Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents

Genomics, the diversification of mammals, and the evolution of placentation

When and why did variations in placental structure and function evolve? Such questions cannot be addressed without a reliable version of mammalian phylogeny. Twenty-five years ago, the mammalian tree was reshaped by molecular phylogenetics. Soon it was shown, in contrast to prevailing theories, that the common ancestor of placental mammals had invasive placentation. Subsequently, evolution of many other features of extraembryonic membranes was addressed. This endeavour stimulated research to fill gaps in our knowledge of placental morphology. Last year the mammalian tree was again revised based on a large set of genomic data. With that in mind, this review provides an update on placentation in the nineteen orders of placental mammals, incorporating much recent data. The principal features such as shape, interdigitation, the interhaemal barrier and the yolk sac are summarized in synoptic tables. The evolution of placental traits and its timing is then explored by reference to the revised mammalian tree. Examples are the early appearance of epitheliochorial placentation in the common ancestor of artiodactyls, perissodactyls, pangolins and carnivores (with reversion to invasive forms in the latter) and later refinements such as the binucleate trophoblast cells and placentomes of ruminants. In primates, the intervillous space gradually evolved from the more basic labyrinth whereas trophoblast invasion of the decidua was a late development in humans and great apes. Only seldom can we glimpse the "why" of placental evolution. The best examples concern placental hormones, including some striking examples of convergent evolution such as the chorionic gonadotropins of primates and equids. In concluding, I review current ideas about what drives placental evolution and identify significant gaps in our knowledge of placentation, including several relevant to the evolution of placentation in primates.

Biogeography of Greater Antillean freshwater fishes, with a review of competing hypotheses

In biogeography, vicariance and long-distance dispersal are often characterised as competing scenarios. However, they are related concepts, both relying on collective geological, ecological, and phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when freshwater connections are temporarily present and later severed (vicariance), or by unusual means when ocean gaps are crossed (long-distance dispersal). Marine barriers have a strong filtering effect on freshwater fishes, limiting immigrants to those most capable of oceanic dispersal. The roles of vicariance and dispersal are debated for freshwater fishes of the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Greater Antilles-Aves Ridge (GAARlandia), long-distance dispersal] and propose long-distance dispersal to be an appropriate model due to limited support for freshwater fish use of landspans. Greater Antillean freshwater fishes have six potential source bioregions (defined from faunal similarity): Northern Gulf of México, Western Gulf of México, Maya Terrane, Chortís Block, Eastern Panamá, and Northern South America. Faunas of the Greater Antilles are composed of taxa immigrating from many of these bioregions, but there is strong compositional disharmony between island and mainland fish faunas (>90% of Antillean species are cyprinodontiforms, compared to <10% in Northern Gulf of México and Northern South America, and ≤50% elsewhere), consistent with a hypothesis of long-distance dispersal. Ancestral-area reconstruction analysis indicates there were 16 or 17 immigration events over the last 51 million years, 14 or 15 of these by cyprinodontiforms. Published divergence estimates and evidence available for each immigration event suggests they occurred at different times and by different pathways, possibly with rafts of vegetation discharged from rivers or washed to sea during storms. If so, ocean currents likely provide critical pathways for immigration when flowing from one landmass to another. On the other hand, currents create dispersal barriers when flowing perpendicularly between landmasses. In addition to high salinity tolerance, cyprinodontiforms collectively display a variety of adaptations that could enhance their ability to live with rafts (small body size, viviparity, low metabolism, amphibiousness, diapause, self-fertilisation). These adaptations likely also helped immigrants establish island populations after arrival and to persist long term thereafter. Cichlids may have used a pseudo bridge (Nicaragua Rise) to reach the Greater Antilles. Gars (Lepisosteidae) may have crossed the Straits of Florida to Cuba, a relatively short crossing that is not a barrier to gene flow for several cyprinodontiform immigrants. Indeed, widespread distributions of Quaternary migrants (Cyprinodon, Gambusia, Kryptolebias), within the Greater Antilles and among neighbouring bioregions, imply that long-distance dispersal is not necessarily inhibitory for well-adapted species, even though it appears to be virtually impossible for all other freshwater fishes.

Historical DNA from a rediscovered nineteenth-century paratype reveals genetic continuity of a Bahamian hutia (Geocapromys ingrahami) population

Past and ongoing human activities have shaped the geographical ranges and diversity of species. New genomic techniques applied to degraded samples, such as those from natural history collections, can uncover the complex evolutionary consequences of human pressures and generate baselines for interpreting magnitudes of species loss or persistence relevant to conservation. Here we integrate mitogenomic data with historical records from a recently rediscovered Bahamian hutia (Geocapromys ingrahami; (FMP Z02816)) specimen at the Fairbanks Museum & Planetarium (Vermont, USA) to determine when and where the specimen was collected and to place it in a phylogenetic context with specimens that both predate (palaeontological) and postdate (archaeological) human arrival in The Bahamas. We determined that this specimen was part of the same population as the named holotype specimen in 1891 on East Plana Cay (EPC). Bahamian hutia populations were widely extirpated following European colonization. Today, EPC hosts the last remaining natural Bahamian hutia population. Mitogenomic data places the focal specimen within the southern Bahamian hutia population, which is now largely restricted to EPC. The results reveal previously undocumented genetic continuity among the EPC population for at least the past 500 years, highlighting how 'dark' museum specimens inform new conservation-relevant understandings of diversity.

Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches

There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.

Paleodietary reconstruction of endemic rodents from the precolumbian Dominican Republic: Discriminating wild feeding behavior from diets linked to human niche construction activities

In the Greater Antilles, certain animal taxa that have long been theorized to have been managed by indigenous peoples prior to AD1492, the main candidates being a group of endemic caviomorph rodents known as hutias (Capromyinae). This isotopic study investigates the paleodiets of several species of endemic rodents from three late precolonial sites in the northern Dominican Republic: El Flaco (cal. ad 990-1452), El Carril (cal. ad 1030-1262), and La Entrada (cal. ad 840-900) to assess whether human influence over animal diets can be determined. We examined bone collagen carbon (δ13Cco) and nitrogen (δ15N) and tooth enamel carbon (δ13Cen) isotope values of three species of hutias, Isolobodon portoricensis, Isolobodon montanus, and Plagiodontia aedium, alongside edible rat (Brotomys sp.), and domestic guinea pig (Cavia porcellus). To estimate dietary source contributions, we employed a Bayesian dietary mixing model (FRUITS v.3.0) and ran three different permutations to assess the relative contributions of C3 or C4/CAM plants. The addition of an extra 79 wild C3 and 40 wild C4/CAM plant species' isotope values from published sources to an established isotopic foodweb for the Caribbean region enabled us to discriminate between wild and domestic C3 and C4/CAM plant food sources in two of these models. Our results provide evidence of the significant consumption of domestic C4/CAM plants by some animals. This likely represents maize (Zea mays) consumption, which is known to have been ubiquitously cultivated by indigenous peoples in the region. This is particularly the case for I. portoricensis, as FRUITS modeling suggests that a few individuals consumed C4/CAM plants well beyond their expected natural diets as determined from feeding studies of extant hutia species. This may indicate human influence over endemic rodent diets due to niche construction activities such as horticultural practices and may reflect either opportunistic feeding on human produce or the purposeful supplementation of hutia diets by humans.

Ancient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits

Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.

Comprehensive total evidence phylogeny of chinchillids (Rodentia, Caviomorpha): Cheek teeth anatomy and evolution

Rodents are the most diverse order of extant mammals, and caviomorph rodents, or New World hystricognaths, have a remarkable morphological disparity and a long fossil record that begins in the Eocene. Chinchilloidea is a poorly understood clade within Caviomorpha, from an evolutionary and phylogenetic perspective. It includes the extant families Chinchillidae and Dinomyidae, the extinct Neoepiblemidae and Cephalomyidae, and several extinct chinchilloids without a clear phylogenetic position, like Eoincamys, Borikenomys, Chambiramys, Ucayalimys, Incamys, Saremmys, Garridomys and Scotamys. The family Chinchillidae includes the extant Chinchilla and Lagidium, grouped in Chinchillinae, and the only living Lagostominae, Lagostomus maximus. Among extinct chinchillids, Eoviscaccia (early Oligocene-early Miocene of Argentina, Bolivia and Chile), Prolagostomus (early-middle Miocene of Argentina, Bolivia and Chile) and Pliolagostomus (early-middle Miocene of Argentina) are the only genera originally described as members of the family. Based on the study of specimens with unworn or little-worn cheek teeth, belonging to extinct and extant taxa, we propose homologies of the cheek teeth structures and perform a combined molecular and morphological phylogenetic analysis including extinct and extant taxa of all families of Chinchilloidea and all genera of Chinchillidae. Our phylogenetic analysis recovered three major lineages in the evolutionary history of Chinchilloidea. The first major lineage is composed of the extant taxa Chinchilla, Lagidium and Lagostomus, and the extinct genera Eoviscaccia, Prolagostomus, Pliolagostomus, Garridomys, Incamys, Loncolicu and Saremmys. Cephalomyid (Banderomys, Cephalomys, Litodontomys, Soriamys) and neoepiblemid (Neoepiblema, Perimys, Phoberomys, Scotamys) genera are part of the second major lineage, while dinomyids such as Dinomys, Drytomomys, Scleromys, 'Scleromys' and Tetrastylus constitute the third major lineage within Chinchilloidea. The phylogenetic position of some taxa previously considered as incertae sedis chinchilloids or without a clear suprageneric group (i.e. Incamys, Saremmys, Garridomys and Loncolicu) show that they belong to pan-Chinchillidae and conform the stem Chinchillidae along with Eoviscaccia. The euhypsodont crown Chinchillidae includes the living subfamilies Chinchillinae and Lagostominae. Dinomyidae and Eoincamys pascuali are recovered as the sisters of a major clade composed by 'Cephalomyidae'+Neopiblemidae and pan-Chinchillidae, and Chambiramys sylvaticus occupies a basal position to the same clade. Four major radiation events are identified in the evolutionary history of Chinchilloidea. The analysis of new morphological characters linked with molecular evidence as well as the addition of taxa of uncertain or unstable phylogenetic position or not considered in previous studies allowed us resolve part of the relationships within Chinchilloidea, particularly that of Chinchillidae, supporting preceding morphological hypotheses.