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Human impacts have been eroding marine ecosystems in such a way that biodiversity patterns are changing. Therefore, policies and science-based solutions are indispensable for monitoring threats to the most impacted species. In such effort, the analysis of elasmobranchs’ environmental traces via eDNA metabarcoding represent a candidate tool for effective monitoring and conservation that is often advocated to be cost-effective and easily replicated. Here, we tested a realistic approach to monitor future changes through elasmobranchs’ metabarcoding with published primers, in which, elasmobranch diversity from the coastal waters of the Fernando de Noronha Archipelago (Brazil) was studied here. We detected a total of three elasmobranch species, namely Hypanus berthalutzae, Ginglymostoma cirratum, and Prionace glauca among numerous other fish species. Even though the technique proved to be a useful tool, some practical constraints were identified, and primarily caused by currently published environmental primers. In order to ensure the broad application of the method, we pointed out feasible adjustments to the problematic parameters based on our survey and other elasmobranch metabarcoding studies. The current drawbacks of the approach need to be considered by managers, conservation actors, and researchers, who are considering this methodology in order to avoid unrealistic promises for the cost incurred.

Identifying factors that create and maintain a hybrid zone is of great interest to ecology, evolution and, more recently, conservation biology. Here, we investigated the role of environmental features in shaping the spatial dynamics of a hybrid zone between the southern tigrina, Leopardus guttulus, and Geoffroy's cat, L. geoffroyi, testing for exogenous selection as the main force acting on its maintenance. These Neotropical felid species are mainly allopatric, with a restricted area of sympatry in the ecotone between the Atlantic Forest and Pampa biomes. As both biomes have experienced high rates of anthropogenic habitat alteration, we also analysed the influence of habitat conversion on the hybrid zone structure. To do this, we used 13 microsatellite loci to identify potential hybrids and generated ecological niche models for them and their parental species. We compared the influence of variables on parental species and hybrid occurrence and calculated the amount of niche overlap among them. Parental species showed different habitat requirements and predicted co-occurrence was restricted to the forest-grassland mosaic of the ecotone. However, hybrids were found beyond this area, mainly in the range of L. geoffroyi. Hybrids demonstrated higher tolerance to habitat alteration than parental types, with a probability of occurrence that was positively related with mosaics of cropland areas and remnants of natural vegetation. These results indicate that exogenous selection alone does not drive the dynamics of the hybrid zone, and that habitat conversion influences its structure, potentially favouring hybrids over parental species.

Yellow Cardinal is an Endangered Species. Its populations are in constant decline due to habitat reduction and loss and illegal capture. There are approximately 50 free-living animals in the south of Brazil (state of Rio Grande do Sul), but estimates indicate more than 1000 in captivity. Our goals were to investigate the genetic variability of captive animals in Brazil, compare it with the genetic variability found in free-living populations, estimate the kinship of captive individuals, and obtain updated data about the number of captive animals. We found only 13% of the registered captive Yellow Cardinals. Analysis of mitochondrial sequences of captive and free-living populations was performed. We obtained 14 haplotypes, one of them (H14) exclusive of captive individuals. Furthermore, we found a haplotype exclusive to the La Pampa population in a male born in captivity in 2013. The most frequent haplotype in captive animals was the same reported for northern Argentina and Uruguay populations, which border Brazil. We found a high number of alleles by locus (mean = 9.6) for microsatellite markers, with high average heterozygosity (HO = 0.605 and HE = 0.727). The global F was 0.168. Kinship analysis of captive birds indicates a degree of kinship means of 0.082. In addition, the probability of relationship indicates that 79.4% of them are unrelated. Our data demonstrated that the captive group retains a high degree of genetic diversity with a low level of kinship. Nevertheless, the presence of haplotype exclusive for Argentina’s population in captive birds, and the low level of parentage among captive animals may be representing cases of illegal wildlife trade.

Endemic, small range species are susceptible to environmental changes and landscape modification. Understanding genetic diversity and distributional patterns is important for implementation of effective conservation measures. In this context, genetic diversity was evaluated to update the conservation status of an endemic tuco-tuco, Ctenomys ibicuiensis. Phylogeographic and population genetic analyses of mitochondrial DNA and microsatellite loci were carried out using 46 individuals sampled across the species’ distribution. Ctenomys ibicuiensis presented moderate to high genetic diversity and highly structured populations with low levels of gene flow and isolation by distance. Anthropogenic landscape changes threaten this restricted-range tuco-tuco. Considering its limited geographic distribution and highly structured populations with low gene flow, we consider C. ibicuiensis to be at significant risk of extinction.

We present a new assessment of the genetic and morphological variation within Oxymycterus quaestor Thomas, 1903, which currently includes the junior synonyms O. judex Thomas, 1909 and O. misionalis Sanborn, 1931. We integrate distinct lines of evidence, including variation of mitochondrial (Cytochrome b [Cytb]) and nuclear (intron 7 of beta fibrinogen gene [Fgb]) sequences, and the assessment of skull quantitative traits based on geometric morphometrics, throughout the Atlantic Forest of Southeastern-Southern Brazil, Argentina, and Paraguay. Phylogenetic relationships based on Cytb indicate that O. quaestor is structured in four well-supported clades (lineages A–D), one of them (lineage C) including topotypes of a previously associated nominal form (O. judex). However, these Cytb lineages exhibit lower levels of differentiation based on the Fgb locus, and are not recovered in the genealogies of this nuclear marker, representing a case of mitonuclear discordance. The Cytb lineages also broadly overlapped in the morphospace both in skull shape and size, which sustain the current wider concept of O. quaestor as one single young species (0.947 Myr) that is recently expanding, and ultimately branching out, in the Atlantic Forest.

Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. Universidade Federal do Para. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil. Universidade Federal de S?o Carlos. Departamento de Gen?tica e Evolu??o. S?o Carlos, SP, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas. S?o Gabriel, RS, Brazil. University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK University of Cambridge. Department of Veterinary Medicine. Cambridge Resource Centre for Comparative Genomics. Cambridge, UK. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular. Porto Alegre, RS, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil / Universidade Federal do Para. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil. In contrast to the ?avian-like? diploid number (2n = 80), most toucans and aracaris (Piciformes: Ramphastidae) have divergent karyotypes, exhibiting a higher 2n. To identify the chromosomal rearrangements that shaped the karyotype of these species, we applied chicken macrochromosome paints 1?10 and 11 microsatellite sequences to the chromosomes of two representative species, Pteroglossus inscriptus and Ramphastos tucannus tucannus. Paints of chicken chromosomes revealed that at least the first five ancestral chromosomes have undergone fissions, and a fusion between a segment of chicken chromosome 1 and a segment from chromosome 3 occurred in both species. The microsatellite sequences were accumulated mainly in the Z chromosome and in several microchromosomes in both species. These results suggest that the genomes of the Ramphastidae have been shaped by extensive fissions and repetitive DNA accumulation as the main driving forces leading to the higher 2n as found in these species. Furthermore, our results suggest that the putative ancestral karyotype of Ramphastidae already had a high diploid number, probably close to 2n = 112, similar to that observed in P. inscriptus and R. t. tucannus.

Anthropogenic pressures have been depleting the global biodiversity. In order to monitor the changes in ecosystems, molecular techniques can be used to characterize species composition. Among molecular markers capable of identifying species, the COI is the most used, and its sequencing is the standard procedure of how taxonomic information can be surveyed. Despite this, new possibilities of biodiversity profiling have become possible through the assessment of highly fragmented DNA molecules in environmental samples. Now, medium- and short-length markers are used in metabarcoding studies. Here, a survey of marine fish from the Saint Peter and Saint Paul Archipelago was barcoded, in which the COI barcode procedure identified 21 species of 11 families of fish. Then, the first extensive COI library of these islands located in isolation was constructed; from these sequences, the most appropriate primer pair for future metabarcoding studies was identified. The new Saint Peter and Saint Paul sequence database has 9,183 sequences from 165 species and 62 families of fish. The overall mean distance among all sequences was 0.4. This distance reveals that the archipelago is a reservoir of biodiversity as this attribute is higher than other islands around the world. Due to this, the protection of the archipelago should be enhanced and well monitored with science-based approaches such as DNA metabarcoding. In this case, the primer pair specifically designed from this library should be considered.

This study was supported by Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq, Proc. PDE 204792/2018-5 and PQ 307382/2019-2), Funda??o de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS, 16/2551-000485-7) and the Biotechnology and Biological Sciences Research Council UK (BB/K008226/1). University of Kent. School of Biosciences. Canterbury, UK; Universidade Federal do Rio Grande do Sul. Instituto de Bioci?ncias. Departamento de Gen?tica. Laborat?rio de Citogen?tica e Evolu??o. Rio Grande do Sul, RS, Brazil. Universidade Federal do Pampa. Laborat?rio de Diversidade Gen?tica Animal. Rio Grande do Sul, RS, Brazil. Universidade Federal do Pampa. Laborat?rio de Diversidade Gen?tica Animal. Rio Grande do Sul, RS, Brazil. Universidade Federal do Rio Grande do Sul. Instituto de Bioci?ncias. Departamento de Gen?tica. Laborat?rio de Citogen?tica e Evolu??o. Rio Grande do Sul, RS, Brazil. Universidade Federal de S?o Carlos. Centro de Ci?ncias Biol?gicas e da Sa?de. Departamento de Gen?tica e Evolu??o. Laborat?rio de Citogen?tica de Peixes. S?o Carlos, SP, Brazil. Universidade Federal de S?o Carlos. Centro de Ci?ncias Biol?gicas e da Sa?de. Departamento de Gen?tica e Evolu??o. Laborat?rio de Citogen?tica de Peixes. S?o Carlos, SP, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Ananindeua, PA, Brasil / Universidade Federal do Par?. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil. University of Kent. School of Biosciences. Canterbury, UK. University of Kent. School of Biosciences. Canterbury, UK. Abstract: Although cytogenetics studies in cuckoos (Aves, Cuculiformes) have demonstrated an interesting karyotype variation, such as variations in the chromosome morphology and diploid number, their chromosome organization and evolution, and relation with other birds are poorly understood. Hence, we combined conventional and molecular cytogenetic approaches to investigate chromosome homologies between chicken and the smooth-billed ani (Crotophaga ani). Our results demonstrate extensive chromosome reorganization in C. ani, with interchromosomal rearrangements involving macro and microchromosomes. Intrachromosomal rearrangements were observed in some macrochromosomes, including the Z chromosome. The most evolutionary notable finding was a Robertsonian translocation between the microchromosome 17 and the Z chromosome, a rare event in birds. Additionally, the simple short repeats (SSRs) tested here were preferentially accumulated in the microchromosomes and in the Z and W chromosomes, showing no relationship with the constitutive heterochromatin regions, except in the W chromosome. Taken together, our results suggest that the avian sex chromosome is more complex than previously postulated and revealed the role of microchromosomes in the avian sex chromosome evolution, especially cuckoos.

The genus Ctenomys has been widely used in karyotype evolution studies due to the variation in their diploid numbers (2n), which range from 2n = 10 to 2n = 70. Ctenomys minutus is characterized by intraspecific variation in diploid number (2n = 42, 46, 48, and 50), which makes it an interesting model to investigate the genomic instability mechanisms that have led to different cytotypes in this species. We aimed to contribute to the knowledge about telomeres’ role in chromosomal instability and global DNA methylation in the genome evolution of C. minutus. This study found that telomere length differs between cytotypes, but only for females (50a

Karyotypic analyses have several applications in studies of chromosome organization, evolution, and cytotaxonomy. They are also essential to genome assembly projects. Here, we present for the first time the karyotype description of the endangered species yellow cardinal, Gubernatrix cristata (Passeriformes, Thraupidae), using conventional staining with Giemsa and 18S rDNA probes. This species has 78 chromosomes, with 12 pairs of macrochromosomes and 27 microchromosome pairs. The 18S rDNA clusters were found in four microchromosomes. Our results revealed that G. cristata has a typical avian karyotype (approximately 80 chromosomes). However, G. cristata has an apomorphic state in relation to the 18S rDNA distribution since the ancestral condition corresponds to only two microchromosomes with these sequences. Probably, duplications and translocations were responsible for increasing the number of 18S rDNA clusters in G. cristata. The results were compared and discussed with respect to other Thraupidae and Passeriformes members. Considering the globally threatened status of G. cristata, we believe that its karyotype description could be a starting point for future cytogenetics and sequencing projects.

The phylogenetic position and taxonomic status of Rhynchocyclidae (Aves: Passeriformes) have been the subject of debate since their first description. In most models, Rhynchocyclidae represents a subfamily-level taxon placed within the Tyrant Flycatchers (Tyrannidae). Considering that this classification does not include cytotaxonomic characters, we tested the hypothesis that the chromosome organization of Rhynchocyclidae members differs from that of Tyrannidae. Hence, we selected two species, Tolmomyias sulphurescens, and Pitangus sulphuratus, representing Rhynchocyclidae and Tyrannidae, respectively. Results revealed a diploid number (2n) of 60 in T. sulphurescens and 2n = 80 in P. sulphuratus, indicating significant chromosomal differences. Chromosome mapping of Gallus gallus (GGA) and Taeniopygia guttata bacterial artificial chromosome (BAC) corresponding to chromosomes GGA1-28 (except 16) revealed that the genome evolution of T. sulphurescens involved extensive chromosome fusions of macrochromosomes and microchromosomes. On the other hand, P. sulphuratus retained the ancestral pattern of organization of macrochromosomes (except the centric fission involving GGA1) and microchromosomes. In conclusion, comparing our results with previous studies in Tyrant Flycatchers and allies indicates that P. sulphuratus has similar karyotypes to other Tyrannidae members. However, T. sulphurescens does not resemble the Tyrannidae family, reinforcing family status to the clade named Rhynchocyclidae.

We describe a new species of the cricetid rodent Oxymycterus (Sigmodontinae), which inhabits a transitional area between the southern Cerrado and the Atlantic Forest in south-southeastern Brazil. Compared to other Oxymycterus, the new species is large-sized with a tawny-brown pelage coloration. The new species could be differentiated from other Oxymycterus species by a combination of cranial characteristics that includes markedly large and inflated auditory bulla; a narrow rostrum and large incisive foramen, with the posterior extremity reaching the posterior region of the M1 protocone or hypoflexus; a wide parapterygoid fossa; the presence of a foramen ovale in the posterior region of the parapterygoid plate; and a thin hamular process of the squamosal. Bayesian analysis based on the mitochondrial and nuclear genes (cytochrome-b and acid phosphatase type V—Intron 2, respectively) recovered from the Oxymycterus sp. nov. showed it to be phylogenetically closely related to O. amazonicus and O. delator, all three species associated with open vegetation. The lineage leading to this clade likely emerged around 1.14 million years ago during the Early-Middle Pleistocene. Genetic distances between the new taxa and these two species calculated from comparison of cytochrome-b sequences are 3.7% and 4.1%, respectively. Currently, Oxymycterus sp. nov. is known from only two unprotected sites, with the type locality inserted in an area under the process of conurbation. Our study raises the number of living species in the genus to 16.

Accurate identification of predator species is a critical requirement to investigate their diet using faecal samples. We used non-invasive sampling and two methods of predator identification to investigate the diets of sympatric carnivores in a highly deforested region of the Brazilian Amazon. Of 108 scats, 81 could be identified at the species level using DNA sequencing and/or trichology. The former performed better than the latter (81.5% vs. 54.3% of the identified samples), and results were quite congruent (89.7% concordance in the 29 samples that could be assessed with both approaches). Nine species were identified, out of which four (crab-eating fox, ocelot, puma and jaguar) presented a sufficient number of samples to allow dietary analyses. The crab-eating fox was the most generalist (BA=0.92); ocelots focused on small- to medium-sized prey; pumas fed mostly on medium-sized items; and jaguars mostly targeted large-sized prey. A considerable overlap was observed between ocelots and pumas in all estimations (O=0.47–0.83). The presence of jaguars in the same region could be driving pumas to select medium- and small-sized prey. The results of this study highlight the importance of reliable predator identification and the need for in-depth ecological studies in areas where carnivore species are sympatric.

Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular (PPGBM). Porto Alegre, RS, Brazil. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular (PPGBM). Porto Alegre, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas (PPGCB). S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Programa de P?s-gradua??o em Ci?ncias Biol?gicas (PPGCB). S?o Gabriel, RS, Brazil. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. University of Cambridge. Cambridge Resource Centre for Comparative Genomics. Cambridge, United Kingdom. Universidade Federal do Par?. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil / Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil. Universidade Federal do Rio Grande do Sul. Programa de P?s-gradua??o em Gen?tica e Biologia Molecular (PPGBM). Porto Alegre, RS, Brazil. Zonotrichia capensis is widely distributed in the Neotropics. Previous cytogenetic studies demonstrated the presence of polymorphisms in two chromosome pairs (ZCA2 and ZCA4). Here, we report results based on comparative chromosome painting, using probes derived from Gallus gallus and Leucopternis albicollis, focused on characterizing the chromosome organization of Z. capensis. Our results demonstrate the conservation of ancestral syntenies as observed previously in other species of passerine. Syntenies were rearranged by a series of inversions in the second chromosome as described in other Passeriformes, but in this species, by using probes derived from L. albicollis we observed an extra inversion in the second chromosome that had not previously been reported. We also report a paracentric inversion in pair 3; this chromosome corresponds to the second chromosome in Zonotrichia albicollis and may indicate the presence of ancestral inversions in the genus. The chromosomal inversions we found might be important for understanding the phenotypic variation that exists throughout the distribution of Z. capensis

Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq, Proc. PDE 204792/2018-5 ), Funda??o de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS, 16/2551-000485-7 and the Biotechnology and Biological Sciences Research Council UK (BB/K008226/1. University of Kent. School of Biosciences. Canterbury, NJ, UK / Universidade Federal do Rio Grande do Sul. Departamento de Gen?tica. Porto Alegre, RS, Brazil. Universidade Federal do Pampa. Laborat?rio de Diversidade Gen?tica Animal. S?o Gabriel, RS, Brazil. Universidade Federal Rural da Amaz?nia. Laborat?rio de Reprodu??o Animal. Parauapebas, PA, Brazil. University of Kent. School of Biosciences. Canterbury, NJ, UK. Universidade Federal do Pampa. Laborat?rio de Diversidade Gen?tica Animal. S?o Gabriel, RS, Brazil. Universidade Federal do Pampa. Laborat?rio de Diversidade Gen?tica Animal. S?o Gabriel, RS, Brazil. Universidade Federal do Rio Grande do Sul. Departamento de Gen?tica. Porto Alegre, RS, Brazil. Minist?rio da Sa?de. Secretaria de Vigil?ncia em Sa?de. Instituto Evandro Chagas. Laborat?rio de Cultura de Tecidos e Citogen?tica. Ananindeua, PA, Brasil / Universidade Federal do Par?. Instituto de Ci?ncias Exatas e Naturais. Bel?m, PA, Brazil. University of Kent. School of Biosciences. Canterbury, NJ, UK. University of Kent. School of Biosciences. Canterbury, NJ, UK. Interchromosomal rearrangements involving microchromosomes are rare events in birds. To date, they have been found mostly in Psittaciformes, Falconiformes, and Cuculiformes, although only a few orders have been analyzed. Hence, cytogenomic studies focusing on microchromosomes in species belonging to different bird orders are essential to shed more light on the avian chromosome and karyotype evolution. Based on this, we performed a comparative chromosome mapping for chicken microchromosomes 10 to 28 using interspecies BAC-based FISH hybridization in five species, representing four Neoaves orders (Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes). Our results suggest that the ancestral microchromosomal syntenies are conserved in Pteroglossus inscriptus (Piciformes), Ramphastos tucanus tucanus (Piciformes), and Trogon surrucura surrucura (Trogoniformes). On the other hand, chromosome reorganization in Phalacrocorax brasilianus (Suliformes) and Hydropsalis torquata (Caprimulgiformes) included fusions involving both macro- and microchromosomes. Fissions in macrochromosomes were observed in P. brasilianus and H. torquata. Relevant hypothetical Neognathae and Neoaves ancestral karyotypes were reconstructed to trace these rearrangements. We found no interchromosomal rearrangement involving microchromosomes to be shared between avian orders where rearrangements were detected. Our findings suggest that convergent evolution involving microchromosomal change is a rare event in birds and may be appropriate in cytotaxonomic inferences in orders where these rearrangements occurred.

The genus Ctenomys is comprised of more than 70 valid living species. It is the largest collection of fossorial mammals that occupy underground habitats, mainly in the grasslands of South America. We investigated different aspects of morphological evolution in the genus Ctenomys, with special attention to the skull. We analyzed 1359 craniums and 830 mandibles of 49 species of Ctenomys. We used geometric morphometric approaches to quantify this morphological diversity across its range. We found geographical structuring in skull shape among the eight clades of Ctenomys structured along east-west and north-south morphological gradients. We observed that many species from the extreme north of the distribution had a robust skull shape, whereas the southern ones had a gracile skull shape. Such structural differences may be following an environmental gradient. The mandible is less variable in shape than the cranium. We found high morphological variation within each of the eight clades and a geographical structuring. The subterranean niche is not homogeneous across space, and morphological adaptation of subterranean species occurs following this spatial gradient.

The genus Ctenomys is one of the most specious among the subterraneous rodent genera. The most recent revision lists 65 species. Regarding speciation models, it has always been accepted that the genus Ctenomys would have diversified due to allopatric processes. However, no reports have discussed the speciation models that might have generated this large group of species. At the same time, the high chromosomal variation that occurs among species is likely to have also caused this explosion of species. Simultaneously, the absence of sympatric distribution between species, except for two areas between two species each, would not promote the occurrence of hybrid zones. In this chapter, we discuss patterns that indicate whether the models of allopatric, sympatric, and chromosome speciation could have generated some of the Ctenomys species. Hybridization zones between and within species and their consequences are also reported. Finally, events that show us a recent process of differentiation of lineages that could be generating new species are also commented.

The vast mammal diversity of the Neotropics is the result of a long evolutionary history. Among mammals, rodents comprise more than half of all Neotropical mammal species, and South America is home to about a quarter of the entire world’s rodent species. However, the economic growth of the region still depends strongly on natural resource exploitation and has high rates of environmental degradation and biodiversity loss. In this context, conservation genetics offers means to help reducing current extinction rates and to preserve biodiversity. In this chapter, we discuss conservation genetics using examples from studies developed in the Neotropical region with rodents from the Sigmodontinae sub-family and rodents from the genus Ctenomys (Caviomorpha). Although some species are well studied and present a large amount of data based on different approaches, long-term genetic studies are needed to understand better the combined impacts of all ‘non-genetic’ and genetic threats faced by populations. Such studies are important because understanding these issues is still far from being accomplished for caviomorphs and sigmodontines in the Neotropical region. Moreover, conservation genetics is essential because it also addresses the conservation of processes like speciation and hybridization.

Although cytogenetics studies in cuckoos (Aves, Cuculiformes) have demonstrated an interesting karyotype variation, such as variations in the chromosome morphology and diploid number, their chromosome organization and evolution, and relation with other birds are poorly understood. Hence, we combined conventional and molecular cytogenetic approaches to investigate chromosome homologies between chicken and the smooth-billed ani (Crotophaga ani). Our results demonstrate extensive chromosome reorganization in C. ani, with interchromosomal rearrangements involving macro and microchromosomes. Intrachromosomal rearrangements were observed in some macrochromosomes, including the Z chromosome. The most evolutionary notable finding was a Robertsonian translocation between the microchromosome 17 and the Z chromosome, a rare event in birds. Additionally, the simple short repeats (SSRs) tested here were preferentially accumulated in the microchromosomes and in the Z and W chromosomes, showing no relationship with the constitutive heterochromatin regions, except in the W chromosome. Taken together, our results suggest that the avian sex chromosome is more complex than previously postulated and revealed the role of microchromosomes in the avian sex chromosome evolution, especially cuckoos.

The Columbidae species (Aves, Columbiformes) show considerable variation in their diploid numbers (2n = 68&ndash, 86), but there is limited understanding of the events that shaped the extant karyotypes. Hence, we performed whole chromosome painting (wcp) for paints GGA1-10 and bacterial artificial chromosome (BAC) probes for chromosomes GGA11-28 for Columbina passerina, Columbina talpacoti, Patagioenas cayennensis, Geotrygon violacea and Geotrygon montana. Streptopelia decaocto was only investigated with paints because BACs for GGA10-28 had been previously analyzed. We also performed phylogenetic analyses in order to trace the evolutionary history of this family in light of chromosomal changes using our wcp data with chicken probes and from Zenaida auriculata, Columbina picui, Columba livia and Leptotila verreauxi, previously published. G-banding was performed on all these species. Comparative chromosome paint and G-banding results suggested that at least one interchromosomal and many intrachromosomal rearrangements had occurred in the diversification of Columbidae species. On the other hand, a high degree of conservation of microchromosome organization was observed in these species. Our cladistic analysis, considering all the chromosome rearrangements detected, provided strong support for L. verreauxi and P. cayennensis, G. montana and G. violacea, C. passerina and C. talpacoti having sister taxa relationships, as well as for all Columbidae species analyzed herein. Additionally, the chromosome characters were mapped in a consensus phylogenetic topology previously proposed, revealing a pericentric inversion in the chromosome homologous to GGA4 in a chromosomal signature unique to small New World ground doves.

Funder: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brazilian Federal Agency for the Support and Evaluation of Graduate Education); doi: https://doi.org/10.13039/501100002322, Funder: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Reproductive compatibility usually decreases according to increasing genetic difference and the time of divergence between species. However, the amount of modification required to influence hybridization may vary in different species. Thus, it is extremely important to conduct studies that seek to understand what and how variables influence the reproductive isolation of species. We have explored a system involving two species of subterranean rodents that present morphological, karyotypic, and evolutionary history differences and are capable of generating hybrids. To gain insight into the karyotype organization of genus Ctenomys, we examined the chromosome evolution by classical and molecular cytogenetics of both parental species and hybrids. Furthermore, we have used different approaches to analyze the differences between the parental species and the hybrids, and determined the origin of the hybrids. The results of our work demonstrate unequivocally that some species that present extensive differences in chromosome organization, phenotype, evolutionary history, sperm morphology and genetic, which are usually associated with reproductive isolation, can generate natural hybrids. The results also demonstrate that females of both species are able to generate hybrids with males of the other species. In addition, the chromosome-specific probes prepared from Ctenomys flamarioni provide an invaluable tool for comparative cytogenetics in closely related species.

As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile-Peru (nnew mtDNA/ microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/ microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile-Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile-Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile-Peru. Fil: Carroll, Emma L. University of St. Andrews; Reino Unido Fil: Ott, Paulo H.. Universidade Federal do Rio Grande do Sul; Brasil Fil: McMillan, Louise F.. University Of Wellington; Nueva Zelanda Fil: Vernazzani, Bárbara Galletti. Centro de Conservación Cetacea; Chile Fil: Neveceralova, Petra. Charles University; República Checa Fil: Vermeulen, Els. University Of Pretoria; Sudáfrica Fil: Gaggiotti, Oscar E.. University of St. Andrews; Reino Unido Fil: Andriolo, Artur. Universidade Federal de Juiz de Fora; Brasil Fil: Scott Baker, C.. State University of Oregon; Estados Unidos Fil: Bamford, Connor. British Antarctic Survey; Reino Unido Fil: Best, Peter. University Of Pretoria; Sudáfrica Fil: Cabrera, Elsa. Centro de Conservación Cetacea; Chile Fil: Calderan, Susannah. Scottish Association For Marine Science; Reino Unido Fil: Chirife, Andrea. Universidad Andrés Bello; Chile Fil: Fewster, Rachel M.. University of Auckland; Nueva Zelanda Fil: Flores, Paulo A. C.. No especifíca; Fil: Frasier, Timothy. Saint Marys University; Canadá Fil: Freitas, Thales R.O.. Universidade Federal do Rio Grande do Sul; Brasil Fil: Groch, Karina. Instituto Australis; Brasil Fil: Hulva, Pavel. Charles University; República Checa Fil: Kennedy, Amy. No especifíca; Fil: Leaper, Russell. No especifíca; Fil: Leslie, Matthew S.. No especifíca; Fil: Moore, Michael. No especifíca; Fil: Oliveira, Larissa. Universidade Federal do Rio Grande do Sul; Brasil Fil: Seger, Jon. University of Utah; Estados Unidos Fil: Stepien, Emilie N.. University Aarhus; Dinamarca Fil: Valenzuela, Luciano Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil; Argentina Fil: Zerbini, Alexandre. University of Washington; Estados Unidos Fil: Jackson, Jennifer A.. No especifíca

Incluye contenido parcial de los autores Biological invasion is one of the main threats to native biodiversity. For a speciesto become invasive, it must be voluntarily or involuntarily introduced by humans into a nonna-tive habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this dataset, we make available occurrence and abundance data on mammal species that (1) transposeda geographical barrier and (2) were voluntarily or involuntarily introduced by humans into theNeotropics. Our data set is composed of 73,738 historical and current georeferenced recordson alien mammal species of which around 96% correspond to occurrence data on 77 speciesbelonging to eight orders and 26 families. Data cover 26 continental countries in the Neotrop-ics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Floridain the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 coun-tries of Caribbean islands. Our data set also includes neotropical species (e.g.,Callithrixsp.,Myocastor coypus,Nasua nasua)considered alien in particular areas of Neotropics. The mostnumerous species in terms of records are fromBossp. (n=37,782),Sus scrofa(n=6,730), andCanis familiaris(n=10,084); 17 species were represented by only one record (e.g., Syncerus caf-fer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of spe-cies in the data set (n=20 species), partly because of uncertainties regarding taxonomicidentification of the generaCallithrix,which includes the speciesCallithrix aurita, Callithrixflaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, andtheir hybrids. This unique data set will be a valuable source of information on invasion riskassessments, biodiversity redistribution and conservation-related research. There are no copy-right restrictions. Please cite this data paper when using the data in publications. We alsorequest that researchers and teachers inform us on how they are using the data

Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the karyotype evolution within Columbiformes remains unclear. To delineate the synteny-conserved segments and karyotypic differences among four Columbidae species, we used chromosome painting from Gallus gallus (GGA, 2n = 78) and Leucopternis albicollis (LAL, 2n = 68). Besides that, a set of painting probes for the eared dove, Zenaida auriculata (ZAU, 2n = 76), was generated from flow-sorted chromosomes. Chromosome painting with GGA and ZAU probes showed conservation of the first ten ancestral pairs in Z. auriculata, Columba livia, and Columbina picui, while in Leptotila verreauxi, fusion of the ancestral chromosomes 6 and 7 was observed. However, LAL probes revealed a complex reorganization of ancestral chromosome 1, involving paracentric and pericentric inversions. Because of the presence of similar intrachromosomal rearrangements in the chromosomes corresponding to GGA1q in the Columbidae and Passeriformes species but without a common origin, these results are consistent with the recent proposal of divergence within Neoaves (Passerea and Columbea). In addition, inversions in chromosome 2 were identified in C. picui and L. verreauxi. Thus, in four species of distinct genera of the Columbidae family, unique chromosomal rearrangements have occurred during karyotype evolution, confirming that despite conservation of the ancestral syntenic groups, these chromosomes have been modified by the occurrence of intrachromosomal rearrangements.

We tested the association between chromosomal polymorphism and skull shape and size variation in two groups of the subterranean rodent Ctenomys. The hypothesis is based on the premise that chromosomal rearrangements in small populations, as it occurs in Ctenomys, produce reproductive isolation and allow the independent diversification of populations. The mendocinus group has species with low chromosomal diploid number variation (2n=46-48), while species from the torquatus group have a higher karyotype variation (2n=42-70). We analyzed the shape and size variation of skull and mandible by a geometric morphometric approach, with univariate and multivariate statistical analysis in 12 species from mendocinus and torquatus groups of the genus Ctenomys. We used 763 adult skulls in dorsal, ventral, and lateral views, and 515 mandibles in lateral view and 93 landmarks in four views. Although we expected more phenotypic variation in the torquatus than the mendocinus group, our results rejected the hypothesis of an association between chromosomal polymorphism and skull shape and size variation. Moreover, the torquatus group did not show more variation than mendocinus. Habitat heterogeneity associated to biomechanical constraints and other factors like geography, phylogeny, and demography, may affect skull morphological evolution in Ctenomys.

The Neotropical region currently harbors 8 recognized species of small cats, including the margay (Leopardus wiedii) and jaguarundi (Puma yagouaroundi). These similar-sized species have broad geographic distributions and commonly occur in sympatry. We constructed species occurrence databases and used the maximum entropy (Maxent) modeling approach to develop models of habitat suitability for each of these species. We identified the environmental predictors with the highest importance for species occurrence and evaluated how they influence habitat suitability for both wild cats. Variables related to temperature and precipitation were good predictors of species occurrence, with both cats responding similarly to them. However, margay showed higher variation in habitat suitability depending on local climatic predictors. The estimated models indicated high niche similarity (> 76%) between these cats, but despite this we identified different areas with the most favorable conditions for each species' occurrence. Approximately 50% and 72% of the entire suitable area were estimated as being moderately to highly suitable for margay and jaguarundi, respectively, with the margay model comprising a higher proportion of forest environments in comparison to that of the jaguarundi. These findings will be relevant in the context of conservation planning when indicating the priority areas for their long-term preservation.

Coexistence between species with similar niche requirements is often facilitated by displacement of morphological, behavioral, or physiological characteristics. Experiments comparing treatments with and without the presence of potential competitors are ideal for testing hypotheses of interspecific competition. Here, we investigate a fundamental aspect in the natural history of a species: the home range. We determined whether co-occurrence can influence the home range size of 2 subterranean rodent species, Ctenomys flamarioni and C. minutus. We evaluated home range size in populations of both species in allopatry and sympatry along the coastal plain of southern Brazil. Animals were radiotracked, and the home range size of each individual was estimated using grid cells and minimum convex polygon methods. We found no significant differences in home range size between sites or species, and the interaction was nonsignificant. We also found no relationship between home range size and body mass or sex. Our results suggest that co-occurrence may not influence home range size in these species, perhaps due to environmental adaptations that facilitate coexistence (e.g., microhabitat segregation and dietary modifications). Further, the characteristics of the sandy dune habitat may act as environmental filters, favoring similar home range sizes for both species.

Patterns of univariate trait variation across metacommunities are widely explored, as are searches for their underlying causes. Surprisingly, patterns of multivariate shape remain unknown, and the search for drivers of functional traits of communities often neglect the biogeographical distribution of phylogenetic clades. Our aim was to investigate multivariate shape distribution across metacommunities and to determine the main environmental drivers of shape beyond/taking into account the phylogenetic distribution of lineages. We obtained mean skull and mandible shape for 228 species of Neotropical sigmodontine rodents through geometric morphometrics (GM), and then calculated mean shapes for 1° × 1° cells across the Neotropics based on the incidence of sigmodontines. We investigated the effects of lineage distribution on mean trait variation by using phylogenetic fuzzy weighting to calculate principal coordinates of phylogenetic structure (PCPS). Effects of environmental variables on shape variation incorporating phylogenetic composition were realized through redundancy analysis. We found that the different distributions of major lineages throughout the Neotropics were responsible for much of the mean shape variation. The association of landscape features with tribal groupings (Oryzomyini with Amazonia and Phyllotini and Abrotrichini with the Andes) were standouts. Environmental variables and lineage distribution explain the same (i.e. shared) portion of shape variation, suggesting phylogenetic niche conservatism at the metacommunity level. Seasonality in temperature and land cover were the best environmental predictors of mean shape: larger tympanic bullae, incisive foramina, and check teeth are all associated with highly seasonal and less vegetated areas. Our new approach of using GM shape across metacommunities was demonstrably useful in understanding large-scale biogeographical patterns of shape variation and identifying its underlying causes. The overlap between environmental variables and phylogenetic lineage distribution suggests that a process of niche conservatism is likely: the phenotype–environment correlation is mediated by the differential biogeographical distribution of the main clades.