Shape variability in topminnows (Fundulus notatus species complex) along the river continuum

We examined intra‐ and interspecific variability in shape of three topminnow species (Funduluidae: Fundulus notatus, F. olivaceus, and F. euryzonus) across ten drainages. Within each drainage, five or more adult male topminnows were digitized at multiple sites (83 total sites) along the river continuum representing a range of stream sizes (cumulative drainage area) and hydrological conditions. Nine of the ten drainages contained two Fundulus species that were longitudinally separated along the river continuum with narrow areas of coexistence. Upstream–downstream distribution patterns were variable by drainage, allowing us to examine patterns repeated across ecologically similar species. More variability in shape was explained by drainage (19.7%) than by species (7.4%) differences. Populations of F. notatus from headwaters (three drainages) converged on a deep‐bodied form similar to F. olivaceus which was typically sampled in headwaters. Fundulus notatus shape was more closely related to stream size than in the other two species. Headwater populations of F. notatus and F. olivaceus had fineness ratios near the hydrodynamic optima of 4.5 whereas downstream populations of F. notatus had shallower bodies. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 612–621.     

Genetic effects of habitat fragmentation and population isolation on Etheostoma raneyi (Percidae)

The use of genetic methods to quantify the effects of anthropogenic habitat fragmentation on population structure has become increasingly common. However, in today’s highly fragmented habitats, researchers have sometimes concluded that populations are currently genetically isolated due to habitat fragmentation without testing the possibility that populations were genetically isolated before European settlement. Etheostoma raneyi is a benthic headwater fish restricted to river drainages in northern Mississippi, USA, that has a suite of adaptive traits that correlate with poor dispersal ability. Aquatic habitat within this area has been extensively modified, primarily by flood-control projects, and populations in headwater streams have possibly become genetically isolated from one another. We used microsatellite markers to quantify genetic structure as well as contemporary and historical gene flow across the range of the species. Results indicated that genetically distinct populations exist in each headwater stream analyzed, current gene flow rates are lower than historical rates, most genetic variation is partitioned among populations, and populations in the Yocona River drainage show lower levels of genetic diversity than populations in the Tallahatchie River drainage and other Etheostoma species. All populations have negative F_IS scores, of which roughly half are significant relative to Hardy–Weinberg expectations, perhaps due to small population sizes. We conclude that anthropogenic habitat alteration and fragmentation has had a profoundly negative impact on the species by isolating E. raneyi within headwater stream reaches. Further research is needed to inform conservation strategies, but populations in the Yocona River drainage are in dire need of management action. Carefully planned human-mediated dispersal and habitat restoration should be explored as management options across the range of the species.     

The effects of age,sex, and habitat on body size and shape of the blackstripe topminnow,Fundulus notatus (Cyprinodontiformes: Fundulidae) (Rafinesque 1820)

Lake and stream habitats pose a variety of challenges to fishes due to differences in variables such as water velocity, habitat structure, prey community, and predator community. These differences can cause divergent selection on body size and/or shape. Here, we measured sex, age, length, and eight different morphological traits of the blackstripe topminnow, Fundulus notatus, from 19 lake and stream populations across four river drainages in central Illinois. Our goal was to determine whether size and shape differed consistently between lake and stream habitats across drainages. We also considered the effects of age and sex as they may affect size and morphology. We found large differences in body size of age 1 topminnows where stream fish were generally larger than lake fish. Body shape mainly varied as a function of sex. Adult male topminnows had larger morphological traits (with the exception of body width) than females, in particular longer dorsal and anal base lengths. Subtle effects of habitat were present. Stream fish had a longer dorsal fin base than lake fish. These phenotypic patterns may be the result of genetic and/or environmental variation. As these lakes are human‐made, the observed differences, if genetic, would have had to occur relatively rapidly (within about 100 years). © 2013 The Linnean Society of London     

Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes

We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch‐based graphical model and then compared within and among three species that co‐occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic‐spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic‐spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most tributary basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross‐basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and in response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage.     

Species invasions and the changing biogeography of Australian freshwater fishes

Aim By dissolving natural physical barriers to movement, human‐mediated species introductions have dramatically reshuffled the present‐day biogeography of freshwater fishes. The present study investigates whether the antiquity of Australia's freshwater ichthyofauna has been altered by the widespread invasion of non‐indigenous fish species. Location Australia. Methods Using fish presence–absence data for historical and present‐day species pools, we quantified changes in faunal similarity among major Australian drainage divisions and among river basins of north‐eastern Australia according to the Sørensen index, and related these changes to major factors of catchment disturbance that significantly alter river processes. Results Human‐mediated fish introductions have increased faunal similarity among primary drainages by an average of 3.0% (from 17.1% to 20.1% similarity). Over three‐quarters of the pairwise changes in drainage similarity were positive, indicating a strong tendency for taxonomic homogenization caused primarily by the widespread introduction of Carassius auratus, Gambusia holbrooki, Oncorhynchus mykiss and Poecilia reticulata. Faunal homogenization was highest in drainages subjected to the greatest degree of disturbance associated with human settlement, infrastructure and change in land use. Scenarios of future species invasions and extinctions indicate the continued homogenization of Australian drainages. In contrast, highly idiosyncratic introductions of species in river basins of north‐eastern Australia have decreased fish faunal similarity by an average of 1.4%. Main conclusions We found that invasive species have significantly changed the present‐day biogeography of fish by homogenizing Australian drainages and differentiating north‐eastern river basins. Decreased faunal similarity at smaller spatial scales is a result of high historical similarity in this region and reflects the dynamic nature of the homogenization process whereby sporadic introductions of new species initially decrease faunal similarity across basins. Our study points to the importance of understanding the role of invasive species in defining patterns of present‐day biogeography and preserving the antiquity of Australia's freshwater biodiversity.     

Phylogeography of Rhinichthys cataractae (Teleostei: Cyprinidae): pre‐glacial colonization across the Continental Divide and Pleistocene diversification within the Rio Grande drainage

The longnose dace, Rhinichthys cataractae, is a primary freshwater fish inhabiting riffle habitats in small headwater rivers and streams across the North American continent, including drainages east and west of the Continental Divide. The mitochondrially encoded cytochrome b gene (1140 bp) and 2298–2346 bp of the nuclear‐encoded genes S7 and RAG1 were obtained from 87 individuals of R. cataractae (collected from 17 sites throughout its range) and from several close relatives. Phylogenetic analyses recovered a monophyletic R. cataractae species‐group that contained Rhinichthys evermanni, Rhinichthys sp. ‘Millicoma dace’, and a non‐exclusive R. cataractae. Within the R. cataractae species‐group, two well‐supported lineages were identified, including a western lineage (containing R. evermanni, R. sp. ‘Millicoma dace’ and individuals of R. cataractae from Pacific slope drainages) and an eastern lineage (containing individuals of R. cataractae from Arctic, Atlantic, and Gulf slope drainages). Within the eastern lineage of R. cataractae, two well‐supported groups were recovered: a south‐eastern group, containing individuals from the Atlantic slope, southern tributaries to the Mississippi River, and the Rio Grande drainage; and a north‐eastern group, containing individuals from the Arctic slope and northern tributaries to the Mississippi River. Estimates of the timing of divergence within the R. cataractae species‐group, combined with ancestral area‐reconstruction methods, indicate a separation between the eastern and western lineages during the Pliocene to early‐Pleistocene, with a direction of colonization from the west of the Continental Divide eastward. Within the southern portion of its range, R. cataractae likely entered the Rio Grande drainage during the Pleistocene via stream capture events between the Arkansas River (Mississippi River drainage) and headwaters of the Rio Grande. A close relationship between populations of R. cataractae in the Rio Grande drainage and the adjacent Canadian River (Mississippi River drainage) is consistent with hypothesized stream capture events between the Pecos (Rio Grande drainage) and Canadian rivers during the late‐Pleistocene. The population of R. cataractae in the lower Rio Grande may have become separated from other populations in the Rio Grande drainage (upper Rio Grande and Pecos River) and Canadian River during the late‐Pleistocene, well before initiation of recent and significant anthropogenic disturbance within the Rio Grande drainage. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 317–333.     

Population genetic structure in the Iberian cyprinid fish Iberochondrostoma lemmingii (Steindachner, 1866): disentangling species fragmentation and colonization processes

Interplay between the complex geography, hydrogeomorphological history, past climatic changes, and anthropogenic pressures is likely responsible for the current diversity and species' distribution of freshwater fishes in the Iberian Peninsula. To further disentangle the evolutionary processes promoting the diversification of endemic Iberian Cyprinids through time and space, we explored the patterns of genetic diversity of the Iberian arched‐mouth nase, Iberochondrostoma lemmingii (Steindachner, 1866), using molecular markers rendering at different timescales: the mitochondrial gene cytochrome b and seven microsatellite loci. Both markers showed significant differentiation of populations though the relative genetic distances among populations were different between markers. Mitochondrial DNA results indicate the isolation of hydrographic basins as the main driver of population differentiation, with Tejo as the centre of diversification. The results also support connections between Tejo, Guadiana, and Guadalquivir, with levels of divergence suggesting an earlier severance of Guadalquivir, whereas Guadiana and Tejo maintained connections until a more recent past. Establishment of more peripherial populations in small southern basins (Quarteira and Almargem) could have been ruled by founder events. However, the analysis of present‐day genetic configuration suggested by microsatellite data implies, for the first time, the involvement of other factors in the evolution of arched‐mouth Iberian nase populations. Relative low genetic distances between inter‐basin populations (Tejo and Guadiana) and the lack of concordance between differentiation and geography suggest a possible influence of human‐mediated translocations in the population genetic patterns of I. lemmingii. High intra‐basin differentiation levels were found within Tejo and Guadiana and may be associated with factors intrinsic to the species (e.g. low dispersal capability) or natural and/or artificial barriers to gene flow. The low vagility of the species appears to be an important factor influencing the evolutionary processes shaping the phylogeographical patterns of I. lemmingii, which could be relevant for the conservation of this threatened species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 559–572.     

Testing the ‘Pleistocene species pump’ in alpine habitats: lineage diversification of flightless ground beetles (Coleoptera: Carabidae: Nebria) in relation to altitudinal zonation

Alpine species often have similar demographic responses to Pleistocene climate changes, but exhibit different spatial patterns of genetic diversity. Using a comparative phylogeographical approach, we examined the factors influencing lineage formation in three alpine carabid beetles of the genus Nebria Latreille inhabiting the California Sierra Nevada. These flightless beetles differ in altitudinal zonation and habitat preferences, but overlap spatially, have limited dispersal capacities and share life history characteristics. Species distribution modelling predicted decreasing population connectivity in relation to increasing altitudinal preferences. Diversity patterns at the cytochrome oxidase subunit I gene revealed north–south genetic structure and recent population growth in all three species. The high‐elevation‐restricted species, Nebria ingens Horn, exhibited a deep phylogeographical split, morphological divergence and evidence of limited, unidirectional gene flow towards the south. This was supported by additional data from three nuclear genes and isolation with migration analysis. Nebria spatulata Van Dyke, inhabiting an intermediate altitudinal range, exhibited fixed morphological differences between northern and southern populations, but showed limited structure. The broadly distributed Nebria ovipennis LeConte showed less structure and lacked morphological variation. Diversification of these Nebria species supports the role of altitudinal zonation in lineage formation and is consistent with the Pleistocene species pump model. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Phylogeography of a pearl oyster (Pinctada maxima) across the Indo‐Australian Archipelago: evidence of strong regional structure and population expansions but no phylogenetic breaks

This study investigates the genetic structure and phylogeography of a broadcast spawning bivalve mollusc, Pinctada maxima, throughout the Indo‐West Pacific and northern Australia. DNA sequence variation of the mitochondrial cytochrome oxidase subunit I (COI) gene was analysed in 367 individuals sampled from nine populations across the Indo‐West Pacific. Hierarchical AMOVA indicated strong genetic structuring amongst populations (Φ_ST = 0.372, P < 0.001); however, sequence divergence between the 47 haplotypes detected was low (maximum 1.8% difference) and no deep phylogenetic divergence was observed. Results suggest the presence of genetic barriers isolating populations of the South China Sea and central Indonesian regions, which, in turn, show patterns of historical separation from northern Australian regions. In P. maxima, historical vicariance during Pleistocene low sea levels is likely to have restricted planktonic larval transport, causing genetic differentiation amongst populations. However, low genetic differentiation is observed where strong ocean currents are present and is most likely due to contemporary larval transport along these pathways. Geographical association with haplotype distributions may indicate signs of early lineage sorting arising from historical population separations, yet an absence of divergent phylogenetic clades related to geography could be the consequence of periodic pulses of high genetic exchange. We compare our results with previous microsatellite DNA analysis of these P. maxima populations, and discuss implications for future conservation management of this species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 632–646.     

The influence of salinity and prey salt content on growth and intestinal Na+/K+-ATPase activity of juvenile bluegill,Lepomis macrochirus

Synopsis Juvenile bluegill,Lepomis macrochirus, collected from Mississippi coastal drainages were held at 0, 5, and 10% S and fed diets containing 0, 2, and 4% dietary NaCl. Over a 58 day period, fish from each of the nine treatments (salinity x diet) were fed ad libitum twice daily for 5 min. Mean treatment growth rates did not differ when adjusted for initial wet weights. Hematocrit and intestinal Na⁺/K⁺-ATPase activity also did not differ. All fish maintained in 0% S had a marginally lower plasma osmolality compared to fish held in 5 and 10% S. Plasma Cl concentration of fish held in 0% S receiving the 0% NaCl diet was lower than that of the other eight treatments. Results indicate that coastal juvenile bluegill can exploit waters up to 10% S while consuming prey items containing up to 4% NaCl with no influence on growth or certain osmoregulatory characteristics.     

Disentangling the divergence and cladogenesis in the freshwater crab species (Potamonautidae: Potamonautes perlatus sensu lato) in the Cape Fold Mountains,South Africa,with the description of two novel cryptic lineages

River networks of major drainages can form barriers that shape the phylogeography of freshwater organisms, particularly those with low dispersal capabilities. Freshwater crab species' distributions can be used to examine hydrological patterns to expose historical drainage interconnectivity. We used molecular sequence data (mitochondrial and nuclear DNA) and divergence time estimations to determine the phylogeography of the freshwater crab, Potamonautes perlatus sensu lato, from six drainage systems along the Cape Fold Mountains, South Africa. Two major clades were detected: clade 1 comprised two geographically discrete haploclades occurring in southern flowing drainages, whereas clade 2 included specimens from western flowing drainages. Divergence time estimations suggested a Pleistocene (c. 2.61 Mya) divergence of P. perlatus s.l. The Pleistocene was associated with arid conditions and drainage contractions. However, it is likely that during the mesic conditions of the Pleistocene, P. perlatus s.l. migrated and diverged into contemporary patterns. We conclude that three lineages are nested within P. perlatus s.l., two representing novel species. Potamonautes perlatus sensu stricto is confined to western flowing drainages. The two novel species both occurring in southern flowing drainages are described here: P otamonautes barbarai sp. nov. occurs in the Gamtoos and Gourits Rivers and P otamonautes barnardi sp. nov. in the Breede River. © 2014 The Linnean Society of London     

Tracing the origins of widespread highland species: a case of Neogene diversification across the Mexican sierras in an endemic lizard

The evolutionary history of the Mexican sierras has been shaped by various geological and climatic events over the past several million years. The relative impacts of these historical events on diversification in highland taxa, however, remain largely uncertain owing to a paucity of studies on broadly‐distributed montane species. We investigated the origins of genetic diversification in widely‐distributed endemic alligator lizards in the genus Barisia to help develop a better understanding of the complex processes structuring biological diversity in the Mexican highlands. We estimated lineage divergence dates and the diversification rate from mitochondrial DNA sequences, and combined divergence dates with reconstructions of ancestral geographical ranges to track lineage diversification across geography through time. Based on our results, we inferred ten geographically structured, well supported mitochondrial lineages within Barisia. Diversification of a widely‐distributed ancestor appears tied to the formation of the Trans‐Mexican Volcanic Belt across central Mexico during the Miocene and Pliocene. The formation of filter barriers such as major river drainages may have later subdivided lineages. The results of the present study provide additional support for the increasing number of studies that suggest Neogene events heavily impacted genetic diversification in widespread montane taxa. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 382–394.     

Hierarchical analysis of genetic structure in the habitat‐specialist Eastern Sand Darter (Ammocrypta pellucida)

Quantifying spatial genetic structure can reveal the relative influences of contemporary and historic factors underlying localized and regional patterns of genetic diversity and gene flow – important considerations for the development of effective conservation efforts. Using 10 polymorphic microsatellite loci, we characterize genetic variation among populations across the range of the Eastern Sand Darter (Ammocrypta pellucida), a small riverine percid that is highly dependent on sandy substrate microhabitats. We tested for fine scale, regional, and historic patterns of genetic structure. As expected, significant differentiation was detected among rivers within drainages and among drainages. At finer scales, an unexpected lack of within‐river genetic structure among fragmented sandy microhabitats suggests that stratified dispersal resulting from unstable sand bar habitat degradation (natural and anthropogenic) may preclude substantial genetic differentiation within rivers. Among‐drainage genetic structure indicates that postglacial (14 kya) drainage connectivity continues to influence contemporary genetic structure among Eastern Sand Darter populations in southern Ontario. These results provide an unexpected contrast to other benthic riverine fish in the Great Lakes drainage and suggest that habitat‐specific fishes, such as the Eastern Sand Darter, can evolve dispersal strategies that overcome fragmented and temporally unstable habitats.     

Hyporheic macroinvertebrates in riffle and pool areas of temporary streams in south eastern Australia

Archived data from a long-term (1973–1988) monitoring study were used to assess the impacts of kraft mill effluents (KME) on fish community dynamics in Elevenmile Creek, a small blackwater stream located in Cantonment, Florida, compared to a neighboring stream, Black Creek, that did not receive KME. The fish community in Elevenmile Creek was generally lower in species richness and diversity than the reference stream. The exception was the mill outfall site, which had similar species richness and diversity to the reference stream. Neither species richness nor diversity changed substantially during the survey period in either stream. Throughout the survey, Elevenmile Creek was numerically dominated by bluegill, Lepomis macrochirus, and eastern mosquitofish, Gambusia affinis. Black Creek had greater abundances of minnows, suckers, and darters. Time series analysis of L. macrochirus for Elevenmile Creek showed that this species was more abundant during winter than summer, but no overall long-term trend was found. Although data used in this study may not be representative of the fish community in Elevenmile Creek as it exists today, results suggest that Elevenmile Creek was highly disturbed during the survey and that species diversity did not increase following mill treatment upgrades.     

The effects of ultraviolet radiation on a freshwater prey fish: physiological stress response,club cell investment,and alarm cue production

Recent anthropogenic activities have caused deleterious effects to the stratospheric ozone layer, resulting in a global increase in the level of ultraviolet radiation (UVR). Understanding the way that organisms respond to such stressors is key to predicting the effects of anthropogenic activities on aquatic ecosystems and the species that inhabit them. The epidermal layer of the skin of fishes is not keratinized and acts as the primary interface between the fish and its environment. The skin of many species of fishes contains large epidermal club cells (ECCs) that are known to release chemicals (alarm cues) serving to warn other fishes of danger. However, the alarm role of the cells is likely secondary to their role in the immune system. Recent research suggests that ECCs in the epidermis may play a role in protecting the fish from damage caused by UVR. In the present study, we examined the effects of in vivo exposure to UVR on fathead minnows (Pimephales promelas), specifically investigating ECC investment, physiological stress responses, and alarm cue production. We found that fish exposed to UVR showed an increase in cortisol levels and a substantive decrease in ECC investment compared to non‐exposed controls. Unexpectedly, our subsequent analysis of the behavioural response of fish to alarm cues revealed no difference in the potency of the cues prepared from the skin of UV‐exposed or non‐exposed minnows. Our results indicate that, although nonlethal, UVR exposure may lead to secondary mortality by altering the fish immune system, although this same exposure may have little influence on chemically‐mediated predator–prey interactions. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 832–841.     

Life‐history variability of non‐native centrarchids in regulated river systems of the lower River Guadiana drainage (south‐west Iberian Peninsula)

Life‐history variability of two non‐native centrarchids, pumpkinseed Lepomis gibbosus and largemouth bass Micropterus salmoides, was evaluated in three stream stretches of the lower River Guadiana drainage (south‐west Iberian Peninsula) with different degrees of regulated flows. Abundance, condition and population structure differed among populations for both species, but invasion success was lower in the least regulated river. Lepomis gibbosus were abundant and had multiple age classes in the three river sites, whereas M. salmoides were less abundant and mainly represented by young‐of‐the‐year fish. Juvenile growth in L. gibbosus was similar in all three populations, though longevity was slightly greater in the population from the River Guadiana mainstream. Lepomis gibbosus exhibited a long reproductive season, but the duration of season, size at maturity and reproductive effort varied among populations. The life‐history differences found demonstrate the importance of species adaptation to local conditions which might favour their invasion success. Lepomis gibbosus were more adaptable and resilient to local conditions, whereas M. salmoides seemed dependent on reservoirs and large rivers for maintenance of riverine populations.     

Patterns of gene flow and source‐sink dynamics in high altitude populations of the common toad Bufo bufo (Anura: Bufonidae)

Understanding patterns of genetic structure is fundamental for developing successful management programmes for deme‐structured organisms, such as amphibians. We used five microsatellite loci and DNA sequences of the mitochondrial control region to assess the relative influences of landscape (geographic distance, altitude and rivers as corridors for dispersal) and historical factors on patterns of gene flow in populations of the toad Bufo bufo in Central Spain. We sampled 175 individuals from eight populations distributed along two major river drainages and used maximum‐likelihood and Bayesian approaches to infer patterns of gene flow and population structure. The mitochondrial DNA data show closely‐related haplotypes distributed across the Iberian Peninsula with no geographic structuring, suggesting recent differentiation of haplotypes and extensive gene flow between populations. On the other hand, microsatellites provide finer resolution, showing that high altitude populations (> 2000 m) exchange lower numbers of migrants with other populations. The results of Bayesian estimates for recent migration rates in high altitude populations suggest source‐sink dynamics between ponds that are consistent with independent data from monitoring over the past 20 years. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 824–839.     

Molecular zoogeography of freshwater fishes in the southeastern United States

Restriction fragment length polymorphisms in mitochondrial DNA (mtDNA) were used to reconstruct evolutionary relationships of conspecific populations in four species of freshwater fish—Amia calva, Lepomis punctatus, L. gulosus, and L. microlophus. A suite of 14-17 endonucleases was employed to assay mtDNAs from 305 specimens collected from 14 river drainages extending from South Carolina to Louisiana. Extensive mtDNA polymorphism was observed within each assayed species. In both phenograms and Wagner parsimony networks, mtDNA clones that were closely related genetically were usually geographically contiguous. Within each species, major mtDNA phylogenetic breaks also distinguished populations from separate geographic regions, demonstrating that dispersal and gene flow have not been sufficient to override geographic influences on population subdivision.—Importantly, there were strong patterns of congruence across species in the geographic placements of the mtDNA phylogenetic breaks. Three major boundary regions were characterized by concentrations of phylogenetic discontinuities, and these zones agree well with previously described zoogeographic boundaries identified by a different kind of data base—distributional limits of species—suggesting that a common set of historical factors may account for both phenomena. Repeated episodes of eustatic sea level change along a relatively static continental morphology are the likely causes of several patterns of drainage isolation and coalescence, and these are discussed in relation to the genetic data.—Overall, results exemplify the positive role that intraspecific genetic analyses may play in historical zoogeographic reconstruction. They also point out the potential inadequacies of any interpretations of population genetic structure that fail to consider the influences of history in shaping that structure.     

Do freshwater ecoregions and continental shelf width predict patterns of historical gene flow in the freshwater fish Poecilia butleri?

We examined historical patterns of gene flow in the freshwater fish Poecilia butleri in western Mexico. We tested the hypothesis that the boundaries between four freshwater ecological communities (ecoregions) might have limited the movement of P. butleri because changes in species compositions might restrict establishment between adjacent ecoregions, even in situations where a physical barrier is absent. Hence, we predicted that boundaries between ecoregions should correspond to phylogeographical breaks in P. butleri. We also tested the hypothesis that the width of the continental shelf affected historical gene flow in P. butleri because a broad continental shelf provides a greater opportunity for rivers to coalesce during historical episodes of low sea levels as opposed to a narrow continental shelf that should restrict the potential for gene flow among adjacent rivers. Hence, we predicted greater amounts of historical gene flow among neighbouring river basins in the region of western Mexico where the continental shelf is wider, whereas, in the region where the continental shelf is narrower, we expected to detect limited levels of historical gene flow. We analyzed mitochondrial DNA sequence data (cytochrome b) taken from 264 individuals of P. butleri collected from 34 locations distributed across four different ecoregions in western Mexico. To examine patterns of phylogenetic diversification and historical gene flow in P. butleri, we employed several analytical approaches, including traditional tree‐based phylogenetic analyses (likelihood and parsimony), haplotype network reconstruction, analyses of molecular variance, and spatial analysis of molecular variance. We found genetic breaks coinciding with two out of three different ecoregion boundaries, suggesting limited historical gene flow. In addition to different species compositions between these adjacent ecoregions, geological features such as the Trans‐Mexican Volcanic Belt and the mountainous topography in south‐western Mexico, likely contributed to these observed genetic breaks. By contrast, no genetic break was evident between two other ecoregions, a result that partially rejects our first hypothesis. Several results were consistent with our second hypothesis. Changes in the width of the continental shelf in western Mexico are associated with the observed patterns of historical gene flow. Our results indicate that the interactions among multiple geological and biological factors affect the spatial patterns of genetic diversity of widespread freshwater species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 399–416.     

Genetic structure of a native cyprinid in a reservoir‐altered stream network

1. Reservoirs modify riverine ecosystems worldwide, and often with deleterious impacts on native biota. The immediate effects of reservoirs on native fish species below dams and in impounded reaches have received considerable attention, but it is unclear how reservoirs may affect fish species at larger spatial and temporal scales. Documented declines of stream fish populations in direct tributaries of reservoirs suggest reservoir pools may reduce gene flow among historically connected populations. 2. Because of increased predator densities in reservoirs and the extent of habitat alteration in impounded reaches, I predicted reservoir habitats would reduce gene flow among small‐bodied fish populations separated by reservoir habitat. I used microsatellite markers to assess the spatial genetic structure of populations of the red shiner (Cyprinella lutrensis), in a reservoir‐fragmented stream network (Lake Texoma, U.S.A.). I also tested the prediction that populations in two direct tributaries that have experienced population declines would have low genetic diversity. Individuals were collected from six sites upstream of the reservoir, three sites in the reservoir and three sites in direct tributaries of the reservoir during 2008 and 2009. 3. Results indicate that most populations were isolated by distance with little divergence among populations. In one direct tributary population, however, there was substantial genetic divergence, and genetic diversity was significantly lower than in other populations. Gene flow also seemed to be lower in reservoir habitats than in intact stream habitats, suggesting reservoir habitats may be reducing gene flow among the reservoir‐separated populations. These results indicate that reservoirs may reduce gene flow among reservoir‐fragmented stream fish populations, altering the evolutionary trajectories of fragmented populations.