Molecular genetic studies of Chilean avifauna: an overview about current progress

The biodiversity of Chilean avifauna has been shaped by geological events, geographical factors and extreme climatic regimens. Molecular genetic studies developed to date have begun to provide valuable information to elucidate the effect of these factors on the evolutionary history of Chilean birds. We conducted a search in two bibliographic databases (PubMed and Scopus) over the period between 1998 and 2018 to identify the number and class of articles published in this research field. The quantification of specific research categories was also performed to assess progress in different molecular genetic issues of Chilean birds. Representative studies of the more active research areas: population structure, phylogeography, systematics and taxonomy and genetic diversity, were briefly commented on. Studies on genetic divergence analysis of cryptic species and the underlying genetics at molecular level of adaptive phenotypes in populations, were very scarce. Several types of mitochondrial and nuclear markers have been used, with COI plus D-loop and microsatellite loci, respectively, being the most widely-used markers. However, high-throughput analyses based on complete mitochondrial genomes have also been published. More than one hundred species have been analyzed; the most studied groups being penguins, followed by New World swallows. Although, to date, molecular genetic studies of Chilean birds still require further analysis, the studies available on some species or groups have provided important data to improve our understanding of the origin and evolution of this avifauna.

Uncovering population structure in the Humboldt penguin (Spheniscus humboldti) along the Pacific coast at South America

The upwelling hypothesis has been proposed to explain reduced or lack of population structure in seabird species specialized in food resources available at cold-water upwellings. However, population genetic structure may be challenging to detect in species with large population sizes, since variation in allele frequencies are more robust under genetic drift. High gene flow among populations, that can be constant or pulses of migration in a short period, may also decrease power of algorithms to detect genetic structure. Penguin species usually have large population sizes, high migratory ability but philopatric behavior, and recent investigations debate the existence of subtle population structure for some species not detected before. Previous study on Humboldt penguins found lack of population genetic structure for colonies of Punta San Juan and from South Chile. Here, we used mtDNA and nuclear markers (10 microsatellites and RAG1 intron) to evaluate population structure for 11 main breeding colonies of Humboldt penguins, covering the whole spatial distribution of this species. Although mtDNA failed to detect population structure, microsatellite loci and nuclear intron detected population structure along its latitudinal distribution. Microsatellite showed significant R_st values between most of pairwise locations (44 of 56 locations, R_st = 0.003 to 0.081) and 86% of individuals were assigned to their sampled colony, suggesting philopatry. STRUCTURE detected three main genetic clusters according to geographical locations: i) Peru; ii) North of Chile; and iii) Central-South of Chile. The Humboldt penguin shows signal population expansion after the Last Glacial Maximum (LGM), suggesting that the genetic structure of the species is a result of population dynamics and foraging colder water upwelling that favor gene flow and phylopatric rate. Our findings thus highlight that variable markers and wide sampling along the species distribution are crucial to better understand genetic population structure in animals with high dispersal ability.

Comparative genome-wide polymorphic microsatellite markers in Antarctic penguins through next generation sequencing

Microsatellites are valuable molecular markers for evolutionary and ecological studies. Next generation sequencing is responsible for the increasing number of microsatellites for non-model species. Penguins of the Pygoscelis genus are comprised of three species: Adélie (P. adeliae), Chinstrap (P. antarcticus) and Gentoo penguin (P. papua), all distributed around Antarctica and the sub-Antarctic. The species have been affected differently by climate change, and the use of microsatellite markers will be crucial to monitor population dynamics. We characterized a large set of genome-wide microsatellites and evaluated polymorphisms in all three species. SOLiD reads were generated from the libraries of each species, identifying a large amount of microsatellite loci: 33,677, 35,265 and 42,057 for P. adeliae, P. antarcticus and P. papua, respectively. A large number of dinucleotide (66,139), trinucleotide (29,490) and tetranucleotide (11,849) microsatellites are described. Microsatellite abundance, diversity and orthology were characterized in penguin genomes. We evaluated polymorphisms in 170 tetranucleotide loci, obtaining 34 polymorphic loci in at least one species and 15 polymorphic loci in all three species, which allow to perform comparative studies. Polymorphic markers presented here enable a number of ecological, population, individual identification, parentage and evolutionary studies of Pygoscelis, with potential use in other penguin species.

Reproductive physiology of the female Magellanic penguin (Spheniscus magellanicus): Insights from the study of a zoological colony

Eight captive female Magellanic penguins (Spheniscus magellanicus) were monitored over a 10week period, commencing at 5weeks prior to egg lay (EL), to increase our understanding of the species' reproductive biology. Females in cordoned nest sites underwent cloacal artificial insemination (AI) every 4-7days with different semen donors for each insemination. The EL interval was 97.9±3.6h (range: 84-108h) and paternity analyses revealed that conceptive inseminations occurred from 11.5 to 4.5days before oviposition. A biphasic pattern of estradiol, testosterone, progesterone and the biochemical analytes triglyceride, iron, calcium and phosphorus occurred in relation to EL, with values increasing (P<0.05) to maximal concentrations during the three weeks preceding oviposition, then decreasing (P<0.05) rapidly after oviposition completion. In comparison with post-lay (baseline) values, concentrations of estradiol and testosterone relative to the first oviposition were elevated at Week-5, and those of triglyceride, a yolk formation index, as well as iron, calcium and phosphorus, became elevated at Week-4 (P<0.05). Collective data indicate an estimated total egg formation interval of 29days, with oviducal transit of the ovulated ovum occurring over the majority of the ∼4day EL interval. These findings indicate that egg formation is prolonged with folliculogenesis initiated at 5weeks or more prior to oviposition. Consequently, the period of folliculogenesis and egg formation is estimated to overlap with the final ∼3weeks that wild females spend at sea prior to returning to land for breeding.

Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations

Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half-siblings or cousins) is strongly suggested.

Paternity testing using microsatellite DNA markers in captive Adélie penguins (Pygoscelis adeliae)

We investigated the paternity of 39 Adélie penguins (Pygoscelis adeliae) hatched at the Port of Nagoya Public Aquarium between 1995 and 2005 breeding seasons using microsatellite DNA markers. Among the 13 microsatellite marker loci tested in this study, eight markers amplified and were found to be polymorphic in the colony's founders of the captive population (n = 26). Multiple marker analysis confirmed that all the hatchlings shared alleles with their social fathers and that none of them were sired by any male (all males ≥4 years old in the exhibit tank during each reproductive season; n = 9-15) other than the one carrying out parental duties, except in the case of two inbred hatchlings whose half-sibling parents shared the same father. These results demonstrated that extra-pair paternity (EPP) did not occur in this captive population and that even if EPP has been detected among them, the probability of excluding all other possible fathers in the exhibit tank is extremely high based on paternity exclusion probabilities across the investigated loci. The paternity exclusion probabilities were almost the same between 1994 and 2005. The probability of identity across the investigated loci declined between the two time points, but was still high. These results are reflected in a very short history of breeding in this captive population. In other words, the parentage analyses using a suite of microsatellite markers will be less effective as generations change in small closed populations, such as zoo and aquarium populations.

Isolation and characterization of macaroni penguin (Eudyptes chrysolophus) microsatellite loci and their utility in other penguin species (Spheniscidae, AVES)

We report the characterization of 25 microsatellite loci isolated from the macaroni penguin (Eudyptes chrysolophus). Thirteen loci were arranged into four multiplex sets for future genetic studies of macaroni penguin populations. All 25 loci were tested separately in each of four other penguin species [Adélie penguin (Pygoscelis adeliae), chinstrap penguin (Pygoscelis antarctica), gentoo penguin (Pygoscelis papua) and king penguin (Aptenodytes patagonicus)]. Between eight and 12 loci were polymorphic per species. These loci are expected to be useful for studies of population genetic structure in a range of penguin species.

Hormonal correlations at transition from reproduction to molting in an annual life cycle of Humboldt penguins (Spheniscus humboldti)

To understand the hormonal mechanism behind a unique strategy of breeding and molting in Humboldt penguins, six pairs of captive Humboldt penguins kept in an outdoor open display pen were observed and blood collected weekly for a year. They all molted between the middle of June and the middle of August within 10 days except one pair that molted about a month later. The late pair had been rearing a hatchling until July due to the successful second clutch after the first clutch failed. A peak of plasma levels of thyroxine and triiodothyronine, respectively, overlapped a period of molting in both sexes. Plasma testosterone concentrations in the males and females were lowest for two month during a period of pre-molt and molting. Plasma concentrations of estradiol were also lowest during the molt in both sexes. Except for the period of molting, sex steroid hormone concentrations were high although there was great individual variation. During the molt, the birds were forced to fast since they did not enter the pool in the display pen where they usually forage live fish. To compensate this forced fasting, they took more food than usual during pre-molting period and gained body mass to about 20% more than the baseline value. Increased flipper thickness was parallel to increased body mass indicating that the gained body mass attributed to fat reservoir. These data indicate that rapid molting in Humboldt penguins is correlated with a drastic increase and decrease of thyroid hormones during the period of lowest concentrations in sex steroid hormones.