Using genomic information for management planning of an endangered perennial,Viola uliginosa

Species occupying habitats subjected to frequent natural and/or anthropogenic changes are a challenge for conservation management. We studied one such species, Viola uliginosa, an endangered perennial wetland species typically inhabiting sporadically flooded meadows alongside rivers/lakes. In order to estimate genomic diversity, population structure, and history, we sampled five sites in Finland, three in Estonia, and one each in Slovenia, Belarus, and Poland using genomic SNP data with double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq). We found monophyletic populations, high levels of inbreeding (mean population F_SNP = 0.407–0.945), low effective population sizes (N_e = 0.8–50.9), indications of past demographic expansion, and rare long‐distance dispersal. Our results are important in implementing conservation strategies for V. uliginosa, which should include founding of seed banks, ex situ cultivations, and reintroductions with individuals of proper origin, combined with continuous population monitoring and habitat management.     

Pollen and stomata morphometrics and polyploidy in Eriotheca (Malvaceae‐Bombacoideae)

Approximately 70% of the angiosperm species are polyploid, an important phenomenon in the evolution of those plants. But ploidy estimates have often been hindered because of the small size and large number of chromosomes in many tropical groups. Since polyploidy affects cell size, morphometric analyses of pollen grains and stomata have been used to infer ploidy level. Polyploidy is present in many species of the Cerrado, the Neotropical savanna region in Central Brazil, and has been linked to apomixis in some taxa. Eriotheca gracilipes and Eriotheca pubescens are common tree species in this region, and present cytotypes that form reproductive mosaics. Hexaploid individuals (2n = 6x = 276) are polyembryonic and apomictic, while tetraploid and diploid individuals (2n = 2x = 92, 2n = 4x = 184) are sexual and monoembryonic. We tested whether morphometric analysis can be used to estimate ploidy levels in E. gracilipes and E. pubescens individuals. Pollen material from diploid and hexaploid individuals of E. gracilipes, and tetraploid and hexaploid individuals of E. pubescens, were fixed in 50% FAA, and expanded leaves were dried in silica gel. Pollen grains and stomata of at least five individuals from each population were measured. The results demonstrate that all measures were significantly different among cytotypes. Individuals with higher levels of ploidy (hexaploid) all presented measurements that were higher than those with lower levels (diploid and tetraploid). There was no overlap between ploidy levels in each species at 95% confidence interval. Thus, the size of the pollen grains and stomata are effective parameters for analysis of ploidy levels in E. gracilipes and E. pubescens.     

Dispersal patterns in black howler monkeys (Alouatta pigra): Integrating multiyear demographic and molecular data

Dispersal is a fundamental process in the functioning of animal societies as it regulates the degree to which closely related individuals are spatially concentrated. A species’ dispersal pattern can be complex as it emerges from individuals’ decisions shaped by the cost–benefit tradeoffs associated with either remaining in the natal group or dispersing. Given the potential complexity, combining long-term demographic information with molecular data can provide important insights into dispersal patterns of a species. Based on a 15-year study that integrates multiyear demographic data on six groups with longitudinal and cross-sectional genetic sampling of 20 groups (N = 169 individuals, N = 21 polymorphic microsatellite loci), we describe the various dispersal strategies of male and female black howler monkeys (Alouatta pigra) inhabiting Palenque National Park, Mexico. Genetically confirmed dispersal events (N = 21 of 59 males; N = 6 of 65 females) together with spatial autocorrelation analyses revealed that the dispersal pattern of black howlers is bisexual with strong sex-biases in both dispersal rate (males disperse more often than females) and dispersal distance (females disperse farther than males). Observational and genetic data confirm that both males and females can successfully immigrate into established groups, as well as form new groups with other dispersing individuals. Additionally, both males and females may disperse singly, as well as in pairs, and both may also disperse secondarily. Overall, our findings suggest multiple dispersal trajectories for black howler males and females, and longer multiyear studies are needed to unravel which demographic, ecological and social factors underlie individuals’ decisions about whether to disperse and which dispersal options to take.     

Spatial distribution of juvenile masu salmon (Oncorhynchus masou) with incongruent genotypic and phenotypic sex in Hokkaido, Japan

To clarify the spatial distribution of masu salmon Oncorhynchus masou with incongruent genotypic and phenotypic sex, we compared the phenotypic sex determined by gonad analysis with the genotypic sex identified by a male-specific genetic marker, Growth hormone pseudogene (GHp), in 584 individuals inhabiting 23 rivers in Hokkaido, Japan. We found that the genotypic sex is different from the phenotypic sex for 39 individuals in 10 rivers. Among them, 35 individuals (89.7?%) were GHp?+?females phenotypically. The opposite feature was noted in the remaining four individuals (10.3?%). This study also revealed that GHp?+?phenotypic females are distributed mainly in the Sea of Japan, whereas GHp- phenotypic male tend to appear in the Sea of Okhotsk. In addition, there was a significant negative correlation between the distance from the Bishabetsu River, where frequency of GHp?+?phenotypic females was the highest, and the frequency of those individuals in each river. These results suggest that the distribution of masu salmon with incongruent genotypic and phenotypic sex would be related to the movement of individuals among the populations and regions.     

Genotypic and phenotypic consequences of reintroduction history in the black-footed ferret (<Emphasis Type="Italic">Mustela nigripes</Emphasis>)

Population augmentation with translocated individuals has been shown to alleviate the effects of bottlenecks and drift. The first step to determine whether restoration for genetic considerations is warranted is to genetically monitor reintroduced populations and compare results to those from the source. To assess the need for genetic restoration, we evaluated genetic diversity and structure of reintroduced (n = 3) and captive populations of the endangered black-footed ferret (Mustela nigripes). We measured genotypic changes among populations using seven microsatellite markers and compared phenotypic changes with eight morphometric characters. Results indicated that for the population which rapidly grew post-reintroduction, genetic diversity was equivalent to the captive, source population. When growth languished, only the population that was augmented yearly maintained diversity. Without augmentation, allelic diversity declined precipitously and phenotypic changes were apparent. Ferrets from the genetically depaupertate population had smaller limbs and smaller overall body size than ferrets from the two populations with greater diversity. Population divergence (F _ST = 0.10 ± 0.01) was surprisingly high given the common source of populations. Thus, it appears that 5–10 years of isolation resulted in both genotypic divergence and phenotypic changes to populations. We recommend translocation of 30–40 captive individuals per annum to reintroduction sites which have not become established quickly. This approach will maximize the retention of genetic diversity, yet maintain the beneficial effects of local adaptation without being swamped by immigration.     

Low genetic variability of <Emphasis Type="Italic">Rhinolophus mehelyi</Emphasis> (Mehely's horseshoe bat) in Romania

Rhinolophus mehelyi (Mehely's horseshoe bat) is a vulnerable species with an increasingly fragmented distribution. In Romania, populations of R. mehelyi have experienced a dramatic decline over the past 50 years, and the current population size is estimated at only 100 adult individuals inhabiting almost exclusively the Limanu cave. In the present study, we investigated the genetic consequences of population decline for the viability of the remaining population of R. mehelyi in Romania. We sequenced and analyzed a 359-bp fragment of the mitochondrial control region from the only known Romanian population and compared it with two geographically close colonies from Bulgaria. A single haplotype was found in the Romanian population compared to 10 in the Bulgarian population, suggesting genetic isolation.     

Identification of natural hybrids between Cottus poecilopus,Heckel, 1837, and Cottus gobio,Linnaeus, 1758, at a hybrid zone on the Svratka River (Czech Republic)

Sculpins occasionally form interspecific hybrids in areas of mutual contact. These can be verified genetically and, potentially, morphologically. At the study site (Svratka River, Czech Republic), Cottus gobio are common whereas C. poecilopus represent a geographically isolated alien population. Potential hybrids between these two species were compared with the parent populations to establish simple identification criteria. Analysis of nuclear and mitochondrial DNA confirmed the existence of a new European hybridisation zone. Hybrids were the result of unidirectional crossing, with female C. gobio taking the maternal position. With the exception of the lateral line position, morphometric characteristics and the epidermis structure were similar in many traits, reflecting the contribution of both species, as well as in the number of sacciform cells where hybrids were similar to C. poecilopus. The vertical position of the lateral line allows recognition of hybrids directly in the field, a useful feature for future studies. The occurrence of these hybrids confirms expansion of non‐native C. poecilopus at the expense of native C. gobio in rivers under anthropogenic pressure.     

Insect morphometry is reproducible under average investigation standards

1. Morphometric research is being applied to a growing number and variety of organisms. Discoveries achieved via morphometric approaches are often considered highly transferable, in contrast to the tacit and idiosyncratic interpretation of discrete character states. The reliability of morphometric workflows in insect systematics has never been a subject of focused research, but such studies are sorely needed. In this paper, we assess the reproducibility of morphometric studies of ants where the mode of data collection is a shared routine.
2. We compared datasets generated by eleven independent gaugers, that is, collaborators, who measured 21 continuous morphometric traits on the same pool of individuals according to the same protocol. The gaugers possessed a wide range of morphometric skills, had varying expertise among insect groups, and differed in their facility with measuring equipment. We used intraclass correlation coefficients (ICC) to calculate repeatability and reproducibility values (i.e., intra‐ and intergauger agreements), and we performed a multivariate permutational multivariate analysis of variance (PERMANOVA) using the Morosita index of dissimilarity with 9,999 iterations.
3. The calculated average measure of intraclass correlation coefficients of different gaugers ranged from R = 0.784 to R = 0.9897 and a significant correlation was found between the repeatability and the morphometric skills of gaugers (p = 0.016). There was no significant association with the magnification of the equipment in the case of these rather small ants. The intergauger agreement, that is the reproducibility, varied between R = 0.872 and R = 0.471 (mean R = 0.690), but all gaugers arrived at the same two‐species conclusion. A PERMANOVA test revealed no significant gauger effect on species identity (R² = 0.69, p = 0.58).
4. Our findings show that morphometric studies are reproducible when observers follow the standard protocol; hence, morphometric findings are widely transferable and will remain a valuable data source for alpha taxonomy.

     

Growth and Development in Wild Owl Monkeys (<Emphasis Type="Italic">Aotus azarai</Emphasis>) of Argentina

Life history predicts that in sexually dimorphic species in which males are the larger sex, males should reach sexual maturity later than females (or vice versa if females are the larger sex). The corresponding prediction that in sexually monomorphic species maturational rates will differ little between the sexes has rarely been tested. We report here sex differences in growth and development to adulthood for 70 female and 69 male wild owl monkeys (Aotus azarai). In addition, using evidence from natal dispersal and first reproduction (mean: 74 mo) for 7 individuals of known age, we assigned ages to categories: infant, 0–6 mo; juvenile, 6.1–24 mo; subadult, 24.1–48 mo; adult >48 mo. We compared von Bertalanffy growth curves and growth rates derived from linear piecewise regressions for juvenile and subadult females and males. Growth rates did not differ between the sexes, although juvenile females were slightly longer than males. Females reached maximum maxillary canine height at ca. 2 yr, about a year earlier than males, and females’ maxillary canines were shorter than males’. Thus apart from canine eruption and possibly crown–rump length, the development of Azara’s owl monkeys conforms to the prediction by life history that in monomorphic species the sexes should develop at similar paces.     

Clonal diversity and turnover in an overwintering Daphnia pulex population,and the effect of fish predation

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Contrasting population genetic structure of two sympatric species of Anthurium (Araceae) along elevation in an Andean mountain forest

The topography of the tropical Andean forest is steep, resulting in physical conditions that change with the elevation, thus driving a high turnover of insect pollinator species over short distances, which may lead to localized gene dispersal, promoting genetic divergence between plant populations distributed along the elevation gradient. In this study, we characterized the population genetic structure of Anthurium caucanum and A. panduriforme, two closely related species that coexist along the elevation gradient in the Andean forest but differ in inflorescence size and abundance of flower visitors. The sampling of both species covered seven elevation bands, from 2,200 to 2,900 MASL. Five microsatellite loci were used to genotype the sampled individuals. Our results indicated that heterozygosity was high for both species. Genotypic richness was significantly lower for A. caucanum (G/N = 0.45) compared with A. panduriforme (G/N = 0.88), while population differentiation was strong for A. caucanum (F_st = 0.23) but low for A. panduriforme (F_st = 0.03). Assignment analysis suggested a low rate of immigration events for A. caucanum populations and a high gene flow between A. panduriforme populations. Based on the seed production of bagged inflorescences, A. caucanum demonstrated the ability to self-pollinate, while A. panduriforme was considered self-incompatible. In addition, genotypic richness decreased with elevation for A. caucanum. In summary, the contrasting population genetic structure of the two Anthurium species along the elevation gradient appear to be the result of different gene flow rates, mating systems, and life-history traits, such as clonal growth, flowering phenology, and density.     

Genetic isolation in an endemic African habitat specialist

The Chestnut‐banded Plover Charadrius pallidus is a Near‐Threatened shorebird species endemic to mainland Africa. We examined levels of genetic differentiation between its two morphologically and geographically distinct subspecies, C. p. pallidus in southern Africa (population size 11 000–16 000) and C. p. venustus in eastern Africa (population size 6500). In contrast to other plover species that maintain genetic connectivity over thousands of kilometres across continental Africa, we found profound genetic differences between remote sampling sites. Phylogenetic network analysis based on four nuclear and two mitochondrial gene regions, and population genetic structure analyses based on 11 microsatellite loci, indicated strong genetic divergence, with 2.36% mitochondrial sequence divergence between individuals sampled in Namibia (southern Africa) and those of Kenya and Tanzania (eastern Africa). This distinction between southern and eastern African populations was also supported by highly distinct genetic clusters based on microsatellite markers (global F_ST = 0.309,  = 0.510, D = 0.182). Behavioural factors that may promote genetic differentiation in this species include habitat specialization, monogamous mating behaviour and sedentariness. Reliance on an extremely small number of saline lakes for breeding and limited dispersal between populations are likely to promote reproductive and genetic isolation between eastern and southern Africa. We suggest that the two Chestnut‐banded Plover subspecies may warrant elevation to full species status. To assess this distinction fully, additional sample collection will be needed, with analysis of genetic and phenotypic traits from across the species’ entire breeding range.     

Population structure and group size of geladas (Theropithecus gelada) at Chenek,Simien Mountains National Park,Ethiopia

The aim of this study was to investigate population structure and group size of geladas (Theropithecus gelada) at Chenek, Simien Mountains National Park. The study was carried out from January 2010 to June 2011 using total count method by classifying the study site into five different blocks. Size of the group was determined by counting individuals of geladas within an hour interval. A total of 397 geladas were counted and the ratio of adult males to adult females was 1 : 1.25, and this difference showed statistical significant (t = 8.157, P < 0.05). There was also significant difference between adult females with juveniles and infants (t = 21.027, P < 0.05). Population structure of geladas in a band comprised a single reproductive male and a number of females, subadults, juveniles and infants. Fission and fusion of individual geladas among different bands were observed during the study period. Geladas at the study site showed population growth and were seen competing for available food. They also stole food from local people and tourists and were seen to be interactive with people. Thus, the interference of people and livestock within the geladas natural habitat should be minimized to avoid human disturbance on the species and its natural habitat.     

Microhabitat use and seasonality of the sexually dimorphic West African centaurus beetle Augosoma centaurus

The sexually dimorphic dynastine centaurus beetle, genus Augosoma (Coleoptera: Scarabeidae), is endemic to tropical Africa where two species are found (A. centaurus and A. hippocrates). These beetles are consumed by rural populations, cause damage in plantations and are targets of insect collectors and traders. We present information on size differences and analyzed intersexual niche divergence and seasonality of A. centaurus in seven study sites in three West African countries (Ivory Coast, Togo and Nigeria). We recorded 711 light-attracted and/or opportunistically encountered individuals, as well as another 97 beetles in standardized transect surveys. In the latter, we found the adult sex ratio was equal, but was significantly skewed towards females in light-attracted and/or opportunistically encountered individuals. In a sample of 298 adult beetles, males were significantly larger than females, with almost no size overlap between sexes. Beetle activity was highly seasonal with most animals observed in November, active from 19:00 h to 24:00 h. Differences in habitat use were not significant between sexes, with most individuals observed in secondary forest. Males were found higher on vegetation than females and beetles of both sexes were found on Pandanus and raffia palms. Beetles were larger in sites with more vegetation cover, and there was a significant effect of tree species on body size of both sexes. Study area or country had no effect on any of the studied parameters. Our study confirms that transect surveys without light trapping can be an effective tool for understanding large-sized tropical beetles of similar ecological characteristics.     

RAD genotyping reveals fine‐scale genetic structuring and provides powerful population assignment in a widely distributed marine species,the American lobster (Homarus americanus)

Deciphering genetic structure and inferring connectivity in marine species have been challenging due to weak genetic differentiation and limited resolution offered by traditional genotypic methods. The main goal of this study was to assess how a population genomics framework could help delineate the genetic structure of the American lobster (Homarus americanus) throughout much of the species’ range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNPs using RAD sequencing to delineate genetic structure and perform population assignment for 586 American lobsters collected in 17 locations distributed across a large portion of the species’ natural distribution range. Our results revealed the existence of a hierarchical genetic structure, first separating lobsters from the northern and southern part of the range (F_CT = 0.0011; P‐value = 0.0002) and then revealing a total of 11 genetically distinguishable populations (mean F_ST = 0.00185; CI: 0.0007–0.0021, P‐value < 0.0002), providing strong evidence for weak, albeit fine‐scale population structuring within each region. A resampling procedure showed that assignment success was highest with a subset of 3000 SNPs having the highest F_ST. Applying Anderson's (Molecular Ecology Resources, 2010, 10, 701) method to avoid ‘high‐grading bias’, 94.2% and 80.8% of individuals were correctly assigned to their region and location of origin, respectively. Lastly, we showed that assignment success was positively associated with sample size. These results demonstrate that using a large number of SNPs improves fine‐scale population structure delineation and population assignment success in a context of weak genetic structure. We discuss the implications of these findings for the conservation and management of highly connected marine species, particularly regarding the geographic scale of demographic independence.     

The wing morphology of limnephilid caddisflies in relation to their habitat preferences

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Using cross-dating techniques to validate ages of aurora rockfish (<Emphasis Type="Italic">Sebastes aurora</Emphasis>): estimates of age,growth and female maturity

Since fishery management regulations have shifted much of the groundfish trawl effort in the northeastern Pacific from the continental shelf to the slope, fishery impacts on unassessed demersal slope rockfish species like the aurora rockfish (Sebastes aurora) may have increased. Understanding the life history of these species is a critical first step in developing management strategies to protect them from overharvest. In this study we employ cross-dating methods to validate the annual periodicity of growth increments and investigate the age, growth and maturity of aurora rockfish, a species for which life history information is quite limited. Specimens were collected on an opportunistic basis from Oregon commercial landings and from research cruises, over the years 2003–2006. Age was estimated for 438 individuals using otoliths processed via the break-and-burn method. The maximum estimated age was 118 years for females (n = 324) and 81 years for males (n = 114). The von Bertalanffy growth function showed that males grow faster and reach a smaller maximum size than females (males: L _inf = 34, K = 0.09, t ₀ = −1.9; females: L _inf = 37, K = 0.06, t ₀ = −5.5), though both sexes demonstrate relatively slow growth. Visual assessment of ovaries showed that the aurora rockfish is a synchronous spawner with parturition occurring in May and June off Oregon. Female age and length at 50% maturity were calculated at 12.6 years and 26 cm, respectively (n = 307). Maturity and age data provided evidence for a protracted adolescence in this species.     

Unraveling the dispersal patterns and the social drivers of natal emigration of a cooperative breeding mammal,the golden lion tamarin

The study of the social drivers of animal dispersal is key to understanding the evolution of social systems. Among the social drivers of natal emigration, the conspecific attraction, aggressive eviction, and reduced social integration hypotheses predict that sexually mature individuals who receive more aggressive behavior and are engaged in less affiliative interactions are more likely to disperse. Few reports have explored these proximate factors affecting emigration in cooperatively breeding species, particularly of Neotropical primates. In this study, we investigated the dispersal patterns and tested the social drivers of natal emigration in the golden lion tamarin (Leontopithecus rosalia) — an endangered species inhabiting Atlantic rainforests fragments in Brazil. We used behavioral and demographic data collected during 7 years from 68 groups of tamarins inhabiting 20 forest fragments. Our analyses from the 160 dispersing individuals showed that dispersal success is higher for males and for those engaged in parallel dispersal, but that males and females use different strategies to enhance their dispersal success, males immigrate into established groups while females form new groups. We did not find high levels of agonistic behavior among group members before natal emigration. Instead we found that conspecific attraction drives natal emigration in both sexes, while additionally the low level of affiliative interactions within the natal group triggers male emigration. We discuss natal emigration in the broader perspective of the cooperative breeding system and the implications of these findings for the conservation of the species.     

Extrinsic and intrinsic factors influence fitness in an avian hybrid zone

The effects of hybridization on evolutionary processes are primarily determined by the differential between hybrid and parental species fitness. Assessing the impacts of hybridization can be challenging, however, as determining the relationship between individual fitness and the extent of introgression in wild populations is difficult. We evaluated the fitness consequences of hybridization for pure and hybrid females in a hybrid zone between two tidal marsh birds, the saltmarsh sparrow (Ammodramus caudacutus), a salt marsh obligate, and Nelson's sparrow (A. nelsoni), which has a broader ecological niche and a much younger evolutionary association with salt marshes. Biotic stressors associated with nesting in tidal environments suggest an important role for differential adaptation in shaping hybrid zone dynamics, with saltmarsh sparrows predicted to be better adapted to nesting in salt marshes. We collected DNA samples from adults (n = 394) and nestlings (n = 431) to determine the extent of introgression using 12 microsatellite loci and tested for the influence of extrinsic (nest placement) and intrinsic (genotype) factors on female reproductive success. We monitored nests (n = 228), collected data on reproductive output, and estimated daily nest survival rates using female genotype and nest characteristics as covariates. To test for reduced survival of hybrid females, we also used capture data to assess the distribution of admixed male and female individuals across age classes. Reproductive success of females varied by genotypic class, but hybrids did not have intermediate success as predicted. Instead, we found that pure Nelson's sparrows had, on average, 33% lower hatching success than any other genotype, whereas F1/F2 hybrids, backcrossed Nelson's sparrows, and backcrossed and pure saltmarsh sparrows all had similar hatching success. We found no effect of genotype or nest placement on daily nest survival probabilities. However, hybrid individuals with a higher proportion of saltmarsh sparrow alleles exhibit nesting behaviours better suited to nesting successfully in tidal marshes. Further, while the proportion of F1/F2 individuals was similar between nestling and adult males, we found that the proportion of F1/F2 individuals was 2.3 times greater in nestling females compared with adult females, indicating reduced survival of F1 females. We conclude that differences in reproductive success among pure and admixed individuals coupled with intrinsic mechanisms (reduced survival in F1 females) shape hybrid zone dynamics in this system.