Opposing demographic histories reveal rapid evolution in grebes (Aves: Podicipedidae)

Ogawa, Lisa M.; Pulgarín, Paulo C.; Vance, Donald A.; Fjeldså, Jon; Tuinen, Marcel van

doi:10.1642/auk-14-259.1

Cited by 6 publications

(4 citation statements)

References 42 publications

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“…BirdLife International (2015b) considered the Northern Silvery Grebe as ‘Near Threatened’ due to its suspected population decline owing to loss and degradation of wetland habitat, and the impact of invasive species. The northernmost populations of the Northern Silvery Grebe (Colombia, Ecuador) appear to be highly geographically isolated from the southern populations (Bolivia, Chile, Perú and Argentina), and may also have diverged genetically (Ogawa et al 2015). Their conservation status is a cause of concern.…”

Section: Introductionmentioning

confidence: 99%

Status of the Northern Silvery Grebe Podiceps juninensis in the northern Andes: recent changes in distribution, population trends and conservation needs

Guevara¹,

Santander²,

Soria³

et al. 2016

Bird Conservation International

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SummaryThe Northern Silvery Grebe Podiceps juninensis is an aquatic bird species considered Vulnerable to extinction in Ecuador and Endangered in Colombia. Globally the species is considered Near Threatened. Herein we report recent changes in distribution and population trends for the subpopulation in the northern Andes (Ecuador, Colombia), which is small and isolated. The Northern Silvery Grebe has undergone two documented extirpations, and at least one colonisation event, over the last three decades. More than 90% of the subpopulation relies on two wetlands, La Mica and Colta lakes in Ecuador, with the latter facing an accelerated sedimentation process which jeopardizes the fate of the wetland, and the species, in the mid-term. The population of La Mica lost 80% of its birds in 2000 after the damming of the lake, but then remained stable over our census period (2004–2013). In contrast, the Colta population results from a recent colonisation in the early 2000s, and has experienced an exponential growth since then (annual population multiplication rate: 1.464). The growth of this population is so fast that it must include an important contribution of immigrants. The temporal coincidence between the drop in population size at lake La Mica and the colonisation of lake Colta suggests that the Colta population was founded by immigrants from La Mica. Finally, the absence of current reports of the species at wetlands in Colombia suggests that the species remains at very low numbers, bolstering the shrinkage in northern distribution.

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Section: Introductionmentioning

confidence: 99%

Status of the Northern Silvery Grebe Podiceps juninensis in the northern Andes: recent changes in distribution, population trends and conservation needs

Guevara¹,

Santander²,

Soria³

et al. 2016

Bird Conservation International

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“…The five primers that could cover the highest number of species were as follows: mCOIR2 (n = 767, 88.36%), K_Bird_F1 (n = 761, 87.67%), the redundant set VertebrateR1 and VR1 (n = 718, 82.72% each), AWCintR4 (n = 706, 81.34%), and BirdF1d (n = 688, 79.26%) (Table 1), with the first one designed based on the avian order Dinornithiformes, the third one for vertebrates in general, and the rest for all birds in general (Supplementary Table 1). On the other hand, the five primers that could cover the lowest number of sequences were as follows: AWCintF2 (Patel et al, 2010), L6615(tTyr)_COI (Sorenson et al, 1999), Pel-F2-COI (Nikulina & Schmölcke, 2015), Schutz03F (Schütz et al, 2020), and BC_392F (Ogawa et al, 2015) (n = 1, 0.12% each). There was a positive but not significant relation between the primer's degeneracy level and its coverage ratio (r = 0.11, p = 0.15).…”

Section: Primer Coveragementioning

confidence: 99%

“…Only three primers were capable of binding to at least one species of all 31 bird orders here analyzed, AWCintR4, BirdF1d, and CO1R (Table 1), and these primers were all designed focused on covering the whole avian group (Supplementary Table 1). Seven primers could bind to sequences of a single avian order: COIaRt_F (Tavares & Baker, 2008), PsEmpCOIF (Kerr, 2010), L6615_(tTyr)_ COI (Sorenson et al, 1999), AWCintF2 (Patel et al, 2010), PelF2COI (Nikulina & Schmölcke, 2015), Schutz03F (Schütz et al, 2020), and BC_392F (Ogawa et al, 2015), with only the first two binding to more than one template sequence (Supplementary Table 4).…”

Section: Primer Coveragementioning

confidence: 99%

“…5) since the complete coverage is achieved with this number, and using more than that is not necessary and can be time and money consuming. So here, for studies that need to try to recover the most number of avian species as possible, such as metabarcoding and forensics, we recommend the following primer sets: the forward primer BC_65 (Ogawa et al, 2015) along with the reverse primers H8121 (Sorenson, 2003) and AvesR (Lee et al, 2010), or with the primer pair BirdF1d (Sonet et al, 2011) and BirdR1dt (Breman et al, 2013) (Fig. 5).…”

Section: In Silico Primer Evaluationmentioning

confidence: 99%

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Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification

2021

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The process of molecular identification of species known as DNA barcoding consists on discriminating taxa based on cumulative differences of their DNA sequences and is widely used within animals, including birds. Finding the best genomic tools, such as primers, to reach most of the species within the studied groups and evaluating the coverage breadth and physicochemical properties of primers before testing in the laboratory, can save time and financial resources. Therefore, this work aimed to retrieve the available primers for the COI gene currently used on the molecular identification of birds and evaluate them for its coverage range, physicochemical properties, and performance on in silico PCR. Afterwards, we provide the best primer subsets to cover the highest number of avian sequences and the best individual primers for each bird order in terms of coverage breadth. Thirty-one bird orders had at least one COI sequence to serve as template, 152 primers available for assessing the COI gene were evaluated, and 118 could bind to at least one template sequence. No primer subset alone could cover all template sequences; however, when combining two subsets, the complete coverage of avian COI sequences analyzed was achieved. We were able to find optimal primer subsets for more specific taxonomic groups or for analysis involving the complete avian group, in order to guide researchers in the process of choosing the best primer set for each individual barcoding goal.

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Macroevolutionary Analyses Suggest That Environmental Factors, Not Venom Apparatus, Play Key Role in Terebridae Marine Snail Diversification

et al. 2019

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How species diversification occurs remains an unanswered question in predatory marine invertebrates, such as sea snails of the family Terebridae. However, the anatomical disparity found throughput the Terebridae provides a unique perspective for investigating diversification patterns in venomous predators. In this study, a new dated molecular phylogeny of the Terebridae is used as a framework for investigating diversification of the family through time, and for testing the putative role of intrinsic and extrinsic traits, such as shell size, larval ecology, bathymetric distribution, and anatomical features of the venom apparatus, as drivers of terebrid species diversification. Macroevolutionary analysis revealed that when diversification rates do not vary across Terebridae clades, the whole family has been increasing its global diversification rate since 25 Ma. We recovered evidence for a concurrent increase in diversification of depth ranges, while shell size appeared to have undergone a fast divergence early in terebrid evolutionary history. Our data also confirm that planktotrophy is the ancestral larval ecology in terebrids, and evolutionary modeling highlighted that shell size is linked to larval ecology of the Terebridae, with species with long-living pelagic larvae tending to be larger and have a broader size range than lecithotrophic species. Although we recovered patterns of size and depth trait diversification through time and across clades, the presence or absence of a venom gland (VG) did not appear to have impacted Terebridae diversification. Terebrids have lost their venom apparatus several times and we confirm that the loss of a VG happened in phylogenetically clustered terminal taxa and that reversal is extremely unlikely. Our findings suggest that environmental factors, and not venom, have had more influence on terebrid evolution.

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Opposing demographic histories reveal rapid evolution in grebes (Aves: Podicipedidae)

Cited by 6 publications

References 42 publications

Status of the Northern Silvery Grebe Podiceps juninensis in the northern Andes: recent changes in distribution, population trends and conservation needs

Status of the Northern Silvery Grebe Podiceps juninensis in the northern Andes: recent changes in distribution, population trends and conservation needs

Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification

Macroevolutionary Analyses Suggest That Environmental Factors, Not Venom Apparatus, Play Key Role in Terebridae Marine Snail Diversification

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