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opencc-zeroDec 2021View details →

Data from: Population genomics of Sitka black-tailed deer supports invasive species management and ecological restoration on islands

<p>Invasive mammals represent a critical threat to island biodiversity; eradications can result in ecological restoration yet may fail in the absence of key population parameters. Over-browsing by invasive Sitka black-tailed deer (<em>Odocoileus hemionus sitkensis</em>) is causing severe ecological and cultural impacts across the Haida Gwaii archipelago (Canada). Previous eradication attempts demonstrate forest regeneration upon deer removal, but reinvasion reverses conservation gains. Here we use restriction-site associated DNA sequencing (12,947 SNPs) to investigate connectivity and gene flow of invasive deer (n=181) across 15 islands, revealing little structure throughout Haida Gwaii and identifying the large, central island of Moresby (>2,600 km2) as the greatest source of migrants. As a result, the archipelago itself should be considered the primary eradication unit, with the exception of geographically isolated islands like SGang Gwaay. Thus, limiting eradications to isolated islands combined with controlled culling and enhanced biosecurity may be the most effective strategies for achieving ecological restoration goals.</p>

FIGURE 1 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 1. Map of sample sites of Pannonian populations of Odontarrhena tortuosa under study. Population codes follow Table 1. Taxa (O. tortuosa subsp. heterophylla and O. tortuosa subsp. tortuosa), ploidy levels and the type of substrate are indicated by symbol colours and shapes.

FIGURE 4 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 4. Canonical discriminant analysis (CDA 1) of 329 individuals of Odontarrhena tortuosa based on 27 morphological characters and three predefined groups corresponding to populations from three geographic regions differing in the type of substrate: (1) sand dunes in southwestern Slovakia, central Hungary and northern Serbia (tetraploid populations 24GRE, 244ORK, 471MCL, 473UZO, 539KIS, 540KSH), (2) sandy and rocky screes in central Hungary (diploid populations 13PIL, 447TOK, 537DOR, 538CSI), (3) calcareous rocks in eastern Slovakia (diploid populations 201JBV, 552KRV, 553HRH). 95 % isodensity circles are depicted. Population codes follow Table 1. For total canonical structure, see Table 5.

FIGURE 5 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 5. Canonical discriminant analyses (CDA) of 329 individuals of Odontarrhena tortuosa based on 27 morphological characters. A. CDA 2 with diploids (black) and tetraploids (white) as two predefined groups, B. CDA 3 with O. tortuosa subsp. tortuosa (white) and O. tortuosa subsp. heterophylla (black) as two predefined groups. For total canonical structure, see Table 5.

FIGURE 3 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 3. Principal coordinate analysis (PCoA) of 13 populations of Odontarrhena tortuosa based on 27 morphological characters and population means. The first three components explain 46.3%, 18.5% and 10.1% of the variation, respectively. Different colours and symbols are used to mark the two ploidy levels, two subspecies and populations from three regions differing in the type of substrate: diploids of O. tortuosa subsp. heterophylla from rocks of the Slovak Karst and Vihorlat Mts in eastern Slovakia (black squares), diploids of O. tortuosa subsp. tortuosa from habitats with sandy and rocky screes in the Gerecse, Pilis and Buda Mts in the northern part of central Hungary (black circles), and tetraploids of O. tortuosa subsp. tortuosa from sand dunes in southwestern Slovakia, central Hungary and northern Serbia (white circles).

FIGURE 2 in Diploid and tetraploid cytotypes and subspecies of Odontarrhena tortuosa (Brassicaceae) in Pannonia: differences in morphology, ecology and genome size

FIGURE 2. Monoploid relative genome size variation of Pannonian populations of Odontarrhena tortuosa sorted into groups based on three criteria: ploidy level (A), assignment to a subspecies (B) and the type of substrate (C). Boxes define the 25th and 75th percentiles, vertical lines within boxes indicate medians, and whiskers extend from minimum to maximum values.

opencc-zeroDec 2010View details →

Data from: Boechera, a model system for ecological genomics

The selection and development of a study system for evolutionary and ecological functional genomics (EEFG) depends on a variety of factors. Here we present the genus Boechera as an exemplary system with which to address ecological and evolutionary questions. Our focus on Boechera is based on several characteristics: 1) native populations in undisturbed habitats where current environments reflect historical conditions over several thousand years; 2) functional genomics benefitting from its close relationship to Arabidopsis thaliana; 3) inbreeding tolerance enabling development of recombinant inbred lines, near-isogenic lines, and positional cloning; 4) interspecific crosses permitting mapping for genetic analysis of speciation; 5) apomixis (asexual reproduction by seeds) in a genetically tractable diploid; and 6) broad geographic distribution in North America, permitting ecological genetics for a large research community. These characteristics, along with the current sequencing of three Boechera species by the Joint Genome Institute, position Boechera as a rapidly advancing system for EEFG studies.

opencc-zeroJul 2019View details →

Data from: Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows

Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage-specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage-specific responses to selection within and among four species of North American sparrows that represent four independent, post-Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection on twelve candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species-specific signatures of selection, including evidence of selection on loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage-specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.