Santiago Sánchez-Ramírez's research while affiliated with SickKids and other places
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Publications (60)
Purpose:
Checkpoint-inhibitors have limited efficacy for children with unselected solid and brain tumors. We report the first prospective pediatric trial (NCT02992964) using nivolumab exclusively for refractory non-hematological cancers harboring tumor mutation burden (TMB) ≥5 mutations/megabase (mut/Mb) and/or mismatch-repair deficiency (MMRD)....
Constitutional mismatch repair deficiency (CMMRD) is an aggressive and highly penetrant cancer predisposition syndrome. Because of its variable clinical presentation and phenotypical overlap with neurofibromatosis, timely diagnosis remains challenging, especially in countries with limited resources. Since current tests are either difficult to imple...
Ectomycorrhizal fungi (ECM) sustain nutrient recycling in most terrestrial ecosystems, yet we know little about what major biogeographical events gave rise to present-day diversity and distribution patterns. Given the strict relationship between some ECM lineages and their hosts, geographically well-sampled phylogenies are central to understanding...
Lentinula (Basidiomycota, Agaricales) includes the most widely cultivated mushroom in the world, Lentinula edodes, also known as shiitake (Japanese) or xiang-gu (Chinese). At present, nine species are recognized in the genus, based on morphology, mating criteria, and geographic distributions. However, analyses of internal transcribed spacers (ITS)...
Trinidad and Tobago are home to three endemic species in the anuran genus Pristimantis, of which two (Pristimantis charlottevillensis and Pristimantis turpinorum) occur in Tobago alone and the third (Pristimantis urichi) is present on both islands. Earlier, the IUCN assessed the conservation status of these species as: P. urichi, Endangered (EN); P...
en The islands of Trinidad and Tobago form a southern extension of the Lesser Antilles. Unlike the continental island of Trinidad, the more northerly Tobago formed as an older oceanic island volcanic arc. Their reptile biodiversity reflects colonization events from the South American mainland through land bridge connections at times of glacial maxi...
Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contributing factors. Extinct taxa or populations might also provide key insights in this respect by means of the DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited numb...
Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contribution factors. Extinct taxa or populations might also provide key insights in this respect from DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited number of recor...
A correction to this paper has been published: https://doi.org/https://doi.org/10.1007/s13127-021-00491-2
Over the last two decades, molecular work on the reptile and amphibian fauna of the island of Trinidad (West Indies) has revealed the presence of cryptic species and island endemics resulting in the re-description of species for northern South America. In this study, we assess the taxonomy of a population of Elachistocleis sp. formerly assigned to...
Changes to regulatory sequences account for important phenotypic differences between species and populations. In heterozygote individuals, regulatory polymorphism typically manifests as allele-specific expression (ASE) of transcripts. ASE data from inter-species and inter-population hybrids, in conjunction with expression data from the parents, can...
When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that generate the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Both cis- and trans-acting regulatory divergence can be hastened by directional selectio...
When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that underlie the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Divergence in cis - and trans -acting regulatory controls evolve despite stabilizing sel...
The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names...
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolut...
Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes...
Background:
Peninsulas often harvest high genetic diversity through repeated southward migrations of species during glacial maxima. Studies addressing within-species evolutionary responses to climate fluctuations in northeast Asia are limited compared to other regions of the world, and more so in the Korean Peninsula. In this study, we conducted t...
Distance, environmental heterogeneity and local adaptation can strongly influence population structure and connectivity. Understanding how these factors shape the genomic landscape of threatened species is a major goal in conservation genomics and wildlife management. Herein, we use thousands (6,859) of single nucleotide polymorphism markers and sp...
Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity).
Two proposals to am...
High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum- and class-level fungal classification accounting for monophyly and di...
Control region alignment raw data.
The effects of ice ages on speciation have been well documented for many European and North American taxa. In contrast, very few studies have addressed the consequences of such environmental and topographical changes in North East Asian species. More precisely, the Korean Peninsula offers a unique model to assess patterns and processes of speciatio...
Concatenated alignment raw data.
Supplementary Information.
Arctic and subarctic environments are among the most inaccessible regions in the world, making biological surveys difficult to conduct. Thus, the insect fauna of these regions has remained inadequately surveyed. The aquatic insect orders Ephemeroptera, Plecoptera, and Trichoptera (EPTs) are particularly abundant and diverse at high latitudes, playi...
In this paper, we provide a phylogenetic overview of Basidiomycota and related phyla in relation to ten years of DNA based phylogenetic studies since the AFTOL publications in 2007. We selected 529 species to address phylogenetic relationships of higher-level taxa using a maximumlikelihood framework and sequence data from six genes traditionally us...
Historical biogeography helps us keep track of organisms over time and space. However, microbial ecology and evolutionary studies are fraught with challenges due to their unknown life histories, a poor fossil record, and problematic taxonomy. Mycorrhizal fungi are key players for most terrestrial ecosystems and interact with a vast number of plants...
Amanita is a diverse and cosmopolitan genus of ectomycorrhizal fungi. Although most species fruit aboveground, some sequestrate taxa have been documented from Australia and the Mediterranean region. We describe A. nouhrae sp. nov., a new hypogeous (‘truffle-like’) species associated with Nothofagus antarctica in northern Patagonia. This constitutes...
Many different evolutionary processes may be responsible for explaining natural variation within genomes, some of which include natural selection at the molecular level and changes in population size. Fungi are highly adaptable organisms, and their relatively small genomes and short generation times make them pliable for evolutionary genomic studie...
Fungal epiphytes are a polyphyletic group found on the surface of plants, particularly on leaves, with a worldwide distribution. They belong in the phylum Ascomycota, which contains the largest known number of fungal genera. There has been little research dating the origins of the common ancestors of fungal epiphytes. This study uses a molecular cl...
Recently the well-known genus Amanita has been split into two genera, Amanita, a genus of putatively
ectomycorrhizal fungi, and Saproamanita, a genus of putatively saprotrophic fungi. We disagree with this generic
split and argue why Amanita should not be split. The proposal to split the genus does not conform to the recently proposed
guidelines fo...
The recognition of taxonomic ranks in the Linnean classification system is largely arbitrary. Some authors have proposed the use of divergence time as a universally standardized criterion. Agaricus (Agaricaceae, Agaricales) is a mushroom genus that contains many species of high commercial value. Recent studies using ITS sequence data discovered 11...
Some of the effects of past climate dynamics on plant and animal diversity make-up have been relatively well studied, but to less extent in fungi. Pleistocene refugia are thought to harbor high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In...
Aim The geographical distributions of most fungal species are still poorly known; consequently, their origins and historical distributions remain largely understudied. High levels of cryptic diversity, scarce fossil records and poorly sampled regions can explain some of these shortcomings. We extensively sampled an iconic group of edible ectomycorr...
Understanding the patterns of biodiversity through time and space is a challenging task. However, phylogeny-based macroevolutionary models allow us to account and measure many of the processes responsible for diversity build-up, namely speciation and extinction. The general latitudinal diversity gradient (LDG) is a well-recognized pattern describin...
The genomes of fungi provide an important resource to resolve issues pertaining to their taxonomy, biology, and evolution. The genomes of Amanita jacksonii, Ceratocystis albifundus, a Fusarium circinatum variant, Huntiella omanensis, Leptographium procerum, Sclerotinia
echinophila, and Rutstroemia sydowiana are presented in this genome announcement...
This study confirms that the two known Chlorociboria species from North America correspond to C. aeruginascens and C. aeruginosa that were originally described from Europe. The anamorphs of these two species are unambiguously identified for the first time: the genetic connection between C. aeruginascens is Dothiorina tulasnei, is here demonstrated...
Marasmius is a widely represented genus in tropical areas, particularly in the Neotropics, which holds exceptional diversity. Previous studies have shown that traditional sections of the genus (e.g. sensu Singer) are still in conflict with phylogenetic data. This paper addresses some issues concerning morphology at the sectional level, section Neos...
Ectomycorrhizal (EM) fungi are essential components of temperate, boreal and tropical ecosystems. However, little is known on what are the processes and patterns affecting their extant diversity and distribution. Well-sampled species-level phylogenies allows us to test hypothesis about processes causing diversity. Recently, it has been proposed tha...
Citations
... Lentinula edodes, shiitake mushroom, is a basidiomycete fungus that is a popular commercially cultivated mushroom. It is mainly found in East Asian countries, including China, Japan, and Korea (Menolli et al., 2022). Genomic DNA sequencing revealed variations in the genome size and gene number as the L. edodes B17 strain (Korea) consists of chromosomal DNA of 46.1 Mb with 13,028 predicted genes (Shim et al., 2016), while the L. edodes W1-26 strain (China) carries chromosomal DNA of 41.8 Mb with 14,889 predicted genes . ...
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... A female ibex, unlike the male, lacked black coloration. For the first year of their lives, young ibex were colored like females (Forcina et al., 2021). ...
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... Accordingly, our study examined the population genetic structure and diversity of N. bathybius in the northern South China Sea using the genetic variability of the mitochondrial DNA (mtDNA) cytochrome b gene (cyt b), with the aim of revealing its demography. The sequences of mtDNA cyt b are usually used to reconstruct demographic history and animal phylogeography (e.g., Garra orientalis [31], Tanichthys albonubes [32], Neocaridina [33], Scatophagus argus [34], Capra pyrenacia pyrenacia [35]). ...
... The only species of the genus Elachistocleis known to occur in the state of Amapá is Elachistocleis helianneae Caramaschi, 2010 (Jowers et al. 2021). We considered the record of Elachistocleis sp. from Pereira-Júnior et al. (2013) to be E. helianneae based on the distribution and the overall morphology of the specimens (Costa-Campos, pers. ...
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... . CC-BY 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is However, some studies focusing on the molecular basis of hybrid incompatibilities have investigated wild species [81,82]. Interestingly both type of studies highlighted the presence of genes having over-expression profiles but gave them a very contrasted interpretation (base of hybrid vigor on one hand and proof of mis-regulation in the other hand (eg., [6,82]). ...
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... Genes that control male-biased traits may evolve especially rapidly due to sexual selection or mutational biases ('faster male' theory), or gene regulatory networks controlling male traits may be unusually sensitive to genetic perturbation in hybrids ('fragile males'), or genes linked the X-chromosome may evolve especially fast ('faster X') (Charlesworth et al., 1987;Wu and Davis, 1993). Consequently, X-linked genes may show distinct patterns of misexpression in hybrids (Moehring et al., 2007;Turner et al., 2014;Civetta, 2016;Sanchez-Ramirez et al., 2020). Developmental pathways related to spermatogenesis seem especially sensitive to disruption in hybrids, perhaps being predisposed to disproportionate compensatory cis-trans regulatory coevolution (Mack et al., 2016;Mack and Nachman, 2017). ...
Reference: Speciation and the developmental alarm clock
... Hispidoderma which included species with the non-metuloid pleurocystidia and hymeniderm or trichoderm pileipellis. More than 500 species of the genus have been described worldwide [9]. However, the species diversity of this genus has not yet been comprehensively studied in Vietnam. ...
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... The full tef1α dataset contained 26 sequences with 535 characters (gaps included). It included Entoloma prunuloides as an outgroup due to its basal position in the Entoloma phylogeny [53,54], and E. luteolamellatum, the type-species of the subgenus Cubospora. In addition to our specimens, 11 more representatives of this subgenus and 1-3 representatives of the other main subgenera of the Entoloma s.l. were included in the analysis. ...
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... Morphological misidentification is unlikely as the voucher specimens were re-verified in detail. These results might be due to inaccurate taxonomy, incomplete lineage sorting, hybridization, or mitonuclear compensation (Bernardo et al., 2019). In addition, they may also indicate the existence of cryptic species. ...
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... Subespecie M.m.migrans. los últimos resultados(Jowers et al., 2019) sugieren que B.r.cirtensis sería en realidad una subespecie de Buteo buteo con presencia de formas intermedias en la mitad sur de España, a los que corresponderían los ejemplares observados a menudo en Extremadura, sobre todo en áreas esteparias y abiertas. ...
Reference: Aves de Extremadura. Volumen 6. 2015-2019
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