Sea Surface Temperatures Drive Historical Demography of Deep-Sea Fishes

Demographic histories are largely understood to be a product of their environment, as populations expand or contract in response to major environmental changes. Deep-pelagic fishes inhabit one of the most temporally and spatially stable habitats on the planet, so they may be resistant to the demographic instability commonly reported in other marine habitats, but their demographic histories are poorly understood. We reconstructed the demographic histories of thirteen species of deep-pelagic fishes using mitochondrial and nuclear DNA sequence data. We uncovered widespread evidence of demographic expansion in our study species, a counterintuitive result bases on the nature of the deep-pelagic. The frequency-based methods detected potential demographic changes in eleven species, while the Extended Bayesian Skyline Plots were more conservative and identified population expansion in five species. The dates of expansion largely coincide with periods of warm sea-surface temperature at the northern and southern boundaries for the ranges these species inhabit. We suggest that this is the result of the pelagic larval phase shared by most deep-pelagic fishes, where the larvae inhabit the upper 200 meters. Changes in sea surface conditions likely alter the suitability of the habitat in a given region for the larval phase, affecting the species range and in turn population size. These results are critical to our understanding of how the deep-pelagic fish community will respond to future climatic changes.

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Reef development and Sea level changes drive Acanthaster Population Expansion in the Indo-Pacific region

10.1101/2020.11.18.388207 ◽

2020 ◽

Author(s):

P.C. Pretorius ◽

T.B. Hoareau

Keyword(s):

Population Size ◽

Sea Level ◽

Environmental Changes ◽

Sequence Data ◽

Demographic History ◽

Population Expansion ◽

Population Level ◽

Sea Level Changes ◽

Reef Development ◽

Curve Fitting Method

AbstractMolecular clock calibration is central in population genetics as it provides an accurate inference of demographic history, whereby helping with the identification of driving factors of population changes in an ecosystem. This is particularly important for coral reef species that are seriously threatened globally and in need of conservation. Biogeographic events and fossils are the main source of calibration, but these are known to overestimate timing and parameters at population level, which leads to a disconnection between environmental changes and inferred reconstructions. Here, we propose the Last Glacial Maximum (LGM) calibration that is based on the assumptions that reef species went through a bottleneck during the LGM, which was followed by an early yet marginal increase in population size. We validated the LGM calibration using simulations and genetic inferences based on Extended Bayesian Skyline Plots. Applying it to mitochondrial sequence data of crown-of-thorns starfish Acanthaster spp., we obtained mutation rates that were higher than phylogenetically based calibrations and varied among populations. The timing of the greatest increase in population size differed slightly among populations, but all started between 10 and 20 kya. Using a curve-fitting method, we showed that Acanthaster populations were more influenced by sea-level changes in the Indian Ocean and by reef development in the Pacific Ocean. Our results illustrate that the LGM calibration is robust and can probably provide accurate demographic inferences in many reef species. Application of this calibration has the potential to help identify population drivers that are central for the conservation and management of these threatened ecosystems.

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Phylogeny, taxonomy, and zoogeography of the genus Gekko Laurenti, 1768 with the revalidation of G. reevesii Gray, 1831 (Sauria: Gekkonidae)

Zootaxa ◽

10.11646/zootaxa.2989.1.1 ◽

2011 ◽

Vol 2989 (1) ◽

pp. 1 ◽

Cited By ~ 26

Author(s):

HERBERT RÖSLER ◽

AARON M. BAUER ◽

MATTHEW P. HEINICKE ◽

ELI GREENBAUM ◽

TODD JACKMAN ◽

...

Keyword(s):

Dna Sequence ◽

Molecular Phylogenetics ◽

Nuclear Dna ◽

Sequence Data ◽

Identification Key ◽

Dna Sequence Data ◽

Preliminary Identification ◽

Specific Rank ◽

Species Groups

A review of the taxonomy, phylogeny, and zoogeography of all currently recognized Gekko species is provided based on morphology (including size, scalation, color, and pattern) and mitochondrial and nuclear DNA sequence data. We distinguish six morphological (phenotypic) species groups within the gekkonid genus Gekko: the G. gecko, G. japonicus, G. monarchus, G. petricolus, G. porosus, and G. vittatus groups, all of which receive support from molecular phylogenetics. The taxon G. reevesii, formerly evaluated as a synonym of G. gekko, is revalidated herein at specific rank. Furthermore, a preliminary identification key of all currently recognized Gekko taxa is provided.

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New genetic lineages within Moroccan day geckos Quedenfeldtia (Sphaerodactylidae) revealed by mitochondrial and nuclear DNA sequence data

Amphibia-Reptilia ◽

10.1163/15685381-00003088 ◽

2017 ◽

Vol 38 (1) ◽

pp. 97-101 ◽

Cited By ~ 1

Author(s):

David James Harris ◽

Daniela Rosado ◽

Raquel Xavier ◽

Daniele Salvi

Keyword(s):

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Reconstruction ◽

Taxonomic Revision ◽

Substantial Portion ◽

Genetic Lineages ◽

Mountainous Regions ◽

Dna Sequence Data ◽

Atlas Mountains ◽

Morphological Assessment

The genus Quedenfeldtia is composed of two species, Q. moerens and Q. trachyblepharus, both endemic to the Atlas Mountains region of Morocco. Previous studies recovered two main genetic lineages within each Quedenfeldtia species, although sampling did not cover a substantial portion of their known distribution. In this study we collected individuals from previously unsampled localities of Quedenfeldtia and carried out genetic analyses in order to assess the range of previously identified lineages and the occurrence of additional lineages. Phylogenetic reconstruction based on both mitochondrial (12S and ND4 + tRNA) and nuclear (MC1R) markers revealed that while the new individuals of Q. moerens belong to previously described lineages, two new lineages of Q. trachyblepharus were uncovered from the northern and southern parts of the range. Genetic divergence of these new lineages (8-9% ND4 + tRNA p-distance) was higher than values observed between other lizard sister species. In the future a thorough morphological assessment is needed to complement this study and allow a taxonomic revision of these taxa. The results of this study highlight the importance of biodiversity assessments in mountainous regions characterized by high endemicity but which are difficult to access.

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Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data

Zootaxa ◽

10.11646/zootaxa.3608.1.4 ◽

2013 ◽

Vol 3608 (1) ◽

pp. 67-74 ◽

Cited By ~ 1

Author(s):

Chris J. LAW ◽

KELLY M. DORGAN ◽

GREG W. ROUSE

Keyword(s):

Dna Sequence ◽

Nuclear Dna ◽

Sequence Data ◽

Hemoglobin Concentration ◽

Sympatric Species ◽

Sandy Beaches ◽

Additional Species ◽

Dna Sequence Data ◽

C Subunit ◽

Coi Sequences

Thoracophelia (Annelida, Opheliidae) are burrowing deposit feeders generally found in the mid- to upper intertidal areas of sandy beaches. Thoracophelia mucronata (Treadwell, 1914) is found along the west coast of North America, including at Dillon Beach, CA. Two additional species, Thoracophelia dillonensis (Hartman, 1938) and T. williamsi (Hartman, 1938) were also described from this beach. These three sympatric species have been primarily distinguished by branchial morphology, and efforts to determine the validity of the species have been based on morphological, reproductive and ecological studies. Here we demonstrate using mitochondrial and nuclear DNA sequence data that these three species are valid. Mitochondrial Cytochrome c subunit 1 (COI) sequences show uncorrected interspecific distances of ~9–13%. We found no inter—specific differences in body color or in hemoglobin concentration, but found that reproductive males were pinkish-red in color and had lower hemoglobin concentrations than purplish—red reproductive females.

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Genetic analyses of the parasitic nematode, Parelaphostrongylus tenuis, in Missouri and Kentucky reveal unexpected levels of diversity and population differentiation

Parasitology ◽

10.1017/s0031182020001912 ◽

2020 ◽

pp. 1-11

Author(s):

L. S. Eggert ◽

L. K. Berkman ◽

K. Budd ◽

B. J. Keller ◽

A. M. Hildreth ◽

...

Keyword(s):

Nuclear Dna ◽

Disease Risk ◽

Sequence Data ◽

Release Site ◽

Primary Host ◽

Dna Sequence Data ◽

Increased Risk ◽

Parelaphostrongylus Tenuis ◽

Risk Of Disease ◽

High Level

Abstract Wildlife translocations, which involve the introduction of naive hosts into new environments with novel pathogens, invariably pose an increased risk of disease. The meningeal worm Parelaphostrongylus tenuis is a nematode parasite of the white-tailed deer (Odocoileus virginianus), which serves as its primary host and rarely suffers adverse effects from infection. Attempts to restore elk (Cervus canadensis) to the eastern US have been hampered by disease caused by this parasite. Using DNA sequence data from mitochondrial and nuclear genes, we examined the hypothesis that elk translocated within the eastern US could be exposed to novel genetic variants of P. tenuis by detailing the genetic structure among P. tenuis taken from white-tailed deer and elk at a source (Kentucky) and a release site (Missouri). We found high levels of diversity at both mitochondrial and nuclear DNA in Missouri and Kentucky and a high level of differentiation between states. Our results highlight the importance of considering the potential for increased disease risk from exposure to novel strains of parasites in the decision-making process of a reintroduction or restoration.

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A new species of cat-eyed snake (Serpentes: Dipsadinae: Leptodeirini) from the Andes of southern Ecuador

Zootaxa ◽

10.11646/zootaxa.4895.3.3 ◽

2020 ◽

Vol 4895 (3) ◽

pp. 357-380

Author(s):

OMAR TORRES-CARVAJAL ◽

JUAN C. SÁNCHEZ-NIVICELA ◽

VALENTINA POSSE ◽

ELVIS CELI ◽

CLAUDIA KOCH

Keyword(s):

New Species ◽

Nuclear Dna ◽

Sequence Data ◽

Molecular Data ◽

Genetic Distances ◽

Dna Sequence Data ◽

The Andes ◽

Southern Ecuador ◽

Morphological And Molecular Data ◽

A New Species

Leptodeira is one of the most widespread and taxonomically problematic snake taxa in the Americas. Here we describe a new species of Leptodeira from the Andes of southern Ecuador based on morphological and molecular data. The new species is geographically close and morphologically similar to L. ornata and L. larcorum, from which it can be distinguished by having smaller dorsal body blotches, a longer tail, and shorter spines on the hemipenial body. The shortest genetic distances between the new species and its congeners are 0.02 (16S), 0.05 (cytb), and 0.18 (ND4). The new species is restricted to the Jubones River Basin in southern Ecuador, an area of endemism for other reptile species. Our phylogenetic analysis based on mitochondrial and nuclear DNA sequence data also supports recognition of the names L. larcorum (restricted to Peru) for “L. septentrionalis larcorum”, and L. ornata for populations of “L. s. ornata” from central and eastern Panama, western Colombia, and western Ecuador. However, some samples of “L. s. ornata” from Panama and Costa Rica, as well as the new species described herein, are not included within or more closely related to L. ornata, which is sister to the clade (L. bakeri, L. ashmeadii).

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