The discrimination of roach Rutilus rutilus (Linnaeus, 1758) populations in different parts of a river system. An investigation using biochemical markers

Roach populations from different parts of the network of the French Upper Rhone and from Lake Geneva were examined. Several populations were discriminated by the electrophoresis of 16 enzymes coded for by 28 gene loci. 90% of the overall genetic variation was due to intrapopulation variation. Some affinity was found between the populations of Lake Geneva and the Rhone immediately downstream, but the stocks of the Rhone farther down proved to be clearly distinct from these (genetic distance D = 0.048) and probably included several independently reproducing populations. One of these populations was only found in the channel, others inhabited a side arm (D between them = 0.035) or succeeded each other in it, presumably in connection with spawning migrations.     

Novel genetic variation in an isolated population of the nationally critical Haast tokoeka (<Emphasis Type="Italic">Apteryx australis</Emphasis> ‘Haast’) reveals extreme short-range structure within this cryptic and flightless bird

There are currently five recognised species of kiwi (Apteryx spp.), and possibly 11 distinct genetic lineages, all of which are threatened or near threatened. Currently, with only approximately 400 individuals left, the most endangered provenance is Haast tokoeka (Apteryx australis ‘Haast’), classified as ‘Nationally Critical’ (Robertson et al. 2017 in Conservation status of New Zealand birds, 2016. New Zealand Threat Classification Series 19. Department of Conservation, Wellington). Several decades ago, a population of tokoeka from the Upper Arawhata region of the Olivine ranges near Haast, New Zealand was discovered, separated from the Lower Arawhata population by the Arawhata River and up to 20 km distance. Here, we used 1283 basepairs from two mitochondrial loci (control region and cytochrome b) and 14 nuclear microsatellites to describe the genetic diversity of this discrete population. Compared to Lower Arawhata, mitochondrial diversity was greater in Upper Arawhata with three mtDNA haplotypes compared to two, despite a lower sample size, and a pairwise nucleotide diversity more than five times as high (π?=?0.00082). No mtDNA haplotypes were shared between the two regions. Microsatellites revealed moderate inbreeding in Upper Arawhata (F_IS = 0.102), lower diversity levels to Lower Arawhata, and indicated this population is closest to but distinct from Lower Arawhata tokoeka when compared to other recognised tokoeka provenances. The marker-specific disparity in diversity measurements in Upper Arawhata may reflect relatedness in the presence of female dispersal. The low mitochondrial diversity in Lower Arawhata may indicate an over-use of productive females in supplementation programs. The distribution of genetic variation across all tokoeka was consistent with an isolation-by-distance model, but this correlation may be disrupted by local and complete barriers to gene flow creating highly structured regional populations. In summary, we provide strong support for the classification of the Upper Arawhata tokoeka as a genetically distinct population, increasing the genetic variation within Haast tokoeka and providing a useful resource for on-going conservation management.     

The genetic structure of roach populations in two contrasted large rivers

Overall heterozygosity was high in all roach populations, and so was gene flow between them. However, genetic diversity was greater in the fast-flowing and more diverse French Upper Rhone than in the uniformly lentic River Saone. Rhone backwaters may be considered as ecotones and reservoirs of genetic diversity, but such is not the case in the Saone owing to the uniformity of the environment.(U.R.A. 1451 Ecologie des Eaux Douces et des Grands Fleuves)     

Presence du Messinien dans la vallee du Rhone

According to the paleontological (molluscs and ostracods) and stratigraphical data, the Congeria rhodanicacclays are of Upper Messinian age. This oligohaline facies points out the local transgression of mediterranean origin in the Rhone basin, following a Lower Messinian erosive episode with coarse subaerial partial valley infill.     

Genetic structuring and transfer of marine dinoflagellate Cochlodinium polykrikoides in Japanese and Korean coastal waters revealed by microsatellites

To determine the process of population expansion and ascertain the origin of the Sea of Japan population, in a noxious red tide forming dinoflagellate Cochlodinium polykrikoides , 13 samples, isolated from 11 different localities in Japanese and Korean coasts, were analysed using 10 polymorphic microsatellites. Analyses by nonmetric multidimensional scaling plots of pairwise F _ST, global amova , and genetic admixture analysis identified three clusters — the Sea of Japan populations, Yatsushiro Sea (Kumamoto Pref.) populations, and other populations — indicating genetic structuring of the 13 samples into three distinct populations. In the proportion of shared alleles by pairwise individuals ( P _SAxy) analyses between the Sea of Japan and the other samples, P _SAxy was extremely low compared with that among the Sea of Japan or among other samples, indicating that a large genetic barrier has occurred between the populations. No significant relationship of isolation-by-distance patterns and almost no genetic distance were detected between pairwise samples of the Sea of Japan, although there is a maximal distance of > 600 km between samples. In addition, P _SAxy data among the samples were extremely high compared with those among other samples, clearly showing that a large-scale transfer from west to east has occurred via the Tushima Warm Current. In the P _SAxy data of the Seto Inland Sea and Pacific samples, individuals showing relatively high P _SAxy were concentrated in the three areas of Nagasaki, Harima, and Mie, suggesting that frequent transfer may have occurred by human-assisted dispersal, although Nagasaki and Mie are separated by a distance of approximately 700 km.     

Genetic differentiation of Anopheles claviger s.s. in France and neighbouring countries

An investigation of polymorphism of 11 autosomal and one sex-linked allozyme loci was made on 18 samples of Anopheles claviger Meigen (Diptera: Culicidae) from localities across France and neighbouring sites in Germany and Switzerland, plus one sample of Anopheles petragnani Del Vecchio from the French Pyrénées. Genetic differentiation between these two sibling species was confirmed (Nei genetic distance 0.33-0.44) and two genetically distinct groups of populations were identified within An. claviger. These two forms of An. claviger showed contiguous geographical distributions, Group I found across western and Central France, Group II in eastern France and nearby parts of Germany and Switzerland. The two groups were in contact in a region near the Rhone Valley where two intermediate samples were found. The taxonomic significance of this finding is discussed in the context of the recent climatic history of Europe and in relation to the vector potential of each member of the An. claviger complex.     

Using genetic monitoring to inform best practice in a captive breeding programme: inbreeding and potential genetic rescue in the freshwater pearl mussel <Emphasis Type="Italic">Margaritifera margaritifera</Emphasis>

Freshwater pearl mussel (Margaritifera margaritifera) populations are declining in Northern Ireland to the extent that a captive breeding programme was established on the Upper Ballinderry river in 1998. Previous genetic analysis of the hatchery broodstock and their first cohort of offspring showed significant levels of inbreeding (F _IS  = 0.166). The broodstock, which currently numbers ca. 90 individuals, was supplemented with new individual mussels, whilst in 2013, a previously unknown population was discovered on the Lower Ballinderry river. The aim of the present study was to determine whether the rotation of the broodstock has led to a decrease in the levels of inbreeding in the second cohort of juveniles, and to determine whether the new population found in the Lower Ballinderry was genetically distinct from the captive bred population and populations from the Upper Ballinderry, which represent the source of the hatchery broodstock. Genotyping using eight microsatellite markers indicated that levels of inbreeding in the second cohort of captive-bred mussels were high, (F _IS  = 0.629), and were comparable to those sampled from the original cohort and the hatchery broodstock (F _IS  = 0.527 and 0.636 respectively). Bayesian analysis of population structure indicated that the newly discovered Lower Ballinderry population was genetically distinct from the broodstock and its source populations on the Upper Ballinderry. The observed differentiation was primarily due to differences in allele frequencies, and was most likely a result of genetic drift. The occurrence of ten alleles, albeit at low frequency, in the Lower Ballinderry population, including four private alleles, suggests that this new population could be incorporated into the broodstock with the aim of decreasing levels of inbreeding in the future.     

Impact of rifting and hydrography on the genetic structure of Clarias gariepinus in eastern Africa

In a study of the genetic structure of Clarias gariepinus at the ND5 and ND6 loci of mitochondrial DNA using RFLP–PCR in 16 populations (267 fish), a total of 18 haplotypes was detected. The most common haplotype was EA1 and represented 46% of all genotypes. Three phylogenetic groups characterized the region, with the East African clade occurring between the western rift in the west, Lake Baringo in the north, the Indian Ocean in the east and the Rufiji River in the south. The Lower Tana River (unlike the Upper Tana River) and Lake Kamnarok grouped with the North clade, while the Ruaha River (tributary of the Rufiji River) represented a contact zone between the East and the South-central African clade. Genetic structure was distinct ( F _ST=0·66), with the Lower Tana River and Lake Mtera forming specific units. Within the East clade, the Oloibortoto River, Upper Tana River and Lake Victoria each formed a distinct population. Lake Baringo grouped either with the eastern rift or the western rift depending on the analysis. Lake Jipe, the Pangani River, Rusizi River, Lake Edward, Nyabugogo River and the Luiche River clustered together. Among group variance explained 66·8% of the total variance; the impact of vicariance (rifting and uplifting) on the phylogeography was considerable. A distribution model of the catfish is proposed which combines the separation by rifting several million years ago with a high gene flow in the western rift due to historical connectivity among lakes and rivers.     

High genetic diversity in cryptic populations of the migratory sutchi catfish Pangasianodon hypophthalmus in the Mekong River

The detection and conservation of spawning units is of crucial importance in highly migratory species. The sutchi catfish Pangasianodon hypophthalmus (Pangasiidae; Teleostei) is a common large-sized tropical fish, which migrates annually to several upstream spawning sites on the Lower Mekong River and feeds on the huge floodplain of the Lower Mekong and Tonle Sap for the other half of the year. We hypothesised that because of the relative size of the feeding and spawning habitat, genetic variability would be high and homogeneous in foraging populations, but that spawning stocks would be distinct in space and time. To test these predictions, 567 individuals from 10 geographic locations separated by up to 1230 km along the Lower Mekong River were genotyped at seven microsatellite loci. The level of genetic diversity was much higher than other freshwater fish and reached values comparable to marine species (mean H(e)=0.757). All samples collected at the potential spawning sites deviated from Hardy-Weinberg expectations, suggesting admixture. Individual-based clustering methods revealed genetic heterogeneity and enabled the detection of three genetically distinct sympatric populations. There was no evidence of recent reduction in effective population size in any population. Contrasting with the vast extent of the feeding grounds, the shortage of spawning grounds seems to have moved sutchi catfish towards diachronous spawning. Hence the sustainable exploitation of this natural resource hinges on the conservation of the limited spawning grounds and open migration routes between the spawning and feeding grounds.     

Pedigree Reconstruction of the Italian Grapevine Aglianico (Vitis vinifera L.) from Campania

A total of 41 accessions of Aglianico belonging to three different biotypes (Taburno, Taurasi, and Vulture) and 9 accessions of Sirica grapes were sampled from diverse areas of Campania (Italy). All accessions were first genotyped using 21 microsatellite markers (SSR) to evaluate possible homonymies, synonymies, and the genetic structure of each group. A larger dataset was then constructed adding Italian and International cultivars. On the basis of results obtained analyzing the first dataset, further investigations were carried out enlarging the number of investigated loci (up to 43). The addition of 22 SSRs was useful in the definition of likely genetic relationships linking Aglianico biotypes, Sirica and Syrah. According to their SSR allelic profiles, the monophyletic origin of the three Aglianico biotypes was confirmed. Among Aglianico Taburno accessions, eight samples (called Aglianico like-to-type) performed a different SSR allelic profile from Aglianico true-to-type. Sirica and Syrah proved to be synonyms. This work allowed to determine the genetic relationship between Aglianico and the cultivars supposed to be related. The parentage analysis was investigated. The most likely pedigree has been reconstructed; revealing a second-degree relationship between the worldwide cultivated Syrah from the Rhone Valley and Aglianico. Aglianico like-to-type appeared related to Aglianico in a parent-offspring fashion.     

Population structure and genetic variability of pearl oyster Pinctada mazatlanica along Pacific coasts from Mexico to Panama

Populations of the Calafia pearl oyster Pinctada mazatlanica ofthe American Pacific coasts have been considered endangeredbecause of overfishing and/or alteration to coastal areas. Weassessed genetic variability and the pattern of populationstructure among 9 samples collected from Mexico to Panama, usingmtDNA RFLP analysis of two genes: 12S rRNA and subunit one ofCytochrome oxydase (COI). Haplotype diversity varied from 0.000to 0.856. The Panama population appeared to be monomorphic, whilethe other samples exhibited a level of haplotypic variabilitysimilar to those reported in the literature for the same kind ofanalysis on other bivalves species. A test for the impact ofdemographic history on genetic diversity was applied on thesequence data, and the results were congruent with a recentdecline of population sizes. Genetic differentiation was shown tofollow a scheme of isolation by distance, with low levels ofdifferentiation at the scales of ten to one hundred kilometres,whereas stronger and significant genetic structure was detectedat a larger scale. Three significantly distinct groups could thenbe defined, which correspond to Northern Mexico, Southern Mexico,and Panama.     

PHYLOGEOGRAPHY AND WITHIN-STREAM GENETIC VARIATION OF BATRACHOSPERMUM HELMENTOSUM (RHODOPHYTA) USING INTER-SIMPLE SEQUENCE REPEATS

A relatively new molecular marker technique, inter-simple sequence repeats (ISSR), was used to assess the within-stream reach genetic variation and phylogeography of the freshwater red alga, Batrachospermum helmentosum. The within-stream reach study was undertaken in Southeastern Ohio, where 58 individuals were collected from an approximately 200 m stream length. Individuals appeared to be congregated into three distinct areas, with no plants between areas. Using three primers, 100 polymorphic bands were scored. Although it was hypothesized that genetic variation would reflect physical distance, the results showed six distinct genetic groupings, some of which consisted of physically distant individuals. Overall, genetic diversity was greater among individuals than between geographic and genetic groups. To investigate phylogeography, 11 stream reaches (3 from Ohio and one each from Connecticut, Massachusetts, Rhode Island, North Carolina, Tennessee, Indiana, Michigan and Louisiana) were sampled throughout the alga's known distribution in North America. Approximately 15 individuals were collected per stream for ISSR analysis. Five primers, yielding 243 polymorphic bands, were used to examine variation among all individuals. Neighbor-joining trees generated from the Dice, Jaccard and Excoffier coefficients showed that individuals from the same stream formed a clade. Among streams there was no distinct correlation between geographic distance and genetic similarity. Genetic groupings varied slightly among distance coefficients employed. Michigan and Tennessee, Connecticut and Rhode Island, and Indiana and Massachusetts streams consistently showed the same relationship, but the relationships among the three Ohio streams and Louisiana stream were variably related to each other.     

Population structure of Hydropsyche exocellata. Genetic homogeneity in a zone of fragmented distribution

Using four allozymic loci, we analysed the genetic structure and differentiation of Hydropsyche exocellata (Trichoptera; Hydropsychidae) larvae in seven sites along the Upper Loire River (France). The genetic differentiation is low for this species despite distribution patchiness, and only due to one locus in one study site. No trend relating genetic differentiation to geographic distance (isolation by distance) was observed. Significant deviations from Hardy-Weinberg equilibrium were observed at most sites and loci. The population genetics analysis of an amphibiotic insect such as H. exocellata in light of current ecological and population genetics knowledge is discussed following two main factors: 1) sampling of partially reproductively isolated, genetically distinct subpopulations, and 2) form of selection. Despite knowledge on several aspects of the ecology of H. exocellata in the River Loire, numerous points limit genetic data interpretation. These points are underlined and discussed with reference to studies on other amphibiotic insects.     

Population genetics of steelhead (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) in the Klamath River

An analysis of population structure and genetic diversity was conducted on samples of Oncorhynchus mykiss (steelhead/rainbow trout) from 33 sites in the Klamath–Trinity River basin. Genotype data from 16 microsatellite loci in almost 1,700 fish revealed genetic differentiation between most sampled locations. Two pairs of samples from the same sites in different years were not significantly different, indicating stability of population structure, at least on a short time scale. Most sampling sites were genetically distinct from all other sampling sites, and there was an evidence of geographic structure within the Klamath–Trinity River basin, although populations from tributaries within the watershed (e.g. Salmon River, Scott River, Clear Creek) did not always constitute distinct genetic lineages. Population structure was evident using phylogeographic trees, isolation by distance analyses and individual assignment tests, which all found a relationship between geographic and genetic distance. Populations in the lower Klamath region, below the confluence with the Trinity River, consistently clustered together in phylogeographic analyses and had patterns of genetic diversity that suggest reduced gene flow between these sites and sites above the confluence. Finally, in an analysis that included data from other coastal California rivers, the populations closest to the mouth of the Klamath River appeared intermediate between populations from adjacent watersheds and the lineage formed by the other populations in the Klamath–Trinity basin.     

Genetic structuring of Patagonian toothfish populations in the Southwest Atlantic Ocean: the effect of the Antarctic Polar Front and deep-water troughs as barriers to genetic exchange

The environmental and/or life history factors affecting genetic exchange in marine species with potential for high dispersal are of great interest, not only from an evolutionary standpoint but also with regard to effective management. Previous genetic studies have demonstrated substantial differentiation among populations of the Patagonian toothfish around the Southern Ocean, indicating breakdown of gene flow across large distances between inhabited shelf areas. The present study examined genetic structuring through analysis of microsatellite loci and restriction fragment length polymorphism (RFLP) of the mitochondrial ND2 gene and control region of the toothfish population in the SW Atlantic, allowing examination of the relative effects of the Antarctic Polar Front (APF), deep-water troughs and distance between sites. Mitochondrial DNA (mtDNA) data indicated a sharp genetic division between the Patagonian Shelf/North Scotia Ridge and the Shag Rocks/South Georgia samples, whereas microsatellite data showed much less distinct structuring and an intermediate position of the North Scotia Ridge samples. We suggest these data indicate that the APF, as a barrier to larval dispersal, is the major inhibitor of genetic exchange between toothfish populations, with deep-water troughs and distance between sites contributing to genetic differentiation by inhibiting migration of relatively sedentary adults. We also suggest that differences between mtDNA and nuclear DNA population patterns may reflect either genome population size effects or (putative) male-biased dispersal.     

Hidden Biodiversity in an Ecologically Important Freshwater Amphipod: Differences in Genetic Structure between Two Cryptic Species

Cryptic species, i.e. species that are morphologically hard to distinguish, have been detected repeatedly in various taxa and ecosystems. In order to evaluate the importance of this finding, we have to know in how far cryptic species differ in various aspects of their biology. The amphipod Gammarus fossarum is a key invertebrate in freshwater streams and contains several cryptic species. We examined the population genetic structure, genetic diversity and demographic history of two of them (type A and type B) using microsatellite markers and asked whether they show significant differences. We present results of population genetic analyses based on a total of 37 populations from the headwaters of two major European drainages, Rhine and Rhone. We found that, in both species, genetic diversity was geographically structured among and within drainages. For type A in the Rhine and type B in the Rhone, we detected significant patterns of isolation by distance. The increase of genetic differentiation with geographical distance, however, was much higher in type A than in type B. This result indicates substantial interspecific differences in population history and/or the extent of current gene flow between populations. In the Rhine, type B does not show evidence of isolation by distance, and population differentiation is relatively low across hundreds of kilometres. The majority of these populations also show signatures of recent bottlenecks. These patterns are consistent with a recent expansion of type B into the Rhine drainage. In summary, our results suggest considerable and previously unrecognized interspecific differences in the genetic structure of these cryptic keystone species.     

泥河湾盆地旧石器中晚期石制品原料初步分析

本文通过对泥河湾盆地旧石器时代中晚期诸遗址中石料产地的调查和石制品颜色、质地及表面状况的分析后认为：泥河湾盆地旧石器中晚期人类选择石料方式变化主要发生在旧石器晚期的早段和晚段之间,在此之前的旧石器时代中期,人类选择石料主要在遗址附近,各遗址的石料表现出强烈的地方色彩,但遗址中的一些优质石料可能来源于10多公里之外的地区;而在旧石器晚期早段,在基本继承这一特点的前提下,仅有很少量的石料输送距离达数10km;石料被带到遗址之前一般并不进行粗选,多是直接进行打片。在此之后,人类对石料的选择则表现出刻意的追求,优质石料大量被输送到数10公里之外,而且石料在输入到遗址之前一般要经过精心选择,与前一阶段形成鲜明对照。     

Sediment dynamics during the Cenomanian-Turonian (cretaceous) oceanic anoxic event in Northwestern Germany

Summary The epicontinental pelagic to hemipelagic Upper Cenomanian and Lower Turonian successons of the Lower Saxony Basin (northwestern Germany) are represented by the Rotpl?ner facies on swells (multicolored marls and marly limestones) and the basinal Black Shales facies (marly limestones (Turbidites), black shales) in the local basins. Facies units are described with their lateral and vertical variation from both depositional environments and their correlation is discussed. The distinct Cenomanian-Turonian boundary facies is due to dilution of pelagic carbonate by siliciclastic material, volcanic ashfall, and substantial changes in carbonate, sedimentation rates by about an order of magnitude. The observed sediment geometries origin from preservation of sediments in areas where normal faults occur and erosion of the formerly deposited units in unfaulted areas (preservation of relicts). Erosion and redeposition on swells occurs in thin (<50 cm thick) debris flow and mud flow channels (1–100 m wide), sheet flows, and by turbidity currents. During the Upper Cenomanian the sediment transport is governed by gravity flow which is increasingly superimposed by storm deposition during the Lower Turonian. Lense-shaped tempestites (probably below average storm wave base) occur at the base of the Turonian (entry ofMytiloides hattini) in morphologically highest swell positions and migrate across the entire basin until the late Lower Turonian. The basinal facies is characterised by laminated and biotrubated black shales and mud turbidites that vary over short distances. Laminae show graded bedding and erosive contacts and were deposited by turbidity currents. Intercalated marly limestones are mud turbidities (some mudflows) that are coarsening upwards until the early Lower Turonian. Larger slides occurred predominantly in the late Upper Cenomanian. The sediment distribution is closely related to sea level changes and reflects short- and long-term fluctuations generating comparable stratigraphic trend in the sections, although basin and swell facies are always clearly distinguished. Lokal basin margins (e.g. primary fordeeps of sal domes) were probably limited by larger normal faults that prevented facies gradation between both depositional environments.     

Evidence for Two Highly Differentiated Herring Groups at Goose Bank in the Barents Sea and the Genetic Relationship to Pacific Herring, Clupea pallasi

Genetic studies on Atlantic herring, Clupea harengus, have generally revealed a low level of genetic variation over large geographic areas. Genetically distinct herring populations in some of the Norwegian fjords are exceptions, and juvenile herring from the large oceanic herring, Norwegian Spring Spawners (NSS), are often found in mixture with local fjord populations as well as widely distributed in the Barents Sea. Research surveys in the eastern Barents Sea (Goose Bank) in 1993, 1994 and 2001 included collection of herring samples for allozyme analyses. As expected the results identified juveniles from NSS stock, but an additional unique group of herring (low vertebrae number), being almost fixed for alternative alleles at several allozyme loci, was detected. In some cases, the two groups of herring were taken in the same trawl catches as documented by highly significant departure from Hardy—Weinberg expectation with large excess of homozygotes providing evidence for population mixing. Large genetic differences (Nei's genetic distance = 1.53; F_ST = 0.754) were detected in pairwise comparisons based on five allozyme loci. The two herring groups were also compared with reference samples of Pacific herring, Clupea pallasi, including one sample from Japan Sea and three Alaskan samples. UPGMA dendrogram based on five allozyme loci revealed a close genetic relationship between the low vertebrae herring in the Barents Sea and the group of samples of Pacific herring. Although significant different in allele frequencies, one of the herring samples clustered together with the reference sample from Bering Sea with genetic distance of 0.008 and F_ST value of 0.032. The close genetic relationship found in this paper, suggest a re-evaluation of the taxonomic status of the Barents Sea herring populations investigated.     

Isolation by distance and Pleistocene expansion of the lowland populations of the white piranha Serrasalmus rhombeus

The genetic variability and distribution of Amazonian fish species have likely been influenced by major disturbance events in recent geological times. Alternatively, the great diversity of aquatic habitat in the Amazon is likely to shape ongoing gene flow and genetic diversity. In this context, complex patterns of genetic structure originating from a joint influence of historical and contemporary gene flow are to be expected. We explored the relative influence of Pleistocene climatic fluctuations and current water chemistry on the genetic structure of a piranha, Serrasalmus rhombeus, in the Upper Amazon by the simultaneous analysis of intron length polymorphism and mitochondrial DNA sequences. The Madeira river is well suited for that purpose as it is characterized by a great diversity of water types, the presence of one of the largest floodplain of the Amazon and the potential occurrence of two Pleistocene refuges. We found evidence of genetic structure even at a small geographical scale (less than 10 km), indicating that the floodplain is not a homogenizing factor promoting interdrainage dispersal in S. rhombeus. Likewise, the hierarchical genetic structure inferred was correlated to geographical distance instead of habitat characteristic. Our results also support the hypothesis that the area underwent population expansion during the last 800 000 years. In addition, a higher level of genetic diversity was found in the samples from the putative Aripuanã refuge. The present findings suggest that Pleistocene refuges contributed significantly to the colonization of the lowlands in the Upper Amazon valley during the Pleistocene.