ResearchPad - evolutionary-biology https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[The two types of society: Computationally revealing recurrent social formations and their evolutionary trajectories]]> https://www.researchpad.co/article/elastic_article_13873 Comparative social science has a long history of attempts to classify societies and cultures in terms of shared characteristics. However, only recently has it become feasible to conduct quantitative analysis of large historical datasets to mathematically approach the study of social complexity and classify shared societal characteristics. Such methods have the potential to identify recurrent social formations in human societies and contribute to social evolutionary theory. However, in order to achieve this potential, repeated studies are needed to assess the robustness of results to changing methods and data sets. Using an improved derivative of the Seshat: Global History Databank, we perform a clustering analysis of 271 past societies from sampling points across the globe to study plausible categorizations inherent in the data. Analysis indicates that the best fit to Seshat data is five subclusters existing as part of two clearly delineated superclusters (that is, two broad “types” of society in terms of social-ecological configuration). Our results add weight to the idea that human societies form recurrent social formations by replicating previous studies with different methods and data. Our results also contribute nuance to previously established measures of social complexity, illustrate diverse trajectories of change, and shed further light on the finite bounds of human social diversity.

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<![CDATA[Genetic diversity of <i>Echinococcus multilocularis</i> and <i>Echinococcus granulosus sensu lato</i> in Kyrgyzstan: The A2 haplotype of <i>E</i>. <i>multilocularis</i> is the predominant variant infecting humans]]> https://www.researchpad.co/article/elastic_article_13871 Analysis of the genetic variability in Echinococcus species from different endemic countries have contributed to the knowledge in the taxonomy and phylogeography of these parasites. The most important species of this genus, Echinococcus granulosus sensu lato and Echinococcus multilocularis, co-exist in Kyrgyzstan causing serious public health issues. E. granulosus s.l. causes cystic echinococcosis and E. multilocularis is the causative agent of alveolar echinococcosis. The most relevant finding of our study is the identification of the cob/nad2/cox1 A2 haplotype of E. multilocularis as the most commonly found in humans and dogs. However, it remains unknown if this variant of E. multilocularis, based on genetic differences in mitochondrial genes, presents differences in virulence which could have contributed to the emergence of alveolar echinococcosis in Kyrgyzstan. The results also show a number of non-previously described genetic variants of E. multilocularis and E. granulosus s.s.

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<![CDATA[Impacts of host gender on <i>Schistosoma mansoni</i> risk in rural Uganda—A mixed-methods approach]]> https://www.researchpad.co/article/elastic_article_13851 Globally, over 230 million people are infected with schistosomiasis, an infectious disease caused by parasitic helminths. Humans can get infected when they contact water which contains Schistosoma parasites. Although the disease can be treated with a drug, people get rapidly reinfected in certain high-transmission settings. Drug treatment alone may not be sufficient to eliminate this disease and additional interventions such as health promotion or improvements in water and sanitation need to be scaled up. To provide recommendations to these control programmes we carried out interdisciplinary research in Eastern Uganda to understand the influence of gender on schistosomiasis risk. We found that the water contact behaviour of boys and girls is quite similar, and we did not see differences in reinfection or genetic diversity of the parasite between boys and girls. Differences in water contact between genders is greater in adults, and further research is required for these individuals. In this setting, infection rates are high in school-aged children and there are no differences between genders. These results emphasise improved control efforts for all school-aged children in communities like these. Our interdisciplinary approach provided complementary findings. Such an integrated approach can therefore have more power to meaningfully inform policy on schistosomiasis control.

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<![CDATA[Interaction between host genes and <i>Mycobacterium tuberculosis</i> lineage can affect tuberculosis severity: Evidence for coevolution?]]> https://www.researchpad.co/article/elastic_article_13824 Susceptibility to tuberculosis (TB) is affected by genetic variation in both the human host and the causative bacterium, Mycobacterium tuberculosis. However, prior studies of the genetics of each species have not explained a large part of TB risk. The possibility exists that risk can be better estimated from patterns of variation in the two species as a unit, such that some combinations provide increased risk, or in the presence of TB, increased disease severity. We hypothesized that alleles in the two species that have co-existed for long periods are more likely to reduce disease severity so as to promote prolonged co-occurrence. We tested this by studying TB severity in two patient cohorts from Uganda for which paired MTB-human DNA were available. We examined severity, as measured by the Bandim TBscore, and assessed whether there was an interaction between MTB lineage and SNPs in the host with this metric. Our results indicate that the most recent TB lineage (L4.6/Uganda) when found together with an ancestral allele in SLC11A1 resulted in more severe disease. This finding is consistent with the conclusion that MTB and human have coevolved to modulate TB severity.

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<![CDATA[Bacterial contribution to genesis of the novel germ line determinant <i>oskar</i>]]> https://www.researchpad.co/article/elastic_article_12752 New cellular functions and developmental processes can evolve by modifying existing genes or creating novel genes. Novel genes can arise not only via duplication or mutation but also by acquiring foreign DNA, also called horizontal gene transfer (HGT). Here we show that HGT likely contributed to the creation of a novel gene indispensable for reproduction in some insects. Long considered a novel gene with unknown origin, oskar has evolved to fulfil a crucial role in insect germ cell formation. Our analysis of over 100 insect Oskar sequences suggests that oskar arose de novo via fusion of eukaryotic and prokaryotic sequences. This work shows that highly unusual gene origin processes can give rise to novel genes that may facilitate evolution of novel developmental mechanisms.

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<![CDATA[Adaptive genetic diversity and evidence of population genetic structure in the endangered Sierra Madre Sparrow (<i>Xenospiza baileyi</i>)]]> https://www.researchpad.co/article/elastic_article_11235 The magnitude and distribution of genetic diversity through space and time can provide useful information relating to evolutionary potential and conservation status in threatened species. In assessing genetic diversity in species that are of conservation concern, several studies have focused on the use of Toll-like receptors (TLRs). TLRs are innate immune genes related to pathogen resistance, and polymorphisms may reflect not only levels of functional diversity, but may also be used to assess genetic diversity within and among populations. Here, we combined four potentially adaptive markers (TLRs) with one mitochondrial (COI) marker to evaluate genetic variation in the endangered Sierra Madre Sparrow (Xenospiza baileyi). This species offers an ideal model to investigate population and evolutionary genetic processes that may be occurring in a habitat restricted endangered species with disjunct populations (Mexico City and Durango), the census sizes of which differ by an order of magnitude. TLRs diversity in the Sierra Madre Sparrow was relatively high, which was not expected given its two small, geographically isolated populations. Genetic diversity was different (but not significantly so) between the two populations, with less diversity seen in the smaller Durango population. Population genetic structure between populations was due to isolation and different selective forces acting on different TLRs; population structure was also evident in COI. Reduction of genetic diversity in COI was observed over 20 years in the Durango population, a result likely caused by habitat loss, a factor which may be the main cause of diversity decline generally. Our results provide information related to the ways in which adaptive variation can be altered by demographic changes due to human-mediated habitat alterations. Furthermore, our findings may help to guide conservation schemes for both populations and their restricted habitat.

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<![CDATA[Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae]]> https://www.researchpad.co/article/elastic_article_11231 In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.

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<![CDATA[Modeling competitive evolution of multiple languages]]> https://www.researchpad.co/article/elastic_article_7854 Increasing evidence demonstrates that in many places language coexistence has become ubiquitous and essential for supporting language and cultural diversity and associated with its financial and economic benefits. The competitive evolution among multiple languages determines the evolution outcome, either coexistence, or decline, or extinction. Here, we extend the Abrams-Strogatz model of language competition to multiple languages and then validate it by analyzing the behavioral transitions of language usage over the recent several decades in Singapore and Hong Kong. In each case, we estimate from data the model parameters that measure each language utility for its speakers and the strength of two biases, the majority preference for their language, and the minority aversion to it. The values of these two biases decide which language is the fastest growing in the competition and what would be the stable state of the system. We also study the system convergence time to stable states and discover the existence of tipping points with multiple attractors. Moreover, the critical slowdown of convergence to the stable fractions of language users appears near and peaks at the tipping points, signaling when the system approaches them. Our analysis furthers our understanding of evolution of various languages and the role of tipping points in behavioral transitions. These insights may help to protect languages from extinction and retain the language and cultural diversity.

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<![CDATA[ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient <i>hsdRMS</i> restriction system broadening conjugation host range]]> https://www.researchpad.co/article/elastic_article_7739 Horizontal gene transfer is the main mechanism by which bacteria acquire and disseminate new traits, such as antibiotic resistance genes, that allow adaptation and evolution. Here we identified a gene, ardC, that enables a plasmid to increase its conjugative host range, and thus positively contributes to plasmid fitness. The crystal structure of the antirestriction protein ArdC revealed a fold different from other antirestriction proteins. Our results have wide implications for understanding how a gene enlarges the environments a plasmid can colonize and point to new targets to harness the bacterial DNA uptake control.

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<![CDATA[Adaptation to unstable coordination patterns in individual and joint actions]]> https://www.researchpad.co/article/elastic_article_7665 Previous research on interlimb coordination has shown that some coordination patterns are more stable than others, and function as attractors in the space of possible phase relations between different rhythmic movements. The canonical coordination patterns, i.e. the two most stable phase relations, are in-phase (0 degree) and anti-phase (180 degrees). Yet, musicians are able to perform other coordination patterns in intrapersonal as well as in interpersonal coordination with remarkable precision. This raises the question of how music experts manage to produce these unstable patterns of movement coordination. In the current study, we invited participants with at least five years of training on a musical instrument. We used an adaptation paradigm to address two factors that may facilitate producing unstable coordination patterns. First, we investigated adaptation in different coordination settings, to test the hypothesis that the lower coupling strength between individuals during joint performance makes it easier to achieve stability outside of the canonical patterns than the stronger coupling during individual bimanual performance. Second, we investigated whether adding to the structure of action effects may support achieving unstable coordination patterns, both intra- and inter-individually. The structure of action effects was strengthened by adding a melodic contour to the action effects, a measure that has been shown to improve the acquisition of bimanual coordination skills. Adaptation performance was measured both in terms of asynchrony and variability thereof. As predicted, we found that producing unstable patterns benefitted from the weaker coupling during joint performance. Surprisingly, the structure of action effects did not help with achieving unstable coordination patterns.

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<![CDATA[Evolutionary trade-off in reproduction of Cambrian arthropods]]> https://www.researchpad.co/article/elastic_article_7741 Trade-offs play a crucial role in the evolution of life-history strategies of extant organisms by shaping traits such as growth pattern, reproductive investment, and lifespan. One important trade-off is between offspring number and energy (nutrition, parental care, etc.) allocated to individual offspring. Exceptional Cambrian fossils allowed us to trace the earliest evidence of trade-offs in arthropod reproduction. †Chuandianella ovata, from the early Cambrian Chengjiang biota of China, brooded numerous (≤100 per clutch), small (Ø, ~0.5 mm) eggs under carapace flaps. The closely related †Waptia fieldensis, from the middle Cambrian Burgess Shale of Canada, also brooded young, but carried fewer (≤ 26 per clutch), larger (Ø, ~2.0 mm) eggs. The notable differences in clutch/egg sizes between these two species suggest an evolutionary trade-off between quantity and quality of offspring. The shift toward fewer, larger eggs might be an adaptive response to marine ecosystem changes through the early-middle Cambrian. We hypothesize that reproductive trade-offs might have facilitated the evolutionary success of early arthropods.

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<![CDATA[Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9]]> https://www.researchpad.co/article/elastic_article_6353 A single protein sometimes does multiple jobs. For instance, our immune system uses a small number of multipurpose proteins to respond quickly to a large number of threats. One example is the protein S100A9. It acts as an antimicrobial by preventing microbes from getting the nutrients they need, while also stimulating inflammation by inducing the release of molecules that recruit white blood cells.

S100A9, like all proteins, is made up of a chain of small building blocks. These building blocks interact with each other and with other molecules in the environment. The sequence of the building blocks thus determines what jobs the protein can do. Therefore, a single change to the sequence of building blocks can have a dramatic effect: one change might render the protein faulty, while another change might allow it to do a new job.

Proteins face similar challenges humans do when trying to do several things at once. A person driving a car while using their phone will not do either task well. Likewise, a protein that does two jobs faces challenges a single-purpose protein does not.

Harman et al. were interested in how S100A9 was able to evolve and maintain its dual functionality, despite this potential problem. They started by asking when S100A9 acquired its two purposes. They measured the antimicrobial and inflammatory activity of S100A9 proteins from humans, mice and opossums. The activities of S100A9 in these species was similar, suggesting that S100A9 acquired its different jobs in the ancestor of mammals, some 160 million years ago.

Next, Harman et al. computationally reconstructed ancestral forms of S100A9 by comparing hundreds of similar proteins and building an evolutionary tree. They then measured the antimicrobial and inflammatory activity of these ancestral proteins. By comparing the last ancestor that did not have these activities to the first ancestor that did, they identified the sequence changes that gave S100A9 its dual activity. Importantly, these changes are located in separate regions of the protein, meaning they could occur independently, without affecting each other. Further, the same sequence change that converted S100A9 into an inflammatory signal also introduced a mechanism to regulate this activity.

The results suggest that a small number of sequence changes – or even a single change – can make a protein more versatile. This means that evolving multipurpose proteins may not be as difficult as is often thought.

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<![CDATA[No Tömösváry organ in flat backed millipedes (, )]]> https://www.researchpad.co/article/Nbb17270b-5ccc-4ebe-8bce-5ada6702d0d2 The Tömösváry organ is a sensory structure of the head in myriapods and some other terrestrial arthropods. Due to its variable shape, size, and position in millipedes () the Tömösváry organ is commonly used as diagnostic character in taxonomic descriptions and often included in phylogenetic analyses. For the , the largest millipede order, the Tömösváry organ is inconsistently stated as being either absent or present as a pear-shaped pit covered by a membrane or cuticular disc. In order to resolve this inconsistency, we investigated the morphology of the presumable Tömösváry organ in four polydesmidan species based on paraffin-histology, semi-thin sections and micro-computed tomography. Our results unambiguously favor the view that the articulation of the cephalic tentorium with the head capsule was misidentified as the Tömösváry organ in previous studies, and thus that the Tömösváry organ indeed is absent in the . The pear-shaped pit proved to represent the distal roundish expansion of the incisura lateralis, to which – similarly as in julidan millipedes – the tentorial transverse bar is articulated. The absence of the Tömösváry organ in the does not affect the topology of the interrelationships among the millipede orders retrieved in previous cladistic analyses based on morphology. As a character shared by and Juliformia, however, absence of a Tömösváry organ in favors the optimization of its presence in nematophoran millipedes as a reversal. Further studies are needed to clarify whether among chilognathan millipedes a Tömösváry organ really exists in taxa such as , and whether the Tömösváry organs are homologous across millipedes.

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<![CDATA[Structure–behaviour correlations between two genetically closely related snail species]]> https://www.researchpad.co/article/N34ae456a-4468-4991-abda-6f0c6f32bda7

Species, through their structure and composition, have evolved to respond to environmental constraints. Predator–prey interactions are among environmental pressures that can lead to speciation, but it remains unclear how this pressure can be related to the material structure and performance. Recently, two land snails, Karaftohelix editha and Karaftohelix gainesi, were found to exhibit divergent phenotypes and responses to predation despite sharing the same habitat and most of their genome. Indeed, under attack from a beetle, K. editha snails retract into their shell whereas K. gainesi snails swing their shell. In this paper, we looked at the microstructure, composition, morphology and mechanics of the shells of those two species and discuss potential relationships between material structure and the snail defence behaviour. The results of this study provide additional arguments for the role of predator–prey interactions on speciation, as well as an unusual approach for the design of biomimetic structures adapted to a particular function.

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<![CDATA[Sexual frequency is associated with age of natural menopause: results from the Study of Women's Health Across the Nation]]> https://www.researchpad.co/article/N9ca572b3-18fc-4cfb-9e0f-7d2629bf6aa4

It is often observed that married women have a later age of natural menopause (ANM) than unmarried women; however, the reason for this association is unknown. We test an original hypothesis that sexual frequency acts as a bio-behavioural mediator between marital status and ANM. We hypothesize that there is a trade-off between continued ovulation and menopause based on the woman's chances of becoming pregnant. If a woman is sexually inactive, then pregnancy is impossible, and continued investment in ovulation would not be adaptive. In addition, we test an existing hypothesis that the observed relationship is because of the exposure to male pheromones. Data from 2936 women were drawn from 11 waves of the Study of Women's Health Across the Nation, which is a longitudinal study conducted in the United States. Using time-varying Cox regression, we found no evidence for the pheromone hypothesis. However, we did observe that women who reported to have sex weekly during the study period were 28% less likely to experience menopause than women who had sex less than monthly. This is an indication that ANM may be somewhat facultative in response to the likelihood of pregnancy.

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<![CDATA[Knowing when to stick: touch receptors found in the remora adhesive disc]]> https://www.researchpad.co/article/Ndb9a3bac-8689-4e18-b01b-2653f16e443d

Remoras are fishes that piggyback onto larger marine fauna via an adhesive disc to increase locomotor efficiency, likelihood of finding mates and access to prey. Attaching rapidly to a large, fast-moving host is no easy task, and while research to date has focused on how the disc supports adhesion, no attention has been paid to how or if remoras are able to sense attachment. We identified push-rod-like mechanoreceptor complexes embedded in the soft lip of the remora adhesive disc that are known in other organisms to respond to touch and shear forces. This is, to our knowledge, the first time such mechanoreceptor complexes are described in fishes as they were only known previously in monotremes. The presence of push-rod-like mechanoreceptor complexes suggests not only that fishes may be able to sense their environment in ways not heretofore described but that specialized tactile mechanoreceptor complexes may be a more basal vertebrate feature than previously thought.

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<![CDATA[What makes a pair bond in a Neotropical primate: female and male contributions]]> https://www.researchpad.co/article/N83ea953f-5c33-488f-a14d-34442f3aac35

Pair living and pair bonding are rare in mammals, and the mechanisms of their maintenance remain a puzzle. Titi monkeys, a ‘textbook example’ for ‘monogamous’ primates, have strong pair bonds and extensive male care. To investigate mechanisms of pair-bond maintenance, we studied seven wild groups of red titis (Plecturocebus cupreus) in Peruvian Amazonia over a period of 14 months. We analysed pair bonds by measuring proximity, grooming and approaches/leaves within pairs, and collected data on intergroup encounters. Females contributed to grooming more than males, especially during infant dependency, when most of the grooming within pairs was done by females. Females were also more active in controlling proximity between pair mates, making most of the approaches and leaves. Males, on the other hand, invested more in territorial defences. They participated in more intergroup encounters than females and were more active during these encounters. Our data is most consistent with the ‘male-services’ hypothesis for pair-bond maintenance, where a female contributes more to the proximity and affiliation maintenance while a male provides beneficial services.

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<![CDATA[Analysis of statistical correlations between properties of adaptive walks in fitness landscapes]]> https://www.researchpad.co/article/N2721638e-c6ac-41d4-8696-8dae5a7fc88a

The fitness landscape metaphor has been central in our way of thinking about adaptation. In this scenario, adaptive walks are idealized dynamics that mimic the uphill movement of an evolving population towards a fitness peak of the landscape. Recent works in experimental evolution have demonstrated that the constraints imposed by epistasis are responsible for reducing the number of accessible mutational pathways towards fitness peaks. Here, we exhaustively analyse the statistical properties of adaptive walks for two empirical fitness landscapes and theoretical NK landscapes. Some general conclusions can be drawn from our simulation study. Regardless of the dynamics, we observe that the shortest paths are more regularly used. Although the accessibility of a given fitness peak is reasonably correlated to the number of monotonic pathways towards it, the two quantities are not exactly proportional. A negative correlation between predictability and mean path divergence is established, and so the decrease of the number of effective mutational pathways ensures the convergence of the attraction basin of fitness peaks. On the other hand, other features are not conserved among fitness landscapes, such as the relationship between accessibility and predictability.

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<![CDATA[An experimental approach to evaluate the potential of drones in terrestrial mammal research: a gregarious ungulate as a study model]]> https://www.researchpad.co/article/N5745988f-3513-4c72-b094-70620994866c

Research on the use of unmanned aircraft systems (UAS) in wildlife has made remarkable progress recently. Few studies to date have experimentally evaluated the effect of UAS on animals and have usually focused primarily on aquatic fauna. In terrestrial open arid ecosystems, with relatively good visibility to detect animals but little environmental noise, there should be a trade-off between flying the UAS at high height above ground level (AGL) to limit the disturbance of animals and flying low enough to maintain count precision. In addition, body size or social aggregation of species can also affect the ability to detect animals from the air and their response to the UAS approach. To address this gap, we used a gregarious ungulate, the guanaco (Lama guanicoe), as a study model. Based on three types of experimental flights, we demonstrated that (i) the likelihood of miscounting guanacos in images increases with UAS height, but only for offspring and (ii) higher height AGL and lower UAS speed reduce disturbance, except for large groups, which always reacted. Our results call into question mostly indirect and observational previous evidence that terrestrial mammals are more tolerant to UAS than other species and highlight the need for experimental and species-specific studies before using UAS methods.

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<![CDATA[An atypical mating system in a neotropical manakin]]> https://www.researchpad.co/article/N3f9e6cbc-e8a0-42c4-bf6d-f36b51f0c46c

Most of the diversity in the mating systems of birds and other animals comes at higher taxonomic levels, such as across orders. Although divergent selective pressures should lead to animal mating systems that diverge sharply from those of close relatives, opportunities to examine the importance of such processes are scarce. We addressed this issue using the Araripe manakin (Antilophia bokermanni), a species endemic to a forest enclave surrounded by xeric shrublands in Brazil. Most manakins exhibit polygynous lekking mating systems that lack territoriality but exhibit strong sexual selection. In sharp contrast, we found that male Araripe manakins defended exclusive territories, and females nested within male territories. However, territoriality and offspring paternity were dissociated: males sired only 7% of nestlings from the nests within their territories and non-territorial males sired numerous nestlings. Moreover, female polyandry was widespread, with most broods exhibiting mixed paternity. Apparently, territories in this species function differently from both lekking arenas and resource-based territories of socially monogamous species. The unexpected territoriality of Araripe manakins and its dissociation from paternity is a unique evolutionary development within the manakin clade. Collectively, our findings underscore how divergences in mating systems might evolve based on selective pressures from novel environmental contexts.

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