Estimating divergence time for two evolutionarily significant units of a protected fish species

The evolutionarily significant unit concept provides a powerful tool for conserving biodiversity below the species level, but temporal criteria are often used explicitly or implicitly in the operational definitions of evolutionarily significant units (ESUs). Such temporal considerations have important implications for recently diverged taxa, as is the case with the White sands pupfish (Cyprinodon tularosa). This species consists of two native populations previously designated as the Malpais Spring and Salt Creek ESUs based on allele frequency differences at nuclear markers and their ecologically divergent habitats; despite a lack of reciprocal monophyly. Isolation of these two ESUs presumably occurred during the mid-Holocene, but an alternative hypothesis is that the populations were isolated due to changes in surface hydrology associated with overgrazing in the late 19th and early 20th centuries. We assayed 13 microsatellite loci and applied an Approximate Bayesian Computation analysis to estimate time of divergence between the two populations. Our reference table consisted of 1,000,000 simulated data sets, and we used three different models, each having different combinations of summary statistics. Estimates of median divergence time varied from approximately 6,500–11,000 generations (3,250–11,000 years). These findings support the hypothesis that Malpais Spring and Salt Creek having been isolated for a least a few millennia, and together with previously documented adaptive divergence, argues for continued management as separate conservation units. We consider the temporal constraints for defining evolutionary significance as it relates to recently diverged populations occupying ecologically divergent habitats.     

Phylogeography,Population Structure,and Conservation of the Javan Gibbon (<Emphasis Type="Italic">Hylobates moloch</Emphasis>)

An understanding of phylogeography and population genetics is needed for a comprehensive long-term conservation management strategy. The Javan gibbon (Hylobates moloch), an Endangered species endemic to the island of Java, has been protected since 1924 but is threatened by ongoing habitat loss, habitat degradation, and the wildlife trade. We studied the phylogeography and population genetic structure of the Javan gibbon, to define the number of Evolutionary Significant Units (ESUs) in the species, and the population genetic structure in each ESU. We sampled 47 individuals, analyzing 35 for variation in mitochondrial DNA control region, 41 for variation in 8 nuclear DNA microsatellites, and 13 for variation in 45 nuclear DNA single nucleotide polymorphisms (SNPs). We found support for two ESUs across the species range: a western ESU, extending from Ujung Kulon to Gunung Gede–Pangrango, and a central ESU, extending from Gunung Masigit–Simpang–Tilu to Gunung Slamet. Analysis of molecular variance and population structure analysis indicate significant structuring in the western ESU between Ujung Kulon and Gunung Halimun–Salak–Gede–Pangrango, and little to moderate structure in the central ESU, underscoring the importance of conserving as many populations as possible to preserve the full array of genetic diversity in this species. Our results will inform future more comprehensive population genetic surveys and the conservation genetic management of the Javan gibbon. This study demonstrates the importance of genetics when designing conservation management strategies for endangered primates.     

Considering evolutionary processes in conservation biology

Conservation biologists assign population distinctiveness by classifying populations as evolutionarily significant units (ESUs). Historically, this classification has included ecological and genetic data. However, recent ESU concepts, coupled with increasing availability of data on neutral genetic variation, have led to criteria based exclusively on molecular phylogenies. We argue that the earlier definitions of ESUs, which incorporated ecological data and genetic variation of adaptive significance, are more relevant for conservation. Furthermore, this dichotomous summary (ESU or not) of a continuum of population differentiation is not adequate for determining appropriate management actions. We argue for a broader categorization of population distinctiveness based on concepts of ecological and genetic exchangeability (sensu Templeton).     

Using microsatellite and MHC variation to identify species, ESUs, and MUs in the endangered Sonoran topminnow

Highly variable loci can provide insight into the recognition of species, evolutionarily significant units (ESUs) and management units (MUs). In general, the ESU and MU categories are thought to be reflective of adaptive differences between them. Here we examine this premise by presenting a comprehensive examination of genetic variation for both microsatellite loci and a major histocompatibility complex (MHC) locus, thought to be of adaptive significance, in the endangered Sonoran topminnow. The extent of variation for the microsatellite loci and the MHC gene within the 13 populations of the Gila topminnow is highly correlated, suggesting that nonselective factors have played an important role in influencing variation within and between populations for the MHC locus. Therefore, using all of these loci, we found that the eight natural populations of the Gila topminnow fell into two different ESUs, one of which had four different MUs. The source of the Boyce Thompson sample, a population that was used extensively for restocking, appeared to be Monkey Spring. The source of the Watson Wash population also appeared to be Monkey Spring (or Boyce Thompson). The newly colonized Santa Cruz River population, which had the most genetic variation of any Gila topminnow population, appeared to descend primarily from Sonoita Creek populations. The Yaqui topminnow, presently considered another subspecies of the Sonoran topminnow, was very distinct for both microsatellite (only two of 25 alleles found in the Yaqui were in any of the Gila topminnow samples) and MHC alleles (nonoverlapping sets of alleles for the two groups). As a result, it appeared that the taxonomic status of the two subspecies should be re-evaluated and that full species status for Gila and Yaqui topminnows was appropriate. There was evidence for the importance of long-term selection at the MHC locus in the higher rate of nonsynonymous than synonymous substitution. In addition, there appeared to have been a duplication of the MHC locus that was present in most of the fish in six of the natural populations of the Gila topminnow.     

The memory remains: application of historical DNA for scaling biodiversity loss

Few species worldwide have attracted as much attention in relation to conservation and sustainable management as Pacific salmon. Most populations have suffered significant reductions, many have disappeared, and even entire evolutionary significant units (ESUs) are believed to have been lost. Until now, no ‘smoking gun’ in terms of direct genetic evidence of the loss of a salmon ESU has been produced. In this issue of Molecular Ecology, Iwamoto et al. (2012) use microsatellite analysis of historical scale samples of Columbia River sockeye salmon (Oncorhynchus nerka) from 1924 ( Fig. 1 ) to ask the pertinent question: Do the historical samples contain salmon from extirpated populations or ESUs? They identified four genetic groups in the historical samples of which two were almost genetically identical to contemporary ESUs in the river, one showed genetic relationship with a third ESU, but one group was not related to any of the contemporary populations. In association with ecological data, the genetic results suggest that an early migrating Columbia River headwater sockeye salmon ESU has been extirpated. The study has significant importance for conservation and reestablishment of sockeye populations in the Columbia River, but also underpins the general significance of shifting baselines in conservation biology, and how to assess loss of genetic biodiversity. The results clearly illustrate the huge and versatile potential of using historical DNA in population and conservation genetics. Because of the extraordinarily plentiful historical samples and rapid advances in fish genomics, fishes are likely to spearhead future studies of temporal ecological and population genomics in non‐model organisms.

Figure 1 Open in figure viewer PowerPoint (a) Kokanee sampling site between Columbia and Windermere lakes on the upper Columbia River at Fairmont Hot Springs, British Columbia, Canada. (b) Bureau of Fisheries scale books that contained sockeye salmon (locally called ‘blueback’ salmon) scales collected from commercial fisheries during the 1920s in the lower Columbia River. (c) Kokanee on spawning beds in Kuskanax Creek, a tributary to Upper Arrow Lake, British Columbia. Photo credit Rick Gustafson and Jim Myers.     

Testing hypotheses on the origin and dispersion of <Emphasis Type="Italic">Limnoperna fortunei</Emphasis> (Bivalvia,Mytilidae) in the Iguassu River (Paraná, Brazil): molecular markers in larvae and adults

The invasive bivalve Limnoperna fortunei (Dunker 1857) was introduced in South America in 1991, with the first occurrence in Brazil in 1998. In the Iguassu River, the species was recorded in 2001; however, it is unknown how it was introduced and spread. Adults and larvae were sampled in Iguassu and Paraná Rivers, and the genetic profiles were compared. The species was absent in the upper reaches and only larvae were found, in low densities, in intermediary reaches. The L. fortunei populations from the lower Iguassu River presented no genetic differentiation among themselves, suggesting strong connectivity, and were significantly different from the Paraná River populations, most likely because of Iguassu Falls. Furthermore, the results suggest that the Paraná River represents the source of propagules to the Iguassu River. Generally, no significant differences were observed between the genetic structure inferred from adults and larvae. Only the population from the Iguassu National Park, a lotic environment, differed from the remaining subpopulations. The characterization of genetic profile using larval stages of L. fortunei populations was satisfactory, and represents an important protocol for studying the population genetics of aquatic species with planktonic larval stages.     

Genomic data indicate ubiquitous evolutionary distinctiveness among populations of California metalmark butterflies

Conservation geneticists have argued that evolutionarily significant units (ESUs) must be both genetically distinct and adaptively significant to be recognized for conservation protection. High-throughput DNA approaches can greatly increase the power to identify genetic distinctiveness, even if inferring adaptive significance remains a challenge. Here we present the first genomic evaluation of Lange’s metalmark, Apodemia mormo langei (Lepidoptera: Riodinidae), a U.S. federally endangered subspecies restricted to sand dune habitats in a single National Wildlife Refuge in California. Previous work based on very few genetic markers detected little genetic distinction for Lange’s metalmark. We use several thousand genome-wide single nucleotide polymorphisms to characterize the population structure of the A. mormo complex across California and determine if Lange’s metalmark qualifies as an ESU. We found that Lange’s metalmark is genetically identifiable, but is no more distinct than many other isolated populations across the study area. It remains unclear whether this genetic variation is adaptive, and so conservation efforts would benefit from more ecological characterization to determine conservation priorities.     

Mesoscale investigations based on microsatellite analysis of the freshwater sponge <Emphasis Type="Italic">Ephydatia fluviatilis</Emphasis> in the River-Sieg system (Germany) reveal a genetic divergence

Freshwater sponges play a major role in freshwater ecological system as important filter-feeding organisms and bioindicators. There are only few data about their ecological diversity and population genetic structure available, though a deeper knowledge is needed to propose proper conservation and effective management. The aim of this study was to assess data on distribution patterns of freshwater sponges to study the connectivity of genotypes of Ephydatia fluviatilis in a river system. We sampled specimens from River-Sieg system (River Agger and River Sieg, Germany). We hypothesized that strong anthropogenic influence would cause a uniform distribution of population structures. The genetic structure of E. fluviatilis populations was analysed with a set of eleven microsatellite loci from seven locations in River-Sieg system. Besides of E. fluviatilis, three other species co-occurred (Ephydatia mülleri, Spongilla lacustris, Eunapius fragilis). In contrast to our hypothesis, we observed an overall correlation between genetic and geographic distances among populations of this sessile species, which follows a clear isolation-by-distance pattern. A significant microsatellite polymorphism and high levels of genetic divergence between populations (F_ST) in upstream reaches were present. These results will provide important information for conservation management of populations with limited dispersal ability in connected river systems.     

Nuclear genetic variation of <Emphasis Type="Italic">Rosa odorata</Emphasis> var. <Emphasis Type="Italic">gigantea</Emphasis> (Rosaceae): population structure and conservation implications

Rosa odorata var. gigantea is one of the most important ancestors of modern roses, which owns many merit traits including large flower, early flowering, and tea scent. Due to habitat loss and fragmentation, it has been listed as a rare and endangered species in China. In this study, a total of 424 accessions from 27 locations across its major distribution range were sampled. Its genetic diversity and population structure were assessed using a combination of seven nuclear microsatellite markers and one single-copy nuclear gene. Moderate to high within-population genetic diversity and moderate differentiation among populations were revealed despite its narrow distribution. The sampled 27 populations were resolved into two genetic clusters with limited contemporary and historical gene flows. The Red River Fault Zone was inferred to be a physical or geographical barrier to gene flow between these two genetic clusters. Genetic distances were significantly associated with geographic distances, indicating the isolation-by-distance model. Our ecological niche modeling indicated that R. odorata var. gigantea had high current potential areas in the central Yunnan province and substantial losses of high potential distribution areas in the western Yunnan in the future. Two detected clusters showed significant genetic differentiation and represented two separate evolutionary lineages, which should be recognized as two evolutionary significant units (ESUs) for conservation concerns. These results could be applied for the decision-making and conservation planning for this important species.     

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (<Emphasis Type="Italic">Oncorhynchus tshawytscha</Emphasis>) within a Snake River watershed

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.     

Differences in Responses of Chinook Salmon to Climate Shifts: Implications for Conservation

Understanding how organisms respond to climate is critical for focusing the debate about ways to recover imperiled or manage exploited species. However, efforts to understand climate effects on biota are complicated by differences among species in life history and physiology. Even within a species it is not clear if different populations will react similarly to large-scale climate trends. Climate regimes exhibit basin-wide effects similar to the El Ni no Southern Oscillation but persist for decades. In the North Pacific Ocean, two regime shifts (abrupt changes from one regime to another) occurred in 1976–1977 and 1989–1990 and had wide ranging effects on many species. We examined the response of chinook salmon from 9 evolutionary significant units (ESUs) to the regime shifts. While there was an average decline in spawner numbers associated with the regime shifts, ESUs did not respond in a uniform manner: some ESUs declined, some did not respond and one may have increased. Four ESUs currently listed under the Endangered Species Act may have declined more across regime boundaries than did the five non-listed ones. Interpretation of this result depends on two ESUs: the Snake River spring/summer run and the Central Valley fall run. The Snake River ESU had the largest decline and most sampling effort. If this ESU was excluded from the analysis, there was no evidence that listed and non-listed stocks responded differently to the regimes. The Central Valley ESU is currently a candidate for listing. If this ESU is considered to be a threatened or endangered, then listed ESUs declined more on average than did non-listed ESUs across the regime boundaries regardless of the Snake River ESU. As a whole, these results suggest that long-term climate trends are important to the dynamics of chinook populations and that sub-units of a species (here ESUs) can respond differently to these regimes.     

Genetic differentiation and the problems of conservation of masu salmon (<Emphasis Type="Italic">Oncorhynchus masou</Emphasis> Brevoort, 1856 (Pisces: Salmonidae)) populations

This study focuses on the strategy for the conservation of masu salmon, Oncorhynchus masou, in the northern part of the species range (via the masu populations in Sakhalin Oblast), based on data of its population structure. It is shown that masu populations that inhabit different rivers genetically differ from each other in allele frequencies at microsatellite markers. In the Naiba River basin, at least two genetically distinct masu populations exist: in the upper reaches and in a tributary, the Bolshoy Takoy River. The masu populations on Iturup Island significantly differ from those on Sakhalin Island; within Sakhalin, the masu salmon from the Chernaya River in the southwestern part of the island is genetically distinct from the southeastern Sakhalin and Aniva Bay populations. The genetic diversity of Iturup populations is substantially lower than that on Sakhalin, probably due to their small sizes. The measures for the conservation and recovery of masu salmon populations should be based primarily on their own genetic resources, or, in the case of a lack of spawners, on the base populations of their ecological/geographical region. In the latter case, masu populations of large rivers can be considered as base ones: for southeastern Sakhalin, this is masu salmon of the Naiba River; for Aniva Bay, this is masu salmon of the Lyutoga River. Transplantation of fish, fertilized eggs, or any other genetic material from a population that is different genetically and inhabits the waters with different ecological gradients should be strongly restricted. The formosan masu salmon from Taiwan Island is studied as an example of a strict genetic isolate.     

The endangered Sonoran topminnow: Examination of species and ESUs using three mtDNA genes

There has been controversy over the species status of Sonoran topminnows and debate about the presence of ESUs in the Gila topminnow. From examination of sequence variation at 2626 base pairs over three mtDNA genes, we found a 29 (1.1%) nucleotide genetic difference between Gila and Yaqui topminnows. This provides strong support that these two taxa are separate species, Poeciliopsis occidentalis (Gila topminnow) and P. sonoriensis (Yaqui topminnow) and have been separated for approximately one million years. All the Gila topminnows within Arizona have the same sequence for the three mtDNA genes, that is, there is not reciprocal monophyly for mtDNA sequence data for the two previously designated ESUs. However, evidence of the unique habitat for Monkey Spring, its long-term isolation from other Gila topminnow habitats, and the presence of unique fish and invertebrate taxa in Monkey Spring support the designation of the Monkey Spring topminnows as an ESU. Finally, theoretical considerations using molecular data and estimates of heterozygosity and genetic distance for nuclear genes between populations of the Gila topminnow show that the lack of mtDNA variation is not inconsistent with the level and pattern of nuclear genetic variation observed.     

Evolution of rough sculpin (<Emphasis Type="Italic">Cottus asperrimus</Emphasis>) genetic divergence and late Quaternary displacement on the Hat Creek fault,California, USA

The rough sculpin (Cottus asperrimus) is a threatened species whose geographic range in northwestern California, USA is disrupted by Hat Creek fault. We tested whether the fluvial barriers (rapids and waterfalls) produced by this fault have generated significant phylogeographic structure among rough sculpin populations by analyzing variation in microsatellites and mitochondrial DNA. Rough sculpin isolated on either side of Hat Creek fault exhibited significant genetic divergence (microsatellite F _ST = 0.36; mitochondrial uncorrected p distance = 1 %). Independently derived estimates for the date of divergence, based upon a molecular clock and upon the age of slip on the Hat Creek fault are concordant and indicate divergence was initiated about 0.5–1 million years ago. Based upon the findings of our genetic analysis and the Pleistocene geologic history of midsections of the Pit River, we present a model of evolution of rough sculpin genetic divergence and late Quaternary displacement on Hat Creek fault. Our findings reveal that rough sculpin exhibit significant population structure and that two management units should be recognized within the species for future conservation planning.     

Molecular phylogeography and population evolution analysis of <Emphasis Type="Italic">Citrus ichangensis</Emphasis> (Rutaceae)

Ichang papeda (Citrus ichangensis), a wild and endemic perennial plant in Rutaceae, is characterized by the existence of wild and natural populations in southwestern and middle-west China. We analyzed a total of 231 individuals across 16 natural populations using chloroplast SSR markers, nuclear SSR markers, and single-copy nuclear genes. Standard population genetic analyses as well as Bayesian and maximum likelihood models were used to clarify the genetic diversity, population differentiation, barriers to gene flow, bottleneck events, isolation by distance, history migration, demographic history among populations, and phylogeny evolution. The chloroplast and nuclear genome analyses revealed a low level of genetic diversity in C. ichangensis. Clear signals of recent bottlenecks and strong patterns of isolation by distance were detected among different subpopulations, indicating a low extent of historical gene flow for this species and that genetic drift would occur after population differentiation. Bayesian clustering analyses revealed a clear pattern of genetic structure, with one cluster spanning the potential refugia in Wuling Mountains and Ta-pa Mountains, and other two clusters covering a more limited distribution range. The demographic history also supported the scenario that two isolated clusters originated in parallel from the genetic diversity center. Taxonomically, Ichang papeda may be a member of subgenus Citrus. Owing to the complicated topography, the mountainous regions and the Yangtze River have provided long-term stable habitats for C. ichangensis and acted as main barriers for its expansion, which might facilitate the process of speciation. Statistical population models and genetic data indicated strong genetic structure in C. ichangensis, which might result from the restricted gene flow, genetic drift, and population bottlenecks.     

Cryptic genetic diversity of <Emphasis Type="Italic">Neverita didyma</Emphasis> in the coast of China revealed by phylogeographic analysis: implications for management and conservation

Revealing cryptic biodiversity and understanding the processes that promote lineage diversification will provide valuable insights into management and protection of exploitable species. Neverita didyma is one of the most common marine species along the coast of China and possesses highly economic and nutritional value. Despite being heavily harvested each year, the genetic diversity of this species has never been assessed in the coastal areas of China. Here, we analyzed the diversity of this species based on the barcode region of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and utilized different species delineation approaches to infer evolutionarily significant units (ESUs). Three distinct ESUs, with high genetic distance among each, were identified. Divergence time estimates suggested that the high genetic distances were probably associated with historical isolation of the marginal seas during Pleistocene low sea level periods. The three ESUs did not map to distinct geographical distribution, possibly attributing to the repeated isolation in different refugia and random postglacial recolonization. Moreover, N. didyma in Haizhou Bay deserves priority protection due to its unique ESU. To improve management regulations in the marine realm, our research also stresses the need for more empirical studies on genetic diversity of commercially exploited species in coastal environments of China.     

Genetic diversity,effective population size,and structure among black bear populations in the Lower Mississippi Alluvial Valley,USA

Multiple small populations of American black bears Ursus americanus, including the recently delisted Louisiana black bear subspecies U. a. luteolus, occupy a fragmented landscape in the Lower Mississippi Alluvial Valley, USA (LMAV). Populations include bears native to the LMAV, bears translocated from Minnesota during the 1960s, and recently reintroduced and colonizing populations sourced from within the LMAV. We estimated population structure, gene flow, and genetic parameters important to conservation of small populations using genotypes at 23 microsatellite markers for 265 bears from seven populations. We inferred five genetic clusters corresponding to the following populations: White River and western Mississippi, Tensas River and Three Rivers, Upper Atchafalaya, Lower Atchafalaya, and Minnesota. Upper Atchafalaya was suggested as the product of Minnesota-sourced translocations, but those populations have since diverged, likely because of a founder effect followed by genetic drift and isolation. An admixture zone recently developed in northeastern Louisiana and western Mississippi between migrants from White River and Tensas River, resulting in a Wahlund effect. However, gene flow among most populations has been limited and considerable genetic differentiation accumulated (global F_ST?=?0.22), particularly among the three Louisiana black bear populations that existed when federal listing occurred. Consistent with previous bottlenecks, founder effects, and persisting isolation, all LMAV bear populations had low genetic diversity (A_R?=?2.08–4.81; H_E?=?0.36–0.63) or small effective population size (N_E?=?3–49). Translocating bears among populations as part of a regional genetic restoration program may help improve genetic diversity and increase effective population sizes.     

Phylogeographic-based conservation implications for the New Zealand long-tailed bat, (<Emphasis Type="Italic">Chalinolobus tuberculatus</Emphasis>): identification of a single ESU and a candidate population for genetic rescue

The New Zealand long-tailed bat (Chalinolobus tuberculatus) is an endemic species threatened with extinction. Since the arrival of humans, massive deforestation has occurred and invasive mammalian predators were introduced. As a result, C. tuberculatus’ distribution shrank dramatically and became fragmented. To aid the management of the remaining populations, two Evolutionary Significant Units (ESUs) were designated: one on each of New Zealand’s main islands. We utilised mitochondrial sequence data (cytb, 703 bp) and 10 nuclear DNA microsatellite loci to reconstruct the demographic history of this species, to characterise the level of genetic diversity in remaining populations, and to assess the current connectivity between them. Our results indicate that the North Island, with the highest genetic diversity, served as a glacial refuge, with a loss of diversity following the path recolonization to the south of the South Island. However, our data are also consistent with continued, or at least very recent, genetic exchange between colonies across the species distribution. The only exception is the Hanging Rock colony on the east coast of the South Island, which appears to be isolated. Thus, there was no support for the previously designated ESUs. Signatures of past population declines were found in three colonies, the most extreme of which was found in Hanging Rock. Consequently, we recommend that it be genetically rescued via translocation from a donor population. In general, future management priorities should treat Chalinolobus tuberculatus as a single unit, focusing on maintaining connectivity between remaining populations, together with continued roost protection and pest control.     

Population genetic structure of the Amazonian black flannelmouth characin (Characiformes,Prochilodontidae: <Emphasis Type="Italic">Prochilodus nigricans</Emphasis> Spix &amp; Agassiz, 1829): contemporary and historical gene flow of a migratory and abundant fishery species

In the present study, sequences of the mtDNA control region (834 bp) were analyzed from 337 specimens of Prochilodus nigricans from sites along the main channel of the Amazonas River and three major tributaries, Madeira, Purus, and Juruá. The results of the analysis of molecular variance revealed that a large part of the genetic variation occurred within the populations analyzed (~85 %). Analysis with SAMOVA and Barriers suggested that the upper Madeira River and Purus Rivers had diverged genetically from the other samples, indicating restricted gene flow among these areas, while sites within the remaining range exhibited relatively little population structure. The high degree of structuring observed in the Madeira River basin population may be attributed to the presence of rapids along its upper course, while the genetic divergence found in the upper Purus River suggests historical connection between the upper Purus and upper Madeira Rivers followed by slow genetic drift due to large effective population sizes. However, given the life history and hypothesized evolutionary strategy of this species, we urge caution in interpreting that this targeted species is not at risk of overexploitation due to contemporary abundance. In order to preserve genetic diversity, we recommend enforcement of management regimes for regional stocks.