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Article: Different patterns of introgression in a three species hybrid zone among European cave salamanders.

Bruni, Giacomo / Chiocchio, Andrea / Nascetti, Giuseppe / Cimmaruta, Roberta

2023 Volume 13, Issue 8, Page(s) e10437

Abstract: Hybrid zones occur where genetically distinct populations meet, mate and produce offspring with mixed ancestry. In Plethodontid salamanders, introgressive hybridization is a common phenomenon, where hybrids backcross with parental populations leading to ... ...

Abstract	Hybrid zones occur where genetically distinct populations meet, mate and produce offspring with mixed ancestry. In Plethodontid salamanders, introgressive hybridization is a common phenomenon, where hybrids backcross with parental populations leading to the spread of new alleles into the parental genomes. Whereas many hybrid zones have been reported in American Plethodontid salamanders, only a single hybrid zone has been documented in European plethodontids so far, which is located at the Apuan Alps in the Italian Peninsula. Here, we describe a previously unreported hybrid zone in the Northern Apennines involving all the three Plethodontid salamander species inhabiting the Italian Peninsula. We found 21 new
Language	English
Publishing date	2023-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.10437
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Distribution and conservation status of threatened endemic amphibians within the Aspromonte mountain region, a hotspot of Mediterranean biodiversity

Martino, Giuseppe / Chiocchio, Andrea / Siclari, Antonino / Canestrelli, Daniele

Nature Conservation. 2022 Sept. 12, v. 50 p.1-22

2022

Abstract: AbstractAmphibian biodiversity loss in recent years has exceeded that of all other groups of vertebrates. In this context, biodiversity hotspots represent priority targets for conservation in amphibian populations. However, little information is ... ...

Abstract	AbstractAmphibian biodiversity loss in recent years has exceeded that of all other groups of vertebrates. In this context, biodiversity hotspots represent priority targets for conservation in amphibian populations. However, little information is available on the distribution and conservation status of amphibian species within most biodiversity hotspots. Here, we characterized the distribution and conservation status of four threatened endemic amphibians (Bombina pachypus, Salamandra salamandra gigliolii, Salamandrina terdigitata, and Rana italica) in the Aspromonte Mountain region, a biodiversity hotspot in southern Italy where the conservation status of amphibians is almost unexplored. We conducted an intensive field survey of 507 potential breeding sites spanning over 2,326 km². We found that all four species were widespread in the study area. We observed 337 species occurrences: 63 for S. s. gigliolii, 29 for S. terdigitata, 84 for B. pachypus, and 161 for R. italica. Species distribution analysis revealed that S. s. gigliolii and R. italica populations had an extended and homogenous distribution. Conversely, S. terdigitata showed a dispersed pattern, with long distances among breeding sites, and B. pachypus an aggregated pattern, associated with the availability of suitable artificial habitats. On the other hand, we reported a decrease in B. pachypus occurrence in its natural habitats, which reflects a negative trend of its populations. Overall, our results provide an encouraging framework for the conservation of amphibian populations in this area, but highlight the low coverage of threatened amphibian populations in protected areas, highlighting the need for a reassessment of conservation policies and spatial conservation planning for the Aspromonte region.
Keywords	Rana ; Salamandra salamandra ; amphibians ; biodiversity ; conservation status ; geographical distribution ; surveys ; Italy ; Amphibian decline ; Apennine yellow-bellied toad ; biodiversity conservation ; biodiversity hotspot ; fire salamander ; Italian peninsula ; Italian stream frog ; spectacled salamander
Language	English
Dates of publication	2022-0912
Size	p. 1-22.
Publishing place	Pensoft Publishers
Document type	Article ; Online
ZDB-ID	2667603-5
ISSN	1314-3301
ISSN	1314-3301
DOI	10.3897/natureconservation.50.86002
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Spatial differentiation of background matching strategies along a Late Pleistocene range expansion route

Spadavecchia, Giada / Chiocchio, Andrea / Costantini, David / Liparoto, Anita / Bisconti, Roberta / Canestrelli, Daniele

Evol Ecol. 2023 Apr., v. 37, no. 2 p.291-303

2023

Abstract: Late Pleistocene climate changes have deeply impacted the range dynamics of temperate species. While the genetic legacy of these dynamics has been widely investigated, little is known about their phenotypic consequences. Anti-predatory strategies offer ... ...

Abstract	Late Pleistocene climate changes have deeply impacted the range dynamics of temperate species. While the genetic legacy of these dynamics has been widely investigated, little is known about their phenotypic consequences. Anti-predatory strategies offer intriguing opportunities to study phenotypic evolution in response to dispersal dynamics since the ability to avoid predation can be pivotal for populations colonising new environments. Here we investigated the spatial differentiation of background colour matching strategies along a Late Pleistocene range expansion route of a temperate species, the Tyrrhenian tree frog Hyla sarda. Using common-garden experiments, we tested whether individuals from the source area (Sardinia) and individuals from the newly founded area (Corsica) differ in two components of the camouflage strategy: colour change abilities and background choice behaviour. We found a remarkable spatial structure in both colour change abilities and background choice behaviour, across the expansion range. Tree frogs from the source area displayed higher colour change abilities and a more pronounced preference for a greener background, with respect to tree frogs from the newly colonised area. Our results support the intriguing hypothesis that Late Pleistocene biogeographic history might be an overlooked major player in shaping current spatial patterns of phenotypic traits variation across animal populations.
Keywords	Hyla ; Pleistocene epoch ; animals ; antipredatory behavior ; camouflage ; climate ; color ; evolution ; geographical distribution ; phenotype ; predation ; spatial variation ; Corsica ; Sardinia
Language	English
Dates of publication	2023-04
Size	p. 291-303.
Publishing place	Springer International Publishing
Document type	Article ; Online
ZDB-ID	15919-0
ISSN	1573-8477 ; 0269-7653
ISSN (online)	1573-8477
ISSN	0269-7653
DOI	10.1007/s10682-022-10216-2
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Paso doble: A two-step Late Pleistocene range expansion in the Tyrrhenian tree frog Hyla sarda.

Spadavecchia, Giada / Chiocchio, Andrea / Bisconti, Roberta / Canestrelli, Daniele

Gene

2021 Volume 780, Page(s) 145489

Abstract: The Tyrrhenian tree frog, Hyla sarda, is an amphibian endemic to the Tyrrhenian islands (Western Mediterranean). Previous investigations of its Pleistocene evolutionary history suggested that it colonised the northern portion of its current range, ... ...

Abstract	The Tyrrhenian tree frog, Hyla sarda, is an amphibian endemic to the Tyrrhenian islands (Western Mediterranean). Previous investigations of its Pleistocene evolutionary history suggested that it colonised the northern portion of its current range, through a spatial diffusion process from the Sardinia island, during the last glaciation. However, southern and northern portions of the species' range experienced markedly different climatic conditions during the Late Pleistocene, suggesting the possibility of an unusual two-step process of demographic expansion. Here, we use Bayesian phylogeographic approaches to locate the ancestral area in Sardinia and to characterise better the demographic component of this expansion event. These analyses located the ancestral area for H. sarda populations along the central-eastern coast of the Sardinia island, within an area previously shown to host suitable bioclimatic conditions for H. sarda populations throughout the Late Pleistocene. Historical demographic reconstructions clearly showed that a two-step process of demographic growth fits well the data, with northern populations expanding later than Sardinia populations. The harsher climatic conditions occurred in northern islands during the glacial epoch, as compared to Sardinia, likely delayed tree frog colonisation of northern territories, and the associated demographic growth.
MeSH term(s)	Animals ; Anura/genetics ; Biological Evolution ; Genetic Variation ; Haplotypes ; Italy ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA
Language	English
Publishing date	2021-02-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2021.145489
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Article: Paso doble: A two-step Late Pleistocene range expansion in the Tyrrhenian tree frog Hyla sarda

Spadavecchia, Giada / Chiocchio, Andrea / Bisconti, Roberta / Canestrelli, Daniele

Gene. 2021 May 15, v. 780

2021

Abstract	The Tyrrhenian tree frog, Hyla sarda, is an amphibian endemic to the Tyrrhenian islands (Western Mediterranean). Previous investigations of its Pleistocene evolutionary history suggested that it colonised the northern portion of its current range, through a spatial diffusion process from the Sardinia island, during the last glaciation. However, southern and northern portions of the species’ range experienced markedly different climatic conditions during the Late Pleistocene, suggesting the possibility of an unusual two-step process of demographic expansion. Here, we use Bayesian phylogeographic approaches to locate the ancestral area in Sardinia and to characterise better the demographic component of this expansion event. These analyses located the ancestral area for H. sarda populations along the central-eastern coast of the Sardinia island, within an area previously shown to host suitable bioclimatic conditions for H. sarda populations throughout the Late Pleistocene. Historical demographic reconstructions clearly showed that a two-step process of demographic growth fits well the data, with northern populations expanding later than Sardinia populations. The harsher climatic conditions occurred in northern islands during the glacial epoch, as compared to Sardinia, likely delayed tree frog colonisation of northern territories, and the associated demographic growth.
Keywords	Bayesian theory ; Hyla ; Pleistocene epoch ; amphibians ; coasts ; genes ; glaciation ; phylogeography ; Sardinia
Language	English
Dates of publication	2021-0515
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2021.145489
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Measuring athletic performance in post-metamorphic fire salamanders

Erica de Rysky / Bisconti Roberta / Chiocchio Andrea / Canestrelli Daniele

BMC Research Notes, Vol 14, Iss 1, Pp 1-

2021 Volume 6

Abstract: Abstract Objective Athletic performances are dynamic movements that are physically challenging and often predict individual success in ecological contexts. They stem from a complex integration of multiple phenotypic traits—e.g., morphological, ... ...

Abstract	Abstract Objective Athletic performances are dynamic movements that are physically challenging and often predict individual success in ecological contexts. They stem from a complex integration of multiple phenotypic traits—e.g., morphological, physiological and behavioural—that dictate animal survival and individual fitness. However, directly quantifying athletic performances can be particularly challenging in cryptic, slow-moving species or not very reactive in attitude. Here we present and describe a rapid, simple, and low-cost method to measure athletic performance in post-metamorphic individuals of the fire salamander Salamandra salamandra. While extremely reactive during the larval stage, adult salamanders are, in fact, cryptic and relatively slow-moving. Results Forcing terrestrial juveniles to swim under standard, albeit ecologically plausible, laboratory conditions, and using an automatic point-mass tracking tool, we were able to measure maximal and average performance indicators of post-metamorphic individuals. This method avoids inter-individual variation in motivation, as it forces individuals to perform at their best. Moreover, with this method, measures of athletic performance will be directly comparable between larval and terrestrial stages, allowing to study the contribution of carryover effects to the wide range of processes implicated in the eco-evo-devo of athletic performance in salamanders.
Keywords	Athletic performance ; Fire salamander ; Salamandra salamandra ; Swimming ; Medicine ; R ; Biology (General) ; QH301-705.5 ; Science (General) ; Q1-390
Subject code	796
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Brain de novo transcriptome assembly of a toad species showing polymorphic anti-predatory behavior.

Chiocchio, Andrea / Libro, Pietro / Martino, Giuseppe / Bisconti, Roberta / Castrignanò, Tiziana / Canestrelli, Daniele

Scientific data

2022 Volume 9, Issue 1, Page(s) 619

Abstract: Understanding the genomic underpinnings of antipredatory behaviors is a hot topic in eco-evolutionary research. Yellow-bellied toad of the genus Bombina are textbook examples of the deimatic display, a time-structured behavior aimed at startling ... ...

Abstract	Understanding the genomic underpinnings of antipredatory behaviors is a hot topic in eco-evolutionary research. Yellow-bellied toad of the genus Bombina are textbook examples of the deimatic display, a time-structured behavior aimed at startling predators. Here, we generated the first de novo brain transcriptome of the Apennine yellow-bellied toad Bombina pachypus, a species showing inter-individual variation in the deimatic display. Through Rna-Seq experiments on a set of individuals showing distinct behavioral phenotypes, we generated 316,329,573 reads, which were assembled and annotated. The high-quality assembly was confirmed by assembly validators and by aligning the contigs against the de novo transcriptome with a mapping percentage higher than 91.0%. The homology annotation with DIAMOND (blastx) led to 77,391 contigs annotated on Nr, Swiss Prot and TrEMBL, whereas the domain and site protein prediction made with InterProScan led to 4747 GO-annotated and 1025 KEGG-annotated contigs. The B. pachypus transcriptome described here will be a valuable resource for further studies on the genomic underpinnings of behavioral variation in amphibians.
MeSH term(s)	Animals ; Anura ; Brain ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Sequence Analysis, RNA ; Transcriptome
Language	English
Publishing date	2022-10-13
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-022-01724-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Evolution of personality and locomotory performance traits during a late Pleistocene island colonization in a tree frog.

Bisconti, Roberta / Carere, Claudio / Costantini, David / Liparoto, Anita / Chiocchio, Andrea / Canestrelli, Daniele

Current zoology

2022 Volume 69, Issue 5, Page(s) 631–641

Abstract: Recent empirical and theoretical studies suggest that personality and locomotory performance traits linked to dispersal abilities are crucial components of the dispersal syndromes, and that they can evolve during range expansions and colonization ... ...

Abstract	Recent empirical and theoretical studies suggest that personality and locomotory performance traits linked to dispersal abilities are crucial components of the dispersal syndromes, and that they can evolve during range expansions and colonization processes. Island colonization is one of the best characterized processes in dispersal biogeography, and its implication in the evolution of phenotypic traits has been investigated over a wide range of temporal scales. However, the effect of island colonization on personality and performance traits of natural populations, and how these traits could drive island colonization, has been little explored. Noteworthy, no studies have addressed these processes in the context of late Pleistocene range expansions. Here, we investigated the contribution of island colonization triggered by postglacial range expansions to intraspecific variation in personality and locomotory performance traits. We compared boldness, exploration, jumping performance, and stickiness abilities in populations from 3 equidistant areas of the Tyrrhenian tree frog
Language	English
Publishing date	2022-08-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2628880-1
ISSN	1674-5507
ISSN	1674-5507
DOI	10.1093/cz/zoac062
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Article ; Online: De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage.

Libro, Pietro / Chiocchio, Andrea / De Rysky, Erika / Di Martino, Jessica / Bisconti, Roberta / Castrignanò, Tiziana / Canestrelli, Daniele

Scientific data

2023 Volume 10, Issue 1, Page(s) 330

Abstract: Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Attitude to disperse is unevenly distributed among individuals within populations, and that individual personality can have pivotal ... ...

Abstract	Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Attitude to disperse is unevenly distributed among individuals within populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we assembled and annotated the first de novo transcriptome of the head tissues of Salamandra salamandra from individuals, representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully assembled and annotated. The high-quality of the assembly was confirmed by three assembly validators. The alignment of contigs against the de novo transcriptome led to a mapping percentage higher than 94%. The homology annotation with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NR, Swiss-Prot and TrEMBL. The domain and site protein prediction led to 9850 GO-annotated contigs. This de novo transcriptome represents reliable reference for comparative gene expression studies between alternative behavioral types, for comparative gene expression studies within Salamandra, and for whole transcriptome and proteome studies in amphibians.
MeSH term(s)	Animals ; Gene Expression Profiling ; Genetic Association Studies ; High-Throughput Nucleotide Sequencing ; Larva/genetics ; Molecular Sequence Annotation ; Salamandra/genetics ; Transcriptome
Language	English
Publishing date	2023-05-27
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-023-02217-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): Assessing the potential causes and consequences

Rota, Jadranka / Twort, Victoria / Chiocchio, Andrea / Peña, Carlos / Wheat, Christopher W. / Kaila, Lauri / Wahlberg, Niklas

Systematic entomology. 2022 Oct., v. 47, no. 4

2022

Abstract: The field of molecular phylogenetics is being revolutionized with next‐generation sequencing technologies making it possible to sequence large numbers of genomes for non‐model organisms ushering us into the era of phylogenomics. The current challenge is ... ...

Abstract	The field of molecular phylogenetics is being revolutionized with next‐generation sequencing technologies making it possible to sequence large numbers of genomes for non‐model organisms ushering us into the era of phylogenomics. The current challenge is no longer how to get enough data, but rather how to analyse the data and how to assess the support for the inferred phylogeny. Here, we focus on one of the largest animal groups on the planet – butterflies and moths (order Lepidoptera), whose phylogeny remains unresolved despite several recent phylogenomic studies. In this study, we assess the potential causes and consequences of the conflicting phylogenetic hypotheses. With a dataset consisting of 331 protein‐coding genes and the alignment length over 290,000 base pairs, including 200 taxa representing 83% of lepidopteran superfamilies, we compare phylogenetic hypotheses inferred from amino acid and nucleotide alignments. The resulting two phylogenies are discordant, especially with respect to the placement of the superfamily Gelechioidea, which is likely due to compositional bias and possible other model violations. Furthermore, we employed a series of analyses to dissect our dataset and demonstrate that there is sufficient phylogenetic signal to resolve much – but not all – of the lepidopteran tree of life. The relationships among superfamilies within Ditrysia, the most species rich lepidopteran clade containing 98% of the extant species, remain poorly resolved. We conclude that taxon sampling remains an issue even in phylogenomic analyses and recommend that poorly sampled highly diverse groups, such as Gelechioidea in Lepidoptera, should receive extra attention in the future.
Keywords	Lepidoptera ; amino acids ; animals ; data collection ; entomology ; genome ; phylogeny
Language	English
Dates of publication	2022-10
Size	p. 531-550.
Publishing place	Blackwell Publishing Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	223608-4
ISSN	0307-6970
ISSN	0307-6970
DOI	10.1111/syen.12545
Database	NAL-Catalogue (AGRICOLA)

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