Hidden endemism,deep polyphyly,and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White‐collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements (UCEs) and mitochondrial DNA to evaluate population differentiation. We find deep levels of molecular divergence between two S. torqueola lineages that are phenotypically diagnosable: One corresponds to S. t. torqueola along the Pacific coast of Mexico, and the other includes S. t. morelleti and S. t. sharpei from the Gulf Coast of Mexico and Central America. Surprisingly, these two lineages are strongly differentiated in both nuclear and mitochondrial markers, and each is more closely related to other Sporophila species than to one another. We infer low levels of gene flow between these two groups based on demographic models, suggesting multiple independent evolutionary lineages within S. torqueola have been obscured by coarse‐scale similarity in plumage patterning. These findings improve our understanding of the biogeographic history of this lineage, which includes multiple dispersal events out of South America and across the Isthmus of Tehuantepec into Mesoamerica. Finally, the phenotypic and genetic distinctiveness of the range‐restricted S. t. torqueola highlights the Pacific Coast of Mexico as an important region of endemism and conservation priority.     

Maternal Prenatal Positive Affect,Depressive and Anxiety Symptoms and Birth Outcomes: The PREDO Study

Background

We investigated whether maternal prenatal emotions are associated with gestational length and birth weight in the large PREDO Study with multiple measurement points of emotions during gestation.

Methods

Altogether 3376 pregnant women self-assessed their positive affect (PA, Positive and Negative Affect Schedule) and depressive (Center for Epidemiologic Studies Depression Scale, CES-D) and anxiety (Spielberger State Anxiety Scale, STAI) symptoms up to 14 times during gestation. Birth characteristics were derived from the National Birth Register and from medical records.

Results

One standard deviation (SD) unit higher PA during the third pregnancy trimester was associated with a 0.05 SD unit longer gestational length, whereas one SD unit higher CES-D and STAI scores during the third trimester were associated with 0.04–0.05 SD unit shorter gestational lengths (P-values ≤ 0.02), corresponding to only 0.1–0.2% of the variation in gestational length. Higher PA during the third trimester was associated with a significantly decreased risk for preterm (< 37 weeks) delivery (for each SD unit higher positive affect, odds ratio was 0.8-fold (P = 0.02). Mothers with preterm delivery showed a decline in PA and an increase in CES-D and STAI during eight weeks prior to delivery. Post-term birth (≥ 42 weeks), birth weight and fetal growth were not associated with maternal prenatal emotions.

Conclusions

This study with 14 measurements of maternal emotions during pregnancy show modest effects of prenatal emotions during the third pregnancy trimester, particularly in the weeks close to delivery, on gestational length. From the clinical perspective, the effects were negligible. No associations were detected between prenatal emotions and birth weight.     

Diatom Cooccurrence Shows Less Segregation than Predicted from Niche Modeling

Species cooccurrence patterns give significant insights into the processes shaping communities. While biotic interactions have been widely studied using cooccurrence analyses in animals and larger plants, studies about cooccurrences among micro-organisms are still relatively rare. We examined stream diatom cooccurrences in France through a national database of samples. In order to test the relative influence of environmental, biotic and spatial constraints on species’ incidence distribution, cooccurrence and nestedness patterns of real communities were compared with the patterns generated from a set of standard and environmentally constrained null models. Real communities showed a higher level of segregation than the most conservative standard null models, but a general aggregation of cooccurrences when compared to environmentally constrained null models. We did not find any evidence of limiting similarity between cooccurring species. Aggregations of species cooccurrences were associated with the high levels of nestedness. Altogether, these results suggested that biotic interactions were not structuring cooccurrences of diatom species at our study scale. Instead, the patterns were more likely to be related with colonization patterns, mass effect, and local temporal dynamics of diatom biofilms. We further highlight that the association of standard and environmentally constrained null models may give realistic insight into the cooccurrence patterns of microbial communities.     

Molecular Diversity of HLA-DQ

HLA-DQ molecules were isolated from a panel of HLA-DR-DQ homozygous cell lines, partially of consanguineous origin, derived by the use of monoclonal antibody SPV-L3, and subsequently analyzed by gel electrophoretic techniques. It is demonstrated that both the DQ alpha and beta chain exhibit an extensive isoelectric point polymorphism. Within a panel of 29 B-cell lines tested, at least 5 distinct alpha and 6 distinct DQ beta chain gene products were observed. Of the 30 theoretically possible DQ alpha-beta dimers, only 10 could be identified within the panel: 5 different dimers are associated with the DQw1 allospecificity; HLA-DQw2 and -DQw3 are associated with 2 types of dimers, whereas another DQ alpha-beta combination was expressed by a cell line with a so-called DQ-blank specificity. The relation between the specificities 2B3 and TA10 appeared to be complicated as far as DQ beta chain isoelectric point differences are concerned: monoclonal antibody IIB3 seems to be reactive with four distinct DQ beta chain alleles whereas monoclonal antibody TA10 only reacted with one type of DQ beta chain. These results suggest that the polymorphic DQ alpha and beta chains may both contribute to the definition of the HLA-DQ allospecificity. A particular DQ beta chain was present in two types of HLA-DQw1 molecules, as well as in one type of HLA-DQw2 and -DQw3 (2133 positive) molecule, and formed dimers with electrophoretic distinct DQ alpha chains. On the other hand, HLA-DQw2 molecules isolated from HLA-DR3-positive cells and one type of HLA-DQw3 (TA10 positive) molecule were found to be constructed of identical alpha chains but appeared to differ in the composition of their DQ beta chain gene products. The implications of these findings will be discussed.     

Ultrastructural study in the diagnosis of various neurolipidoses

We have studied the sphingolipidosis, principally, ceroid-lipofuscinosis and other complex lipid storage diseases. We examined biopsy tissue of fourteen patients with diseases of the various types given above. The biopsy tissue was usually skin, muscle or peripheral nerve, and occassionally brain or various visceral tissue.     

Biochemical complexity of serum HLA class I molecules

Human serum was found to contain a variety of class I-like molecules by Western blotting with anti-class I heavy chain reagents: major bands usually are observed around M _r 44 000, 40 000, and 35 000–37 000. HLA-A24-positive individuals are distinguished by higher serum levels of M _r 44 000 and 40 000 class I-like molecules than those found in HLA-A24-negative individuals. The M _r 44 000 serum molecules are probably intact class I molecules that have been shed from the cell membrane, because they contain both a transmembrane segment (TM), as deduced from detergent-binding experiments, and a cytoplasmic tail (CT), as inferred from reactivity with an antipeptide serum specific for the cytoplasmic domain of class I antigens (RaCT). The M _r 35 000 and 37 000 molecules contain neither a TM nor a CT region and therefore are probably proteolytic breakdown products of cellular and/or serum M _r 44 000 molecules, although the existence of Q10-like molecules in man cannot be ruled out. The M _r 40 000 molecules do not contain a TM region. M _r 40 000 molecules reactive with the RaCT serum were found in the minority (2/13) of sera tested. We conclude that alternative splicing resulting in a precise excision of the TM exon plays a minor role in the generation of serum HLA class I antigens.Abbreviations used in this paper B2m beta-2 microglobulin - BSA bovine serum albumin - EBV-BLCL Epstein-Barr virus-transformed B lymphoblastoid cell line - mAb monoclonal antibody - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis - TCA trichloroacetic acid     

Polymorphism and complexity of HLA-DR: evidence for intra-HLA-DR region crossing-over events

HLA-DR molecules were isolated from HLA-DR3, –5, and –w6 positive homozygous B-cell lines by immunoprecipitation with monoclonal antibodies and analyzed by gel electrophoretic techniques. DNA isolated from the same cell lines was digested with the restriction enzyme Taq I and hybridized with a DR beta full-length cDNA probe. We demonstrated that certain DR I alleles are found in combination with different DR III alleles as defined by Southern blotting, protein chemistry, a functional assay using purified protein derivative-specific T-cell lines, and, in one case, also alloreactive T-cell reagents. Our results indicate that within the family of HLA-DRw52-associated haplotypes DR beta chain genes may have been transferred from one haplotype to another. The implications of these findings are discussed.     

Possible functional roles of cortical depsides and medullary depsidones in the foliose lichen Hypogymnia physodes

Secondary compounds were quantified in 75 thalli of the foliose lichen Hypogymnia physodes collected in habitats along a natural shade-sun gradient from dark spruce forests to sun-exposed sea cliffs. The irradiance in all the 75 lichen sites was estimated from hemispherical photographs. The content of lichen compounds per thallus area correlated positively with irradiance level (r²=0.73), and the mean concentration increased from 6.7% in the spruce forest to 14.4% on sea cliffs. The medullary depsidones, physodic, physodalic and protocetraric acids, constituted >95% of the total pool of extractable secondary compounds, the cortical depsides, atranorin and chloratranorin, represented <5%. Both cortical compounds correlated well with direct and with diffuse radiation, whereas the three medullary compounds correlated better with diffuse than with direct radiation. Mentioned trends are consistent with a solar radiation screening hypothesis of both groups of these colourless compounds occuring as tiny crystals outside fungal hyphae. However, the UV-B protective hypothesis of the compounds was further tested in a lab experiment. Unnaturally high UV-B doses were required to significantly reduce the PSII efficiency (F_V/F_M) of symbiotic algae. Removal of the major pool of secondary compounds with acetone did not increase photobiont susceptibility to UV-B. Therefore, the main functional role of the UV-B absorbing secondary compounds in H. physodes is hardly UV-B screening. Other roles such as PAR-screening and defence against herbivores and pathogenic organisms are discussed.     

Mollusc assemblages of the Pontian and Dacian deposits from the Topolog-Arge? area (southern Carpathian foredeep - Romania)

A better understanding of Mediterranean-Paratethys water-exchange during the Messinian Salinity Crisis has since long been hampered by the absence of a reliable time frame for the Paratethys. High-resolution magnetostratigraphic studies on the sedimentary sequences of the eastern and southern Carpathian foredeep recently resulted in an accurate chronology for the Mio-Pliocene deposits of the Dacic Basin of Romania. This allowed a straightforward correlation of the Pontian and Dacian stages to the geological time scale, which revived earlier discussions on Mediterranean-Paratethys connectivity. Here, we present Pontian and Dacian mollusc assemblages of the Getic Depression (Topolog-Arge? area, southern Carpathians) of Romania, which are incorporated in a magnetostratigraphic time frame. They indicate that a hiatus - comprising the Early Pontian - is present in the stratigraphic successions, which could be related to a base level drop of the Paratethys water column or to more local tectonic processes. The mollusc assemblages furthermore show a gradual transition at the Pontian/Dacian boundary, which is magnetostratigraphically dated at ∼4.9 Ma. This is significantly later (by more than 400 kyrs) than the Mio-Pliocene boundary in the Mediterranean sequences.