Spatial genetic variation and habitat association of <Emphasis Type="Italic">Rhinichthys cataractae</Emphasis>, the longnose dace,in the Driftless Area of the upper Mississippi River basin

The Driftless Area of the upper Mississippi River drainage is a unique geographic region because of its complex geological history and the influence of recent, intensive human activities. The longnose dace, Rhinichthys cataractae, is a relatively common, small freshwater fish that is distributed in swift, cool streams within the region. The aim of this study was to determine the spatial genetic differentiation of the longnose dace and define the broad scale environmental variables that shape the distribution of the species in the southwestern portion of the Driftless Area. Genotypic data from seven microsatellite loci were analyzed for 276 individuals from 15 localities representing major drainages within the region in northeast Iowa. Broad scale environmental variables including hydrologic, soil, and climatic factors were evaluated to construct an ecological niche model (ENM) to predict the suitability of habitat for the species within the region. Results of the genetic analyses revealed two distinct, but somewhat admixed genetic clusters of longnose dace in Iowa. The genetic differentiation between localities and between drainages was low to moderate with some evidence of isolation by distance. Most of the variation was observed by differences between individuals within local populations. The ENM generated largely reflected the known distribution of the species in Iowa with a decreasing probability of suitable habitat from northern to southern drainages. Geologic factors played a key role in the model. The distribution and population structure of the longnose dace in the northeast Iowa revealed that isolation by distance, historical processes and the underlying geology are primarily responsible for the observed spatial distribution of genetic variation.     

Morphological and genetic analysis of sympatric dace within the Rhinichthys cataractae species complex: a case of isolation lost

The Nooksack dace (Pisces: an undescribed putative taxon within Rhinichthys) and longnose dace (Rhinichthys cataractae) are two forms within the R. cataractae species complex that are distinguishable from one another by mitochondrial (mt) DNA divergence of 2–3%, as well as by subtle morphological differences. The two forms are found in allopatry in south‐eastern British Columbia (BC), Canada, and adjacent areas of western Washington, USA, and are sympatric in three streams in the lower Fraser River valley, BC, and may represent cryptic species. We assayed 12 morphometric traits and two meristic characters (N = 582; 23 sampling locations) to test for diagnosability of the two dace, as well as to test for morphological differentiation by mtDNA type in sympatry. We then employed a 10‐locus microsatellite DNA assay (N = 374; 12 sampling locations) to test for genetic distinction between Nooksack dace and longnose dace in sympatry. We found that the two dace could not be reliably differentiated morphologically: there was overlap in all characters measured, and sampling location had a much larger effect on morphology than mtDNA group. Microsatellite analysis showed no distinction by mtDNA type in localities with sympatric dace, indicating complete admixture between the sympatric Nooksack dace and longnose dace. The Nooksack dace and longnose dace provide an example of ‘ephemeral speciation’: two lineages that, despite an estimated 1.1 Myr of isolation, have developed no apparent barriers to reproduction and appear to have collapsed into a single interbreeding population where they come into secondary contact. Nonetheless, the zone of secondary contact and the diagnosability of the Nooksack dace in terms of mtDNA represent significant aspects of the evolutionary legacy within R. cataractae and support its conservation importance.     

The Functional Gene Diversity in Natural Populations over Postglacial Areas: The Shaping Mechanisms Behind Genetic Composition of Longnose Dace (Rhinichthys cataractae) in Northeastern North America

The diversity of functional genes and the related processes are important issues for conservation biology. This is especially relevant for populations that have suffered from demographic reduction as a consequence of the processes of postglacial colonization. In this perspective, the aims of the present study are (1) to quantify the genetic diversity of functional genes and (2) to disentangle the long- and short-term effects of natural selection that shapes genetic diversity from those of drift, mutation, and allopatric fragmentation. This research was conducted using an extensive genetic polymorphism analysis of populations of longnose dace (Rhinichthys cataractae) living over an area once covered by Pleistocene glaciations. The sequence and diversity of one exon of three genes (MHC IIβ, growth hormone, and trypsin) were jointly analyzed with non-coding nuclear loci from 27 populations; these populations were sampled over four major basins of northeastern North America. The survey revealed a surprisingly low allelic richness, especially for the MHC gene, considering the number of individuals and populations sampled. The results suggest that there is a complex mixture of different evolutionary processes shaping the level of polymorphism among longnose dace. While our study underlines the importance of the short-term effects of neutral processes and the major impact of post-glacial colonization on gene diversity, locally dependent balancing selection was detected on MHC. From this perspective, our results support an understanding of the importance of drift on functional gene diversity but also highlight the transient effects of natural selection on allelic composition, even in populations that show drastic reduction of genetic diversity.     

Multi-scale effects of resource patchiness on foraging behaviour and habitat use by longnose dace, Rhinichthys cataractae

1. We examined the response of a predatory benthic fish, the longnose dace ( Rhinichthys cataractae ), to patchiness in the distribution of benthic macroinvertebrates on cobbles at three hierarchical spatial scales during summer and autumn 1996, and spring 1997 in a southern Appalachian stream. 2. At the primary scale (four to five individual cobbles separated by <1 m), the intensity of foraging was not correlated with the biomass of benthic macroinvertebrates/cobble, regardless of season. 3. At the secondary scale (i.e. foraging patches <5 m in diameter) we found that benthic macroinvertebrates were patchily distributed in summer, but not in autumn or spring. Concomitantly, in summer, longnose dace foraged on cobbles with a significantly higher biomass of benthic macronvertebrates than nearby, randomly selected cobbles with similar physical conditions (i.e. longnose dace tended to avoid low-prey foraging patches). In contrast, when benthic macroinvertebrates were distributed homogeneously (spring and autumn), dace did not select patches with a significantly higher biomass of benthic macroinvertebrates than that available on randomly selected cobbles. 4. At the tertiary scale (i.e. stream reaches 11–19 m long), the biomass of benthic macroinvertebrates (per cobble per reach) was patchily distributed (i.e. differed significantly among reaches) in all seasons. Among reaches with physical characteristics preferred by longnose dace, (i.e. erosional reaches dominated by cobble/boulder substratum and high current velocity), we detected a significant, positive correlation between the biomass of benthic macroinvertebrates/cobble and longnose dace density in all seasons. 5. Our results demonstrated that both spatial and temporal patchiness in resource availability influenced significantly the use of both foraging patches and stream reaches by longnose dace.     

Populational structure of three fish species (Cypriniformes: Cyprinidae) living in rivers of the Ob-Irtysh basin,by the data of isoenzyme analysis

Data are presented on genetic subdivision of populations of roach Rutilus rutilus lacustris, ide Leuciscus idus, and dace L. leuciscus baicalensis living in rivers of West Siberia. These fish species have comparable levels of variation of allozyme loci and similar populational structure which well agrees with geography of the river network of the Ob-Irtysh basin. The populational differentiation is more expressed in ide than in roach and dace.     

The spring development of phytoplankton in Lake Erken: species composition,biomass, primary production and nutrient conditions — a review

Relative abundance and within-lake distributions of three fishes, northern redbelly dace (Phoxinus eos), finescale dace (Phoxinus neogaeus), and central mudminnow (Umbra limi), were examined using minnow traps in Tuesday Lake, a small bog lake in the Upper Peninsula, Michigan. For these species, catches in minnow traps placed at the perimeter of the lake were 21 to 52 times higher than catches in midlake traps. Variance: mean ratios of perimeter trap catches indicated that both dace species were highly aggregated while the distribution of mudminnows was less aggregated or random. Over an 11 day period during which all fish caught were removed from the lake, catch per unit effort (CPUE) of both dace species declined in response to fish removal. In contrast, CPUE for mudminnows was low initially, increased to an asymptote and then declined only in the last 5 days of the fish removal. The patterns of CPUE for mudminnows indicated that mudminnow trapability and/or activity was reduced in the presence of high densities of dace. The low abundance of dace in traps with many mudminnows suggested mudminnows avoided traps already containing dace. Throughout the removal period, CPUE provided an accurate index of dace abundance, whereas this was true for mudmnnows only after dace populations had been reduced drastically. Therefore, in any use of minnow traps to estimate populations, both spatial distributions and relative species abundance of small fishes must be taken into account.     

Isolation and characterization of simple sequence repeat loci in Rubus hochstetterorum and their use in other species from the Rosaceae family

The identification of microsatellite loci in Rubus hochstetterorum provides an important tool for the characterization and conservation of wild populations of this species. Cross‐species amplification of markers may be of particular interest for the study of other Rubus species. In this study, 41 simple sequence repeat markers were identified in a genomic library of R. hochstetterorum. Fifteen of the identified microsatellite loci were characterized in a set of 30 samples and revealed to be polymorphic with three to 19 alleles per locus. All the identified markers allowed cross‐species amplification in at least one of the other three tested species from the Rosaceae family.     

Evaluating the genetic status of a Great Basin endemic minnow: the relict dace (<Emphasis Type="Italic">Relictus solitarius</Emphasis>)

The relict dace (Relictus solitarius) is an endemic minnow restricted to isolated spring systems within Butte, Goshute, Ruby and Steptoe valleys in the eastern Nevada portion of the Great Basin. It is the only native fish in these basins, but speckled dace (Rhinichthys osculus) have been introduced into some localities in Ruby Valley and, based on morphology, the two species are believed to have hybridized in those areas. We used DNA sequence data from one mitochondrial gene (cytochrome b) and one nuclear intron (S7) to determine if putative relict dace populations in Ruby Valley share mtDNA haplotypes with speckled dace, or show signs of hybridization. Results of our analyses show that 11 of 16 Ruby Valley populations sampled contain only speckled dace, and one speckled dace population exhibited signs of limited introgressive hybridization. The remaining five Ruby Valley populations that were sampled contain relict dace that remain genetically distinct from speckled dace. The integrity of the Ruby Valley relict dace populations should be actively protected, particularly in the area surrounding Ruby Lake where speckled dace have been widely introduced.     

Genetic Divergence of Far-Eastern Dace Species Belonging to the Genus Tribolodon (Pisces, Cyprinidae) and Closely Related Taxa

Based on a biochemical–genetic approach, heterozygosity and divergence of structural genes at 30 enzyme loci were analyzed in six dace species. In addition, intra- and interspecific divergence of gene expression was analyzed based on a sample of 12 to 15 loci. Mean heterozygosities per individual varied as follows: Tribolodon species, H _obs = 0.007 ± 0.007 and H _exp = 0.007 ± 0.007; T. ezoe, H _obs = 0.045 ± 0.016 and H _exp = 0.067 ± 0.029. Several variants of genetic distances were estimated. Standard Nei's distances (D _N) varied from 0.145 to 0.284 in four dace species studied. As related to Tribolodon dace species, the following genetic distances were obtained for two members of other genera:Pseudaspius leptocephalus, D _N = 0.269; Leuciscus waleckii, D _N = 0.769. Based on the distance matrices, different clustering algorithms were realized. The main feature shared by different dendrograms was a separate position of the cluster joining Far-Eastern dace species, to whichP. leptocephalus and L. waleckii are successively added. Among the species studied, the proportion of loci similar by expression (E) varied from 87 to 100%. The greatest difference was found between landlocked and landlocked ecotypes of T. hakonensis, E = 67%. The following conclusions can be made: (1) Four studied species of the genus Tribolodon are rather well genetically differentiated. Diagnostic loci are available. (2) A nominal dace species, T. species, should be considered the fourth unambigous species of this genus, which is confirmed by its recent zoological acceptance of this species. (3) The origin and divergence of dace species belonging to the genus Tribolodon are relatively late (1 to 3 Myr ago) historical events. (4) Taxonomically, the genus Tribolodon belong to the tribe Pseudaspinini together with P. leptocephalus, which is confirmed by genetic data. (5) Data on heterozygosity and the divergence of structural and regulatory elements of genome, along with the proposed scheme of speciation types, suggest the following speciation modes for the species studied: for four species, adaptive divergence and for two species, genetic transformation.     

Behavior and Physiology of the Redside Dace, Clinostomus elongatus, a Threatened Species in Michigan

The threatened status of redside dace, Clinostomus elongatus, in Michigan inhibits study and management of remnant populations of the species. We present a phenotypic approach to evaluate the use of redside dace from New York as behavioral and physiological models for Michigan populations. We evaluated behavioral similarity by comparing patterns of microhabitat use and physiological similarity by comparing resting routine metabolic rates measured in the field. Variation between sites in available microhabitat made direct comparisons difficult; however, redside dace in Michigan and New York showed a common preference for mid-water positions in the deepest parts of pools under overhanging structure. Field measurements at 10°C showed that Michigan fish had higher metabolic rates than rates predicted for New York fish at the same temperature, though biological significance of this difference is questionable. In laboratory experiments, we measured metabolic rate and upper thermal tolerance in relation to acclimation temperatures of 6–20°C using redside dace collected from four streams in New York. Redside dace showed a significant increase in metabolic rate as acclimation temperature increased (Q₁₀=2.3). Critical thermal maxima (CTM) of New York redside dace also increased with acclimation temperature. Obstacles related to the transferability of habitat use data and variation in physiology due to uncontrolled and unmeasured environmental factors in the field lead us to urge caution when extrapolating behavioral and physiological characteristics between widely-separated populations of a species. Despite these obstacles, we described useful patterns of microhabitat use and provided estimates of physiological tolerances that will assist resource managers in the recovery of Michigan redside dace.     

Polymorphic microsatellite loci in the sponge Crambe crambe (Porifera: Poecilosclerida) and their variation in two distant populations

Seven polymorphic microsatellite loci were characterized in the marine encrusting sponge Crambe crambe from a partial genomic DNA‐enriched library. Preliminary data on allelic variation of these loci in two distant populations of C. crambe are presented to assess their potential utility as high‐resolution genetic markers for this species. The number of alleles per locus ranged between three and 16 and the distributions of allele frequencies differed considerably between the two populations, indicating a marked genetic differentiation between them. These are the first microsatellite loci reported from any species in the phylum.     

Host-parasite relationships of longnose dace, Rhinichthys cataractae, from the Ford River, Michigan.

A total of 1,115 longnose dace, Rhinichthys cataractae (family Cyprinidae), were examined for parasites from May 1983 through October 1986 from 3 localities in the Ford River in Michigan's Upper Peninsula. Thirteen parasite species (1 Monogenea, 2 Digenea, 2 Cestoda, 4 Nematoda, 1 Acanthocephala, 3 Protozoa) infected dace. The parasite faunas of dace, taxonomically and in species number, were similar between localities. Posthodiplostomum minimum minimum, Neascus sp., and Rhabdochona canadensis were the most common helminths infecting dace from each locality. The first 2 species did not exhibit consistent seasonal infection patterns between years, whereas the prevalence and mean intensity of R. canadensis in dace from the downriver locality were higher in summer 1983, 1984, and 1985. The intensity of infection of each of these helminth species significantly increased with host length. The prevalences and mean intensities of P. m. minimum, Neascus sp., and R. canadensis as well as the helminth infracommunity diversity were highest in dace from the upriver locality. The major factors that influenced parasite intensity were environmental factors that occurred when and where a fish began its life, the sequence of events that occurred in each habitat the fish encountered during its life, and the length of exposure (age of fish). Dace have isolationist helminth infracommunities arising from factors including ectothermy, a simple enteric system, restricted vagility, and being gape-limited. Allogenic helminths with indirect life cycles predominate in the depauperate helminth fauna of dace.     

Genetic divergence of Far Eastern dace species belonging to the genus Tribolodon (Pisces,Cyprinidae) and closely related taxa

Based on a biochemical-genetic approach, heterozygosity and divergence of structural genes of 30 enzyme loci were analyzed in six dace species. In addition, intra- and interspecific divergence of gene expression was analyzed based on a sample of 12 to 15 loci. Mean heterozygosities per individual varied as follows: Tribolodon species, Hobs = 0.007 +/- 0.007 and Hexp = 0.007 +/- 0.007; T. ezoe, Hobs = 0.045 +/- 0.016 and Hexp = 0.067 +/- 0.029. Several variants of genetic distances were estimated. Standard Nei's distances (DN) varied from 0.145 to 0.284 in four dace species studied. As related to Tribolodon dace species, the following genetic distances were obtained for two members of other genera: Pseudaspius leptocephalus, DN = 0.269; Leuciscus waleckii, DN = 0.769. Based on the distance matrices, different clustering algorithms were realized. The main feature shared by different dendrograms was a separate position of the cluster joining Far-Eastern dace species, to which P. leptocephalus and L. waleckii are successively added. Among the species studied, the proportion of loci similar by expression (E) varied from 87 to 100%. The greatest difference was found between anadromous and nonanadromous ecotypes of T. hakonensis, E = 67%. The following conclusions can be made: (1) Four studied species of the genus Tribolodon are rather well genetically differentiated. Diagnostic loci are available. (2) A nominal dace species, T. species, should be considered the fourth isolated species of this genus, which is confirmed by its recent zoological acceptance of this species. (3) The origin and divergence of dace species belonging to the genus Tribolodon are relatively late (1 to 3 Myr ago) historical events. (4) Taxonomically, the genus Tribolodon belong to the tribe Pseudaspinini together with P. leptocephalus, which is confirmed by genetic data. (5) Data on heterozygosity and the divergence of structural and regulatory elements of genome, along with the proposed scheme of speciation types, suggest the following speciation modes for the species studied: for four species, adaptive divergence and for two species, genetic transformation.     

Isolation and characterization of microsatellites in the woody shrub,Calothamnus quadrifidus (Myrtaceae)

Microsatellite loci were developed for genetic analysis of the bird pollinated woody shrub Calothamnus quadrifidus. A genomic library was constructed and screened with dinucleotide and trinucleotide repeat sequences. Ten dinucleotide microsatellite markers were developed, and polymorphism in a population of C. quadrifidus was investigated for six of these markers, which showed an average of 12.7 alleles per locus. Mendelian inheritance of the loci was confirmed through analysis of open pollinated progeny arrays of 10 plants. These loci will be used to study gene flow patterns between isolated populations of this species in southwest Western Australia.     

Isolation and characterization of highly polymorphic microsatellite markers in Hypochaeris radicata (Asteraceae)

We developed five highly polymorphic dinucleotide microsatellite loci for the grassland species Hypochaeris radicata (Asteraceae). Polymorphism of these markers was examined in six populations in the Netherlands. All loci were polymorphic in all populations. The number of alleles per locus varied between 18 and 43. Expected heterozygosity was between 0.86 and 0.91. Cross‐species amplification was tested in six Hypochaeris species and was successful for three different loci in four species. These microsatellites are a useful tool in population genetic, dispersal and metapopulation studies or in testing levels of inbreeding.     

Isolation and characterization of polymorphic microsatellite loci for the dace complex: Leuciscus leuciscus (Teleostei: Cyprinidae)

Ten novel polymorphic microsatellites were isolated from the dace complex (Leuciscus leuciscus), which is a European cyprinid species. Four multiplex polymerase chain reaction sets were optimized in order to genotype 26 polymorphic loci in all, including 16 previously published cyprinid-specific loci. The level of genetic diversity was assessed in 142 dace individuals. We also successfully applied 26 of the microsatellites to 10 related species. These primers thus will be useful to assess population structure of the dace and other cyprinid species, with application for conservation issues and phylogeographical approaches.     

Microsatellites for use in Nothofagus cunninghamii (Nothofagaceae) and related species

Nothofagus cunninghamii (myrtle) has a widespread distribution through the temperate rainforest of southeastern Australia with some disjunct populations existing in putative glacial refugia. Polymorphic nuclear markers are required to resolve the biogeographical history of the species and will also be useful for conservation and forestry applications in this and other species of Nothofagus. Fourteen polymorphic microsatellite loci were isolated from N. cunninghamii, with four to 10 alleles amplified in 15 individuals tested. Transferability to other species of Nothofagus was successful, with six loci transferring to all eight other species tested.     

Characterization of microsatellite markers in the threatened sand skink (Neoseps reynoldsi)

We characterized microsatellite loci for the sand skink (Neoseps reynoldsi) for future studies of genetic structure in this threatened taxon. We screened a partial genomic library enriched for microsatellites, designed primers for eight loci and assessed these markers for polymorphism across 11 populations in central Florida. Preliminary analyses indicate deviations from Hardy–Weinberg expectations for most loci, suggesting population genetic structure across the sampled populations; therefore, understanding genetic connectivity is critical for maintaining genetic variation in this species.     

Isolation and characterization of polymorphic microsatellite markers from fireweed,Senecio madagascariensis Poir. (Asteraceae)

Ten polymorphic microsatellite loci were isolated and characterized from invasive fireweed (Senecio madagascariensis) populations in the Hawaiian archipelago. These loci provided markers with polymorphism of six to 24 alleles per locus within 96 individuals collected from two populations from the island of Maui. The expected and observed heterozygosities ranged from 0.31 to 0.91 and from 0.056 to 1. These markers should be useful to study the importance of genetic diversity in invasion success of this species.     

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.