Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.     

Phenological Changes in the Southern Hemisphere

Current evidence of phenological responses to recent climate change is substantially biased towards northern hemisphere temperate regions. Given regional differences in climate change, shifts in phenology will not be uniform across the globe, and conclusions drawn from temperate systems in the northern hemisphere might not be applicable to other regions on the planet. We conduct the largest meta-analysis to date of phenological drivers and trends among southern hemisphere species, assessing 1208 long-term datasets from 89 studies on 347 species. Data were mostly from Australasia (Australia and New Zealand), South America and the Antarctic/subantarctic, and focused primarily on plants and birds. This meta-analysis shows an advance in the timing of spring events (with a strong Australian data bias), although substantial differences in trends were apparent among taxonomic groups and regions. When only statistically significant trends were considered, 82% of terrestrial datasets and 42% of marine datasets demonstrated an advance in phenology. Temperature was most frequently identified as the primary driver of phenological changes; however, in many studies it was the only climate variable considered. When precipitation was examined, it often played a key role but, in contrast with temperature, the direction of phenological shifts in response to precipitation variation was difficult to predict a priori. We discuss how phenological information can inform the adaptive capacity of species, their resilience, and constraints on autonomous adaptation. We also highlight serious weaknesses in past and current data collection and analyses at large regional scales (with very few studies in the tropics or from Africa) and dramatic taxonomic biases. If accurate predictions regarding the general effects of climate change on the biology of organisms are to be made, data collection policies focussing on targeting data-deficient regions and taxa need to be financially and logistically supported.     

中国块菌要览及其保护策略

截至目前报道的中国块菌有28种,其中黑块菌4种,白块菌24种.具有重要经济价值和生态价值的黑块菌类有印度块菌复合种和中国夏块菌,其中印度块菌复合种与欧洲法国黑孢块菌属于姊妹类群,中国夏块菌与欧洲夏块菌也是姊妹类群.虽然欧洲意大利白块菌在中国尚未找到、波氏块菌在中国的存在尚待最终确认,但是,最近的更多白块菌新种的发现,说...     

Historical and Life History Factors in the Biogeography of Mayflies

SYNOPSIS. Cladistic analysis of mayflies suggests that dispersalwas very asymmetrical after the new land connection betweenNorth and South America. Twenty-one genera apparently movedfrom South to North and Central America, but there is good evidencefor only one North American genus moving into the south. Testablepredictions are possible once the boreal (Laurasian) or austral(Gondwanian) designations are made. For example, Paracloeodes,a genus of austral origin, was predicted to be found in SouthAmerica, and in North America in warm rivers north and eastof its known distribution. These predictions have been confirmed.Other characteristics of tropical mayflies, such as length oflarval period and emergence and mating patterns, may be usedto predict habitats and characteristics of present North Americangenera. Merger events and consequent dispersal of organismshave profound influences on distributional patterns, and fromsuch information, biologically useful generalities can be made.     

Tuberculous Lymphadenitis in Ethiopia Predominantly Caused by Strains Belonging to the Delhi/CAS Lineage and Newly Identified Ethiopian Clades of the Mycobacterium tuberculosis Complex

Background

Recently, newly defined clades of Mycobacterium tuberculosis complex (MTBC) strains, namely Ethiopia 1–3 and Ethiopia H37Rv-like strains, and other clades associated with pulmonary TB (PTB) were identified in Ethiopia. In this study, we investigated whether these new strain types exhibit an increased ability to cause TB lymphadenitis (TBLN) and raised the question, if particular MTBC strains derived from TBLN patients in northern Ethiopia are genetically adapted to their local hosts and/or to the TBLN.

Methods

Genotyping of 196 MTBC strains isolated from TBLN patients was performed by spoligotyping and 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing. A statistical analysis was carried out to see possible associations between patient characteristics and phylogenetic MTBC strain classification.

Results

Among 196 isolates, the majority of strains belonged to the Delhi/CAS (38.8%) lineage, followed by Ethiopia 1 (9.7%), Ethiopia 3 (8.7%), Ethiopia H37RV-like (8.2%), Ethiopia 2 and Haarlem (7.7% each), URAL (3.6%), Uganda l and LAM (2% each), S-type (1.5%), X-type (1%), and 0.5% isolates of TUR, EAI, and Beijing genotype, respectively. Overall, 15 strains (7.7%) could not be allocated to a previously described phylogenetic lineage. The distribution of MTBC lineages is similar to that found in studies of PTB samples. The cluster rate (35%) in this study is significantly lower (P = 0.035) compared to 45% in the study of PTB in northwestern Ethiopia.

Conclusion

In the studied area, lymph node samples are dominated by Dehli/CAS genotype strains and strains of largely not yet defined clades based on MIRU-VNTR 24-loci nomenclature. We found no indication that strains of particular genotypes are specifically associated with TBLN. However, a detailed analysis of specific genetic variants of the locally contained Ethiopian clades by whole genome sequencing may reveal new insights into the host-pathogen co-evolution and specific features that are related to the local host immune system.     

Historical Biogeography: Evolution in Time and Space

Biogeography is the discipline of biology that studies the present and past distribution patterns of biological diversity and their underlying environmental and historical causes. For most of its history, biogeography has been divided into proponents of vicariance explanations, who defend that distribution patterns can mainly be explained by geological, tectonic-isolating events; and dispersalists, who argue that current distribution patterns are largely the result of recent migration events. This paper provides an overview of the evolution of the discipline from methods focused on finding general patterns of distribution (cladistic biogeography), to those that integrate biogeographic processes (event-based biogeography), to modern probabilistic approaches (parametric biogeography). The latter allows incorporating into biogeographic inference estimates of the divergence time between lineages (usually based on DNA sequences) and external sources of evidence, such as information on past climate and geography, the organism fossil record, or its ecological tolerance. This has revolutionized the discipline, allowing it to escape the dispersal versus vicariance dilemma and to address a wider range of evolutionary questions, including the role of ecological and historical factors in the construction of biomes or the existence of contrasting patterns of range evolution in animals and plants.     

Historical and Ecological Factors in the Biogeography of Aposematic Neotropical Butterflies

SYNOPSIS. Quantitative analysis of low-level (mostly subspecific)geographic differentiation of aposematic color patterns in threegroups of forest butterflies (Heliconiini, Ithomiinae, and Troidini),in 1,550 half-degree quadrants throughout the Neotropics, indicatesfour principal species-endemicity regions, 44 principal subspecies-endemicitycenters, and 300 quadrants of subspecies hybridization. Theendemism centers are different in outline but nearly identicalin position for each of the three ecologically different groups.Basic data on present and past physical environments (climate,soils, geomorphology, and vegetation structures), when integratedinto maps, show 1) regions of favorable ecological conditionsfor forest organisms in the present, 2) regions of environmentalconformities and rapid transitions in the present, and 3) regionsof high probability for humid forest persistence during themajor landscape changes at the end of the last glacial period,13,000–20,000 yr ago. Species diversity (a local phenomenon)is readily related to favorable modern ecological conditionsand environmental microheterogeneity, promoted by unpredictablemild disturbance. Biogeographical patterns of evolution at thelevel of regional subspecies correlate very well with presumedpaleoecological conditions. The biogeographical data also supportan hypothesis of differentiation resulting from areas of rapidenvironmental change; most of the hybridization quadrants fallwithin transition zones. There is lower correlation betweencenters of endemism and zones of en vironmental conformity,but some individual cases of differentiation in the butterfliesmay be adequately explained by modern ecological factors. Speciespresently undergoing differentiation in isolated habitat islands(Amazonian savannas and high-altitude Andean forests and paramos)may offer the best opportunities for observation of evolutionaryprocesses in the present.     

块菌名实考证及其资源保护

块菌是指Tuber属的真菌种类,属于子囊菌门(Ascomycota),生在地下,其中包含着世界上最美味和价值最昂贵的食用菌.中国食与药用真菌文化悠久,历代本草都不乏各种菌类的记载,但在本草中记载的与块菌有关系的菌类唯有1245年陈仁玉编撰的“菌谱”中称之为“麦蕈”和俗名为“麦丹蕈”的一种地下真菌.日本本草对“麦蕈”也屡有记载,并把“麦蕈”叫“地肾”和“松露”.这是“松露”一名的最早记载,“麦蕈”或“松露”可能是被现代菌物学称之为须腹菌(Rhizopogon spp.)的真菌种类.因而,“松露”一名虽是汉字,但是所指并非真正的块菌,应是须腹菌(Rhizopogon spp.),也称“假块菌”(false truffle),所以松露和块菌寓意各异.产于我国西南地区的食用黑块菌主要是印度块菌(Tuber indi-cum)或中华块菌(T.sinernse)、夏块菌(T.aestivum=T.uncinatu)和拟喜马拉雅块菌(T.pseudohimalayense=T.pseudoexcavatum),近年来身价倍增,成为中国野生食用菌出口种类中名列前三甲的菌类,在世界块菌市场上也颇受欢迎.喜马拉雅块菌(T.himalayense)在我国尚未发现它的踪迹.印度块菌和中华块菌形态上有差异,若把中国产的类似黑孢块菌的黑块菌统称为印度块菌(T.indicum)尚值得商榷.中华块菌或印度块菌形态和遗传变异多样,尚需进一步研究.2010年在云南和四川相继发现的大型香味浓郁的白块菌,近似于波氏块菌(T.borchii)组的块菌,颇具研究和巨大的商业价值,表明我国块菌资源比原有记载的要丰富的多.由于利益之驱动和疏于管理,掠夺式的采收方法造成了块菌产区生态环境毁灭性的破坏,一些商业化采集区的块菌已濒临灭绝,中国西南地区的块菌资源的保护问题迫在眉睫.本文对产自欧洲、美洲的块菌、沙漠块菌,以及块菌的生态意义和种植作了简要介绍和讨论.     

Global warming caused by afforestation in the Southern Hemisphere

Using an earth system model of intermediate complexity (EMIC), the McGill Paleoclimate Model-2 (MPM-2), this paper examines the climatic biogeophysical effects of afforestation in the southern hemisphere (SH) with a focus on land–atmosphere interactions and the modeling influence of the dynamic ocean in the background of the earth system. Increased forest cover affects the albedo feedback and the supply of water, which in turn influences temperature. These changes largely control the net impact of the SH afforestation based on latitudinal band. In response to afforestation in 0–15°S and 0–40°S, the local surface air temperature significantly increases at a maximum value around 5°S during autumn. This warming is attributed to decreased land surface albedo dominating over enhanced precipitation which is resulted from increased tree cover. Forest expansions in 15–30°S and 30–40°S induce diminished land surface albedo and precipitation locally, leading to a warming around 25°S during spring and a warming around 35°S in winter, respectively. The maximum differences in the modeled responses of afforestation on latitude band basis are seen to be 7–10 times larger for the same season. Our results show that capturing how and where biogeophysical changes due to forest expansion warm a specific region requires an accurate global simulation of afforestation geographically. This provides potential for further improving detection and attribution of regional afforestation effects. Furthermore, a dynamic ocean simulation results in a warming compared with a fixed one over most forcing originating areas in response to afforestation. We demonstrate that unless the dynamic ocean is considered we risk influenced conclusions regarding the drivers of temperature changes over regions of afforestation.     

Southern Ocean Biogeography of Tintinnid Ciliates of the Marine Plankton

Ciliate microzooplankton are important grazers in most pelagic ecosystems and among them, tintinnids, with their largely species‐specific loricas, allow relatively easy assessment of questions of diversity and distributions. Herein, we present the results of a survey of species records of tintinnids from the Southern Ocean (locations below 40°S) reported in 56 publications yielding 2,047 species records (synonyms included) from 402 locations. The 192 species reported can be parsed into two main groups: 32 endemic Southern Ocean species, known only from 40°S and further south, and a second group of 181 widespread species, forms with extensive geographic ranges extending into the Southern Ocean. Widespread species reported from the Southern Ocean can be further divided into a group of 81 species, each recorded multiple times in the Southern Ocean waters and 70 apparent “stray” species which have only been found but once. The endemic and widespread species of the Southern Ocean show both distinct distributional patterns and morphological differences. The assemblage of Southern Ocean endemics is found mostly within the Antarctic zone delimited by the average location of the Polar Front and contains a relatively large portion of wide‐mouthed forms. We give suggestions for future study.     

Pleistocene Niche Stability and Lineage Diversification in the Subtropical Spider Araneus omnicolor (Araneidae)

The influence of Quaternary climate oscillations on the diversification of the South American fauna is being increasingly explored. However, most of these studies have focused on taxa that are endemic to tropical environments, and relatively few have treated organisms restricted to subtropical biomes. Here we used an integrative phylogeographical framework to investigate the effects of these climate events on the ecological niche and genetic patterns of the subtropical orb-weaver spider Araneus omnicolor (Araneidae). We analyzed the mitochondrial (Cytochrome Oxidase I, COI) and nuclear (Internal Transcribed Subunit II, ITS2) DNA of 130 individuals throughout the species’ range, and generated distribution models in three different climate scenarios [present, Last Glacial Maximum (LGM), and Last Interglacial Maximum (LIG)]. Additionally, we used an Approximate Bayesian Computation (ABC) approach to compare possible demographic scenarios and select the hypothesis that better explains the genetic patterns of A. omnicolor. We obtained high haplotype diversity but low nucleotide variation among sequences. The population structure and demographic analyses showed discrepancies between markers, suggesting male-biased dispersal in the species. The time-calibrated COI phylogenetic inference showed a recent diversification of lineages (Middle/Late Pleistocene), while the paleoclimate modeling indicated niche stability since ~120 Kya. The ABC results agreed with the niche models, supporting a panmictic population as the most likely historical scenario for the species. These results indicate that A. omnicolor experienced no niche or population reductions during the Late Pleistocene, despite the intense landscape modifications that occurred in the subtropical region, and that other factors beside LGM and LIG climate oscillations might have contributed to the demographic history of this species. This pattern may be related to the high dispersal ability and wide environmental tolerance of A. omnicolor, highlighting the need for more phylogeographical studies with invertebrates and other generalist taxa, in order to understand the effects of Quaternary climate changes on Neotropical biodiversity.     

The Role of Historical Barriers in the Diversification Processes in Open Vegetation Formations during the Miocene/Pliocene Using an Ancient Rodent Lineage as a Model

The Neotropics harbors a high diversity of species and several hypotheses have been proposed to account for this pattern. However, while species of forested domains are frequently studied, less is known of species from open vegetation formations occupying, altogether, a larger area than the Amazon Forest. Here we evaluate the role of historical barriers and the riverine hypothesis in the speciation patterns of small mammals by analyzing an ancient rodent lineage (Thrichomys, Hystricomorpha). Phylogenetic and biogeographic analyses were carried out with mitochondrial and nuclear DNA markers to analyze the evolutionary relationships between Thrichomys lineages occurring in dry domains along both banks of the Rio São Francisco. This river is one of the longest of South America whose course and water flow have been modified by inland tectonic activities and climate changes. Molecular data showed a higher number of lineages than previously described. The T. inermis species complex with 2n = 26, FN = 48 was observed in both banks of the river showing a paraphyletic arrangement, suggesting that river crossing had occurred, from east to west. A similar pattern was also observed for the T. apereoides complex. Thrichomys speciation occurred in Late Miocene when the river followed a different course. The current geographic distribution of Thrichomys species and their phylogenetic relationships suggested the existence of frequent past connections between both banks in the middle section of the Rio São Francisco. The extensive palaeodune region found in this area has been identified as a centre of endemism of several vertebrate species and is likely to be a center of Thrichomys diversification.     

Biogeography of Cephalopods in the Southern Ocean Using Habitat Suitability Prediction Models

Our understanding of how environmental change in the Southern Ocean will affect marine diversity, habitats and distribution remain limited. The habitats and distributions of Southern Ocean cephalopods are generally poorly understood, and yet such knowledge is necessary for research and conservation management purposes, as well as for assessing the potential impacts of environmental change. We used net-catch data to develop habitat suitability models for 15 of the most common cephalopods in the Southern Ocean. Using modeled habitat suitability, we assessed favorable areas for each species and examined the relationships between species distribution and environmental parameters. The results compared favorably with the known ecology of these species and with spatial patterns from diet studies of squid predators. The individual habitat suitability models were overlaid to generate a “hotspot” index of species richness, which showed higher numbers of squid species associated with various fronts of the Antarctic circumpolar current. Finally, we reviewed the overall distribution of these species and their importance in the diet of Southern Ocean predators. There is a need for further studies to explore the potential impacts of future climate change on Southern Ocean squid.     

Plate tectonics and the distribution of cool temperate Southern Hemisphere macrolichens

GALLOWAY, D. J., 1988. Plate tectonics and the distribution of cool temperate Southern Hemisphere macrolichens. Several macrolichen genera in the families Lobariaceae and Pannariaceae speciate richly in cool temperate areas of the Southern Hemisphere between latitudes 35 and 55°S, being common in Nothofagus forests, subalpine shrubland, bog and grassland habitats. Affinities of southern cool temperate lichens are discussed in terms of plate tectonics and tectono-stratigraphic terranes.