Omar Chassin-Noria

Conservation Genetics of the East Pacific Green Turtle (Chelonia mydas) in Michoacan, Mexico

The main continental nesting rookeries of the east Pacific green turtle (EPGT), Chelonia mydas, on the Michoacan (Mexico) coast suffered drastic population declines following intense exploitation in the 1960s–1970s with annual abundance of nesting females plummeting from about 25,000 to an average of about 1400 between 1982 and 2001. Analyses of data from three nDNA microsatellite loci and 400 bp mtDNA control region sequences from a total of 123 nesting females sampled from four Michoacan rookeries found no evidence of population sub-structuring. The recent order of magnitude reduction in the population size shows no apparent impact on genetic diversity in either control region sequences (overall h= 0.48; π= 0.0036) or microsatellite loci (overall Na= 20.8; Hexp= 0.895). Our estimates of annual effective female population size (Nef; from θ= 2Neμ) of 1.9–2.3 × 103, in spite of being an order of magnitude below historical records, appear to be sufficient to allow recovery of this population without significant loss of genetic diversity. These findings highlight the importance of continued conservation to reverse the decline of this population before it becomes vulnerable to genetic erosion.

Population structure and phylogeography reveal pathways of colonization by a migratory marine reptile (Chelonia mydas) in the central and eastern Pacific.

Climate, behavior, ecology, and oceanography shape patterns of biodiversity in marine faunas in the absence of obvious geographic barriers. Marine turtles are an example of highly migratory creatures with deep evolutionary lineages and complex life histories that span both terrestrial and marine environments. Previous studies have focused on the deep isolation of evolutionary lineages (>3 mya) through vicariance; however, little attention has been given to the pathways of colonization of the eastern Pacific and the processes that have shaped diversity within the most recent evolutionary time. We sequenced 770 bp of the mtDNA control region to examine the stock structure and phylogeography of 545 green turtles from eight different rookeries in the central and eastern Pacific. We found significant differentiation between the geographically separated nesting populations and identified five distinct stocks (FST = 0.08–0.44, P < 0.005). Central and eastern Pacific Chelonia mydas form a monophyletic group containing 3 subclades, with Hawaii more closely related to the eastern Pacific than western Pacific populations. The split between sampled central/eastern and western Pacific haplotypes was estimated at around 0.34 mya, suggesting that the Pacific region west of Hawaii has been a more formidable barrier to gene flow in C. mydas than the East Pacific Barrier. Our results suggest that the eastern Pacific was colonized from the western Pacific via the Central North Pacific and that the Revillagigedos Islands provided a stepping-stone for radiation of green turtles from the Hawaiian Archipelago to the eastern Pacific. Our results fit with a broader paradigm that has been described for marine biodiversity, where oceanic islands, such as Hawaii and Revillagigedo, rather than being peripheral evolutionary “graveyards”, serve as sources and recipients of diversity and provide a mechanism for further radiation.

Genetic diversity and population structure of Escherichia coli from neighboring small-scale dairy farms.

The genetic diversity and population structure of Escherichia coli isolates from small-scale dairy farms were used to assess the ability of E. coli to spread within the farm environment and between neighboring farms. A total of 164 E. coli isolates were obtained from bovine feces, bedding, cow teats and milk from 6 small-scale dairy farms. Ward’s clustering grouped the isolates into 54 different random amplified polymorphic DNA (RAPD) types at 95% similarity, regardless of either the sample type or the farm of isolation. This suggests that RAPD types are shared between bovine feces, bedding, cow teats, and milk. In addition, transmission of RAPD types between the studied farms was suggested by the Ward grouping pattern of the isolates, Nei’s and AMOVA population analyses, and genetic landscape shape analysis. For the first time, the latter analytical tool was used to assess the ability of E. coli to disseminate between small-scale dairy farms within the same producing region. Although a number of dispersal mechanisms could exist between farms, the genetic landscape shape analysis associated the flow of E. coli RAPD types with the movement of forage and milking staff between farms. This study will aid in planning disease prevention strategies and optimizing husbandry practices.

Genetic shifts in the transition from wild to farmed white-tailed deer (Odocoileus virginianus) population

The white-tailed deer (Odocoileus virginianus) is one of the most important species related to sport hunting in northern Mexico. During the last decade, this species has been subjected to intensive breeding to achieve improvements in certain desired traits (i.e., antlers). This alleged intensive management of bringing originally wild populations into captivity might have harmful consequences on genetic diversity. In this short research paper we estimate and discuss the consequences of that transition, as assessed by a microsatellite genetic marker analysis. The results show that no short-term changes in genetic diversity parameters were promoted by captivity; however, a genetic diversity condition maintained by artificial genetic flow was identified, perhaps allowing for the required introgression of gene diversity into this closed population. A wider analysis is recommended and the implications are discussed. Within a realistic forecast of expanding sport hunting, the achievement of useful, pragmatic, and strict conservancy programs of this species, considering approaches such as those used here, will be necessary.

The complete mitochondrial genomes of nine white-tailed deer subspecies and their genomic differences

The white-tailed deer (Odocoileus virginianus) is an important, sustainable-use species in Mexico; 14 subspecies are widely distributed throughout the Mexican territory. The criteria for classifying subspecies is based on morphological features throughout their geographical range; however, the complete genetic characterization of Mexican subspecies has not been established. The objective of the present work is to report the mitogenomes of 9 of the 14 white-tailed deer subspecies from Mexico and identify their unique variations. Typical vertebrate mitogenomes structures (i.e., 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) were observed in the studied subspecies. The greatest numbers of polymorphisms were identified in the D-loop, ND4, ND5, CYTB/ COI, ATP6, and COIII genes. Phylogenetic analyses showed that the southern and southeastern subspecies were distinct from the central and northern subspecies; the greatest genetic distances were also observed between these 2 groups. These subspecies-specific variations could be useful for designing a strategy to genetically characterize the studied subspecies.