Cross-Amplification in Strigiformes: A New STR Panel for Forensic Purposes

Strigiformes are affected by a substantial decline mainly caused by habitat loss and destruction, poaching, and trapping. Moreover, the increasing trend in bird trade and the growing interest in wild-caught rather than captive-bred birds are expected to encourage illegal trade. The biomolecular investigation represents a valuable tool to track illegal trade and to explore the genetic variability to preserving biodiversity. Microsatellite loci (STRs) are the most used markers to study genetic variability. Despite the availability of species-specific microsatellite loci in Strigiformes, a unique panel permitting the description of the genetic variability across species has not been identified yet. We tested 32 highly polymorphic microsatellite markers to evaluate the reliability of a unique microsatellite panel in different species of Strigiformes and its use for conservation and forensic purposes. We included in the study 84 individuals belonging to 28 parental groups and 11 species of Strigiformes. After screening polymorphic microsatellite loci, the description of genetic variability, and the kinship assessment, we characterized a final panel of 12 microsatellite loci able to identify individuals in 9 Strigiformes species. This STR panel might support the authorities in the forensic investigation for suspected smugglers and false parental claims; moreover, it can be useful to evaluate relatedness among individuals in captive-bred populations and to implement research projects finalized to the description of the genetic variability in wild populations.

Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes

We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106 nt. We calculated the genome-wide fixation index (FST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates.

Genetic Signatures of Demographic Changes in an Avian Top Predator during the Last Century: Bottlenecks and Expansions of the Eurasian Eagle Owl in the Iberian Peninsula

The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo) in the Iberian Peninsula. During the last century, the species was the object of extermination programs, suffering direct persecution by hunters until the 70's. Moreover, during the last decades the eagle owl was severely impacted by increased mortality due to electrocution and the decline of its main prey species, the European rabbit (Oryctolagus cuniculus). In recent times, the decrease of direct persecution and the implementation of some conservation schemes have allowed the species' demographic recovery. Yet, it remains unknown to which extent the past population decline and the later expansion have influenced the current species' pattern of genetic diversity. We used eight microsatellite markers to genotype 235 eagle owls from ten Spanish subpopulations and analyse the presence of genetic signatures attributable to the recent population fluctuations experienced by the species. We found moderate levels of differentiation among the studied subpopulations and Bayesian analyses revealed the existence of three genetic clusters that grouped subpopulations from central, south-western and south-eastern Spain. The observed genetic structure could have resulted from recent human-induced population fragmentation, a patchy distribution of prey populations and/or the philopatric behaviour and habitat selection of the species. We detected an old population bottleneck, which occurred approximately 10,000 years ago, and significant signatures of recent demographic expansions. However, we did not find genetic signatures for a recent bottleneck, which may indicate that population declines were not severe enough to leave detectable signals on the species genetic makeup or that such signals have been eroded by the rapid demographic recovery experienced by the species in recent years.

Population characteristics may reduce the levels of individual call identity

Individual variability influences the demographic and evolutionary dynamics of spatially structured populations, and conversely ecological and evolutionary dynamics provide the context under which variations at the individual level occur. Therefore, it is essential to identify and characterize the importance of the different factors that may promote or hinder individual variability. Animal signaling is a prime example of a type of behavior that is largely dependent on both the features of individuals and the characteristics of the population to which they belong. After 10 years studying the dynamics of a population of a long-lived species, the eagle owl (Bubo bubo), we investigated the emergence and maintenance of traits that reveal individual identity by focusing on vocal features. We found that individuals inhabiting a high density population characterized by a relative lack of heterogeneity (in terms of prey availability and breeding success) among breeding sites might be selected for reducing the levels of identity. Two non-mutually exclusive hypotheses may explain the structural call patterns we detected: (1) similarity in calls may be principally a consequence of the particular characteristics of the population; and (2) high density may encourage individuals to mimic each other’s vocalizations in a cascade effect, leading to a widespread and unique communication network.

Introgression and dispersal among spotted owl (Strix occidentalis) subspecies

Population genetics plays an increasingly important role in the conservation and management of declining species, particularly for defining taxonomic units. Subspecies are recognized by several conservation organizations and countries and receive legal protection under the US Endangered Species Act (ESA). Two subspecies of spotted owls, northern (Strix occidentalis caurina) and Mexican (S. o. lucida) spotted owls, are ESA-listed as threatened, but the California (S. o. occidentalis) spotted owl is not listed. Thus, determining the boundaries of these subspecies is critical for effective enforcement of the ESA. We tested the validity of previously recognized spotted owl subspecies by analysing 394 spotted owls at 10 microsatellite loci. We also tested whether northern and California spotted owls hybridize as suggested by previous mitochondrial DNA studies. Our results supported current recognition of three subspecies. We also found bi-directional hybridization and dispersal between northern and California spotted owls centered in southern Oregon and northern California. Surprisingly, we also detected introgression of Mexican spotted owls into the range of northern spotted owls, primarily in the northern part of the subspecies' range in Washington, indicating long-distance dispersal of Mexican spotted owls. We conclude with a discussion of the conservation implications of our study.

Microsatellite markers in an invasive strain of Asparagopsis taxiformis (Bonnemaisoniales, Rhodophyta): insights in ploidy level and sexual reproduction

Eight polymorphic nuclear microsatellite loci were identified from the invasive Indo-Pacific Mediterranean strain of Asparagopsis taxiformis. Microsatellite markers were tested against a panel of specimens collected along the Italian (Elba, Naples) and Californian (Catalina Island) coasts, all belonging to the same mitochondrial lineage. In addition, we used Hawaiian specimens, belonging to a closely related mitochondrial lineage. The markers amplified in all of the specimens but failed consistently in thalli of two more distantly related mitochondrial lineages of A. taxiformis as well as in specimens belonging to the sister species Asparagopsis armata. Since haploid female individuals among the Mediterranean specimens contained cystocarps, genotyping was performed on supposedly haploid female specimens and supposedly diploid cystocarps separately. As expected, external allelic contribution was detected in the cystocarps. However, even after removal of these reproductive structures, gametophyte thalli exhibited patterns consisting of up to three alleles in all of the tested populations indicating polyploidy. An elevated number of distinct genotypes (up to 85%) were found per population, suggesting high intra-population variation. Results showed high genetic similarity between the two Mediterranean populations screened and lower similarity between these two and the Californian one within the same mitochondrial lineage. Lowest similarity was found between these three and the Hawaiian population belonging to the other related mitochondrial lineage 1.

Contrasting patterns of mitochondrial and microsatellite genetic structure among Western European populations of tawny owls (Strix aluco)

A recent study of mitochondrial phylogeography of tawny owls (Strix aluco) in western Europe suggested that this species survived the Pleistocene glaciations in three allopatric refugia located in Iberia, Italy, and the Balkans, and the latter was likely the predominant source of postglacial colonization of northern Europe. New data from seven microsatellite loci from 184 individual owls distributed among 14 populations were used to assess the genetic congruence between nuclear and mitochondrial DNA (mtDNA) markers. Microsatellites corroborated the major phylogeographical conclusions reached on the basis of the mtDNA sequences, but also showed important differences leading to novel inferences. Microsatellites corroborated the three major refugia and supported the Balkan origin of northern populations. When corrected for differences in effective population size, microsatellites and mtDNA yielded generally congruent overall estimates of population structure (N*ST=0.12 vs. RST=0.16); however, there was substantial heterogeneity in the RST among the seven nuclear loci that was not correlated with heterozygosity. Populations representing the Balkans postglacial expansion interact with populations from the other two refugia forming two clines near the Alps and the Pyrenees. In both cases, the apparent position of the contact zones differed substantially between markers due to the genetic composition of populations sampled in northern Italy and Madrid. Microsatellite data did not corroborate the lower genetic diversity of northern, recently populated regions as was found with mtDNA; this discrepancy was taken as evidence for a recent bottleneck recovery. Finally, this study suggests that congruence among genetic markers should be more likely in cases of range expansion into new areas than when populations interact across contact zones.

Inbreeding and endangered species management: is New Zealand out of step with the rest of the world?

There is growing evidence that inbreeding can negatively affect small, isolated populations. This contrasts with the perception in New Zealand, where it has been claimed that native birds are less affected by inbreeding depression than threatened species from continental regions. It has been argued that New Zealand's terrestrial birds have had a long history of small population size with frequent inbreeding and that this has 'purged" deleterious alleles. The rapid recovery of many tiny and inbred populations after introduced predators have been controlled, and without input from more genetically diverse populations, has further supported the view that inbreeding is not a problem. This has led to a general neglect of inbreeding as a factor in recovery programs for highly endangered species such as the Black Robin (Petroica traversi) and Kakapo (Strigops habroptilis). We examined the reasons for this situation and review the New Zealand evidence for genetic purging. Complete purging of the genetic load and elimination of inbreeding depression are unlikely to occur in natural populations, although partial purging may be more likely where small populations have become inbred over an extended period of time, such as on small isolated islands. Recent molecular data are consistent with the view that island endemics, including New Zealand's threatened birds, have low genetic variation and hence have possibly gone through longer periods of inbreeding than threatened species from continental regions. Nevertheless, results from recent field studies in New Zealand indicate that, despite the opportunity for purging, inbreeding depression is evident in many threatened species. Although inbreeding depression has not prevented some populations from recovering from severe bottlenecks, the long-term consequences of inbreeding and small population size--the loss of genetic variation--are potentially much more insidious. The degrees to which genetic factors reduce population viability generally remain unquantified in New Zealand. Although minimizing ecological risks (e.g., preventing reinvasion of islands by mammalian predators) will continue to receive high priority in New Zealand because of their much larger impacts, we advocate that genetic considerations be better integrated into recovery plans.