A new species of <Emphasis Type="Italic">Alloneuron</Emphasis> (Melastomataceae) from northern Peru

Alloneuron glomeratum, a new species of Melastomataceae from the Marañón Valley in northern Peru, is described and illustrated. This new species can be quickly recognized and differentiated from other species in Alloneuron by the presence of pseudo-glomerulate inflorescences.     

The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru

Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic divergence in allopatry, we employed a comparative phylogeographic approach consisting of replicates of ecologically similar Andean bird species isolated across a major biogeographic barrier, the Marañon Valley of Peru. Our study design leverages variation among codistributed taxa in their degree of plumage, morphometric, and vocal differentiation across the Marañon to examine the tempo of phenotypic evolution. We found that substantial plumage differences between populations required roughly two million years to evolve. In contrast, morphometric trait evolution showed greater idiosyncrasy and stasis. Our results demonstrate that despite a large degree of idiosyncrasy in the relationship between genetic and phenotypic divergence across taxa and environments, comparative studies within regions may reveal predictability in the pace of phenotypic divergence. Our results also suggest that social selection is important for driving differentiation of populations found in similar environments.     

Limited gene flow among brown bear populations in far Northern Europe? Genetic analysis of the east–west border population in the Pasvik Valley

Noninvasively collected genetic data can be used to analyse large‐scale connectivity patterns among populations of large predators without disturbing them, which may contribute to unravel the species’ roles in natural ecosystems and their requirements for long‐term survival. The demographic history of brown bears (Ursus arctos) in Northern Europe indicates several extinction and recolonization events, but little is known about present gene flow between populations of the east and west. We used 12 validated microsatellite markers to analyse 1580 hair and faecal samples collected during six consecutive years (2005–2010) in the Pasvik Valley at 70°N on the border of Norway, Finland and Russia. Our results showed an overall high correlation between the annual estimates of population size (N_c), density (D), effective size (N_e) and N_e/N_c ratio. Furthermore, we observed a genetic heterogeneity of ～0.8 and high N_e/N_c ratios of ～0.6, which suggests gene flow from the east. Thus, we expanded the population genetic study to include Karelia (Russia, Finland), Västerbotten (Sweden) and Troms (Norway) (477 individuals in total) and detected four distinct genetic clusters with low migration rates among the regions. More specifically, we found that differentiation was relatively low from the Pasvik Valley towards the south and east, whereas, in contrast, moderately high pairwise F_ST values (0.91–0.12) were detected between the east and the west. Our results indicate ongoing limits to gene flow towards the west, and the existence of barriers to migration between eastern and western brown bear populations in Northern Europe.     

A new species of Anchoviella (Clupeiformes: Engraulidae) from the western Amazon River in Peru,with comments on congeners in the Peruvian Amazon River

Anchoviella hernanni sp. nov. is described from the upper Amazon River basin, in tributaries of the Marañon, Ucayali and Madre de Dios river drainages that drain the Peruvian Andes. The new taxon can be distinguished from all congeners except Anchoviella jamesi, Anchoviella manamensis and Anchoviella perezi, by having 12–15 gill rakers in the lower branch of the first gill arch (v·16–35) and from those species by the distance between verticals through the posterior margin of the orbit to the posterior margin of the upper jaw 9·5–14·8% head length; L_H (v. up to 6·0% L_H). An updated identification key of all freshwater species of Anchoviella and morphological comparisons between all species of the genus occurring in Peru are provided.     

Consequences of multiple mating‐system shifts for population and range‐wide genetic structure in a coastal dune plant

Evolutionary transitions from outcrossing to selfing can strongly affect the genetic diversity and structure of species at multiple spatial scales. We investigated the genetic consequences of mating‐system shifts in the North American, Pacific coast dune endemic plant Camissoniopsis cheiranthifolia (Onagraceae) by assaying variation at 13 nuclear (n) and six chloroplast (cp) microsatellite (SSR) loci for 38 populations across the species range. As predicted from the expected reduction in effective population size (N_e) caused by selfing, small‐flowered, predominantly selfing (SF) populations had much lower nSSR diversity (but not cpSSR) than large‐flowered, predominantly outcrossing (LF) populations. The reduction in nSSR diversity was greater than expected from the effects of selfing on N_e alone, but could not be accounted for by indirect effects of selfing on population density. Although selfing should reduce gene flow, SF populations were not more genetically differentiated than LF populations. We detected five clusters of nSSR genotypes and three groups of cpSSR haplotypes across the species range consisting of parapatric groups of populations that usually (but not always) differed in mating system, suggesting that selfing may often initiate ecogeographic isolation. However, lineage‐wide genetic variation was not lower for selfing clusters, failing to support the hypothesis that selection for reproductive assurance spurred the evolution of selfing in this species. Within three populations where LF and SF plants coexist, we detected genetic differentiation among diverged floral phenotypes suggesting that reproductive isolation (probably postzygotic) may help maintain the striking mating‐system differentiation observed across the range of this species.     

PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐white Ficedula flycatchers

Climatic fluctuations during the Quaternary period governed the demography of species and contributed to population differentiation and ultimately speciation. Studies of these past processes have previously been hindered by a lack of means and genetic data to model changes in effective population size (N_e) through time. However, based on diploid genome sequences of high quality, the recently developed pairwise sequentially Markovian coalescent (PSMC) can estimate trajectories of changes in N_e over considerable time periods. We applied this approach to resequencing data from nearly 200 genomes of four species and several populations of the Ficedula species complex of black‐and‐white flycatchers. N_e curves of Atlas, collared, pied and semicollared flycatcher converged 1–2 million years ago (Ma) at an N_e of ≈ 200 000, likely reflecting the time when all four species last shared a common ancestor. Subsequent separate N_e trajectories are consistent with lineage splitting and speciation. All species showed evidence of population growth up until 100–200 thousand years ago (kya), followed by decline and then start of a new phase of population expansion. However, timing and amplitude of changes in N_e differed among species, and for pied flycatcher, the temporal dynamics of N_e differed between Spanish birds and central/northern European populations. This cautions against extrapolation of demographic inference between lineages and calls for adequate sampling to provide representative pictures of the coalescence process in different species or populations. We also empirically evaluate criteria for proper inference of demographic histories using PSMC and arrive at recommendations of using sequencing data with a mean genome coverage of ≥18X, a per‐site filter of ≥10 reads and no more than 25% of missing data.     

Zur kenntnis der in peru lebenden tauben der gattung columbigallina boie∗

Contribución al conocimiento de los representantes peruanos de palomas del género Cotumbi‐ gallina Boie (con la descripción de una nueva subespecie).—Se conoce dos especies de Columbigallina en el Perú: C. minuta y C. talpacoti. La Columbigallina buckleyi tratado hasta ahora como especie separada es solamente una subespecie de C. talpacoti como ya supone Dorst (1957). Las Columbigallinas que viven en el dominio del Rio Marañón no presentan una verdadera población de transición entre C. talpacoti y C. buckleyi como anota Dorst (1957) sino que ellas poseen caracteres propias que justifican la fundación de una nueva subespecie: Columbigallina talpacoti dorsti n. ssp. Eupelia cruziana, incluido por Peters (1937) en el género Columbigallina está consi‐derado aquí como género aparte.     

Sweepstakes reproductive success is absent in a New Zealand snapper (Chrysophrus auratus) population protected from fishing despite “tiny” Ne/N ratios elsewhere

A landmark study published in 2002 estimated a very small N_e/N ratio (around 10^–5) in a population of pink snapper (Chrysophrys auratus, Forster, 1801) in the Hauraki Gulf in New Zealand. It epitomized the tiny N_e/N ratios (<10^–3) reported in marine species due to the hypothesized operation of sweepstakes reproductive success (SRS). Here we re‐evaluate the occurrence of SRS in marine species and the potential effect of fishing on the N_e/N ratio by studying the same species in the same region, but in a population that has been protected from fishing since 1975. We combine empirical, simulation and model‐based approaches to estimate N_e (and N_b) from genotypes of 1,044 adult fish and estimate N using recapture‐probabilities. The estimated N_e/N ratio was much larger (0.33, SE: 0.14) than expected. The magnitude of estimates of population‐wide variance in individual lifetime reproductive success (10–18) suggested that the sweepstakes effect was negligible in the study population. After evaluating factors that could explain the contrast between studies – experimental design, life history differences, environmental effects and the influence of exploitation on the N_e/N ratio – we conclude that the low N_e of the Hauraki Gulf population is associated with demographic instability in the harvested compared to the protected population despite circumstantial evidence that the 2002 study may have underestimated N_e. This study has broad implications for the prevailing view that reproductive success in the sea is largely driven by chance, and for genetic monitoring of populations using the N_e/N ratio and N_b.     

A genetic demographic analysis of Lake Malawi rock‐dwelling cichlids using spatio‐temporal sampling

We estimated the effective population sizes (N_e) and tested for short‐term temporal demographic stability of populations of two Lake Malawi cichlids: Maylandia benetos, a micro‐endemic, and Maylandia zebra, a widespread species found across the lake. We sampled a total of 351 individuals, genotyped them at 13 microsatellite loci and sequenced their mitochondrial D‐loop to estimate genetic diversity, population structure, demographic history and effective population sizes. At the microsatellite loci, genetic diversity was high in all populations. Yet, genetic diversity was relatively low for the sequence data. Microsatellites yielded mean N_e estimates of 481 individuals (±99 SD) for M. benetos and between 597 (±106.3 SD) and 1524 (±483.9 SD) individuals for local populations of M. zebra. The microsatellite data indicated no deviations from mutation–drift equilibrium. Maylandia zebra was further found to be in migration–drift equilibrium. Temporal fluctuations in allele frequencies were limited across the sampling period for both species. Bayesian Skyline analyses suggested a recent expansion of M. zebra populations in line with lake‐level fluctuations, whereas the demographic history of M. benetos could only be estimated for the very recent past. Divergence time estimates placed the origin of M. benetos within the last 100 ka after the refilling of the lake and suggested that it split off the sympatric M. zebra population. Overall, our data indicate that micro‐endemics and populations in less favourable habitats have smaller N_e, indicating that drift may play an important role driving their divergence. Yet, despite small population sizes, high genetic variation can be maintained.     

MICROHABITAT DIFFERENCES IMPACT PHYLOGEOGRAPHIC CONCORDANCE OF CODISTRIBUTED SPECIES: GENOMIC EVIDENCE IN MONTANE SEDGES (CAREX L.) FROM THE ROCKY MOUNTAINS

By selecting codistributed, closely related montane sedges from the Rocky Mountains that are similar in virtually all respects but one—their microhabitat affinities—we test predictions about how patterns of genetic variation are expected to differ between Carex nova, an inhabitant of wetlands, and Carex chalciolepis, an inhabitant of drier meadows, slopes, and ridges. Although contemporary populations of the taxa are similarly isolated, the distribution of glacial moraines suggests that their past population connectedness would have differed. Sampling of codistributed population pairs from different mountain ranges combined with the resolution provided by over 24,000 single nucleotide polymorphism loci supports microhabitat‐mediated differences in the sedges’ patterns of genetic variation that are consistent with their predicted differences in the degree of isolation of ancestral source populations. Our results highlight how microhabitat preferences may interact with glaciations to produce fundamental differences in the past distributions of presently codistributed species. We discuss the implications of these findings for generalizing the impacts of climate‐induced distributional shifts for communities, as well as for the prospects of gaining insights about species‐specific deterministic processes, not just deterministic community‐level responses, from comparative phylogeographic study.     

Environmental and topographic variables shape genetic structure and effective population sizes in the endangered Yosemite toad

Aim Describing the landscape variables that accurately reflect how environmental and topographic variations affect population connectivity and demography is a major goal of landscape genetics and conservation biology. However, few landscape genetics studies have quantified the relationships between landscape variables and effective population size (N_e), although N_e is a key conservation and population genetics parameter. In this study, I estimated genetic structure and effective population sizes in the Yosemite toad (Bufo canorus) and tested for associations with environmental and geographic variables. Location Yosemite National Park, California, USA. Methods I estimated F_ST, D_ps and N_e using 10 microsatellite loci amplified from 781 individuals from 24 populations. I used three landscape variables (environmental variation, topography and slope) to generate geographic distance models and a series of regression analyses to identify the variables that contributed to genetic structure in this species. I also tested for correlations between N_e and a suite of variables, including geographic and genetic isolation, habitat suitability, elevation, temperature and precipitation. Results I found substantial variation in genetic distances between populations (F_ST = 0.004–0.396, D_ps = 0.045–0.839) and in effective population sizes (N_e = 9–52). Environmental variation and slope played important roles in explaining variation in genetic distances, and precipitation variables were significantly correlated with N_e. Main conclusions These results show that environmental and topographic variables are both important for understanding population connectivity in B. canorus and provide some of the first evidence, in any species, for a link between environmental variables and effective population size.     

Multiple estimates of effective population size for monitoring a long‐lived vertebrate: an application to Yellowstone grizzly bears

Effective population size (N_e) is a key parameter for monitoring the genetic health of threatened populations because it reflects a population's evolutionary potential and risk of extinction due to genetic stochasticity. However, its application to wildlife monitoring has been limited because it is difficult to measure in natural populations. The isolated and well‐studied population of grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem provides a rare opportunity to examine the usefulness of different N_e estimators for monitoring. We genotyped 729 Yellowstone grizzly bears using 20 microsatellites and applied three single‐sample estimators to examine contemporary trends in generation interval (GI), effective number of breeders (N_b) and N_e during 1982–2007. We also used multisample methods to estimate variance (N_eV) and inbreeding N_e (N_eI). Single‐sample estimates revealed positive trajectories, with over a fourfold increase in N_e (≈100 to 450) and near doubling of the GI (≈8 to 14) from the 1980s to 2000s. N_eV (240–319) and N_eI (256) were comparable with the harmonic mean single‐sample N_e (213) over the time period. Reanalysing historical data, we found N_eV increased from ≈80 in the 1910s–1960s to ≈280 in the contemporary population. The estimated ratio of effective to total census size (N_e/N_c) was stable and high (0.42–0.66) compared to previous brown bear studies. These results support independent demographic evidence for Yellowstone grizzly bear population growth since the 1980s. They further demonstrate how genetic monitoring of N_e can complement demographic‐based monitoring of N_c and vital rates, providing a valuable tool for wildlife managers.     

Genetic variation and effective population size in isolated populations of coastal cutthroat trout

Following glacial recession in southeast Alaska, waterfalls created by isostatic rebound have isolated numerous replicate populations of coastal cutthroat trout (Oncorhynchus clarkii clarkii) in short coastal streams. These replicate isolated populations offer an unusual opportunity to examine factors associated with the maintenance of genetic diversity. We used eight microsatellites to examine genetic variation within and differentiation among 12 population pairs sampled from above and below these natural migration barriers. Geological evidence indicated that the above-barrier populations have been isolated for 8,000–12,500 years. Genetic differentiation among below-barrier populations (F _ST = 0.10, 95% C.I. 0.08–0.12) was similar to a previous study of more southern populations of this species. Above-barrier populations were highly differentiated from adjacent below-barrier populations (mean pairwise F _ST = 0.28; SD 0.18) and multiple lines of evidence were consistent with asymmetric downstream gene flow that varied among streams. Each above-barrier population had reduced within-population genetic variation when compared to the adjacent below-barrier population. Within-population genetic diversity was significantly correlated with the amount of available habitat in above-barrier sites. Increased genetic differentiation of above-barrier populations with lower genetic diversity suggests that genetic drift has been the primary cause of genetic divergence. Long-term estimates of N _e based on loss of heterozygosity over the time since isolation were large (3,170; range 1,077–7,606) and established an upper limit for N _e if drift were the only evolutionary process responsible for loss of genetic diversity. However, it is likely that a combination of mutation, selection, and gene flow have also contributed to the genetic diversity of above-barrier populations. Contemporary above-barrier N _e estimates were much smaller than long-term N _e estimates, not correlated with within-population genetic diversity, and not consistent with the amount of genetic variation retained, given the approximate 10,000-year period of isolation. The populations isolated by waterfalls in this study that occur in larger stream networks have retained substantial genetic variation, which suggests that the amount of habitat in headwater streams is an important consideration for maintaining the evolutionary potential of isolated populations.     

Sea‐level variations have influenced the demographic history of estuarine and freshwater fishes of the coastal plain of Paraná, Brazil

This study surveyed the mitochondrial haplotype diversity of nine freshwater fish species and two estuarine–marine species from the coastal basins and drainages of the highland plateaus of Paraná, Brazil. Portions of the cytochrome b gene or the control region were sequenced. The demographic history of each species was inferred using the Bayesian skyline method, mismatch distribution analysis and statistical neutrality tests. Demographic reconstruction analyses revealed a single pattern of variation in the effective population size (N_e) among species. No dramatic changes in N_e were detected in upland species. By contrast, evidence of population expansion over the past 200 000 years was detected in all coastal plain and estuarine species. These findings correspond to periods of low sea‐level (regressions) followed by a rapid increase in the sea‐level by >100 m. The resulting reconnections and subsequent fragmentation and isolation between the estuarine and freshwater bodies were putatively relevant to the historical demography of the fish species in these areas.     

The large Amazonian peatland carbon sink in the subsiding Pastaza‐Marañón foreland basin,Peru

The carbon (C) dynamics of tropical peatlands can be of global importance, because, particularly in Southeast Asia, they are the source of considerable amounts of C released to the atmosphere as a result of land‐use change and fire. In contrast, the existence of tropical peatlands in Amazonia has been documented only recently. According to a recent study, the 120 000 km² subsiding Pastaza‐Marañón foreland basin in Peruvian Amazonia harbours previously unstudied and up to 7.5 m thick peat deposits. We studied the role of these peat deposits as a C reserve and sink by measuring peat depth, radiocarbon age and peat and C accumulation rates at 5–13 sites. The basal ages varied from 1975 to 8870 cal yr bp , peat accumulation rates from 0.46 to 9.31 mm yr^?1 and C accumulation rates from 28 to 108 g m^?2 yr^?1. The total peatland area and current peat C stock within the area of two studied satellite images were 21 929 km² and 3.116 Gt (with a range of 0.837–9.461 Gt). The C stock is 32% (with a range of 8.7–98%) of the best estimate of the South American tropical peatland C stock and 3.5% (with a range of 0.9–10.7%) of the best estimate of the global tropical peatland C stock. The whole Pastaza‐Marañón basin probably supports about twice this peatland area and peat C stock. In addition to their contemporary geographical extent, these peatlands probably also have a large historical (vertical) extension because of their location in a foreland basin characterized by extensive river sedimentation, peat burial and subsidence for most of the Quaternary period. Burial of peat layers in deposits of up to 1 km thick Quaternary river sediments removes C from the short‐term C cycle between the biosphere and atmosphere, generating a long‐term C sink.     

ESTIMATION OF PARAMETERS OF INBREEDING AND GENETIC DRIFT IN POPULATIONS WITH OVERLAPPING GENERATIONS

Many long‐lived plant and animal species have nondiscrete overlapping generations. Although numerous models have been developed to predict the effective sizes (N_e) of populations with overlapping generations, they are extremely difficult to apply to natural populations because of the large array of unknown and elusive life‐table parameters involved. Unfortunately, little work has been done to estimate the N_e of populations with overlapping generations from marker data, in sharp contrast to the situation of populations with discrete generations for which quite a few estimators are available. In this study, we propose an estimator (EPA, estimator by parentage assignments) of the current N_e of populations with overlapping generations, using the sex, age, and multilocus genotype information of a single sample of individuals taken at random from the population. Simulations show that EPA provides unbiased and accurate estimates of N_e under realistic sampling and genotyping effort. Additionally, it yields estimates of other interesting parameters such as generation interval, the variances and covariances of lifetime family size, effective number of breeders of each age class, and life‐table variables. Data from wild populations of baboons and hihi (stitchbird) were analyzed by EPA to demonstrate the use of the estimator in practical sampling and genotyping situations.     

Genetic divergence predicts reproductive isolation in damselflies

Reproductive isolation is the defining characteristic of a biological species, and a common, but often untested prediction is a positive correlation between reproductive isolation and genetic divergence. Here, we test for this correlation in odonates, an order characterized by strong sexual selection. First, we measure reproductive isolation and genetic divergence in eight damselfly genera (30 species pairs) and test for a positive correlation. Second, we estimate the genetic threshold preventing hybrid formation and empirically test this threshold using wild populations of species within the Ischnura genus. Our results indicate a positive and strong correlation between reproductive isolation and genetic distance using both mitochondrial and nuclear genes cytochrome oxidase II (COII: r = 0.781 and 18S–28S: r = 0.658). Hybridization thresholds range from ?0.43 to 1.78% for COII and ?0.052–0.71% for 18S–28S, and both F₁‐hybrids and backcrosses were detected in wild populations of two pairs of Ischnura species with overlapping thresholds. Our study suggests that threshold values are suitable to identify species prone to hybridization and that positive isolation–divergence relationships are taxonomically widespread.     

Habitat Specialization by Birds in Western Amazonian White‐sand Forests

In the Peruvian Amazon, white‐sand forests are patchily distributed and restricted to a few localities in the North. Although recent studies have documented patterns of habitat specialization by plants in these unique forests, very few studies of the fauna of these habitats have been conducted. The species composition of the avifauna of the white‐sand forests at six localities in the region was sampled by conducting transects and point counts. Surrounding habitats were also sampled to compare avifaunal communities and to determine the degree of restriction of bird species to white‐sand habitats. Non‐metric multidimensional scaling analysis showed that bird communities of white‐sand forests were more similar to each other than they were to terra firme or flooded forest communities. Sites on either side of the Amazon‐Marañón barrier were the most similar within habitat type consistent with the hypothesis that these rivers represent a major biogeographic barrier. Twenty‐six species, belonging to 13 families, were to some degree specialized to white‐sand forests. This is the first comprehensive ornithological assessment carried out on these habitats in Peru. The high degree of habitat specialization found in these 26 bird species highlights the need for conservation and management measures that will protect white‐sand forests.     

Genetic diversity in Dactylorhiza majalis subsp. majalis populations (Orchidaceae) of northern Poland

We analysed 16 populations of Dactylorhiza majalis subsp. majalis from northern Poland, simultaneously utilizing both morphological and molecular data. Genetic differentiation was examined using five microsatellite loci, and morphological variation was assessed for 23 characters. At the species level, our results showed a moderate level of genetic diversity (A = 6.00; A_e = 1.86; H_o = 0.387; F_IS = 0.139) which varied between the studied populations (A = 2.60–4.20; A_e = 1.68–2.39; H_o = 0.270–0.523; F_IS = ?0.064–0.355). A significant excess of homozygotes was detected in five population, while excess of heterozygotes was observed in four populations, but the latter values were statistically insignificant. Moderate, but clear between population genetic differentiation was found (F_ST = 0.101; p < 0.001). Considering pairwise‐F_ST and number of migrants among populations, we recognized three population groups (I, II, III), where the first could be further divided into two subgroups (Ia, Ib). These three groups differed with respect to gene flow values (N_m = 0.39–1.12). The highest number of migrants per generation was noticed among populations of subgroup Ia (8.58), indicative of a central panmictic population with free gene flow surrounded by peripatric local populations (Ib) with more limited gene flow. Geographic isolation, habitat fragmentation and limited seed dispersal are inferred to have caused limitations to gene flow among the three indicated population groups. There was a significant correlation between the morphological and genetic distance matrices. A weak but significant pattern of isolation by distance was also observed (r = 0.351; p < 0.05).