Search

In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500–1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of Mammillaria. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was M. solisioides (256), whereas M. pectinifera contained the highest amount of SSRs (84). In contrast, M. zephyranthoides contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.

In angiosperms, huge advances in massive DNA sequencing technologies have impacted phylogenetic studies. Probe sets have been developed with the purpose of recovering hundreds of orthologous loci of targeted DNA sequences (TDS) across different plant lineages. We tested in silico the effectiveness of two universal probe sets in the whole available genomes of Caryophyllids, emphasizing phylogenetic issues in cacti species. A total of 870 TDS (517 TDS from Angiosperm v.1 and 353 from Angiosperms353) were individually tested in nine cacti species and Amaranthus hypochondriacus (external group) with ≥17 Gbp of available DNA data. The effectiveness was measured by the total number of orthologous loci recovered and their length, the percentage of loci discarded by paralogy, and the proportion of informative sites (PIS) in the alignments. The results showed that, on average, Angiosperms353 was better than Angiosperm v.1 for cacti species, since the former obtained an average of 275.6 loci that represent 123,687 bp, 2.48% of paralogous loci, and 4.32% of PIS in alignments, whereas the latter recovered 148.4 loci (37,683 bp), 10.38% of paralogous loci, and 3.49% of PIS. We recommend the use of predesigned universal probe sets for Caryophyllids, since these recover a high number of orthologous loci that resolve phylogenetic relationships.

In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500&ndash, 1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of Mammillaria. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was M. solisioides (256), whereas M. pectinifera contained the highest amount of SSRs (84). In contrast, M. zephyranthoides contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.

Florestina is shown to consist of six annual species occurring mostly in arid and semiarid regions of Mexico. Florestina species are morphologically similar and consequently phylogenetic relationships within the genus are poorly understood. We present a phylogenetic study based on morphological characters, DNA sequences of nuclear non-coding spacers (ETS and ITS) and chloroplast non-coding spacers (rpl32-trnL and trnC-petN). The ETS and ITS spacer-based phylogenies allowed several well-supported conclusions: (1) the genus Florestina is monophyletic and Palafoxia is its closest relative; (2) Florestina latifolia and F. platyphylla form a strongly supported clade; (3) four taxa that are morphologically very similar, F. liebmannii, F. pedata, F. simplicifolia, and F. tripteris, are phylogenetically closely related and based on the sequence data we suggest that these should be recognized as only two species, one comprising F. pedata and F. simplicifolia, which shows wide morphological variation throughout its distributional range; and the other comprising F. liebmannii and F. tripteris; (4) F. lobata and F. purpurea are species very distinct from the remainder of the species in Florestina. Our phylogenetic analyses suggest that hybridization and introgression may be involved in the evolutionary history of Florestina.

Forest structure and composition have been used to assess the habitat characteristics that determine bird distributions. The patterns of distribution have been shaped by historical and ecological factors that play different roles at both temporal and spatial scales. The objectives of this research were to characterize the habitat of the endangered Military Macaw (Ara militaris) and evaluate the potential distribution of this species based on trends of land use changes in Mexico. We characterized the community structure and floristic composition of 8 forests that are currently used by the Military Macaw for breeding and feeding and compared the results with 6 similar forests characterized in other studies but without historical records of the presence of the Military Macaw. The Military Macaw preferred sites with high diversity of plant species dominated by trees from 4 to 15m in height and from 5 to 90cm in diameter at breast height. We identified 236 plant species in the 8 forests with 20 species (8.4%) used for nesting and feeding by the Military Macaw. The floristic composition is important for the presence of the Military Macaw because there were significant differences between forests with and without its presence. The potential area of distribution of the Military Macaw had decreased by 32% and the remnant areas are included in only 8 National Protected Areas. The protected areas of natural forests should be increased to preserve the sites of potential distribution and consequently the habitat of the Military Macaw in Mexico.

Mammillaria agrupa a 200 especies, 164 registradas en México, 85 % son endémicas y 113 están en la Norma Oficial Mexicana NOM-059 SEMARNAT-2010. A pesar de su importancia en la biodiversidad y de su grave crisis de conservación, la escasa información documentada en estas especies no permite proponer estrategias para protegerlas. Nuestro objetivo fue estimar los niveles de diversidad genética poblacional en M. hernandezii, M. kraehenbuehlii y M. napina para identificar unidades genéticas de conservación. Se genotiparon con 10 loci de microsatélites 24 individuos de dos poblaciones de M. hernandezii y 120 individuos de cinco poblaciones para cada una de las otras dos especies. En las tres especies se estimaron niveles de heterocigosidad observada menores que los esperados (M. hernandezii 0.58, 0.65; M. kraehenbuehlii 0.61, 0.73; y M. napina 0.56, 0.74), la diversidad alélica varió de cinco (M. hernandezii) a ocho alelos en las otras dos especies. Las tres especies mostraron una deficiencia de heterocigotos que puede deberse a deriva genética porque sus poblaciones son pequeñas, aunque la autofecundación también podría participar. Entre las poblaciones de las tres especies los niveles de flujo génico fueron altos, lo que indica que podría ser la deriva genética y el sistema de dispersión de polen y semillas lo que determina la estructura genética. Para M. kraehenbuehlii y M. napina se proponen tres grupos genéticos para que sean considerados como referencias para programas de conservación de estas especies y de sus hábitats. Las principales amenazas para las tres especies son la severa transformación del paisaje que aisla a sus poblaciones y el saqueo. En M. hernandezii se debe incrementar el número de poblaciones estudiadas para tener resultados concluyentes de su diversidad genética poblacional, por el momento el patrón de distribución geográfica en parches pequeños indica una severa fragmentación que insta a tomar medidas urgentes para su protección y manejo.

We evaluated the impacts of land-cover changes of evergreen cloud forests on the distribution of quetzals in the four mountain regions of Chiapas, Mexico. The land-cover changes were estimated comparing satellite images of 1970 and 2000. We also simulated the amount of remnant forests 50 years in the future. The past and the current distributions of quetzals were based on literature records and recent field surveys. Our results showed that in 1970 the forests occupied 973 km 2 , and in 2000, 312 km 2 , and annual loss from 3.34 to 6.85%. Our simulation suggests that 50 years from now, only one region will maintain evergreen cloud forests. In addition, we documented literature reports of 39 forests inhabited by quetzals, but in 2001 there remained 11 smallisolated forests. In order to guarantee the survival of this species, conversation efforts must be made to protect the quetzal and its habitat throughout the entire Mesoamerica region. # 2003 Elsevier Ltd. All rights reserved.

Nearly 168 species of Mammillaria are endangered at the global level; most of these cactus species exhibit a narrow distribution range and/or small population size. Recently, the first population genetics studies showed low to moderate levels of heterozygosity in this genus. This study examines Mammillaria huitzilopochtli and M. supertexta, 2 threatened species endemic to the central semiarid region of Mexico, to propose conservation actions, as well as to identify the underlying processes that determine the levels of population genetic diversity in these species. A total of 106 and 148 individuals from 5 populations were sampled for M. huitzilopochtli and M. supertexta, respectively. Each individual was genotyped at 8 microsatellite loci. The levels of heterozygosity were high in the 2 species, but differences in allelic richness were detected. Genetic differentiation between populations was significant in both species, with evidence for isolation by distance in M. supertexta but not in M. huitzilopochtli. We postulated that genetic drift; geographic isolation and inbreeding are the most important processes shaping the populations' genetic variability and differentiation. We identified 3 and 4 genetic groups for M. huitzilopochtli and M. supertexta, respectively. In the Tehuacán-Cuicatlán valley these groups may be used as references to guide plant conservation efforts under ecosystem-based approach.

The endemic plant species with extremely narrow geographical range (

The Military Macaw (Ara militaris) is a globally threatened species with a fragmented distribution, and assessing the genetics of populations could help identify conservation units. Nine microsatel...

The cactus Mammillaria crucigera is a threatened species endemic to central Mexico. As a means of assessing population genetic status of these species, eight microsatellite markers were developed. These primers were tested in 40 individual from two wild populations. The results showed that these primers will be useful to describe population structure and aid to the conservation of species. The eight primers were tested in other Mammillaria species and most of them showed successful amplification.

The resplendent Quetzal (Pharomachrus mocinno) is an endemic Mesoamerican bird species of conservation concern. Within this species, the subspecies P. m. costaricensis and P. m. mocinno, have been recognized by apparent morphometric differences; however, presently there is no sufficient data for confirmation. We analyzed eight morphometric attributes of the body from 41 quetzals: body length, tarsus and cord wing, as well as the length, wide and depth of the bill, body weight; and in the case of the males, the length of the long upper-tail cover feathers. We used multivariate analyses to discriminate morphometric differences between subspecies and contrasted each morphometric attribute between and within subspecies with paired non-parametric Wilcoxon test. In order to review the intraspecific taxonomic status of this bird, we added phylogenetic analysis, and genetic divergence and differentiation based on nucleotide variations in four sequences of mtDNA. The nucleotide variation was estimated in control region, subunit NDH6, and tRNA Glu and tRNA Phe in 26 quetzals from eight localities distributed in five countries. We estimated the genetic divergence and differentiation between subspecies according to a mutation-drift equilibrium model. We obtained the best mutation nucleotide model following the procedure implemented in model test program. We constructed the phylogenetic relationships between subspecies by maximum parsimony and maximum likelihood using PAUP, as well as with Bayesian statistics. The multivariate analyses showed two different morphometric groups, and individuals clustered according to the subspecies that they belong. The paired comparisons between subspecies showed strong differences in most of the attributes analyzed. Along the four mtDNA sequences, we identified 32 nucleotide positions that have a particular nucleotide according to the quetzals subspecies. The genetic divergence and the differentiation was strong and markedly showed two groups within P. mocinno that corresponded to the quetzals subspecies. The model selected for our data was TVM+G. The three phylogenetic methods here used recovered two clear monophyletic clades corresponding to each subspecies, and evidenced a significant and true partition of P. mocinno species into two different genetic, morphometric and ecologic groups. Additionally, according to our calculations, the gene flow between subspecies is interrupted at least from three million years ago. Thus we propose that P. mocinno be divided in two independent species: P. mocinno (Northern species, from Mexico to Nicaragua) and in P. costaricensis (Southern species, Costa Rica and Panama). This new taxonomic classification of the quetzal subspecies allows us to get well conservation achievements because the evaluation about the kind and magnitude of the threats could be more precise. Rev. Biol. Trop. 58 (1): 357-371. Epub 2010 March 01.El Quetzal (Pharomachrus mocinno) es un ave endémica mesoamericana de interés en conservación. Dentro de esta especie, se reconocen a las subespecies P. m. costaricensis y P. m. mocinno por aparentes diferencias morfométricas, sin embargo, hasta el momento no hay datos suficientes que las confirmen. En este estudio, analizamos ocho rasgos morfométricos de 41 quetzales: la longitud del cuerpo, del tarso y de la cuerda alar, así como la longitud, el ancho y la profundidad del pico, el peso corporal, y en el caso de los machos, la longitud de las plumas cobertoras supracaudales. Usamos análisis multivariados para discriminar diferencias morfométricas entre las subespecies. Comparamos cada rasgo morfométrico dentro y entre las subespecies a partir de comparaciones pareadas con el análisis no-paramétrico de Wilcoxon. Realizamos análisis filogenéticos, y de diferenciación y divergencia genéticas fundamentados en las variaciones nucleotídicas de cuatro secuencias de ADNm con la finalidad de revisar el estatus taxonómico de esta ave. La variación nucleotídica fue estimada en la región control, la subunidad NDH6 y los tRNA Glu y tRNA Phe en 26 quetzales de ocho localidades de cinco países. Estimamos la divergencia y la diferenciación genética entre subespecies con base en el modelo de equilibrio mutación-deriva. Obtuvimos el mejor modelo de mutación nucleotídica siguiendo el procedimiento implementado en el programa Model test. Construimos las relaciones filogenéticas entre las subespecies con máxima parsimonia y máxima verosimilitud usando PAUP, así con estadística Bayesiana. Los análisis multivariados discriminaron dos grupos morfométricos, y los individuos se agruparon de acuerdo con la subespecie a la que pertenecen. Las comparaciones pareadas entre las subespecies mostraron fuertes diferencias en la mayoría de los rasgos analizados. En las cuatro secuencias de ADNmt identificamos 32 posiciones nucleotídicas que tienen un nucleótido particular de acuerdo con la subespecie de quetzal. La divergencia genética y la diferenciación fueron marcadas y mostraron dos grupos dentro de P. mocinno que correspondieron a las subespecies de quetzales. El modelo seleccionado para nuestros datos fue el TVM+G. Los tres métodos filogenéticos usados recuperaron dos clados monofiléticos robustos correspondiendo a cada una de las subespecies. Consideramos que nuestros resultados muestran una significativa y real división de P. mocinno en dos grupos genéticos, morfométricos y ecológicos. Además de acuerdo con nuestras estimaciones, el flujo génico está interrumpido entre las subespecies desde al menos hace tres millones de años. Por ello, proponemos que P. mocinno sea dividido en dos especies independientes: P. mocinno (especie norteña, desde México hasta Nicaragua) y P. costaricensis (especie sureña, Costa Rica y Panamá). Esta nueva clasificación de las subespecies de quetzal permitirá mejores logros en su conservación, dado que la evaluación de la clase y magnitud de las amenazas serán más precisas.

In this study, we analyzed the genetic variation of quetzals ( Pharomachrus mocinno ) throughout their geographic distribution to determine conservation targets. This species is found in patchy isolated cloud forests from Mexico to Panama. A multidimensional scaling and UPGMA analysis of a 286 RAPD fragment set resolved 3 genetic groups: cluster 1 (Mexican localities), cluster 2 (Guatemala, Nicaragua and El Salvador) and cluster 3 (Panama). The mean genetic diversity estimated by the Shannon index was 0.38, 0.22 and 0.32, for clusters 1, 2, and 3, respectively. The genetic differentiation among clusters was statistically significant. The highest percentage of genetic variation (70.86%) was found within populations using an AMOVA analysis. Our results suggest that within the quetzal species, there are 3 genetic groups that should be considered as independent conservation targets and included in a global Mesoamerican conservation program.

The Resplendent Quetzal (Pharomachrus mocinno) is an altitudinal migrant that nests in high elevation cloud forests and migrates toward lower areas during the summer rainy season. It has been suggested that its migratory movements are related to the abundance of ripe Lauraceae fruits. We studied the quetzal diet during two consecutive years, as well as changes in fruit abundance of the plant species on which the bird feeds at El Triunfo Biosphere Reserve, southeastern Mexico. The quetzal was observed feeding on 32 plant species; of these, 24 are new records in its diet. We chose 20 of these 32 species and studied their fruit phenology for two years in order to describe the relationship between fruit and quetzal abundance. Our results showed that quetzal abundance in the breeding area was correlated with the total number of fruiting species, whereas the correlation between quetzal abundance and the number of fruiting Lauraceae species was only marginal. Additionally, a correlation test showed that quetzal abundance was marginally correlated with total fruit availability (total no. of fruits per month); however, the correlation between quetzal abundance and the number of fruits in the Lauraceae was not significant. Our results suggest that the dynamics of food resources may be playing a major role in the quetzal's migratory behavior. Knowing the bird's diet may aid in characterizing the type of habitat adequate for its conservation. Our observations in this respect suggest that conservation efforts to preserve this bird species should concentrate on the protection of its habitat, including both breeding and nonbreeding (migration) locations.