Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).

BACKGROUND AND AIMS: Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. METHODS: Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. KEY RESULTS: The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. CONCLUSIONS: The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.

Two new species of Calonectria (Hypocreales, Nectriaceae) causing Eucalyptus leaf blight in Brazil.

In recent decades, commercial Eucalyptus plantations have expanded toward the warm and humid regions of northern and northeastern Brazil, where Calonectria leaf blight (CLB) has become the primary fungal leaf disease of this crop. CLB can be caused by different Calonectria species, and previous studies have indicated that Calonectria might have high species diversity in Brazil. During a disease survey conducted in three commercial plantations of Eucalyptus in northeastern Brazil, diseased leaves from Eucalyptus trees with typical symptoms of CLB were collected, and Calonectria fungi were isolated. Based on phylogenetic analyses of six gene regions (act, cmdA, his3, rpb2, tef1, and tub2) and morphological characteristics, two new species of Calonectria were identified. Five isolates were named as C.paragominensis sp. nov. and four were named as C.imperata sp. nov. The pathogenicity to Eucalyptus of both species was confirmed by fulfilling the Koch's postulates.

ROP18 and ROP5 alleles combinations are related with virulence of T. gondii isolates from Argentina.

The allelic combination of ROP18/ROP5 genes of Toxoplasma gondii has been shown to be highly predictive of mouse virulence in canonical isolates and strains. The aims of this study were to analyze the alleles present in the ROP18/ROP5 genes from T. gondii isolates obtained in Argentina, to associate the results with the virulence registered in mouse model, and to compare with other isolates and reference strains using a phylogenetic network. Fourteen T. gondii isolates from Argentina were analyzed by nPCR-RFLP for ROP18/ROP5. Phylogenetic network analysis was inferred using the ToxoDB genotypes and the ROPs molecular markers. All isolates and reference strains were categorized as lethal or non-lethal. As results, combinations 2/2, 3/3 and 4/3 for ROP18/ROP5 were detected in 12 isolates, whereas only alleles 1 and 2 of ROP5 were detected in 2 isolates. The majority of the isolates had a mouse virulence matching to that predicted by the ROP18/ROP5 allele combination. The 3 isolates that differed from the expected virulence presented non-clonal genotypes. ROPs incorporation increased the accuracy of the phylogenetic network relations among the T. gondii samples, prevailing the clustering according to regions. Our results indicate a predominance of type 3 allele in both ROP18 and ROP5 markers and an association of allelic profiles 3/3 and 4/3 of non-clonal genotypes from Argentina, both with virulent and avirulent profiles in mice.

Population structure of Toxoplasma gondii in Argentina.

The protozoan Toxoplasma gondii is worldwide distributed showing a particular population structure that may differ among continents and countries. The aim of this study was to analyze the T. gondii population structure in Argentina and compare it with genotyping information from other South American countries. For the analysis, 39 samples from Argentina (isolates from the provinces of Buenos Aires, Misiones, Entre Ríos and San Luis) were genotyped using 10 multilocus PCR-RFLP markers including SAG1, SAG2 (5'-3'SAG2, alt. SAG2), SAG3, BTUB, GRA6, C22-8, C29-2, L358, PK1, and Apico. The T. gondii DNA samples were obtained from domestics animals (chickens n = 20; cats n = 3; pigs n = 2; goat n = 1; rabbit n = 1), humans (n = 6), zoo animals (n = 5) and a rat (n = 1). Phylogenetic relationship of these Argentinean isolates together with representative reference genotypes was determined by phylogenetic network analysis. Thirty-seven Argentinean samples belonged to 21 genotypes and two samples were genotyped at 8 of the 10 loci and considered incomplete characterized. Among these 37 typed samples, five genotypes were not previously reported. The majority of the samples grouped with the Type III (ToxoDB PCR-RFLP genotype #2) lineage. The clonal Type II (ToxoDB genotypes #1 and #3) was also identified. Our results suggest a unique population structure with combination of unique genotypes and the common Type II and Type III lineages in Argentina. Nevertheless, different regions showed distinctive pattern of genotypes, revealing a higher variability in Northern provinces.

Uncovering the hidden biodiversity of natural history collections: Insights from DNA barcoding and morphological characters of the Neotropical genus Orthocomotis Dognin (Lepidoptera: Tortricidae).

We used a 227-bp fragment of the mitochondrial gene cytochrome oxidase I (DNA "barcode") in conjunction with morphological data to study specimens of the Neotropical genus Orthocomotis Dognin, 1906, acquired from natural history collections. We examined over 20 species of Orthocomotis from 17 localities in Colombia, Ecuador, and Peru. The analysis identified 32 haplotypes among the 62 specimens and found no haplotypes shared among species. The molecular study revealed not only the usefulness of short COI sequences in discriminating among Orthocomotis species but also showed distinctness of four clusters which correspond to those based on morphological (genitalia) characters. Moreover, the molecular results suggest the occurrence of rapid speciation in Orthocomotis. We hypothesize that this may be linked to the great biodiversity of potential host plants in Neotropical ecosystems.