Shedding light: A phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves

Abstract Background Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. Results In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae, and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade. Conclusions The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exadaptation existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.

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Shedding light: A phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves

10.21203/rs.2.16100/v4 ◽

2020 ◽

Author(s):

Jingchun Li ◽

Sarah Lemer ◽

Lisa Kirkendale ◽

Rüdiger Bieler ◽

Colleen Cavanaugh ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Structural Integrity ◽

Sister Group ◽

Sister Group Relationship ◽

Last Common Ancestor ◽

Ancestral State ◽

Marine Animals ◽

Giant Clams ◽

Rapid Divergence ◽

Anatomical Adaptations

Abstract Background: Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. Results: In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae, and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade.Conclusions: The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exadaptation existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.

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Shedding light: A phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves

10.21203/rs.2.16100/v3 ◽

2020 ◽

Author(s):

Jingchun Li ◽

Sarah Lemer ◽

Lisa Kirkendale ◽

Rüdiger Bieler ◽

Colleen Cavanaugh ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Structural Integrity ◽

Sister Group ◽

Sister Group Relationship ◽

Last Common Ancestor ◽

Ancestral State ◽

Marine Animals ◽

Giant Clams ◽

Rapid Divergence ◽

Anatomical Adaptations

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Shedding light: A phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves

10.21203/rs.2.16100/v1 ◽

2019 ◽

Author(s):

Jingchun Li ◽

Sarah Lemer ◽

Lisa Kirkendale ◽

Rüdiger Bieler ◽

Colleen Cavanaugh ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Structural Integrity ◽

Sister Group ◽

Sister Group Relationship ◽

Last Common Ancestor ◽

Ancestral State ◽

Marine Animals ◽

Giant Clams ◽

Rapid Divergence ◽

Anatomical Adaptations

Abstract Background Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice.Results In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae, and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade.Conclusions The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exadaptation existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.

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Systematics of the spider genus Neoleptoneta Brignoli, 1972 (Araneae:Leptonetidae) with a discussion of the morphology and relationships for the North American Leptonetidae

Invertebrate Systematics ◽

10.1071/is11014 ◽

2011 ◽

Vol 25 (4) ◽

pp. 334 ◽

Cited By ~ 8

Author(s):

Joel Ledford ◽

Pierre Paquin ◽

James Cokendolpher ◽

Josh Campbell ◽

Charles Griswold

Keyword(s):

North American ◽

Sister Group ◽

Morphological Data ◽

New Combination ◽

Sister Group Relationship ◽

Ancestral State ◽

New Combinations ◽

Molecular Sequence ◽

North East ◽

The North

A phylogenetic analysis of the spider genus Neoleptoneta Brignoli, 1972 is presented based on molecular sequence variation from three genes (mitochondrial cytochrome c oxidase subunit I, nuclear histone H3 and nuclear 28S rDNA) and including exemplars for all North American leptonetid genera except the ecribellate archoleptonetine Darkoneta. Analysis of concatenated data and independent genes using Bayesian, maximum likelihood and parsimony methods failed to recover Neoleptoneta as monophyletic. The genera Archoleptoneta, Appaleptoneta and Calileptoneta are monophyletic and a sister group relationship is supported between Appaleptoneta and Calileptoneta. Morphological data based on a survey of leptonetid genera using scanning electron and compound light microscopy are discussed and traced on the molecular phylogeny. Images for each North American leptonetine genus are provided, including comparison with Asian and European outgroups. Images of the incertae sedis species Leptoneta brunnea Gertsch, 1974 and Leptoneta sandra Gertsch, 1974 are provided and their generic placement is re-evaluated. Ancestral state reconstruction is used to assess patterns of cave evolution and shows that most species are descended from troglophilic ancestors and that troglobites have evolved at least nine times independently within the North American Leptonetidae. Neoleptoneta is relimited to include seven species restricted to central Mexico including N. bonita (Gertsch, 1974), N. capilla (Gertsch, 1971), N. delicata (Gertsch, 1971), N. limpida (Gertsch, 1974), N. rainesi (Gertsch, 1971) and N. reclusa (Gertsch, 1971) and to include Leptoneta brunnea, giving the new combination N. brunnea (Gertsch, 1974). The remaining species described in Neoleptoneta are placed in three new genera: (1) Chisoneta, gen. nov. from south-western Texas and Nuevo Leon, Mexico, including the four species C. chisosea (Gertsch, 1974), C. isolata (Gertsch, 1971), C. modica (Gertsch, 1974) and C. pecki (Gertsch, 1971), new combinations; (2) Ozarkia, gen. nov. from Arizona and New Mexico north-east to Arkansas, Alabama and Georgia, including the nine species O. alabama (Gertsch, 1974), O. apachea (Gertsch, 1974), O. archeri (Gertsch, 1974), O. arkansa (Gertsch, 1974), O. blanda (Gertsch, 1974), O. georgia (Gertsch, 1974), O. ivei (Gertsch, 1974), O. novaegalleciae (Brignoli, 1979) and O. serena (Gertsch, 1974), new combinations; and (3) Tayshaneta, gen. nov. from Texas south to Coahuila, Mexico, with the eleven species T. anopica (Gertsch, 1974), T. bullis (Cokendolpher, 2004), T. coeca (Chamberlin & Ivie, 1942), T. concinna (Gertsch, 1974), T. devia (Gertsch, 1974), T. furtiva (Gertsch, 1974), T. microps (Gertsch, 1974), T. myopica (Gertsch, 1974), T. paraconcinna (Cokendolpher & Reddell, 2001), T. uvaldea (Gertsch, 1974) and T. valverdae (Gertsch, 1974), new combinations. Leptoneta sandra Gertsch, 1974 cannot be placed in any North American, European or Asian genus and is thus transferred to the new genus Montanineta, gen. nov., giving the new combination Montanineta sandra (Gertsch, 1974).

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First description of the male of Cretaconiopteryx grandis Liu & Lu, 2017 (Neuroptera: Coniopterygidae) from the Cretaceous Burmese amber

Zootaxa ◽

10.11646/zootaxa.4674.4.7 ◽

2019 ◽

Vol 4674 (4) ◽

pp. 482-490 ◽

Cited By ~ 1

Author(s):

HONGYU LI ◽

BO WANG ◽

XINGYUE LIU

Keyword(s):

Male Genitalia ◽

Upper Cretaceous ◽

Sister Group ◽

Sister Group Relationship ◽

Burmese Amber ◽

Representative Species ◽

First Time

The male of Cretaconiopteryx grandis Liu & Lu, 2017, which is the only representative species of the extinct dustywing subfamily Cretaconiopteryginae, is described for the first time from the Upper Cretaceous Burmese amber. The male genitalia, well preserved in the examined specimen, show a number of plesiomorphic characters, which support the sister group relationship between Coniopterygidae and the rest of extant lacewing families.

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The postcranial skeleton, phylogenetic position, and probable lifestyle of the Early Triassic reptile Procolophon trigoniceps

Canadian Journal of Earth Sciences ◽

10.1139/e02-082 ◽

2003 ◽

Vol 40 (4) ◽

pp. 527-556 ◽

Cited By ~ 44

Author(s):

Michael deBraga

Keyword(s):

South Africa ◽

Morphological Study ◽

Lower Triassic ◽

Sister Group ◽

Phylogenetic Position ◽

Sister Group Relationship ◽

Early Triassic ◽

Postcranial Skeleton ◽

Sister Clade ◽

Key Innovations

A morphological study of the postcranial skeleton of Procolophon trigoniceps from the Lower Triassic of South Africa and Antarctica is undertaken. Procolophon shares a sister-group relationship with the procolophonid Tichvinskia from the Lower Triassic of Russia and is a basal member of Procolophonidae. This clade also includes the enigmatic taxon Sclerosaurus, believed most recently to be a pareiasaur relative. Owenettids form a separate lineage from Procolophonidae and are predominantly restricted to the Permian of both South Africa and Madagascar. A phylogenetically based assessment is considered, in which specialized modern taxa (sand lizards) are compared to their nonfossorial sister clade, allowing for "key innovations" to be identified. A similar comparison between owenettids and procolophonids reveals a number of apparent "key innovations" within procolophonids that are suggestive of a burrowing lifestyle for Procolophon.

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Ordosemys leios, n.gen., n.sp., a new turtle from the Early Cretaceous of the Ordos Basin, Inner Mongolia

Canadian Journal of Earth Sciences ◽

10.1139/e93-184 ◽

1993 ◽

Vol 30 (10) ◽

pp. 2128-2138 ◽

Cited By ~ 50

Author(s):

Donald B. Brinkman ◽

Jiang-Hua Peng

Keyword(s):

Early Cretaceous ◽

Inner Mongolia ◽

Cervical Vertebrae ◽

Ordos Basin ◽

Sister Group ◽

Sister Group Relationship ◽

Articular Surfaces ◽

Caudal Vertebrae ◽

The Ordos Basin

Ordosemys leios, n.gen., n.sp., from the Early Cretaceous Luohandong Formation, Zhidan Group, Ordos Basin, Inner Mongolia, is a primitive aquatic turtle with a reduced, fenestrated plastron. It shares with the members of the Centrocryptodira the presence of well-formed articular surfaces on the cervical and caudal vertebrae. Within the Centrocryptodira, characters of the cervical vertebrae suggest it is more closely related to the Polycryptodira than is the Meiolaniidae. Ordosemys shares with the Chelydridae the presence of two procoelous anterior caudals, but this character may be primitive for the Polycryptodira. Characters of the basicranial region of the braincase shared by Ordosemys and the Chelonioidea support a sister-group relationship between these two taxa, but a sister-group relationship between Ordosemys and the Polycryptodira is more strongly supported by characters shared by the Chelonioidea and other members of the Polycryptodira.

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Improved resolution of recalcitrant nodes in the animal phylogeny through the analysis of genome gene content and morphology

10.1101/2021.11.19.469253 ◽

2021 ◽

Author(s):

Ksenia Juravel ◽

Luis Porras ◽

Sebastian Hoehna ◽

Davide Pisani ◽

Gert Wörheide

Keyword(s):

Common Ancestor ◽

Sister Group ◽

The Other ◽

Gene Content ◽

Statistical Hypothesis ◽

Phylogenetic Position ◽

Last Common Ancestor ◽

Statistical Hypothesis Testing ◽

Animal Phylogeny ◽

Phylogenetic Hypotheses

An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the "Superphylum" Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

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The male genitalia of Agathiphaga (Lepidoptera: Agathiphagidae) and the lepidopteran ground plan

Insect Systematics & Evolution ◽

10.1163/187631284x00127 ◽

1984 ◽

Vol 15 (2) ◽

pp. 151-178 ◽

Cited By ~ 13

Author(s):

Niels P. Kristensen

Keyword(s):

Male Genitalia ◽

Ejaculatory Duct ◽

Posterior Part ◽

Sister Group ◽

Sister Group Relationship ◽

Ground Plan ◽

Accessory Glands ◽

Internal Genitalia ◽

Genital Structure ◽

Segment Viii

AbstractThe genital segments and internal genitalia of Agathiphaga vitiensis are described. Sternum VIII is anteriorly produced into blunt paired apophyses and posteriorly into a tongue-shaped lobe. Segment IX is a complete ring, very short in the dorsal and ventral midlines; its anterolateral lobes are largely apodemal. The long and curved gonopod ("valva") consists of a single piece. There is no median sclerite between the gonopod bases, but an open, softwalled "subgenital crypt" below the entrance of the phallocrypt may be homologous with the "median plate" in other primitive homoneurous moths. Tergum X bears a pair of broad "superior lobes" and the postgenital complex terminates in a medially intended, sclerotized "terminal lobe" above the eversible perianal area. The roof of the posterior part of the genital chamber bears a median aggregation of cuticular spines (the "spiny plate"), and a pair of smooth lateral sclerotizations ("presocii") tentatively attributed to venter X: a pair of setose sclerites (socii) are tentatively attributed to the paraprocts. The area bearing the spiny plate and presocii may in repose be folded down behind the phallus, thereby closing the phallocrypt. The phallus comprises a tubular phallotheca and an eversible aedeagus; the thick basal margen of the phallotheca is posteriorly expanded and forms the floor of the greater part of the phallocrypt; there is no ventral aedeagal branch. The musculature comprises two IX/X muscles, a segment IX muscle inserting on the subgenital crypt, phallic pro- and retractors (the former originating in the gonopod), intrinsic phallic muscles, a single segment IX muscle (adductor) to the gonopod and five intrinsic muscles of the postgenital complex. Each testis comprises four large, separate follicles. The spermatozoa do not remain grouped in discrete bundles in the vas deferens. Seminal vesicles are located on the vasa deferentia close to the testis and are doubtfully homologous with the vesicles in other Lepidoptera. The unpaired ejaculatory duct is very short. The evidence bearing on a reconstruction of the ground plan of the lepidopteran male genitalia is reviewed. Segment VIII was similar to the preceding segments. It is tentatively suggested that tergum and sternum IX were fused, that the gonopod was undivided and that a tubular, partly sclerotized aedeagus was present; deviations from these states within the order are therefore considered to be autapomorphic. The base of the aedeagus was probably surrounded by a short, collarlike phallotheca. It is suggested that there was a median sclerite between the gonopod bases, but the presence of discrete, paired and muscular "valvellae" in the lepidopteran ground plan is considered doubtful. It is further suggested that dorsum X bore a pair of lobes and that there were paired sclerotizations in venter X. The X/XI boundary is very difficult to trace. Seventeen muscle sets are ascribed to the lepidopteran ground plan; it is considered an autapomorphy of this ground plan that the phallic protractor originates within the gonopod. The testes presumably had large, separate follicles and there may have been two pairs of tubular accessory glands. The testes and the double set of accessory glands of Agathiphaga could be cited in support of a sistergroup relationship to all other Lepidoptera whereas the phallic structure (and possibly the "spiny plate") might support a sister group relationship to the Heterobathmiina. There is no support in male genital structure for a sistergroup relationship to the Heterobathmiina + Glossata; the latter phylogenetic hypothesis may be preferable on other grounds, however.

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