Mitochondrial gene divergence of Colombian Drosophila pseudoobscura

Isolated populations of drosophila pseudoobscura, separated from North American populations by about 2,400 km, were found in Colombia in 1960. We compared for sequences of the small ribosomal RNA (srRNA) gene on the mitochondria between North American and Colombian D. pseudoobscura in order to clarify the age of the Colombian isolates. The North American populations were not genetically different from each other but were genetically different from the Colombian populations. The Mexican strains represent the area from which the Colombian founders might have come. The estimated net nucleotide divergence between Mexican and Colombian D. pseudoobscura indicates that the Colombian population is not an ancient lineage. Phylogenies using both distance and parsimony methodologies reinforced this conclusion. The Colombian samples group together with both methods but, according to the bootstrap analysis, not significantly. It appears that the populations have not been separated long enough for their DNA sequences to show much divergence.      

GENETIC DIFFERENTIATION AMONG ANCESTRAL AND INTRODUCED POPULATIONS OF THE EURASIAN TREE SPARROW (PASSER MONTANUS)

We compared genetic variation in three introduced North American populations of Passer montanus with an ancestral German population, a native Swedish population, and an introduced Australian population. The North American P. montanus were less variable genetically than the ancestral German birds, presumably a result of the founding event. The genetic structure of all six populations of P. montanus can be explained in terms of interaction among mutation, genetic drift, effective population size, and unknown selective factors. Cluster analyses and an ordination of distance measures derived from electrophoretic data generally showed relationships in phenetic space among populations consistent with the magnitude of their geographic separation. An exception occurred with the Swedish population, which was closer in the ordination to a North American population than to the geographically neighboring German population. This seemingly anomolous juxtaposition was attributed to the relative abundance of alleles present in the Swedish birds. Populations of P. montanus seem to have diverged in a manner similar to that seen in conspecific disjunct populations, i.e., at present showing no trenchant indication of genetic speciation.     

Coat Gene Profiles of Several Cat Populations in Cuba,Costa Rica,Colombia, Paraguay,Chile and Argentina,and Possible Genetic Origins of These Cat Populations

Until the present moment, only a scarce number of Latin American domestic cat populations have been studied from a population genetic standpoint. For this reason, the cat populations of La Havana (Cuba), San José (Costa Rica), Bogotá and Ibagué (Colombia), Asunción (Paraguay), Santiago (Chile) and Buenos Aires (Argentina) were sampled for several coat genes. The results obtained were as follows: (1) there was a strong genetic resemblence between several Hispanic American cat populations (especially, those of Buenos Aires, San José and the two Colombian populations studied) and those from South Western United States (California, Texas and Colorado), which adds suport to the suspicion that these populations probably have a common origin; (2) The cat population of Santiago (Chile), contrarily to the other Hispanic American populations studied, showed a strong genetic resemblance with some Anglo North American populations; and (3) The I (long hair) and d(dilution) alleles showed systematic higher frequencies in the Hispanic American populations than those observed in Spain. Although the Hispanic American populations were not identical to the current Spanish populations (with the exception of Asuncion), this historic genetic experiment was very different to that found for the British populations and their overseas colonies.     

Morphometric characterization of thalassohaline Artemia franciscana populations from the Colombian Caribbean

Aim To establish possible interpopulation relationships among Colombian Artemia franciscana (Crustacea, Anostraca) populations. Location Colombian Caribbean coast (Manaure, Galerazamba, Salina Cero and Tayrona) and a similar thalassohaline reference population from San Francisco Bay (SFB‐USA). Methods Morphometric characters of male and female cultured individuals of A. franciscana were measured. The populations were grouped according to: (1) population type (populations grouped according to two broad regions of origin: North America and the Caribbean coast), and (2) specific geographical origin (populations selected according to five specific local origins: Manaure, Galerazamba, Salina Cero, Tayrona and SFB) and evaluated using forward stepwise discriminant analysis (SPSS, Ver. 10). Results Optimal discriminant variables for males grouped by the type of population were left setae and antenna length, and for females they were abdominal length and antenna length. However, for males grouped by their specific geographical origin, the optimal variables were furca length, left setae, antenna length, eye separation, abdominal width and abdominal length, and for the females, they were furca length, abdominal length, left setae and eye separation. Male and female Colombian Caribbean populations were separated from the North American populations. However, our results show that the classification based on male characters provides better group membership than females. Main conclusions Male morphometric characters separated the type of population groups more clearly than the female characters, because all Colombian populations were correctly positioned in the Caribbean coast region and the SFB population in the North American region, with no overlapping between the two types, as was the case for the female individuals. Likewise, male individuals correctly position the Salina Cero population to its neighbouring Galerazamba population and to the other Colombian populations. In contrast, female individuals from Salina Cero did not cluster with the other Colombian coast populations (Galerazamba, Tayrona and Manaure) or with the SFB population.     

Weedy adaptation in Setaria spp. II. Genetic diversity and population genetic structure in S. glauca,S. geniculata,and S. faberii (Poaceae)

Setaria glauca (yellow foxtail), S. geniculata (knotroot foxtail), and S. faberii (giant foxtail) are important cosmopolitan weeds of temperate and tropical regions. Isozyme markers were used to investigate genetic diversity and population genetic structure in 94 accessions of yellow foxtail, 24 accessions of knotroot foxtail, and 51 accessions of giant foxtail, collected mainly from North America and Eurasia. Giant foxtail populations were nearly identical genetically, with only one population exhibiting isozyme polymorphism. Yellow and knotroot foxtail populations had low genetic diversity but marked population differentiation. Although the latter species are similar morphologically, they are readily distinguished electrophoretically, with Nei's genetic identity being 0.83. In both species, genetic divergence between accessions from Eurasia and North America was minimal. Populations from the native ranges had slightly greater genetic diversity than those from the respective introduced ranges. Yellow foxtail populations genetically clustered into Asian, European, and North American groups. Within North America, yellow foxtail populations from Iowa were genetically diverse whereas populations collected from other North American locations were nearly monomorphic for the same multilocus genotype. Knotroot foxtail populations in North America were genetically differentiated into northern and southern groups on either side of a line at ≈37° N latitude. No genetic patterning was evident in knotroot foxtail populations from Eurasia. In both yellow and knotroot foxtail, patterns of population genetic structure have been influenced by several factors, including genetic bottlenecks associated with founder events, genetic drift, and natural selection.     

Examining the genetic diversity of the orange blossom wheat midge,Sitodiplosis mosellana (Géhin), across North America

The orange blossom wheat midge, Sitodiplosis mosellana (Géhin) (Diptera: Cecidomyiidae), is a significant pest of wheat (Triticum spp.) grown in the Northern Hemisphere. It was accidently introduced to North America over 200 years ago and has subsequently spread throughout the northern Great Plains. Since 2010, several Canadian spring wheat varieties containing the resistance gene Sm1 have been released. Due to the potential of wheat midge populations to evolve virulent biotypes to Sm1, cultivars containing Sm1 are grown with a susceptible cultivar in an interspersed refuge. An understanding of the genetic diversity of wheat midge populations could provide important information on the potential development of resistance to Sm1. In the current study, we used two mitochondrial genes (CO1 and ND4) from wheat midge collected across the northern Great Plains and Québec in North America to assess population structure and genetic diversity. We found limited genetic diversity and population structure across the sampled North American populations. We also assessed North American haplotype similarity to wheat midge collected from Europe and China and found high similarity between North American and European populations, although sampling in Europe was limited. This supports the hypothesis that North American populations originated from Europe.     

Conservation genetics of American Dipper (<Emphasis Type="Italic">Cinclus mexicanus</Emphasis>): the genetic status of a population in severe decline

American Dippers (Cinclus mexicanus) were once known to occur in streams throughout the Black Hills of South Dakota and Wyoming, but now dippers number about 50–75 individuals and reside almost exclusively in a single stream. The recent decline of the American Dipper in the Black Hills of South Dakota is thought to be due to local stream degradation. As a result of the decline of C. mexicanus in the Black Hills of South Dakota and Wyoming, the Black Hills population of American Dippers is a candidate for designation as a distinct population segement (DPS) and might warrant protection and special management. One criterion for DPS designation is genetic uniqueness. Here we present the results of a genetic assessment of the Black Hills population of C. mexicanus. Data presented here indicate that the dipper population in the Black Hills is genetically distinct from other sampled populations. Further population sampling will be needed to understand the genetic population structure of C. mexicanus throughout its range. Furthermore, the recent decline in the Black Hills dipper population should be a warning that other populations (and other species) may be experiencing similar declines and that such montane habitats are worthy of special management.     

Genetic diversity of the black mangrove (Avicennia germinans L.) in Colombia

This study analyzed the genetic diversity and patterns of genetic structure in Colombian populations of Avicennia germinans L. using microsatellite loci. A lower genetic diversity was found on both the Caribbean (Ho = 0.439) and the Pacific coasts (Ho = 0.277) than reported for the same species in other locations of Central American Pacific, suggesting the deterioration of genetic diversity. All the populations showed high inbreeding coefficients (0.131–0.462) indicating heterozygotes deficience. The genetic structure between the Colombian coasts separated by Central American Isthmus was high (F_RT = 0.39) and the analyses of the genetic patterns of A. germinans revealed a clear differentiation of populations and no-recent gene flow evidence between coasts. Genetic structure was found within each coast (F_ST = 0.10 for the Caribbean coast and F_ST = 0.22 for the Pacific coast). The genetic patterns along the two coasts appear to reflect a forcing by local geomorphology and marine currents. Both coasts constitute a different Evolutionary Significant Unit, so we suggest for future transplantations plans that propagules or saplings of the populations of the Caribbean coast should not be mixed with those of the Pacific Colombian coast. Besides, we suggest that reforestation efforts should carefully distinguish propagules sources within each coast.     

Mitochondrial DNA analysis reveals hidden genetic diversity in captive populations of the threatened American crocodile (Crocodylus acutus) in Colombia

Identification of units within species worthy of separate management consideration is an important area within conservation. Mitochondrial DNA (mtDNA) surveys can potentially contribute to this by identifying phylogenetic and population structure below the species level. The American crocodile (Crocodylus acutus) is broadly distributed throughout the Neotropics. Its numbers have been reduced severely with the species threatened throughout much of its distribution. In Colombia, the release of individuals from commercial captive populations has emerged as a possible conservation strategy that could contribute to species recovery. However, no studies have addressed levels of genetic differentiation or diversity within C. acutus in Colombia, thus complicating conservation and management decisions. Here, sequence variation was studied in mtDNA cytochrome b and cytochrome oxidase I gene sequences in three Colombian captive populations of C. acutus. Two distinct lineages were identified: C. acutus‐I, corresponding to haplotypes from Colombia and closely related Central American haplotypes; and C. acutus‐II, corresponding to all remaining haplotypes from Colombia. Comparison with findings from other studies indicates the presence of a single “northern” lineage (corresponding to C. acutus‐I) distributed from North America (southern Florida), through Central America and into northern South America. The absence of C. acutus‐II haplotypes from North and Central America indicates that the C. acutus‐II lineage probably represents a separate South American lineage. There appears to be sufficient divergence between lineages to suggest that they could represent two distinct evolutionary units. We suggest that this differentiation needs to be recognized for conservation purposes because it clearly contributes to the overall genetic diversity of the species. All Colombian captive populations included in this study contained a mixture of representatives of both lineages. As such, we recommend against the use of captive‐bred individuals for conservation strategies until further genetic information is available.     

High genetic diversity in the blue-listed British Columbia population of the purple martin maintained by multiple sources of immigrants

To assess genetic diversity in the blue-listed purple martin (Progne subis) population in British Columbia, we analysed mitochondrial control region sequences of 93 individuals from British Columbia and 121 individuals collected from seven localities of the western and eastern North American subspecies P. s. arboricola and P. s. subis, respectively. Of the 47 haplotypes we detected, 34 were found exclusively in western populations, and 12 were found only in eastern populations. The most common eastern haplotype (25) was also found in three nestlings in British Columbia and one in Washington. Another British Columbia nestling had a haplotype (35) that differed by a C to T transition from haplotype 25. Coalescent analysis indicated that these five nestlings are probably descendents of recent immigrants dispersing from east to the west, because populations were estimated to have diverged about 200,000–400,000 ybp, making ancestral polymorphism a less likely explanation. Maximum likelihood estimates of gene flow among all populations detected asymmetrical gene flow into British Columbia not only of rare migrants from the eastern subspecies in Alberta but also a substantial number of migrants from the adjacent Washington population, and progressively lower numbers from Oregon in an isolation-by distance pattern. The influx of migrants from different populations is consistent with the migrant-pool model of recolonization which has maintained high genetic diversity in the small recovering population in British Columbia. Thus, the risk to this population is not from genetic erosion or inbreeding following a severe population crash, but from demographic stochasticity and extinction in small populations.     

Preliminary genetic data on some Caribbean Artemia franciscana strains based on RAPD's

A total of fourteen Artemia samples from Colombia, Venezuela, Curaçao (Netherlands Antilles), Puerto Rico, and reference samples from U.S.A. (San Francisco Bay, SFB) belonging to the superspecies Artemia franciscana, and Argentina (A. persimilis), were analysed with the RAPD technique in order to demonstrate genetic dissimilarities. Pearson's correlation coefficients between the DNA banding patterns were calculated. They served as input values for the construction of UPGMA dendrograms. The results indicate that, within the collection of Colombian, Venezuelan and the two Netherlands Antilles Artemiacyst samples examined, two different groups seem to exist. Geographically, the mountainous area of Sierra Nevada de Santa Marta separates these two groups (lower Caribbean to the South and middle Caribbean to the North). Although the Caribbean, North and South American populations belong to A. franciscana, genetic discontinuities are to be expected due to habitat differences and geographic isolation. The Sierra Nevada (with an altitude of about 5800 m) emerges as the barrier very likely to explain the observed RAPD differences. Little genetic variability was present in the Colombian samples from Manaure that were collected almost every ten years, nor in the samples from Galerazamba collected almost two decades apart, although these samples were more likely subjected to different prevailing environmental conditions. The SFB population did not show a very close relation with all Caribbean populations analyzed, including the Puerto Rican. All A. franciscana populations analyzed were divergent from A. persimilis(Argentina).     

Genetic variability and level of differentiation among Brazilian pantanal wood stork populations

The Wood Stork (Mycteria americana) is a colonial wading bird of the tropical and lower subtropical zones. We assessed genetic structure within and among five stork colonies from the Brazilian Pantanal and compared our data with those from North American populations. Samples of 234 individuals were studied using protein electrophoresis to evaluate genetic variability and interpopulation differentiation. Of 22 loci examined, 7 were polymorphic (mean heterozygosity = 0.068). The low Fst value (0.005) indicated little intraspecific variation among breeding colonies. Estimated number of migrants per generation based on private alleles (Nm = 11.3) and on Fst (48.8) suggests high gene flow. Nei's genetic distance values among Pantanal colonies ranged from 0.0001 to 0.0034, demonstrating low genetic divergence among populations. Our data can be explained by supposing high gene flow levels among Pantanal colonies, and between North and South American populations, intermediated by a probable interbreeding population in Central America.     

Neutral and functionally important genes shed light on phylogeography and the history of high‐altitude colonization in a widespread New World duck

Phylogeographic studies often infer historical demographic processes underlying species distributions based on patterns of neutral genetic variation, but spatial variation in functionally important genes can provide additional insights about biogeographic history allowing for inferences about the potential role of adaptation in geographic range evolution. Integrating data from neutral markers and genes involved in oxygen (O₂)‐transport physiology, we test historical hypotheses about colonization and gene flow across low‐ and high‐altitude regions in the Ruddy Duck (Oxyura jamaicensis), a widely distributed species in the New World. Using multilocus analyses that for the first time include populations from the Colombian Andes, we also examined the hypothesis that Ruddy Duck populations from northern South America are of hybrid origin. We found that neutral and functional genes appear to have moved into the Colombian Andes from both North America and southern South America, and that high‐altitude Colombian populations do not exhibit evidence of adaptation to hypoxia in hemoglobin genes. Therefore, the biogeographic history of Ruddy Ducks is likely more complex than previously inferred. Our new data raise questions about the hypothesis that adaptation via natural selection to high‐altitude conditions through amino acid replacements in the hemoglobin protein allowed Ruddy Ducks to disperse south along the high Andes into southern South America. The existence of shared genetic variation with populations from both North America and southern South America as well as private alleles suggests that the Colombian population of Ruddy Ducks may be of old hybrid origin. This study illustrates the breadth of inferences one can make by combining data from nuclear and functionally important loci in phylogeography, and underscores the importance of complete range‐wide sampling to study species history in complex landscapes.     

Subspecific identity and a comparison of genetic diversity between wild and ex situ wildebeest

The original North American ex situ wildebeest population was believed to originate from the white-bearded wildebeest (Connochaetes taurinus albojubatus), which is both morphologically distinct and geographically separated from the brindled wildebeest (C. t. taurinus). However, after an import of wildebeest into North America in 2001, managers have suspected that white-bearded and brindled wildebeest were mixed in herds at multiple institutions. We sequenced the mitochondrial control region (d-loop) from a portion of the managed North American population and compared our sequences with previously published sequences from wild individuals to determine the subspecific identity and genetic diversity of our ex situ population. We were able to confidently identify C. t. albojubatus as the subspecies identity of the sampled portion of our population. Within our population, haplotype and nucleotide diversity were low (0.169 and 0.001, respectively) with a single common haplotype (H1) containing 41 of the 45 individuals sequenced, while two rare haplotypes (H2 and H3) were derived from three individuals and a single individual, respectively. Nucleotide and haplotype diversity were greater overall in the wild populations compared with our managed population. However, C. t. albojubatus was found to exhibit lower nucleotide diversity in both wild and ex situ populations when compared to other wild subspecies. Though the overall goal of the North American wildebeest population is for public education and not reintroduction, maintaining genetic diversity is vital for the long-term viability of this managed population, which may benefit from periodic supplementation of wild animals.     

Genetic diversity of North American captive‐born gorillas (Gorilla gorilla gorilla)

Western lowland gorillas (Gorilla gorilla gorilla) are designated as critically endangered and wild populations are dramatically declining as a result of habitat destruction, fragmentation, diseases (e.g., Ebola) and the illegal bushmeat trade. As wild populations continue to decline, the genetic management of the North American captive western lowland gorilla population will be an important component of the long‐term conservation of the species. We genotyped 26 individuals from the North American captive gorilla collection at 11 autosomal microsatellite loci in order to compare levels of genetic diversity to wild populations, investigate genetic signatures of a population bottleneck and identify the genetic structure of the captive‐born population. Captive gorillas had significantly higher levels of allelic diversity (t₇ = 4.49, P = 0.002) and heterozygosity (t₇ = 4.15, P = 0.004) than comparative wild populations, yet the population has lost significant allelic diversity while in captivity when compared to founders (t₇ = 2.44, P = 0.04). Analyses suggested no genetic evidence for a population bottleneck of the captive population. Genetic structure results supported the management of North American captive gorillas as a single population. Our results highlight the utility of genetic management approaches for endangered nonhuman primate species.     

Population Genetic Structure of Neotropical Mangrove Species on the Colombian Pacific Coast: Avicennia germinans (Avicenniaceae)1

We investigated the genetic variation of Avicennia germinans using 172 AFLP (Amplified Fragment Length Polymorphism) bands of 45 plants from four localities on the Colombian Pacific coast: 11 from Virudó (Chocó), 10 from La Plata (Valle), 12 from Tumaco (Nariño), and 12 from Chontal (Nariño). AFLP variation among localities (16.2%) was highly significant (AMOVA; P < 0.0001). All the analyses showed that Tumaco was the most genetically distinct locality of the four under study. The other three localities, La Plata, Virudó, and Chontal, apparently form a large single subpopulation with high‐to‐moderate gene flow among localities. We also found the genetic diversity of A. germinans on the Colombian Pacific coast (H_E= 0.251) higher than that estimated by others over the broad geographic range of A. germinans. All these results together show that mangroves on the Colombian Pacific coast deserve a strong investigative effort to improve our ecological, evolutionary, and biogeographic knowledge of this important tropical forest type.     

Reproductive Strategies Explain Genetic Diversity in Atlantic Salmon, Salmo salar

Synopsis We investigated the relationship between conservation status and genetic variability in European and North American Atlantic salmon, Salmo salar, populations, many of which have suffered severe bottlenecks. A negative north--south cline exists for the status of population conservation in this species. A literature review of genetic variability and demographic parameters of wild Atlantic salmon populations resulted in no statistical associations between population conservation status and genetic variation at enzyme or VNTR loci. We found however, a negative relationship between male parr maturation rates and geographical latitude for both American and European populations. The increase in effective population size due to participation by mature male parr and the increased proportions of these males in smaller (southern) populations could explain the lack of expected relationship between genetic variation and conservation status.     

Genetic variability and population differentiation in captive baird's Tapirs (Tapirus bairdii)

The objectives of this study were to assess the level of genetic variability and population differentiation within captive populations of an endangered large mammal, Baird's tapir (Tapirus bairdii). We genotyped 37 captive animals from North American (NA) and Central American (CA) zoos and conservation ranches using six polymorphic microsatellite loci. Standard indices of genetic variability (allelic richness and diversity, and heterozygosity) were estimated and compared between captive populations, and between captive and wild population samples. In addition, we evaluated levels of population differentiation using Weir and Cockerham's version of Wright's F-statistics. The results indicate that the NA and CA captive populations of Baird's tapirs have retained levels of genetic variability similar to that measured in a wild population. However, inbreeding coefficients estimated from the molecular data indicate that the CA captive population is at increased risk of losing genetic variability due to inbreeding. Despite this, estimated levels of population differentiation indicate limited divergence of the CA captive population from the wild population. Careful management appears to have kept inbreeding coefficients low in the NA captive population; however, population differentiation levels indicate that the NA population has experienced increased divergence from wild populations due to a founder effect and isolation. Based on these results, we conclude that intermittent exchanges of Baird's tapirs between the NA and CA captive populations will benefit both populations by increasing genetic variability and effective population size, while reducing inbreeding and divergence from wild populations. Zoo Biol 23:521–531, 2004. © 2004 Wiley-Liss, Inc.     

Genetic analysis of Drosophila melanogaster in the French West Indies and comparison with populations from other parts of the world

Four natural populations of Drosophila melanogaster, three from Guadeloupe and one from Martinique (French West Indies), were studied with respect to four types of genetically determined traits, namely allozyme frequencies, morphology, ethanol tolerance, and oviposition rhythm. These populations were compared to European (France) and tropical African populations, and, with respect to allozymes alone, to an American population. The four populations from the West Indies were found to be genetically similar; this may reflect a common historical origin, or an adaptive response to similar environmental pressures or possibly some gene flow between the two islands. The comparisons with distant populations led to different conclusions depending upon the trait considered. In the case of allozymes, flies from the West Indies were more similar to tropical African populations than to an American population from Texas, but the main difference observed was in comparison with European populations. The morphology of the West Indies flies resembled a smaller, tropical type, but the size was even smaller than observed in Africa. Both ethanol tolerance and oviposition rhythm were intermediate between flies from tropical Africa and Europe. All these results can be explained in terms of interactions between selection imposed by a tropical environment and the genetic properties of the founder population which first colonized the islands.     

Morphological adaptation to coastal marshes in spite of limited genetic structure in the Neotropical passerine Spartonoica maluroides (Aves: Furnariidae)

Tidal marshes present profound adaptive challenges to terrestrial vertebrates. For example, North American sparrows have relatively longer and thinner bills and darker dorsal plumage in coastal saltmarshes than in interior marshes. Bay‐capped wren‐spinetail (Furnariidae; Spartonoica maluroides) show a strong association with South American saltmarshes. We hypothesized that bay‐capped wren‐spinetail have similar morphological adaptations to North American sparrows to the saltmarsh environment, which would be indicative of the generality of selection on these traits in the coastal saltmarsh ecosystem. We captured individuals of S. maluroides from coastal saltmarshes and interior marshes. Populations were compared based on morphology and molecular markers. We found significant phenotypic differences in bill shape and plumage coloration (melanism) between S. maluroides populations from coastal and inland marshes. The low levels of genetic variation, weak geographical structure and shallow divergences, based on mitochondrial DNA and microsatellite data, suggest that coastal populations had a recent demographic expansion. Our results are consistent with the pattern of morphological divergence found between North American Emberizids. The possibility of convergent evolutionary adaptations between saltmarsh North American Emberizids and South American Furnariids suggests that there are strong selective pressures associated with saltmarsh environments on the beak, leading to adaptations for food acquisition, and on plumage coloration for better camouflage for predator avoidance (melanism). © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 78–91.