‐based test of the secondary contact model in Baja California and show that populations of C. ruber were isolated before coming back into contact near Loreto, a region that shows phylogeographic breaks for other taxa. Given the timing of divergence and contact, we suggest that climatic fluctuations have driven the observed phylogeographic structure observed in C. ruber and that they may have driven similar patterns in other taxa.     

Basin-scale Patterns in the Drift of Embryonic and Larval Fishes and Lamprey Ammocoetes in two Coastal Rivers

We studied the distribution and abundance of drifting embryonic and larval fishes and lampreys in the Smith and Van Duzen rivers of northern California, U.S.A. We collected seven fish species in four families and at least one lamprey species in the drift. All taxa drifted almost exclusively at night. Sculpins, Cottus aleuticus and C. asper, outnumbered all other taxa, comprising 63% of the catch in the Van Duzen River and 90% of the catch in the Smith River. We estimated that sculpin drift reached 3×10⁷ individualsh^–1 during the relatively high flow period from late winter through early summer. Most sculpin in these two rivers appeared to drift to the estuaries; we estimated 2.5×10⁹ sculpin embryos and larvae reached the Smith River estuary in 1995. In contrast to the sculpins, the patterns in the drift of other taxa suggest limited transport to the estuaries. Suckers, Catostomus occidentalis in the Van Duzen River, C. rimiculus in the Smith River, threespine stickleback, Gasterosteus aculeatus, and lamprey, Lampetra tridentata and possibly L. richardsoni, drifted at much lower rates and later in the year than sculpins. In the Van Duzen River, drift appeared to serve as a dispersal mechanism for only one of three introduced cyprinids. California roach, Lavinia symmetricus, drifted at low rates throughout the summer while we captured only seven Sacramento pikeminnow, Ptychocheilus grandis, and no speckled dace, Rhynichthys osculus. The information gathered on the drift of early life history phases is germane to both the conservation of native fishes and management of non-indigenous species in coastal rivers.     

Characterization of microsatellite loci in chinook salmon (Oncorhynchus tshawytscha) and cross‐species amplification in other salmonids

Previous studies of population genetic structure of fall‐run chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley have either not focused on or have been unable to resolve intertributary differences within the San Joaquin River basin. The authors describe the isolation, the polymerase chain reaction conditions, and characterize the cross‐species amplification of 17 microsatellite loci in six species of salmonids. Fourteen of these loci are polymorphic in fall‐run chinook from the San Joaquin River drainage. These results indicate the potential utility of microsatellite markers developed for one species, for both congenerics and species within a closely related genus.     

Fish Communities of the Sacramento River Basin: Implications for Conservation of Native Fishes in the Central Valley, California

The associations of resident fish communities with environmental variables and stream condition were evaluated at representative sites within the Sacramento River Basin, California between 1996 and 1998 using multivariate ordination techniques and by calculating six fish community metrics. In addition, the results of the current study were compared with recent studies in the San Joaquin River drainage to provide a wider perspective of the condition of resident fish communities in the Central Valley of California as a whole. Within the Sacramento drainage, species distributions were correlated with elevational and substrate size gradients; however, the elevation of a sampling site was correlated with a suite of water-quality and habitat variables that are indicative of land use effects on physio-chemical stream parameters. Four fish community metrics – percentage of native fish, percentage of intolerant fish, number of tolerant species, and percentage of fish with external anomalies – were responsive to environmental quality. Comparisons between the current study and recent studies in the San Joaquin River drainage suggested that differences in water-management practices may have significant effects on native species fish community structure. Additionally, the results of the current study suggest that index of biotic integrity-type indices can be developed for the Sacramento River Basin and possibly the entire Central Valley, California. The protection of native fish communities in the Central Valley and other arid environments continues to be a conflict between human needs for water resources and the requirements of aquatic ecosystems; preservation of these ecosystems will require innovative management strategies.     

Extensive diversification of pebblesnails (Lithoglyphidae: Fluminicola) in the upper Sacramento River basin, northwestern USA

Mitochondrial DNA sequences from the cytochrome c oxidase subunit I (COI) and cytochrome b (cytb) genes were obtained from the nine extant, previously described species of the northwestern North American freshwater gastropod genus Fluminicola (commonly known as pebblesnails) and from a large number of taxonomically undescribed populations of these animals from the upper Sacramento River basin, California and Oregon, which is composed of the Sacramento River headwaters, and the McCloud and Pit Rivers. Phylogenetic analyses of separate and combined molecular datasets yielded well‐supported and largely congruent trees delineating 13 genetically divergent and morphologically distinctive upper Sacramento basin lineages, which we describe as new species. These include two groups of closely related and geographically proximal species that are further united by unique radular or shell features. Most of these novelties have narrow geographical distributions and are restricted to headspring areas, whereas several are more wide ranging and typically occupy larger, well‐integrated habitats. The highly endemic fauna of upper Sacramento River pebblesnails is not a single species flock, but instead a polyphyletic assemblage spread among four separate clades. Our phylogeny, together with the application of a COI molecular clock for Fluminicola, suggests that upper Sacramento River clades originated as a result of late Neogene separation of this basin from neighbouring regions (northwestern Great Basin, Klamath River basin), which is consistent with previous biogeographical hypotheses based on the distributions of fishes. The upper Sacramento River pebblesnails evolved in association with the complex late Cenozoic history of regional landscape and drainage and diversification was also facilitated by the invasion of and adaptation to insular spring habitats. Our findings are consistent with the generally limited dispersal ability and geologically ancient (mid‐Tertiary) age of this genus and imply that other portions of northwestern North America may also harbour a large number of undescribed pebblesnail species. Journal compilation © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149 , 371–422. No claim to original US government works.     

Molecular data and ecological niche modelling reveal the phylogeographic pattern of Cotinus coggygria (Anacardiaceae) in China's warm‐temperate zone

The phylogeography of common and widespread species helps to elucidate the history of local flora and vegetation. In this study, we selected Cotinus coggygria, a species widely distributed in China's warm‐temperate zone. One chloroplast DNA (cpDNA) region and ecological niche modelling were used to examine the phylogeographic pattern of C. coggygria. The cpDNA data revealed two phylogeographic groups (Southern and Northern) corresponding to the geographic regions. Divergence time analyses revealed that divergence of the two groups occurred at approximately 147,000 years before the present (BP), which coincided with the formation of the downstream area of the Yellow River, indicating that the Yellow River was a weak phylogeographic divide for C. coggygria. The molecular data and ecological niche modelling also indicated that C. coggyria did not experience population expansion after glaciations. This study thus supports the fact that Pleistocene glacial cycles only slightly affected C. coggygria, which survived in situ and occupied multiple localised glacial refugia during glaciations. This finding is contrary to the hypothesis of large‐scale range habitat contraction and retreat into a few main refugia.     

Speciation with gene flow in whiptail lizards from a Neotropical xeric biome

Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well‐delimited lineages (Northeast and Southwest) that have diverged along the Cerrado–Caatinga border during the Mid‐Late Miocene (6–14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado–Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.     

Phylogeography of the chestnut‐tailed antbird (Myrmeciza hemimelaena) clarifies the role of rivers in Amazonian biogeography

Aim We examined patterns of spatial and temporal diversification of the Amazonian endemic chestnut‐tailed antbird, Mymeciza hemimelaena (Thamnophilidae), to evaluate the diversification of a widespread avian taxon across rivers that potentially represent major natural barriers. Location Lowland Amazonia. Methods Sequences of the mitochondrial ND2 and cytochrome b genes were investigated from 65 individuals distributed throughout the entire range of M. hemimelaena, and including the two currently valid subspecies M. h. hemimelaena and M. h. pallens. Based on a combination of phylogeographic tools, molecular dating, and population genetic methods, we reconstructed a spatio‐temporal scenario of diversification of M. hemimelaena in the Amazon. Results The data revealed three genetically divergent and monophyletic groups in M. hemimelaena, which can also be distinguished by a combination of morphological and vocal characters. Two of these clades correspond to the previously described taxa M. h. hemimelaena and M. h. pallens, which are separated by the upper Madeira River, a main Amazonian tributary. The third clade is distributed between the middle reaches of the Madeira River and the much smaller tributaries Jiparaná and Aripuanã, and, although currently treated as M. h. pallens, clearly constitutes an independent evolutionary lineage probably deserving separate species status. Molecular clock and population genetic analyses indicate that diversification in this group occurred throughout the Pleistocene, with demographic fluctuations assumed for M. h. hemimelaena and M. h. pallens. Main conclusions The findings implicate rivers as barriers driving diversification in the M. hemimelaena complex. Levels of mitochondrial DNA divergence and associated morphological and vocal traits support its division into at least three separate species with comparatively small ranges. The existence of a previously unrecognized lineage in the M. hemimelaena complex, and the high degree of population structuring found in M. h. hemimelaena underscore the pervasiveness of cryptic endemism throughout Amazonia and the importance of DNA‐based taxonomic and phylogeographic studies in providing the accurate estimates of diversity that are essential for conservation planning.     

Comparative phylogeography of codistributed aquatic insects in western North America: insights into dispersal and regional patterns of genetic structure

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Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: concerted,independent, or multiple evolutionary responses?

A central goal of comparative phylogeography is determining whether codistributed species experienced (1) concerted evolutionary responses to past geological and climatic events, indicated by congruent spatial and temporal patterns (“concerted‐response hypothesis”); (2) independent responses, indicated by spatial incongruence (“independent‐response hypothesis”); or (3) multiple responses (“multiple‐response hypothesis”), indicated by spatial congruence but temporal incongruence (“pseudocongruence”) or spatial and temporal incongruence (“pseudoincongruence”). We tested these competing hypotheses using DNA sequence data from three livebearing fish species codistributed in the Nicaraguan depression of Central America (Alfaro cultratus, Poecilia gillii, and Xenophallus umbratilis) that we predicted might display congruent responses due to co‐occurrence in identical freshwater drainages. Spatial analyses recovered different subdivisions of genetic structure for each species, despite shared finer‐scale breaks in northwestern Costa Rica (also supported by phylogenetic results). Isolation‐with‐migration models estimated incongruent timelines of among‐region divergences, with A. cultratus and Xenophallus populations diverging over Miocene–mid‐Pleistocene while P. gillii populations diverged over mid‐late Pleistocene. Approximate Bayesian computation also lent substantial support to multiple discrete divergences over a model of simultaneous divergence across shared spatial breaks (e.g., Bayes factor [B₁₀] = 4.303 for Ψ [no. of divergences] > 1 vs. Ψ = 1). Thus, the data support phylogeographic pseudoincongruence consistent with the multiple‐response hypothesis. Model comparisons also indicated incongruence in historical demography, for example, support for intraspecific late Pleistocene population growth was unique to P. gillii, despite evidence for finer‐scale population expansions in the other taxa. Empirical tests for phylogeographic congruence indicate that multiple evolutionary responses to historical events have shaped the population structure of freshwater species codistributed within the complex landscapes in/around the Nicaraguan depression. Recent community assembly through different routes (i.e., different past distributions or colonization routes), and intrinsic ecological differences among species, has likely contributed to the unique phylogeographical patterns displayed by these Neotropical fishes.