Insular populations are typically more vulnerable to the loss of genetic diversity than their mainland counterparts and are often of conservation concern. The Bijagós Archipelago in Guinea-Bissau is a West African biodiversity hotspot and a recently designated UNESCO World Heritage Site. It hosts the westernmost populations of the spot-nosed monkey ( Cercopithecus petaurista ), a species thought to have been extirpated from mainland and threatened by anthropogenic activities. Here, we conducted a non-invasive DNA survey across five of the largest islands with known occurrences. We used eleven microsatellite loci and a fragment of the mitochondrial d-loop to estimate genetic diversity and population structure. Using 64 individual profiles we found that populations may have lost genetic diversity but were not depauperated. Genetic diversity was heterogeneous and populations were structured by island. Higher levels of historical gene flow between distant islands than between nearby ones suggest a pattern that is inconsistent with stepwise colonisation typical of island systems. Our study suggests a complex colonisation history which may have been influenced by human movements in the area. Canhabaque Island holds the most diverse populations and may support reintroductions in the mainland. We suggest conservation management should be carried out by island to safeguard long-term persistence.

The Quaternary period was marked by significant climatic and sea-level fluctuations that had a strong impact on coastal ecosystems worldwide. Sea-level changes played a key role in the formation of restinga ecosystems along the Brazilian coast. These Quaternary sandy beach-dune deposits support unique ecosystems, characterized by their recent origin, constant environmental dynamics, and strong influence of saline, aeolian, and solar factors. The lizards Tropidurus hygomi, Glaucomastix abaetensis, and Glaucomastix itabaianensis are endemic and sympatric species found in restinga formations along the northern coast of Bahia and Sergipe. We used ddRADseq genomic data and ecological niche modeling to unravel the spatiotemporal diversification of these lizards across restinga areas. We found eight well-supported genetic population lineages in both lizard genera, revealing strong population structure. Spatial patterns of population clustering show a high degree of concordance across taxa. Gene flow among some lineages was associated with coastal plains, while barriers were linked to rivers, wetlands, and aeolian dune formations. We observed synchronous expansion of population lineages over the continental shelf during sea-level lowstands associated with glacial cycles, followed by synchronous population contraction during transgressive events in all population lineages. These patterns are associated with habitat availability and loss due to climatic changes and continental shelf exposure during the late Quaternary. Wetlands and river systems likely acted as barriers to gene flow, contributing to the observed population structure. We highlight the importance of genomic studies in other taxa to reveal the evolutionary and biogeographic processes linked to restinga ecosystems, and the urgent need for conservation efforts targeting these species and their habitats.

Studies in the Neotropical region consistently highlight high levels of endemism and biodiversity. However, challenges persist, particularly in uncovering the cryptic diversity among species. Various approaches are needed to address this, including morphological, genetic, and environmental data. This study focused on genetic and morphological variation in three endemic, sympatric lizard species: Tropidurus hygomi, Glaucomastix abaetensis, and Glaucomastix itabaianensis in the coastal sand dunes of Northeastern Brazil. These lizards are confined to sandy Pleistocene-formed environments with limited distribution. While earlier research revealed substantial genetic diversity, gaps remained in distribution sampling, morphological data, and understanding the correlation between this variation and environmental factors. We aimed to identify genetic clusters to assess the alignment of phenotypic differences with these clusters and explore potential relationships between climatic and geographical factors and morphometric variations. We utilized mtDNA data to assess population clusters. Geometric and linear morphometrics were employed to analyze morphological data, which was then correlated with climatic information. Results unveiled genetic and morphological variations signifying the presence of cryptic diversity. Our analyses also highlighted the influence of geography and climate on morphometric variations. These findings underscore hidden diversity and a complex evolutionary history within the confined Pleistocene sand dunes. Further genomic analyses could contribute to comprehending these patterns and enhancing the conservation strategies for these endangered species.

Large ungulates across the world are threatened with extinction due to habitat loss, land use change, and other anthropogenic pressures. While conservation measures are critical, for many populations the implementation of conservation measures is often not practical, either due to a lack of information on the species' biology or their conservation status. Here we consider 2 large ungulates, the roan ( Hippotragus equinus ) and sable ( H. niger ) antelopes, occurring in Mudumu National Park (MNP) Namibia, for which data on populations trends and habitat use are largely unknown. Here, we used camera trapping data collected in the dry and wet seasons between March and September 2021 in visit frequency models to understand the relationship between habitat variables and the distribution dynamics of roan and sable over time at MNP. Our results showed that roans in the wet season were detected more at sites with increased grass cover and detected less at sites near the Kwando River. In the dry season, roans were detected more at sites with increased grass cover and more termite mounds but detected less at sites near the Kwando River. In the wet season, sables were detected more at sites with fewer termite mounds. In the dry season, sables were detected more at sites with increased grass cover. We hypothesized that roan and sable use fewer areas near permanent water to avoid high predator densities and high grazing intensity by dense herds of short‐grass grazers. The study findings are useful knowledge on 2 threatened ungulates and will be used to inform and develop comprehensive conservation programs and strategies that aim to lower the risk of extinction for roan and sable at a Namibian protected area.

As the sole obligate symbiotic birds in Africa, oxpeckers offer a unique model for studying symbiotic relationships. Due to the multitrophic level they occupy and the context dependent foraging behavior they exhibit, the type of symbiotic relationship can be variable. In addition to providing a cleaning service to the host by removing ticks, oxpeckers frequently feed on blood, mucus, and saliva, inflicting potential damage on the host. Here, we used DNA metabarcoding on faecal samples to analyze the taxonomic composition of the trophic interactions of the Yellow-billed Oxpecker (Buphagus africanus) and Red-billed Oxpecker (B. erythrorhynchus) in northeastern Namibia. In contrast to conventional methods, DNA metabarcoding allows for a detailed identification of dietary resources encompassing both mammal hosts and consumed arthropods within the same samples. With this information, we examined differences in the diet composition between oxpecker species and localities, as well as the co-occurrence between host and arthropod species. Our findings revealed that oxpeckers predominantly source their diet from mammals, ticks, and flies; however, ticks and flies rarely co-occur in the diet of an individual. We observed variability among individuals in their feeding ecology, which is strongly correlated with locality and, to a lesser extent, with the mammal host. We noted a high degree of mobility between hosts within relatively short periods, with 32% of the samples showing traces of at least two mammal hosts. This study illustrates the dynamic foraging behavior of these specialized symbiotic birds, shedding light on their potential role in pest control services and disease transmission.

Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.

Birds are the vertebrate group most used in studies that attempts to decipher the events that have molded the diversification of the Amazonian biota. However, inconsistencies related to the existence of polytypic species, associated with the limited samples available for many regions, hamper the accurate reconstruction of phylogeographic patterns. In particular, no molecular study has yet included all the subspecific taxa currently recognized in the Band-tailed Manakin, Pipra fasciicauda . This species encompasses a complex of subspecies differentiated by their morphological traits and distinct regional distributions. The present study investigated the current taxonomic and phylogeographic configuration of P. fasciicauda using a multilocus molecular approach to decipher the biogeographic events that determined the diversification of this group. This analysis included all the recognized subspecies, sampled widely throughout their respective areas of occurrence. The molecular data indicate the existence of three monophyletic lineages that coincide only partially with the current subspecific classification of the group. Lineage 1 grouped all the specimens of the subspecies Pipra fasciicauda purusiana and Pipra fasciicauda saturata . Lineage 2 was composed of the individuals of Pipra fasciicauda fasciicauda and Pipra fasciicauda calamae , while lineage 3 was formed by the specimens of Pipra fasciicauda scarlatina . Lineage 1 was estimated to have diverged from the other lineages by around 0.43 Mya, while lineages 2 and 3 would have separated by 0.17 Mya, which indicates that their current phylogeographic configuration was determined by events occurring during the middle Pleistocene. The demographic analyses revealed a process of recent geographic expansion, with dispersal events molding the gene flow among lineages. As observed in other bird taxa, the diversification of P. fasciicauda has been associated with the hydrographic dynamics of the Amazon basin, together with climatic shifts, which have combined to determine the differentiation of the populations from west to east within the basin.

This dataset includes - cyt-b sequence alignment (fasta format, .fas) for R. parvipalmata and associated metadata (excel sheet), including origin, taxonomic assignment and lineage identity of the corresponding samples - RAD-seq sequence alignment (fasta format, .fas) and SNP matrix (structure format, .str) for R. parvipalmata, and associated metadata (excel sheet), including origin, taxonomic assignment and lineage identity of the corresponding samples - Raw morphometric data for R. parvipalmata and nearby R. temporaria (excel sheet), including body size (SVL) and 18 biometric characters, and associated metadata (sample origin, taxonomic assignement and lineage identity)

Theoretical and empirical studies suggest that the structure and position of hybrid zones can change over time. Evidence for moving hybrid zones has been directly inferred by repeated sampling over time, or indirectly through the detection of genetic footprints left by the receding species and the resulting asymmetric patterns of introgression across markers. We here investigate a hybrid zone formed by two subspecies of the Iberian golden-striped salamander, Chioglossa lusitanica, using a panel of 35 nuclear loci (31 SNPs and 4 allozymes) and one mitochondrial locus in a transect in central Portugal. We found concordant and coincident clines for most of the nuclear loci (n = 22, 63%), defining a narrow hybrid zone of ca. 6 km wide, with the centre positioned ca. 15 km south of the Mondego River. Asymmetric introgression was observed at another 14 loci. Their clines are displaced towards the north, with positions located either close to the Mondego River (n = 6) or further northwards (n = 8). We interpret these profiles as genetic traces of the southward displacement of C. lusitanica lusitanica by C. l. longipes over the wider Mondego River valley. We noted the absence of significant linkage disequilibrium, and we inferred low levels of effective selection per locus against hybrids, suggesting that introgression in the area of species replacement occurred under a neutral diffusion process. A species distribution model suggests that the C. lusitanica hybrid zone coincides with a narrow corridor of fragmented habitat. From the position of the displaced clines, we infer that patches of locally suitable habitat trapped some genetic variants that became disassociated from the southward moving hybrid zone. This study highlights the influence of habitat availability on hybrid zone movement.

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.

The golden-striped salamander is a streamside species endemic to the northwestern corner of the Iberian Peninsula. In the first half of the twentieth century, an undisclosed number of individuals of this species were reportedly captured in Buçaco, Central Portugal, and deliberately introduced in Sintra Mountains, 170 km south of its native distribution range. The discovery of a breeding population of this salamander in Sintra during 2015 prompted this work: we used neutral genetic markers, the mitochondrial DNA cytochrome b (cytb), and seven microsatellite loci to elucidate on the relict/human-introduced nature of Sintra population, identify the potential source population, and infer the severity of founder effect. Our results support a human-mediated introduction. First, sequencing analysis of cytb showed the presence of a unique haplotype (h31) in Sintra, which was detected only in Buçaco and in two additional populations located close to Mondego river. Second, microsatellite analysis showed that Sintra is more closely related to populations in between Douro and Mondego rivers (Central Portugal), instead of its geographically closest populations (southernmost), as would be expected if Sintra was a relict population isolated in an interglacial refuge. Third, Sintra presents both reduced levels of genetic variability and effective population size when compared to native populations, particularly to those of Central Portugal. Consistent with an isolated population funded by a small number of individuals (inferred herein to be ca. 10–11 salamanders), Sintra forms a geographically coherent genetic unit that is significantly differentiated from the extant native C. lusitanica populations. Although our data provide supporting evidence for Buçaco as a likely source population, as documented in the literature, overall, we cannot unequivocally exclude other populations close to Mondego river as a potential source of the introduced individuals in Sintra.

Protected-area systems should conserve intraspecific genetic diversity. Because genetic data require resources to obtain, several approaches have been proposed for generating plans for protected-area systems (prioritizations) when genetic data are not available. Yet such surrogate-based approaches remain poorly tested. We evaluated the effectiveness of potential surrogate-based approaches based on microsatellite genetic data collected across the Iberian Peninsula for 7 amphibian and 3 reptilian species. Long-term environmental suitability did not effectively represent sites containing high genetic diversity (allelic richness). Prioritizations based on long-term environmental suitability had similar performance to random prioritizations. Geographic distances and resistance distances based on contemporary environmental suitability were not always effective surrogates for identification of combinations of sites that contain individuals with different genetic compositions. Our results demonstrate that population genetic data based on commonly used neutral markers can inform prioritizations, and we could not find an adequate substitute. Conservation planners need to weigh the potential benefits of genetic data against their acquisition costs.

The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south‐western and south‐eastern) of the Iberian endemic Bosca's newt ( Lissotriton boscai ) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south‐western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south‐eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150‐km transect across the hybrid zone showed broadly coincident cline widths ( ca. 3.2–27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population‐level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.

The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.

The Amazon is the primary source of Neotropical diversity and a nexus for discussions on processes that drive biotic diversification. Biogeographers have focused on the roles of rivers and Pleistocene climate change in explaining high rates of speciation. We combine phylogeographic and niche-based paleodistributional projections for 23 upland terra firme forest bird lineages from across the Amazon to derive a new model of regional biological diversification. We found that climate-driven refugial dynamics interact with dynamic riverine barriers to produce a dominant pattern: Older lineages in the wetter western and northern parts of the Amazon gave rise to lineages in the drier southern and eastern parts. This climate/drainage basin evolution interaction links landscape dynamics with biotic diversification and explains the east-west diversity gradients across the Amazon.

Genetic studies on green sea turtles (Chelonia mydas) in the Eastern Atlantic have mostly focused on reproductive females, with limited information available regarding juveniles and foraging grounds. Improved understanding of genetic diversity and patterns of connectivity between nesting and foraging grounds is critical to identify management units and delineate suitable conservation strategies. Here we analyzed data from 11 microsatellite markers and sequences of the mitochondrial control region from both juveniles and females sampled in foraging and nesting aggregations around São Tomé and Príncipe islands, in the Gulf of Guinea, West Africa. Both nuclear and mtDNA data were congruent in showing that São Tomé and Príncipe's green turtles population exhibit high levels of genetic diversity, which are similar to those reported for other foraging aggregates in the Atlantic. Although signs of population substructure among foraging and nesting grounds of São Tomé and Príncipe islands were not apparent, our analysis based on mtDNA marker showed that both juvenile and adult turtles were genetically differentiated from other foraging and nesting Atlantic populations. The similar levels of genetic diversity found in both juveniles and females are consistent with the results from mixed stock analyses, which suggested that São Tomé and Príncipe's rookery is the primary source of juveniles to the local foraging aggregation. Taken these aspects in consideration, we argue that São Tomé and Príncipe green turtles show limited dispersal and should be considered an important management unit, and conservation actions in this archipelago must be implemented not only at the level of the rookery but should also include the foraging aggregations.

Miniaturisation is an important evolutionary trend for amphibians and has occurred several times in independent anuran lineages. Most miniaturised frogs live in the leaf litter of tropical forests and have terrestrial reproductive modes. They are expected to have reduced fecundity in number of eggs than larger-bodied related species, but little is known about reproductive cycles and proportion of reproductive females. Lower vagility is also assumed, however, as they are difficult to observe, there is little empirical evidence about their dispersal. We studied the reproductive biology (sex ratio, sexual size dimorphism and fecundity parameters) and population ecology (growth, dispersal, and phenology) of the miniature Guanabara Frog Euparkerella aff. brasiliensis (⩽ 20 mm). We collected and analysed 75 specimens of E. aff. brasiliensis, of which 27 were adult females with vitellogenic oocytes in their ovaries. Fecundity was low for number of eggs (average number = 9.7), but only one adult female had no vitellogenic oocytes. Sex ratio was relatively balanced among sexes, being female-biased (0.92) for all individuals and male-biased (1.17) for adults. Juveniles and ovigerous females were observed throughout the year during the two years of mark-recapture study, which indicates continuous breeding. We captured 121 individuals, of which 12% were recaptured in their original collection sites, suggesting low vagility. We discuss our findings considering the current knowledge about the ecology of miniaturised frogs and other Terraranae and suggest future directions for ecological studies and conservation planning.