Community replacement of a Pleistocene Crepidula biostrome

A sequence of fossil associations preserved in early Pleistocene mudstone, exposed on the Neuse River, eastern North Carolina, illustrates community replacement by species turnover, in this case involving addition of new species with rank demotions of formerly important community members. Here, a Crepidula biostrome is replaced by more diverse fossil associations dominated by oysters and infaunal bivalves. Biostrome deposits represent an extensive Crepidula snail bank that occupied a subtropical bay environment with low turbidity, near-normal marine salinity, and temporally stable water currents and food supplies. Because of local shoaling, extensive substrate coverage by these sessile epifaunal gastropods was gradually disrupted. A patchier subtidal environment, with more varied habitats for benthic organisms, succeeded the snail bank, thus giving rise to species-rich Oslrea clump and Anadara-Noetia associations containing only a few remaining Crepidula aggregations. Community replacement, species turnover, addition with rank demotions, autochthonous fossils, subtropical marine bay .     

Transgression, regression and fossil community succession

Recent paleoecological studies have emphasized the recognition of successional stages of level-bottom communities, but have neglected to point out techniques for distinguishing succession within a fossil community from the temporal and spatial replacement of one fossil community by another. The physical integrity of a marine level-bottom community is discernible, in most instances, through careful temporal and spatial study, and one community can be distinguished from another by judicious application of the 'end-member' concept. Community boundaries are only as distinct as the associated environmental stress gradient. Of first-order significance in understanding fossil community succession and replacement is appreciation of the basic asymmetry of the community dynamics involved in transgression-regression events. Of second-order importance is appreciation of the nature of the onshore-offshore environmental stress gradient, which, in turn, is controlled by the physical setting of transgression-regression (e.g. progradation versus eustatic control; high topographic relief versus low topographic relief, etc.). The application of the preceding concepts is shown by detailed study of community succession and replacement in the Cambridge Limestone (Upper Pennsylvanian), Guernsey County, Ohio.     

Earliest fossil record of bacterial-cyanobacterial mat consortia: the early Silurian Passage Creek biota (440 Ma, Virginia, USA)

Cyanobacteria in terrestrial and aquatic habitats are frequently associated with heterotrophic bacteria, and such associations are most often metabolically interactive. Functionally, the members of such bacterial–cyanobacterial consortia benefit from diverse metabolic capabilities of their associates, thus exceeding the sum of their parts. Such associations may have been just as ubiquitous in the past, but the fossil record has not produced any direct evidence for such associations to date. In this paper, we document fossil bacteria associated with a macrophytic cyanobacterial mat in the early Silurian (Llandovery) Massanutten Sandstone of Virginia, USA. Both the bacterial and the cyanobacterial cells are preserved by mineral replacement (pyrite subsequently replaced by iron oxyhydroxides) within an amorphous carbonaceous matrix which represents the common exopolysaccharide investment of the cyanobacterial colony. The bacteria are rod-shaped, over 370 nm long and 100 nm in diameter, and occur both as isolated cells and as short filaments. This occurrence represents the oldest fossil evidence for bacterial–cyanobacterial associations, documenting that such consortia were present 440 Ma ago, and revealing the potential for them to be recognized deeper in the fossil record.     

Trace fossil associations related to facies of an upper Ordovician low wave energy shoreface and shelf, Oslo-Asker district, Norway

Three trace fossil associations have been identified from facies interpreted as low wave energy upper, middle and lower shoreface deposits, transitional shoreface/shelf deposits and open epicontinental shelf deposits. These were developed in pre-regressive, regressive and transgressive phases associated with eustatic sea level changes caused by the upper Ordovician glaciation. The three associations are the Skolithos-Diplocraterion association, the Diplichnites-Phycodes association and the Thalassinoides association. The Skolithos-Diplocraterion association inhabited upper, middle and lower shoreface environments, the Diplichnites-Phycodes association a lowermost shoreface environment and the Thalassinoides association inhabited offshore epicontinental shelf environmcnts. The Skolithos-Diplocraferion and Diplichnites-Phycodes associations bear strong affinities with previously described Skolithos ichnofacies assemblages (indicating shoreline environments) and the Cruziana ichnofacies forms (indicating shallow water environments down to wave base) respectively. The Thalassinoides assemblage, however, closely compares with assemblages described from Mesozoic epicontinental shelf sequences. Trace fossil diversity achieves a maximum in the lowermost shoreface environment and reduces in deeper water and shallower water environments. This accords with diversity patterns identified in analogous Jurassic epicontinental palaeonvironments. The stratigraphic distribution of some trace fossil association boundaries accords with those of contemporary body fossil associations. However, several body fossil associations are included within the volume of distribution of a single trace fossil assemblage. □ Trace fossil association, shoreface and shelf, Oslo district, upper Ordovician.     

Mitochondrial phylogeography of a leafminer parasitoid, Diglyphus isaea (Hymenoptera: Eulophidae) in China

Diglyphus isaea is one of the primary parasitoids of agromyzid leafminers. Mitochondrial cytochrome oxidase subunit I sequences from 10 Chinese localities were used to investigate geographic variation within this widespread and morphologically uniform parasitoid. Phylogeographic analyses and sequence variation indicated that this species was actually a species-complex. We used an amber fossil record of the genus Entedon (Eulophidae: Entedoninae) as a reference to estimate the divergence time of major clades within D. isaea. With reference to the fossil record of its hosts, our results indicate that associations between parasitoids and leaf-miners could have been possibly established 38.2 million years ago.     

Gaps in fossil teeth: Saltations or sampling errors?

All evolutionists accept that there are gaps in the fossil record. To some, gaps are data: they mark sudden transitions, unlikely to be preserved, between one species and its descendants that have arisen by a brief genetic revolution within an otherwise stable lineage. However, recent studies of sediment gain and loss show that few fossil beds can be complete enough to give details of the process of speciation, so that most gaps are gaps, and nothing more. Differences in the perception of time and sampling completeness mean that paleontologists and geneticists see the rate and pattern of evolution in different ways. Just how misleading each view may be is seen by analysing the laws of life governing change in living populations using the limitations intrinsic to studies of past times; and by a new insight into the details of species formation now emerging from some remarkably complete primate fossil sequences.     

They are young,and they are many: dating freshwater lineages in unicellular dinophytes

Dinophytes are one of few protist groups that have an extensive fossil record and are therefore appropriate for time estimations. However, insufficient sequence data and strong rate heterogeneity have been hindering to put dinophyte evolution into a time frame until now. Marine-to-freshwater transitions within this group are considered geologically old and evolutionarily exceptional due to strong physiological constraints that prevent such processes. Phylogenies based on concatenated rRNA sequences (including 19 new GenBank entries) of two major dinophyte lineages, Gymnodiniaceae and Peridiniales, were carried out using an uncorrelated molecular clock and five calibration points based on fossils. Contrarily to previous assumptions, marine-to-freshwater transitions are more frequent in dinophytes (i.e. five marine-freshwater transitions in Gymnodiniaceae, up to ten but seven strongly supported transitions in Peridiniales), and none of them occurred as early as 140 MYA. Furthermore, most marine-to-freshwater transitions, and the followed diversification, took place after the Cretaceous–Paleogene boundary. Not older than 40 MYA, the youngest transitions within Gymnodiniaceae and Peridiniales occurred under the influence of the Eocene climate shift. Our evolutionary scenario indicates a gradual diversification of dinophytes without noticeable impact of catastrophic events, and their freshwater lineages have originated several times independently at different points in time.     

The large-mammal fauna from the Kibish Formation

The Kibish faunal remains are useful for reconstructing the habitat of the earliest documented Homo sapiens and for understanding the community within which early modern humans existed. A diverse assemblage of large mammals, including many species of bovids, suids, and equids, has been recovered from the Kibish Formation. There are no extinct large mammals represented in the fossil assemblage, and the overall taxonomic composition of the fossil fauna is similar to the modern-day wildlife community living near the Omo River. The fossil faunal assemblage shows a paucity of arboreal primates, and carnivore species are rare. However, the faunal sample includes possible Cephalophus (duiker) remains and Hylochoerus meinertzhageni (giant forest hog), taxa that are extremely rare in the African fossil record, and both indicate more closed habitats. Comparative analyses of the Kibish faunal remains using the ecological-diversity approach document close associations with edaphic grassland and woodland vegetation types. These vegetation forms are similar to current habitats surrounding the Omo River.     

Long-term retrospection on mangrove development using sediment cores and pollen analysis: A review

Mangroves are biogenic systems that accumulate sedimentary sequences, where cores can provide records of mangrove species variation in distribution with past climate change and sea-level change. Fossil evidence used for palaeoecological reconstruction is based on organic remains that preserve identifying features so that they can be identified to generic levels at least. This includes macrofossils such as fruit, flowers, wood or leaves, or microfossils particularly pollen. Anaerobic conditions in mangrove sediment allow the long-term preservation of these fossil records. Fossil pollen from core samples is concentrated for microscopic examination by use of standard chemical treatments, but refinements of these are necessary for the peculiarities of mangrove peat. Pollen diagrams are expressed in concentrations, or more usefully in mangrove environments as proportions relative to others, as this has been shown to demonstrate the depositional environment actually underneath the mangrove forest. Radiocarbon dating of sedimentary sequences is used to date palaeoecological successions shown by fossil sequences, or long-term sedimentation rates. Sediment accretion in the last 50–200 years can been analysed better using Cs¹³⁷ and Pb²¹⁰ analyses. From pollen and macrofossils mostly recovered from stratigraphic cores of sedimentary rock and more recent sediment, the evolution and dispersal of mangroves through geological time has been reconstructed. While reconstruction of actual temperatures in these earlier records is associative to the fossil types present, it is apparent that mangroves have always been tropical species, extending to higher latitudes only during global warm periods. Many sedimentary records show mangroves deeper than the present lower limit of mangrove growth at mean sea-level. These indicate sea-level rising over time, and mangroves keeping pace with rising sea-level. Stratigraphic dating shows accretion rates of 1 mm a⁻¹ for low island locations, and up to 1.5 mm a⁻¹ in high islands/continental margins. Sedimentary records can also show die-off of mangroves with more rapid sea-level rise and replacement by open water during rising sea-level, landward retreat of mangrove zones, or replacement of mangroves by freshwater forest with sedimentary infill. The causes of mangrove community changes identified in the palaeoecological record can only be inferred by comparison with ecological studies in the modern environment, the link between the two that may be possible through long-term mangrove monitoring being poorly established.     

THE MACROEVOLUTIONARY CONSEQUENCES OF ECOLOGICAL DIFFERENCES AMONG SPECIES

Abstract:  In this paper, I examine the dynamics of species richness in a model system in which multiple species compete in a metacommunity (multiple patches linked by dispersal). Patches lie along an environmental gradient, and new species are introduced into the system by speciation of existing species. This model is used to explore how the ecological similarity of species influences the patterns in community structure that result and to determine whether patterns in fossil and systematics data may be signatures for different types of community structure. Making species more similar overall along the entire gradient or making new species that have more similar optimal positions along the gradient to their progenitor both increase the time required to drive species extinction. As a result, making species more similar ecologically to one another increases overall species richness because of an increased frequency of transient species in the system. Having more transient species in systems shifted the longevity distributions of species in the fossil record towards having a greater frequency of shorter duration species, and the age distribution of extant species that would be estimated from molecular phylogenies also had a higher frequency of younger aged species. Comparisons of these results with species longevity distributions extracted from two data sets and with species ages derived from species-level molecular phylogenies strongly suggest that transient species are an important component of real biological communities.     

The implications of palaeontological evidence for theories of ecological communities and species richness

Abstract Palaeontological evidence raises several questions that relate to current explanations of ecological communities, to the classification of communities and to interpretations of species richness. The first question relates to the stability of species detected in the fossil record. Coupled with that is the issue of incidental association of species on the same trophic level through differential effects of climatic change on the different species. Such observations are seen to support the ‘individualistic’ concept of communities. Recent statements about this concept leave unresolved questions about the acquisition of adaptation, and about the place of adaptation theory in theories of ecological communities and interpretations of ‘regional species richness’. At issue is whether there is justification for continuing to classify communities as a basis for understanding them. There is good reason to reject this approach for one in which questions about communities and ‘local’ and ‘regional’ species richness are replaced by more specific and basic questions about the relationship between adaptation, distribution and abundance, and ecological interactions. Some recent efforts to incorporate species theory into community theory fail because their basis remains the flawed concept of ‘local community’.     

Protein structural changes induced by their uptake at interfaces

For insertion into lipidic media, most hydrosoluble proteins must cross the lipid-water interface and thus undergo conformational transitions. According to their chemical sequences these transitions may be restricted to changes involving only the tertiary structure, while for other proteins this environment modification will induce drastic changes such as the unfolding of large domains. The structural transitions are mainly governed by the presence of hydrophobic domains and/or by the existence of induced amphipathic properties.     

Bay and shoreface benthic communities in the Lower Cretaceous

Lower Cretaceous marine rocks exposed in New Mexico, southcastcrn Colorado, Oklahoma, and Kansas contain well-preserved faunal assemblages that formed either as in-place, disturbed-neighborhood, or transported assemblages. Five faunal associations characterize lithofacies of the bay-to-shoreface depositional model and possess uniquc structures. The Nucula-Nuculana association represents a speciediverse, infaunal detritus-suspension community occupying the open-bay muddy substrate. The Corbula-Breviarca association was a species-dominant, infaunal suspension feeding community on the lower shoreface. The Texigryphaea-Lopha community formed biostromes on the shoreface. The mid-shoreface supported a species-diverse, infaunol suspension feeding community of Scabrotrigonia and Turritella . The Arenicolites trace fossil association characterizes the upper shoreface-beach habitat.     

Taphonomy of modern and fossil intertidal gastropod associations from Isla Santa Cruz and Isla Santa Fe, Galápagos Islands

Examination of modern gastropod associations from the low intertidal zone of Isla Santa Cruz suggests that fossil rocky intertidal deposits from this tropical locality will be taphonomically compromised in three ways: (1) Marine hermit crabs, by their use of empty gastropod shells, will mix the shells from varying tidal heights and habitats, thus facilitating mixed associations of such shells in the fossil record, (2) encrusting organisms on crab-inhabited shells are abundant, while boring organisms are almost non-existent, indicating possible differences in postmortem shell retention, and (3) intertidal shells are further taphonomically altered by terrestrial hermit crabs, which transport the shells onto land as well as physically modify the shells. Gastropod fossils from beach and terrace deposits on Isla Santa Fe are interpreted to be a mixed assemblage of rocky intertidal assemblage with few shells indicating influence from marine hermit crabs. Modification of the shell by marine and terrestrial hermit crabs was also evident. A unique polish to the shells at one locality is attributed to the marine iguanas and is only found in the terrace site biologically bulldozed by egg-laying iguanas. Few studies exist on modern rocky intertidal associations in the Galápagos, and the fossil record of rocky shores may provide a baseline for future studies in how community structure has changed over since the advent of humans. Galapagos, C oenobita C ompressus , gastropods, humans, Gulf of California, bionts, nutrients.
Sally E. Walker, Department of Geology, The University of Georgia, Athens, Georgia, USA; 8th September, 1994; revised 28th June, 1995.     

Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine --> guanine and thymine --> cytosine) and type 2 transitions (cytosine --> thymine and guanine --> adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nuDNA sequences. We argue that the problems presented by postmortem damage, as well as problems with contamination from exogenous sources of conserved nuclear genes, allelic variation, and the reliance on single nucleotide polymorphisms, call for great caution in studies relying on ancient nuDNA sequences.     

Mutations induced by ultraviolet light

The different ultraviolet (UV) wavelength components, UVA (320-400 nm), UVB (280-320 nm), and UVC (200-280 nm), have distinct mutagenic properties. A hallmark of UVC and UVB mutagenesis is the high frequency of transition mutations at dipyrimidine sequences containing cytosine. In human skin cancers, about 35% of all mutations in the p53 gene are transitions at dipyrimidines within the sequence 5'-TCG and 5'-CCG, and these are localized at several mutational hotspots. Since 5'-CG sequences are methylated along the p53 coding sequence in human cells, these mutations may be derived from sunlight-induced pyrimidine dimers forming at sequences that contain 5-methylcytosine. Cyclobutane pyrimidine dimers (CPDs) form preferentially at dipyrimidines containing 5-methylcytosine when cells are irradiated with UVB or sunlight. In order to define the contribution of 5-methylcytosine to sunlight-induced mutations, the lacI and cII transgenes in mouse fibroblasts were used as mutational targets. After 254 nm UVC irradiation, only 6-9% of the base substitutions were at dipyrimidines containing 5-methylcytosine. However, 24-32% of the solar light-induced mutations were at dipyrimidines that contain 5-methylcytosine and most of these mutations were transitions. Thus, CPDs forming preferentially at dipyrimidines with 5-methylcytosine are responsible for a considerable fraction of the mutations induced by sunlight in mammalian cells. Using mouse cell lines harboring photoproduct-specific photolyases and mutational reporter genes, we showed that CPDs (rather than 6-4 photoproducts or other lesions) are responsible for the great majority of UVB-induced mutations. An important component of UVB mutagenesis is the deamination of cytosine and 5-methylcytosine within CPDs. The mutational specificity of long-wave UVA (340-400 nm) is distinct from that of the shorter wavelength UV and is characterized mainly by G to T transversions presumably arising through mechanisms involving oxidized DNA bases. We also discuss the role of DNA damage-tolerant DNA polymerases in UV lesion bypass and mutagenesis.     

Historical biogeography and cryptic diversity in the Callichthyinae (Siluriformes,Callichthyidae)

The family Callichthyidae, divided into the subfamilies Corydoradinae and Callichthyinae, contains more than 200 species of armoured catfishes distributed throughout the Neotropics, as well as fossil species dating from the Palaeocene. Both subfamilies are very widely distributed throughout the continent, with some species ranges extending across multiple hypothesized biogeographical barriers. Species with such vast geographical ranges could be made up of multiple cryptic populations that are genetically distinct and have diverged over time. Although relationships among Callichthyinae genera have been thoroughly investigated, the historical biogeography of the Callichthyinae and the presence of species complexes have yet to be examined. Furthermore, there is a lack of fossil‐calibrated molecular phylogenies providing a time frame for the evolution of the Callichthyinae. Here, we present a novel molecular data set for all Callichthyinae genera composed of partial sequences of mitochondrial and nuclear markers. These data were used to construct a fossil‐calibrated tree for the Callichthyinae and to reconstruct patterns of spatiotemporal evolution. All phylogenetic analyses [Bayesian, maximum likelihood and maximum parsimony (MP)] resulted in a single fully resolved and well‐supported hypothesis for the Callichthyinae, where Dianema is the sister group of all the remaining genera. Results suggest that the ancestry of most Callichthyinae genera originated in the Amazonas basin, with a number of subsequent ancestral dispersal events between adjacent basins. High divergences in sequences and time were observed for several samples of Hoplosternum littorale, Megalechis picta and Callichthys callichthys, suggesting that these species may contain cryptic diversity. The results highlight the need for a taxonomic revision of species complexes within the Callichthyinae, which may reveal more diversity within this relatively species‐poor lineage.     

Southern Africa and modern human origins.

This paper argues that southern Africa was a remote part of the Old World in the late Pleistocene (125-10 ka ago). Because of this isolated position there was continuity without significant replacement in the resident population. Isolation and the relatively recent spread of agriculture to the region has allowed a section of this population to survive into the present. They are the Bushmen (San). Studies of geographic patterning in conventional genetic markers and mitochondrial DNA indicate that the Bushman clade has a long evolutionary history in southern Africa. Estimates of more than 100 ka for the continued presence of this population in the region are supported in archaeological investigations of sites with long sequences such as Klasies River main site and Border Cave. Human remains dating to the earlier part of the late Pleistocene have been recovered from these sites and the samples form a morphological series with the Klasies River remains possibly 20 ka older than those from Border Cave. There is no fossil record for the later Pleistocene, however, at a period when selection for a gracile morphology may have been pronounced. The cultural associations in the earlier late Pleistocene are with the Middle Stone Age. Expressions of cultural 'style' and the occurrence of similar artefact design types in the Middle and Later Stone Ages can be interpreted with reference to the ethnographic present. Temporal continuity can be shown in the geographical distribution of stylistic markers and this suggests participation in a shared cognitive system.(ABSTRACT TRUNCATED AT 250 WORDS)     

海南岛吊罗山热带山地雨林两个演替阶段的种间联结性

种间联结一直是群落演替理论研究的焦点之一, 关于物种间相互作用与群落演替之间的动态关系仍然存在争议。本文中, 作者通过出现-不出现数据的方差比例、基于2×2列联表的种间联结分析和 ²检验, 对海南岛吊罗山热带山地雨林演替前期和演替后期群落的种间联结性进行了研究, 以揭示种间联结与群落演替的相互作用。结果表明: (1)在演替前期, 群落内所有树种间总体呈正联结, 但不显著; 发展至演替后期达到显著正联结。群落内所有物种间正、负联结种对数占总种对数的比例随演替进程呈现下降趋势, 而无联结种对数的比例则大幅上升; 优势种和伴生种间呈现相同的趋势。这表明群落演替正朝着有利于物种稳定共存的方向发展。(2)演替前期建群种和后期侵入种间正联结与无联结种对数的比例(分别为37.8%与41.5%)远大于负联结的比例(20.7%), 但正联结均不显著; 前期定居树种和后期侵入种通过分割资源而共存, 而且也趋于独立存在。(3)后期侵入种间不存在负联结, 所有正联结(占总对数的33.3%)均达显著水平, 显示它们对生境有相似的适应和相互重叠的生态位。     

Subfamily structure and evolution of the human L1 family of repetive sequences

Summary Comparative analysis of the available 3′-portions of the human L1 (LINE-1) family of repeated sequences indicates that all the sequences can be classified in two major subfamilies. The division is based on patterns of diagnostic bases shared within L1 subfamilies of sequences but differing between them. The overall ratio of replacement to synonymous positions, occupied by the diagnostic bases in the large open reading frame of the L1 sequence, is 1.15. This indicates that both subfamilies were obtained from genes coding for functional proteins. The L1 subfamilies appear to be of different ages and may represent a “fossil record” of the same active gene at different times in the history of primates. The younger subfamily can be split further into at least two closely related branches of sequences. The above facts combined with the recent data for the Alu subfamily structure show that LINE and SINE families of interspersed repeats share discontinuous patterns in their evolution. These data are consistent with the model that both Alu and L1 families, as well as other pseudogene families, contain active genes producing discrete layers of pseudogenes throughout the history of primates. Models of evolutionary processes that could generate these discontinuities are discussed together with the possible biological role of Alu and L1 genes.