Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola

The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data. Received: 12 January 1996 / Accepted: 10 August 1996     

三江平原农田土壤跳虫多尺度空间自相关性

土壤动物多尺度空间自相关性特征是土壤动物空间异质性和空间共存格局研究的重要基础。以土壤跳虫为研究对象,以中国科学院三江平原沼泽湿地生态实验站为研究区,于2011年8月和10月,选取具30 a以上耕作历史的旱地为实验样地,以5 m为步长设置一个50 m×50 m的实验样地,采用地统计中的全局Moran's I指数和局部Moran's I指数相结合的方法,研究土壤跳虫多尺度空间自相关性特征。全局空间自相关结果表明,土壤跳虫群落总密度和多数跳虫种类存在显著的多尺度空间自相关特征,多数为显著的正的空间自相关性,形成明显的空间集群。局部空间自相关结果表明,土壤跳虫群落总密度和所有跳虫种类均存在显著的局部空间自相关性,在局部地区形成"高—高"和/或"低—低"的空间集群,并和"高—低"和/或"低—高"的空间孤立区相伴发生,即形成"斑块"和"孔隙"相间分布的水平镶嵌格局;这种镶嵌格局具一定的时间动态特征,从夏季到秋季斑块大小和空间分布范围略有变化。研究表明,土壤跳虫具有明显的多尺度空间自相关性;空间集群是土壤跳虫的常见空间分布格局,在样地内形成"斑块"和"孔隙"相间分布的水平镶嵌格局,这种格局具年内时间变异性。     

Springtails (Collembola) of eastern Chukotka: Characteristics of the fauna and species assemblages

A total of 139 collembolan species from 55 genera were found in coastal tundra near the settlement of Lavrentiya in the eastern part of the Chukchi Peninsula. The local fauna of the region is quite “Beringian” in species composition but its structure appears to be in full agreement with the known characteristics of southern tundra faunas of other sectors in the Arctic. The specificity of collembolan complexes of the main plant associations in the studied area is not very high because the predominant collembolan species usually inhabit a wide range of communities. The performed study on Collembola fails to confirm the conventional view of a significantly higher diversity of northeastern Palaearctic faunas. Despite the rather southern position of the studied coastal tundra, the species richness of its collembolan fauna seems to be the same as or only slightly higher than that of analogous landscapes in the other Arctic sectors. The apparent discrepancy between relatively low diversity of Collembola at the local level as shown herein and its rich regional fauna may be the result of increased differentiation of the collembolan fauna of the region characterized by very complex orography and extremely contrasting climatic conditions.     

Genomic Consequences of Ecological Speciation in Astyanax Cavefish

The cave environment is consistently radically different than the surface environment because it lacks light, and animals adapting to cave life are subject to strong selective forces much different than those experienced by their ancestors who evolved in the presence of light. As such, their divergence from surface ancestors and eventual speciation is likely to be driven by the shift in ecology. We report here that hybrids between cave and surface Astyanax mexicanus fishes produce offspring with allelic frequencies that differ significantly from Mendelian expectations both for transmission ratios and for independent assortment of unlinked markers. Comparison of allelic content of DNA from fin clips and sperm pools show that the transmission ratio distortion likely occurs during spermatogenesis. Departures from expectations of independent assortment are essentially epistatic phenomena generating linkage disequilibrium. A novel analysis of the epistatic interactions reveals an apparent network of interactions among genes known or suspected to be involved in cave adaptation, implying that the epistasis arose as a “by product” of the divergence due to cave adaptation.     

Cyto‐nuclear discordance suggests complex evolutionary history in the cave‐dwelling salamander,Eurycea lucifuga

Our understanding of the evolutionary history and ecology of cave‐associated species has been driven historically by studies of morphologically adapted cave‐restricted species. Our understanding of the evolutionary history and ecology of nonrestricted cave species, troglophiles, is limited to a few studies, which present differing accounts of troglophiles’ relationship with the cave habitat, and its impact on population dynamics. Here, we used phylogenetics, demographic statistics, and population genetic methods to study lineage divergence, dates of divergence, and population structure in the Cave Salamander, Eurycea lucifuga, across its range. In order to perform these analyses, we sampled 233 individuals from 49 populations, using sequence data from three gene loci as well as genotyping data from 19 newly designed microsatellite markers. We find, as in many other species studied in a phylogeographic context, discordance between patterns inferred from mitochondrial relationships and those inferred by nuclear markers indicating a complicated evolutionary history in this species. Our results suggest Pleistocene‐based divergence among three main lineages within E. lucifuga corresponding to the western, central, and eastern regions of the range, similar to patterns seen in species separated in multiple refugia during climatic shifts. The conflict between mitochondrial and nuclear patterns is consistent with what we would expect from secondary contact between regional populations following expansion from multiple refugia.     

Revisiting the phylogeny of Wolbachia in Collembola

The endosymbiont Wolbachia has been detected in a few parthenogenetic collembolans sampled in Europe and America, including three species of Poduromorpha, two species of Entomobryomorpha, and two species of Neelipleona. Based on 16S rRNA and ftsZ gene sequences, most of the Wolbachia infecting parthenogenetic collembolans were characterized as members of supergroup E and showed concordant phylogeny with their hosts. However, the two neelipleonan symbionts form another unique group, indicating that Wolbachia has infected parthenogenetic collembolans multiple times. In this study, five parthenogenetic collembolan species were identified as hosts of Wolbachia, and four new Wolbachia strains were reported for four collembolan species sampled in China, respectively, including a neelipleonan strain from Megalothorax incertus (wMinc). Our results demonstrated that the Wolbachia multilocus sequence typing (MLST) system is superior to the 16S rRNA + ftsZ approach for phylogenetic analyses of collembolan Wolbachia. The MLST system assigned these Wolbachia of parthenogenetic collembolans to supergroup E as a unique clade, which included wMinc, supporting the monophyletic origin of Wolbachia in parthenogenetic collembolan species. Moreover, our data suggested supergroup E as one of the most divergent lineages in Wolbachia and revealed the discrepancy between the phylogenies of Wolbachia from parthenogenetic collembolans and their hosts, which may result from the high level of genetic divergence between collembolan Wolbachia, in association with the geographic differentiation of their hosts, or the possible horizontal transmission of Wolbachia between different collembolan species.     

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.     

Seasonal changes in soil arthropod abundance in the dry evergreen forest of north-east Thailand,with special reference to collembolan communities

A soil arthropod community was studied in a dry evergreen forest over a 3-year period from May 1998 to April 2001. Population abundance, species composition, and community structure were investigated over the 3-year study period. The soil arthropods consisted of Acari (75.38%), Collembola (16.11%), and others (8.51%), and their abundances showed a clear difference between the rainy and dry seasons. Population abundance of Collembola and Acari were low during drought conditions. The humidity was the most important factor determining distribution, abundance, and survival of soil Collembola in this tropical forest. High predation and low accumulation of organic matter caused low population abundance of Collembola in the tropical habitat. The collembolan community was dominated by a few dominant species over the study period. The pattern of seasonal changes in numbers of Collembola was similar over the 3-year study period. The species composition of the collembolan community was constant and persistent throughout a 3-year study period. Thus, the collembolan community showed constancy in its species composition with seasonal variability over the 3-year study period.     

Molecular phylogeny of the extinct cave lion Panthera leo spelaea

To reconstruct the phylogenetic position of the extinct cave lion (Panthera leo spelaea), we sequenced 1 kb of the mitochondrial cytochrome b gene from two Pleistocene cave lion DNA samples (47 and 32 ky B.P.). Phylogenetic analysis shows that the ancient sequences form a clade that is most closely related to the extant lions from Africa and Asia; at the same time, cave lions appear to be highly distinct from their living relatives. Our data show that these cave lion sequences represent lineages that were isolated from lions in Africa and Asia since their dispersal over Europe about 600 ky B.P., as they are not found among our sample of extant populations. The cave lion lineages presented here went extinct without mitochondrial descendants on other continents. The high sequence divergence in the cytochrome b gene between cave and modern lions is notable.     

Flow field,swimming velocity and boundary layer: parameters which affect the stimulus for the lateral line organ in blind fish

The data presented support the hypothesis that the flow field supplies the stimulus to the lateral line organ (LLO) in blind cave fish (Anoptichthys jordani). Two basic predictions from the theoretical analysis of the flow field were confirmed: (i) individual blind cave fish prefer particular swimming velocities, (ii) the velocity preferred depends on the cross-sectional area (CSA) of the fish, i.e. the smaller the CSA the higher the swimming velocity. This relationship was found also in experimentally blinded fish of other species. Furthermore, when placed in unfamiliar surroundings, blind cave fish swim at higher velocities than in familiar surroundings for a certain habituation period. The boundary layer which surrounds the fish attenuates the amplitude of the hydrodynamic stimulus because of its damping properties. Computations of the current velocity distribution within the boundary layer indicate that the stimulus for freestanding neuromasts is considerable even during swimming in open water.     

Molecular and evolutionary analyses of formyl peptide receptors suggest the absence of VNO-specific FPRs in primates

Formyl peptide receptors (FPRs) were observed to expand in rodents and were recently suggested as candidate vomeronasal chemo-sensory receptors. Since vomeronasal chemosensory receptors usually underwent positive selection and evolved concordantiy with the vomeronasal organ (VNO) morphology, we surveyed FPRs in primates in which VNO morphology is greatly diverse and thus it would provide us a clearer view of VNO-FPRs evolution. By screening available primate genome sequences, we obtained the FPR repertoires in representative primate species. As a result, we did not find FPR family size expansion in primates. Further analyses showed no evolutionary force variance between primates with or without VNO structure, which indicated that there was no functional divergence among primates FPRs. Our results suggest that primates lack the VNO-specific FPRs and the FPR expansion is not a common phenomenon in mammals outside rodent lineage, regardless of VNO complexity.     

Phylogeography of surface and cave Astyanax (Teleostei) from Central and North America based on cytochrome b sequence data

Astyanax fasciatus has become a model organism for the study of regressive and adaptive evolution in cave animals. To fully understand these processes, it is important to have background information on the systematics and phylogeography of surface and cave populations of this species. Here we investigate the phylogeography of A. fasciatus in North and Central America and also the historical biogeography of this region. Phylogenetic analysis of part of the mtDNA cytochrome b gene from 26 surface and nine cave A. fasciatus populations revealed seven major clades, which, in principle, represent geographical patterns of distribution. However, the four strongly eye and pigment reduced cave populations, Piedras, Sabinos, Tinaja, and Curva, form a separate cluster, which is not sister group to the surface populations from the same locality. Similarly the Belizean populations do not cluster with their geographic neighbors from the Yucatan. The analyses indicate that there have been recurrent invasions of surface Astyanax from the south, that were most likely influenced by major climate changes during the Pleistocene. During this period, ancestors of the strongly eye and pigment reduced cave populations were able to survive underground as thermophilic relics when the surface populations became extinct. The high level of genetic divergence among the different clades shows that differing haplotype lineages must have reinvaded the surface waters from the south and/or back-colonized them from residual habitats and also penetrated into the caves. Nested clade analyses show that recurrent gene flow as well as historic processes like past fragmentation and range expansion have influenced current populations of A. fasciatus in Central and North America. Different haplotype clades of the phylogeny are not compatible with the present taxonomy of Astyanax and, therefore, we propose the application of a single systematic unit, called A. fasciatus.     

Molecular evolution and functional divergence of the cytochrome P450 3 (CYP3) Family in Actinopterygii (ray-finned fish)

Background

The cytochrome P450 (CYP) superfamily is a multifunctional hemethiolate enzyme that is widely distributed from Bacteria to Eukarya. The CYP3 family contains mainly the four subfamilies CYP3A, CYP3B, CYP3C and CYP3D in vertebrates; however, only the Actinopterygii (ray-finned fish) have all four subfamilies and detailed understanding of the evolutionary relationship of Actinopterygii CYP3 family members would be valuable.

Methods and Findings

Phylogenetic relationships were constructed to trace the evolutionary history of the Actinopterygii CYP3 family genes. Selection analysis, relative rate tests and functional divergence analysis were combined to interpret the relationship of the site-specific evolution and functional divergence in the Actinopterygii CYP3 family. The results showed that the four CYP3 subfamilies in Actinopterygii might be formed by gene duplication. The first gene duplication event was responsible for divergence of the CYP3B/C clusters from ancient CYP3 before the origin of the Actinopterygii, which corresponded to the fish-specific whole genome duplication (WGD). Tandem repeat duplication in each of the homologue clusters produced stable CYP3B, CYP3C, CYP3A and CYP3D subfamilies. Acceleration of asymmetric evolutionary rates and purifying selection together were the main force for the production of new subfamilies and functional divergence in the new subset after gene duplication, whereas positive selection was detected only in the retained CYP3A subfamily. Furthermore, nearly half of the functional divergence sites appear to be related to substrate recognition, which suggests that site-specific evolution is closely related with functional divergence in the Actinopterygii CYP3 family.

Conclusions

The split of fish-specific CYP3 subfamilies was related to the fish-specific WGD, and site-specific acceleration of asymmetric evolutionary rates and purifying selection was the main force for the origin of the new subfamilies and functional divergence in the new subset after gene duplication. Site-specific evolution in substrate recognition was related to functional divergence in the Actinopterygii CYP3 family.     

Population genetics of grotto sculpin (Cottus specus), a new cave-adapted fish species

The grotto sculpin (Cottus specus) is a troglomorphic fish endemic to cave systems in Perry County, Missouri. These fish are state-threatened and were recently listed as federally endangered under the Endangered Species Act (ESA). Due to the unstable nature of the cave environment, grotto sculpins are highly susceptible to pollution via agricultural and waste runoff. Here we provide a summary of population genetic diversity within the range of the grotto sculpin. Samples from twenty-one cave, surface, and resurgence sites within and surrounding the Bois Brule drainage in Perry County, southeast Missouri, USA were collected and sequence data from the mitochondrial control were analyzed using analysis of molecular variance, maximum likelihood, parsimony, and Bayesian techniques. We found a substantial degree of divergence from surface populations of Midlands and Black River banded sculpin races (7.7–8.0 %). Within the Bois Brule drainage, two distinct lineages of grotto sculpin were identified which correspond with northern and southern cave system boundaries and may represent independent cave invasions.     

Ultrastructure and function of the labial nephridia and the rectum of Orchesella cincta (L.) (Collembola)

Summary The collembolan Orchesella cincta possesses a well-developed coelomoduct kidney. The presence of podocytes in the wall of the sacculus and the fact that the epithelium of the nephridial tubule has the ultrastructural characteristics of resorbing cells, indicate that this is an ultrafiltration-reabsorption kidney.Apparently also the rectum is lined by a reabsorptive epithelium; the cells possess an extensive system of apical and basal infoldings. This view is sustained by the fact that the stereology of the apical channel system varies in animals kept under different moisture conditions. During the intermoult period, both organs are subject to strong morphological changes, which are obviously related to the feeding rhythm.The authors wish to thank Dr. T. Sminia for his stimulating interest during the investigations, Dr. J.C. Jager for statistical advice and Mr. G.W.H. van den Berg for drawing the figures     

Experimental Detritus Manipulations Unite Surface and Cave Stream Ecosystems Along a Common Energy Gradient

Subsidies of detritus from donor habitats are important energy sources for many ecosystems, but understanding their role in structuring recipient food webs requires comparative experimental studies along the full spectrum of detrital fluxes. Here we report results from an experimental addition of maize (Zea mays L.) litter to a detritus-poor cave stream ecosystem, which we then compare with analogous, past experiments using detritus-rich surface stream ecosystems that similarly have detritus-based food webs and extremely low in situ primary production. Bulk-tissue and compound-specific stable isotope analyses showed that maize litter carbon (C) was rapidly assimilated by microbes and transferred via successive trophic levels to the top of the cave stream food web (omnivorous crayfishes and predatory salamanders). All trophic levels increased in abundance and biomass, but only facultative cave taxa, that is those also found in surface streams, contributed to this numerical response. The lack of response by obligate cave species presumably occurred because evolutionary trade-offs associated with adaptations to low-C environments constrained their population-level responses during the one-year period of the litter addition. Comparison of the responses of the cave community with the analogous litter manipulation experiments in surface streams showed strong convergence in the functional relationship between invertebrate and detritus biomass (R ² = 0.72, P < 0.0001). Our results suggest that these seemingly disparate stream food webs lie along a single, common gradient of detritus supply, occupied at its extreme minimum by communities of obligate cave taxa adapted to low-energy environments.     

Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals?

The brown bear has proved a useful model for studying Late Quaternary mammalian phylogeography. However, information is lacking from northern continental Eurasia, which constitutes a large part of the species' current distribution. We analysed mitochondrial DNA sequences (totalling 1943 bp) from 205 bears from northeast Europe and Russia in order to characterize the maternal phylogeography of bears in this region. We also estimated the formation times of the sampled brown bear lineages and those of its extinct relative, the cave bear.
Four closely related haplogroups belonging to a single mitochondrial subclade were identified in northern continental Eurasia. Several haplotypes were found throughout the whole study area, while one haplogroup was restricted to Kamchatka. The haplotype network, estimated divergence times and various statistical tests indicated that bears in northern continental Eurasia recently underwent a sudden expansion, preceded by a severe bottleneck. This brown bear population was therefore most likely founded by a small number of bears that were restricted to a single refuge area during the last glacial maximum. This pattern has been described previously for other mammal species and as such may represent one general model for the phylogeography of Eurasian mammals. Bayesian divergence time estimates are presented for different brown and cave bear clades. Moreover, our results demonstrate the extent of substitution rate variation occurring throughout the phylogenetic tree, highlighting the need for appropriate calibration when estimating divergence times.     

The ontogeny and maintenance of adult symmetry properties in the ctenophore, Mnemiopsis mccradyi

Ctenophores are biradially symmetrical animals. The body is composed of four identical quadrants which are organized along an oral-aboral axis. Most species have eight comb rows, two tentacles, and an apical organ (located on the aboral surface). During embryogenesis there is a fixed pattern of cleavage, a precocious specification of blastomere developmental potential, and an inability to regulate for portions of the embryo that have been removed. When blastomeres are separated at the two-cell stage each blastomere develops into a "half-animal" with four comb rows, one tentacle, and half an apical organ. In contrast, adult ctenophores regenerate readily. When an adult ctenophore is cut in half to produce "half-animals," in most cases each half regenerates the missing half. In some cases, however, bisected animals remain as "half-animals" which repair the wound site but do not replace all of the missing structures. When animals are cut in half along the tentacular or esophageal axis at different stages of embryogenesis a transition period is detected when the capacity for adult regeneration begins. This transition occurs at the time when the formation of the apical organ is complete and comb row function becomes coordinated. Embryos bisected prior to this time remain as "half-animals" even after growing to large reproductive sizes, while animals bisected after the transition period usually regenerate the missing structures within 2-3 days. When adult "half-animals" (produced by bisection either before or after the transition period) are cut into "quarter-pieces," the pieces regenerate to form either "half-animals" or whole animals. Thus, "half-animals" produced prior to the transition period--although they failed to undergo embryonic regulation--have not irreversibly lost the capacity to form whole animals if challenged to regenerate during adult stages. When aboral blastomeres destined to form the apical organ, tentacles, and comb rows are removed from early cleavage stages (prior to the transition period), the embryo does not form these structures at the appropriate time. However, the resulting deficient adults spontaneously form these structures from remaining blastomere lineages soon after hatching. These experiments suggest that as long as some quadrant-specific cells of the oral pole are present at the time of the transition period, the structures of that quadrant will be spontaneously replaced during the adult period.(ABSTRACT TRUNCATED AT 400 WORDS)     

Ultrafine structure of the integument of the tick Hyalomma asiaticum P. Sch. et E. Schl. in starvation and feeding]

Integument fine structure of H. asiaticum nymphs during their feeding and starvation has been studied. In hungry nymphs hypoderma has an ultrastructure typical for hypodermal cells of arthropods in the intermoulting period and is characterized by a poor development of granular endoplasmic reticulum, small number of mitochondrial and absence of Golgi complexes. The apical surface of the cells is covered with short irregularly scattered microvilli. The cuticle consists of the procuticle, which has a homogenous fine-granular structure, and four-layered epicuticle. During the feeding period hypodermal cells greatly increase in volume and the elements of granular endoplasmic reticulum and metachondria increase in number. Golgi complexes and a variety of apical vesicles have been observed. The number of microvilli on the apical surface increases that is accompanied by a cuticle growth. Procuticle, which is being formed within this period, has a lamellar structure.     

Evidence for stabilizing selection and slow divergent evolution of male genitalia in a millipede (Antichiropus variabilis)

It is generally accepted that postcopulatory sexual selection drives rapid divergence of genital morphology among isolated populations. The mode of selection operating upon genitalia can be explored by comparing patterns of population divergence in genetic and genitalic traits. We collected Antichiropus variabilis millipedes from eight localities across the species range. Levels of among-population genetic divergence, at microsatellite loci, and the mitochondrial COI gene were very high. Following geometric morphometric analyses, genital morphology was also found to be highly divergent among the populations surveyed, whereas head morphology had not diverged as markedly. However, pairwise comparisons of F(ST) and P(ST) showed that among-population divergence in both genital and head shape was significantly lower than that experienced by neutral genetic markers. Our results suggest that the genitalia of A. variabilis are currently experiencing a period of stabilizing selection, the mode of selection expected for genitalia that function in species recognition via a "lock-and-key" mechanism. Our results demonstrate that although genital morphology can clearly diverge among genetically isolated populations, divergence is not necessarily as rapid as commonly argued, and continuous directional sexual selection may not always underpin the evolutionary divergence of male genitalia.