Genetic population structure in an equatorial sparrow: roles for culture and geography

Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous‐collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence.     

Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps

Altitudinal gradients in mountain regions are short‐range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19–29 individuals from each population. The sample includes two pairs of low‐ and high‐altitude populations from two different valleys. High‐altitude populations showed a lower nucleotide diversity and negative Tajima's D values and were more closely related to each other than to low‐altitude populations from the same valley. Despite their close geographic proximity, demographic analysis revealed that low‐ and high‐altitude populations split between 260 000 and 15 000 years before present. Single nucleotide polymorphisms whose allele frequencies were highly differentiated between low‐ and high‐altitude populations identified genomic regions of up to 50 kb length where patterns of genetic diversity are consistent with signatures of local selective sweeps. These regions harbour multiple genes involved in stress response. Variation among populations in two putative adaptive phenotypic traits, frost tolerance and response to light/UV stress was not correlated with altitude. Taken together, the spatial distribution of genetic diversity reflects a potentially adaptive differentiation between low‐ and high‐altitude populations, whereas the phenotypic differentiation in the two traits investigated does not. It may resemble an interaction between adaptation to the local microhabitat and demographic history influenced by historical glaciation cycles, recent seed dispersal and genetic drift in local populations.     

Test of the adaptive modulation hypothesis in rodents: dietary flexibility and enzyme plasticity.

The phenotypic response of digestive enzymes was assessed in two species of rodents with different foods habits. Species were Phyllotis darwini (omnivorous) and Octodon degus (herbivorous). The activity of sucrase, maltase and aminopeptidase-N were determined in vitro in animals feeding two contrasting diets. No effect of dietary chemistry on sucrase and maltase activities was observed. Nevertheless, aminopeptidase-N showed a reversible response to diet in P. darwini but not in O. degus. Through Principal Component Analysis we separated the specific and non-specific modulation of the enzymes. The analysis showed that aminopeptidase-N activity is up-regulated by dietary protein in P. darwini. Differences in the phenotypic response of this species apparently reflect the historic levels of specific substrates of the natural diets for this enzyme, linking dietary flexibility and digestive plasticity in an evolutionary context.     

Phenotypic consequences of polyploidy and genome size at the microevolutionary scale: a multivariate morphological approach

? Chromosomal duplications and increases in DNA amount have the potential to alter quantitative plant traits like flower number, plant stature or stomata size. This has been documented often across species, but information on whether such effects also occur within species (i.e. at the microevolutionary or population scale) is scarce. ? We studied trait covariation associated with polyploidy and genome size (both monoploid and total) in 22 populations of Dianthus broteri s.l., a perennial herb with several cytotypes (2x, 4x, 6x and 12x) that do not coexist spatially. Principal component scores of organ size/number variations were assessed as correlates of polyploidy, and phylogenetic relatedness among populations was controlled using phylogenetic generalized least squares. ? Polyploidy covaried with organ dimensions, causing multivariate characters to increase, remain unchanged, or decrease with DNA amount. Variations in monoploid DNA amount had detectable consequences on some phenotypic traits. According to the analyses, some traits would experience phenotypic selection, while others would not. ? We show that polyploidy contributes to decouple variation among traits in D. broteri, and hypothesize that polyploids may experience an evolutionary advantage in this plant lineage, for example, if it helps to overcome the constraints imposed by trait integration.     

Population status of Andean Condors in central and southern Bolivia

Andean Condors (Vultur gryphus) are a Near Threatened species that was formerly distributed along the entire length of the Andes from western Venezuela to Tierra del Fuego. Populations have been severely reduced north of Peru, but several thousand Andean Condors still exist in the southern portion of their range in Argentina and Chile. Little is known, however, about the size of the Andean Condor population in the central part of their range in Peru and Bolivia. From June to September 2012, we used feeding stations to attract Andean Condors and estimate the size and structure of the population in the eastern Andes of central and southern Bolivia. We estimated a minimum population of 253 condors, an adult male‐to‐female ratio of 1:0.6, an immature male‐to‐female ratio of 1:0.9, and an adult‐to‐immature ratio of 1:1.1. At our five survey areas, estimated abundance ranged from 15 to 100 condors per area. Males outnumbered females in three areas and the opposite was true in two areas. Our estimated adult‐to‐immature ratio, overall and in each area, suggests that the populations could be reproducing at a high rate. As previously observed in other Andean Condor populations, skewed sex ratios could be associated with differences between sexes and age classes in habitat selection. Although our results suggest that Bolivian populations of Andean Condors are still reasonably large, population monitoring is urgently needed, including use of feeding stations throughout the entire Bolivian range of the species and intensive searches for roosting and nesting sites.     

Psorophora columbiae and Psorophora toltecum (Diptera: Culicidae) Colombian populations cannot be differentiated by isoenzymes

Two populations of the mosquito Psorophora columbiae from the central Andean area of Colombia and one population of Ps. toltecum from the Atlantic coast of Colombia were analyzed for 11 isoenzyme markers. Psorophora columbiae and Ps. toltecum are two of the main vectors of Venezuelan equine encephalitis. We found no conspicuous genetic differences between the two species. The relatively high gene flow levels among these populations indicate that these are not two different species or that there has been recent divergence between these taxa. In addition, no global differential selection among the loci was detected, although the alpha-GDH locus showed significantly less genetic heterogeneity than the remaining loci, which could mean that homogenizing natural selection acts at this locus. No isolation by distance was detected among the populations, and a spatial population analysis showed opposite spatial trends among the 31 alleles analyzed. Multiregression analyses showed that both expected heterozygosity and the average number of alleles per locus were totally determined by three variables: altitude, temperature and size of the human population at the locality. Individually, the expected heterozygosity is more related to these three variables than to the average number of alleles.     

Altitude, migration, and fertility in the Andes

In order to examine the relationship between hypoxia and reduced fertility of high Andean populations, a sample of 241 females living in the low-altitude Tambo Valley of Peru was studied. 63 of the subjects were born in the low-altitude valley, 121 were migrants from high altitudes, and 57 were migrants born in low altitudes. The rate of abortion was low among high-altitude subjects before they migrated, but became greater after migrating. It was found that the high-altitude populations had almost twice as long parity intervals than the low-altitude populations. Compared to migrants born at low altitudes, the high-altitude-born subjects who migrated to low altitudes had higher fertility rates. The results of the study are consistent with the hypothesis that high altitudes, through anoxia, have a lowering effect on fertility. Of the several possible explanations which might account for the increase in fertility of downward migrants on migration from high to low altitude (migration, socioeconomic factors, acculturation, seasonal male emigration from high altitude, and removal of hypoxia stress), altitude appears to be the most significant.     

海拔对全缘叶绿绒蒿植株性状和花特征的表型选择分析

为了研究海拔差异对植株性状、花特征表型选择的影响,以青藏高原高寒草甸的全缘叶绿绒蒿（Meconopsis integrifolia）为研究材料,于盛花期内,测定不同海拔（4 452、4 081和3 681 m）种群中个体植株性状、花特征、单果结实数并进行统计分析,采用线性回归模型估计不同海拔种群间植株性状、花特征所受的表型选择（选择差与选择梯度）。结果表明：（1）随着海拔升高,全缘叶绿绒蒿植株性状、花特征及单果结实数显著降低,海拔越高的种群中株高越矮、叶面积越小、花数越少、花越小、单果结实数越低。（2）不同海拔种群中各性状的表型选择存在差异,较低海拔（3 681 m）种群中花数、花大小具有显著的选择差和选择梯度,表现为花越多、花越大的个体雌性适合度越高;海拔较高（4 081 m）的种群中株高、叶面积及花数更容易受到选择,表现为植株越高、叶面积越大、花越多的个体雌性适合度越高;海拔最高（4 452 m）的种群中叶面积与花数的选择梯度接近显著。（3）植物性状分化伴随着海拔的变化而呈现出差异,较低海拔种群中花特征容易受到选择,而较高海拔种群中可能由于传粉者稀少、资源限制等因素使得株高、叶面积更容易受到选择。     

Genetic differences and phenotypic plasticity in body size between high- and low-altitude populations of the ground beetle Carabus tosanus

The body size of a univoltine carabid beetle Carabus tosanus on Shikoku Island, Japan, was clearly smaller in higher‐altitude populations (subspecies), which possibly represents incipient speciation. To explore the determinants of altitudinal differences in body size in this species, we studied the degree of phenotypic plasticity by conducting rearing experiments at two constant temperatures and examined genetic differences through interpopulation crosses. At 15 °C, C. tosanus had a longer developmental period and a shorter adult body than at 20 °C. Nevertheless, variation in body size due to temperature effects (phenotypic plasticity) was small compared to the interpopulation differences, which suggests substantial genetic differences between populations (subspecies) at different altitudes. In F₁ offspring from crosses between a low‐altitude (subspecies tosanus) and a high‐altitude population (subspecies ishizuchianus), adult body length was affected by the genotypes of both parents, with an interaction effect of parental genotype and offspring sex. Further analyses revealed that adult body length was affected by sex‐linked factors in addition to autosomal factors. These genetic differences in body size may have resulted from adaptations to different altitudes and may be important for the process of incipient speciation because body size differences could contribute to premating reproductive isolation.     

Extent of phenotypic flexibility during long‐distance flight is determined by tissue‐specific turnover rates: a new hypothesis

Phenotypic flexibility in organ size of migratory birds is typically explained in functional terms in accordance with the principal of economic design. However, proposed functional hypotheses do not adequately explain differences in phenotypic flexibility between organs during fasting and in‐flight starvation. We show that the extent of phenotypic flexibility in organ mass in five species of migratory birds during actual migration or simulated in‐flight starvation consistently ranked as follows from highest to lowest mass change: small intestine, liver, kidney, gizzard, heart, flight and leg muscle. This pattern of phenotypic flexibility in organ mass was not consistent with proposed functional hypotheses, and was almost completely explained by differences in tissue‐specific turnover rate measured in vivo using nutrients differing in their isotopic values. Thus, the fundamental process of tissue‐specific protein turnover determines extent of organ mass changes for birds during migration, this likely applies to other organisms during fasting, and no further functional explanation(s) for differences in the magnitude of phenotypic flexibility between organs is required.     

Genetic evaluation of eri silkworm <Emphasis Type="Italic">Samia cynthia ricini</Emphasis>: ISSR loci specific to high and low altitude regimes and quantitative attributes

Genetic structure of populations is under constant pressure from varying geographical conditions that induce phenotypic plasticity in insects. Spatial distribution of 15 populations of Indian eri silkworm, Samia cynthia ricini originated at various altitudes of sub Himalayas based on Euclidean distance realized from yield attributes showed two population clusters irrespective of their place of origin and altitude. However, DNA amplification profile by inter SSR (ISSR) markers showed genetic variations among the populations depend on low and high altitudes. One ISSR locus each specific to high and low altitude population was identified. The locus from high altitude showed deviation from Hardy-Weinberg equilibrium but that from low altitude was in neutrality suggests that the high altitude loci could be under pressure from the altitudinal variations. In association with different yield traits, 18 loci were identified. Of which, three markers showed association with more than one trait indicative of pleiotropic influence. Stepwise addition of markers enhanced the correlation between markers and the associated trait pointed to polygenic influence. Association of markers with altitude and yield traits suggests an imperative relation of rare genetic loci with gene-environment interaction and phenotypic variability in S. c. ricini.     

Altitude,heredity and body proportions in northern Chile

Recent studies of the effects of hypoxia on human growth and adult size have focused mainly on the variability of single measurements. In this paper we explore changes with altitude and ethnicity (Spanish-Aymara ancestry) in body proportions of permanent residents of an altitudinal gradient (0–4000 meters) in northern Chile. Body proportion or shape is assessed by anthropometric indices and principal components of 14 bone measurements. Ethnicity independent of altitude had its major effect on proportions and a lesser effect on size. Aymara had larger relative sitting heights, broader builds and prominent facial development as compared to non-Aymara (Spanish). Altitude also affected head and chest proportions during growth. On the whole, the effects of altitude and Aymara ancestry on the measurements and indices were independent (not necessarily of similar direction or magnitude), in spite of a correlation of ethnicity and altitude in Andean populations.     

Hemoglobin levels in a Himalayan high altitude population

This report presents data on hemoglobin concentrations in a sample of Himalayan high altitude natives measured at their habitual altitude of residence. In this sample of 270 healthy Tibetan adults resident at 3250–3560 m in Upper Chumik, Nepal, the mean hemoglobin concentration is 16.1 ± 1.2 gm/dl among adult males, 14.4 ± 1.4 gm/dl among premenopausal and 15.0 ± 1.1 gm/dl among postmenopausal adult females. 123 of 126 (98%) males, 96 of 100 (96%) premenopausal and 36 of 44 (82%) postmenopausal females have hemoglobin concentrations within two standard deviations of the sea level mean. These data demonstrate that a healthy population may reside at high altitude without the degree of elevation in hemoglobin widely known and cited for Andean highlanders. Comparing published data on mean hemoglobin concentrations of adult Himalayan and Andean samples residing between 3200 m and 4100 m reveals that Himalayan means are systematically lower. This in turn may account for the reported population differences in the prevalence of chronic mountain sickness (Monge's disease). It is hypothesized that Himalayan and Andean highlanders represent alternative patterns of high altitude hematological adaptation.     

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure) exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans) separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2), shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association studies necessary to confirm the role of selection-nominated candidate genes and gene regions in adaptation to altitude.     

Fine-scale phenotypic change across a species transition zone in the genus neotoma: disentangling independent evolution from phylogenetic history

Zones of secondary contact between closely related species provide a rare opportunity to examine evidence of evolutionary processes that reinforce species boundaries and/or promote diversification. Here, we report on genetic and morphological variation in two sister species of woodrats, Neotoma fuscipes and N. macrotis, across a 30-km transition zone in the Sierra Nevada of California. We assessed whether these lineages readily hybridize, and whether their morphology suggests ecological interactions favoring phenotypic diversification. We combined measurements of body size and 11 craniodental traits from nine populations with genetic data to examine patterns of variation within and between species. We used phylogenetic autocorrelation methods to estimate the degree to which phenotypic variation in our dataset arose from independent evolution within populations versus phylogenetic history. Although no current sympatry or hybridization was evident, craniodental morphology diverged in both lineages near their distributional limits, whereas body size converged. The shift in craniodental morphology arose independently within populations whereas body size retained a strong phylogenetic signal, yet both patterns are consistent with expectations of phenotypic change based on different models of resource competition. Our findings demonstrate the importance of examining a suite of morphological traits across contact zones to provide a more complete picture of potential ecological interactions: competition may drive both diversification and convergence in different phenotypic traits.     

Stepwise colonization of the Andes by Ruddy Ducks and the evolution of novel β‐globin variants

Andean uplift played a key role in Neotropical bird diversification, yet past dispersal and genetic adaptation to high‐altitude environments remain little understood. Here we use multilocus population genetics to study population history and historical demographic processes in the ruddy duck (Oxyura jamaicensis), a stiff‐tailed diving duck comprising three subspecies distributed from Canada to Tierra del Fuego and inhabiting wetlands from sea level to 4500 m in the Andes. We sequenced the mitochondrial DNA, four autosomal introns and three haemoglobin genes (α^A, α^D, β^A) and used isolation‐with‐migration (IM) models to study gene flow between North America and South America, and between the tropical and southern Andes. Our analyses indicated that ruddy ducks dispersed first from North America to the tropical Andes, then from the tropical Andes to the southern Andes. While no nonsynonymous substitutions were found in either α globin gene, three amino acid substitutions were observed in the β^A globin. Based on phylogenetic reconstruction and power analysis, the first β^A substitution, found in all Andean individuals, was acquired when ruddy ducks dispersed from low altitude in North America to high altitude in the tropical Andes, whereas the two additional substitutions occurred more recently, when ruddy ducks dispersed from high altitude in the tropical Andes to low altitude in the southern Andes. This stepwise colonization pattern accompanied by polarized β^A globin amino acid replacements suggest that ruddy ducks first acclimatized or adapted to the Andean highlands and then again to the lowlands. In addition, ruddy ducks colonized the Andean highlands via a less common route as compared to other waterbird species that colonized the Andes northwards from the southern cone of South America.     

Comparative population genetics of two dominant plant species of high Andean wetlands reveals complex evolutionary histories and conservation perspectives in Chile’s Norte Chico

High Andean wetlands are naturally fragmented ecosystems that are impacted by anthropogenic activities. Although they constitute important reservoirs of biodiversity and ecosystem service providers, many aspects of their ecology are still unknown. In this study, we investigated the population genetic structure of two dominant and highly interactive plant species of high altitude wetlands, Patosia clandestina (Juncaceae) and Carex gayana (Cyperaceae), in 21 high Andean wetlands of Chile’s Norte Chico. Using rbcL gene sequences and AFLP markers, we found that both species displayed low levels of within-wetland genetic diversity, high inter-population genetic differentiation, and spatially-dependent genetic variation arising from isolation-by-distance. The distance at which populations become genetically independent was of the same order of magnitude in both species (125–175 km). Despite these similarities, idiosyncratic spatial patterns were detected. C. gayana in the three most northeastern wetlands demonstrated marked differences relative to the rest of the populations, with the latter group following a latitudinal stepping-stone pattern. In P. clandestina, a genetic barrier was found to divide the northern and southern populations into two balanced groups, and spatial genetic variation was consistent with a hierarchical island model. The data indicate that each of the two species likely responded to different geological and ecological events, resulting in the definition of unique evolutionarily significant units in both. These results suggest that the implementation of global conservation programs at regional scales would likely result in the loss of important components of biodiversity in these ecosystems, and underscore the need for caution in designing effective conservation strategies.     

Phenotypic evolution in high‐elevation populations of western fence lizards (Sceloporus occidentalis) in the Sierra Nevada Mountains

Adaptive divergence in response to variable habitats, climates, and altitude is often accentuated along elevation gradients. We investigate phenotypic evolution in body size and coloration in the western fence lizard (Sceloporus occidentalis Baird & Girard, 1852) across elevation gradients in Yosemite National Park, California, situated in the Sierra Nevada mountains of Western North America. High‐elevation populations occurring above 2100 m a.s.l. are recognized as a separate subspecies (Sceloporus occidentalis taylori Camp, 1916), with a distinctive phenotype characterized by a large body size and extensive blue ventral pigmentation. We sampled S. occidentalis from across elevation gradients in Yosemite National Park, California, and collected phenotypic data (body size and ventral coloration measurements; 410 specimens) and mitochondrial DNA sequence data (complete NADH1 gene; 969 bp, 181 specimens) to infer phylogenetic relationships, and examine the genetic and phenotypic diversity among populations. Populations of S. occidentalis in Yosemite National Park follow Bergmann's rule and exhibit larger body sizes in colder, high‐elevation environments. The high‐elevation subspecies S. o. taylori is not monophyletic, and the mitochondrial DNA genealogy supports a model of convergent phenotypic evolution among high‐elevation populations belonging to different river drainages. The hypothesis that separate populations of S. occidentalis expanded up river drainages after the recession of glaciers is supported by population demographic analyses, and suggest that Bergmann's clines can evolve rapidly along elevation gradients. The distinctive high‐elevation phenotype that is attributable to S. o. taylori has evolved independently several times, and includes adaptive phenotypic changes associated with increases in body size and ventral coloration. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 630–641.     

The rate of fitness-valley crossing in sexual populations

Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a "fitness valley" to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population.