scholarly journals Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation

2018 ◽  
Vol 115 (50) ◽  
pp. 12769-12774 ◽  
Author(s):  
Roseina Woods ◽  
Samuel T. Turvey ◽  
Selina Brace ◽  
Ross D. E. MacPhee ◽  
Ian Barnes
Keyword(s):  
Ancient Dna ◽  
Nuclear Genome ◽  
Primate Species ◽  
Morphological Studies ◽  
Mammal Fauna ◽  
Titi Monkey ◽  
The Caribbean ◽  
Primate Diversity ◽  
Entire Mitochondrial Genome ◽  
Limited Coverage

The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori. We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus. These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5–18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations.

Description of two new Caribbean species from the Hypnea musciformis complex (Cystocloniaceae, Rhodophyta)

Phytotaxa ◽  
2019 ◽  
Vol 408 (2) ◽  
pp. 85-98 ◽  
Author(s):  
FABIO NAUER ◽  
VALÉRIA CASSANO ◽  
MARIANA C. OLIVEIRA
Keyword(s):  
New Species ◽  
Dna Barcode ◽  
Economic Importance ◽  
Hypnea Musciformis ◽  
Widespread Species ◽  
Macroalgal Species ◽  
Morphological Studies ◽  
Molecular Studies ◽  
Two New Species ◽  
The Caribbean

Hypnea musciformis is a red macroalgal species with economic importance as a source for production of carrageenan. Recent phylogeographic studies revealed a hidden diversity of cryptic species, putting in check its cosmopolitan distribution. The DNA barcode marker COI-5P and plastid rbcL, in addition to morphological studies, were used to investigate the species in this complex and to compare them with specimens from other countries including the type locality in Italy. The divergences between sequences within the H. musciformis complex were significantly high for both markers. Based on these analyses two new species are described, Hypnea caraibica Nauer, Cassano & M.C. Oliveira sp. nov. and Hypnea schneideri Nauer, Cassano & M.C. Oliveira sp. nov. Hypnea caraibica seems to be a common, widespread species in the Gulf of Mexico and the Caribbean and was recently introduced into Hawaii. This species was unnoticed due to lack of phylogeographic studies in the region. Hypnea schneideri seems to be more geographically restricted, but further surveys are needed to understand the distribution of this species. Because the identification of Hypnea species is complicated by their relatively simple and plastic morphology, DNA barcoding surveys and other molecular studies are essential to uncover hidden biodiversity in the genus and to supplement traditional studies based on morphology.

scholarly journals Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama

2020 ◽  
Author(s):  
Alexis P. Sullivan ◽  
Stephanie Marciniak ◽  
Aaron O’Dea ◽  
Thomas A. Wake ◽  
George H. Perry
Keyword(s):  
Mitochondrial Genome ◽  
Ancient Dna ◽  
Evolutionary Biology ◽  
High Throughput Sequencing ◽  
Dna Analysis ◽  
Nuclear Genome ◽  
Average Frequency ◽  
Land Snail ◽  
Marine Bivalve ◽  
Bocas Del Toro

ABSTRACTAlthough protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n=3), Late Holocene (984-1258 BP) archaeological midden (n=5), and a mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n=5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n=5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7x higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behavior on mollusc evolutionary biology.

scholarly journals Origins and genetic legacies of the Caribbean Taino

2018 ◽  
Vol 115 (10) ◽  
pp. 2341-2346 ◽  
Author(s):  
Hannes Schroeder ◽  
Martin Sikora ◽  
Shyam Gopalakrishnan ◽  
Lara M. Cassidy ◽  
Pierpaolo Maisano Delser ◽  
...  
Keyword(s):  
Native American ◽  
South America ◽  
Population Size ◽  
Ancient Dna ◽  
Effective Population ◽  
The Bahamas ◽  
Dna Preservation ◽  
Large Effective Population Size ◽  
The Caribbean ◽  
Northern South America

The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

scholarly journals First nuclear genome assembly of an extinct moa species, the little bush moa (Anomalopteryx didiformis)

2018 ◽  
Author(s):  
Alison Cloutier ◽  
Timothy B. Sackton ◽  
Phil Grayson ◽  
Scott V. Edwards ◽  
Allan J. Baker
Keyword(s):  
Ancient Dna ◽  
Genome Assembly ◽  
Limb Development ◽  
High Throughput Sequencing ◽  
Nuclear Dna ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Population Level ◽  
Single Copy ◽  
Vertebrate Limb Development

AbstractHigh throughput sequencing (HTS) has revolutionized the field of ancient DNA (aDNA) by facilitating recovery of nuclear DNA for greater inference of evolutionary processes in extinct species than is possible from mitochondrial DNA alone. We used HTS to obtain ancient DNA from the little bush moa (Anomalopteryx didiformis), one of the iconic species of large, flightless birds that became extinct following human settlement of New Zealand in the 13 th century. In addition to a complete mitochondrial genome at 249.9X depth of coverage, we recover almost 900 Mb of the moa nuclear genome by mapping reads to a high quality reference genome for the emu (Dromaius novaehollandiae). This first nuclear genome assembly for moa covers approximately 75% of the 1.2 Gb emu reference with sequence contiguity sufficient to identify more than 85% of bird universal single-copy orthologs. From this assembly, we isolate 40 polymorphic microsatellites to serve as a community resource for future population-level studies in moa. We also compile data for a suite of candidate genes associated with vertebrate limb development and show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization among this candidate set. We also identify potential function-altering coding sequence variants in moa for future experimental assays.

scholarly journals Oxytocin receptor binding in the titi monkey hippocampal formation is associated with parental status and partner affiliation

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alexander Baxter ◽  
M. Anderson ◽  
A. M. Seelke ◽  
E. L. Kinnally ◽  
S. M. Freeman ◽  
...  
Keyword(s):  
Hippocampal Formation ◽  
Average Frequency ◽  
Postmortem Brain ◽  
Primate Species ◽  
Pair Bonding ◽  
Infant Carrying ◽  
Titi Monkey ◽  
Postmortem Brain Tissue ◽  
Titi Monkeys ◽  
The Impact

Abstract Social cognition is facilitated by oxytocin receptors (OXTR) in the hippocampus, a brain region that changes dynamically with pregnancy, parturition, and parenting experience. We investigated the impact of parenthood on hippocampal OXTR in male and female titi monkeys, a pair-bonding primate species that exhibits biparental care of offspring. We hypothesized that in postmortem brain tissue, OXTR binding in the hippocampal formation would differ between parents and non-parents, and that OXTR density would correlate with frequencies of observed parenting and affiliative behaviors between partners. Subjects were 10 adult titi monkeys. OXTR binding in the hippocampus (CA1, CA2/3, CA4, dentate gyrus, subiculum) and presubiculum layers (PSB1, PSB3) was determined using receptor autoradiography. The average frequency of partner affiliation (Proximity, Contact, and Tail Twining) and infant carrying were determined from longitudinal observations (5–6 per day). Analyses showed that parents exhibited higher OXTR binding than non-parents in PSB1 (t(8) = − 2.33, p = 0.048), and that OXTR binding in the total presubiculm correlated negatively with Proximity (r = − 0.88) and Contact (r = − 0.91), but not Tail Twining or infant carrying. These results suggest that OXTR binding in the presubiculum supports pair bonding and parenting behavior, potentially by mediating changes in hippocampal plasticity.

scholarly journals A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives

2021 ◽  
Vol 1 ◽  
pp. 25
Author(s):  
Michael V Westbury ◽  
Ross Barnett ◽  
Marcela Sandoval-Velasco ◽  
Graham Gower ◽  
Filipe Garrett Vieira ◽  
...  
Keyword(s):  
Gene Flow ◽  
South America ◽  
Ancient Dna ◽  
Empirical Data ◽  
Phylogenetic Relationships ◽  
Middle Miocene ◽  
Nuclear Genome ◽  
Evolutionary Relationships ◽  
Grade Group ◽  
Dna Preservation

Background: The evolutionary relationships of Felidae during their Early–Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths. Methods: Here, we sequenced a draft nuclear genome of Smilodon populator, dated to 13,182 ± 90 cal BP, making this the oldest palaeogenome from South America to date, a region known to be problematic for ancient DNA preservation. We analysed this genome, together with genomes from other extinct and extant cats to investigate their phylogenetic relationships. Results: We confirm a deep divergence (~20.65 Ma) within sabre-toothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae. Conclusions: Given that some species traditionally assigned to Pseudaelurus originated in the Early Miocene ~20 Ma, this indicates that some species of Pseudaelurus may be younger than the lineages they purportedly gave rise to, further supporting the hypothesis that Pseudaelurus was paraphyletic.

scholarly journals Primates, Pitheciidae, Callicebus barbarabrownae Hershkovitz, 1990: new localities for the critically endangered titi monkey in the São Francisco basin, state of Sergipe, Brazil [with erratum]

Check List ◽  
2013 ◽  
Vol 9 (1) ◽  
pp. 113 ◽  
Author(s):  
Eduardo La Noce Marques ◽  
Raone Beltrão-Mendes ◽  
Stephen Francis Ferrari
Keyword(s):  
The State ◽  
Critically Endangered ◽  
Primate Species ◽  
Titi Monkey ◽  
New Localities ◽  
Important Extension ◽  
Few Data ◽  
Occurrence Records

Barbara Brown’s titi monkey, Callicebus barbarabrownae Hershkovitz, 1990, appears to be endemic to the Caatinga of northern Bahia and western Sergipe, although few data are available for the northernmost portion of its range. The present study presents seven new occurrence records of the species, in the São Francisco basin of northern Sergipe, extending its range in the state over a distance of more than 50 km from west to east. This represents an important extension of the known range and total number of populations of this critically endangered primate species.

scholarly journals Reclassification of the Angraecum-alliance (Orchidaceae, Vandoideae) based on molecular and morphological data

2013 ◽  
Vol 29 (1) ◽  
pp. 1-23 ◽  
Author(s):  
Dariusz L. Szlachetko ◽  
Piotr Tukałło ◽  
Joanna Mytnik-Ejsmont ◽  
Elżbieta Grochocka
Keyword(s):  
Bayesian Analysis ◽  
Molecular Analysis ◽  
Nuclear Genome ◽  
Intergenic Spacer ◽  
Its Region ◽  
The Other ◽  
Morphological Data ◽  
New Genera ◽  
New Classification ◽  
Morphological Studies

Abstract Results of molecular analysis compared with morphological studies were used for reclassification of the Angraecumalliance (Orchidaceae). For the purpose of this study we sequenced the ITS region (ITS1-5.8S-ITS2) of nrDNA representing nuclear genome and the plastid region trnL-F (including intron of trnL gene and trnL-trnF intergenic spacer). The ITS matrix includes 97 samples representing 86 species and the trnL-F matrix includes 94 samples representing 86 species. We focus mainly on the genus Angraecum, however the other genera of Angraecinae are also included (Aeranthes, Campylocentrum, Dendrophylax, Cryptopus, Calyptrochilum, Lemurorchis, Jumellea, Neobathiea, Oeonia, Oeoniella, Sobennikoffia). Additional 43 sequences, including an outgroup (Polystachya modesta) and other representatives of the subtribes Aeridinae (Aerides) and Aerangidinae (Aerangis, Angraecopsis, Erasanthe, Solenangis), were obtained from NCBI resources. Bayesian analysis using MrBayes 3.1.2 on the combined ITS/trnL-F matrix were performed. The monophyly of Angraecinae with an inclusion of Aerangidinae is highly supported by both methods (93 BP/100 PP). The Angraecoid taxa formed two well supported clades, namely clade I (89 BP/100 PP) and clade II (84 BP/100 PP). New classification based on both molecular and classical taxonomy studies is presented including a key to the genera. The subtribe Angraecinae includes 36 genera, 18 of them, included within Angraecum by different authors so far, are treated here. Five new genera are described: Eichlerangraecum, Hermansia, Lesliegraecum, Pectianriella and Rudolfangraecum. Ten sections of Angraecum are raised to the generic status.

Sign in / Sign up

Export Citation Format

Share Document