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1.
Mol Biol Evol ; 41(7)2024 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-38916488

RESUMEN

Nest building is a vital behavior exhibited during breeding in birds, and is possibly induced by environmental and social cues. Although such behavioral plasticity has been hypothesized to be controlled by adult neuronal plasticity, empirical evidence, especially at the neurogenomic level, remains limited. Here, we aim to uncover the gene regulatory networks that govern avian nest construction and examine whether they are associated with circuit rewiring. We designed an experiment to dissect this complex behavior into components in response to pair bonding and nest material acquisition by manipulating the presence of mates and nest materials in 30 pairs of zebra finches. Whole-transcriptome analysis of 300 samples from five brain regions linked to avian nesting behaviors revealed nesting-associated gene expression enriched with neural rewiring functions, including neurogenesis and neuron projection. The enriched expression was observed in the motor/sensorimotor and social behavior networks of female finches, and in the dopaminergic reward system of males. Female birds exhibited predominant neurotranscriptomic changes to initiate the nesting stage, while males showed major changes after entering this stage, underscoring sex-specific roles in nesting behavior. Notably, major neurotranscriptomic changes occurred during pair bonding, with minor changes during nest material acquisition, emphasizing social interactions in nest construction. We also revealed gene expression associated with reproductive behaviors and tactile sensing for nesting behavior. This study presents novel neurogenomic evidence supporting the hypothesis of adult neural plasticity underlying avian nest-construction behavior. By uncovering the genetic toolkits involved, we offer novel insights into the evolution of animals' innate ability to construct nests.


Asunto(s)
Encéfalo , Pinzones , Redes Reguladoras de Genes , Comportamiento de Nidificación , Animales , Pinzones/genética , Pinzones/fisiología , Encéfalo/metabolismo , Encéfalo/fisiología , Femenino , Masculino , Conducta Social , Transcriptoma
2.
BMC Biol ; 21(1): 57, 2023 03 20.
Artículo en Inglés | MEDLINE | ID: mdl-36941675

RESUMEN

BACKGROUND: Individual organisms may exhibit phenotypic plasticity when they acclimate to different conditions. Such plastic responses may facilitate or constrain the adaptation of their descendant populations to new environments, complicating their evolutionary trajectories beyond the genetic blueprint. Intriguingly, phenotypic plasticity itself can evolve in terms of its direction and magnitude during adaptation. However, we know little about what determines the evolution of phenotypic plasticity, including gene expression plasticity. Recent laboratory-based studies suggest dominance of reversing gene expression plasticity-plastic responses that move the levels of gene expression away from the new optima. Nevertheless, evidence from natural populations is still limited. RESULTS: Here, we studied gene expression plasticity and its evolution in the montane and lowland populations of an elevationally widespread songbird-the Rufous-capped Babbler (Cyanoderma ruficeps)-with reciprocal transplant experiments and transcriptomic analyses; we set common gardens at altitudes close to these populations' native ranges. We confirmed the prevalence of reversing plasticity in genes associated with altitudinal adaptation. Interestingly, we found a positive relationship between magnitude and degree of evolution in gene expression plasticity, which was pertinent to not only adaptation-associated genes but also the whole transcriptomes from multiple tissues. Furthermore, we revealed that genes with weaker expressional interactions with other genes tended to exhibit stronger plasticity and higher degree of plasticity evolution, which explains the positive magnitude-evolution relationship. CONCLUSIONS: Our experimental evidence demonstrates that species may initiate their adaptation to new habitats with genes exhibiting strong expression plasticity. We also highlight the role of expression interdependence among genes in regulating the magnitude and evolution of expression plasticity. This study illuminates how the evolution of phenotypic plasticity in gene expression facilitates the adaptation of species to challenging environments in nature.


Asunto(s)
Aclimatación , Adaptación Fisiológica , Fenotipo , Adaptación Fisiológica/genética , Altitud , Expresión Génica , Evolución Biológica
3.
Mol Ecol ; 32(9): 2234-2251, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-36748940

RESUMEN

Organisms often acquire physiological and morphological modifications to conquer ecological challenges when colonizing new environments which lead to their adaptive evolution. However, deciphering the genomic mechanism of ecological adaptation is difficult because ecological environments are often too complex for straightforward interpretation. Thus, we examined the adaptation of a widespread songbird-the rufous-capped babbler (Cyanoderma ruficeps)-to a relatively simple system: distinct environments across elevational gradients on the mountainous island of Taiwan. We focused on the genomic sequences of 43 birds from five populations to show that the Taiwan group split from its sister group in mainland China around 1-2 million years ago (Ma) and colonized the montane habitats of Taiwan at least twice around 0.03-0.22 Ma. The montane and lowland Taiwan populations diverged with gene flow between them, suggesting strong selection associated with different elevations. We found that the montane babblers had smaller beaks than the lowland ones, consistent with Allen's rule, and identified candidate genes-COL9A1 and SOX11-underlying the beak size changes. We also found that altitudinally divergent mutations were mostly located in noncoding regions and tended to accumulate in chromosomal inversions and autosomes. The altitudinally divergent mutations might regulate genes related to haematopoietic, metabolic, immune, auditory and vision functions, as well as cerebrum morphology and plumage development. The results reveal the genomic bases of morphological and physiological adaptation in this species to the low temperature, hypoxia and high UV light environment at high elevation. These findings improve our understanding of how ecological adaptation drives population divergence from the perspective of genomic architecture.


Asunto(s)
Passeriformes , Pájaros Cantores , Animales , Pájaros Cantores/genética , Adaptación Fisiológica/genética , Genoma/genética , Genómica , Passeriformes/genética
4.
Ecol Lett ; 25(6): 1421-1431, 2022 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-35291055

RESUMEN

Eggs and nests are two critical traits for the ecological success of birds. Their functional interactions, however, remain unclear. Here, we examined the functional connections between egg stiffness and nest attachment, site and structure for 1350 avian species. We revealed high eggshell stiffness for eggs in nests with a pensile attachment, located on non-tree vegetation or having a domed shape, suggesting that birds produce stiffer eggs in response to higher egg-collision risk in unstable or enclosed nests. Interdependence models suggested that the evolution of eggshell stiffness was more likely to be driven by than drive that of nest characters. Our results implied a trade-off between investment in competing for established nesting niches and producing stiff eggs to explore novel niches with high collision risk, possibly mediated by predation or thermoregulation. This study highlights an overlooked connection between nests and eggshells that may have broadened the ecological niches of birds.


Asunto(s)
Cáscara de Huevo , Comportamiento de Nidificación , Animales , Aves/fisiología , Regulación de la Temperatura Corporal , Ecosistema , Cáscara de Huevo/fisiología , Comportamiento de Nidificación/fisiología
5.
Mol Ecol ; 31(3): 752-766, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-34779057

RESUMEN

Domesticated species are valuable models to examine phenotypic evolution, and knowledge on domestication history is critical for understanding the trajectories of evolutionary changes. Sequentially Markov Coalescent models are often used to infer domestication history. However, domestication practices may obscure the signal left by population history, affecting demographic inference. Here we assembled the genomes of a recently domesticated species-the society finch-and its parent species-the white-rumped munia-to examine its domestication history. We applied genomic analyses to two society finch breeds and white-rumped munias to test whether domestication of the former resulted from inbreeding or hybridization. The society finch showed longer and more runs of homozygosity and lower genomic heterozygosity than the white-rumped munia, supporting an inbreeding origin in the former. Blocks of white-rumped munia and other ancestry in society finch genomes showed similar genetic distance between the two taxa, inconsistent with the hybridization origin hypothesis. We then applied two Sequentially Markov Coalescent models-psmc and smc++-to infer the demographic histories of both. Surprisingly, the two models did not reveal a recent population bottleneck, but instead the psmc model showed a specious, dramatic population increase in the society finch. Subsequently, we used simulated genomes based on an array of demographic scenarios to demonstrate that recent inbreeding, not hybridization, caused the distorted psmc population trajectory. Such analyses could have misled our understanding of the domestication process. Our findings stress caution when interpreting the histories of recently domesticated species inferred by psmc, arguing that these histories require multiple analyses to validate.


Asunto(s)
Domesticación , Genoma , Genómica , Endogamia , Densidad de Población
6.
Proc Natl Acad Sci U S A ; 116(6): 2152-2157, 2019 02 05.
Artículo en Inglés | MEDLINE | ID: mdl-30659151

RESUMEN

What kind of genetic variation contributes the most to adaptation is a fundamental question in evolutionary biology. By resequencing genomes of 80 individuals, we inferred the origin of genomic variants associated with a complex adaptive syndrome involving multiple quantitative traits, namely, adaptation between high and low altitudes, in the vinous-throated parrotbill (Sinosuthora webbiana) in Taiwan. By comparing these variants with those in the Asian mainland population, we revealed standing variation in 24 noncoding genomic regions to be the predominant genetic source of adaptation. Parrotbills at both high and low altitudes exhibited signatures of recent selection, suggesting that not only the front but also the trailing edges of postglacial expanding populations could be subjected to environmental stresses. This study verifies and quantifies the importance of standing variation in adaptation in a cohort of genes, illustrating that the evolutionary potential of a population depends significantly on its preexisting genetic diversity. These findings provide important context for understanding adaptation and conservation of species in the Anthropocene.


Asunto(s)
Adaptación Biológica , Evolución Biológica , Variación Genética , Pájaros Cantores/genética , Animales , Ambiente , Genética de Población , Genoma , Genómica/métodos , Polimorfismo de Nucleótido Simple , ARN no Traducido , Selección Genética , Taiwán
7.
Proc Biol Sci ; 288(1948): 20210073, 2021 04 14.
Artículo en Inglés | MEDLINE | ID: mdl-33823666

RESUMEN

Both anthropogenic impacts and historical climate change could contribute to population decline and species extinction, but their relative importance is still unclear. Emerging approaches based on genomic, climatic and anthropogenic data provide a promising analytical framework to address this question. This study applied such an integrative approach to examine potential drivers for the endangerment of the green peafowl (Pavo muticus). Several demographic reconstructions based on population genomes congruently retrieved a drastic population declination since the mid-Holocene. Furthermore, a comparison between historical and modern genomes suggested genetic diversity decrease during the last 50 years. However, climate-based ecological niche models predicted stationary general range during these periods and imply the little impact of climate change. Further analyses suggested that human disturbance intensities were negatively correlated with the green peafowl's effective population sizes and significantly associated with its survival status (extirpation or persistence). Archaeological and historical records corroborate the critical role of humans, leaving the footprint of low genomic diversity and high inbreeding in the survival populations. This study sheds light on the potential deep-time effects of human disturbance on species endangerment and offers a multi-evidential approach in examining underlying forces for population declines.


Asunto(s)
Genoma , Metagenómica , Animales , Cambio Climático , Ecosistema , Extinción Biológica , Humanos
8.
BMC Evol Biol ; 20(1): 147, 2020 11 07.
Artículo en Inglés | MEDLINE | ID: mdl-33160317

RESUMEN

BACKGROUND: Phenotypic convergence between distinct species provides an opportunity to examine the predictability of genetic evolution. Unrelated species sharing genetic underpinnings for phenotypic convergence suggests strong genetic constraints, and thus high predictability of evolution. However, there is no clear big picture of the genomic constraints on convergent evolution. Genome-based phylogenies have confirmed many cases of phenotypic convergence in birds, making them a good system for examining genetic constraints in phenotypic convergence. In this study, we used hierarchical genomic approaches to estimate genetic constraints in three convergent avian traits: nocturnality, raptorial behavior and foot-propelled diving. RESULTS: Phylogeny-based hypothesis tests and positive selection tests were applied to compare 16 avian genomes, representing 14 orders, and identify genes with strong convergence signals. We found 43 adaptively convergent genes (ACGs) associated with the three phenotypic convergence cases and assessed genetic constraints in all three cases, from (amino acid) site mutations to genetic pathways. We found that the avian orders shared few site mutations in the ACGs that contributed to the convergent phenotypes, and that these ACGs were not enriched in any genetic pathways. In addition, different pairs of orders with convergent foot-propelled diving or raptorial behaviors shared few ACGs. We also found that closely related orders that shared foot-propelled diving behavior did not share more ACGs than did distinct orders, suggesting that convergence among these orders could not be explained by their initial genomic backgrounds. CONCLUSIONS: Our analyses of three avian convergence events suggest low constraints for phenotypic convergence across multiple genetic levels, implying that genetic evolution is unpredictable at the phylogenetic level of avian order. Ours is one of first studies to apply hierarchical genomic examination to multiple avian convergent cases to assess the genetic constraints in life history trait evolution.


Asunto(s)
Aves/clasificación , Evolución Molecular , Fenotipo , Filogenia , Animales , Conducta Animal , Genómica , Selección Genética
9.
Mol Phylogenet Evol ; 143: 106671, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31707139

RESUMEN

The geographical context of speciation is important for understanding speciation and community assembly. However, the predominant mode of speciation in the Himalayan-Hengduan Mountains (HHMs), a global biodiversity hotspot, remains unknown. Here, we examined the role of geography in speciation using four pairs of sister or closely related avian species that currently co-occur in the HHMs. While multilocus network analyses based on nine to eleven genes revealed deep splits between these species, several allelic networks based on individual loci suggested phylogenetic paraphyly implying a recent history of divergence. Following extensive sampling in the contact zones of these species pairs, the coalescence-based approximate Bayesian computation approach supported no gene flow during their divergence and was consistent with an allopatric speciation model. We further estimated the divergence times of the four species pairs during the middle and late Pleistocene, which were characterized by increased amplitudes of glacial variability. We found a positive relationship between their divergence times and current sympatry levels, supporting a scenario of secondary contact following allopatric speciation. The Pleistocene glacial-interglacial cycles may have led to the initial geographic population isolation; ecological divergence or mate choice might further accelerate their differentiation during secondary contact, facilitating their speciation and species accumulation in the mountainous landscape. Our findings reveal the critical role of geographic isolation in speciation in the HHMs and shed light on how this biodiversity hotspot aggregates numerous species.


Asunto(s)
Aves/genética , Especiación Genética , Animales , Teorema de Bayes , Biodiversidad , Aves/clasificación , Flujo Génico , Filogenia , Simpatría
10.
Mol Ecol ; 28(4): 772-784, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30580492

RESUMEN

Specialization in narrow ecological niches may not only help species to survive in competitive or unique environments but also contribute to their extermination over evolutionary time. Although the "evolutionary dead end" hypothesis has long been debated, empirical evidence from species with detailed information on niche specialization and evolutionary history remains rare. Here we use a group of four closely related Cnemaspis gecko species that depend highly on granite boulder caves in the Mekong Delta to investigate the potential impact of ecological specialization on their evolution and population dynamics. Isolated by unsuitable floodplain habitats, these boulder-dwelling geckos are among the most narrowly distributed Squamata in the world. We applied several coalescence-based approaches combined with the RAD-seq technique to estimate their divergence times, gene flow and demographic fluctuations during the speciation and population differentiation processes. Our results reveal long-term population shrinkage in the four geckos and limited gene flow during their divergence. The results suggest that the erosion and fragmentation of the granite boulder hills have greatly impacted population divergence and declines. The habitat specialization of these geckos has led to fine-scaled speciation in these granite rocky hills; in contrast, specialization might also have pushed these species toward the edge of extinction. Our study also emphasizes the conservation urgency of these vulnerable, cave-dependent geckos.


Asunto(s)
Lagartos/genética , Animales , Demografía , Ecosistema , Evolución Molecular , Flujo Génico/genética , Especiación Genética , Variación Genética/genética , Lagartos/clasificación , Filogenia , Dinámica Poblacional
11.
Mol Ecol ; 28(4): 803-817, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30565765

RESUMEN

Ecological niche evolution can promote or hinder the differentiation of taxa and determine their distribution. Niche-mediated evolution may differ among climatic regimes, and thus, species that occur across a wide latitudinal range offer a chance to test these heterogeneous evolutionary processes. In this study, we examine (a) how many lineages have evolved across the continent-wide range of the Eurasian nuthatch (Sitta europaea), (b) whether the lineages' niches are significantly divergent or conserved and (c) how their niche evolution explains their geographic distribution. Phylogenetic reconstruction and ecological niche models (ENMs) showed that the Eurasian nuthatch contained six parapatric lineages that diverged within 2 Myr and did not share identical climatic niches. However, the niche discrepancy between these distinct lineages was relatively conserved compared with the environmental differences between their ranges and thus was unlikely to drive lineage divergence. The ENMs of southern lineages tended to cross-predict with their neighbouring lineages whereas those of northern lineages generally matched with their abutting ranges. The coalescence-based analyses revealed more stable populations for the southern lineages than the northern ones during the last glaciation cycle. In contrast to the overlapping ENMs, the smaller parapatric distribution suggests that the southern lineages might have experienced competitive exclusion to prevent them from becoming sympatric. On the other hand, the northern lineages have expanded their ranges and their current abutting distribution might have resulted from lineages adapting to different climatic conditions in allopatry. This study suggests that niche evolution may affect lineage distribution in different ways across latitude.


Asunto(s)
Ecosistema , Modelos Teóricos , Animales , Especiación Genética , Passeriformes , Filogenia
12.
BMC Evol Biol ; 17(1): 244, 2017 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-29212454

RESUMEN

BACKGROUND: The glacial-interglacial cycles in the Pleistocene caused repeated range expansion and contraction of species in several regions in the world. However, it remains uncertain whether such climate oscillations had similar impact on East Asian biota, despite its widely recognized importance in global biodiversity. Here we use both molecular and ecological niche profiles on 11 East Asian avian species with various elevational ranges to reveal their response to the late Pleistocene climate changes. RESULTS: The ecological niche models (ENM) consistently showed that these avian species might substantially contract their ranges to the south during the Last Interglacial period (LIG) and expanded their northern range margins through the Last Glacial Maximum (LGM), leading to the LGM ranges observed for all 11 species. Consistently, coalescent simulations based on 25-30 nuclear genes retrieved signatures of significant population growth through the last glacial period across all species studied. Climate statistics suggested that high climatic variability during the LIG and a relatively mild climate at the LGM potentially explained the historical population dynamics of these birds. CONCLUSIONS: This is the first study based on multiple species and both lines of ecological niche profiles and genetic data to characterize the unique response of East Asian biota to late Pleistocene climate. The present study highlights regional differences in the evolutionary consequence of climate change during the last glacial cycle and implies that global warming might pose a great risk to species in this region given potentially higher climatic variation in the future analogous to that during the LIG.


Asunto(s)
Aves/fisiología , Cambio Climático , Cubierta de Hielo , Animales , Ecosistema , Asia Oriental , Modelos Biológicos , Filogeografía , Dinámica Poblacional , Especificidad de la Especie , Temperatura
13.
Mol Ecol ; 26(14): 3775-3784, 2017 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-28437589

RESUMEN

Organismal traits such as ecological specialization and migratory behaviour may affect colonization potential, population persistence and degree of isolation, factors that determine the composition and genetic structure of communities. However, studies focusing on community assembly rarely consider these factors jointly. We sequenced 16 nuclear genes and one mitochondrial gene from Caucasian and European populations of 30 forest-dwelling avian species that represent diverse ecological (specialist-generalist) and behavioural (migratory-resident) backgrounds. We tested the effects of organismal traits on population divergence and community assembly in the Caucasus forest, a continental mountain island setting. We found that (i) there is no concordance in divergence times between the Caucasus forest bird populations and their European counterparts, (ii) habitat specialists tend to be more divergent than generalists and (iii) residents tend to be more divergent than migrants. Thus, specialists and residents contribute to the high level of endemism of Caucasus forest avifauna more than do generalists and migrants. Patterns of genetic differentiation are better explained by differences in effective population sizes, an often overlooked factor in comparative studies of phylogeography and speciation, than by divergence times or levels of gene flow. Our results suggest that the Caucasus forest avifauna was assembled through time via dispersal and/or multiple vicariant events, rather than originating simultaneously via a single isolation event. Our study is one of the first multilocus, multispecies analyses revealing how ecological and migratory traits impact the evolutionary history of community formation on a continental island.


Asunto(s)
Evolución Biológica , Biota , Aves/clasificación , Migración Animal , Animales , Núcleo Celular/genética , ADN Mitocondrial/genética , Ecología , Bosques , Flujo Génico , Filogeografía , Densidad de Población
14.
Proc Natl Acad Sci U S A ; 111(29): 10636-41, 2014 Jul 22.
Artículo en Inglés | MEDLINE | ID: mdl-24979776

RESUMEN

To assess the role of human disturbances in species' extinction requires an understanding of the species population history before human impact. The passenger pigeon was once the most abundant bird in the world, with a population size estimated at 3-5 billion in the 1800s; its abrupt extinction in 1914 raises the question of how such an abundant bird could have been driven to extinction in mere decades. Although human exploitation is often blamed, the role of natural population dynamics in the passenger pigeon's extinction remains unexplored. Applying high-throughput sequencing technologies to obtain sequences from most of the genome, we calculated that the passenger pigeon's effective population size throughout the last million years was persistently about 1/10,000 of the 1800's estimated number of individuals, a ratio 1,000-times lower than typically found. This result suggests that the passenger pigeon was not always super abundant but experienced dramatic population fluctuations, resembling those of an "outbreak" species. Ecological niche models supported inference of drastic changes in the extent of its breeding range over the last glacial-interglacial cycle. An estimate of acorn-based carrying capacity during the past 21,000 y showed great year-to-year variations. Based on our results, we hypothesize that ecological conditions that dramatically reduced population size under natural conditions could have interacted with human exploitation in causing the passenger pigeon's rapid demise. Our study illustrates that even species as abundant as the passenger pigeon can be vulnerable to human threats if they are subject to dramatic population fluctuations, and provides a new perspective on the greatest human-caused extinction in recorded history.


Asunto(s)
Columbidae/fisiología , Extinción Biológica , Animales , Mapeo Cromosómico , Abastecimiento de Alimentos , Genoma/genética , Geografía , Cadenas de Markov , Densidad de Población , Dinámica Poblacional , Quercus/fisiología , Estados Unidos
15.
Proc Biol Sci ; 283(1826): 20152340, 2016 Mar 16.
Artículo en Inglés | MEDLINE | ID: mdl-26962145

RESUMEN

Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller Ne and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed.


Asunto(s)
ADN/genética , Variación Genética , Filogeografía/métodos , Pájaros Cantores/genética , Animales , Núcleo Celular/genética , ADN Mitocondrial/genética , Europa (Continente) , Intrones , Densidad de Población , Simpatría
16.
G3 (Bethesda) ; 14(6)2024 Jun 05.
Artículo en Inglés | MEDLINE | ID: mdl-38607414

RESUMEN

The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. The discoveries of feathers on the hind limbs of basal birds and dinosaurs have sparked an interest in the evolutionary origin and genetic mechanism of feathered feet. However, the majority of studies investigating the genes associated with this trait focused on domestic populations. Understanding the genetic mechanism underpinned feathered-foot development in wild birds is still in its infancy. Here, we assembled a chromosome-level genome of the Asian house martin (Delichon dasypus) using the long-read High Fidelity sequencing approach to initiate the search for genes associated with its feathered feet. We employed the whole-genome alignment of D. dasypus with other swallow species to identify high-SNP regions and chromosomal inversions in the D. dasypus genome. After filtering out variations unrelated to D. dasypus evolution, we found six genes related to feather development near the high-SNP regions. We also detected three feather development genes in chromosomal inversions between the Asian house martin and the barn swallow genomes. We discussed their association with the wingless/integrated (WNT), bone morphogenetic protein, and fibroblast growth factor pathways and their potential roles in feathered-foot development. Future studies are encouraged to utilize the D. dasypus genome to explore the evolutionary process of the feathered-foot trait in avian species. This endeavor will shed light on the evolutionary path of feathers in birds.


Asunto(s)
Plumas , Genoma , Animales , Polimorfismo de Nucleótido Simple , Cromosomas/genética , Fenotipo , Pie , Inversión Cromosómica , Genómica/métodos
17.
BMC Zool ; 9(1): 12, 2024 Jun 26.
Artículo en Inglés | MEDLINE | ID: mdl-38926885

RESUMEN

The Middle Eastern endemic genus Asaccus comprises Southwest Asian leaf-toed geckos. To date, this genus includes 19 species of leaf-toed geckos (seven in Arabia and 12 in the Zagros Mountains). Despite a recent study on the taxonomy and phylogeny of Asaccus species in Iran, controversies still remain surrounding the phylogeny and phylogeography of the genus. Here, we used an integrative approach to determine the phylogeny and phylogeography of Asaccus species using two mitochondrial genes (12 S and Cyt b), and one nuclear gene (c-mos). Our results uncovered 22 distinct lineages, demonstrating a significant cryptic diversity that challenges the current morphological classifications of these species. Phylogenetic analyses reinforce the monophyly of the Asaccus group, positioning A. montanus as a basal lineage, which supports a deep evolutionary divergence dating back to the Late Oligocene, approximately 27.94 million years ago. This genetic diversity also highlights the impact of historical climatic and geographical changes on species diversification. The findings advocate for an integrative approach combining both molecular and morphological data to resolve species identities accurately, thereby enhancing conservation strategies to protect these genetically distinct lineages.

18.
Mol Phylogenet Evol ; 66(1): 103-11, 2013 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-23022139

RESUMEN

A previously published phylogeographic analysis of mtDNA sequences from the widespread Palearctic common rosefinch (Carpodacus erythrinus) suggested the existence of three recently diverged groups, corresponding to the Caucasus, central-western Eurasia, and northeastern Eurasia. We re-evaluated the mtDNA data using coalescence methods and added sequence data from a sex-linked gene. The mtDNA gene tree and SAMOVA supported the distinctiveness of the Caucasian group but not the other two groups. However, UPGMA clustering of mtDNA Φ(ST)-values among populations recovered the three groups. The sex-linked gene tree recovered no phylogeographic signal, which was attributed to recent divergence and insufficient time for sorting of alleles. Overall, coalescence methods indicated a lack of gene flow among the three groups, and population expansion in the central-western and northeastern Eurasia groups. These three groups corresponded to named subspecies, further supporting their validity. A species distribution model revealed potential refugia at the Last Glacial Maximum. These three groups, which we hypothesized are in the early stages of speciation, provided an opportunity for testing tenets of ecological speciation. We showed that the early stages of speciation were not accompanied by ecological niche divergence, consistent with other avian studies.


Asunto(s)
Evolución Biológica , Pinzones/genética , Filogenia , Animales , Asia , ADN Mitocondrial/genética , Ecosistema , Europa (Continente) , Pinzones/clasificación , Flujo Génico , Genética de Población , Haplotipos , Modelos Biológicos , Filogeografía , Análisis de Secuencia de ADN
19.
Sci Data ; 10(1): 923, 2023 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-38129417

RESUMEN

The reproductive success of birds is closely tied to the characteristics of their nests. It is crucial to understand the distribution of nest traits across phylogenetic and geographic dimensions to gain insight into bird evolution and adaptation. Despite the extensive historical documentation on breeding behavior, a structured dataset describing bird nest characteristics has been lacking. To address this gap, we have compiled a comprehensive dataset that characterizes three ecologically and evolutionarily significant nest traits-site, structure, and attachment-for 9,248 bird species, representing all 36 orders and 241 out of the 244 families. By defining seven sites, seven structures, and four attachment types, we have systematically classified the nests of each species using information from text descriptions, photos, and videos sourced from online databases and literature. This nest traits dataset serves as a valuable addition to the existing body of morphological and ecological trait data for bird species, providing a useful resource for a wide range of avian macroecological and macroevolutionary research.


Asunto(s)
Aves , Comportamiento de Nidificación , Animales , Cruzamiento , Filogenia , Reproducción
20.
Ecol Evol ; 12(8): e9188, 2022 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-35949538

RESUMEN

Species with similar ecological characters often compete with each other; however, a species may also facilitate the survival or reproduction of another ecologically similar species, although such interaction is rarely documented in birds. Here, we reported a facilitative species interaction between Asian house martins (Delichon dasypus) and russet sparrows (Passer cinnamomeus), both passerines using closed nests, in a montane farming area of Taiwan. We found that Asian house martins constructed dome-shaped nests in human houses that provided additional nest sites for russet sparrows, secondary cavity nesters with greatly declining populations in Taiwan. Russet sparrows that used house martin nests had reproductive success comparable to those that used artificial nest boxes. However, Asian house martins avoided reclaiming sparrow-used nests, which reduced their available nest sites. Interestingly, our results imply that man-made structures may be used as a conservation tool to improve the breeding of the endangered russet sparrows via this facilitative interaction.

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