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Phylogenetic tree inferred by ML from the combined data set with a reduced number of outgroups. The identical topology with similar branch lengths resulted from Bayesian analysis of the same data. Numbers above branches indicate bootstrap support counted in minimum evolution analysis under the same model of substitution used in ML analysis (values >50 shown). Numbers under the nodes indicate Bayesian posterior probabilities. Vertical lines beside taxon names correspond to Papilio sections sensu Munroe (1961).  

Phylogenetic tree inferred by ML from the combined data set with a reduced number of outgroups. The identical topology with similar branch lengths resulted from Bayesian analysis of the same data. Numbers above branches indicate bootstrap support counted in minimum evolution analysis under the same model of substitution used in ML analysis (values >50 shown). Numbers under the nodes indicate Bayesian posterior probabilities. Vertical lines beside taxon names correspond to Papilio sections sensu Munroe (1961).  

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Swallowtail butterflies are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. We inferred phylogenetic relationships for 51 of about 205 species of the genus Papilio (sensu lato) from 3.3-Kilobase (kb) sequences of mitochondrial and nuclear DNA (...

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... ML analysis for combined data revealed a sin- gle tree with a negative log-likelihood score (-ln L) of 31023.619 that was identical to the combined MP boot- strap consensus tree (Fig. 2). In the expanded ML tree for combined data that shows all species (Fig. 3), group- ing within the major terminal subclades (corresponding to species groups and subgenera) is usually congruent with the relationships inferred by the MP combined data tree (Fig. 1). However, relationships among many major clades remain weakly ...
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... independent analyses for the combined data set converged on similar log-likelihood scores and reached stationarity before generation 300,000. For the COI-COII data, the initial 3,000 trees from each analysis were dis- carded. A consensus tree was constructed from the com- bined set of 21,000 trees (Fig. 3). The branching pattern of the tree is completely identical to that of the MP bootstrap consensus and ML trees from combined analyses. The average posterior probability for the inferred phylogeny was 0.97. Thirty-eight ingroup nodes (of 53) had poste- rior probabilities of 1.0, and 46 nodes were supported with significance level >0.9. ...

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... The family is distributed worldwide and currently includes 32 genera, seven tribes, and three subfamilies (Häuser et al., 2005;Van Nieukerken et al., 2011b). As the largest subfamily, Papilioninae includes about 490 species worldwide, but with the greatest diversity found in the tropics (Wallace, 1865;Zakharov et al., 2004). The subfamily Parnassiinae includes 80 species, which are mainly distributed in the Palearctic region (Nazari et al., 2007). ...
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Swallowtail butterflies (Papilionidae) are a historically significant butterfly group due to their colorful wing patterns, extensive morphological diversity, and phylogenetically important position as a sister group to all other butterflies and have been widely studied regarding ecological adaption, phylogeny, genetics, and evolution. Notably, they contain a unique class of pigments, i.e., papiliochromes, which contribute to their color diversity and various biological functions such as predator avoidance and mate preference. To date, however, the genomic and genetic basis of their color diversity and papiliochrome origin in a phylogenetic and evolutionary context remain largely unknown. Here, we obtained high-quality reference genomes of 11 swallowtail butterfly species covering all tribes of Papilioninae and Parnassiinae using long-read sequencing technology. Combined with previously published butterfly genomes, we obtained robust phylogenetic relationships among tribes, overcoming the challenges of incomplete lineage sorting (ILS) and gene flow. Comprehensive genomic analyses indicated that the evolution of Papilionidae-specific conserved non-exonic elements (PSCNEs) and transcription factor binding sites (TFBSs) of patterning and transporter/cofactor genes, together with the rapid evolution of transporters/cofactors, likely promoted the origin and evolution of papiliochromes. These findings not only provide novel insights into the genomic basis of color diversity, especially papiliochrome origin in swallowtail butterflies, but also provide important data resources for exploring the evolution, ecology, and conservation of butterflies.
... Por su parte, las mariposas de la familia Papilionidae, con unas 560 especies descritas en todo el mundo, de las cuales 129 se distribuyen desde Texas hasta Argentina, incluyendo las islas de Cuba, Jamaica, Haití y Puerto Rico (Rothschild y Jordan, 1906;Tyler et al., 1994;Paim y Di Mare, 2002; Graça y Nunes-Gutjahr, 2014), son de las Lepidoptera más conocidas y estudiadas (Gaston, 1991;Zakharov et al., 2004;Kawahara y Breinholt, 2014). Sin embargo, a pesar de los importantes esfuerzos de investigación, la familia todavía presenta muchas dificultades taxonómicas y muchos aspectos ecológicos y biológicos por descifrar, especialmente la interacción con sus enemigos naturales. ...
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... Two species, P. garcia and P. alexiares, are found in Mexico and western parts of Texas and are closely related to the eastern group (Hagen and Scriber, 1991;Kunte et al., 2011;Sperling, 1993). Relationships within the species group have been explored using interspecific hybridization data (Ae, 1979), allozymes (Hagen and Scriber, 1991), mitochondrial DNA restriction sites (Sperling, 1993), mitochondrial and nuclear gene sequences (Wu et al., 2015;Zakharov et al., 2004), amplified fragment length polymorphisms (Kunte et al., 2011), and whole genome sequence data, albeit for a limited number of specimens (Allio et al., 2021;Zhang et al., 2019). Despite the presence of mito-nuclear discordance in the western species (Sperling, 1993), relationships within the group are relatively stable. ...
... Considerably older ages (Early to Late Miocene for the P. glaucus group origin) were obtained in analysis using penalized maximum likelihood molecular dating implemented in the program r8s (Zakharov et al., 2004). In contrast, estimation of divergence dates within the (P. ...
... We found that phylogenetic relationships within the P. glaucus group were consistent with previous studies (Allio et al., 2021;Condamine et al., 2013;Condamine et al., 2012;Kunte et al., 2011;Wu et al., 2015;Zakharov et al., 2004;Zhang et al., 2019) and recovered similar mitonuclear discordance within the P. glaucus/P. canadensis and P. rutulus/ P. eurymedon species pairs (Kunte et al., 2011;Sperling, 1993). ...
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... 1-3). Both tribe-and genus-level relationships are mostly consistent with previous results using multilocus datasets 18,34,[42][43][44][45][46] . However, our species tree benefits from a phylogenomic backbone that we recently inferred at the genus level for the Papilionidae using genome scale data 47 . ...
Thesis
The phenomenon of evolutionary convergence is a fascinating process in which distantly related species independently acquire similar characteristics in response to similar selective pressures. Ant- and termite-eating mammals are among the most famous examples of morphological convergence. Indeed, this particular lifestyle evolved in five distinct lineages of mammals: the aardvark (Tubulidentata), the aardwolf (Carnivora), the anteaters (Pilosa), the giant armadillo (Cingulata), and the pangolins (Pholidota). To better undestand the evolution of these organisms, several approaches were developed in this thesis. First, I present an original strategy to characterize the precise diet of myrmecophagous mammals taking advantage of metagenomic sequencing data generated from fecal samples and a reference mitogenomic database of termites and ants. Second, with the final objective of detecting molecular convergence at the genomic scale in ant-eating mammals, we generated nine high quality mammlian genomes using Oxford Nanopore technologies. The different strategies developed from the set-up of MinION qesuencing to annotation of the resulting assemblies are presented together with a first case study illustrating the use of two of these new reference genomes for species delineation. Finally, I present comparative transcriptomic analyses of salivary glands and other organs in ant-eating mammals suggesting that historical contingency and molecular evolutionary tinkering of chitinase genes played a major role in the convergent evolution of myrmecophagy.
... 1-3). Both tribe-and genus-level relationships are mostly consistent with previous results using multilocus datasets 18,34,35,[42][43][44][45] . However, our species tree benefits from a phylogenomic backbone that we recently inferred at the genus level for the Papilionidae using genome-scale data 46 . ...
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... may be monomorphic or polymorphic (Kunte, 2009a;Zakharov, Caterino, & Sperling, 2004). Some butterfly species of the family Papilionidae display sex-limited polymorphic Batesian mimicry in which only a portion of females mimic heterospecific model butterflies whereas the rest are nonmimetic and uniform in appearance throughout their range; in these species, males are always nonmimetic (Clarke & Sheppard, 1972;Kunte, 2009b). ...
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Batesian mimicry, in which harmless organisms resemble unpalatable or harmful species, is a well‐studied adaptation for predation avoidance. The females of some Batesian mimic species comprise mimetic and nonmimetic individuals. Mimetic females of such polymorphic species clearly have a selective advantage due to decreased predation pressure, but the selective forces that maintain nonmimetic females in a population remain unclear. In the swallowtail butterfly, Papilio polytes, female polymorphism is controlled by the H (mimetic) and h (nonmimetic) alleles at a single autosomal locus. Here, we examined whether the dominant H allele has a deleterious effect on the pre‐adult survival rate (egg‐to‐adult emergence rate). We repeated an assortative mating‐like treatment—that is breeding of males and females whose mothers had the same phenotype (mimetic or nonmimetic)—for three consecutive generations, while avoiding inbreeding. Results showed that pre‐adult survival rate decreased over generations only in lines derived from mothers with the mimetic phenotype (hereafter, mimetic‐assorted lines). This lowered survival was due to an increased mortality at the final instar larval stage and the pupal stages. Interestingly, the pre‐adult mortality in the mimetic‐assorted lines seemed to be associated with a male‐biased sex ratio at adult emergence. These results suggest that the dominant H allele displays a mildly deleterious effect that is expressed more strongly in females and homozygous individuals than in heterozygous individuals. We propose that this cost of mimicry in larval and pupal stages contributes to the maintenance of female‐limited polymorphism in P. polytes.
... We then mapped that node onto available phylogenies to estimate timing, drawing from 15 different studies. Existing time-calibrated phylogenies allowed quantification of most host shifts within Pieridae (Wheat et al. 2007;Cao et al. 2016;Woronik 2017;Espeland et al. 2018), Nymphalidae (Kodandaramaiah and Wahlberg 2007;Wahlberg et al. 2009;Simonsen et al. 2010;Mullen et al. 2011;de Moya 2016;Su et al. 2017;Espeland et al. 2018), and Papilionidae (Zakharov et al. 2004;Michel et al. 2008;Condamine et al. 2018). The timing of host shifts in Lycaenidae was quantifiable in "millions of years" for over half of the species in the study (Pratt et al. 2011;Stekolnikov et al. 2013;Espeland et al. 2018). ...
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... The second new finding was that P. hospiton was sister to the remainder of the species group (excluding P. indra). Previous phylogenies based on mtDNA alone (Dupuis and Sperling, 2015) or mtDNA and a single nuclear gene (Condamine et al., 2012;Zakharov et al., 2004) had placed P. hospiton as sister only to P. machaon. Hybridization between P. hospiton and P. machaon has been documented, although contemporary gene flow seems low (Aubert et al., 1997;Cianchi et al., 2003), but all analyses here support its genomic distinctness from P. machaon. ...
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Genomics has revolutionized our understanding of hybridization and introgression, but most of the early evidence for these processes came from studies of mitochondrial introgression. To expand these evolutionary insights from mitochondrial patterns, we evaluate phylogenetic discordance across the nuclear genomes of a hybridizing system, the Papilio machaon group of swallowtail butterflies. This species group contains three hybrid lineages (P. brevicauda, P. joanae, and P. m. kahli) that are geographically disjunct across North America and have complete fixation of a mitochondrial lineage that is otherwise primarily found in P. m. hudsonianus, a boreal subspecies of the Holarctic P. machaon. Genome-wide nuclear markers place the three hybrid lineages as a monophyletic group that is sister to P. polyxenes/P. zelicaon rather than P. machaon, although ancient hybridization between a subspecies of P. machaon and the ancestor of these three lineages is also shown by their greater nuclear affinity to P. m. hudsonianus than to other subspecies of P. machaon. Individuals from contemporary hybrid swarms in Alberta, where mitochondrial DNA fixation has not occurred, were more intermediate between their respective parent species, demonstrating diversity in mito-nuclear discordance following hybrid interactions. Our new phylogenetic findings for the P. machaon species group also include: subspecific paraphyly within P. machaon itself across its Holarctic distribution; paraphyly of P. zelicaon relative to P. polyxenes; and more divergent placement of a Mediterranean species, P. hospiton. These results provide the first comprehensive genomic evaluation of relationships within this species group and provide insight into the evolutionary dynamics of hybridization and mitochondrial introgression.