Aim: The central and western Amazonia underwent several landscape changes during the Quaternary. Whereas the Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of Amazonia biota. Here, we tested how river rearrangements influenced the evolutionary history of uakari monkeys, genus Cacajao, a primate genus primarily associated with seasonally flooded forests in central and western Amazonia. Location: Central and Western Amazonia. Taxon: The genus Cacajao, including the black uakaris (C. melanocephalus, C. ayresi, C. hosomi); and the bald-headed uakaris (C. calvus, C. amuna, C. rubicundus, C. ucayalii, C. novaesi). Methods: We performed a continuous phylogeographic analysis using 77 cytochrome b sequences to identify the origin and dispersal of Cacajao lineages. We used genome-wide SNP variation (ddRADseq) to investigate population structure, gene flow and demographic history in Cacajao populations and used digital elevation models to identify landscape and riverscape characteristics that may have influenced the geographic distribution of Cacajao. Results: Our continuous phylogeographic reconstruction pointed out that the ancestral Cacajao lineage occupied the flooded forests of the Solimoes River, in central Amazonia, at similar to 1.7 Mya and descendant lineages dispersed throughout central and western Amazonia more recently. We identified gene flow in both black and bald-headed uakari populations, even across rivers considered barriers (e.g. the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. Historical demographic analyses suggest varied scenarios of population size changes among Cacajao monkeys consistent with periods of intense dynamism in flooded habitats and the formation of non-flooded upland forests. Main Conclusion: Our results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent changes in demographic histories in species with a restricted geographic distribution.

Population genomics applied to game species conservation can help delineate management units, ensure appropriate harvest levels and identify populations needing genetic rescue to safeguard their adaptive potential. The ruffed grouse (Bonasa umbellus) is rapidly declining in much of the eastern USA due to a combination of forest maturation and habitat fragmentation. More recently, mortality from West Nile Virus may have affected connectivity of local populations; however, genetic approaches have never explicitly investigated this issue. In this study, we sequenced 54 individual low-coverage (~5X) grouse genomes to characterize population structure, assess migration rates across the landscape to detect potential barriers to gene flow and identify genomic regions with high differentiation. We identified two genomic clusters with no clear geographic correlation, with large blocks of genomic differentiation associated with chromosomes 4 and 20, likely due to chromosomal inversions. After excluding these putative inversions from the data set, we found weak but nonsignificant signals of population subdivision. Estimated gene flow revealed reduced rates of migration in areas with extensive habitat fragmentation and increased genetic connectivity in areas with less habitat fragmentation. Our findings provide a benchmark for wildlife managers to compare and scale the genetic diversity and structure of ruffed grouse populations in Pennsylvania and across the eastern USA, and we also reveal structural variation in the grouse genome that requires further study to understand its possible effects on individual fitness and population distribution.

Investigating parallel roles of geography and environmental heterogeneity in diversification provides insights on how neutral and selective forces drive evolution of biological systems. Here, we investigate whether geographic and climatic distances explain either genetic or phenotypic variation in Blue-crowned Manakins ( Lepidothrix coronata ), a polychromatic bird species that is broadly distributed in the Neotropics. We tested the hypotheses of isolation by distance and environment through an integrative approach using genetic, colorimetric, geographic, and environmental data. Through structural equation modeling and multiple matrix regression with randomization statistics, we tested whether intraspecific genetic or phenotypic (plumage color) diversity is associated with variation in geographic and environmental distances among localities. Genetic and color diversity were not correlated: color variation was marginally associated with latitude; and genetic distances were explained by linear and least-cost geographic distances, conforming to predictions of isolation by distance and by environment. We suggest a combined effect of genetic drift and environmental heterogeneity in driving the genetic diversification at the regional scale, and adaptation to local environments operating in the diversification of adult male plumage coloration.

ABSTRACT Aim Western Amazonia is a region that underwent several landscape changes during the Quaternary. While Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of the Amazonia biota. Here we test how river rearrangements in western Amazonia influenced the evolutionary history of uakari monkeys, a primate group most associated with seasonally flooded forests in western Amazonia. Location Western Amazonia Taxon The uakari monkey (genus Cacajao ) Methods We performed a continuous phylogeographic analysis using 77 cytochrome b sequences and used digital elevation models to identify the role of landscape and riverscape characteristics in the geographic distribution of Cacajao . Finally, we used genome-wide SNPs variation (ddRADseq) to investigate population structure, gene flow and demographic history in three Cacajao species that were impacted by river rearrangements. Results Our continuous phylogeographical reconstruction points that the ancestral Cacajao lineage occupied the flooded forests of the Solimões River at ∼1.7 Mya, and descendant lineages dispersed throughout western Amazonia more recently. We identified gene flow among both black and bald-headed uakari populations, even across rivers considered barriers (e.g., the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao . The demographic analysis indicates that C. calvus, C. amuna , and C. rubicundus went through a population decline in the last 70 Kya and have a low effective population size. Main conclusion Our results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent population decline in species with a restricted geographic distribution.

We, as Associate Editors (AEs) for the Journal of Biogeography, have serious concerns about the widespread shifts by John Wiley & Sons Ltd (Wiley) and other academic publishers to full Open Access (OA), which appears to be imminent for journals in the Wiley portfolio (Rieseberg et al., 2023) and has been discussed as a possibility for the Journal of Biogeography itself. We commend the philosophy of OA—to make research freely available online, but for many journals that shift to full OA, article publication is accompanied by expensive article processing charges (APCs) payable by the authors (see Laakso et al., 2011; Tennant et al., 2016). This creates a financial burden that falls heaviest on early career scientists and scientists from low- to middle-income countries, erecting barriers to equity in publishing. The typical APC fees for OA range from 2000 to 3500 USD but can even surpass 11,000 USD, while the Journal of Biogeography APC is currently 4800 USD per article. A shift from subscription-based to full OA-based business models with APCs also clearly shifts the economic incentives for journals away from quality and toward quantity. High-throughput and high-output publishing models in academia severely risk lowering research standards and jeopardise the reputation of journals that adopt this practice. Researchers in low-to-middle income (LMI) countries (e.g., in Africa, Latin America and the Caribbean, parts of Asia and Oceania)—collectively identified as the ‘Global South’ or ‘GS’ (Dados & Connell, 2012) face many systematic, logistical and economic challenges to achieve academic productivity (e.g. as may be measured by h-index, # citations, research grants awarded) not experienced by counterparts from high-income countries (e.g., in Western, Central and Northern Europe, North America, Australia, among others). GS researchers have limited access to basic infrastructure, financial resources, and new technologies as well as fewer opportunities for upskilling (Guedes et al., 2023; Reidpath & Allotey, 2019). This situation has created a well-known disparity in academic productivity (Beheregaray, 2008; Gonzalez-Brambila et al., 2016) and uptake of content produced by GS researchers (Gomez et al., 2022; Lund, 2019). This simultaneously favours researchers in more developed countries and increases opportunities for better-resourced researchers to fill research gaps and gain prominence in scientific fields (Demeter, 2019; Gonzalez-Brambila et al., 2016; Odeny & Bosurgi, 2022), particularly in biodiverse regions (Wilson et al., 2016). Already struggling GS researchers now face an additional challenge—the widespread adoption of OA publishing with mandatory and unaffordable APCs. Originally a well-intentioned solution for allowing research to be visible outside paywalls (Laakso et al., 2011; Willinsky, 2006), OA has been co-opted by many journals into a problematic pay-to-publish business model, primarily by for-profit publishing houses (Tennant et al., 2016). Some academic institutions now require their researchers to only, or primarily, e.g. publish under the OA model. The full OA model is problematic for most researchers from GS countries because they simply lack the financial resources to cover high APCs (Kwon, 2022). GS countries tend to contribute only 1%–2% toward the total annual global research investment, while high-income countries contribute proportionally much more (Gonzalez-Brambila et al., 2016). Such small investment is compounded by a significant purchase-power disparity for GS researchers because APCs are charged in GBP, EUR or USD, and currencies from LMI economies depreciate against stronger currencies (Agénor & Montiel, 2015). The APC fee for a single article can be equivalent to several months of basic salary for researchers in GS countries (Dawson et al., 2023; Mekonnen et al., 2021). The financial imbalance produces a lower proportion of OA publications by GS-based researchers because many authors opt out of publishing in OA journals (Kwon, 2022; Smith et al., 2022), particularly in biogeographic fields (Edwards et al., 2022). The knock-on effect is that GS-based researchers have lower visibility and potentially fewer citations than their counterparts based in high-income countries, which leads to a disparity in research profiles (Gomez et al., 2022). Researchers from many fields have spoken out, demanding greater diversity in authorship (Nuñez et al., 2021; Odeny & Bosurgi, 2022; Raja et al., 2022) brought about by fundamental changes to the OA model to level the playing field. Without a radical shift in the OA business model, a cadre of researchers will increasingly be marginalised, equating to systemic epistemic injustice (Fricker, 2007; Grasswick, 2017; Pitts, 2017) by excluding GS perspectives and approaches that would otherwise advance science (Thorp, 2023). This effect is particularly poignant for biogeographic research because most of the world's remaining biodiversity is situated in GS countries, and hence contributions from the GS are of special importance to combat the ongoing global biodiversity crisis. Although most academic publishers offer APC fee waivers to some GS-based authors, the eligibility list is short and based on the per capita GDP of the researchers' country. This typically provides some opportunity for researchers in low-income countries, but those from middle-income countries (MIC) often fall through the cracks. Some publishers offer discounts to MIC researchers, but these discounts are insufficient to address the financial disparity. Moreover, applications for discounts are sometimes not granted depending on e.g. the combination of authors on the article. On the surface, OA publishers appear to be addressing inequality, but the number of genuine waivers granted is few relative to the need (Kowaltowski et al., 2023). The reality is that MIC is fraught with income and wealth inequality, and by basing waivers on simple measures, such as per capita GDP, most GS researchers do not qualify. We therefore strongly advocate that the criteria for APC waivers and substantial discounts are based on more nuanced metrics such as wealth distribution, purchasing power (e.g., Gini-Index, PPP, CPI, among others), and percentage of GDP invested in science and technology. The signing of reasonable transformative agreements with GS countries that cover an array of research institutions must advance, as the contributions of GS researchers are being excluded from the most visible global scientific literature. True transformation will dismantle the barriers set up by APCs and be measured not in company profits but in bringing equity to OA academic publishing. Early career researchers (ECRs), defined here as any scientist within 10 years of PhD completion (Christian et al., 2021), are at the forefront of bringing new insights into the field of biogeography and thus play a critical role in advancing the discipline. For decades, Journal of Biogeography has served as a major source of research inspiration for ECRs, many of whom published their first papers in the journal and continue to do so as they advance in their careers. The 'ECR Featured Researchers' section on the journal's blog highlights recently published research in the Journal of Biogeography by ECRs and is written by ECRs. These highlights allow ECR authors to share with readers a more personal perspective on the motivations, challenges and novelty associated with their research, thus building a community around and beyond the journal itself. Finally, the Journal of Biogeography ‘Innovation Awards’ aim to acknowledge outstanding research contributions of ECRs in advancing the field of biogeography (Dawson et al., 2023). Together, these initiatives led by the senior editors have demonstrated a strong commitment by the Journal of Biogeography to support ECRs through advancing their professional growth, providing a platform for networking and knowledge sharing while also increasing their visibility and overall recognition within the wider research community. Unfortunately, the shift to excessive APCs for OA by for-profit publishers threatens the ECRs that these worthy initiatives seek to support. Because of the precarity of ECRs, both financially and with respect to the career stage, the high APCs associated with OA have particularly detrimental effects on career development. Moreover, a shift to full OA with high APCs would raise serious concerns about scientific integrity and compatibility with the values upheld by the biogeography community, including ECRs. ECRs represent the future of the discipline, and we have written this section to voice our concerns on behalf of ECRs everywhere. In summary, ECRs play a key role on editorial boards by promoting diversity and inclusion, helping the progression of other ECRs, and contributing novel perspectives and ideas that support journal development (e.g., new methodologies, emerging topics). We commend the Journal of Biogeography for its past commitments to supporting ECRs, and we strongly advocate against any consideration of a shift to a full-OA model that would jeopardise these commitments. Going forward, we recommend that academic journals prioritise ECRs' career growth and provide financial support for ECR publishing and editing, such as through APC fee waivers and compensation for reviewing and editing (Hotaling et al., 2023). These changes are essential for a sustainable academic publishing landscape. We also recommend stabilising or reducing targets for the number of special issues and general submissions, which are oversimplistic and subject to perverse incentives (see above), and instead focusing on helping authors of regular submissions publish their best work possible in a journal of high quality. Publishing high-quality scientific journals costs money, and we support a reasonable cost-recovery model for academic publishers based on charges to authors, institutions or subscribers. We also support the principle of OA that makes scientific content freely available. However, to keep advancing the field of biogeography and science in general, a new paradigm needs to be reached, one that keeps the costs of publishing affordable for authors and that compensates scientists for their professional services instead of one that is designed to produce a high-profit margin for the publisher. We have written this editorial and engaged in the work stoppage as a way of communicating to our colleagues and to profit-based journals the seriousness and depth of our concerns and as a way of promoting further dialogue. We are willing to discuss these concerns to reach a mutually beneficial compromise with the publisher of JBI. However, we are also ready to resign our positions as AEs if the publisher of JBI were to take the unfortunate step of shifting to a full OA model with high APCs without considering full equity for GS and ECR researchers. We recognise that some steps have been made along these lines, but this is yet inadequate and disproportionate to the considerable profits made by many publishers. AEs usually work without financial compensation or other incentives (such as discounts or credits), with the ultimate goal of advancing the field of biogeography by supporting high-quality, peer-reviewed, cutting-edge research. In contrast, Wiley, the owner and publisher of the Journal of Biogeography, has had a reported annual revenue in recent years of over 2 billion USD per annum with a gross profit margin averaging nearly 70%. Wiley reports their performance using the —i.e., operating profit as a percentage of revenue—controversial adjusted EBITDA profit metric, and this shows the company operates at a very satisfactory level of a 20% margin. Research-related publications reportedly form a large part of their revenue. Other academic publishers such as Elsevier show similar revenues and gross profits. Given that the Journal of Biogeography has a proud history as a thought leader in our discipline, we are firmly against a business model that maintains the already substantial profits made by academic publishing houses at the cost of the increased financial burden to authors, increased workload of volunteer editors and reducing the scientific quality of academic journals in jeopardy. We are grateful for advice and support from the senior editors of the Journal of Biogeography and in particular for their commitment to mentoring the Early Career Researchers on the editorial team. The authors of this editorial are currently Associate Editors or on the Editorial Board of the Journal of Biogeography, and most have recently participated in a temporary work stoppage. Many of the authors have previously published their research in the Journal of Biogeography or other Wiley outlets. Data sharing is not applicable to this article as no new data were created or analyzed in this study. The authors are Associate Editors or on the Editorial Board of the Journal of Biogeography, and most are Early Career Researchers and/or researchers from the Global South. Author contributions: This team of authors conceived and co-wrote the article.

Populations peripheral to a species’ distribution are more susceptible to new selective pressures, changes, differentiation, and extinction. The Sooty Swift Cypseloides fumigatus (Apodidae) is a rare bird found mainly in central and southeastern South America. Populations of this species are resident in some localities throughout the year, whereas other populations migrate following the breeding season. Recently, a northern population was found well beyond the limits of its known distribution, with approximately 1000 km of occurrence gap between this newly discovered population and the southern distribution. Here, we reveal changes in species distribution over time, as well as compare the morphometric and genetic patterns of populations in the central-southern distribution of the Atlantic Forest and the northern peripheral population within the Caatinga. Our climate niche models indicate a scenario of expanding species distribution during the Last Glacial Maximum, which potentially drove the colonization of the northernmost population. This scenario of peripheral isolation is also supported by the spatial morphometric and genetic variation among populations of the humid forest enclave within the Caatinga and the Cerrado–Atlantic Forest populations. These findings provide important insights into the connectivity between distant Sooty Swift populations, the species' migratory behavior, as well as implications for conservation.

The Cerrado encompasses a complex network of hydrographic basins, which is responsible for the formation and maintenance of the riparian and gallery forests. Alterations in the vegetation resulting from the paleoclimatic changes that occurred during the Pleistocene influenced the current distribution of these humid forests. To understand of the evolutionary dynamics of this landscape on the population structure of the associated organisms, we studied the population genetics of the Antilophia galeata (Pipridae), a bird endemic to the gallery forests of the Cerrado. For this, we evaluated the variability of the mitochondrial control region of 71 A. galeata specimens from 18 localities distributed throughout the Cerrado. The results indicated the existence of significant substructure among the populations located in the peripheral areas of the Cerrado, in comparison with the populations found in the central portion, reflecting historical changes in the environment. We also found high levels of diversity in all the populations, while the analysis of the demographic history revealed a scenario of stability. Overall, then, these findings indicate that the historical modifications of the gallery forest distribution may have been most accentuated in the peripheral zones, with a greater stability and connectivity persisting in the central portion of the biome.

Ecological, climatic and palaeogeographical processes drive biological diversification. However, the evolutionary outcomes of those mechanisms are complex and difficult to discriminate. Here, we test how alternative drivers affected connectivity along the Amazonian floodplains generating current patterns of population structure and diversity within the Striped Woodcreeper, a widespread bird species tied to forests seasonally flooded by Amazonian rivers.

Genetic information is still underestimated in conservation policies, seldom being monitored or included in management strategies. Monitoring changes in genetic diversity over time in endangered species is useful to anticipate possible risks associated with reduced genetic variation. The Araripe Manakin (Antilophia bokermanni) is a Critically Endangered species, probably with a historically low level of genetic diversity and currently facing demographic population decline. This is the first study to present a fine-scale spatio-temporal genetic monitoring for the Araripe Manakin. Using microsatellite loci, genotyped at two time periods (2003–2004 and 2015–2017), we conclude that genetic diversity has been relatively stable in this short-term assessment, with limited signs of population structure between time frames, and no current population structure within past or present species distribution. However, we also detect signs of genetic bottleneck and evidence that suggest that mating is not presently random. Our results corroborate that the species is a resilient bird, but habitat loss and degradation are jeopardizing Araripe Manakin’s persistence. The species comprises a unique small population, and restoration of habitat quality and connectivity should continue to maintain its viability. Nonetheless, given the low genetic diversity observed, we further identify some challenges and recommend solutions for the implementation of genetic information in the current conservation effort of the Araripe Manakin.

Although vicariant processes are expected to leave similar genomic signatures among codistributed taxa, ecological traits such as habitat and stratum can influence genetic divergence within species. Here, we combined landscape history and habitat specialization to understand the historical and ecological factors responsible for current levels of genetic divergence in three species of birds specialized in seasonally flooded habitats in muddy rivers and which are widespread in the Amazon basin but have isolated populations in the Rio Branco. Populations of the white-bellied spinetail (Mazaria propinqua), lesser wagtail-tyrant (Stigmatura napensis) and bicolored conebill (Conirostrum bicolor) are currently isolated in the Rio Branco by the black-waters of the lower Rio Negro, offering a unique opportunity to test the effect of river colour as a barrier to gene flow. We used ultraconserved elements (UCEs) to test alternative hypotheses of population history in a comparative phylogeographical approach by modelling genetic structure, demographic history and testing for shared divergence time among codistributed taxa. Our analyses revealed that (i) all three populations from the Rio Branco floodplains are genetically distinct from other populations along the Amazon River floodplains; (ii) these divergences are the result of at least two distinct events, consistent with species habitat specialization; and (iii) the most likely model of population evolution includes lower population connectivity during the Late Pleistocene transition (~250,000 years ago), with gene flow being completely disrupted after the Last Glacial Maximum (~21,000 years ago). Our findings highlight how landscape evolution modulates population connectivity in habitat specialist species and how organisms can have different responses to the same historical processes of environmental change, depending on their habitat affinity.

Aim Amazonian floodplains include distinct types of seasonally flooded habitats, determined by the flooding regime and sedimentation dynamics. Some bird species prefer specific habitat types within the floodplains. To investigate whether distinct habitats are differentially affected by geologic and climatic history, we compare population history in a sympatric and closely related pair of ovenbird species with different habitat associations. Location Amazonian floodplains. Taxa Synallaxis albigularis and Mazaria propinqua (Aves; Furnariidae). Methods Occurrence records were obtained from museums and public databases. Genomic data included nuclear loci (UCE) and the mitogenome for 49 samples. SNPs from UCE data were used to infer population genetic structure and effective migration. Mitogenomes were used to build phylogenetic trees and chronograms. Both datasets were used to infer historical demographic changes and test demographic scenarios. Results S. albigularis includes geographically structured mtDNA clades with a crown age of 250 ka, whereas M. propinqua includes a single clade with a crown age of 38 ka. Effective migration is lower at the base of the Andes for S. albigularis and at the lower Negro River for M. propinqua. Population expansion is detected for both species during the Quaternary, but was steeper and more recent in M. propinqua. Main conclusions The differences in population histories relate to distinct habitat associations along Amazonian floodplains. Preference of M. propinqua for more ephemeral island habitats may favour local extinctions, leading to demographic change, low genetic variability, no population structure and smaller effective population size. In contrast, more resilient habitats along the floodplains inhabited by S. albigularis may sustain local populations, generating and maintaining local diversity. Our results suggest that climatic variations of the late Pleistocene and Holocene caused changes in distribution and connectivity of the different types of habitats along the Amazonian floodplains, affecting gene flow and population sizes of associated bird populations.

The two species of the genus Antilophia , Antilophia bokermanni and Antilophia galeata , are found in environments that are undergoing extensive modification, which may be provoking the loss of their genetic diversity. Nine polymorphic microsatellite loci were characterized and analyzed in each of these species. The distribution of allele frequencies revealed two clusters that reflected the distinct genetic profile of each species. Observed levels of heterozygosity were low for each species, with the lowest allelic diversity found in the critically endangered A. bokermanni . The set of loci described here, in contrast with other genetic markers that have been analyzed previously, effectively diagnosed the genetic diversity of different populations of the two species.

Establishing links between phenotypic and genotypic variation is a central goal of evolutionary biology, as they might provide important insights into evolutionary processes shaping genetic and species diversity in nature. One of the more intriguing possibilities is when no genetic divergence is found to be associated with conspicuous phenotypic divergence. In that case, speciation theory predicts that phenotypic divergence may still occur in the presence of significant gene flow-thereby resulting in little genomic divergence-when genetic loci underpinning phenotypes are under strong divergent selection. However, a finding of phenotypic distinctiveness with weak or no population genetic structure may simply result from low statistical power to detect shallow genetic divergences when small data sets are used. Here, we used a subgenomic data set of 2,386 ultraconserved elements to explore genomewide divergence between two species of Antilophia manakins, which are phenotypically distinct yet evidently lack strong genetic differentiation according to previous studies based on a limited number of loci. Our results revealed clear population structure that matches the two phenotypes, supporting the idea that smaller data sets lacked the power to detect this recent divergence event (likely <100 k ya). Indeed, we found little or no introgression between the species, as well as evidence of genomewide divergence. One implication of our study is that the Araripe plateau may be a hot spot of cryptic-diverging forest Cerrado populations. Besides their use in biogeography, subgenomic data sets may help redefine local conservation programmes by revealing cryptic population structure that may be key to population management.

The melanocortin-1 receptor gene is the most widely-used marker for the investigation of the genetic determination of melanic plumage patterns. Studies of a number of wild bird species have shown an association between non-synonymous mutations of the MC1R gene and the presence of melanic variants. The genus Antilophia (Pipridae) includes only two manakin species (A. galeata and A. bokermanni), which are distinguished primarily by the differences in the pattern of melanic coloration of the plumage of the mantle in the adult males. In A. galeata, this plumage is black, while in A. bokermanni, it is predominantly white. This study investigates the possible association between mutations of the MC1R marker and the variation in plumage coloration observed in the two species. The MC1R sequences of the two species was analyzed, and the observed nucleotide variation was compared. Six polymorphic sites were identified, representing seven distinct genotypes. Five of these polymorphic mutations were non-synonymous, but were not related to the different phenotypes. Neutral evolution and the absence of any systematic association between the variants of the MC1R and plumage coloration in the Antilophia species indicate that alternative mechanisms regulate the expression of the coloration of the plumage in the adult males.

To determine a hypothetical scenario that accounts for the diversification of the two species of the genus Antilophia, we conducted multilocus molecular comparisons and species distribution modeling for the two taxa, which have distinct male plumage coloration patterns and allopatric geographic distributions, despite the high degree of genetic similarity indicated by recent studies. Three mitochondrial and three nuclear fragments were analyzed. The results indicate clear differences in the genetic diversity of the two species, but with ample sharing of haplotypes in all the markers analyzed, reflecting the absence of reciprocal monophyly, presumably due to the relatively recent and still incomplete separation of the two species. The paleoclimatic distribution models, together with the observed genetic profile indicate a recent process of divergence by geographic isolation in the ancestral populations of the two species. This scenario coincides with the recent climatic events of the South American dry diagonal, which involves the gallery forests of the Cerrado biome and the cloud forest enclaves of the seasonal tropical dry forest of the Caatinga between the late Pleistocene and the mid Holocene.

The Araripe Manakin (Antilophia bokermanni) is a "Critically endangered" bird species endemic to northeastern Brazil. The habitat of the species has suffered intense fragmentation and degradation in recent years, resulting in a decline in population numbers. The present study evaluated the genetic diversity and structure of this population through the analysis of the Hypervariable Domain I of the mitochondrial Control Region and two nuclear introns (I7BF and G3PDH). Results revealed an absence of population substructuring and population decline beginning during the late Pleistocene, approximately 50,000 years ago. The evidence indicates that the effective population size of the Araripe Manakin has declined gradually over time ever since, a process that may have been intensified as a result of the recent anthropogenic impacts on the habitat of the species.

The Araripe manakin is a critically endangered species of bird endemic to northeastern Brazil. The species’ habitat has suffered intense fragmentation and degradation in recent years, resulting in a decline in population numbers and a probable loss of viability. The present study evaluated the genetic diversity and structure of this population through the analysis of Hypervariable Domain I of the mitochondrial Control Region and two nuclear introns (I7BF and G3PDH). The results, based primarily on mitochondrial data, revealed an absence of any population substructuring and a marked tendency for population decline during the demographic history of the species, which began during the late Pleistocene, approximately 40,000 years ago. The evidence indicates that the effective size of the population of the Araripe manakin has declined gradually over time, a process that may be intensifying as a result of the recent anthropogenic impacts on the species’ habitat.