Vicariance and endemism in a Neotropical savanna hotspot: distribution patterns of Cerrado squamate reptiles

Aim To test predictions of the vicariance model, to define basic biogeographical units for Cerrado squamates, and to discuss previous biogeographical hypotheses. Location Cerrado; South American savannas south of the Amazon, extending across central Brazil, with marginal areas in Bolivia and Paraguay and isolated relictual enclaves in adjacent regions. Methods We compiled species occurrence records via field sampling and revision of museum specimens and taxonomic literature. All species were mapped according to georeferenced locality records, and classified as (1) endemic or non‐endemic, (2) typical of plateaus or depressions, and (3) typical of open or forested habitats. We tested predictions of the vicariance model using biotic element analysis, searching for non‐random clusters of species ranges. Spatial congruence of biotic elements was compared with putative areas of endemism revealed by sympatric restricted‐range species. Effects of topographical and vegetational mosaics on distribution patterns were studied according to species composition in biotic elements and areas of endemism. Results We recorded 267 Cerrado squamates, of which 103 (39%) are endemics, including 20 amphisbaenians (61% endemism), 32 lizards (42%) and 51 snakes (32%). Distribution patterns corroborated predictions of the vicariance model, revealing groups of species with significantly clustered ranges. An analysis of endemic species recovered seven biotic elements, corroborating results including non‐endemics. Sympatric restricted‐range taxa delimited 10 putative areas of endemism, largely coincident with core areas of biotic elements detected with endemic taxa. Distribution patterns were associated with major topographical and vegetational divisions of the Cerrado. Endemism prevailed in open, elevated plateaus, whereas faunal interchange, mostly associated with forest habitats, was more common in peripheral depressions. Main conclusions Our results indicate that vicariant speciation has strongly shaped Cerrado squamate diversity, in contrast to earlier studies emphasizing faunal interchange and low endemism in the Cerrado vertebrate fauna. Levels of squamate endemism are higher than in any other Cerrado vertebrate group. The high number of recovered endemics revealed previously undetected areas of evolutionary relevance, indicating that biogeographical patterns in the Cerrado were poorly represented in previous analyses. Although still largely undocumented, effects of vicariant speciation may be prevalent in a large fraction of Cerrado and Neotropical biodiversity.     

Recent origin,active speciation and dispersal for the lichen genus Nephroma (Peltigerales) in Macaronesia

Aim We reconstructed the phylogeny of the lichen genus Nephroma (Peltigerales) to assess the relationships of species endemic to Macaronesia. We estimated dates of divergences to test the hypothesis that the species arose in Macaronesia (neo‐endemism) versus the oceanic archipelagos serving as refugia for formerly widespread taxa (palaeo‐endemism). Location Cosmopolitan with a special focus on the archipelagos of the Azores, Madeira and the Canary Islands. Methods DNA sequences were obtained from 18 species for three loci and analysed using maximum parsimony, maximum likelihood and Bayesian inferences. Divergence dates were estimated for the internal transcribed spacer (ITS)‐based phylogeny using a relaxed molecular clock. Reconstruction of the ancestral geographical range was conducted using the Bayesian 50% majority rule consensus tree under a parsimony method. Results The backbone phylogenetic tree was fully supported, with Nephroma plumbeum as sister to all other species. Four strongly supported clades were detected: the Nephroma helveticum, the N. bellum, the N. laevigatum and the N. parile clades. The latter two share a common ancestor and each includes a widespread Holarctic species (N. laevigatum and N. parile, respectively) and all species endemic to Macaronesia. The data suggest a neo‐endemic origin of Macaronesian taxa, a recent range expansion from Macaronesia of both widespread species, a range expansion limited to the Mediteranean Basin and south‐western Europe for another taxon, and a long dispersal event that resulted in a speciation event in the western parts of North America. Main conclusions The Macaronesian endemic species belong to two sister clades and originated from a most recent common ancestor (MRCA) shared with one widely distributed taxon, either N. parile or N. laevigatum. Estimates of the mean divergence dates suggest that the endemics originated in the archipelagos after the rise of the volcanic islands, along with the ancestor to the now widespread species, which probably expanded their range beyond Macaronesia via long‐distance dispersal. This study provides the first phylogenetic evidence of Macaronesian neo‐endemism in lichenized fungi and provides support for the hypothesis that oceanic islands may serve as a source for the colonization of continents. However, further data are needed to properly assess the alternative hypothesis, namely colonization from western North America.     

Palaeodistribution modelling does not support disjunct Pleistocene refugia in several Central American plant taxa

Aim We combine evidence from palaeoniche modelling studies of several tree species to estimate the extent of Central American forest during the Last Glacial Maximum (LGM). In particular, we ask whether the distributions of these species are likely to have changed since the LGM, and whether LGM distributions coincide with previously proposed Pleistocene refugia in this area. Location Central American wet and seasonally dry forests. Methods We developed ecological niche models using two simulations of Pleistocene climate and occurrence data for 15 Neotropical plant species. We focused on palaeodistribution models of three ‘focal’ tree species that occur in wet and seasonally dry Central American forests, where recent phylogeographic data suggest Pleistocene differentiation coincident with previously proposed refugia. We added predictions from six wet‐forest and six seasonally dry‐forest obligate plant species to gauge whether Pleistocene range shifts were specific to habitat type. Correlation analyses were performed between projected LGM and present distributions, LGM distributions and previously proposed refugia. We also asked whether modelled palaeodistributions were smaller than their current extents. Results According to our models, the ranges of the study species were not reduced during the LGM, and did not correlate with refugial models, regardless of habitat type. Relative range sizes between present and LGM distributions did not indicate significant range changes since the LGM. However, relative range sizes differed overall between the two palaeoclimate models. Main conclusions Many of the modelled palaeodistributions of study species were not restricted to refugia during the LGM, regardless of forest type. While constrained from higher elevations, most species found suitable habitat at coastal margins and on newly exposed land due to lowered sea levels during the LGM. These results offer no corroboration for Pleistocene climate change as a driver of genetic differentiation in the ‘focal’ species. We offer alternative explanations for genetic differentiation found in plant species in this area.     

Inhibition of co-operative enzymes by substrate-analogues: Possible implications for the physiological significance of negative co-operativity illustrated by phenylalanine metabolism in higher plants

The “Hill” equation for co-operative binding-systems has been extended to describe the effect of substrate-analogue on the binding of substrate to an oligomeric protein. It is demonstrated that the more negatively co-operative the binding-system, the more sensitive is the binding of substrate to inhibition by increases in the relative concentration of substrate-analogue. It is proposed that the physiological significance of negative co-operativity for enzymes may be complementary to the physiological significance of positive co-operativity. The effect of negative co-operativity is to make substrate binding more sensitive to inhibition by relative increases in the concentration of substrate-analogue (e.g. for many enzymes product of the reaction) at the expense of decreased sensitivity of substrate binding to relative changes in substrate concentration compared to a system with equivalent, independent substrate binding sites. In contrast, the effect of positive co-operativity is to make the enzyme more sensitive to relative changes in substrate concentration at the expense of decreased sensitivity to inhibition by relative increases in product concentration, compared to an enzyme without co-operative binding.     

Introduction of the African Catfish Clarias gariepinus (BURCHELL, 1822) into Southern Brazil

We record here the introduction of the African catfish Clarias gariepinus into the Guaraguaçu River basin in Paraná State, Brazil, an area with an extremely rich endemic fish fauna, including many catfishes. C. gariepinus was introduced as escapees from ponds built for recreational angling. These catfishes are very large and hard predators, thus posing serious potential for impact on the native fish fauna. The impact of C. gariepinus needs study with emphasis on finding means for controlling its spread.     

Leaf size of woody dicots predicts ecosystem primary productivity

A key challenge in ecology is to understand the relationships between organismal traits and ecosystem processes. Here, with a novel dataset of leaf length and width for 10 480 woody dicots in China and 2374 in North America, we show that the variation in community mean leaf size is highly correlated with the variation in climate and ecosystem primary productivity, independent of plant life form. These relationships likely reflect how natural selection modifies leaf size across varying climates in conjunction with how climate influences canopy total leaf area. We find that the leaf size?primary productivity functions based on the Chinese dataset can predict productivity in North America and vice‐versa. In addition to advancing understanding of the relationship between a climate‐driven trait and ecosystem functioning, our findings suggest that leaf size can also be a promising tool in palaeoecology for scaling from fossil leaves to palaeo‐primary productivity of woody ecosystems.     

Stromatolite-dominated microbialites at the Permian–Triassic boundary of the Xikou section on South Qinling Block,China

Permian–Triassic boundary microbialites (PTBMs) are organosedimentary carbonates formed immediately after the end-Permian mass extinction. All those reported PTBMs constrained by convincing conodont biozones are present stratigraphycally not higher than the Hindeodus parvus zone and most of them are dominated by thrombolites. This paper provides the first record of a brief, but spectacular development of stromatolite-dominated PTBMs within the basal Isarcicella isarcica conodont zone of the earliest Triassic from the Xikou section of South Qinling Block that was at the margin of the North China Block during the Permian–Triassic transition and was geographically separated from the major occurrence of post-extinction microbialites in the South China Block. This stromatolite cap overlies a 3.7-m-thick oolitic limestone and is composed of a lower 0.2-m-thick bed and an upper 0.5-m-thick bed, separated by a 0.2-m-thick greyish green siliciclastic mudstone. These two stromatolite beds mainly consist of columnar stromatolites with subordinate domal stromatolites. The intercolumn and interstitial spaces within the stromatolites are filled with oolitic grainstones. At the microscopic scale, laminoid structures in stromatolites comprise wavy, millimetric-domical and tangled laminae. The increased grain and fossil contents and/or bioturbation in the domical and tangled laminae indicate that the formation of these laminae is likely related to an increase in the populations and the disruptions by benthic metazoans, as well as an influx of sediment grains. The δ¹³C_carb values fluctuate between 2‰ and 3‰ in the uppermost Permian strata; a distinct negative shift of 1.9‰ occurs at the topmost oolitic grainstone, just below the lower stromatolite bed, and the lowest value of −0.1‰ is located at the base of the upper stromatolite bed. The stratigraphic succession from stromatolites to thrombolites of the PTBMs may represent a transgressive succession and/or a transient ecosystem recovery immediately after the end-Permian mass extinction. The thrombolites-dominated PTBMs mainly developed in near-equator shallow marine geographic locations, and stromatolite-dominated PTBMs mainly developed at higher latitude settings, which probably indicates that a relatively lower diversity and abundance of marine benthic metazoans existed at higher latitudes after the end-Permian mass extinction.     

广西百色盆地高岭坡遗址的地层及年代

广西百色盆地旧石器工业因含有众多的手斧且年代早到803 kaBP而闻名于世。盆地内发育有7级河流阶地,其中第IV级阶地发现有手斧和玻璃陨石。自从1973年第一个石器地点被发现,越来越多的遗址或地点被调查发现和发掘。以前研究认为,百色盆地旧石器只出自网纹红土层,年代均为803 kaBP。2013年以前,通常只在土状堆积的上部发掘,从来没有人对第IV级阶地的沉积物从地表到底部砾石层进行系统发掘,因此关于第IV级阶地的整体地层堆积情况及含石器层位很模糊。2013-2014年,广西文物保护与考古研究所会同田东县博物馆对百色盆地最重要的旧石器遗址之一——田东高岭坡遗址进行了系统的考古发掘。此次发掘从遗址的地表往下一直发掘到砾石层,揭露出厚度超过7m的完整地层序列,发现1处小型石器制造场和1处用火遗迹。在不同地层中发现石制品800多件,包括砍砸器、手镐、刮削器等。涵盖旧石器和新石器两个时代。根据地层对比和石制品的特征及测年结果,我们把旧石器时代文化遗存可分为3期：第一期的年代早于或等于803 kaBP,第二期为15 kaBP,第三期约为10 kaBP。     

Genotyping‐by‐sequencing and ecological niche modeling illuminate phylogeography,admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides)

Populus tremuloides is the widest‐ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome‐wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal–Cascades (cluster 1), east‐slope Cascades–Sierra Nevadas–Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the “stable‐edge hypothesis” that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited “trailing‐edge” dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the “inland dispersal hypothesis” predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific‐coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable‐edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific‐coastal genetic lineage of quaking aspen.     

Genetic diversity of mitochondrial D-LOOP sequences in the spotted scat (Scatophagus argus) from different geographical populations along the northern coast of the South China Sea

The genetic diversity of 289 spotted scat (Scatophagus argus) from seven populations along the northern coast of the South China Sea was studied by analyzing the full-length sequences of the mitochondrial control region (D-LOOP). The S. argus D-LOOP sequence was 1,004–1,010 bp long and contained 156 variant sites. The seven studied S. argus populations had a high degree of genetic diversity (haplotype diversity [Hd] = 0.99135; nucleotide diversity (π) = 0.01313). There was no obvious genetic differentiation among the seven geographical populations and gene exchange was frequent (Fst = −0.01867–0.01117, p > .05). Four distinct mitochondrial lineages were identified in the phylogenetic tree and the haplotype network. The between-lineage Fst was 0.71690–0.84940 (p < .001), but these lineages showed no obvious phylogeographic pattern. Based on D-LOOP mutation rates, we estimated that the four lineages diverged approximately 513,800–93,600 years ago, during the Eocene ice age, at which time falling sea levels may have led to population segregation. We estimated that S. argus population expansion occurred approximately 2.29–0.68 million years ago, during the late Pleistocene. During this period, sea levels rose again, allowing previously separated lineages to come into sympatry, which eventually gave rise to a highly genetically diverse population without pyhlogeographic structure. Here, we characterized the genetic structure and differentiation of seven S. argus populations from the northern coast of the South China Sea. Our results suggested that the seven S. argus populations from the northern coast of the South China Sea have a relatively low level of genetic variation and can be considered a single unit for the purposes of fishery development, utilization, and management.