Isolation and characterization of novel microsatellite loci for parentage assessment in the lance‐tailed manakin (Chiroxiphia lanceolata)

The lance‐tailed manakin (Chiroxiphia lanceolata) is a lek‐breeding bird from Central America in which males court females with complex cooperative displays. To resolve detailed patterns of paternity in the wild, we isolated and characterized 12 novel microsatellite loci in this species. Eleven of these loci were polymorphic (five to 14 alleles), with observed heterozygosities ranging from 0.36 to 0.87 (N = 574 individuals). We tested for linkage disequilibrium using randomized subsamples of adults to control for known family structure among long‐lived and sedentary individuals. These loci will be valuable in resolving paternity among many candidate fathers in this species.     

Characterization of new microsatellite loci for the ring‐tailed lemur (Lemur catta)

In this report we describe the development and characterization of six dinucleotide microsatellite loci for the ring‐tailed lemur (Lemur catta). The new markers were isolated from the genomic DNA of L. catta and all loci were found to be polymorphic when evaluated by genotyping a minimum of 34 individuals. Mendelian inheritance of each locus was verified using four families of captive ring‐tailed lemurs. The loci presented will facilitate the genetic survey of free‐ranging L. catta, enabling study of their social organization and mating patterns.     

Distribution and at‐sea behavior of Bermudan White‐tailed Tropicbirds (Phaethon lepturus catesbyi) during the non‐breeding season

The movements and behavior of many taxa of seabirds during the non‐breeding season remain poorly known. For example, although studies conducted in the Pacific and Indian oceans suggest that White‐tailed Tropicbirds (Phaethon lepturus) seldom fly more than a few thousand kilometers from nest colonies after breeding, little is known about the post‐breeding movements and behavior of a subspecies of White‐tailed Tropicbirds (P. l. catesbyi) that breeds on islands in the North Atlantic Ocean. Our objective, therefore, was to use light‐based geolocators to identify the ranges and pelagic activities of White‐tailed Tropicbirds from Bermuda during the non‐breeding periods in 2014–2015 (N = 25) and 2015–2016 (N = 16). Locations were estimated based on changes in light intensity across time, and pelagic activities were determined based on whether geolocators attached to leg bands were wet (i.e., birds resting on the water's surface) or dry (i.e., birds in flight). In 2014, birds spent late summer (July–September) near Bermuda and the British Virgin Islands; by mid‐September, most (N = 17; 68%) birds took a direct easterly route to the Sargasso Sea. In 2015, most post‐breeders (N = 15; 94%) flew east from Bermuda and to the Sargasso before the end of late summer. For both years combined, fall and winter (October–February) ranges extended as far west as North Carolina and as far east as the mid‐Atlantic Ridge. In both years, all birds were located between Bermuda and the British Virgin Islands during the spring (April–May). All birds then flew north to Bermuda in both years, with variations in timing, during April and May. We also found extensive overlap in the ranges of males and females during the non‐breeding season in both years. During the non‐breeding season, White‐tailed Tropicbirds spent 5% of night periods and 41% of day periods in flight in 2014; in 2015, birds spent 8% and 42% of night and day periods, respectively, in flight. Tropicbirds spent more time flying during the day because they hunt by day, detecting prey on the wing by sight. Overall, our results suggest that White‐tailed Tropicbirds that breed in Bermuda are diurnal, nomadic wanderers that range over an extensive area of the Atlantic Ocean during the non‐breeding season.     

Year‐round movements of sympatric Fork‐tailed (Oceanodroma furcata) and Leach's (O. leucorhoa) storm‐petrels

Long‐distance movements are characteristic of most seabirds in the order Procellariiformes. However, little is known about the migration and foraging ranges of many of the smaller species in this order, especially storm‐petrels (Hydrobatidae). We used Global Location Sensors to document the year‐round movements of sympatrically breeding Fork‐tailed Storm‐Petrels (Oceanodroma furcata) and Leach's Storm‐Petrels (O. leucorhoa) from the Gillam Islands located northwest of Vancouver Island, British Columbia, Canada. In 2016, breeding Fork‐tailed (N = 5) and Leach's (N = 2) storm‐petrels traveled maximum distances of ~1550–1600 km from their colony to a region that has a wide shelf with major canyons creating a highly productive foraging area. After the breeding season, Fork‐tailed Storm‐Petrels (N = 2) traveled to similar areas west of the Gillam Islands, a maximum distance of ~3600 km from the breeding colony, and remained in the North Pacific Ocean and north of the Subarctic Boundary for an average of 5.4 mo. Post‐breeding Leach's Storm‐Petrels (N = 2) moved south to the Eastern Tropical Pacific, west of central Mexico, Ecuador, and northern Peru, an estimated maximum distance of ~6700 km from their breeding colony, and remained there for an average of 7.2 mo. Carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope analyses of feathers revealed niche separation between Fork‐tailed (N = 21) and Leach's (N = 53) storm‐petrels. The wide range of δ¹⁵N values in the feathers of Leach's Storm‐Petrels (N = 53) suggests that they foraged at a variety of trophic levels during the non‐breeding season. Our results demonstrate that storm‐petrels have large core foraging areas and occupy vast oceanic areas in the Pacific during their annual cycle. However, given the coarse precision of Global Location Sensors, additional study is needed to identify the specific areas used by each species during both breeding and non‐breeding periods.     

Characterization of 20 microsatellite loci in the long‐tailed tit Aegithalos caudatus (Aegithalidae,AVES)

We characterized 20 microsatellite loci in the long‐tailed tit, Aegithalos caudatus. Polymorphic loci were identified by testing 114 loci that had been originally isolated in other avian species. The loci were characterized in 23–163 unrelated long‐tailed tits from a British population and displayed between two and 42 alleles, with observed heterozygosity ranging between 0.09 and 0.97.     

White‐tailed deer as the last megafauna dispersing seeds in Neotropical dry forests: the role of fruit and seed traits

Endozoochory is a prominent form of seed dispersal in tropical dry forests. Most extant megafauna that perform such seed dispersal are ungulates, which can also be seed predators. White‐tailed deer (Odocoileus virginianus) is one of the last extant megafauna of Neotropical dry forests, but whether it serves as a legitimate seed disperser is poorly understood. We studied seed dispersal patterns and germination after white‐tailed deer gut passage in a tropical dry forest in southwest Ecuador. Over 23 mo, we recorded ca 2000 seeds of 11 species in 385 fecal samples. Most seeds belonged to four species of Fabaceae: Chloroleucon mangense, Senna mollissima, Piptadenia flava, and Caesalpinia glabrata. Seeds from eight of the 11 species dispersed by white‐tailed deer germinated under controlled conditions. Ingestion did not affect germination of C. mangense and S. mollissima, whereas C. glabrata showed reduced germination. Nevertheless, the removal of fruit pulp resulting from ingestion by white‐tailed deer could have a deinhibition effect on germination due to seed release. Thus, white‐tailed deer play an important role as legitimate seed dispersers of woody species formerly considered autochorous. Our results suggest that more research is needed to fully understand the ecological and evolutionary effects of the remaining extant megafauna on plant regeneration dynamics in the dry Neotropics.     

Genetic structure offers insights into the evolution of migration and the taxonomy of the Barred Long‐tailed Cuckoo Cercococcyx montanus species complex

Barred Long‐tailed Cuckoo (Cercococcyx montanus) currently comprises two morphologically distinct subspecies, one resident in the Albertine Rift (montanus) and one in east and southeast Africa (patulus) in which there are migrations that are poorly understood. Based on nuclear and mitochondrial DNA sequences, we find that two specimens collected in relatively low‐elevation forest in the Albertine Rift were correctly identified from plumage as the migratory subspecies whose closest known breeding area is > 800 km to the east. We discuss ways in which this unique migratory pattern could have evolved and argue that migration was gained and then lost in the C. montanus complex. Based on consistent morphological and genetic differences, we suggest that Barred Long‐tailed Cuckoo is best treated as two species, one of which (C. montanus) is a non‐migratory Albertine Rift endemic.     

Using heterozygosity–fitness correlations to study inbreeding depression in an isolated population of white‐tailed deer founded by few individuals

A heterozygosity–fitness correlations (HFCs) may reflect inbreeding depression, but the extent to which they do so is debated. HFCs are particularly likely to occur after demographic disturbances such as population bottleneck or admixture. We here study HFC in an introduced and isolated ungulate population of white‐tailed deer Odocoileus virginianus in Finland founded in 1934 by four individuals. A total of 422 ≥ 1‐year‐old white‐tailed deer were collected in the 2012 hunting season in southern Finland and genotyped for 14 microsatellite loci. We find significant identity disequilibrium as estimated by g₂. Heterozygosity was positively associated with size‐ and age‐corrected body mass, but not with jaw size or (in males) antler score. Because of the relatively high identity disequilibrium, heterozygosity of the marker panel explained 51% of variation in inbreeding. Inbreeding explained approximately 4% of the variation in body mass and is thus a minor, although significant source of variation in body mass in this population. The study of HFC is attractive for game‐ and conservation‐oriented wildlife management because it presents an affordable and readily used approach for genetic monitoring that allowing identification of fitness costs associated with genetic substructuring in what may seem like a homogeneous population.     

The effect of terrain and female density on survival of neonatal white‐tailed deer and mule deer fawns

Juvenile survival is a highly variable life‐history trait that is critical to population growth. Antipredator tactics, including an animal's use of its physical and social environment, are critical to juvenile survival. Here, we tested the hypothesis that habitat and social characteristics influence coyote (Canis latrans) predation on white‐tailed deer (Odocoileus virginianus) and mule deer (O. hemionus) fawns in similar ways during the neonatal period. This would contrast to winter when the habitat and social characteristics that provide the most safety for each species differ. We monitored seven cohorts of white‐tailed deer and mule deer fawns at a grassland study site in Alberta, Canada. We used logistic regression and a model selection procedure to determine how habitat characteristics, climatic conditions, and female density influenced fawn survival during the first 8 weeks of life. Fawn survival improved after springs with productive vegetation (high integrated Normalized Difference Vegetation Index values). Fawns that used steeper terrain were more likely to survive. Fawns of both species had improved survival in years with higher densities of mule deer females, but not with higher densities of white‐tailed deer females, as predicted if they benefit from protection by mule deer. Our results suggest that topographical variation is a critical resource for neonates of many ungulate species, even species like white‐tailed deer that use more gentle terrain when older. Further, our results raise the possibility that neonatal white‐tailed fawns may benefit from associating with mule deer females, which may contribute to the expansion of white‐tailed deer into areas occupied by mule deer.     

Development of EST‐derived microsatellite markers for Arabidopsis lyrata subspecies petraea (L.)

A set of expressed sequence tag–simple sequence repeat (EST‐SSR) loci has been developed for Arabidopsis lyrata ssp. petraea. From 768 root cDNA clones, 126 microsatellites, including di‐, tri‐, tetra‐ and pentanucleotide repeat motifs were identified and primers were designed to 24 EST‐SSRs. Eleven loci were subsequently screened on 150 individuals sampled from five natural populations, which revealed three to nine alleles per locus (mean 5.36) and expected heterozygosity (H_E) estimates ranging from 0.046 to 0.698. Significant deviations from random mating were observed at 10 EST‐SSR loci, likely due to inbreeding (global F_IS = 0.151) and population structure (global F_ST = 0.246).     

Isolation of 22 new Haliaeetus microsatellite loci and their characterization in the critically endangered Madagascar fish‐eagle (Haliaeetus vociferoides) and three other Haliaeetus eagle species

We isolated a total of 22 microsatellite loci from two Haliaeetus species: the Madagascar fish‐eagle (Haliaeetus vociferoides) and the bald eagle (Haliaeetus leucocephalus). Five loci were monomorphic in both the Madagascar fish‐eagle (n = 24–43) and the bald eagle (n = 2–8) but were found to be polymorphic in other Haliaeetus species. Haliaeetus loci have proved useful for investigating gene flow in Haliaeetus and Aquila eagles. Ten loci were polymorphic in the critically endangered Madagascar fish‐eagle and will be used to investigate the genetic population structure and mating system in this species.     

Isolation and characterization of polymorphic microsatellite markers in the gray,short‐tailed opossum (Monodelphis domestica)

Twenty‐six polymorphic microsatellite markers were isolated from (AC)_n and (AG)_n microsatellite‐enhanced genomic libraries of the gray, short‐tailed opossum Monodelphis domestica. All 26 loci showed high allelic diversity, with allele numbers ranging from five to 11 in a subset of 35 animals. Normal Mendelian inheritance was confirmed for 24 loci by analysing allelic segregation in 10, two‐generation, families. Non‐amplifying (null) alleles were detected at two loci, which we recommend be used only if pedigree data are available. We conclude that all of these microsatellite markers would be useful for quantitative trait locus mapping and population genetic studies.     

What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper,Lissotriton helveticus,and Triturus cristatus) and comparison with Illumina‐based approaches

The development of microsatellite loci has become more efficient using next‐generation sequencing (NGS) approaches, and many studies imply that the amount of applicable loci is large. However, few studies have sought to quantify the number of loci that are retained for use out of the thousands of sequence reads initially obtained. We analyzed the success rate of microsatellite loci development for three amphibian species using a 454 NGS approach on tetra‐nucleotide motif‐enriched species‐specific libraries. The number of sequence reads obtained differed strongly between species and ranged from 19,562 for Triturus cristatus to 55,626 for Lissotriton helveticus, with 52,075 reads obtained for Calotriton asper. PHOBOS was used to identify sequences with tetra‐nucleotide repeat motifs with a minimum repeat number of ten and high quality primer binding sites. Of 107 sequences for T. cristatus, 316 for C. asper and 319 for L. helveticus, we tested the amplification success, polymorphism, and degree of heterozygosity for 41 primer combinations each for C. asper and T. cristatus, and 22 for L. helveticus. We found 11 polymorphic loci for T. cristatus, 20 loci for C. asper, and 15 loci for L. helveticus. Extrapolated, the number of potentially amplifiable loci (PALs) resulted in estimated species‐specific success rates of 0.15% (T. cristatus), 0.30% (C. asper), and 0.39% (L. helveticus). Compared with representative Illumina NGS approaches, our applied 454‐sequencing approach on specifically enriched sublibraries proved to be quite competitive in terms of success rates and number of finally applicable loci.     

Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits

To study effects from natural selection acting on brown trout in a natural stream habitat compared with a hatchery environment, 3,781 single nucleotide polymorphism (SNP) markers were analyzed in three closely related groups of brown trout (Salmo trutta L.). Autumn (W/0+, n = 48) and consecutive spring (W/1+, n = 47) samples of brown trout individuals belonging to the same cohort and stream were retrieved using electrofishing. A third group (H/1+, n = 48) comprised hatchery‐reared individuals, bred from a mixture of wild parents of the strain of the two former groups and from a neighboring stream. Pairwise analysis of F_ST outliers and analysis under a hierarchical model by means of ARLEQUIN software detected 421 (10.8%) candidates of selection, before multitest correction. BAYESCAN software detected 10 candidate loci, all of which were included among the ARLEQUIN candidate loci. Body length was significantly different across genotypes at 10 candidate loci in the W/0+, at 34 candidate loci in the W/1+ and at 21 candidate loci in the H/1+ group. The W/1+ sample was tested for genotype‐specific body length at all loci, and significant differences were found in 10.6% of all loci, and of these, 14.2% had higher frequency of the largest genotype in the W/1+ sample than in W/0+. The corresponding proportion among the candidate loci of W/1+ was 22.7% with genotype‐specific body length, and 88.2% of these had increased frequency of the largest genotype from W/0+ to W/1+, indicating a linkage between these loci and traits affecting growth and survival under this stream's environmental conditions. Bayesian structuring of all loci, and of the noncandidate loci suggested two (K = 2), alternatively four clusters (K = 4). This differed from the candidate SNPs, which suggested only two clusters. In both cases, the hatchery fish dominated one cluster, and body length of W/1+ fish was positively correlated with membership of one cluster both from the K = 2 and the K = 4 structure. Our analysis demonstrates profound genetic differentiation that can be linked to differential selection on a fitness‐related trait (individual growth) in brown trout living under natural vs. hatchery conditions. Candidate SNP loci linked to genes affecting individual growth were identified and provide important inputs into future mapping of the genetic basis of brown trout body size selection.     

Novel polymorphic microsatellite markers for paternity analysis in the red‐capped robin (Petroica goodenovii: Aves)

Seven microsatellite loci were isolated and characterized from the red‐capped robin Petroica goodenovii, using nonradioactive polymerase chain reaction (PCR)‐based techniques to screen an enriched genomic library. Five loci showed no evidence of null alleles and were variable [mean heterozygosity (H_E) = 0.440, mean number of alleles = 8]. Cross‐amplification using primers for microsatellites in Phylloscopus occipitalis and Emberiza schoeniclus yielded another two polymorphic loci. The combined set of five red‐capped robin and two cross‐amplified loci are suitable for paternity assignment (exclusion probability for seven unlinked loci = 0.9760).     

Characterization of seven polymorphic microsatellite loci in the Baja California endemic black‐tailed brush lizard Urosaurus nigricaudus

Seven microsatellite loci were developed for the Baja California endemic black‐tailed brush lizard Urosaurus nigricaudus, using an enriched genomic DNA library. All loci were polymorphic and overall presented high levels of variation. Number of alleles ranged from five to 16 (average 12.14), and observed heterozygosities from 0.535 to 0.923 (average 0.752). Cross‐species amplification was successful and polymorphism was detected for all the loci using the congeners Urosaurus lahtelai and Urosaurus ornatus. These markers will be useful to study fragmented populations of U. nigricaudus on agricultural landscape of the Baja California Peninsula.     

A multiplex panel of microsatellite markers for widespread sub‐Saharan rodents of the genus Mastomys

We isolated and characterized 12 polymorphic microsatellite loci in the sub‐Saharan rodent Mastomys huberti. We tested cross‐species amplification of all these loci in three closely related Mastomys species: M. coucha, M. erythroleucus and M. natalensis. Multiplex panels comprising 11 loci were developed and their application to a set of individuals in each species allowed clear and easy characterization of allele sizes. Statistics from 31 M. huberti coming from one locality in Mali showed no deviation from Hardy–Weinberg equilibrium except for one locus, and no significant linkage disequilibria between loci.     

Isolation and characterization of polymorphic microsatellite loci for the study of paternity and population structure in the little penguin Eudyptula minor

We isolated and characterized eight novel microsatellite loci in the little penguin Eudyptula minor, using nonradioactive polymerase chain reaction‐based techniques to screen GA and GAAA repeats from enriched genomic DNA libraries. All eight loci were polymorphic and seven were variable in our main study population (mean H_E = 0.613, mean N_A = 7.14). Cross‐amplification using a microsatellite primer developed in Spheniscus demersus (African penguin) yielded one additional polymorphic locus. This locus combined with six of the little penguin loci is suitable for paternity assignment in little penguins (exclusion probability for seven unlinked loci = 0.993).     

Isolation and characterization of microsatellite markers in the southern emu‐wren (Stipiturus malachurus: Aves)

We isolated and characterized eight novel microsatellite loci in the southern emu‐wren (Stipiturus malachurus). We used nonradioactive polymerase chain reaction (PCR)‐based techniques to screen an enriched genomic DNA library. Based on genotypes from a single population, six loci showed no evidence of null alleles and were polymorphic (allele range = 2–9, mean heterozygosity = 0.57), and one locus was sex‐linked (N_A = 4). These loci were variable and had different allele size ranges in three other populations of southern emu‐wrens, and are therefore useful for determining levels of genetic diversity within and between populations of the species.