Tiago Marafiga Degrandi

The evolution of the amniote genome is characterized by a striking dichotomy between extreme karyotypic stasis and rapid structural innovation. To identify the mechanisms governing this variation, we provide a comprehensive synthesis of chromosome number and karyotype data across non‐avian reptiles, birds and mammals, integrating a century of classical cytogenetics with modern chromosome‐scale genomics. Amniote chromosome numbers span a range from 2 n = 6 to 142 and have been shaped primarily by chromosomal fusions and fissions rather than by polyploidization common in non‐amniotes. Recent ancestral state reconstructions suggest a highly fragmented ancestral amniote karyotype of 2 n = 88 with a bipartite organization of macro‐ and microchromosomes. They also support environmental sex determination as the plesiomorphic state. We explore the evolutionary mechanisms facilitating chromosomal turnover, including lineage‐specific transposable element activity, hybridization‐driven genomic instability and genetic hitchhiking, alongside the canalization model and the position‐effect hypothesis as primary responses to environmental transitions. Social structure, such as polygynous harem systems, can further contribute to rearrangement fixation via genetic drift in some, but not all, lineages. Chromosomal divergence across these lineages serves as a useful cytotaxonomic marker and, in some cases, a barrier to gene flow, as in the postzygotic incompatibility of equid and cervid hybrids. In contrast, introgression persists across karyotypically divergent rock‐wallabies and crocodilians, indicating that the reproductive consequences of karyotypic divergence are lineage‐specific rather than a fixed function of karyotypic distance. This synthesis presents an updated atlas of amniote chromosomal evolution and provides a conceptual framework for understanding how molecular mechanisms, ecological shifts and behavioural factors interact to shape genomic structure.

Catfishes of the genus Hypancistrus are among the most emblematic endemic species of the Xingu River rapids, a biodiversity hotspot of the Amazon Basin. In the unique Volta Grande region, the distribution of Hypancistrus zebra , Hypancistrus seideli , and Hypancistrus yudja overlap, creating a potential zone of biological interaction, and previous morphological analyses suggest the occurrence of hybridization between H. seideli and H. yudja . We investigated maternal inheritance and phylogenetic relationships among the three species and hybrids using complete mitochondrial genomes and nuclear genome size estimates. Phylogenetic analyses revealed that hybrids carried maternal lineages exclusively from H. zebra and H. seideli , with no evidence of contribution from H. yudja . Nuclear genome size analyses support this pattern, with hybrids exhibiting intermediate values consistent with additive inheritance. Divergence time estimates indicated a very recent evolutionary radiation (< 0.5 Ma), explaining the persistence of reproductive compatibility among the species. These findings raise conservation concerns, particularly for the zebra pleco H. zebra , a critically endangered species at risk of genetic introgression. Our study provides the first complete mitochondrial genome data for these species and emphasizes the importance of integrating morphological and genomic approaches to understand hybridization dynamics and guide conservation strategies in the Xingu River.

Seaports are introduction hotspots for invasive alien species (IAS). This is especially true for rodents, which have accompanied humans around the globe since the earliest days of ocean-going voyages. The rapid spread of IAS soon after arrival in a new environment is facilitated by further human-mediated transport or landscape features, like roads. By measuring genetic diversity and structure to investigate dispersal pathways, we gained insight into the transport, spread and establishment stages of a biological invasion, leveraging the most common rodent species (R. norvegicus) in this setting. We characterized the genetic structure of three Norway rat populations along a busy industrial road used by trucks to access the Port area in Paranaguá city (Brazil). A total of 71 rats were genotyped using 11 microsatellite markers. The results revealed a pattern of gene flow contrary to the expected stepping-stone model along the linear transect, with the two furthest apart populations being clustered together. We hypothesize that the observed outcome is explained by natural dispersal along the corridor being lower than human-mediated transport. The sampled area furthest from the port is a gas station frequented by trucks which are considered the most likely mode of transportation. In terms of management strategies, we suggest more emphasis should be put on cargo surveillance to lower the risk of Norway rat dispersal, not only for biosecurity, but also for sanitary reasons, as this port is a major grain trading point.

Hummingbirds (Trochilidae) are one of the most enigmatic avian groups, and also among the most diverse, with approximately 360 recognized species in 106 genera, of which 43 are monotypic. This fact has generated considerable interest in the evolutionary biology of the hummingbirds, which is reflected in a number of DNA-based studies. However, only a few of them explored chromosomal data. Given this, the present study provides an analysis of the karyotypes of three species of Neotropical hummingbirds, Anthracothorax nigricollis (ANI), Campylopterus largipennis (CLA), and Hylocharis chrysura (HCH), in order to analyze the chromosomal processes associated with the evolution of the Trochilidae. The diploid number of ANI is 2n=80 chromosomes, while CLA and HCH have identical karyotypes, with 2n=78. Chromosome painting with Gallus gallus probes (GGA1-12) shows that the hummingbirds have a karyotype close to the proposed ancestral bird karyotype. Despite this, an informative rearrangement was detected: an in-tandem fusion between GGA7 and GGA9 found in CLA and HCH, but absent in ANI. A comparative analysis with the tree of life of the hummingbirds indicated that this fusion must have arisen following the divergence of a number of hummingbird species.

The distribution of 45S rDNA cluster in avian karyotypes varies in different aspects, such as position, number of bearer chromosomes, and bearers being macro- or microchromosomes. The present study investigated the patterns of variation in the 45S rDNA-bearer chromosomes of birds in order to understand the evolutionary dynamics of the cluster configuration and its contribution to the evolution of bird karyotypes. A total of 73 bird species were analyzed, including both published data and species for which rDNA-FISH was conducted for the first time. In most birds, the 45S rDNA clusters were located in a single pair of microchromosomes. Hence, the location of 45S rDNA in macrochromosomes, observed only in Neognathae species, seems to be a derived state, probably the result of chromosomal fusion between microchromosomes and distinct macrochromosomes. Additionally, the 45S rDNA was observed in multiple microchromosomes in different branches of the bird phylogeny, suggesting recurrence of dispersion processeses, such as duplications and translocations. Overall, this study indicated that the redistribution of the 45S rDNA sites in bird chromosomes followed different evolutionary trajectories with respect to each lineage of the class Aves.

Despite the richness of species in the Hirudinidae family, little is known about the genome organization of swallows. The Progne tapera species presents genetic and morphological difference when compared to other members of the same genus. Hence, the aims of this study were to analyze the chromosomal evolution of three species Progne tapera, Progne chalybea and Pygochelidon cyanoleuca - by comparative chromosome painting using two sets of probes, Gallus gallus and Zenaida auriculata, in order to determine chromosome homologies and the relationship between these species. All karyotypes exhibited 76 chromosomes with similar morphology, except for the 5th, 6th and 7th chromosome pairs in P. cyanoleuca. Additionally, comparative chromosome painting demonstrated the same hybridization pattern in the two Progne, which was similar to the putative avian ancestral karyotype, except for the centric fission in the first pair, as found in other Passeriformes. Thus, these data display a close relationship between the Progne species. Although P. cyanoleuca demonstrated the same fission in the first pair of the ancestral syntenic (GGA1), it also showed an additional chromosomal rearrangement for this species, namely a fusion with a microchromosome in the seventh pair.

The order Charadriiformes comprises three major clades: Lari and Scolopaci as sister group to Charadrii. Until now, only three Charadriiformes species have been studied by chromosome painting: Larus argentatus (Lari), Burhinus oedicnemus and Vanellus chilensis (Charadrii). Hence, there is a lack of information concerning the third clade, Scolapaci. Based on this, and to gain a better understanding of karyotype evolution in the order Charadriiformes, we applied conventional and molecular cytogenetic approaches in a species belonging to clade Scolopaci - the wattled jacana (Jacana jacana) - using Gallus gallus and Zenaida auriculata chromosome-specific probes. Cross-species evaluation of J. jacana chromosomes shows extensive genomic reshuffling within macrochromosomes during evolution, with multiple fission and fusion events, although the diploid number remains at high level (2n=82). Interestingly, this species does not have the GGA7-8 fusion, which was found in two representatives of Charadrii clade, reinforcing the idea that this fusion may be exclusive to the Charadrii clade. In addition, it is shown that the chromosome evolution in Charadriiformes is complex and resulted in species with typical and atypical karyotypes. The karyotypic features of Scolopaci are very different from those of Charadrii and Lari, indicating that after divergence, each suborder has undergone different chromosome rearrangements.

Kingfishers comprise about 115 species of the family Alcedinidae, and are an interesting group for cytogenetic studies, for they are among birds with most heterogeneous karyotypes. However, cytogenetics knowledge in Kingfishers is extremely limited. Thus, the aim of this study was to describe the karyotype structure of the Ringed Kingfisher (Megaceryle torquata Linnaeus, 1766) and Green Kingfisher (Chloroceryle americana Gmelin, 1788) and also compare them with related species in order to identify chromosomal rearrangements. The Ringed Kingfisher presented 2n = 84 and the Green Kingfisher had 2n = 94. The increase of the chromosome number in the Green Kingfisher possibly originated by centric fissions in macrochromosomes. In addition, karyotype comparisons in Alcedinidae show a heterogeneity in the size and morphology of macrochromosomes, and chromosome numbers ranging from 2n = 76 to 132. Thus, it is possible chromosomal fissions in macrochromosomes resulted in the increase of the diploid number, whereas chromosome fusions have originated the karyotypes with low diploid number.

Domestic buffaloes are divided into two group based on cytogenetic characteristics and habitats: the "river buffaloes" with 2n = 50 and the "swamp buffaloes", 2n = 48. Nevertheless, their hybrids are viable, fertile and identified by a 2n = 49. In order to have a better characterization of these different cytotypes of buffaloes, and considering that NOR-bearing chromosomes are involved in the rearrangements responsible for the karyotypic differences, we applied silver staining (Ag-NOR) and performed fluorescent in situ hybridization (FISH) experiments using 18S rDNA as probe. Metaphases were obtained through blood lymphocyte culture of 21 individuals, including river, swamp and hybrid cytotypes. Ag-NOR staining revealed active NORs on six chromosome pairs (3p, 4p, 6, 21, 23, 24) in the river buffaloes, whereas the swamp buffaloes presented only five NOR-bearing pairs (4p, 6, 20, 22, 23). The F1 crossbreed had 11 chromosomes with active NORs, indicating expression of both parental chromosomes. FISH analysis confirmed the numerical divergence identified with Ag-NOR. This result is explained by the loss of the NOR located on chromosome 4p in the river buffalo, which is involved in the tandem fusion with chromosome 9 in this subspecies. A comparison with the ancestral cattle karyotype suggests that the NOR found on the 3p of the river buffalo may have originated from a duplication of ribosomal genes, resulting in the formation of new NOR sites in this subspecies.

The order Passeriformes is the largest group of species karyotyped among birds, however little is known about the cytogenetic of the Mimidae family, registering only karyology basic data (giemsa staining). The aim of this study was to analyze the chromosomal complement from the species Mimus saturninus by conventional staining and differential chromosome banding. Diploid number and chromosome morphology were determined, as well as the distribution pattern of constitutive heterochromatin (CBG-banding), GTG-banding andAgNOR staining (NORs). The Chalk-browed Mockingbird has 2n=80. The first and fourth pairs are submetacentric and the second, third and fifth are acrocentric. The remaining chromosomes pairs of the complement have telocentric morphology. The Z chromosome is submetacentric and the W is metacentric. CBG-banding showed positive staining in the pericentromeric region of most macrochromosomes and microchromosomes and also at Z chromosome, differently from W chromosome which appeared totally heterochromatic. The GTG-banding was similar to Gallus gallus and in other species which have already been GTG-banded. The NORs were identified in a pair of microchromosomes characterized by presenting a remarkable secondary constriction. This can be considered as a plesiomorphic characteristic for M. saturninus once baseline groups (Paleognathae) also showed a pair of microchromosomes bearing NORs.