Microsatellite Markers Reveal Strong Genetic Structure in the Endemic Chilean Dolphin

Abstract

Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (FST = 0.15 and RST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies.

Fine‐scale habitat partitioning of Chilean and Peale's dolphins and their overlap with aquaculture

“…Predicted mean occurrence of Chilean dolphins (a) and Peale's dolphins (d) in the northern study area, together with upper (b, e) and lower (c, f) 95% CIFIGURE 5Occurrence of Peale's dolphins as a smooth function of different covariates: depth, distance to shore, salinity, SST, distance to nearest river and distance to nearest shellfish farm. The availability of suitable habitat and resulting effects on dolphin carrying capacity could be important factors in determining overall distribution, abundance and population structure.Genetic studies have shown clear population differences betweenChilean dolphins along the open coast north of Chiloé and to the south in the deep fjords(Pérez-Alvarez et al, 2015). Data points are represented as rug plots on the horizontal axesFIGURE 6 Predicted mean dolphin occurrence of Chilean and Peale's dolphins overlaid with concessions for salmon and shellfish farms in 2015 in the southern (a) and northern (b) study areas.…”

“…Data points are represented as rug plots on the horizontal axesFIGURE 6 Predicted mean dolphin occurrence of Chilean and Peale's dolphins overlaid with concessions for salmon and shellfish farms in 2015 in the southern (a) and northern (b) study areas. Unfortunately, Chilean dolphins in the intermediate Chiloé region have not been sampled(Pérez-Alvarez et al, 2015), so finerscale population structure remains unknown, but obtaining such information should be a priority given the distinct and stable habitat use patterns described here.Sheltered, shallow nearshore waters might also confer a lower risk of predation. Mark-recapture studies of identifiable individuals at southern Chiloé indicate that the local population of Chilean dolphins is small (c. 60 adults) with individuals showing high site fidelity and lim-ited along-shore movements(Heinrich, 2006).…”

Genomewide identification and development of microsatellite markers for Marssonina brunnea and their applications in two populations

“…The program LOSITAN (Antao, Lopes, Lopes, Beja-Pereira, & Luikart, 2008) was used to detect putative loci under selection with two options: neutral mean FST' and force mean FST'. STRUCTURE version 2.3.4 (Falush, Stephens, & Pritchard, 2003;Pritchard, Stephens, & Donnelly, 2000) was used to analyse the genetic structure of the populations using the Bayesian clustering approach, which has been proven to be suitable and is widely used for genetic structure analysis using SSRs (Al-Jawabreh et al, 2008;Pérez-Alvarez et al, 2015). The specific program parameters were as follows: the replicates were set with K from 1 to 7, and the repeats of each replicate were 30.…”

The ecological value of long-term studies of birds and mammals in Central America, South America and Antarctica

“…Pérez-Alvarez et al [68] conducted a 14-year study of the Chilean dolphin (Cephalorhynchus eutropia), a species endemic to coastal Chile. Although there are no geographical barriers in its distribution, analysis of microsatellite markers revealed that northern [found in habitat ranging from Valparaíso (33°020 S) to Chiloé (42°000 S)] and southern populations [(from Chiloé to Navarino Island (55°140 S)] are genetically distinct.…”

“…Although there are no geographical barriers in its distribution, analysis of microsatellite markers revealed that northern [found in habitat ranging from Valparaíso (33°020 S) to Chiloé (42°000 S)] and southern populations [(from Chiloé to Navarino Island (55°140 S)] are genetically distinct. The individuals sampled were located at sites spanning the Chilean coast from 35°20′S to 52°40′S, but despite lacking a physical barrier, there is limited gene flow between the two populations [68]. Potentially, there are ecological or behavioral adaptations to the local habitats that maintain a genetic subdivision of the population.…”