Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideriinferred from mtDNA and nuclear markers

BACKGROUND: The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3) we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. RESULTS: All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB), while R. marina sequences from the left Amazon bank (LAB) are monophyletic. An Isolation-with-Migration (IM) analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene), while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene). This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr), which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. CONCLUSIONS: The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these two closely related toad species. Overall, our results suggest a phenomenon of extensive mtDNA unidirectional introgression from the previously occurring R. schneideri into the invading R. marina. We hypothesize that climatic-induced range shifts during the Pleistocene/Holocene may have played an important role in the observed patterns of introgression

New occurrence records of Lepidodactylus lugubris (Duméril & Bibron, 1836) (Squamata: Gekkonidae) for the amazon and atlantic forest in Brazil

The gecko Lepidodactylus lugubris is native to southwest Pacific but is widely introduced into the neotropics. In Brazil, its known distribution was limited to the city of Belém in the Amazon. This work presents three new records of the species for the states of Pará and Bahia. Records from Pará were made in Capitão Poço and in Marajó island, while the third one was in Salvador, Bahia. We believe these records represent independent colonizations, with specimens arriving in Capitão Poço in auto-vehicles coming from Belém, while colonizations of Salvador and Breves may have occurred by ships. Introductions of L. lugubris were described as accidental or due to pet trade, so the latter alternative cannot be discarded. It seems likely that L. lugubris has already spread to other states and biomes across the north and northeast of Brazil, but its occurrence is yet to be documented in these regions.Asociación Herpetológica Argentin

Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads <it>Rhinella marina </it>and <it>R. schneideri </it>inferred from mtDNA and nuclear markers

Abstract Background The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3) we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. Results All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB), while R. marina sequences from the left Amazon bank (LAB) are monophyletic. An Isolation-with-Migration (IM) analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene), while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene). This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr), which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. Conclusions The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these two closely related toad species. Overall, our results suggest a phenomenon of extensive mtDNA unidirectional introgression from the previously occurring R. schneideri into the invading R. marina. We hypothesize that climatic-induced range shifts during the Pleistocene/Holocene may have played an important role in the observed patterns of introgression.</p

SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses

Abstract Background The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained. Results To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers. Conclusions The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature. Graphical abstrac

Inclusion of South American samples reveals new population structuring of the blacktip shark (Carcharhinus limbatus) in the western Atlantic

Carcharhinus limbatus has a cosmopolitan distribution and marked genetic structuring, mainly because of its philopatric behavior. However, analysis of this structuring has not previously included South American populations. In the present study, we analyzed a sample of adult individuals collected on the northern coast of Brazil and compared the sequences of the mitochondrial control region with those of populations already genotyped. Relatively high haplotype diversity (12 haplotypes, genetic diversity of 0.796) was observed, similar to that in other populations but with a much larger number of private alleles. In contrast to populations studied previously, which were represented by neonates, the pronounced allelic variability found in the South American individuals may have resulted from migrations from other populations in the region that have yet to be genotyped. This population was also genetically distinct from the other Atlantic populations (Fst > 0.8), probably because of female philopatry, and apparently separated from the northwestern Atlantic group 1.39 million years ago. These findings indicate that the C. limbatus population from northern Brazil is genetically distinct from all other populations and should be considered as a different management unit for the protection of stocks

Additional file 1 of SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses

Additional file 1: List of Chordata genomes analyzed in this study, including their taxonomic classification and accession numbers

Using copepods to develop a didactic strategy for teaching species concepts in the classroom

10 pages, 4 figuresWhile there is little doubt that the species is the lowest independent evolutionary unit, understanding the many different species concepts is a difficult task, even for university students. In the present study, we propose a didactic sequence that involves fieldwork, laboratory analyses, experimental cultures, and computational work in an integrated strategy for the comprehension of the phenetic, ecological, biological, and phylogenetic species concepts. This activity is based on the observation of the morphological, ecological, biological, and phylogenetic characteristics of samples of two copepod crustaceans, Acartia tonsa Dana, 1849 and Acartia lilljeborgi Giesbrecht, 1889 (Copepoda, Calanoida). These species were the focus of a simple practical that contributes to the effective comprehension of the four species concepts mentioned above, using straightforward methods that can be standardized easily in the laboratory and classroom. The practical activities developed for the didactic sequence presented here not only made the classes more interesting and motivational, but also contributed to the more effective assimilation of the content, as well as the more effective consolidation of the knowledge presented in the class. It is important to note that these activities can be developed at different educational levels (i.e., undergraduate and graduate students), and can be applied to other types of organism (e.g., amphibians, insects or other copepods), as long as their characteristics are adequate for the systematic exploration of the four species concepts included hereThis study was financed by CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) through a graduate scholarship to CG and research productivity (PQ) fellowships to MV (308217/2019-5) and SFF (310852/2017-0)With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe