Figure - available via license: Creative Commons Attribution 2.0 Generic
Content may be subject to copyright.
Phylogeny of Charadriiformes. Optimal maximum likelihood phylogenetic reconstruction of Charadriiformes and selected outgroups based on combined data of ADH5, GPD3-5, FGB7, 12S rDNA, 16S rDNA, and tRNA Valine using GTR + G. Both mixed model Bayesian analysis and maximum parsimony produce trees of identical topology. Bootstrap values obtained from 500 ML pseudoreplicates are indicated above branches or positioned by arrows. Asterisks indicate bootstrap values of 100%. Charadriiformes are indicated by bold font and subordinal epithets.
Source publication
The phylogeny of shorebirds (Aves: Charadriiformes) and their putative sister groups was reconstructed using approximately 5 kilobases of data from three nuclear loci and two mitochondrial genes, and compared to that based on two other nuclear loci.
Charadriiformes represent a monophyletic group that consists of three monophyletic suborders Lari (i...
Citations
... The Eurasian Woodcock (Scolopax rusticola L.) is a monotypic species [1,2] classified within the highly diverse order of Charadriiformes in the family Scolopacidae, genus Scolopax [3][4][5][6][7][8]. Its global distribution is in the Palaearctic faunal range [9], with breeding ranges from Norway, the British Isles, western France to northern Spain, and from the Azores, Canary Islands and Madeira eastwards to East Asia. ...
In the present study, 7344 spring observations of a short-distance migratory species, the Eurasian Woodcock, from the Carpathian Basin between 1894 and 1926 were used to investigate the timing of the species’ migration and how different environmental factors influenced it. We used a generalized additive model (GAM) to explore migratory patterns by using environmental and geographical variables. In years when the weather was colder and snowier, the birds migrated weeks later than in years with milder weather. This may be due to the availability of earthworms, which are the most important food for the species. In areas at lower altitudes, migration occurred earlier than in mountainous areas, which may also be due to the different weather. Furthermore, a two week difference was observed between the south-western and north-eastern parts of the Carpathian Basin. This difference is still present nowadays, but the timing of migration has shifted earlier than in the past, probably due to climate change. It would also be important to compare the historical data with recent data to gain a better understanding of the effects of climate change on the migration of the Eurasian Woodcock.
... The phylogenetic relationships within Charadriiformes based on morphological characteristics and biochemical methods show distinct differences [3,4]. Molecular studies have classified Charadriiformes into the three monophyletic suborders Scolopaci, Lari, and Charadrii [5,6]. The family Scolopacidae, which includes a diverse array of bird species with about 97 species in 15 genera [7], is known for its strong migratory capabilities. ...
Citation: Li, Q.; Jiang, P.; Li, M.; Du, J.; Sun, J.; Chen, N.; Wu, Y.; Chang, Q.; Hu, C. Structure and Phylogenetic Relationships of Scolopacidae Mitogenomes (Charadriiformes: Scolopacidae). Curr. Issues Mol. Biol. 2024, 46, 6186-6198. https://doi. Abstract: The family Scolopacidae presents a valuable subject for evolutionary research; however, molecular studies of Scolopacidae are still relatively understudied, and the phylogenetic relationships of certain species remain unclear. In this study, we sequenced and obtained complete mitochondrial DNA (mtDNA) from Actitis hypoleucos and partial mtDNA from Numenius arquata, Limosa limosa, and Limnodromus semipalmatus. The complete mtDNA contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 tRNA genes, and a control region. Scolopacidae contained three types of start codons and five types of stop codons (including one incomplete stop codon, TIn In 13 protein-coding genes, average uncorrected pairwise distances (Aupd) revealed that ATP8 was the least conserved while COX3 had the lowest evolutionary rate. The ratio of Ka/Ks suggested that all PCGs were under purifying selection. Using two methods (maximum likelihood and Bayesian inference) to analyze the phylogenetic relationships of the family Scolopacidae, it was found that the genera Xenus and Actitis were clustered into another sister group, while the genus Phalaropus is more closely related to the genus Tringa. The genera Limnodromus, Gallinago, and Scolopax form a monophyletic group. This study improves our understanding of the evolutionary patterns and phylogenetic relationships of the family Scolopacidae.
... The birds Charadriiformes are a diverse order that can be taxonomically divided into three main clades, Lari (buttonquails, allies, and their auks, along with gulls) is a sister group to Scolopaci (allies, jacanas, and sandpipers) whilst Charadrii (plovers, oystercatchers and allies) is placed at the base [1][2][3][4]. The variation in morphological traits, behavioral ecology, and ecological relationships makes Charadriiformes a popular subject to study [5][6][7]. ...
Background
The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy.
Method
In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of nonsynonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection.
Result
Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family.
Conclusion
This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.
... Three suborders are present in Charadriiformes, (Björklund, 1994;Pereira & Baker, 2010), and Charadriidae is included in Charadrii. Charadriiformes is an effective clade for phylogenetic research because it shows not only various specifications but also distinctive traits in evolutionary history (Fain & Houde, 2007;Sibley et al., 1988). Additionally, Charadriiformes is useful for modeling, which is ideal for investigating the macroevolution of waterbirds (Thomas et al., 2004a). ...
... Phylogenetic studies support three major clades: Lari (gulls, auks, and allies plus buttonquails), Scolopaci (sandpipers, jacanas, and allies), and Charadrii (plovers, oystercatchers, and allies) [2]. This order is a monophiletic clade where the genus Vanellus from clade Charadrii is more basal than the genera Tringa and Jacana from clade Scolopaci [3]. Considering the great diversity in the number of species, shorebirds are an excellent model group to investigate several biological questions, such as morphology, ecological diversification, and phylogenetic relationships [4]. ...
Microchromosomes, once considered unimportant elements of the genome, represent fundamental building blocks of bird karyotypes. Shorebirds (Charadriiformes) comprise a wide variety of approximately 390 species and are considered a valuable model group for biological studies. Despite this variety, cytogenetic analysis is still very scarce in this bird order. Thus, the aim of this study was to provide insight into the Charadriiformes karyotype, with emphasis on microchromosome evolution in three species of shorebirds—Calidris canutus, Jacana jacana, and Vanellus chilensis—combining classical and molecular approaches. Cross-species FISH mapping applied two BAC probes for each microchromosome, GGA10–28 (except GGA16). The experiments revealed different patterns of microchromosome organization in the species investigated. Hence, while in C. canutus, we found two microchromosomes involved in chromosome fusions, they were present as single pairs in V. chilensis. We also described a new chromosome number for C. canutus (2n = 92). Hence, this study contributed to the understanding of genome organization and evolution of three shorebird species.
... The ibisbill (Ibidorhyncha struthersii) has been recovered as the sister group to the Recurvirostridae in morphological (Chu, 1995;Livezey, 2010) and supertree (Thomas et al., 2004) studies, while molecular analyses have allied it with the Haematopodidae (Baker et al., 2007;Chen et al., 2018) or a (Haematopodidae + Recurvirostridae) clade (Burleigh et al., 2015). The monotypic crab plover (Dromas ardeola) was not represented in the early molecular phylogenetic studies on charadriiforms (Paton et al., 2003;Paton and Baker, 2006;Baker et al., 2007;Fain and Houde, 2007), and larger phylogenomic studies that did include it failed to sample shorebirds densely enough to unambiguously resolve its position within the order (Hackett et al., 2008;Reddy et al., 2017). Recent molecular evidence indicates a sister-group relationship of Dromas to the coursers and pratincoles (Glareolidae), albeit with varying degrees of support (Pereira and Baker, 2010;Burleigh et al., 2015;De Pietri et al., 2020; see also the supertree of Kimball et al. (2019)). ...
... Recent molecular evidence indicates a sister-group relationship of Dromas to the coursers and pratincoles (Glareolidae), albeit with varying degrees of support (Pereira and Baker, 2010;Burleigh et al., 2015;De Pietri et al., 2020; see also the supertree of Kimball et al. (2019)). Finally, the monophyly of lapwings and plovers (Charadriidae) has been contested, with multiple studies finding the gray and golden plovers (genus Pluvialis) to be more closely related to the Haematopodoidea than to the rest of the family (Baker et al., 2007;Fain and Houde, 2007;Burleigh et al., 2015;Chen et al., 2018), or to fall outside of the clade formed by the Haematopodoidea and other plovers (Ericson et al., 2003). This contradicts the traditional morphological hypothesis of charadriid monophyly (Chu, 1995;Livezey, 2010) as well as the nuclear sequence analysis of Baker et al. (2012), who attributed the earlier molecular results to stochastic gene tree estimation error stemming primarily from the use of fast-evolving mitochondrial loci. ...
... Such sequences were not excluded unless they exhibited other problems. In addition, we further monitored for gene tree misrooting, which has been shown to negatively impact phylogenomic studies (Simmons et al., 2022), following the unanimous consensus among molecular analyses that the correct root lies between a monophyletic Charadrii and all other shorebirds (Ericson et al., 2003;Baker et al., 2007;Fain and Houde, 2007;Hackett et al., 2008;Prum et al., 2015;Kuhl et al., 2020). Rooting errors were often successfully addressed by the removal of the outgroup, whose relatively short branch in the nuclear gene trees frequently caused the root to fall inside the ingroup (cf. ...
Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.
... Introduction Charadriiformes represent one of the largest orders of birds, with 19 families and 383 species. This order is divided into three large monophyletic suborders: Charadrii (plovers), Scolopaci (snipes, partridges) and Lari (seagulls, terns and mandrels) [1]. Members of this order are quite diverse in morphology, behavior and reproduction, which make them an excellent model for studying evolution in different groups [2]. ...
... Molecular data analyses suggest that these three suborders arose in the late Cretaceous and that at least 14 modern Charadriiformes lineages have survived the late Cretaceous mass extinction [3]. Molecular data reveal that Lari and Scolopaci are sister branches and Charadrii is in a more basal position [1]. ...
... As Charadriiformes is an order where the phylogenetic relationships of a major higher-level clade have been successfully resolved [1], comparative chromosome painting analysis of the three suborders using BOE painting probes could shed new light on phylogenetic relationships and define karyotype evolution in the order. Our hypothesis is that this approach will allow us to find chromosome signatures specific for each suborder. ...
Charadriiformes represent one of the largest orders of birds; members of this order are diverse in morphology, behavior and reproduction, making them an excellent model for studying evolution. It is accepted that the avian putative ancestral karyotype, with 2n = 80, remains conserved for about 100 million years. So far, only a few species of Charadriiformes have been studied using molecular cytogenetics. Here, we performed chromosome painting on metphase chromosomes of two species of Charadriidae, Charadrius collaris and Vanellus chilensis, with whole chromosome paint probes from Burhinus oedicnemus. Charadrius collaris has a diploid number of 76, with both sex chromosomes being submetacentric. In V. chilensi a diploid number of 78 was identified, and the Z chromosome is submetacentric. Chromosome painting suggests that chromosome conservation is a characteristic common to the family Charadriidae. The results allowed a comparative analysis between the three suborders of Charadriiformes and the order Gruiformes using chromosome rearrangements to understand phylogenetic relationships between species and karyotypic evolution. However, the comparative analysis between the Charadriiformes suborders so far has not revealed any shared rearrangements, indicating that each suborder follows an independent evolutionary path, as previously proposed. Likewise, although the orders Charadriiformes and Gruiformes are placed on sister branches, they do not share any signature chromosomal rearrangements.
... The suborder Scolopaci appeared 70 million years ago and is formed by five families: Jacanidae, Rostratulidae, Thinocoridae, Pedionomidae and Scolopacidae; the latter is the most specious, with about 100 species [2]. Phylogenetically, this suborder is divided into two major branches: one leads to Scolopacidae, and one leads to the other families [2][3][4]. ...
... The rearrangements described here are restricted to suborder Scolopaci, since chromosomal painting in Larus argentatus [20], a species of suborder Lari (a sister group of Scolopaci) [1,4], revealed a karyotype similar to the ancestral birds in pairs PAK1-4, with fusions Fig. 2 Actitis macularius karyotype with genomic mapping performed using Burhinus oedicnemus (BOE) whole-chromosome probes, with the correspondence shown on the right. The microchromosomes were organized by size, as the correct homologies could not be detected due to the lack of reliable markers of microchromosomes with macrochromosomes (LAR4 and 7-9) and none of the fissions observed in Scolopaci ( Table 2). ...
Background
The Scolopacidae family (Suborder Scolopaci, Charadriiformes) is composed of sandpipers and snipes; these birds are long-distance migrants that show great diversity in their behavior and habitat use. Cytogenetic studies in the Scolopacidae family show the highest diploid numbers for order Charadriiformes. This work analyzes for the first time the karyotype of Actitis macularius by classic cytogenetics and chromosome painting.
Results
The species has a diploid number of 92, composed mostly of telocentric pairs. This high 2n is greater than the proposed 80 for the avian ancestral putative karyotype (a common feature among Scolopaci), suggesting that fission rearrangements have formed smaller macrochromosomes and microchromosomes. Fluorescence in situ hybridization using Burhinus oedicnemus whole chromosome probes confirmed the fissions in pairs 1, 2, 3, 4 and 6 of macrochromosomes.
Conclusion
Comparative analysis with other species of Charadriiformes studied by chromosome painting together with the molecular phylogenies for the order allowed us to raise hypotheses about the chromosomal evolution in suborder Scolopaci. From this, we can establish a clear idea of how chromosomal evolution occurred in this suborder.
... Owing to the convergent plumage evolution, the taxonomic approach often flunks to resolve the phylogenetic relationship of Charadriiformes birds . Later on, the genetic analyses evidenced that, the order Charadriiformes can be classified into three major clades (Paton and Baker 2006;Fain and Houde 2007;Livezey 2010). However, the evolutionary relationship of this group is still perplexing while examining in-depth phylogenetic analysis. ...
The complete mitogenome sequence of the brown-headed gull, Chroicocephalus brunnicephalus was determined in this study. The 16,771 bp genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, and a control region (CR). The decoded mitogenome was AT-rich (54.77%) with nine overlapping and 17 intergenic spacer regions. Most of the PCGs were started by a typical ATG initiation codon except for cox1 and nad3. Further, the usual termination codons (AGG, TAG, TAA, and AGA) were used by 11 PCGs except for cox3 and nad4. The concatenated PCGs based Bayesian phylogeny clearly discriminates all the Laridae species and reflects the sister relationship of C. brunnicephalus with C. ridibundus. The present mitogenome-based phylogeny was congruent with the earlier hypothesis and confirmed the evolutionary position of the brown-headed gull as masked species. The generated mitogenome of C. brunnicephalus is almost identical to the previously generated mitogenome from China except for two base pairs in CR. To visualize the population structure of this migratory species, we propose more sampling from different geographical locations and the generation of additional molecular data to clarify the reality.
... The rearrangements described here are restricted to suborder Scolopaci, since chromosomal painting in Larus argentatus [20], a species of suborder Lari (a sister group of Scolopaci) [1,4], revealed a karyotype similar to the ancestral birds in pairs PAK1-4, with fusions of microchromosomes with macrochromosomes (LAR4 and 7-9) and none of the ssions observed in Scolopaci ( Table 2). ...
Background: The Scolopacidae family (Suborder Scolopaci, Charadriiformes) is composed of sandpipers and snipes; these birds are long-distance migrants that show great diversity in their behavior and habitat use. Cytogenetic studies in the Scolopacidae family show the highest diploid numbers for order Charadriiformes. This work analyzes for the first time the karyotype of Actitis macularius by classic cytogenetics and chromosome painting.
Results: The species has a diploid number of 92, composed mostly of telocentric pairs. This high 2n is greater than the proposed 80 for the avian ancestral putative karyotype (a common feature among Scolopaci), suggesting that fission rearrangements have formed smaller macrochromosomes and microchromosomes. Fluorescence In Situ Hybridization using Burhinus oedicnemus whole chromosome probes confirmed the fissions in pairs 1, 2, 3, 4 and 6 of macrochromosomes.
Conclusion: Comparative analysis with other species of Charadriiformes studied by chromosome painting together with the molecular phylogenies for the order allowed us to raise hypotheses about the chromosomal evolution in suborder Scolopaci. From this, we can establish a clear idea of how chromosomal evolution occurred in this suborder.
