Genetic Differentiation between Geographically Distant Populations of DROSOPHILA MELANOGASTER

We have studied allozyme variation at 26 gene loci in nine populations of Drosophila melanogaster originating on five different continents. The distant populations show significant genetic differentiation. However, only half of the loci studied have contributed to this differentiation; the other half show identical patterns in all populations. The genetic differentiation in North American, European and African populations is correlated with the major climatic differences between north and south. These differences arise mainly from seven loci that show gene-frequency patterns suggestive of latitudinal clines in allele frequencies. The clinal variation is such that subtropical populations are more heterozygous than temperate populations. These results are discussed in relation to the selectionist and neutralist hypotheses of genetic variation in natural populations.     

Genetic variability and divergence between populations and species of Nesticus cave spiders

Genetic variability and divergence at 21 enzyme loci were studied in and between Italian populations of the cave spiders Nesticus eremita (13 populations), N. menozzii and N. sbordonii (one population each). The three species differ with respect to the degree of specialization to cave life, dispersion ability, isolation of populations, abundancy, extent of the distribution area, and range from the troglophilic and widespread N. eremita to the troglobitic N. sbordonii, endemic to a single cave in the Central Appennines.Heterozygosity ranges from 0.05 to 0.15 in N. eremita populations and appears to be largely controlled by the occurrence and the extent of gene flow among populations. The relatively low polymorphism levels of N. menozzii (H=0.081) and N. sbordonii (H=0.106) are also associated with reduced gene flow and small population sizes.Genetic distances between N. eremita populations vary considerably and are strictly related to the geographical distances involved, again indicating a major role of gene flow in determining the patterns of genetic differentiation between populations. This view is strongly supported by the results of a principal component analysis applied to the gene-frequency data. Estimates of genetic divergence between species suggest that the major cladogenetic events leading to complete separation of these three Nesticus species occurred in the Middle-late Pliocene.     

Genetic population structure in a troglobitic beetle (Speonomus zophosinus)

Genetic variation of five variable loci was analyzed for troglobitic beetles within and between populations along the Salat and Arac Rivers in the central Pyrenees; the patterns of variation are described. Significant genetic differentiation was found for Speonomus zophosinus from populations in close proximity (10 km), largely due to differences between two groups of three populations. F_ST values range from 0.004 (Phi) to 0.354 (Est-6). Within a region, populations on opposite banks are genetically similar. Within populations genotypic frequencies were not in Hardy-Weinberg equilibrium. For troglobitic species such as S. zophosinus, gene flow is a function of intrinsic (active movement and reproductive strategy) and extrinsic factors (geologic structure of the subterranean environment). It seems that natural selection has played little, if any, role in generating the observed gene frequency patterns. The patterns of variation are most reasonably explained as having resulted from genetic dirft occurring between two areas separated by an inhospitable habitat which acts as a dispersal barrier or limits gene flow.     

Free-Running Locomotor Activity Rhythms in Cave-Dwelling Catfishes,Trichomycterus sp., from Brazil (Teleostei,Siluriformes)

Locomotor activity of troglobitic (cave restricted) catfishes, Trichomycterus sp., was recorded in the laboratory under constant darkness for ten consecutive days. Infra-red photocell beam crossings were totalled every thirty minutes and stored for later analysis. Spectral analysis of the data followed by a statistical test designed for the detection of significant components was then performed. The results of 14 individuals, seven pigmented and seven albino fishes, are reported here. In eight individuals, four pigmented and four albinos, we were not able to detect significant components in the circadian range, although ultradian and/or infradian significant components were found in all cases. Former studies on other two Brazilian cave catfishes, Pimelodella kronei and Imparfinis sp., showed similar results, suggesting a picture of gradual loss of circadian rhythmicity and persistence of ultradian and infradian rhythms in the locomotor activity of troglobitic populations. The proportion of specimens without significant circadian components was higher in Trichomycterus sp., supposedly less specialized to cave life than the other two species. This is tentatively correlated with a higher environmental stability during the time of evolutionary isolation in the subterranean biotope. These results provide strong arguments for the importance of external selection over circadian rhythmicity.     

Free-Running Locomotor Activity Rhythms in Cave-Dwelling Catfishes, Trichomycterus sp., from Brazil (Teleostei, Siluriformes)

Locomotor activity of troglobitic (cave restricted) catfishes, Trichomycterus sp., was recorded in the laboratory under constant darkness for ten consecutive days. Infra-red photocell beam crossings were totalled every thirty minutes and stored for later analysis. Spectral analysis of the data followed by a statistical test designed for the detection of significant components was then performed. The results of 14 individuals, seven pigmented and seven albino fishes, are reported here. In eight individuals, four pigmented and four albinos, we were not able to detect significant components in the circadian range, although ultradian and/or infradian significant components were found in all cases. Former studies on other two Brazilian cave catfishes, Pimelodella kronei and Imparfinis sp., showed similar results, suggesting a picture of gradual loss of circadian rhythmicity and persistence of ultradian and infradian rhythms in the locomotor activity of troglobitic populations. The proportion of specimens without significant circadian components was higher in Trichomycterus sp., supposedly less specialized to cave life than the other two species. This is tentatively correlated with a higher environmental stability during the time of evolutionary isolation in the subterranean biotope. These results provide strong arguments for the importance of external selection over circadian rhythmicity.     

The genus Vietbocap Lourenço & Pham, 2010 in the Thien Duong cave,Vietnam: A possible case of subterranean speciation in scorpions (Scorpiones: Pseudochactidae)

Two new species of scorpion belonging to the family Pseudochactidae and to the genus Vietbocap are described based on specimens collected in the Thien Duong cave, which belongs to the Vom cave system, in the Phong Nha–Ke Bang National Park, Quang Binh Province, Vietnam. The previously described species from this cave, Vietbocap thienduongensis Lourenço & Pham, 2012 was collected in the initial section of the cave (1500 to 1800 m from the cave entrance) and proved to be a true troglobitic element. The diagnosis of this species, only known from males, is completed based on females collected at 750 m from the cave entrance. The two new species described here were collected respectively at 3000 and 5000 m from the cave entrance and are also true troglobitic elements, very similar to V. thienduongensis, but showing some clear morphological differences. This observed situation suggests a possible case of speciation within the cave system, the first one ever reported for scorpions. The population found at 5000 m from the entrance of the cave is a total new record of distance from a cave entrance for scorpions.     

The first troglobitic species of freshwater flatworm of the suborder Continenticola (Platyhelminthes) from South America

Brazilian cave diversity, especially of invertebrates, is poorly known. The Bodoquena Plateau, which is located in the Cerrado Biome in central Brazil, has approximately 200 recorded caves with a rich system of subterranean water resources and high troglobitic diversity. Herein we describe a new troglobitic species of Girardia that represents the first obligate cave-dwelling species of the suborder Continenticola in South America. Specimens of the new species, which occur in a limestone cave in the Bodoquena Plateau, in the Cerrado biome, are unpigmented and eyeless. Species recognition in the genus Girardia is difficult, due to their great morphological resemblance. However, the new species can be easily recognized by a unique feature in its copulatory apparatus, namely a large, branched bulbar cavity with multiple diverticula.     

Studies in cave life evolution: a rationale for future theoretical developments using phylogenetic inference

As in every field of comparative biology, phylogeny provides an independent reference system in studies on cave life evolution to test current theoretical proposals. Using phylogeny, sound hypotheses on the ancestral states of characters and their subsequent changes can be made by polarizing the characters between related taxa. Hypotheses on evolutionary processes can also be tested by comparing the patterns they imply with independently inferred phylogenetic patterns. The power of the tests relies upon the independence of phylogenetic patterns (built with cladistics using Wagner parsimony) and the theoretical proposals under study. Classical assumptions on the evolution of troglobitic life are analysed with this methodology. The following points are discussed: what is a troglobitic taxon? Are there features characteristic of troglobitic taxa? Is troglobitic life an evolutionary dead end? What circumstances favour troglobitic evolution? Using phylogenetic analysis, the presence or absence of so-called troglomorphic features were inferred in troglobitic taxa. In fact these taxa can be characterized only by their behavioural ecology. Pre-adaptations (exaptations) can also be precisely defined. Cave living does not appear to be an evolutionary dead end. Two patterns subsequent to cave life appearance have been documented: speciation of troglobitic taxa in the subterranean environment, and reversal to an epigean habitat. Troglobitic life thus turns out to be one step in the diversification of clades. Troglobitic life is usually explained as an evolution under the pressure of unfavourable environmental conditions, or the conquest of a new resource, or the result of biological interactions (competition, predation). Phylogenetic analyses show that none of these hypotheses propose clear alternatives on cave life evolution. Moreover most of their a priori statements cannot easily be falsified. As such they have only limited explanatory power.     

Mapping a cave fish genome: polygenic systems and regressive evolution

We used random amplified polymorphic DNA (RAPD) fingerprinting to generate anonymous DNA markers in the fish Astyanax mexicanus, a species with both surface and cave populations. Surface individuals are eyed and pigmented; troglobitic forms are blind and depigmented. We hybridized surface fish and Pachon population cave fish and produced a RAPD genomic map 1064 cM in length (about half the total length of the genome) that was used to screen for quantitative trait loci (QTL) for troglomorphic traits. Three QTL for reduced eye size, two for decreased numbers of melanophores, two for condition factor, and the locus for the unifactorial trait, albinism, were mapped. These factors account for an average of 46% of the variance in these traits in the backcross. The results are the first direct demonstration that troglomorphic changes in this population are multifactorial. Two closely linked pairs of QTL were found. Each consisted of a regressive and a constructive trait QTL. These close linkages are unlikely to have occurred by chance (P <.05 for each) and suggest that troglomorphic evolution might be facilitated by pleiotropy or by genetic hitchhiking.     

Genetic divergence between populations of two closely related troglobitic beetle species (Speonomus: Bathysciinae,Coleoptera)

Genetic variability and divergence at 13 enzyme loci were studied in two species of troglobitic beetles (Speonomus zophosinus andhydrophilus 12 populations) collected from the Pyrenees mountains. These allopatric species exhibit a high degree of specialization to underground life and a very small geographical range. Four diagnostic loci arePgi, Est-2, Pac-1, Phi. Within each species polymorphic loci exhibited marked spatial variation of allele frequencies, sometimes over short distances (5–10 km). The levels of genetic variability are comparable to those observed in non-cave invertebrates (frequency of polymorphic loci: 0.31; average expected heterozygosity: 0.112±0.015). Moreover, a single species showed variability in the average level of heterozygosity (0.06 to 0.172). Patterns of genetic differentiation among species were also studied; mean genetic distance (D: 0.263±0.010) between the twoSpeonomus species was of the same order of magnitude as most data reported in the literature between species. A significant heterozygote deficiency occurs in local populations and for all loci. This deficit does not vary from locus to locus. Several hypotheses were examined in an attempt to account for these observations in connection with the species biology. This deficit probably is due to the breeding structure of the population (inbreeding and assortative mating) coupled with limited dispersal ability.     

Parallel speciation in Astyanax cave fish (Teleostei) in Northern Mexico

We investigated differentiation processes in the Neotropical fish Astyanax that represents a model system for examining adaptation to caves, including regressive evolution. In particular, we analyzed microsatellite and mitochondrial data of seven cave and seven surface populations from Mexico to test whether the evolution of the cave fish represents a case of parallel evolution. Our data revealed that Astyanax invaded northern Mexico across the Trans-Mexican Volcanic Belt at least three times and that populations of all three invasions adapted to subterranean habitats. Significant differentiation was found between the cave and surface populations. We did not observe gene flow between the strongly eye and pigment reduced old cave populations (Sabinos, Tinaja, Pachon) and the surface fish, even when syntopically occurring like in Yerbaniz cave. Little gene flow, if any, was found between cave populations, which are variable in eye and pigmentation (Micos, Chica, Caballo Moro caves), and surface fish. This suggests that the variability is due to their more recent origin rather than to hybridization. Finally, admixture of the young Chica cave fish population with nuclear markers from older cave fish demonstrates that gene flow between populations that independently colonized caves occurs. Thus, all criteria of parallel speciation are fulfilled. Moreover, the microsatellite data provide evidence that two co-occurring groups with small sunken eyes and externally visible eyes, respectively, differentiated within the partly lightened Caballo Moro karst window cave and might represent an example for incipient sympatric speciation.     

Evolutionary convergence on sleep loss in cavefish populations

Patterns of sleep vary widely among species, but the functional and evolutionary principles responsible for this diversity remain unknown. The characin fish, Astyanax mexicanus, has eyed surface and numerous blind cave populations. The cave populations are largely independent in their origins, and the species is ideal for studying the genetic bases of convergent evolution. Here we show that this system is also uniquely valuable for the investigation of variability in patterns of sleep. We find that a clearly defined change in ecological conditions, from surface to cave, is correlated with a dramatic reduction in sleep in three independently derived cave populations of A. mexicanus. Analyses of surface × cave hybrids show that the alleles for reduced sleep in the Pachón and Tinaja cave populations are dominant in effect to the surface alleles. Genetic analysis of hybrids between surface and Pachón cavefish suggests that only a small number of loci with dominant effects are involved. Our results demonstrate that sleep is an evolutionarily labile phenotype, highly responsive to changes in ecological conditions. To our knowledge, this is the first example of a single species with a convergence on sleep loss exhibited by several independently evolved populations correlated with population-specific ecologies.     

Genetic diversity and structure of the endangered species Megaleranthis saniculifolia in Korea as revealed by allozyme and ISSR markers

The genetic diversity and structure of 12 populations of Megaleranthis saniculifolia, a rare endemic Korean plant, were analyzed using 14 allozyme loci coding 10 enzymes and 78 ISSR loci using seven primers. The genetic diversity of M. saniculifolia at the species level was similar to that observed in out-crossing and long-lived perennials, while at the population level, it was significantly low. The high F _IS value of many populations as well as homozygote excess occurred relatively evenly in many populations in relation to the Hardy-Weinberg expectation, suggesting that inbreeding was occurring within the M. saniculifolia populations. The degree of genetic differentiation based on the two markers was high, and there was no correlation between geographic and genetic distance. Bayesian cluster analysis did not reveal any remarkable geographic trends. Positive correlations were observed between genetic diversity (H _e and h) and population size. Therefore, low genetic diversity within the population and high population differentiation of M. saniculifolia were closely related to the influence of genetic drift, particularly in highly isolated populations. In addition, the fixation of the main alleles at several loci in the opposite direction provided good evidence for genetic drift. The genetic diversity of M. saniculifolia could be compromised if the distribution area or the size of the population were further reduced. In particular, the isolated populations that are fragmented within an area could be at high risk of extinction due to accelerated inbreeding or genetic drift. Considering this, a close monitoring of the population size and of the changes in the genetic structure must be performed. Some practical measures for genetic conservation are also proposed.     

Dwindling genetic diversity in European ground squirrels?

The European ground squirrel (Spermophilus citellus) is endangered and in decline. Populations are increasingly fragmented, and only a coordinated conservation effort at the European level may guarantee its long-term survival. To obtain a general population genetic picture on a larger geographic scale, we screened 117 individuals from seven local populations in Hungary, Romania, and Austria for allelic variation at eleven microsatellite loci. We found a high (23.4%) proportion of private alleles, and a moderate to somewhat elevated level (15.27%) of partitioning of genetic diversity among populations, compared to that found in many other terrestrial mammals. Genetic variability was significantly higher than in earlier studied Czech populations that are considered genetically depleted, but significantly lower than in undisturbed populations of S. suslicus and S. brunneus, that are similar to the European ground squirrel in their ecological requirements, reproductive biology, and social organization. Genetic diversity was also lower than in most presumably “undisturbed” populations of other Sciurid species. This, together with the observed level and pattern of genetic differentiation among populations, such as no significant increase of genetic differentiation with geographic distance and similar variance of genetic differentiation between populations independent of geographic distance, indicated the prevalence of relatively strong drift effects for all populations. A Bayesian STRUCTURE analysis and a factorial correspondence analysis concordantly revealed a fairly complex genetic composition of local populations, but no major geographic trend in the pattern of the genetic composition. Overall, the results suggest disintegration of local colonies that might earlier have been more connected genetically. The STRUCTURE analysis also suggested anthropogenic translocations among single Hungarian populations. Our data on genetic diversity and its distribution do not object to such conservation measures. Translocation of individuals particularly from nearby populations may increase the chances of survival of small and isolated populations and counteract inbreeding at low densities.     

Low genetic differentiation among widely separated populations of the pearl oyster Pinctada fucata as revealed by AFLP

Genetic variation within and among five populations of the pearl oyster Pinctada fucata, from China (Daya Bay, Sanya Bay and Beibu Bay), Japan (Mie Prefecture) and Australia (Port Stephens) was studied using AFLP. Three primer pairs generated 184 loci among which 91.8-97.3% is polymorphic. An overall genetic diversity of 0.38 among populations and an average of 0.37 within populations (ranging from 0.35 in Japanese population to 0.39 in Beibu Bay population) were observed. Genetic differentiation among the five populations is low but significant as indicated by pairwise G_ST (0.0079-0.0404). AMOVA further shows that differentiation is significant among the five populations but is not significant at a broader geographical scale, among the three groups of Chinese, Japanese and Australian populations or among the two groups of Australian and north Pacific populations. The low level of genetic differentiation indicated that P. fucata populations in the west Pacific are genetically linked. Among the five populations, the Australian one is more differentiated from the others, based on both pairwise AMOVA and G_ST analyses, and is genetically isolated by distance as indicated by Mantel test. However, genetic differences among the three Chinese populations are not correlated with the geographic distances, suggesting that Hainan Island and Leizhou Peninsula may act as barriers blocking gene flow.     

The cave population of Chaerilus Simon, 1877 from Palawan,Philippines, and description of a new species (Scorpiones: Chaerilidae)

The study of an important collection of scorpions, belonging to the genus Chaerilus, recently collected from a cave in the Palawan Island, Philippines, allows the clarification of the identity of this population, often misidentified with Chaerilus chapmani Vachon & Lourenço, 1985 known from caves in the Gunong Mulu National Park in Sarawak (Borneo). Chaerilus agnellivanniorum sp. n. is described from the Puerto Princesa Underground River Cave in Palawan Island based on 14 specimens, males, females, and juveniles. The new species is totally distinct morphologically from Chaerilus chapmani, a true troglobitic species. Chaerilus agnellivanniorum sp. n. may also be a true troglobitic element, but with a less marked degree of regression for several characters. Some comments on the ecology of the new species and on regional biogeography of Borneo and Palawan islands are also proposed.     

Genetic variability, population size and reproduction potential in Ligularia sibirica (L.) populations in Estonia

Ligularia sibirica (L.) Cass. (Asteraceae) is a EU Habitats Directive Annex II plant species that has suffered a lot from human-caused major changes in quality and availability of habitats in Estonia. The aim of this study was to find out if the observed decline in population size is reflected in the amount of genetic variation and fertility in remnant populations of this species. AFLP technique was used for that purpose. Genetic diversity within populations was assessed as the percentage of polymorphic loci in a given population and average gene diversity over loci. The degree of genetic differentiation among populations and genetic differentiation between pairs of populations was estimated. The amount of viable seeds per flower stem was compared among populations and between years (2007 and 2008). Average genetic diversity over loci and proportion of polymorphic loci in L. sibirica populations were significantly correlated with population size, suggesting the action of genetic drift and/or inbreeding. No correlation was found between genetic and geographic distances. Natural barriers like forests may have been efficiently preventing seed migration even between geographically closer populations. Results of this study suggest that genetic erosion could be partially responsible for the lower fitness in smaller populations of this species.     

Population studies on an endemic troglobitic beetle: geographical patterns of genetic variation, gene flow and genetic structure compared with morphometric data

Highly specialized obligatory cave beetles endemic to the French Pyrenees offer an opportunity to investigate the relative importance of environmental conditions and ecological characteristics on the organization of genetic variability, to describe the genetic structure of populations, and to assess the extent of gene flow between local populations in relation to geologic structure. Twenty-three geographically close populations of the beetle Speonomus hydrophilus occurring both in caves (reduced fluctuations in many abiotic parameters) and under the deepest layer of soil in mountains (more exposed to climatic variations) were studied. Significant genetic differentiation at 17 allozyme loci was found among populations in close proximity, as well as among those from distant parts of range. On a larger scale, genetic differences among populations appear to result from low dispersal rates between populations. The spatial patterning observed suggests that allozyme frequencies are not responding to environmentally controlled selection. Substantial genetic divergence (F(ST) = 0.112) occurred throughout the range, with important variation in levels of genetic variability (H: 0.065-0.184) among populations. A significant level of substructuring has occurred among the populations with four major geographic areas of similarity indicated. The substructuring of the species into regions suggests an influence of paleoclimatic gradient and paleoenvironment on the population's genetic structure. Also, founder effect and reduced gene flow appear to have influenced populations in the southeastern portion of the range.     

Complex genetic structures of Sardinella zunasi in the Northwest Pacific detected by AFLP markers

Seventy-one Sardinella zunasi individuals collected from 5 locations in the Northwest Pacific were used in an AFLP analysis to examine the population genetic structure of S. zunasi. Using 4 selective primer combinations, 414 putative loci were detected, including 340 polymorphic loci (82.13%). Both AMOVA and pairwise F_ST analysis detected significant population genetic structure between Chinese and Japanese populations, supporting separate stocks in this species. The UPGMA trees also detected significant spatial structure within S. zunasi. Pleistocene glaciations are hypothesized to be responsible for the genetic differentiation. The significant genetic differentiation found among S. zunasi populations might also be due to geographic isolation, because a pattern of isolation-by-distance was observed. The weaker but significant structures between the Japanese Aichi and Kagawa populations might be impacted by the semi-enclosed coastal topography there. No significant genetic structure was detected among the Chinese populations, perhaps because of S. zunasi’s migratory behavior and ocean current patterns.     

A Comprehensive Study of Genic Variation in Natural Populations of Drosophila melanogaster. III. Variations in Genetic Structure and Their Causes between Drosophila melanogaster and Its Sibling Species Drosophila simulans

The natural populations of Drosophila melanogaster and Drosophila simulans were compared for their genetic structure. A total of 114 gene-protein loci were studied in four mainland (from Europe and Africa) and an island (Seychelle) populations of D. simulans and the results were compared with those obtained on the same set of homologous loci in fifteen worldwide populations of D. melanogaster. The main results are as follows: (1) D. melanogaster shows a significantly higher proportion of loci polymorphic than D. simulans (52% vs. 39%, P<0.05), (2) both species have similar mean heterozygosity and mean number of alleles per locus, (3) the two species share some highly polymorphic loci but they do not share loci that show high geographic differentiation, and (4) D. simulans shows significantly less geographic differentiation than D. melanogaster. The differences in genetic differentiation between the two species are limited to loci located on the X and second chromosomes only; loci on the third chromosome show similar level of geographic differentiation in both species. These two species have previously been shown to differ in their pattern of variation for chromosomal polymorphisms, quantitative and physiological characters, two-dimensional electrophoretic (2DE) proteins, middle repetitive DNA and mitochondrial DNA. Variation in niche-widths and/or genetic "strategies" of adaptation appear to be the main causes of differences in the genetic structure of these two species.