Phylogeography of a widespread Australian freshwater fish, western carp gudgeon (Eleotridae: Hypseleotris klunzingeri): Cryptic species, hybrid zones, and strong intra-specific divergences

Despite belonging to the most abundant and widespread genus of freshwater fishes in the region, the carp gudgeons of eastern Australia (genus Hypseleotris) have proved taxonomically and ecologically problematic to science since the 19th century. Several molecular studies and a recent taxonomic revision have now shed light on the complex biology and evolutionary history that underlies this group. These studies have demonstrated that carp gudgeons include a sexual/unisexual complex (five sexual species plus an assortment of hemiclonal lineages), many members of which also co-occur with an independent sexual relative, the western carp gudgeon (H. klunzingeri). Here, we fill yet another knowledge gap for this important group by presenting a detailed molecular phylogeographic assessment of the western carp gudgeon across its entire and extensive geographic range. We use a suite of nuclear genetic markers (SNPs and allozymes) plus a matrilineal genealogy (cytb) to demonstrate that H. klunzingeri s.l. also displays considerable taxonomic and phylogeographic complexity. All molecular datasets concur in recognizing the presence of multiple candidate species, two instances of historic between-species admixture, and the existence of a natural hybrid zone between two of the three candidate species found in the Murray-Darling Basin. We also discuss the major phylogeographic patterns evident within each taxon. Together, these analyses provide a robust molecular, taxonomic, and distributional framework to underpin future morphological and ecological investigations on this prominent member of regional freshwater ecosystems in eastern Australia.

Infrasound detection of approaching lahars

Infrasound may be used to detect the approach of hazardous volcanic mudflows, known as lahars, tens of minutes before their flow fronts arrive. We have analyzed signals from more than 20 secondary lahars caused by precipitation events at Fuego Volcano during Guatemala's rainy season in May through October of 2022. We are able to quantify the capabilities of infrasound monitoring through comparison with seismic data, time lapse camera imagery, and high-resolution video of a well-recorded event on August 17. We determine that infrasound sensors, deployed adjacent to the lahar path and in small-aperture (10 s of meters) arrays, are particularly sensitive to remote detection of lahars, including small-sized events, at distances of at least 5 km. At Fuego Volcano these detections could be used to provide timely alerts of up to 30 min before lahars arrive at a downstream monitoring site, such as in the frequently impacted Ceniza drainage. We propose that continuous infrasound monitoring, from locations adjacent to a drainage, may complement seismic monitoring and serve as a valuable tool to help identify approaching hazards. On the other hand, infrasound arrays located a kilometer or more from the lahar path can be effectively used to track a lahar's progression.

Predation history has no effect on lateralized behavior in Brachyrhaphis rhabdophora

Evolutionary biologists have grown increasingly interested in laterality, a phenomenon where bilaterally symmetrical organisms show a side bias in some trait. Lateralized behavior is particularly interesting because it is not necessarily tied to morphological asymmetry. What causes lateralized behavior remains largely unknown, although previous research in fishes suggest that fish might favor one eye over another to view potential food sources, mates, and to assess predation risk. Here we test the hypothesis that a history of predation risk predicts lateralized behavior in the livebearing fish Brachyrhaphis rhabdophora. To do this, we used a detour assay to test for eye bias when a focal fish approached various stimuli (predator, potential mate, novel object, and empty tank control). Contrary to our predictions, we found no differences in lateralized behavior between fish from populations that co-occurred with fish predators relative to those that do not co-occur with predators. In fact, we found no evidence for behavioral lateralization at all in response to any of the stimuli. We explore several possible explanations for why lateralized behavior is absent in this species, especially considering a large body of work in other livebearing fishes that shows that lateralized behavior does occur.

Morphologic and genetic variation within a relict Andean catfish, Hatcheria macraei , and its relationship with Trichomycterus areolatus and Bullockia maldonadoi (Siluriformes: Trichomycteridae)

The South American siluriform fishes are found primarily in the Neotropical region, north and east of the Colorado River of Argentina, with a few relict species distributed southward and westward on both sides of the Andes Mountains. Three of these, the closely related trichomycterids Hatcheria macraei, Trichomycterus areolatus and Bullockia maldonadoi, have been subject to historical taxonomic and nomenclatural arrangements. Here, we amplify a 652-bp fragment of COI mtDNA from 55 H. macraei individuals and use publicly available Cytb mtDNA sequences of the three taxa to assess their relationship, genetic variation and haplotype distribution in relation to hydrographic basins. In addition, we extend a recent morphometric study on H. macraei by analyzing body shape in 447 individuals collected from 24 populations across their entire cis-Andean distribution. We identified some lineages previously assigned to T. areolatus that show a closer relationship to either B. maldonadoi or H. macraei, revealing new boundaries to their currently known trans-Andean distribution. We found a great morphologic variation among H. macraei populations and a high genetic variation in H. macraei, T. areolatus and B. maldonadoi associated with river basins. We highlight further integrative studies are needed to enhance our knowledge of the southern Andean trichomycterid diversity.

Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

A recent study argued that coalescent-based models of species delimitation mostly delineate population structure, not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here, we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (1) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles and to hold aside individuals involved in contemporary admixture for independent consideration; (2) apply phylogenetic techniques to identify lineages; (3) assess diagnosability of those lineages as potential candidate species; (4) interpret the diagnosable lineages in a geographical context (sympatry, parapatry, allopatry); (5) assess significance of difference or trends in the context of sampling intensity; and (6) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We adopt this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (Retropinna spp.). Our framework addresses two cornerstone issues in systematics that are often not discussed explicitly in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.

Predator Environment Does Not Predict Life History in the Morphologically Constrained Fish Alfaro cultratus (Cyprinodontiformes: Poeciliidae)

Predation is known to have a significant effect on life history diversification in a variety of species. However, physical constraints of body shape and size can sometimes limit life history divergence. We test this idea in the Costa Rican livebearing fishAlfaro cultratus. Individuals in this species have a narrow body and keeled ventral surface, and females do not develop a distended abdomen when pregnant like other livebearing fishes. Here, we describe the life history ofA. cultratusfrom 20 different populations across both high-predation and low-predation environments. We found significantly lower reproductive allotment in females from high-predation environments than in females from low-predation environments, but no significant difference in female or male size at maturity, number of offspring produced by females, or size of offspring. We found thatA. cultratusexhibit isometric patterns of allocation for clutch dry mass in relation to female dry mass in high-predation and low-predation environments. Our results suggest that body shape constraints in this species limit the life history divergence we typically see between populations from high-predation and low-predation environments in other species.

What Drives Life-History Variation in the Livebearing Fish Poeciliopsis prolifica? An Assessment of Multiple Putative Selective Agents

Life-history traits are directly linked to fitness, and therefore, can be highly adaptive. Livebearers have been used as models for understanding the evolution of life histories due to their wide diversity in these traits. Several different selective pressures, including population density, predation, and resource levels, can shape life-history traits. However, these selective pressures are usually considered independently in livebearers and we lack a clear understanding of how they interact in shaping life-history evolution. Furthermore, selective pressures such as interspecific competition are rarely considered as drivers of life-history evolution in poeciliids. Here we test the simultaneous effects of several potential selective pressures on life-history traits in the livebearing fish Poeciliopsis prolifica. We employ a multi-model inference approach. We focus on four known agents of selection: resource availability, stream velocity, population density, and interspecific competition, and their effect on four life-history traits: reproductive allocation, superfetation, number of embryos, and individual embryo size. We found that models with population density and interspecific competition alone were strongly supported in our data and, hence, indicated that these two factors are the most important selective agents for most life-history traits, except for embryo size. When population density and interspecific competition increase there is an increase in each of the three life-history traits (reproductive allocation, superfetation, and number of embryos). For individual embryo size, we found that all single-agent models were equivalent and it was unclear which selective agent best explained variation. We also found that models that included population density and interspecific competition as direct effects were better supported than those that included them as indirect effects through their influence on resource availability. Our study underscores the importance of interspecific competitive interactions on shaping life-history traits and suggests that these interactions should be considered in future life-history studies.

Does Asymmetrical Gonopodium Morphology Predict Lateralized Behavior in the Fish Xenophallus umbratilis?

Why bilaterally symmetrical organisms express handedness remains an important question in evolutionary biology. In some species, anatomical asymmetries have evolved that accompany behavioral handedness, yet we know remarkably little about causal links between asymmetric morphological traits and behavior. Here, we explore if a dextral or sinistral orientation of the male intromittent organ predicts side preferences in male behaviors. Our study addresses this question in the Costa Rican livebearing fish, Xenophallus umbratilis. This fish has a bilaterally symmetrical body plan, with one exception—the male anal fin (gonopodium), used to inseminate females, terminates with a distinct left- or right-handed corkscrew morphology. We used a detour assay to test males for side biases in approach behavior when exposed to four different stimuli (predator, potential mate, novel object, empty tank control). We found that left morph males preferred using their right eye to view potential mates, predators, and the control, and that right morph males preferred to use their left eye to view potential mates and predators, and their right eye to view the control. Males of both morphs displayed no eye bias when approaching the novel object. Our results suggest that there is a strong link between behavior and gonopodium orientation, with right and left morph males responding with opposite directional behaviors when presented with the same stimuli. This presents the intriguing possibility that mating preferences—in this case constrained by gonopodial morphology—could be driving lateralized decision making in a variety of non-mating behaviors.

Beyond Pairwise Interactions: Multispecies Character Displacement in Mexican Freshwater Fish Communities

Competition has long been recognized as a central force in shaping evolution, particularly through character displacement. Yet research on character displacement is biased, as it has focused almost exclusively on pairs of interacting species while ignoring multispecies interactions. Communities are seldom so simple that only pairs of species interact, and it is not clear whether inferences from pairwise interactions are sufficient to explain patterns of phenotypes in nature. Here, we test for character displacement in a natural system of freshwater fishes in western Mexico that contains up to four congeneric species of the genus Poeciliopsis. We analyzed body shape differences between populations with different numbers of competitors while accounting for confounding environmental variables. Surprisingly, we found evidence for convergent character displacement in populations of P. prolifica, P. viriosa, and P. latidens. We also found that the convergence in body shape was not consistently in the same direction, meaning that when three or more competitors co-occurred, we did not find more extreme body shapes compared with when there were only two competitors. Instead, when three or more competitors co-occurred, body shape was intermediate between the shape found with a pair of species and the shape found with no competitor present. This intermediate shape suggests that evolution in multispecies communities likely occurs in response to several competitors rather than to simple pairwise interactions. Overall, our results suggest that competition among multiple species is more complex than simple pairwise competitive interactions.

Testes mass in the livebearing fish Brachyrhaphis rhabdophora (Poeciliidae) varies hypoallometrically with body size but not between predation environments

In this study, we considered potential causes of variation in testis size in the livebearing fish Brachyrhaphis rhabdophora. We evaluated variation in testes mass among individual males and among populations that occupy different selective environments. First, we predicted that small males should allocate more to testes mass than large males (i.e., hypoallometric pattern) based on a sperm competition argument. Second, based on life history theory and associated differences in mortality rates between populations that coexist with many fish predators and those with few predators, we predicted that males in high-predation environments should allocate more to testes mass than males in habitats with few predators. Our results showed that small males allocated proportionally more to testes mass than larger males (slope of testes mass to body mass was hypoallometric). However, there was no effect of predator environment on testes mass independent of body size differences. In this system, size-specific patterns of reproductive allocation in males (hypoallometry) differ from that seen in females (hyperallometry). Allocation to testes mass may respond to differences in mortality rate through selection on body size.

Anal fin pigmentation in Brachyrhaphis fishes is not used for sexual mimicry

Mimicry can occur in several contexts, including sexual interactions. In some cases, males mimic females to gain access to potential mates. In contrast, there are relatively few examples of species where females mimic males, and we know very little about what drives these patterns. Two hypotheses have been advanced to explain female mimicry of males. The first is that mimicry is used to reduce harassment of females by males. The second is that mimicry is used to display dominance over other females. In this study, we tested these hypotheses in Brachyrhaphis fishes, wherein females of several species have pigmentation on their anal fin of the same coloration and shape, and in the same location, as the genitalia of males. To test if female mimicry of males reduces male harassment, we experimentally manipulated female pigmentation and observed male preference for females with and without male-like pigmentation. To test the effect that female mimicry of males has on female dominance, we observed how females respond to anal fin pigmentation patterns of companion females. We found that neither of these hypotheses was supported by our data. We conclude that similarities in anal fin pigmentation between male and female Brachyrhaphis fishes is not an adaptation to reduce male harassment or to signal dominance between females. Alternative explanations must exist, including the possibility that these similarities are simply non-adaptive.

Divergent predation environment between two sister species of livebearing fishes (Cyprinodontiformes: Poeciliidae) predicts boldness, activity, and exploration behavior

Predators can influence a variety of prey traits, including behavior. Traits such as boldness, activity rate, and tendency to explore can all be shaped by predation risk. Our study examines the effects of predation on these behaviors by considering a natural system in which two sister species of livebearing fishes, Brachyrhaphis roseni and B. terrabensis, experience divergent predation environments. In February of 2013, we collected fish in the Río Chiriquí Nuevo drainage, Chiriquí, Panama, and conducted behavioral assays. Using open-field behavioral assays, we evaluated both juveniles and adults, and males and females, to determine if there were differences in behavior between ontogenetic stages or between sexes. We assessed boldness as ‘time to emerge’ from a shelter into a novel environment, and subsequently measured activity and exploration within that novel environment. We predicted that B. roseni (a species that co-occurs with predators) would be more bold, more active, and more prone to explore, than B. terrabensis (a species that does not co-occur with predators). In total, we tested 17 juveniles, 21 adult males, and 20 adult females of B. roseni, and 19 juveniles, 19 adult males, and 18 adult females of B. terrabensis. We collected all animals from streams in Chiriquí, Panama in February 2013, and tested them following a short acclimation period to laboratory conditions. As predicted, we found that predation environment was associated with several differences in behavior. Both adult and juvenile B. roseni were more active and more prone to explore than B. terrabensis. However, we found no differences in boldness in either adults or juveniles. We also found a significant interaction between ‘sex’ and ‘species’ as predictors of boldness and exploration, indicating that predation environment can affect behaviors of males and females differently in each species. Our work demonstrates the importance of considering sex and life history stage when evaluating the evolution of behavior.

Modulatory effects of Zn2+ ions on the toxicity of citrate- and PVP-capped gold nanoparticles towards freshwater algae, Scenedesmus obliquus

Gold nanoparticles (GNPs) are widely used for medical purposes, both in diagnostics as well as drug delivery, and hence are prone to release and distribution in the environment. Thus, we have explored the effects of GNPs with two distinct surface capping (citrate and PVP), and three different sizes (16, 27, and 37 nm) at 0.01-, 0.1-, and 1-mg L^-1 concentrations on a predominant freshwater alga Scenedesmus obliquus in the sterile freshwater matrix. We have also investigated how an abundant metal ion from freshwater, i.e., Zn²⁺ ions may modulate the effects of the selected GNPs (40 nm, citrate, and PVP capped). Preliminary toxicity results revealed that gold nanoparticles were highly toxic in comparison to zinc ions alone. A significant modulation in the toxicity of Zn ions was not noticed in the presence of GNPs. In contrast, zinc ions minimized the toxicity produced by GNPs (both CIT-37 and PVP-37), despite its individual toxicity. Approximately, about 42, 33, and 25% toxicity reduction was noted at 0.05-, 0.5-, and 5-mg L^-1 Zn ions, respectively, for CIT-37 GNPs, while 31% (0.05 mg L^-1), 24% (0.5 mg L^-1), and 9% (5 mg L^-1) of toxicity reduction were noted for PVP-37 GNPs. Maximum toxicity reduction was seen at 0.05 mg L^-1 of Zn ions. Abbott modeling substantiated antagonistic effects offered by Zn²⁺ ions on GNPs. Stability and sedimentation data revealed that the addition of zinc ions gradually induced the aggregation of NPs and in turn significantly reduced the toxicity of GNPs. Thus, the naturally existing ions like Zn²⁺ have an ability to modulate the toxicity of GNPs in a real-world environment scenario.

Sympatry Predicts Spot Pigmentation Patterns and Female Association Behavior in the Livebearing Fish Poeciliopsis baenschi

In this study, we explored the possibility that differences in pigmentation patterns among populations of the fish Poeciliopsis baenschi were associated with the presence or absence of the closely related species P. turneri. If reproductive character displacement is responsible, spotting patterns in these two species should diverge in sympatry, but not allopatry. We predicted that female P. baenschi from sympatric sites should show a preference for associating with conspecifics vs. heterospecific males, but females from allopatric sites should show no such preferences. To evaluate these predictions, we compared spotting patterns and female association behaviors in populations of P. baenschi from Central Mexico. We found that both of our predictions were supported. Poeciliopsis baenschi that co-occured with P. turneri had spotting patterns significantly different than their counterparts from allopatric sites. Using a simultaneous choice test of video presentations of males, we also found that female P. baenschi from populations that co-occured with P. turneri spent significantly more time with males of their own species than with P. turneri males. In contrast, females from allopatric populations of P. baenschi showed no differences in the amount of time they spent with either conspecific or heterospecific males. Together, our results are consistent with the hypothesis that reproductive character displacement may be responsible for behavioral and spotting pattern differences in these populations of P. baenschi.

Selection is stronger in early-versus-late stages of divergence in a Neotropical livebearing fish

How selection acts to drive trait evolution at different stages of divergence is of fundamental importance in our understanding of the origins of biodiversity. Yet, most studies have focused on a single point along an evolutionary trajectory. Here, we provide a case study evaluating the strength of divergent selection acting on life-history traits at early-versus-late stages of divergence in Brachyrhaphis fishes. We find that the difference in selection is stronger in the early-diverged population than the late-diverged population, and that trait differences acquired early are maintained over time.

Co-occurrence of eosinophilic esophagitis and potential/probable celiac disease in an adult cohort: a possible association with implications for clinical practice

We describe an adult cohort with eosinophilic esophagitis (EoE) and evidence of celiac disease (CD), propose a change in diagnostic practice to better characterize these conditions, and hypothesize new directions for research. Pediatric studies postulate association between gluten sensitivity and EoE. However, few publications describe the prevalence, detection, or therapeutic and pathophysiologic implications of such association in adults. Retrospective chart review was done on patients diagnosed with EoE from 2009 to 2010 at University of Utah Hospitals and Clinics. Data included sex, age, presentation, duodenal pathology, tissue transglutaminase immunoglobulin A antibody (TTG) positivity, human leukocyte antigen (HLA) type (when indicated), and gross and microscopic Esophagogastroduodenoscopy (EGD) findings. Duodenal biopsy, TTG results, and HLA type were correlated. Endoscopy was repeated after gluten-free diet. Forty-four of 75 patients were followed in EoE specialty clinic with duodenal biopsy and TTG testing per protocol. Six EoE patients had potential or probable CD. No sex or age differences were noted between those with findings of CD and EoE and those with EoE alone. Six patients with findings of CD and EoE followed gluten-free diet. Five underwent repeat endoscopy. Three had resolution of esophageal eosinophilia. Potential or probable CD was commonly found in adults with EoE. Diagnosis of CD may be challenging due to nonspecific symptoms and insufficient duodenal biopsy and serologic testing. Furthermore, gluten-free diet resolved EoE findings in some patients, suggesting possible shared pathophysiology in some cases of EoE and CD. TTG testing and adequate duodenal biopsy may further direct clinical care for EoE patients, and studies are needed to elucidate mechanisms linking EoE and CD.

Low Genetic Diversity in Diplomystes camposensis, an Endemic and Endangered Catfish from South Chile

Carlos P. Muñoz-Ramírez, Evelyn Habit, Peter J. Unmack, Jerald B. Johnson, and Pedro F. Victoriano (2016) Despite the fundamental importance of the family Diplomystidae for understanding catfish evolution, its species are poorly known and most of them endangered. Diplomystes camposensis, restricted to a single river basin in southern Chile, is perhaps the most vulnerable species due to its small geographic range and imminent habitat alterations by dam constructions. Using mitochondrial DNA sequences, we describe the genetic diversity across its entire distribution in the Valdivia basin and test hypotheses related to the impact of glacial cycles on the genetic diversity and structure. We found that Diplomystes camposensis has low genetic diversity and structure across the entire Valdivia basin along with a pattern of decreasing nucleotide and haplotype diversity from West to East. Demographic analyses showed evidence of population expansion in agreement with the glaciated history of the basin. Analyses of population structure showed no evidence of population subdivision. However, coalescent analyses indicated that very recent subdivision (in the last 50 years) cannot be ruled out. Low genetic diversity and genetic structure across the entire basin suggest that the species might be highly vulnerable to habitat fragmentation. Thus, the imminent construction of hydropower dams represents a serious threat to its conservation. Our results suggest that the low genetic diversity can be the product of the glaciated history of the basin, although the influence of species-specific biological traits may also add to this condition. Despite the overall low genetic diversity, higher diversity was found in the central portion of the basin suggesting high priority of conservation for this area as it might be used as a source population in case translocations are required among potential management plans.

Surface capping and size-dependent toxicity of gold nanoparticles on different trophic levels

In the present study, the toxicity of gold nanoparticles (Au NPs) was evaluated on various trophic organisms. Bacteria, algae, cell line, and mice were used as models representing different trophic levels. Two different sizes (CIT30 and CIT40) and surface-capped (CIT30-polyvinyl pyrrolidone (PVP)-capped) Au NPs were selected. CIT30 Au NP aggregated more rapidly than CIT40 Au NP, while an additional capping of PVP (CIT30-PVP capped Au NP) was found to enhance its stability in sterile lake water medium. Interestingly, all the forms of NPs evaluated were stable in the cell culture medium during the exposure period. Size- and dose-dependent cytotoxicities were observed in both bacteria and algae, with a strong dependence on reactive oxygen species (ROS) generation and lactate dehydrogenase (LDH) release. CIT30-PVP capped Au NP showed a significant decrease in toxicity compared to CIT30 Au NP in bacteria and algae. In the SiHa cell line, dose- and exposure-dependent decline in cell viability were noted for all three types of Au NPs. In mice, the induction of DNA damage was size and dose dependent, and surface functionalization with PVP reduced the toxic effects of CIT30 Au NP. The exposure to CIT30, CIT40, and CIT30-PVP capped Au NPs caused an alteration of the oxidative stress-related endpoints in mice hepatocytes. The toxic effects of the gold nanoparticles were found to vary in diverse test systems, accentuating the importance of size and surface functionalization at different trophic levels.

Phylogenetic analyses provide insights into the historical biogeography and evolution of Brachyrhaphis fishes

The livebearing fish genus Brachyrhaphis (Poeciliidae) has become an increasingly important model in evolution and ecology research, yet the phylogeny of this group is not well understood, nor has it been examined thoroughly using modern phylogenetic methods. Here, we present the first comprehensive phylogenetic analysis of Brachyrhaphis by using four molecular markers (3mtDNA, 1nucDNA) to infer relationships among species in this genus. We tested the validity of this genus as a monophyletic group using extensive outgroup sampling based on recent phylogenetic hypotheses of Poeciliidae. We also tested the validity of recently described species of Brachyrhaphis that are part of the B. episcopi complex in Panama. Finally, we examined the impact of historical events on diversification of Brachyrhaphis, and made predictions regarding the role of different ecological environments on evolutionary diversification where known historical events apparently fail to explain speciation. Based on our results, we reject the monophyly of Brachyrhaphis, and question the validity of two recently described species (B. hessfeldi and B. roswithae). Historical biogeography of Brachyrhaphis generally agrees with patterns found in other freshwater taxa in Lower Central America, which show that geological barriers frequently predict speciation. Specifically, we find evidence in support of an 'island' model of Lower Central American formation, which posits that the nascent isthmus was partitioned by several marine connections before linking North and South America. In some cases where historic events (e.g., vicariance) fail to explain allopatric species breaks in Brachyrhaphis, ecological processes (e.g., divergent predation environments) offer additional insight into our understanding of phylogenetic diversification in this group.

Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae)

Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.

Size doesn't matter, sex does: a test for boldness in sister species of Brachyrhaphis fishes

The effect of divergent natural selection on the evolution of behavioral traits has long been a focus of behavioral ecologists. Predation, due to its ubiquity in nature and strength as a selective agent, has been considered an important environmental driver of behavior. Predation is often confounded with other environmental factors that could also play a role in behavioral evolution. For example, environments that contain predators are often more ecologically complex and “risky” (i.e., exposed and dangerous). Previous work shows that individuals from risky environments are often more bold, active, and explorative than those from low-risk environments. To date, most comparative studies of environmentally driven behavioral divergence are limited to comparisons among populations within species that occur in divergent selective environments but neglect comparisons between species following speciation. This limits our understanding of how behavior evolves post-speciation. The Central American live-bearing fish genus Brachyrhaphis provides an ideal system for examining the relationship between selective environments and behavior, within and between species. Here, we test for differences in boldness between sister species B. roseni and B. terrabensis that occur in streams with and without piscivorous predators, respectively. We found that species do differ in boldness, with species that occur with predators being bolder than those that do not. Within each species, we found that sexes differed in boldness, with males being bolder than females. We also tested for a relationship between size (a surrogate for metabolic rate) and boldness, but found no size effects. Therefore, sex, not size, affects boldness. These results are consistent with the hypothesis that complex and risky environments favor individuals with more bold behavioral traits, but they are not consistent with the hypothesis that size (and therefore metabolic rate) drives divergence in boldness. Finally, our results provide evidence that behavioral trait divergence continues even after speciation is complete.

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 [B 10] = 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.

Morphological divergence driven by predation environment within and between species of Brachyrhaphis fishes

Natural selection often results in profound differences in body shape among populations from divergent selective environments. Predation is a well-studied driver of divergence, with predators having a strong effect on the evolution of prey body shape, especially for traits related to escape behavior. Comparative studies, both at the population level and between species, show that the presence or absence of predators can alter prey morphology. Although this pattern is well documented in various species or population pairs, few studies have tested for similar patterns of body shape evolution at multiple stages of divergence within a taxonomic group. Here, we examine morphological divergence associated with predation environment in the livebearing fish genus Brachyrhaphis. We compare differences in body shape between populations of B. rhabdophora from different predation environments to differences in body shape between B. roseni and B. terrabensis (sister species) from predator and predator free habitats, respectively. We found that in each lineage, shape differed between predation environments, consistent with the hypothesis that locomotor function is optimized for either steady swimming (predator free) or escape behavior (predator). Although differences in body shape were greatest between B. roseni and B. terrabensis, we found that much of the total morphological diversification between these species had already been achieved within B. rhabdophora (29% in females and 47% in males). Interestingly, at both levels of divergence we found that early in ontogenetic development, females differed in shape between predation environments; however, as females matured, their body shapes converged on a similar phenotype, likely due to the constraints of pregnancy. Finally, we found that body shape varies with body size in a similar way, regardless of predation environment, in each lineage. Our findings are important because they provide evidence that the same source of selection can drive similar phenotypic divergence independently at multiple divergence levels.

Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas

Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi-taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional-scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low-structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long-distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene-Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in-depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.

Phylogeography of the ancient catfish family Diplomystidae: biogeographic, systematic, and conservation implications

The catfish family Diplomystidae is one of the earliest branching lineages within the diverse order Siluriformes and shows a deep phylogenetic split from all other extant and extinct major catfish groups. Despite its relevance in the evolution of siluriforms, phylogenetic relationships within the Diplomystidae are poorly understood, and prior to this study, no phylogenetic hypotheses using molecular data had been published. By conducting a phylogeographic study across the entire distribution of the family, that encompasses river systems from Central-South Chile and Argentina, we provide the first molecular phylogenetic hypothesis among all known species of Diplomystidae, and in addition, investigate how their evolutionary history relates to major historical events that took place in southern South America. Our phylogenetic analyses show four main lineages and nine sub-lineages strongly structured geographically. All Pacific basin populations, with one exception (those found in the Baker basin) clustered within three of the four main lineages (clades I-III), while all populations from Atlantic basins and those from the Baker basin clustered in a single main clade (clade IV). There was a tendency for genetic diversity to decrease from north to south for Pacific basins consistent with an increasing north-south ice coverage during the last glacial maximum. However, we did not find a statistically significant correlation between genetic diversity and latitude. Analysis of molecular variance (AMOVA) showed that river basins and the barrier created by the Andes Mountains explained a high percentage of the genetic variation. Interestingly, most of the genetic variation among drainages was explained among Pacific basins. Molecular phylogenetic analyses agree only partially with current systematics. The geographical distribution of main lineages did not match species distribution and suggests a new taxonomic hypothesis with support for four species of Diplomystes, three species distributed allopatrically from the Rapel to the Valdivia basin, and only one species distributed in Baker and Atlantic basins. High genetic differentiation among river basins suggests that conservation efforts should focus on protecting populations in each basin in order to preserve the genetic diversity of one of the oldest groups of catfishes on the earth today.

Paleoclimatic modeling and phylogeography of least killifish, Heterandria formosa: insights into Pleistocene expansion-contraction dynamics and evolutionary history of North American Coastal Plain freshwater biota

BACKGROUND

Climatic and sea-level fluctuations throughout the last Pleistocene glacial cycle (~130-0 ka) profoundly influenced present-day distributions and genetic diversity of Northern Hemisphere biotas by forcing range contractions in many species during the glacial advance and allowing expansion following glacial retreat ('expansion-contraction' model). Evidence for such range dynamics and refugia in the unglaciated Gulf-Atlantic Coastal Plain stems largely from terrestrial species, and aquatic species Pleistocene responses remain relatively uninvestigated. Heterandria formosa, a wide-ranging regional endemic, presents an ideal system to test the expansion-contraction model within this biota. By integrating ecological niche modeling and phylogeography, we infer the Pleistocene history of this livebearing fish (Poeciliidae) and test for several predicted distributional and genetic effects of the last glaciation.

RESULTS

Paleoclimatic models predicted range contraction to a single southwest Florida peninsula refugium during the Last Glacial Maximum, followed by northward expansion. We inferred spatial-population subdivision into four groups that reflect genetic barriers outside this refuge. Several other features of the genetic data were consistent with predictions derived from an expansion-contraction model: limited intraspecific divergence (e.g. mean mtDNA p-distance = 0.66%); a pattern of mtDNA diversity (mean Hd = 0.934; mean π = 0.007) consistent with rapid, recent population expansion; a lack of mtDNA isolation-by-distance; and clinal variation in allozyme diversity with higher diversity at lower latitudes near the predicted refugium. Statistical tests of mismatch distributions and coalescent simulations of the gene tree lent greater support to a scenario of post-glacial expansion and diversification from a single refugium than to any other model examined (e.g. multiple-refugia scenarios).

CONCLUSIONS

Congruent results from diverse data indicate H. formosa fits the classic Pleistocene expansion-contraction model, even as the genetic data suggest additional ecological influences on population structure. While evidence for Plio-Pleistocene Gulf Coast vicariance is well described for many freshwater species presently codistributed with H. formosa, this species demography and diversification departs notably from this pattern. Species-specific expansion-contraction dynamics may therefore have figured more prominently in shaping Coastal Plain evolutionary history than previously thought. Our findings bolster growing appreciation for the complexity of phylogeographical structuring within North America's southern refugia, including responses of Coastal Plain freshwater biota to Pleistocene climatic fluctuations.

Comparative life histories of fishes in the genus Phallichthys (Pisces: Poeciliidae)

This study presents a description of the life histories of all four species of the genus Phallichthys, found primarily in the Atlantic slope of Central America (ranging from northern Panama to Mexico), based on a combination of data collected from preserved and living specimens. All species produced a single litter of offspring before developing another brood (i.e. no superfoetation). In the laboratory, the mean time interval between successive litters ranged from 24 to 48 days, further suggesting that they lack superfoetation. Embryos lose from 15 to 65% of their dry mass during development, meaning all or the large majority of resources required for development are provided prior to fertilization (lecithotrophy). All mature male size distributions were platykurtotic and appeared either bimodal or multimodal. Multimodal and skewed size distributions have been associated with genetic polymorphisms for size at maturity in other species of Poeciliidae. As the sister clade to Phallichthys includes genera in which all species have superfoetation (Neoheterandria and Poeciliopsis), these results suggest that their common ancestor with Phallichthys also had superfoetation and that the trait has been lost.

Effects of predation environment and food availability on somatic growth in the Livebearing Fish Brachyrhaphis rhabdophora (Pisces: Poeciliidae)

Variation in somatic growth rates is of great interest to biologists because of the relationship between growth and other fitness-determining traits, and it results from both genetic and environmentally induced variation (i.e. plasticity). Theoretical predictions suggest that mean somatic growth rates and the shape of the reaction norm for growth can be influenced by variation in predator-induced mortality rates. Few studies have focused on variation in reaction norms for growth in response to resource availability between high-predation and low-predation environments. We used juvenile Brachyrhaphis rhabdophora from high-predation and low-predation environments to test for variation in mean growth rates and for variation in reaction norms for growth at two levels of food availability in a common-environment experiment. To test for variation in growth rates in the field, we compared somatic growth rates in juveniles in high-predation and low-predation environments. In the common-environment experiment, mean growth rates did not differ between fish from differing predation environments, but the interaction between predation environment and food level took the form of a crossing reaction norm for both growth in length and mass. Fish from low-predation environments exhibited no significant difference in growth rate between high and low food treatments. In contrast, fish from high-predation environments exhibited variation in growth rates between high and low food treatments, with higher food availability resulting in higher growth rates. In the field, individuals in the high-predation environment grow at a faster rate than those in low-predation environments at the smallest sizes (comparable to sizes in the common-environment experiment). These data provide no evidence for evolved differences in mean growth rates between predation environments. However, fish from high-predation environments exhibited greater plasticity in growth rates in response to resource availability suggesting that predation environments may exhibit increased variation in food availability for prey fish and consequent selection for plasticity.

Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf galaxias (G. pusilla)

The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate Southern Australia. We also tested if continental shelf width has influenced connectivity among populations during low sea levels when rivers, now isolated, could have been connected. We addressed these questions by sampling each species across its range using multiple molecular markers (mitochondrial cytochrome b sequences, nuclear S7 intron sequences, and 49 allozyme loci). These data also allowed us to assess species boundaries, to refine phylogenetic affinities, and to estimate species ages. Interestingly, we found compelling evidence for cryptic species in G. pusilla, manifesting as allopatric eastern and western taxa. Our combined phylogeny and dating analysis point to an origin for the genus dating to the early Cenozoic, with three of the four species originating during the Oligocene-Miocene. Each Galaxiella species showed high levels of genetic divergences between all but the most proximate populations. Despite extensive drainage connections during recent low sea levels in southeastern Australia, populations of both species within G. pusilla maintained high levels of genetic structure. All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum. High levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.

What can phylogeographic breaks in the livebearer Poeciliopsis turrubarensis tell about fish community boundaries in western Costa Rica?

This study asks if the geographic boundary delineating two fish communities in western Costa Rica is congruent with a phylogeographic break in a single widespread fish species Poeciliopsis turrubarensis (Poeciliidae) that spans this area. Such congruence would suggest that a common historical event (e.g. geological or climatic) could be responsible for both patterns. It was found that there was a shared break across a region in central Costa Rica suggesting a common cause may be responsible for both the abrupt shift in fish community composition and the genetic break in P. turrubarensis.

Phylogeography of the catfish Hatcheria macraei reveals a negligible role of drainage divides in structuring populations

Southern South America provides a set of unusual geographic features that make it particularly interesting for studying phylogeography. The Andes Mountains run along a north-to-south axis and act as a barrier to gene flow for much of the biota of this region, with southern portions experiencing extensive historical glaciation. Geological data reveal a series of drainage reversals, shifting from Pacific Ocean outlets to Atlantic Ocean outlets because of glacier formation that dammed and reversed rivers. Once glaciers melted around 13 000 years ago, drainages returned to the Pacific Ocean. This geologic history predicts that aquatic organisms in Pacific rivers should have their closest relationships to their counterparts in Atlantic rivers immediately to their east. We tested this prediction in the trichomycterid catfish Hatcheria macraei from 38 locations using the mitochondrial cytochrome b gene. Our results show that most populations found in Pacific rivers were closely related to fish found in the adjacent Atlantic draining Río Chubut. Surprisingly, one documented drainage reversal (from Río Deseado into Río Baker) did not result in movement of H. macraei. Overall, we found the lowest levels of genetic structure between most Pacific rivers that are adjacent to the Atlantic draining Río Chubut. We also found low levels of population structuring among three of four contemporary river basins that drain to the Atlantic Ocean. Our findings suggest that drainage basin boundaries have historically not played an important long-term role in structuring between nine of 11 drainages, an unusual finding in freshwater biogeography.

Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage

Background

Understanding how freshwater assemblages have been formed and maintained is a fundamental goal in evolutionary and ecological disciplines. Here we use a historical approach to test the hypothesis of codivergence in three clades of the Chilean freshwater species assemblage. Molecular studies of freshwater crabs (Aegla: Aeglidae: Anomura) and catfish (Trichomycterus arealatus: Trichomycteridae: Teleostei) exhibited similar levels of genetic divergences of mitochondrial lineages between species of crabs and phylogroups of the catfish, suggesting a shared evolutionary history among the three clades in this species assemblage.

Results

A phylogeny was constructed for Trichomycterus areolatus under the following best-fit molecular models of evolution GTR + I + R, HKY + I, and HKY for cytochrome b, growth hormone, and rag 1 respectively. A GTR + I + R model provided the best fit for both 28S and mitochondrial loci and was used to construct both Aegla phylogenies. Three different diversification models were observed and the three groups arose during different time periods, from 2.25 to 5.05 million years ago (Ma). Cladogenesis within Trichomycterus areolatus was initiated roughly 2.25 Ma (Late Pliocene - Early Pleistocene) some 1.7 - 2.8 million years after the basal divergences observed in both Aegla clades. These results reject the hypothesis of codivergence.

Conclusions

The similar genetic distances between terminal sister-lineages observed in these select taxa from the freshwater Chilean species assemblage were formed by different processes occurring over the last ~5.0 Ma. Dramatic changes in historic sea levels documented in the region appear to have independently shaped the evolutionary history of each group. Our study illustrates the important role that history plays in shaping a species assemblage and argues against assuming similar patterns equal a shared evolutionary history.

Morphological and reproductive variation among populations of the Pacific molly Poecilia butleri

In viviparous organisms, pregnant females typically experience an increase in body mass and body volume. In this study, the prediction that variation in reproductive traits among populations of viviparous organisms should be related to variation among populations in body shape was tested in the Pacific molly Poecilia butleri, a viviparous fish that inhabits western Mexico and northern Central America. Variation among 10 populations in four reproductive traits was examined: brood size, individual embryo mass, total reproductive allotment and degree of maternal provisioning of nutrients to developing embryos. Variation among these populations in body shape was also examined. Significant variation among populations was observed in both brood size and reproductive allotment but not in embryo mass or degree of maternal provisioning. Significant variation among populations was also observed in body shape. After correcting for female size, however, reproductive traits and body shape were not associated among populations. This suggests that selective pressures acting on reproduction do not necessarily affect morphology and vice versa. Several factors might contribute to this unexpected lack of association between reproductive traits and morphology.

Use of congeneric assessment to reveal the linked genetic histories of two threatened fishes in the Murray-Darling Basin, Australia

The intensely regulated Murray-Darling Basin in southeastern Australia is the nation's most extensive and economically important river system, and it contains fragmented populations of numerous fish species. Among these is the Murray hardyhead (Craterocephalus fluviatilis), a species listed as endangered (International Union for Conservation of Nature Red List) in the mid-1990 s prior to its acute decline with the progression of a severe drought that began in 1997. We compared the genetic structure of Murray hardyhead with 4 congeneric species (Darling hardyhead[C. amniculus], Finke hardyhead[C. centralis], Lake Eyre hardyhead[C. eyresii], and unspecked hardyhead[C. stercusmuscarum]), selected on the basis of their taxonomic or biological similarity to Murray hardyhead, in order to affirm species boundaries and test for instances of introgressive hybridization, which may influence species ecology and conservation prospects. We used allozyme (52 loci) and mtDNA markers (1999 bp of ATPase and cytochrome b) to provide a comparative genetic assessment of 139 Murray hardyhead, which represented all extant and some recently extirpated populations, and 71 congeneric specimens from 12 populations. We confirmed that Murray hardyhead and Darling hardyhead are taxonomically distinct and identified a number of potential conservation units, defined with genetic criteria, in both species. We also found allozyme and mtDNA evidence of historic genetic exchange between these 2 allopatric species, apparently involving one population of each species at the geographic edge of the species' ranges, not in the most proximate populations sampled. Our results provide information on species boundaries and offer insight into the likely causes of high genetic diversity in certain populations, results which are already being used to guide national recovery planning and local action. Given the prevalence of incorrect taxonomies and introgression in many organismal groups, we believe these data point to the need to commence genetic investigations of any threatened species from an initially broad taxonomic focus.

Tracking near-surface atmospheric conditions using an infrasound network

Continuous volcanic infrasound signal was recorded on a three-microphone network at Kilauea in July 2008 and inverted for near-surface horizontal winds. Inter-station phase delays, determined by signal cross-correlation, vary by up to 4% and are attributable to variable atmospheric conditions. The results suggest two predominant weather regimes during the study period: (1) 6-9 m/s easterly trade winds and (2) lower-intensity 2-5 m/s mountain breezes from Mauna Loa. The results demonstrate the potential of using infrasound for tracking local averaged meteorological conditions, which has implications for modeling plume dispersal and quantifying gas flux.