scholarly journals Evolutionary history of the porpoises (Phocoenidae) across the speciation continuum: a mitogenome phylogeographic perspective

2019 ◽  
Author(s):  
Yacine Ben Chehida ◽  
Julie Thumloup ◽  
Cassie Schumacher ◽  
Timothy Harkins ◽  
Alex Aguilar ◽  
...  
Keyword(s):  
Marine Mammals ◽  
Evolutionary History ◽  
Environmental Changes ◽  
Phylogenetic Analyses ◽  
Food Resources ◽  
Recent Common Ancestor ◽  
Cetacean Species ◽  
Evolutionary Patterns ◽  
Speciation Continuum ◽  
Southern Species

AbstractHistorical changes affecting food resources are a major driver of cetacean evolution. Small cetaceans like porpoises (Phocoenidae) are among the most metabolically challenged marine mammals and are particularly sensitive to changes in their food resources. The seven species of this family inhabit mostly temperate waters and constitute a textbook example of antitropical distribution. Yet, their evolutionary history remains poorly known despite major conservation issues threatening the survival of some porpoises (e.g., vaquita and Yangzte finless porpoises). Here, we reconstructed their evolutionary history across the speciation continuum, from intraspecific subdivisions to species divergence. Phylogenetic analyses of 63 mitochondrial genomes suggest that, like other toothed whales, porpoises radiated during the Pliocene in response to deep environmental changes. However, all intra-specific phylogeographic patterns were shaped during the Quaternary Glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent adaptations to coastal versus oceanic environments. This result suggests that the mechanism(s) driving species diversification in the relatively well-known species from the northern hemisphere may apply also to the poorly-known southern species. In contrast to previous studies, we showed that the spectacled and Burmeister’s porpoises share a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size throughout at least the last 5,000 years, leaving one single relict mitochondrial lineage. Finally, we observed unreported subspecies level divergence within Dall’s, spectacled and Pacific harbor porpoises, suggesting a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanism driving the adaptation and speciation processes involved in the diversification of cetacean species. This knowledge can illuminate their demographic trends and provide an evolutionary framework for their conservation.

scholarly journals Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yacine Ben Chehida ◽  
Julie Thumloup ◽  
Cassie Schumacher ◽  
Timothy Harkins ◽  
Alex Aguilar ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Environmental Changes ◽  
Phylogenetic Analyses ◽  
Recent Common Ancestor ◽  
Evolutionary Patterns ◽  
Low Genetic Diversity ◽  
Speciation Continuum ◽  
New Perspective ◽  
Historical Variation ◽  
Southern Species

Abstract Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall’s) and southern species (spectacled and Burmeister’s). In contrast to previous studies, spectacled and Burmeister’s porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall’s, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.

scholarly journals Out of Africa: A New Afrotheria Lineage Rises From Extinct South American Mammals

2021 ◽  
Vol 9 ◽  
Author(s):  
Leonardo S. Avilla ◽  
Dimila Mothé
Keyword(s):  
Environmental Changes ◽  
Phylogenetic Analyses ◽  
South American ◽  
Evolutionary Patterns ◽  
Natural Group ◽  
Phylogenetic Studies ◽  
Monophyletic Lineage ◽  
Early Paleocene ◽  
History Of ◽  
Out Of Africa

The South American native ungulates (SANUs) are usually overlooked in Eutherian phylogenetic studies. In the rare studies where they were included, the diversity of SANUs was underrated, keeping their evolutionary history poorly known. Some authors recognized the SANUs as a monophyletic lineage and formally named it Meridiungulata. Here, we recognized and defined a new supraordinal lineage of Eutheria, the Sudamericungulata, after performing morphological phylogenetic analyses including all lineages of SANUs and Eutheria. The SANUs resulted as non-monophyletic; thus, Meridiungulata is not a natural group; Litopterna and “Didolodontidae” are Panameriungulata and closer to Laurasiatheria than to other “Meridiungulata” (Astrapotheria, Notoungulata, Pyrotheria, and Xenungulata). The other “Meridiungulata” is grouped in the Sudamericungulata, as a new monophyletic lineage of Afrotheria Paenungulata, and shared a common ancestor with Hyracoidea. The divergence between the African and South American lineages is estimated to Early Paleocene, and their interrelationships support the Atlantogea biogeographic model. Shortly afterward, the Sudamericungulata explosively diversified in its four lineages. Confronting the Sudamericungulata evolutionary patterns and the Cenozoic natural events (such as tectonics and climatic and environmental changes, among others) helps to unveil a new chapter in the evolution of Gondwanan Eutheria, as well as the natural history of South America during the Cenozoic.

Recommendations for Sustainable Cetacean-Based Tourism in French Territories: A Review on the Industry and Current Management Actions

2020 ◽  
Vol 15 (3) ◽  
pp. 211-235
Author(s):  
Josephine Chazot ◽  
Ludovic Hoarau ◽  
Pamela Carzon ◽  
Jeanne Wagner ◽  
Stéphanie Sorby ◽  
...  
Keyword(s):  
Marine Mammal ◽  
Marine Mammals ◽  
French Polynesia ◽  
Legal Framework ◽  
Whale Watching ◽  
Cetacean Species ◽  
Commercial Activities ◽  
Management Actions ◽  
Overseas Territories ◽  
Socioeconomic Benefits

Whale-watching activities provide important socioeconomic benefits for local communities and constitute powerful platform incentives for marine mammals' protection or more broadly marine environments. However, these activities can cause adverse effects on targeted populations, with considerable downside associated risks of injuries and fatality for whale watchers during inwater interactions. France with its overseas territories has the second largest exclusive economic zone (EEZ), in which more than half of existing cetacean species are encountered. In these territories, recreational and commercial whale watching, including swim-with cetacean activities, have recently developed. Yet few studies focused on these activities and their associated impacts across French territories, leading to an unclear assessment of the situation. To address this issue, we reviewed cetaceans' occurrence within the French EEZ, whale-watching industry, targeted species, local management of marine mammal-based tourism activities, and regulations in France mainland and some overseas territories (Reunion Island, Mayotte, and French Polynesia). Fortyeight species are encountered in the French EEZ, and 15 are targeted by whale-watching activities. A total of 185 operators, including 34% offering swim-with-cetaceans tours, offered trips in France and overseas in 2019. While several more or less restrictive regulations exist locally, our results indicate that French's national legal framework for marine mammals' protection remains inadequate and insufficient to cope with the recent development of this activity. As conservation biologists, managers, and stakeholders from these French territories, we cooperated to provide general guidelines for a sustainable development of whale watching at a national scale. We urge (1) to legally acknowledge and regulate whale-watching commercial activities; (2) to create a national legal framework regarding whale watching and swim-with marine mammals practices, while accounting for local distinctiveness and disparities across regions; (3) to conduct more research to evaluate local short- and long-term impacts on targeted marine mammal populations as well as the socioeconomic benefits; and (4) to reinforce synergetic relations between the different stakeholders.

First record of Norwegian killer whales attacking and feeding on a harbour porpoise

2015 ◽  
Vol 8 ◽  
Author(s):  
A. Mel Cosentino
Keyword(s):  
North Atlantic ◽  
Marine Mammals ◽  
First Record ◽  
Harbour Porpoise ◽  
Sperm Whales ◽  
Killer Whales ◽  
Strait Of Gibraltar ◽  
Cetacean Species ◽  
The North ◽  
Northern Bottlenose Whales

Orcinus orcais a cosmopolitan species and the most widely distributed marine mammal. Its diet includes over 140 species of fish, cephalopods, sea birds and marine mammals. However, many populations are specialised on certain specific prey items. Three genetically distinct populations have been described in the North Atlantic. Population A (that includes the Icelandic and Norwegian sub-populations) is believed to be piscivorous, as is population C, which includes fish-eating killer whales from the Strait of Gibraltar. In contrast, population B feeds on both fish and marine mammals. Norwegian killer whales follow the Norwegian spring spawning herring stock. The only description in the literature of Norwegian killer whales feeding on another cetacean species is a predation event on northern bottlenose whales in 1968. Daily land-based surveys targeting sperm whales were conducted from the Andenes lighthouse using BigEyes®binoculars (25×, 80 mm). The location of animals at sea was approximated through the use of an internal reticule system and a graduated wheel. On 24 June 2012 at 3:12 am, an opportunistic sighting of 11 killer whales was made off Andenes harbour. The whales hunted and fed on a harbour porpoise. Despite these species having overlapping distributions in Norwegian waters, this is the first predatory event reported in the literature.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

The evolutionary history and conservation value of disjunct Bartonia paniculata subsp. paniculata (Branched Bartonia) populations in Canada

Botany ◽  
2013 ◽  
Vol 91 (9) ◽  
pp. 605-613 ◽  
Author(s):  
Claudia Ciotir ◽  
Chris Yesson ◽  
Joanna Freeland
Keyword(s):  
Great Lakes ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Great Lakes Region ◽  
Conservation Value ◽  
Most Recent Common Ancestor ◽  
Disjunct Populations ◽  
Management Plans ◽  
Global Status

Understanding the spatial distribution of genetic diversity and its evolutionary history is an essential part of developing effective biodiversity management plans. This may be particularly true when considering the value of peripheral or disjunct populations. Although conservation decisions are often made with reference to geopolitical boundaries, many policy-makers also consider global distributions, and therefore a species’ global status may temper its regional status. Many disjunct populations can be found in the Great Lakes region of North America, including those of Bartonia paniculata subsp. paniculata, a species that has been designated as threatened in Canada but globally secure. We compared chloroplast sequences between disjunct (Canada) and core (USA) populations of B. paniculata subsp. paniculata separated by 600 km, which is the minimum distance between disjunct and core populations in this subspecies. We found that although lineages within the disjunct populations shared a relatively recent common ancestor, the genetic divergence between plants from Ontario and New Jersey was substantially greater than expected for a consubspecific comparison. A coalescence-based analysis dated the most recent common ancestor of the Canadian and US populations at approximately 534 000 years ago with the lower confidence estimate at 226 000 years ago. This substantially predates the Last Glacial Maximum and suggests that disjunct and core populations have followed independent evolutionary trajectories throughout multiple glacial–interglacial cycles. Our findings provide important insight into the diverse processes that have resulted in numerous disjunct species in the Great Lakes region and highlight a need for additional work on Canadian B. paniculata subsp. paniculata taxonomy prior to a reevaluation of its conservation value.

scholarly journals Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shingo Nishiki ◽  
Kenichi Lee ◽  
Mizue Kanai ◽  
Shu-ichi Nakayama ◽  
Makoto Ohnishi
Keyword(s):  
Genetic Difference ◽  
Phylogenetic Analyses ◽  
Treponema Pallidum ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Global Perspectives ◽  
Most Recent Common Ancestor ◽  
Sex With Men

AbstractJapan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.

Cone visual pigments of aquatic mammals

2005 ◽  
Vol 22 (6) ◽  
pp. 873-879 ◽  
Author(s):  
LUCY A. NEWMAN ◽  
PHYLLIS R. ROBINSON
Keyword(s):  
Color Vision ◽  
Mammalian Cells ◽  
Marine Mammals ◽  
Light Availability ◽  
Splice Site Mutation ◽  
Harbor Seal ◽  
Site Mutation ◽  
Cetacean Species ◽  
Cone Opsin ◽  
Aquatic Mammals

It has long been hypothesized that the visual systems of animals are evolutionarily adapted to their visual environment. The entrance many millions of years ago of mammals into the sea gave these new aquatic mammals completely novel visual surroundings with respect to light availability and predominant wavelengths. This study examines the cone opsins of marine mammals, hypothesizing, based on previous studies [Fasick et al. (1998) and Levenson & Dizon (2003)], that the deep-dwelling marine mammals would not have color vision because the pressure to maintain color vision in the dark monochromatic ocean environment has been relaxed. Short-wavelength-sensitive (SWS) and long-wavelength-sensitive (LWS) cone opsin genes from two orders (Cetacea and Sirenia) and an additional suborder (Pinnipedia) of aquatic mammals were amplified from genomic DNA (for SWS) and cDNA (for LWS) by PCR, cloned, and sequenced. All animals studied from the order Cetacea have SWS pseudogenes, whereas a representative from the order Sirenia has an intact SWS gene, for which the corresponding mRNA was found in the retina. One of the pinnipeds studied (harp seal) has an SWS pseudogene, while another species (harbor seal) appeared to have an intact SWS gene. However, no SWS cone opsin mRNA was found in the harbor seal retina, suggesting a promoter or splice site mutation preventing transcription of the gene. The LWS opsins from the different species were expressed in mammalian cells and reconstituted with the 11-cis-retinal chromophore in order to determine maximal absorption wavelengths (λmax) for each. The deeper dwelling Cetacean species had blue shifted λmax values compared to shallower-dwelling aquatic species. Taken together, these findings support the hypothesis that in the monochromatic oceanic habitat, the pressure to maintain color vision has been relaxed and mutations are retained in the SWS genes, resulting in pseudogenes. Additionally, LWS opsins are retained in the retina and, in deeper-dwelling animals, are blue shifted in λmax.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

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