The avifauna of Chile comprises more than 500 species, which inhabit different environments across the continental territory (17°S to 56°S), including the Antarctic peninsula and the oceanic islands (Couve et al. 2016). Research about this group has involved different issues, although most studies have focused on morphological, ecological, reproductive, distribution and diet analyses. An example are raptor birds, a group comprising 26 species according to Marín (2004), that has been the subject of around 160 studies between 1970 and 2010, focusing on the aforementioned aspects (Raimilla et al. 2012).

However, molecular genetic studies, a well-recognized approach that can also contribute to resolving various problems, have received little attention. The taxonomic status of subspecies reported in these raptor birds (e.g., Geranoaetus polyosoma exsul and Accipiter bicolor chilensis), or the level of divergence among closely related species of caracara of the genus Phalcoboenus D’Orbigny, 1834 (Raimilla et al. 2012) are included in such problematic issues.

Taxonomic problems identified in raptor birds are also common to other Chilean birds. In fact, Jaramillo (2005) listed 80 issues of this nature affecting Chilean birds, which are recommended for further study to clarify their taxonomic status. Thus, data on genetic differentiation within and between species and the phylogenetic relations of closely related and cryptic species may provide key evidence to evaluate current taxonomic status, contrasted with molecular data.

Despite the limited genetic studies based on molecular genetic markers performed to date on Chilean birds, they have revealed their usefulness in assessing taxonomic problems, suggesting more efforts that should be carried out to contribute further data. In addition, these studies have also provided valuable information to elucidate the effect of different factors, such as geographic isolation and geological events that have driven the evolutionary history of these birds. These phenomena have resulted in a particular pattern of biodiversity, represented by depleted species richness and a high level of endemism (Kelt et al. 2016), along with scarce morphological divergence (Vuilleumier 1991).

Thus, to address the progress of molecular genetic studies in Chilean birds, we briefly comment on some representative studies that reveal how they contribute significantly to progress on these issues, based on the analysis of the more active research categories that include population structure, phylogeography, systematics and taxonomy and genetic diversity. In addition, analyses of genetic divergence and phylogeny of cryptic Patagonian birds were conducted to explore the level of interspecific divergence present in these birds and the usefulness of molecular genetic markers to unequivocally identify the species.

The search allowed us to recover 31 articles on this subject over the period between 1998 and 2018 (Table 1). These studies were carried out by national or foreign researchers, or through the collaboration of both, and included at least one species of bird distributed in Chile. Most studies involved the analysis of only one species (15 articles, 48.4%), although there were reports that analyzed a large number of species, either 2–10 species (15 articles, 48.4%) or 24 species (1 article, 3.2%). In total, articles involved the analysis of 110 species, with penguins being the most studied group (10 species) followed by New World swallows (9 species) and the genera Phrygilus (6 species), Chloephaga (6 species) and Anairetes (6 species). It should be noted that the interest of different researcher teams in studying penguin species is reflected in 9 articles which only targeted this group. With regard to the molecular genetic markers reported in the articles, most studies used different types of mitochondrial and/or nuclear markers, such as HVRI, COI, D-loop, ND2, Cyt b, ATPase 6/8 and 12S markers for the former and ODC, AK1, ACOI9, Fib5, α- and β-globin genes, βfibint7, ENO1, ODC1, MB, CHD1Z, ISSR and microsatellite loci markers for the latter. However, among these markers the mitochondrial COI and/or D-loop have been by far the most widely-used markers (11 articles), followed by microsatellite loci markers (8 articles). Of note is that three articles also report the use of complete mitochondrial genomes; in two of these the genomes data were used either to construct phylogenies (Cerasale et al. 2012) or to describe interspecific genetic variation (Ramos et al. 2018). In addition, the articles classified into research categories according to the criteria of Torres-Florez et al. (2018) showed that most papers involved the study of population structure and phylogeography or both (8 articles), and systematics and taxonomy (8 articles). On the other hand, a less represented research field in the papers analyzed corresponded to genetic diversity (3 articles), parentage and kinship related to the analysis of hybridization among species (2 articles), cytogenetics (2 articles), DNA markers (2 articles) and landscapes genetics (1). It should be noted that, thanks to the currently available high-throughput technology for sequencing complete genomes, two articles used complete mitochondrial genome data to assess genetic diversity among species and to identify signatures of selection in New World swallows (Cerasale et al. 2012) and penguins (Ramos et al. 2018).

In this respect, Masello et al. (2011) represent an interesting study on the population structure and phylogeography of a characteristic bird from north-central Chile. In this report, using the cytochrome c oxidase subunit I gene sequence (COI), they provided an insight into the phylogeography of the burrowing parrot, Cyanoliseus patagonus (Vieillot, 1818), a species comprising different subspecies that inhabit the arid to semi-arid landscapes of Chile and Argentina. By analyzing samples obtained across this distribution range, Masello et al. (2011) found a strong population structure in C. patagonus that was composed of four clusters. One of the four clusters corresponded exactly to the bloxami phenotype that is found exclusively on the Chilean side of the species range, while within Argentina, one cluster corresponded mainly to the Andinus phenotype (northern morph), and two clusters belonged to the patagonus phenotype (southern morph). In addition, no support for a specific cluster for the conlara phenotype was found, a morph present in an intermediate location in Argentina (e.g. San Luis region), whose origin could be hybrid between Andinus and patagonus phenotypes, as was indicated by the phylogenetic and networks analyses. This analysis also revealed a Chilean origin for this species, with a single migration occurring across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean lineages. Thus, the Andes have constituted an important geographic barrier to dispersal of this species across southern South America, which has affected the way in which populations have diverged, and, therefore, driving their genetic structure.

Another interesting study that addressed the issue of the population structure and phylogeography of Chilean birds is the report of Alvares-Varas et al. (2015). In this study, by using the COI genetic marker, they found great intrageneric divergence in closely related species of Phrygilus CABANIS, 1844, a complex of six species distributed mainly in central and northern Chile. This divergence pattern appears to be related to the marked phylogeographic structure of these species, since it was associated with the broad altitudinal and latitudinal distribution of these species across the Andean mountains. For instance, some species of this group, such as P. alaudinus (Kittlitz, 1833), P. atriceps (D’Orbigny & Lafresnaye, 1837), and P. unicolor (D’Orbigny & Lafresnaye, 1837), showed genetic differentiation mediated by allopatric mechanisms in response to specific geographic barriers, which reveals that allopatric events acted as a major factor in the population differentiation of Phrygilus species. In addition, this study showed no relationship between geographic range size and genetic structure in Phrygilus species. For example, P. unicolor, P. alaudinus and P. gayi, which have broad geographic distributions, showed a pattern of genetic variation similar to P. atriceps (Gervais, 1834), the species with the most restricted geographic distribution. This result contrasts with data published for other passerine birds widely distributed in America (e.g., Chaves and Smith 2011), and suggested, as was found in other widespread species of South America, such as the aquatic songbird Chrysomus icterocephalus (Linnaeus, 1766) (Cadena et al. 2011), that the non-detectable genetic structure across the distribution range, may be associated with ecological features related to the high dispersal capacity of Phrygilus species, a condition that facilitates gene flow between populations. Another issue addressed by Alvares-Varas et al. (2015) was the congruence in the intraspecific taxonomy of Phrygilus genus, based on the comparison of morphological and molecular data, since the Phrygilus species possess great morphological variation across its distribution ranges, revealed by variations in plumage color pattern, body size and shape and size of beak (Couve et al. 2016). Thus, various subspecies have been described for each species, particularly, six subspecies for P. alaudinus and P. unicolor, three for P. fruticeti (Kittlitz, 1833) and P. gayi and two subspecies for P. plebejus (Tschudi, 1844) (Clements et al. 2016). This analysis showed a high congruence in the intraspecific taxonomy of this genus considering only Chilean localities, i.e., the lack of morphological differentiation observed among populations with multivariate analysis was in accordance with molecular data in most species, since no intraspecific genetic divergence was observed. This result contrasts with findings reported in other bird species, where incongruence in the delimitation of subspecies by means of morphological features and molecular data usually occurs (e.g., Cheviron et al. 2005; Weir et al. 2008).

Another noteworthy work on population structure and phylogeography was undertaken by Vianna et al. (2017), who studied a common bird of the Antarctic Peninsula and sub-Antarctic islands, as the Gentoo penguin Pygoscelis papua (J. R. Forster, 1781). Two subspecies have been described for this species based on morphology with distribution limited by 60°S latitude: P. p. papua, distributed up to 60°S (e.g. on the Falkland and South Georgia islands) and P. p. ellsworthii (smaller in size) that ranges from 60°S to 65°S (e.g. on the South Shetland Islands and the Antarctic Peninsula). Using the mtDNA, HVRI and microsatellite loci markers that include the analysis of 12 colonies, these authors found a strong population genetic structure in this species for both markers based on Bayesian analysis of population structure, which was also in accordance with the phylogenetic and network analyses of these populations. In fact, the Bayesian analysis revealed at least four distinct genetic clades; one for the Western Antarctic Peninsula and three for the sub-Antarctic islands. Moreover, in comparison to colonies from the sub-Antarctic Islands, colonies from the Western Antarctic Peninsula presented high genetic differentiation for both genetic markers (e.g. microsatellite F_ST = 0.110–0.290). These results suggested that dispersal around the Southern Ocean is very limited and the Antarctic Polar Front, located between the Antarctic and sub-Antarctic provinces, appears to be a significant biogeographical boundary for Gentoo penguin populations. In addition, given the existence of various distinct genetic clades within P. papua, assessment of the subspecies status was also proposed since these may correspond to distinct Evolutionarily Units.

As was indicated above, issues on systematics and taxonomy are another research area within molecular genetic studies of Chilean birds that have been addressed in various articles. Among these, one study analyzed the taxonomic status of closely related species distributed in island and continental areas of Chile, an issue that to date remains largely uncertain for several birds. For example, Roy et al. (1998), based on the cytochrome b and ND2 markers, found that the hummingbirds Sephanoides fernandensis (King, 1831), from the Juan Fernández Islands, a site separated by about 700 km from the continent, had a marked divergence with the congeneric species distributed on the Chilean mainland, Sephanoides sephanoides (Lesson, 1827), and even with individuals of S. sephanoides living in the same islands. The phylogenetic analysis of these hummingbirds also revealed that both species belonged to a sister taxa. Thus, this study contributed to supporting the traditional taxonomic relations of these species that had not previously been the subject of in-depth analysis. Likewise, the study of wide-ranging species that inhabit Chile and other continents is another issue that has been addressed within the systematics and taxonomy subject to assess taxonomic status, since geographic isolation can promote the evolutionary divergence. This is the case of the barn owl, Tyto alba (Scopoli, 1769), a species that inhabits Chile and the rest of America, as well as Europe, Africa, Asia and Oceania. The genetic divergence analysis of this species from southern Chile using the COI marker (Colihueque et al. 2015) revealed no major divergence with populations from different locations in America, but strong differentiation with Old World populations. The genetic distance registered in the aforementioned study among Chilean and Old World populations of this species was in the upper limit of the mean intraspecific distances reported previously for Strigiformes (Nijman and Aliabadian 2013). This result was, therefore, extremely interesting, and implied the need for additional studies to evaluate the taxonomic position of Chilean barn owl populations, due to their particular divergence pattern. Further analysis has recently confirmed the high degree of genetic divergence registered for barn owls from different continents, a report that even suggests treating barn owls from these geographic areas as different species, for example, Tyto alba for Africa and Europe and Tyto furcata for the New World (Aliabadian et al. 2016).

Analysis of genetic diversity among bird populations and its association with geological events or geographic barriers (e.g., Andes mountains), which are phenomena typical of Chile, is another issue addressed in some articles. For example, by using the inter-simple-sequence-repeats and the cytochrome b markers, González and Wink (2010) have found that glaciation processes, a climatic phenomenon that occurred during the Last Glacial Maximum 21,000–14,000 years ago, may have impacted the genetic structure of the Thorn-tailed Rayadito, Aphrastura spinicauda (Gmelin, 1789). This notion is based on the finding that within this species, populations currently inhabiting palaeorefuge sites (e.g., Mocha Island) show greater genetic variation than populations located in regions that were covered by ice sheets. After the glaciation event, the population of palaeorefuge sites probably has diversified by genetic drift during colonization of new environments, a process that may explain their current broad distribution in continental areas of the country. Likewise, in the Andean Condor Vultur gryphus (Linnaeus, 1758), a typical highland bird that presents a wide distribution range throughout the Andes mountains of South America, the genetic divergence analysis within and among population using the D-loop and the 12S markers, showed a low level of genetic variability, even lower than for most other birds analyzed for these loci (Hendrickson et al. 2003). In fact, the analysis of 38 individuals from 12 localities in Ecuador, Colombia, Peru, Bolivia, Argentina and Chile, showed a total of five haplotypes based on the presence of four variable sites in the sequences. This result revealed that, in spite of the current widespread distribution range of the Andean Condor across the Andes Mountains, this is a genetically highly homogenous species. These authors inferred that this particular genetic pattern is likely to be related to its condition as a large predatory or scavenging bird, and not to its endangered status, since this species maintains a substantial geographic range. It is expected that this trophic condition generates a small effective population size due to its high position in the food chain, which will lead to a reduction of genetic variation, as has been suggested in other birds, such as the spotted owl Strix occidentalis (Xántus de Vésey, 1860) (Barrowclough and Gutierrez 1990).

Studies analyzing the genetic diversity in cryptic birds distributed in Chile are scarce. Nevertheless this is an interesting issue given that several species present from incipient to full speciation, accompanied by weak morphological differentiation. Vuilleumier (1991) found, for example, that about a third of Patagonian species exhibit the latter phenomenon, a process that seems to have occurred as a result of different vicariance events, mainly ascribed to the Pleistocene age. Thus, the assignment of Chilean birds to particular species or subspecies is challenging in some cases, given their cryptic differentiation as can be exemplified in the genera Chloephaga (Eyton, 1838), Haematopus (Linnaeus, 1758) and Tachyeres (Owen, 1875) (Figure 1). In addition, these species also show little interspecific genetic differentiation, which may make it difficult to achieve their unequivocal identification through the use of molecular genetic markers. In other words, in some cases inconsistency exists between their traditional taxonomic classification, which defines them as different species, and their degree of genetic divergence. This lack of intergeneric genetic differentiation can be supported by a genetic divergence analysis based on published sequences of mtDNA markers (COI and D-loop), since the Haematopus and Tachyeres genera, in contrast to the Chloephaga genus, shows interspecific comparisons with low genetic differentiation (Figure 2). In fact, comparisons among Chloephaga species exhibit high genetic divergences (K2P = 3.82–6.26%), these values being well above the 10× rule (2.4%), a threshold whose value has been suggested as a reference value for the interspecific differentiation of the temperate birds of southern South America, according to Kerr et al. (2009). Therefore, this result supports the existence of a strong intrageneric differentiation in Chloephaga. However, in Haematopus and Tachyeres, some interspecific comparisons show very low genetic differentiation, for example, 0.92% among H. ater and H. palliatus, and 0.54% between T. patachonicus and T. pteneres, revealing divergence levels close to the intraspecific differentiation registered for these genera. Thus, no consistent separation is observed among these species which may reflect the existence of a single taxa. This is an interesting result and indicates that the taxonomic status of these species requires more detailed taxonomic study. Ideally, studies should include multiple lines of evidence, for example, morphology, reproduction and feeding, in addition to molecular data. Moreover, the phylogenetic analysis shows a close phylogenetic relationship in these genera, i.e., some species clustered together within the same branch (Figure 3), a result that is discordant with their current taxonomic classification as distinctive species. For example, Chloephaga species were consistently grouped in a separated cluster, revealing the monophyletic condition of each species. However, in Haematopus and Tachyeres, some species clustered together consistently within the same branch, e.g. H. ater with H. palliatus and T. patachonicus with T. pteneres plus T. brachypterus (83% and 100% of nodal support, respectively), showing a close phylogenetic relation of these species, a result that is discordant with their current taxonomic status as distinctive species. In fact, Fulton et al. (2012) reported no support for monophyly of any species within Tachyeres, despite having registered a certain amount of genetic differentiation between them for example, 0.1–0.8% between continental individuals from southern South America, which included three species. As the species of this group are characterized as presenting flight, e.g., flying steamer duck, T. patachonicus (King, 1828) or flightless, e.g., Magellanic flightless steamer duck, T. pteneres (Forster, 1844) conditions, this result was interpreted as a different stage of the evolution of flightlessness. In the case of Chloephaga, Bulgarella et al. (2014) using the mtDNA D-loop marker had also reported a well-defined monophyletic clade for each species of this group, since C. rubidiceps (P. L. Sclater, 1861) was sister to C. poliocephala (Sclater, 1857), the latter clade being in turn, sister to C. picta (Gmelin, 1789). However, when they compared insular (Falkland Islands) and continental populations of C. rubidiceps and C. picta, significant intraspecific differentiation was found (1.0% and 0.6%, respectively), these populations being reciprocally monophyletic in the mitochondrial gene tree. This result suggested that these species may be affected either by lack of gene flow between the islands and the continent, or by female-biased philopatry, or both.

Genetic diversity data can be an important source of information to understand how selection operates at gene level, when species or populations are under natural selection regimens during their adaptation to environmental conditions. With this aim, the study of markers derived from coding genes, including their regulatory mechanism, is required, since variation in neutral molecular genetic markers (e.g. microsatellite loci) cannot provide direct information on selective processes involved in the interaction among individuals and their environment. This type of analysis contributes to clarifying the underlying genetics of adaptive phenotypes in natural populations (Höglung, 2009). In birds, genetic molecular data have been analyzed to assess the action of natural selection mainly in association with geographic isolation, as this factor can affect the evolution of organisms, as has been documented in different bird species (Cheviron and Brumfield 2009; Kerr 2011; Ribeiro et al. 2011; Barreira et al. 2016). However, no major studies have been published on this issue for Chilean birds, except those that have analyzed the variation among species to assess evidence of signatures of selection on the mitochondrial genome based on the complete genome sequences (Cerasale et al. 2012; Ramos et al. 2018). For example, the recent study of Ramos et al. (2018) applied this molecular aspect in a comparative approach to study patterns of selection in the mitochondrial genome. Using ten penguin species they correlated this genetic data against the spatial environmental data obtained through remote sensing, such as sea surface temperature (SST), chlorophyll and both variables combined. This analysis identified mtDNA candidate genes under positive selection, such as ND4 gene, which could be involved in broad-scale adaptations of penguins to their environment, particularly to SST, and thus are likely related to climate adaptation throughout penguin speciation. In addition, this analysis also supported the signature of purifying selection across the mitochondrial genome, a result that is consistent with the hypothesis that purifying selection is constraining mitogenome evolution to maintain oxidative phosphorylation proteins and functionality. Therefore, this type of study represents a useful approach to better understand adaptation to the environment occurring at molecular levels in penguins, by using large-scale remote sensing data. Thus, the application of this method to other bird groups from Chile has great potential.

In conclusion, a bibliographic analysis of articles published between 1998 and 2018 on the topic of molecular genetics in Chilean birds indicates that over 30 articles of this class were published during this period. The articles focused mainly on research areas related to population structure, phylogeography, systematics and taxonomy and genetic diversity. Mitochondrial DNA D-loop and Cyt b markers along with microsatellite loci were the most widely used markers, while penguins were the most studied taxa in terms of number of species analyzed and articles published. These molecular genetic analyses have contributed to improving our understanding of the evolutionary history of some species and bird groups, which, according to this evidence, seems to have been shaped by geological events, geographical factors or extreme climatic regimens. For example, the population genetic structure and phylogeographic analysis of the burrowing parrot (Cyanoliseus patagonus), a typical bird of the semi-arid zones of north-central Chile, indicates that geographical barriers (i.e., Andean mountains) may have constituted an important dispersal factor of this species across southern South America, affecting the way in which populations have diverged though time. A second example is the Gentoo penguin (Pygoscelis papua), common to the Antarctic Peninsula and sub-Antarctic islands, where genetic data reflect a highly structured species, a genetic pattern that appears to be related to its dispersal capacity around the Southern Ocean that is mostly limited by the Antarctic Polar Front. A third example is the complex of closely related species of Phrygilus, a bird group distributed mainly in central and northern Chile. In this case, genetic data indicate the existence of high levels of intrageneric divergence, whose origin appears to be related to the marked phylogeographic structure of these species and the effect of geographic barriers (e.g. the Andean mountains) acting as a major factor in the differentiation of these species. The use of molecular genetic analysis to address issues related to the taxonomic status of different birds has also been useful, as occurred with hummingbirds from the Juan Fernández Islands (Sephanoides fernandensis) and the barn owl (Tyto alba). In addition, the complete genomes analysis of some bird groups was also carried out. For example, the study of the mitochondrial genome in penguins has provided important evidence on the existence of signatures of selection in several genes of this genome. This class of analysis may be useful in future studies on other bird groups from Chile, to better understand how adaptation to the environment operates at the molecular level.